diff --git a/2.7.0-dev0/_modules/MDAnalysis/analysis/dielectric.html b/2.7.0-dev0/_modules/MDAnalysis/analysis/dielectric.html index 39d8cccbc2..c5cc48733c 100644 --- a/2.7.0-dev0/_modules/MDAnalysis/analysis/dielectric.html +++ b/2.7.0-dev0/_modules/MDAnalysis/analysis/dielectric.html @@ -162,6 +162,10 @@

Source code for MDAnalysis.analysis.dielectric

the usual case if electrostatics are handled with a Ewald summation technique. See [Neumann1983]_ for details on the derivation. + .. warning:: + Applying this class requires that no free charges, such as ions or + charged fragments, are present in the simulation. + Parameters ---------- atomgroup : MDAnalysis.core.groups.AtomGroup diff --git a/2.7.0-dev0/documentation_pages/analysis/dielectric.html b/2.7.0-dev0/documentation_pages/analysis/dielectric.html index 5e74a3ed7b..16da310be1 100644 --- a/2.7.0-dev0/documentation_pages/analysis/dielectric.html +++ b/2.7.0-dev0/documentation_pages/analysis/dielectric.html @@ -147,6 +147,11 @@

4.8.4. Dielectric — [Neumann1983] for details on the derivation.

+
+

Warning

+

Applying this class requires that no free charges, such as ions or +charged fragments, are present in the simulation.

+
Parameters

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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.2.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.1.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.2.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.2.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.11.1. Analysis data files", "4.8.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.8.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.9.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.7.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.2.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.2.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.2.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.2.7.1.2. Clustering", "4.2.7.1.4. 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TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.26. Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.27. MDAnalysis topology tables", "5.28. Utility functions for the TPR topology parser", "5. Topology modules", "8. Trajectory transformations (\u201con-the-fly\u201d transformations)", "8.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "8.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "8.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "8.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "8.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "8.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "8.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "8.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "15. Constants and unit conversion \u2014 MDAnalysis.units", "14. Version information for MDAnalysis - MDAnalysis.version", "12.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "12.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "12. Visualization modules", "MDAnalysis documentation"], "terms": {"author": [0, 1, 3, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 59, 81, 99, 108, 109, 163, 164], "oliv": [0, 6, 9, 23, 34, 36], "beckstein": [0, 6, 9, 23, 34, 36, 112, 113], "joshua": [0, 108], "adelman": [0, 108], "year": [0, 1, 3, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 81, 99, 108, 163, 164], "2010": [0, 108, 109, 113, 161], "2013": [0, 4, 23, 26, 52, 113], "copyright": [0, 1, 3, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 81, 99, 163, 164], "gnu": [0, 1, 3, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 69, 81, 99, 105, 163, 164, 166], "public": [0, 1, 3, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 81, 99, 105, 108, 111, 113, 162, 163, 164, 166], "licens": [0, 1, 3, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 29, 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157, 158, 159, 160, 161, 162, 165, 166], "optim": [0, 13, 20, 34, 36, 100, 108, 109, 110, 113, 152], "whole": [0, 3, 6, 7, 9, 17, 26, 32, 36, 38, 65, 69, 80, 81, 84, 87, 88, 104, 149, 152, 155, 156, 166], "1ake": [0, 36], "trj": [0, 34, 61, 80, 83, 85], "4ake": [0, 36, 67, 87, 112, 114], "filenam": [0, 3, 5, 6, 14, 17, 19, 23, 25, 26, 34, 36, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 87, 93, 95, 101, 102, 106, 110, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148], "rmsfit": 0, "run": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 48, 56, 59, 81, 87, 89, 110, 112, 114, 148, 151, 153, 166], "object": [0, 2, 8, 12, 13, 14, 15, 16, 17, 18, 20, 23, 24, 25, 28, 30, 34, 35, 37, 38, 40, 42, 44, 47, 48, 49, 52, 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55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 78, 79, 80, 81, 87, 89, 91, 92, 93, 104, 110, 114, 115, 121, 161], "fasta2select": [0, 34, 36], "feed": [0, 23, 26], "result": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 91, 92, 93, 99, 100, 104, 105, 107, 108, 109, 110, 112, 114, 147, 148, 152, 155], "dictionari": [0, 2, 4, 6, 17, 18, 19, 20, 23, 26, 28, 34, 36, 38, 40, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 70, 71, 72, 73, 74, 76, 80, 81, 89, 92, 110, 148, 149], "seldict": 0, "see": [0, 1, 2, 3, 6, 7, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 36, 37, 38, 39, 42, 44, 47, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 83, 87, 89, 91, 93, 95, 99, 100, 102, 103, 104, 110, 114, 121, 133, 137, 141, 142, 147, 149, 150, 151, 152, 153, 161, 163, 164, 165, 166], "document": [0, 2, 5, 6, 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150, 156, 161, 163, 164], "now": [0, 2, 4, 6, 8, 9, 10, 19, 20, 23, 28, 29, 30, 32, 33, 34, 36, 37, 42, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 79, 81, 84, 86, 87, 89, 91, 92, 93, 95, 96, 100, 103, 104, 110, 114, 115, 133, 134, 135, 137, 139, 141, 142, 147, 150], "exclus": [0, 20, 23, 35, 37, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 105, 106, 142], "access": [0, 1, 2, 3, 5, 6, 9, 18, 21, 23, 24, 25, 28, 29, 30, 34, 38, 39, 40, 42, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 86, 87, 89, 91, 92, 93, 95, 100, 105, 106, 110, 111, 112, 114, 136, 148, 166], "16": [0, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 32, 34, 36, 57, 59, 62, 65, 66, 79, 81, 84, 87, 90, 93, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 134, 139, 148, 149, 150, 163], "rms_fit_trj": 0, "deprec": [0, 4, 6, 8, 9, 19, 23, 24, 28, 30, 32, 33, 34, 35, 36, 37, 38, 39, 52, 55, 57, 59, 61, 70, 73, 74, 75, 76, 81, 87, 91, 92, 103, 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157, 161, 166], "wai": [0, 2, 4, 6, 8, 9, 13, 14, 19, 23, 24, 25, 29, 37, 40, 42, 49, 69, 76, 77, 80, 83, 86, 93, 109, 111, 112, 114, 115, 116, 117, 118, 119, 120, 136, 152, 155], "A": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 19, 22, 23, 24, 25, 28, 29, 30, 32, 34, 35, 36, 37, 38, 40, 44, 52, 54, 55, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 79, 80, 81, 82, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 104, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 132, 135, 139, 141, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161], "sel1": [0, 34, 36], "sel2": [0, 34, 36], "befor": [0, 2, 3, 4, 6, 10, 13, 14, 17, 24, 32, 36, 38, 39, 42, 44, 59, 65, 66, 69, 75, 76, 80, 87, 90, 91, 93, 99, 101, 102, 107, 108, 110, 114, 115, 139, 150, 152, 157, 158, 159], "its": [0, 3, 4, 8, 12, 13, 19, 23, 29, 32, 34, 37, 38, 40, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 79, 80, 82, 83, 86, 87, 89, 91, 93, 100, 104, 105, 106, 110, 113, 114, 121, 149, 152, 155], "coincid": [0, 100], "below": [0, 4, 5, 10, 17, 23, 29, 31, 32, 34, 36, 40, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 79, 80, 81, 86, 87, 103, 114, 121, 132], "explan": [0, 29, 59, 110, 149], "deriv": [0, 2, 6, 7, 11, 17, 38, 42, 44, 76, 80, 84, 93, 103, 110, 115, 145, 148], "shift": [0, 26, 87, 100, 105, 160], "behavior": [0, 34, 38, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 110, 114], "through": [0, 4, 6, 10, 11, 17, 20, 21, 23, 24, 25, 35, 38, 40, 41, 44, 49, 52, 55, 56, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 80, 81, 84, 86, 87, 89, 93, 100, 110, 112, 114, 123, 148, 160, 166], "construct": [0, 6, 8, 13, 19, 20, 34, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 86, 89, 93, 100, 105, 107, 110, 122, 148, 152], "alreadi": [0, 6, 7, 8, 23, 32, 42, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 83, 87, 93, 107, 114], "match": [0, 13, 16, 20, 23, 30, 34, 36, 49, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 78, 81, 87, 89, 91, 92, 155], "should": [0, 2, 3, 4, 6, 8, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 33, 34, 35, 36, 37, 38, 42, 44, 49, 52, 57, 59, 61, 62, 63, 65, 67, 75, 76, 80, 83, 85, 87, 89, 90, 91, 92, 96, 100, 103, 105, 106, 107, 110, 116, 117, 118, 119, 120, 131, 133, 134, 141, 142, 147, 148, 149, 156], "therefor": [0, 2, 6, 14, 17, 26, 27, 59, 65, 69, 75, 87, 104, 110, 141, 147], "preserv": [0, 8, 32, 34, 57, 61, 63, 65, 87], "exact": [0, 4, 17, 23, 29, 34, 69, 87], "either": [0, 4, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 28, 34, 36, 38, 40, 42, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 87, 92, 93, 99, 100, 101, 102, 104, 106, 107, 110, 111, 112, 114, 123, 133, 141, 148, 152, 159, 160, 166], "ani": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 16, 17, 23, 24, 25, 26, 28, 29, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 103, 104, 105, 106, 107, 110, 111, 113, 114, 121, 127, 128, 130, 132, 133, 137, 147, 148, 152, 153, 161, 166], "other": [0, 2, 3, 4, 6, 8, 9, 13, 16, 17, 19, 23, 25, 26, 28, 29, 30, 32, 34, 37, 38, 39, 40, 41, 42, 46, 47, 49, 50, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 104, 106, 110, 111, 114, 132, 133, 141, 147, 148, 149, 152, 153, 157, 161, 164, 166], "new": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 44, 46, 47, 48, 49, 50, 51, 52, 53, 55, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 104, 105, 106, 109, 110, 112, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 153, 161, 166], "made": [0, 4, 5, 6, 8, 9, 15, 17, 19, 25, 32, 49, 79, 80, 81, 87, 89, 92, 93, 99, 110, 114, 148, 152], "sort": [0, 23, 24, 26, 32, 33, 38, 45, 87, 89, 90, 91, 92, 110, 114], "index": [0, 2, 6, 8, 23, 24, 25, 26, 28, 29, 30, 32, 34, 36, 37, 38, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 90, 91, 92, 100, 102, 110, 115, 116, 117, 118, 119, 120, 121, 130, 141, 142, 148, 149, 166], "destroi": 0, "correspond": [0, 3, 6, 8, 9, 12, 13, 18, 23, 25, 32, 34, 36, 37, 38, 39, 42, 43, 49, 52, 55, 58, 59, 61, 62, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 99, 100, 103, 105, 107, 110, 113, 114, 130, 150, 155, 157, 158], "safest": 0, "mix": [0, 38], "string": [0, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 29, 32, 34, 36, 37, 38, 40, 42, 48, 58, 59, 62, 63, 65, 67, 69, 78, 79, 80, 81, 86, 87, 89, 91, 93, 101, 103, 106, 109, 111, 114, 115, 116, 117, 118, 119, 120, 121, 133, 135, 141, 142, 149, 150, 155, 162, 163, 164], "paramet": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "str": [0, 2, 3, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 51, 52, 55, 57, 58, 59, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 86, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 106, 107, 110, 113, 114, 116, 118, 121, 132, 139, 145, 149, 155, 159, 163, 164], "dict": [0, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 25, 26, 29, 30, 32, 34, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 81, 82, 84, 87, 89, 90, 92, 93, 101, 103, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 161], "tupl": [0, 4, 6, 10, 18, 19, 20, 26, 32, 34, 35, 36, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 79, 81, 87, 90, 91, 92, 93, 99, 103, 104, 109, 110, 141, 147, 148, 150, 152], "option": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "oper": [0, 2, 6, 18, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 81, 87, 89, 92, 100, 101, 104, 105, 107, 110, 111, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 160], "valid": [0, 8, 9, 32, 34, 35, 36, 42, 44, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 81, 105, 110, 137, 142, 143, 149], "ident": [0, 17, 20, 32, 34, 36, 57, 58, 87, 92, 93, 109, 110, 130, 148], "where": [0, 1, 5, 6, 7, 8, 15, 17, 18, 19, 20, 23, 29, 32, 33, 34, 35, 36, 37, 38, 40, 44, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 110, 112, 114, 133, 141, 147, 152, 155, 156, 158, 161], "return": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "clustalw": [0, 34, 36], "stamp": [0, 2, 23, 34, 36], "2": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 46, 47, 48, 49, 51, 52, 53, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 106, 109, 110, 113, 114, 132, 133, 134, 135, 137, 141, 142, 143, 145, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164, 166], "3": [0, 2, 3, 4, 6, 7, 8, 9, 10, 13, 15, 16, 17, 18, 20, 21, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 81, 84, 87, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 113, 114, 132, 133, 134, 137, 141, 142, 147, 148, 149, 150, 152, 157, 158, 159, 160, 161, 163, 164, 166], "gener": [0, 1, 5, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 32, 34, 35, 36, 38, 39, 40, 44, 47, 52, 58, 59, 61, 62, 63, 65, 70, 73, 74, 76, 78, 80, 81, 82, 87, 89, 91, 92, 93, 100, 102, 105, 107, 109, 110, 112, 113, 114, 130, 131, 134, 139, 141, 147, 148, 156, 161, 163, 164, 166], "equival": [0, 6, 18, 22, 24, 29, 36, 37, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 82, 87, 106, 107, 114, 142], "each": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 70, 72, 73, 74, 75, 76, 77, 80, 81, 86, 87, 89, 90, 91, 92, 93, 99, 100, 103, 104, 105, 108, 110, 112, 115, 121, 132, 141, 147, 148, 149, 155, 158, 160], "list": [0, 2, 3, 4, 6, 9, 12, 13, 14, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 109, 112, 113, 114, 115, 121, 123, 126, 127, 128, 129, 131, 137, 138, 141, 142, 143, 144, 147, 148, 149, 152, 158, 161, 166], "defin": [0, 2, 3, 4, 6, 13, 16, 17, 20, 23, 24, 25, 28, 34, 36, 37, 38, 40, 44, 52, 57, 59, 61, 65, 66, 69, 75, 76, 79, 80, 87, 91, 92, 93, 100, 101, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 132, 141, 145, 147, 148, 150, 152, 153, 155, 158, 159, 161], "describ": [0, 2, 3, 11, 13, 15, 16, 17, 18, 23, 25, 29, 31, 34, 36, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 103, 104, 105, 110, 112, 113, 114, 121, 139, 142, 151, 152, 162], "under": [0, 17, 23, 25, 26, 34, 36, 37, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 81, 87, 93, 99, 100, 103, 105, 110, 120, 148, 152, 166], "bool": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 96, 100, 101, 103, 104, 107, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 153, 154, 155, 156, 157, 158, 159, 160], "whether": [0, 9, 13, 14, 16, 17, 20, 23, 24, 26, 34, 40, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 89, 91, 103, 106, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152], "default": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 26, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 44, 47, 48, 49, 50, 51, 52, 53, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 103, 104, 106, 107, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 149, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "array_lik": [0, 2, 3, 6, 9, 10, 14, 15, 17, 18, 23, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 92, 100, 101, 102, 104, 107, 109, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 155, 158], "choos": [0, 6, 8, 20, 23, 32, 34, 77, 80, 87, 89, 91, 155, 159], "With": [0, 6, 15, 20, 26, 34, 36, 37, 40, 46, 77, 99, 155, 158], "weigh": [0, 34, 36, 155, 158], "equal": [0, 1, 8, 13, 18, 23, 32, 34, 36, 37, 38, 44, 59, 89, 92, 99, 100, 103, 110, 155, 158, 163], "float": [0, 4, 6, 7, 8, 10, 13, 15, 16, 17, 19, 20, 23, 24, 25, 28, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 44, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 81, 84, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 114, 147, 149, 150, 154, 155, 158, 161, 163, 164], "same": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 16, 17, 20, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 44, 48, 49, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 92, 93, 99, 100, 101, 104, 105, 109, 110, 114, 121, 130, 147, 148, 150, 155, 157, 158, 160], "length": [0, 2, 3, 6, 8, 10, 13, 14, 17, 19, 20, 22, 23, 24, 29, 30, 32, 33, 34, 36, 38, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 84, 87, 90, 91, 92, 93, 100, 101, 104, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 158, 161], "element": [0, 3, 6, 12, 13, 14, 16, 17, 18, 23, 32, 34, 36, 37, 38, 48, 49, 59, 65, 75, 87, 90, 91, 99, 105, 110, 114, 115, 123, 126, 128, 135, 137, 138, 141, 142, 143, 149, 150, 155, 158], "reject": [0, 25, 34, 36], "differ": [0, 1, 2, 3, 4, 6, 8, 11, 13, 16, 17, 19, 20, 23, 24, 25, 32, 34, 36, 37, 38, 42, 44, 49, 52, 55, 56, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 83, 84, 86, 87, 91, 92, 93, 101, 109, 110, 112, 113, 114, 121, 126, 137, 142, 148, 152, 161], "more": [0, 1, 2, 3, 4, 8, 9, 10, 11, 13, 16, 17, 23, 24, 25, 32, 34, 36, 37, 38, 39, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 88, 91, 93, 100, 101, 102, 103, 105, 106, 109, 110, 111, 112, 114, 141, 142, 147, 148, 152, 156, 164, 166], "than": [0, 3, 4, 6, 8, 9, 10, 15, 17, 19, 20, 23, 24, 32, 34, 36, 37, 38, 41, 42, 51, 57, 59, 65, 67, 69, 75, 77, 81, 87, 91, 92, 93, 99, 100, 104, 105, 106, 110, 114, 147, 150, 156], "Will": [0, 4, 6, 8, 9, 17, 18, 20, 24, 28, 32, 33, 35, 36, 38, 44, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 93, 104], "rais": [0, 2, 3, 6, 9, 23, 26, 29, 30, 32, 36, 40, 42, 43, 44, 49, 52, 55, 57, 58, 59, 60, 61, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 93, 95, 102, 103, 104, 106, 109, 110, 114, 121, 135, 137, 145, 147, 157, 161], "selectionerror": [0, 36, 89, 95], "doe": [0, 3, 6, 13, 14, 23, 24, 29, 32, 34, 36, 37, 59, 61, 64, 65, 67, 69, 70, 77, 78, 80, 82, 84, 87, 91, 93, 95, 100, 101, 103, 104, 110, 114, 121, 131, 138, 141, 151, 153, 156], "try": [0, 20, 23, 42, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 79, 81, 83, 85, 110, 131, 133, 142, 147, 162], "prepar": [0, 93], "drop": [0, 17, 58, 87, 110], "residu": [0, 3, 6, 9, 10, 19, 23, 25, 28, 30, 31, 32, 35, 36, 37, 38, 48, 65, 66, 67, 80, 86, 87, 89, 90, 91, 93, 95, 96, 110, 112, 114, 123, 125, 126, 127, 128, 130, 131, 132, 134, 137, 139, 140, 141, 142, 144, 148, 159, 160], "non": [0, 2, 3, 6, 8, 9, 17, 23, 24, 25, 29, 30, 32, 33, 36, 38, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 89, 103, 104, 105, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 126, 141, 156, 157], "get_matching_atom": 0, "detail": [0, 4, 6, 7, 8, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 49, 52, 59, 61, 65, 75, 79, 80, 90, 102, 103, 110, 111, 114, 141, 142, 148, 152, 166], "e": [0, 2, 4, 6, 9, 13, 17, 18, 23, 24, 25, 26, 28, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 86, 87, 89, 91, 92, 93, 99, 100, 101, 103, 104, 105, 109, 110, 111, 112, 113, 114, 115, 137, 141, 147, 148, 149, 150, 152, 153, 154, 157, 158, 161, 162, 163, 164, 166], "context": [0, 23, 44, 48, 58, 59, 65, 69, 76, 78, 80, 101, 102, 106, 110, 121, 153], "rest": [0, 3, 6, 150], "ligand": [0, 3, 6, 19, 35, 38, 78, 93], "surround": 0, "water": [0, 6, 7, 8, 10, 20, 23, 24, 39, 87, 88, 93, 99, 112, 113, 114, 132, 150, 161], "old_rmsd": 0, "new_rmsd": 0, "after": [0, 1, 2, 3, 6, 8, 10, 17, 18, 20, 23, 24, 26, 32, 34, 35, 36, 37, 38, 42, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 86, 87, 91, 93, 103, 106, 107, 110, 114, 141, 147, 149, 152, 157, 158, 162], "effici": [0, 1, 10, 18, 34, 65, 68, 69, 73, 103, 113, 148], "method": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 16, 17, 19, 20, 22, 23, 25, 26, 28, 29, 31, 32, 33, 35, 36, 37, 38, 40, 42, 46, 49, 52, 55, 56, 57, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 77, 81, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 100, 101, 102, 103, 105, 107, 108, 109, 110, 112, 113, 114, 115, 121, 136, 145, 147, 148, 150, 152, 156, 159], "ad": [0, 1, 2, 3, 4, 6, 9, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 30, 32, 36, 37, 42, 49, 52, 55, 56, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 87, 89, 90, 91, 92, 93, 99, 100, 102, 103, 104, 110, 132, 133, 135, 137, 138, 139, 141, 142, 143, 145, 147, 149, 152], "toggl": [0, 38, 93, 142], "8": [0, 2, 4, 9, 26, 31, 34, 36, 37, 40, 48, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 70, 72, 73, 74, 76, 78, 81, 84, 87, 89, 91, 92, 93, 100, 104, 110, 114, 115, 116, 117, 118, 119, 120, 126, 137, 142, 148, 149, 150, 160, 161, 163, 164], "check": [0, 4, 6, 9, 10, 13, 19, 20, 23, 31, 32, 33, 34, 36, 38, 42, 44, 52, 55, 58, 59, 61, 65, 70, 71, 72, 73, 74, 76, 77, 78, 81, 87, 92, 100, 105, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160], "includ": [0, 1, 3, 5, 9, 11, 13, 17, 23, 24, 25, 29, 32, 34, 36, 38, 42, 44, 48, 52, 55, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 89, 90, 93, 99, 100, 103, 106, 109, 110, 114, 121, 132, 138, 142, 148, 150, 152, 166], "work": [0, 2, 4, 6, 8, 9, 10, 11, 13, 16, 17, 18, 23, 28, 31, 36, 37, 38, 39, 40, 49, 52, 55, 58, 59, 61, 68, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 95, 100, 103, 104, 105, 106, 110, 112, 113, 114, 115, 121, 132, 142, 147, 152, 155, 160, 166], "incomplet": [0, 9, 27], "lenient": 0, "wherea": [0, 8, 32, 34, 87, 110, 111], "old": [0, 52, 80, 86, 87, 93, 110, 148], "kwarg": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 18, 23, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 86, 87, 91, 92, 93, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 147, 153], "replac": [0, 6, 12, 23, 58, 87, 93, 99, 100, 106, 110, 147, 148], "mass_weight": [0, 34, 36], "sinc": [0, 4, 6, 8, 9, 14, 17, 19, 21, 23, 24, 28, 32, 33, 34, 35, 36, 38, 39, 49, 52, 65, 69, 75, 76, 81, 87, 91, 114, 141, 156], "instead": [0, 2, 3, 4, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 42, 49, 51, 52, 53, 54, 55, 56, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 80, 81, 87, 89, 91, 92, 93, 96, 99, 100, 101, 102, 104, 105, 110, 114, 115, 116, 117, 118, 119, 120, 121, 126, 137, 148, 152, 159], "prefix": [0, 23, 34, 87, 103, 114], "rmsfit_": 0, "forc": [0, 20, 30, 31, 39, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 82, 84, 85, 87, 89, 92, 93, 100, 102, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 161], "in_memori": [0, 17, 36, 37, 81, 93], "both": [0, 2, 3, 4, 6, 9, 10, 14, 17, 23, 24, 26, 29, 30, 32, 34, 36, 38, 40, 49, 54, 56, 58, 61, 65, 69, 72, 80, 87, 92, 99, 102, 103, 112, 113, 114, 130, 133, 140, 141, 164], "must": [0, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 18, 20, 23, 24, 26, 29, 32, 34, 36, 38, 40, 42, 44, 49, 52, 55, 59, 61, 65, 67, 68, 69, 70, 71, 73, 74, 76, 77, 80, 81, 84, 87, 90, 91, 93, 99, 100, 104, 105, 106, 107, 108, 110, 114, 115, 141, 145, 147, 152, 155, 157, 161], "instanc": [0, 2, 3, 4, 6, 7, 8, 9, 13, 16, 17, 18, 23, 25, 28, 29, 32, 33, 34, 35, 36, 39, 40, 42, 43, 44, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 84, 86, 87, 88, 91, 92, 93, 100, 101, 103, 105, 106, 110, 112, 114, 115, 141, 145, 148, 150, 152, 159, 163, 164, 165, 166], "output": [0, 2, 6, 13, 14, 17, 18, 19, 23, 26, 32, 34, 35, 36, 40, 49, 50, 51, 52, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 86, 87, 89, 91, 100, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 128, 148, 157], "format": [0, 3, 4, 6, 10, 13, 14, 15, 16, 17, 18, 23, 25, 26, 34, 37, 38, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 56, 58, 59, 60, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 77, 78, 79, 81, 82, 84, 85, 87, 91, 92, 93, 95, 100, 103, 104, 105, 109, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 143, 145, 147, 149, 150, 151, 162, 166], "determin": [0, 3, 4, 6, 8, 9, 10, 13, 18, 22, 23, 24, 25, 26, 29, 32, 33, 34, 38, 42, 44, 59, 65, 79, 80, 87, 91, 93, 100, 104, 108, 110, 113, 147, 157], "extens": [0, 4, 6, 17, 23, 25, 34, 44, 51, 59, 65, 66, 67, 68, 69, 77, 78, 79, 80, 85, 87, 93, 110, 111, 116, 117, 118, 119, 120, 132, 148, 151, 162], "One": [0, 2, 3, 6, 13, 16, 23, 24, 25, 26, 34, 37, 38, 48, 87, 93, 101, 114, 152, 161], "save": [0, 3, 4, 6, 7, 8, 10, 14, 17, 18, 20, 26, 28, 29, 32, 34, 36, 37, 52, 58, 59, 61, 63, 65, 69, 73, 74, 78, 83, 100, 101, 102, 106], "an": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 52, 55, 56, 57, 58, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "altern": [0, 6, 9, 17, 19, 22, 23, 24, 28, 32, 41, 44, 49, 62, 65, 66, 87, 92, 93, 104, 110, 114, 121, 134, 152], "np": [0, 2, 3, 4, 5, 6, 8, 17, 20, 23, 24, 26, 28, 29, 32, 34, 36, 37, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 93, 100, 101, 102, 104, 108, 109, 110, 114, 147, 149, 152, 163, 164], "savetxt": [0, 4, 28, 36], "subdomain": [0, 105], "against": [0, 17, 69, 92, 105], "written": [0, 2, 6, 14, 17, 19, 23, 34, 38, 40, 48, 51, 52, 55, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 80, 83, 84, 87, 91, 93, 101, 102, 103, 104, 106, 110, 115, 116, 117, 118, 119, 120, 121, 139, 142, 148, 152, 166], "prepend": [0, 34], "toler": [0, 4, 87, 89, 163, 164], "given": [0, 3, 4, 5, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 29, 30, 32, 34, 35, 36, 37, 38, 40, 42, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 101, 102, 106, 110, 114, 132, 136, 141, 147, 150, 152, 155, 156, 157, 158, 159, 160, 162], "find": [0, 9, 10, 13, 19, 20, 23, 24, 25, 32, 34, 38, 40, 42, 43, 46, 52, 61, 77, 83, 87, 90, 96, 101, 110, 111, 114, 131, 141, 147], "fail": [0, 6, 26, 28, 38, 49, 59, 65, 67, 69, 73, 83, 85, 87, 95, 104, 110, 145], "t": [0, 2, 4, 7, 17, 20, 22, 24, 29, 30, 32, 34, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 52, 55, 56, 58, 59, 60, 61, 64, 65, 66, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 90, 91, 99, 100, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 152, 153, 156, 157, 158, 159, 160, 161], "found": [0, 2, 9, 19, 20, 23, 24, 25, 34, 38, 40, 42, 43, 49, 59, 65, 70, 77, 78, 79, 86, 87, 89, 91, 93, 108, 110, 111, 132, 147, 148, 166], "overwrit": [0, 20, 35, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "perman": [0, 37, 93], "switch": [0, 4, 9, 24, 38, 40, 105], "memori": [0, 8, 10, 13, 14, 18, 29, 36, 37, 40, 41, 42, 44, 53, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 85, 87, 90, 93, 110, 147, 157], "place": [0, 6, 9, 14, 17, 23, 38, 40, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 90, 93, 100, 102, 104, 108, 109, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 154, 160], "which": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 23, 24, 25, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 46, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 165, 166], "improv": [0, 15, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 89, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "substanti": [0, 81], "some": [0, 4, 8, 9, 17, 20, 23, 26, 28, 32, 37, 38, 39, 40, 42, 47, 48, 49, 59, 61, 65, 68, 69, 76, 78, 79, 80, 83, 87, 89, 91, 104, 109, 110, 111, 135, 146, 147, 148, 150, 152, 161, 165, 166], "out": [0, 4, 17, 22, 23, 32, 36, 37, 38, 39, 40, 42, 44, 45, 52, 55, 56, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 80, 81, 87, 93, 103, 109, 115, 141, 148, 161, 162, 165, 166], "ignor": [0, 6, 13, 16, 18, 23, 42, 44, 59, 63, 65, 66, 75, 80, 81, 82, 84, 87, 91, 92, 93, 103, 104, 114, 126, 132, 133, 135, 137, 141, 147, 149], "verbos": [0, 2, 3, 4, 6, 7, 8, 9, 13, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 81, 93, 103], "logger": [0, 38, 103], "inform": [0, 8, 9, 13, 16, 17, 20, 23, 24, 25, 33, 34, 37, 38, 42, 49, 50, 52, 55, 57, 59, 61, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 80, 83, 84, 87, 90, 91, 93, 100, 101, 102, 104, 110, 114, 122, 123, 126, 127, 128, 130, 132, 133, 137, 138, 139, 140, 141, 142, 143, 144, 146, 148, 151, 165, 166], "progress": [0, 2, 3, 4, 6, 7, 8, 9, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 93, 103], "reference_atom": [0, 104], "mobile_atom": 0, "insid": [0, 2, 5, 20, 23, 37, 80, 83, 87, 89, 92, 99, 105, 111, 113, 121, 152, 160], "rmsd_align": 0, "valu": [0, 2, 3, 4, 6, 8, 9, 13, 14, 16, 17, 20, 23, 24, 26, 29, 30, 32, 34, 35, 36, 37, 38, 40, 41, 42, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 149, 150, 153, 161, 163, 164], "least": [0, 2, 3, 4, 6, 8, 9, 13, 15, 19, 23, 25, 29, 30, 32, 36, 44, 52, 55, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 77, 81, 106, 108, 110, 126, 137, 142], "minimim": 0, "numpi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 44, 52, 53, 55, 59, 61, 70, 73, 74, 76, 79, 80, 84, 87, 88, 89, 90, 91, 92, 93, 100, 104, 105, 109, 110, 112, 147, 152, 153, 164, 166], "ndarrai": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 19, 20, 23, 24, 28, 29, 30, 33, 34, 35, 36, 40, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 84, 87, 91, 92, 93, 100, 102, 104, 105, 107, 108, 109, 110, 112, 147], "alia": [0, 4, 6, 9, 23, 24, 28, 30, 32, 33, 35, 36, 38, 87, 89, 91, 150], "attribut": [0, 2, 3, 4, 6, 7, 9, 18, 19, 20, 23, 24, 26, 28, 30, 32, 33, 34, 35, 36, 38, 39, 40, 42, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 81, 83, 84, 87, 89, 90, 92, 93, 94, 100, 101, 102, 107, 110, 112, 114, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 152, 153, 161], "reflect": [0, 32, 77, 79, 84, 87, 105, 109, 110, 114], "upon": [0, 20, 59, 61, 75, 76, 77, 78, 92, 93, 103, 145, 147, 152], "recommend": [0, 2, 24, 38, 59, 65, 110, 111, 112, 114, 147, 166], "wrap": [0, 2, 3, 6, 13, 16, 18, 29, 36, 61, 65, 87, 91, 106, 107, 110, 152, 156, 158, 159], "statement": [0, 32, 80, 110, 115], "final": [0, 4, 6, 9, 13, 16, 17, 18, 20, 28, 32, 37, 38, 49, 57, 65, 75, 87, 90, 92, 107, 112, 114], "guarante": [0, 6, 24, 67, 104, 110], "restor": [0, 6], "log": [0, 2, 3, 6, 9, 17, 29, 30, 32, 36, 38, 80, 111, 148], "level": [0, 5, 23, 59, 73, 76, 78, 89, 90, 96, 103, 106, 110], "except": [0, 23, 26, 35, 38, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 81, 84, 87, 89, 91, 93, 110, 111, 148, 152], "represent": [0, 14, 18, 23, 34, 38, 52, 55, 57, 61, 71, 80, 92, 93, 104, 120, 121, 126, 137, 138], "remaind": [0, 112], "python": [0, 2, 6, 17, 23, 26, 39, 40, 46, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 83, 84, 86, 87, 88, 89, 91, 101, 102, 103, 106, 108, 109, 110, 111, 113, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 149, 150, 152, 165, 166], "session": [0, 69, 112], "memoryread": [0, 36, 79, 80, 93], "alwai": [0, 2, 4, 6, 13, 16, 17, 26, 32, 33, 36, 40, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 76, 80, 81, 87, 91, 93, 109, 110, 112, 114, 139, 147, 148, 152, 161], "treat": [0, 6, 19, 22, 24, 37, 38, 42, 59, 62, 77, 87, 92, 93, 104, 112, 132, 141, 148, 163, 164], "had": [0, 35, 156], "directori": [0, 23, 26, 34, 73, 106, 112, 113, 132], "19": [0, 9, 10, 32, 35, 61, 65, 66, 69, 76, 77, 81, 87, 91, 92, 93, 95, 99, 100, 104, 105, 110, 133, 141, 149, 150, 161], "support": [0, 2, 4, 6, 10, 17, 18, 23, 26, 28, 35, 36, 37, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 83, 85, 87, 89, 93, 100, 101, 102, 106, 110, 111, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 151, 155, 161, 166], "start": [0, 1, 2, 3, 4, 6, 8, 9, 16, 18, 20, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 79, 80, 81, 84, 88, 93, 101, 103, 110, 112, 114, 139, 142, 148, 149, 157, 166], "stop": [0, 2, 3, 4, 6, 8, 9, 23, 24, 26, 28, 29, 30, 32, 34, 35, 36, 37, 39, 41, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 84, 93, 101, 103], "These": [0, 1, 2, 4, 5, 9, 17, 28, 29, 32, 34, 35, 36, 37, 40, 52, 55, 57, 58, 59, 61, 65, 68, 70, 72, 73, 74, 76, 80, 81, 87, 89, 91, 100, 101, 102, 105, 106, 107, 132, 157, 165], "pass": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 34, 35, 36, 37, 38, 40, 42, 44, 46, 47, 48, 49, 50, 52, 55, 56, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 85, 86, 87, 89, 91, 92, 93, 99, 103, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148], "store": [0, 2, 3, 4, 5, 6, 8, 9, 13, 14, 19, 23, 25, 28, 32, 33, 34, 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61, 65, 69, 75, 92, 106, 110, 150], "hold": [6, 40, 44, 65, 80, 81, 84, 90, 105], "annot": [6, 34, 65], "readabl": [6, 40, 110], "understand": [6, 49, 68, 87, 94, 105, 110], "known": [6, 29, 43, 59, 80, 110, 112, 142, 161], "issu": [6, 8, 26, 27, 40, 42, 49, 52, 59, 61, 65, 69, 75, 80, 81, 87, 90, 100, 110, 114, 134, 137, 141, 142, 148, 153, 166], "griddataformat": 6, "right": [6, 20, 23, 33, 36, 55, 65, 75, 83, 87, 91, 110, 114], "awai": [6, 38, 87, 114], "becaus": [6, 10, 12, 32, 34, 36, 38, 40, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 77, 80, 81, 87, 92, 93, 104, 110, 113, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 152, 161], "reliabl": [6, 32, 69, 80, 100, 152], "detect": [6, 49, 52, 58, 59, 61, 69, 79, 93, 110, 121, 123, 141, 157], "conveni": [6, 18, 23, 32, 34, 40, 44, 69, 87, 93, 115, 152, 161], "less": [6, 8, 19, 20, 23, 24, 32, 34, 38, 42, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 99, 100, 104, 147], "demonstr": [6, 29, 89], "itself": [6, 13, 17, 18, 23, 24, 26, 35, 40, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 87, 110, 111, 112, 114, 121], "algebra": [6, 87, 114], "subtract": [6, 13, 36, 87], "saniti": 6, "sure": [6, 31, 42, 59, 83, 87, 91, 114, 166], "ndindex": 6, "check_compat": 6, "arithmet": 6, "scalar": [6, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 104, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "resampl": [6, 12, 17], "typeerror": [6, 36, 59, 79, 80, 81, 87, 91, 93, 110], "particl": [6, 10, 19, 29, 35, 37, 58, 59, 68, 87, 93, 99, 100, 105, 107, 130, 150, 156, 163, 164], "spc": [6, 38, 87, 114, 161], "tip3p": [6, 38, 161], "997": [6, 161], "cm": [6, 23, 28, 149, 161], "molar": [6, 161], "mol": [6, 23, 28, 47, 49, 63, 68, 69, 70, 112, 161], "runtimeerror": [6, 23, 59, 137], "unknown": [6, 135, 137, 138, 141, 151], "go": 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"hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel-deprecated"]], "HELANAL \u2014 analysis of protein helices": [[22, "helanal-analysis-of-protein-helices"]], "Example use": [[22, "example-use"]], "HOLE analysis \u2014 MDAnalysis.analysis.hole2": [[23, "hole-analysis-mdanalysis-analysis-hole2"]], "Module": [[23, "module-MDAnalysis.analysis.hole2"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2": [[23, "id3"]], "Using HOLE on a PDB file": [[23, "using-hole-on-a-pdb-file"]], "Using HOLE on a trajectory": [[23, "using-hole-on-a-trajectory"]], "Using HOLE with VMD": [[23, "using-hole-with-vmd"]], "Analyzing a full trajectory": [[23, "analyzing-a-full-trajectory"]], "Creating subsampled HOLE surface": [[23, "creating-subsampled-hole-surface"]], "Loading a trajectory into VMD with subsampling": [[23, "loading-a-trajectory-into-vmd-with-subsampling"]], "Creating a subsampled trajectory": [[23, "creating-a-subsampled-trajectory"]], "Functions and classes": [[23, "functions-and-classes"]], "Utility functions and templates": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.helper": [[23, "hole-analysis-mdanalysis-analysis-hole2-helper"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.templates": [[23, "hole-analysis-mdanalysis-analysis-hole2-templates"]], "Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "hydrogen-bond-analysis-mdanalysis-analysis-hydrogenbonds-hbond-analysis"]], "Example use of HydrogenBondAnalysis": [[24, "example-use-of-hydrogenbondanalysis"]], "The class and its methods": [[24, "the-class-and-its-methods"]], "Leaflet identification \u2014 MDAnalysis.analysis.leaflet": [[25, "leaflet-identification-mdanalysis-analysis-leaflet"]], "Algorithm": [[25, "algorithm"]], "Classes and Functions": [[25, "classes-and-functions"], [32, "classes-and-functions"]], "Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna": [[26, "generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-legacy-x3dna"]], "Single structure": [[26, "single-structure"]], "Trajectory": [[26, "trajectory"]], "Utilities": [[26, "utilities"]], "MDAnalysis.analysis.legacy \u2014 Legacy analysis code": [[27, "mdanalysis-analysis-legacy-legacy-analysis-code"]], "Legacy modules": [[27, "legacy-modules"]], "Linear Density \u2014 MDAnalysis.analysis.lineardensity": [[28, "linear-density-mdanalysis-analysis-lineardensity"]], "Mean Squared Displacement \u2014 MDAnalysis.analysis.msd": [[29, "mean-squared-displacement-mdanalysis-analysis-msd"]], "Computing an MSD": [[29, "computing-an-msd"]], "Computing Self-Diffusivity": [[29, "computing-self-diffusivity"]], "Combining Multiple Replicates": [[29, "combining-multiple-replicates"]], "Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids": [[30, "updated-nucleic-acid-analysis-mdanalysis-analysis-nucleicacids"]], "Distances": [[30, "distances"], [31, "distances"]], "Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo": [[31, "nucleic-acid-analysis-mdanalysis-analysis-nuclinfo"]], "Phases": [[31, "phases"]], "Dihedral angles": [[31, "dihedral-angles"]], "Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca": [[32, "principal-component-analysis-pca-mdanalysis-analysis-pca"]], "PCA Tutorial": [[32, "pca-tutorial"]], "Polymer analysis \u2014 MDAnalysis.analysis.polymer": [[33, "polymer-analysis-mdanalysis-analysis-polymer"]], "Calculating path similarity \u2014 MDAnalysis.analysis.psa": [[34, "calculating-path-similarity-mdanalysis-analysis-psa"]], "Helper functions and variables": [[34, "helper-functions-and-variables"]], "Classes, methods, and functions": [[34, "classes-methods-and-functions"]], "Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf": [[35, "radial-distribution-functions-mdanalysis-analysis-rdf"]], "Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms": [[36, "calculating-root-mean-square-quantities-mdanalysis-analysis-rms"]], "Calculating RMSD for multiple domains": [[36, "calculating-rmsd-for-multiple-domains"]], "Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics": [[37, "water-dynamics-analysis-mdanalysis-analysis-waterdynamics"]], "Example use of the analysis classes": [[37, "example-use-of-the-analysis-classes"]], "HydrogenBondLifetimes": [[37, "hydrogenbondlifetimes"]], "WaterOrientationalRelaxation": [[37, "waterorientationalrelaxation"], [37, "id76"]], "AngularDistribution": [[37, "angulardistribution"], [37, "id77"]], "MeanSquareDisplacement": [[37, "meansquaredisplacement"], [37, "id78"]], "SurvivalProbability": [[37, "survivalprobability"], [37, "id79"]], "Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis": [[38, "water-bridge-analysis-mdanalysis-analysis-hydrogenbonds-waterbridgeanalysis"]], "Theory": [[38, "theory"]], "Output as Network": [[38, "output-as-network"]], "Output as Timeseries": [[38, "output-as-timeseries"]], "Detection of water bridges": [[38, "detection-of-water-bridges"]], "Default heavy atom names for CHARMM27 force field.": [[38, "id69"]], "Heavy atom types for GLYCAM06 force field.": [[38, "id70"]], "How to perform WaterBridgeAnalysis": [[38, "how-to-perform-waterbridgeanalysis"]], "Use count_by_type": [[38, "use-count-by-type"]], "Use count_by_time": [[38, "use-count-by-time"]], "Analysis modules": [[39, "analysis-modules"]], "Building blocks for Analysis": [[39, "building-blocks-for-analysis"]], "Distances and contacts": [[39, "distances-and-contacts"]], "Hydrogen bonding": [[39, "hydrogen-bonding"]], "Membranes and membrane proteins": [[39, "membranes-and-membrane-proteins"]], "Nucleic acids": [[39, "nucleic-acids"]], "Polymers": [[39, "polymers"]], "Structure": [[39, "structure"]], "Macromolecules": [[39, "macromolecules"]], "Liquids": [[39, "liquids"]], "Volumetric analysis": [[39, "volumetric-analysis"]], "Dimensionality Reduction": [[39, "dimensionality-reduction"]], "Legacy analysis modules": [[39, "legacy-analysis-modules"]], "Data": [[39, "data"], [161, "data"], [162, "data"]], "EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR": [[40, "edr-auxiliary-reader-mdanalysis-auxiliary-edr"]], "Background": [[40, "background"]], "Standalone Usage of the EDRReader": [[40, "standalone-usage-of-the-edrreader"]], "Adding EDR data to trajectories": [[40, "adding-edr-data-to-trajectories"]], "XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG": [[41, "xvg-auxiliary-reader-mdanalysis-auxiliary-xvg"]], "XVG Readers": [[41, "xvg-readers"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary.base": [[42, "auxiliary-readers-mdanalysis-auxiliary-base"]], "Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core": [[43, "common-functions-for-auxiliary-reading-mdanalysis-auxiliary-core"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary": [[44, "auxiliary-readers-mdanalysis-auxiliary"]], "Supported formats": [[44, "supported-formats"]], "Auxiliary API": [[44, "auxiliary-api"]], "Auxiliaries and trajectories": [[44, "auxiliaries-and-trajectories"]], "Adding an auxiliary to a trajectory": [[44, "adding-an-auxiliary-to-a-trajectory"]], "Iterating by an auxiliary": [[44, "iterating-by-an-auxiliary"]], "Accessing auxiliary attributes": [[44, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[44, "recreating-auxiliaries"]], "AuxStep class": [[44, "auxstep-class"]], "Attributes": [[44, "attributes"], [44, "id2"], [80, "attributes"], [80, "id19"], [80, "id21"]], "Methods": [[44, "methods"], [44, "id3"], [80, "methods"], [80, "id18"], [80, "id20"], [80, "id22"]], "AuxReader class": [[44, "auxreader-class"]], "Registry": [[44, "registry"], [80, "registry"]], "Replicating auxiliaries": [[44, "replicating-auxiliaries"]], "Auxiliary modules": [[45, "auxiliary-modules"]], "Converter modules": [[46, "converter-modules"]], "OpenMM topology parser MDAnalysis.converters.OpenMMParser": [[47, "openmm-topology-parser-mdanalysis-converters-openmmparser"]], "OpenMM structure I/O \u2014 MDAnalysis.converters.OpenMM": [[47, "openmm-structure-i-o-mdanalysis-converters-openmm"]], "ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser": [[48, "parmed-topology-parser-mdanalysis-converters-parmedparser"]], "ParmEd structure I/O \u2014 MDAnalysis.converters.ParmEd": [[48, "parmed-structure-i-o-mdanalysis-converters-parmed"]], "RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser": [[49, "rdkit-topology-parser-mdanalysis-converters-rdkitparser"]], "RDKit molecule I/O \u2014 MDAnalysis.converters.RDKit": [[49, "rdkit-molecule-i-o-mdanalysis-converters-rdkit"]], "Base classes \u2014 MDAnalysis.converters.base": [[50, "base-classes-mdanalysis-converters-base"]], "CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD": [[51, "crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd"]], "DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD": [[52, "dcd-trajectory-i-o-mdanalysis-coordinates-dcd"]], "DL_Poly format reader MDAnalysis.coordinates.DLPoly": [[53, "dl-poly-format-reader-mdanalysis-coordinates-dlpoly"]], "DESRES file format \u2014 MDAnalysis.coordinates.DMS": [[54, "desres-file-format-mdanalysis-coordinates-dms"]], "FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS": [[55, "fhi-aims-file-format-mdanalysis-coordinates-fhiaims"]], "Developer notes: FHIAIMSWriter format strings": [[55, "developer-notes-fhiaimswriter-format-strings"]], "GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS": [[56, "gamess-trajectory-reader-mdanalysis-coordinates-gms"]], "GRO file format \u2014 MDAnalysis.coordinates.GRO": [[57, "gro-file-format-mdanalysis-coordinates-gro"]], "Writing GRO files": [[57, "writing-gro-files"]], "Developer notes: GROWriter format strings": [[57, "developer-notes-growriter-format-strings"]], "GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD": [[58, "gsd-trajectory-reader-mdanalysis-coordinates-gsd"]], "H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD": [[59, "h5md-trajectories-mdanalysis-coordinates-h5md"]], "Units": [[59, "units"]], "Example: Loading an H5MD simulation": [[59, "example-loading-an-h5md-simulation"]], "Example: Writing an H5MD file": [[59, "example-writing-an-h5md-file"]], "Example: Opening an H5MD file in parallel": [[59, "example-opening-an-h5md-file-in-parallel"]], "Building parallel h5py and HDF5 on Linux": [[59, "building-parallel-h5py-and-hdf5-on-linux"]], "INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD": [[60, "inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd"]], "LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS": [[61, "lammps-dcd-trajectory-and-data-i-o-mdanalysis-coordinates-lammps"]], "Data file formats": [[61, "data-file-formats"]], "Dump files": [[61, "dump-files"]], "Example: Loading a LAMMPS simulation": [[61, "example-loading-a-lammps-simulation"]], "MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF": [[62, "mmtf-trajectory-reader-mdanalysis-coordinates-mmtf"]], "MOL2 file format \u2014 MDAnalysis.coordinates.MOL2": [[63, "mol2-file-format-mdanalysis-coordinates-mol2"], [135, "mol2-file-format-mdanalysis-coordinates-mol2"]], "Example for working with mol2 files": [[63, "example-for-working-with-mol2-files"]], "MOL2 format notes": [[63, "mol2-format-notes"]], "NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN": [[64, "namdbin-files-format-mdanalysis-coordinates-namdbin"]], "PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB": [[65, "pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb"]], "Capabilities": [[65, "capabilities"]], "Examples for working with PDB files": [[65, "examples-for-working-with-pdb-files"]], "PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT": [[66, "pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt"]], "PQR file format \u2014 MDAnalysis.coordinates.PQR": [[67, "pqr-file-format-mdanalysis-coordinates-pqr"]], "TNG trajectory files \u2014 MDAnalysis.coordinates.TNG": [[68, "tng-trajectory-files-mdanalysis-coordinates-tng"]], "Current Limitations": [[68, "current-limitations"]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[69, "amber-trajectories-mdanalysis-coordinates-trj"]], "Binary NetCDF trajectories": [[69, "binary-netcdf-trajectories"]], "ASCII TRAJ trajectories": [[69, "ascii-traj-trajectories"]], "TRR trajectory files \u2014 MDAnalysis.coordinates.TRR": [[70, "trr-trajectory-files-mdanalysis-coordinates-trr"]], "TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ": [[71, "trz-trajectory-i-o-mdanalysis-coordinates-trz"]], "TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ": [[72, "txyz-file-format-mdanalysis-coordinates-txyz"]], "XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR": [[73, "xdr-based-trajectory-files-mdanalysis-coordinates-xdr"]], "XTC trajectory files \u2014 MDAnalysis.coordinates.XTC": [[74, "xtc-trajectory-files-mdanalysis-coordinates-xtc"]], "XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ": [[75, "xyz-trajectory-reader-mdanalysis-coordinates-xyz"]], "XYZ File format": [[75, "xyz-file-format"]], "Base classes \u2014 MDAnalysis.coordinates.base": [[76, "base-classes-mdanalysis-coordinates-base"]], "FrameIterators": [[76, "frameiterators"]], "Readers": [[76, "readers"], [80, "readers"]], "Writers": [[76, "writers"], [80, "writers"]], "Converters": [[76, "converters"]], "Helper classes": [[76, "helper-classes"]], "ChainReader \u2014 MDAnalysis.coordinates.chain": [[77, "chainreader-mdanalysis-coordinates-chain"]], "Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles": [[78, "reading-trajectories-with-chemfiles-mdanalysis-coordinates-chemfiles"]], "Using the CHEMFILES reader": [[78, "using-the-chemfiles-reader"]], "Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core": [[79, "common-functions-for-coordinate-reading-mdanalysis-coordinates-core"]], "Trajectory Readers and Writers \u2014 MDAnalysis.coordinates": [[80, "trajectory-readers-and-writers-mdanalysis-coordinates"]], "Timesteps": [[80, "timesteps"]], "Supported coordinate formats": [[80, "supported-coordinate-formats"]], "Table of supported coordinate formats": [[80, "id23"]], "Trajectory API": [[80, "trajectory-api"]], "Timestep class": [[80, "timestep-class"]], "Private attributes": [[80, "private-attributes"]], "Trajectory Reader class": [[80, "trajectory-reader-class"]], "Trajectory Writer class": [[80, "trajectory-writer-class"]], "Single Frame Writer class": [[80, "single-frame-writer-class"]], "Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory": [[81, "reading-trajectories-from-memory-mdanalysis-coordinates-memory"]], "How to use the MemoryReader": [[81, "how-to-use-the-memoryreader"]], "In-memory representation of arbitrary trajectories": [[81, "in-memory-representation-of-arbitrary-trajectories"]], "Switching a trajectory to an in-memory representation": [[81, "switching-a-trajectory-to-an-in-memory-representation"]], "Constructing a Reader from a numpy array": [[81, "constructing-a-reader-from-a-numpy-array"]], "Creating an in-memory trajectory of a sub-system": [[81, "creating-an-in-memory-trajectory-of-a-sub-system"]], "Null output \u2014 MDAnalysis.coordinates.null": [[82, "null-output-mdanalysis-coordinates-null"]], "Serialization of Coordinate Readers": [[83, "serialization-of-coordinate-readers"]], "How to serialize a new reader": [[83, "how-to-serialize-a-new-reader"]], "File Access": [[83, "file-access"]], "To seek or not to seek": [[83, "to-seek-or-not-to-seek"]], "Miscellaneous": [[83, "miscellaneous"]], "Tests": [[83, "tests"], [166, "tests"]], "_SingleFrameReader Test": [[83, "singleframereader-test"]], "BaseReaderTest and MultiframeReaderTest": [[83, "basereadertest-and-multiframereadertest"]], "File handler Test": [[83, "file-handler-test"]], "Currently implemented picklable IO Formats": [[83, "currently-implemented-picklable-io-formats"]], "Timestep Class \u2014 MDAnalysis.coordinates.timestep": [[84, "timestep-class-mdanalysis-coordinates-timestep"]], "Timestep": [[84, "timestep"]], "Coordinates modules": [[85, "coordinates-modules"]], "AtomGroup accessors \u2014 MDAnalysis.core.accessors": [[86, "atomgroup-accessors-mdanalysis-core-accessors"]], "Core objects: Containers \u2014 MDAnalysis.core.groups": [[87, "core-objects-containers-mdanalysis-core-groups"]], "Collections": [[87, "collections"]], "Chemical units": [[87, "chemical-units"]], "Levels": [[87, "levels"]], "Core functions of MDAnalysis": [[88, "core-functions-of-mdanalysis"]], "Atom selection Hierarchy \u2014 MDAnalysis.core.selection": [[89, "atom-selection-hierarchy-mdanalysis-core-selection"]], "Core Topology object \u2014 MDAnalysis.core.topology": [[90, "core-topology-object-mdanalysis-core-topology"]], "Topology attribute objects \u2014 MDAnalysis.core.topologyattrs": [[91, "topology-attribute-objects-mdanalysis-core-topologyattrs"]], "Core Topology Objects \u2014 MDAnalysis.core.topologyobjects": [[92, "core-topology-objects-mdanalysis-core-topologyobjects"]], "Core object: Universe \u2014 MDAnalysis.core.universe": [[93, "core-object-universe-mdanalysis-core-universe"]], "Core modules": [[94, "core-modules"]], "Important objects for users": [[94, "important-objects-for-users"]], "Topology system": [[94, "topology-system"]], "Selection system": [[94, "selection-system"]], "Custom exceptions and warnings \u2014 MDAnalysis.exceptions": [[95, "custom-exceptions-and-warnings-mdanalysis-exceptions"]], "Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch": [[96, "neighbor-search-wrapper-for-mdanalysis-mdanalysis-lib-neighborsearch"]], "Distance calculation library \u2014 MDAnalysis.lib.c_distances": [[97, "distance-calculation-library-mdanalysis-lib-c-distances"]], "Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp": [[98, "parallel-distance-calculation-library-mdanalysis-lib-c-distances-openmp"]], "Correlations utilities \u2014 MDAnalysis.lib.correlations": [[99, "correlations-utilities-mdanalysis-lib-correlations"]], "Autocorrelation Function": [[99, "autocorrelation-function"]], "Intermittency Function": [[99, "intermittency-function"]], "Fast distance array computation \u2014 MDAnalysis.lib.distances": [[100, "fast-distance-array-computation-mdanalysis-lib-distances"]], "Selection of acceleration (\u201cbackend\u201d)": [[100, "selection-of-acceleration-backend"]], "Available backends for accelerated distance functions.": [[100, "id1"]], "Use of the distopia library": [[100, "use-of-the-distopia-library"]], "Functions available using the distopia backend.": [[100, "id2"]], "Low-level modules for MDAnalysis.lib.distances": [[100, "low-level-modules-for-mdanalysis-lib-distances"]], "Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd": [[101, "low-level-dcd-trajectory-reading-mdanalysis-lib-formats-libdcd"]], "Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr": [[102, "low-level-gromacs-xdr-trajectory-reading-mdanalysis-lib-formats-libmdaxdr"]], "Setting up logging \u2014 MDAnalysis.lib.log": [[103, "setting-up-logging-mdanalysis-lib-log"]], "Convenience functions": [[103, "convenience-functions"]], "Other functions and classes for logging purposes": [[103, "other-functions-and-classes-for-logging-purposes"]], "Mathematical helper functions \u2014 MDAnalysis.lib.mdamath": [[104, "mathematical-helper-functions-mdanalysis-lib-mdamath"]], "Linear algebra": [[104, "linear-algebra"]], "Connectivity": [[104, "connectivity"]], "Neighbor search library \u2014 MDAnalysis.lib.nsgrid": [[105, "neighbor-search-library-mdanalysis-lib-nsgrid"]], "About the code": [[105, "about-the-code"]], "About the algorithm": [[105, "about-the-algorithm"]], "Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io": [[106, "picklable-read-only-i-o-classes-mdanalysis-lib-picklable-file-io"]], "PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree": [[107, "periodickdtree-mdanalysis-lib-pkdtree"]], "Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot": [[108, "fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot"]], "Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations": [[109, "homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations"]], "Requirements": [[109, "requirements"]], "Helper functions \u2014 MDAnalysis.lib.util": [[110, "helper-functions-mdanalysis-lib-util"]], "Files and directories": [[110, "files-and-directories"]], "Streams": [[110, "streams"]], "Containers and lists": [[110, "containers-and-lists"]], "Arrays": [[110, "arrays"]], "File parsing": [[110, "file-parsing"]], "Data manipulation and handling": [[110, "data-manipulation-and-handling"]], "Strings": [[110, "strings"]], "Class decorators": [[110, "class-decorators"]], "Function decorators": [[110, "function-decorators"]], "Code management": [[110, "code-management"]], "Data format checks": [[110, "data-format-checks"]], "Library functions \u2014 MDAnalysis.lib": [[111, "module-MDAnalysis.lib"]], "Overview": [[111, "overview"]], "List of modules": [[111, "list-of-modules"]], "Low level file formats": [[111, "low-level-file-formats"]], "Libmdanalysis": [[111, "libmdanalysis"]], "Overview over MDAnalysis": [[112, "overview-over-mdanalysis"]], "Using MDAnalysis in python": [[112, "using-mdanalysis-in-python"]], "Examples": [[112, "examples"]], "Included trajectories": [[112, "included-trajectories"]], "Code snippets": [[112, "code-snippets"]], "Citations for the whole MDAnalysis library": [[113, "citations-for-the-whole-mdanalysis-library"]], "Citations for included algorithms and modules": [[113, "citations-for-included-algorithms-and-modules"]], "Citations using Duecredit": [[113, "citations-using-duecredit"]], "Selection commands": [[114, "selection-commands"]], "Selection Keywords": [[114, "selection-keywords"]], "Simple selections": [[114, "simple-selections"]], "Pattern matching": [[114, "pattern-matching"]], "Boolean": [[114, "boolean"]], "Geometric": [[114, "geometric"]], "Similarity and connectivity": [[114, "similarity-and-connectivity"]], "Index": [[114, "index"]], "Preexisting selections and modifiers": [[114, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[114, "dynamic-selections"]], "Ordered selections": [[114, "ordered-selections"]], "Base classes for the selection writers": [[115, "base-classes-for-the-selection-writers"]], "CHARMM selections": [[116, "charmm-selections"]], "Gromacs selections": [[117, "gromacs-selections"]], "Jmol selections": [[118, "jmol-selections"]], "PyMOL selections": [[119, "pymol-selections"]], "VMD selections": [[120, "vmd-selections"]], "Selection exporters": [[121, "selection-exporters"]], "Table of supported exporters and recognized file name extensions.": [[121, "id2"]], "How to write selections": [[121, "how-to-write-selections"]], "Single AtomGroup": [[121, "single-atomgroup"]], "Multiple selections": [[121, "multiple-selections"]], "Selection writers": [[121, "selection-writers"]], "The topology system": [[122, "the-topology-system"]], "CRD topology parser": [[123, "crd-topology-parser"]], "Todo": [[123, "id1"], [141, "id1"]], "DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser": [[124, "dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser"]], "DESRES Molecular Structure file format topology parser": [[125, "desres-molecular-structure-file-format-topology-parser"]], "Extended PDB topology parser": [[126, "extended-pdb-topology-parser"]], "FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser": [[127, "fhi-aims-topology-parser-mdanalysis-topolgy-fhiaimsparser"]], "GAMESS Topology Parser": [[128, "gamess-topology-parser"]], "GRO topology parser": [[129, "gro-topology-parser"]], "GSD topology parser": [[130, "gsd-topology-parser"]], "HOOMD XML topology parser": [[131, "hoomd-xml-topology-parser"]], "ITP topology parser": [[132, "itp-topology-parser"]], "Preprocessor variables": [[132, "preprocessor-variables"]], "LAMMPSParser": [[133, "lammpsparser"]], "Atom styles": [[133, "atom-styles"]], "MMTF Topology Parser": [[134, "mmtf-topology-parser"]], "Minimal topology parser": [[136, "minimal-topology-parser"]], "PDB Topology Parser": [[137, "pdb-topology-parser"]], "PDBQT topology parser": [[138, "pdbqt-topology-parser"]], "PQR topology parser": [[139, "pqr-topology-parser"]], "PSF topology parser": [[140, "psf-topology-parser"]], "AMBER PRMTOP topology parser": [[141, "amber-prmtop-topology-parser"]], "Gromacs portable run input TPR format parser": [[142, "gromacs-portable-run-input-tpr-format-parser"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[142, "id4"]], "Development notes": [[142, "development-notes"]], "TXYZ topology parser": [[143, "txyz-topology-parser"]], "XYZ Topology Parser": [[144, "xyz-topology-parser"]], "Base topology reader classes \u2014 MDAnalysis.topology.base": [[145, "base-topology-reader-classes-mdanalysis-topology-base"]], "Common functions for topology building \u2014 MDAnalysis.topology.core": [[146, "common-functions-for-topology-building-mdanalysis-topology-core"]], "Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers": [[147, "guessing-unknown-topology-information-mdanalysis-topology-guessers"]], "Example uses of guessers": [[147, "example-uses-of-guessers"]], "Guessing elements from atom names": [[147, "guessing-elements-from-atom-names"]], "Topology readers \u2014 MDAnalysis.topology": [[148, "topology-readers-mdanalysis-topology"]], "Table of Supported Topology Formats": [[148, "id19"]], "Developer Notes": [[148, "developer-notes"]], "atoms": [[148, "atoms"]], "bonds": [[148, "bonds"]], "bondorder": [[148, "bondorder"]], "angles": [[148, "angles"]], "dihedrals": [[148, "dihedrals"]], "impropers": [[148, "impropers"]], "MDAnalysis topology tables": [[149, "mdanalysis-topology-tables"]], "Utility functions for the TPR topology parser": [[150, "utility-functions-for-the-tpr-topology-parser"]], "TPR support": [[150, "tpr-support"]], "TPRParser settings": [[150, "tprparser-settings"]], "Class definitions for the TPRParser": [[150, "class-definitions-for-the-tprparser"]], "Utilities for the TPRParser": [[150, "utilities-for-the-tprparser"]], "Topology modules": [[151, "topology-modules"]], "Trajectory transformations (\u201con-the-fly\u201d transformations)": [[152, "module-MDAnalysis.transformations"]], "Workflows": [[152, "workflows"]], "Creating transformations": [[152, "creating-transformations"]], "Creating complex transformation classes": [[152, "creating-complex-transformation-classes"]], "Creating complex transformation closure functions": [[152, "creating-complex-transformation-closure-functions"]], "Transformations in MDAnalysis": [[152, "transformations-in-mdanalysis"]], "How to transformations": [[152, "how-to-transformations"]], "Building blocks for Transformation Classes": [[152, "building-blocks-for-transformation-classes"]], "Currently implemented transformations": [[152, "currently-implemented-transformations"]], "Transformations Base Class \u2014 MDAnalysis.transformations.base": [[153, "transformations-base-class-mdanalysis-transformations-base"]], "Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions": [[154, "set-box-dimensions-mdanalysis-transformations-boxdimensions"]], "Fitting transformations \u2014 MDAnalysis.transformations.fit": [[155, "fitting-transformations-mdanalysis-transformations-fit"]], "No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump": [[156, "no-jump-trajectory-unwrapping-mdanalysis-transformations-nojump"]], "Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging": [[157, "trajectory-coordinate-averaging-mdanalysis-transformations-positionaveraging"]], "Trajectory rotation \u2014 MDAnalysis.transformations.rotate": [[158, "trajectory-rotation-mdanalysis-transformations-rotate"]], "Trajectory translation \u2014 MDAnalysis.transformations.translate": [[159, "trajectory-translation-mdanalysis-transformations-translate"]], "Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap": [[160, "wrap-unwrap-transformations-mdanalysis-transformations-wrap"]], "Constants and unit conversion \u2014 MDAnalysis.units": [[161, "constants-and-unit-conversion-mdanalysis-units"]], "Base units in MDAnalysis as encoded in MDANALYSIS_BASE_UNITS": [[161, "id71"]], "Implementation notes": [[161, "implementation-notes"]], "Conversions": [[161, "conversions"]], "References and footnotes": [[161, "references-and-footnotes"]], "Version information for MDAnalysis - MDAnalysis.version": [[162, "version-information-for-mdanalysis-mdanalysis-version"]], "Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines": [[163, "streamplots-2d-mdanalysis-visualization-streamlines"]], "Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D": [[164, "streamplots-3d-mdanalysis-visualization-streamlines-3d"]], "Visualization modules": [[165, "visualization-modules"]], "Visualization of Lipid Flow": [[165, "visualization-of-lipid-flow"]], "MDAnalysis documentation": [[166, "mdanalysis-documentation"]], "Getting involved": [[166, "getting-involved"]], "User Guide": [[166, "user-guide"]], "Installing MDAnalysis": [[166, "installing-mdanalysis"]], "conda": [[166, "conda"]], "pip": [[166, "pip"]], "Source Code": [[166, "source-code"]], "Citation": [[166, "citation"]], "Indices and tables": [[166, "indices-and-tables"]]}, "indexentries": {"aligntraj (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AlignTraj"]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure"]], "mdanalysis.analysis.align": [[0, "module-MDAnalysis.analysis.align"]], "_fit_to() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align._fit_to"]], "alignto() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.alignto"]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select"]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename"]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename"]], "get_matching_atoms() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.get_matching_atoms"]], "mobile_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.mobile_atoms"]], "mobile_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.mobile_atoms"]], "module": [[0, "module-MDAnalysis.analysis.align"], [1, "module-MDAnalysis.analysis.atomicdistances"], [2, "module-MDAnalysis.analysis.base"], [3, "module-MDAnalysis.analysis.bat"], [4, "module-MDAnalysis.analysis.contacts"], [5, "module-MDAnalysis.analysis.data.filenames"], [6, "module-MDAnalysis.analysis.density"], [7, "module-MDAnalysis.analysis.dielectric"], [8, "module-MDAnalysis.analysis.diffusionmap"], [9, "module-MDAnalysis.analysis.dihedrals"], [10, "module-MDAnalysis.analysis.distances"], [12, "module-MDAnalysis.analysis.encore.bootstrap"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"], [13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"], [13, "module-MDAnalysis.analysis.encore.clustering.cluster"], [14, "module-MDAnalysis.analysis.encore.confdistmatrix"], [15, "module-MDAnalysis.analysis.encore.covariance"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"], [17, "module-MDAnalysis.analysis.encore.similarity"], [18, "module-MDAnalysis.analysis.encore.utils"], [19, "module-MDAnalysis.analysis.gnm"], [20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"], [21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"], [22, "module-MDAnalysis.analysis.helix_analysis"], [23, "module-MDAnalysis.analysis.hole2"], [23, "module-MDAnalysis.analysis.hole2.templates"], [23, "module-MDAnalysis.analysis.hole2.utils"], [24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"], [25, "module-MDAnalysis.analysis.leaflet"], [26, "module-MDAnalysis.analysis.legacy.x3dna"], [28, "module-MDAnalysis.analysis.lineardensity"], [29, "module-MDAnalysis.analysis.msd"], [30, "module-MDAnalysis.analysis.nucleicacids"], [31, "module-MDAnalysis.analysis.nuclinfo"], [32, "module-MDAnalysis.analysis.pca"], [33, "module-MDAnalysis.analysis.polymer"], [34, "module-MDAnalysis.analysis.psa"], [35, "module-MDAnalysis.analysis.rdf"], [36, "module-MDAnalysis.analysis.rms"], [37, "module-MDAnalysis.analysis.waterdynamics"], [38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"], [40, "module-MDAnalysis.auxiliary.EDR"], [41, "module-MDAnalysis.auxiliary.XVG"], [42, "module-MDAnalysis.auxiliary.base"], [43, "module-MDAnalysis.auxiliary.core"], [44, "module-MDAnalysis.auxiliary.__init__"], [46, "module-MDAnalysis.converters"], [47, "module-MDAnalysis.converters.OpenMM"], [47, "module-MDAnalysis.converters.OpenMMParser"], [48, "module-MDAnalysis.converters.ParmEd"], [48, "module-MDAnalysis.converters.ParmEdParser"], [49, "module-MDAnalysis.converters.RDKit"], [49, "module-MDAnalysis.converters.RDKitParser"], [50, "module-MDAnalysis.converters.base"], [51, "module-MDAnalysis.coordinates.CRD"], [52, "module-MDAnalysis.coordinates.DCD"], [53, "module-MDAnalysis.coordinates.DLPoly"], [54, "module-MDAnalysis.coordinates.DMS"], [55, "module-MDAnalysis.coordinates.FHIAIMS"], [56, "module-MDAnalysis.coordinates.GMS"], [57, "module-MDAnalysis.coordinates.GRO"], [58, "module-MDAnalysis.coordinates.GSD"], [59, "module-MDAnalysis.coordinates.H5MD"], [60, "module-MDAnalysis.coordinates.INPCRD"], [61, "module-MDAnalysis.coordinates.LAMMPS"], [62, "module-MDAnalysis.coordinates.MMTF"], [63, "module-MDAnalysis.coordinates.MOL2"], [64, "module-MDAnalysis.coordinates.NAMDBIN"], [65, "module-MDAnalysis.coordinates.PDB"], [66, "module-MDAnalysis.coordinates.PDBQT"], [67, "module-MDAnalysis.coordinates.PQR"], [68, "module-MDAnalysis.coordinates.TNG"], [69, "module-MDAnalysis.coordinates.TRJ"], [70, "module-MDAnalysis.coordinates.TRR"], [71, "module-MDAnalysis.coordinates.TRZ"], [72, "module-MDAnalysis.coordinates.TXYZ"], [73, "module-MDAnalysis.coordinates.XDR"], [74, "module-MDAnalysis.coordinates.XTC"], [75, "module-MDAnalysis.coordinates.XYZ"], [76, "module-MDAnalysis.coordinates.base"], [77, "module-MDAnalysis.coordinates.chain"], [78, "module-MDAnalysis.coordinates.chemfiles"], [79, "module-MDAnalysis.coordinates.core"], [80, "module-MDAnalysis.coordinates.__init__"], [81, "module-MDAnalysis.coordinates.memory"], [82, "module-MDAnalysis.coordinates.null"], [84, "module-MDAnalysis.coordinates.timestep"], [86, "module-MDAnalysis.core.accessors"], [87, "module-MDAnalysis.core.groups"], [88, "module-MDAnalysis.core.__init__"], [89, "module-MDAnalysis.core.selection"], [90, "module-MDAnalysis.core.topology"], [91, "module-MDAnalysis.core.topologyattrs"], [92, "module-MDAnalysis.core.topologyobjects"], [93, "module-MDAnalysis.core.universe"], [95, "module-MDAnalysis.exceptions"], [96, "module-MDAnalysis.lib.NeighborSearch"], [97, "module-MDAnalysis.lib.c_distances"], [98, "module-MDAnalysis.lib.c_distances_openmp"], [99, "module-MDAnalysis.lib.correlations"], [100, "module-MDAnalysis.lib.distances"], [101, "module-MDAnalysis.lib.formats.libdcd"], [102, "module-MDAnalysis.lib.formats.libmdaxdr"], [103, "module-MDAnalysis.lib.log"], [104, "module-MDAnalysis.lib.mdamath"], [105, "module-MDAnalysis.lib.nsgrid"], [106, "module-MDAnalysis.lib.picklable_file_io"], [107, "module-MDAnalysis.lib.pkdtree"], [108, "module-MDAnalysis.lib.qcprot"], [109, "module-MDAnalysis.lib.transformations"], [110, "module-MDAnalysis.lib.util"], [111, "module-MDAnalysis.lib"], [115, "module-MDAnalysis.selections.base"], [116, "module-MDAnalysis.selections.charmm"], [117, "module-MDAnalysis.selections.gromacs"], [118, "module-MDAnalysis.selections.jmol"], [119, "module-MDAnalysis.selections.pymol"], [120, "module-MDAnalysis.selections.vmd"], [123, "module-MDAnalysis.topology.CRDParser"], [124, "module-MDAnalysis.topology.DLPolyParser"], [125, "module-MDAnalysis.topology.DMSParser"], [126, "module-MDAnalysis.topology.ExtendedPDBParser"], [127, "module-MDAnalysis.topology.FHIAIMSParser"], [128, "module-MDAnalysis.topology.GMSParser"], [129, "module-MDAnalysis.topology.GROParser"], [130, "module-MDAnalysis.topology.GSDParser"], [131, "module-MDAnalysis.topology.HoomdXMLParser"], [132, "module-MDAnalysis.topology.ITPParser"], [133, "module-MDAnalysis.topology.LAMMPSParser"], [134, "module-MDAnalysis.topology.MMTFParser"], [135, "module-MDAnalysis.topology.MOL2Parser"], [136, "module-MDAnalysis.topology.MinimalParser"], [137, "module-MDAnalysis.topology.PDBParser"], [138, "module-MDAnalysis.topology.PDBQTParser"], [139, "module-MDAnalysis.topology.PQRParser"], [140, "module-MDAnalysis.topology.PSFParser"], [141, "module-MDAnalysis.topology.TOPParser"], [142, "module-MDAnalysis.topology.TPRParser"], [143, "module-MDAnalysis.topology.TXYZParser"], [144, "module-MDAnalysis.topology.XYZParser"], [145, "module-MDAnalysis.topology.base"], [146, "module-MDAnalysis.topology.core"], [147, "module-MDAnalysis.topology.guessers"], [148, "module-MDAnalysis.topology.__init__"], [149, "module-MDAnalysis.topology.tables"], [150, "module-MDAnalysis.topology.tpr"], [150, "module-MDAnalysis.topology.tpr.obj"], [150, "module-MDAnalysis.topology.tpr.setting"], [150, "module-MDAnalysis.topology.tpr.utils"], [152, "module-MDAnalysis.transformations"], [153, "module-MDAnalysis.transformations.base"], [154, "module-MDAnalysis.transformations.boxdimensions"], [155, "module-MDAnalysis.transformations.fit"], [156, "module-MDAnalysis.transformations.nojump"], [157, "module-MDAnalysis.transformations.positionaveraging"], [158, "module-MDAnalysis.transformations.rotate"], [159, "module-MDAnalysis.transformations.translate"], [160, "module-MDAnalysis.transformations.wrap"], [161, "module-MDAnalysis.units"], [162, "module-MDAnalysis.version"], [163, "module-MDAnalysis.visualization.streamlines"], [164, "module-MDAnalysis.visualization.streamlines_3D"]], "positions (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.positions"]], "positions (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.positions"]], "reference_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.reference_atoms"]], "reference_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.reference_atoms"]], "rmsd (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.rmsd"]], "rmsd (mdanalysis.analysis.align.aligntraj.results attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.results.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.rmsd"]], "rotation_matrix() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.rotation_matrix"]], "sequence_alignment() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.sequence_alignment"]], "universe (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.universe"]], "universe (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.universe"]], "atomicdistances (class in mdanalysis.analysis.atomicdistances)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances"]], "mdanalysis.analysis.atomicdistances": [[1, "module-MDAnalysis.analysis.atomicdistances"]], "n_atoms (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_atoms"]], "n_frames (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_frames"]], "results (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.results"]], "analysisbase (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisBase"]], "analysisfromfunction (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction"]], "mdanalysis.analysis.base": [[2, "module-MDAnalysis.analysis.base"]], "results (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.Results"]], "analysis_class() (in module mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.analysis_class"]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.frames"]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames"]], "frames (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.frames"]], "results (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.results"]], "run() (mdanalysis.analysis.base.analysisbase method)": [[2, "MDAnalysis.analysis.base.AnalysisBase.run"]], "times (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.times"]], "times (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.times"]], "times (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.times"]], "timeseries (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.timeseries"]], "timeseries (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.timeseries"]], "bat (class in mdanalysis.analysis.bat)": [[3, "MDAnalysis.analysis.bat.BAT"]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.Cartesian"]], "mdanalysis.analysis.bat": [[3, "module-MDAnalysis.analysis.bat"]], "atoms (mdanalysis.analysis.bat.bat property)": [[3, "MDAnalysis.analysis.bat.BAT.atoms"]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[3, "MDAnalysis.analysis.bat.BAT.results.bat"]], "load() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.load"]], "run() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.run"]], "save() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.save"]], "contacts (class in mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.Contacts"]], "mdanalysis.analysis.contacts": [[4, "module-MDAnalysis.analysis.contacts"]], "contact_matrix() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.contact_matrix"]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.hard_cut_q"]], "q1q2() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.q1q2"]], "radius_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.radius_cut_q"]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.soft_cut_q"]], "timeseries (mdanalysis.analysis.contacts.contacts attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.timeseries"]], "timeseries (mdanalysis.analysis.contacts.contacts.results attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.results.timeseries"]], "janin_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Janin_ref"]], "mdanalysis.analysis.data.filenames": [[5, "module-MDAnalysis.analysis.data.filenames"]], "rama_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Rama_ref"]], "density (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.Density"]], "densityanalysis (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.DensityAnalysis"]], "mdanalysis.analysis.density": [[6, "module-MDAnalysis.analysis.density"]], "_set_user_grid() (mdanalysis.analysis.density.densityanalysis static method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis._set_user_grid"]], "centers() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.centers"]], "check_compatible() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.check_compatible"]], "convert_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_density"]], "convert_length() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_length"]], "default_format (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.default_format"]], "delta (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.delta"]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.density"]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.results.density"]], "edges (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.edges"]], "export() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.export"]], "grid (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.grid"]], "interpolated (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolated"]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolation_spline_order"]], "load() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.load"]], "make_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.make_density"]], "origin (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.origin"]], "resample() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample"]], "resample_factor() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample_factor"]], "run() (mdanalysis.analysis.density.densityanalysis method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.run"]], "save() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.save"]], "units (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.units"]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant"]], "m (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M"]], "m2 (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M2"]], "mdanalysis.analysis.dielectric": [[7, "module-MDAnalysis.analysis.dielectric"]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps"]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean"]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct"]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap"]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix"]], "mdanalysis.analysis.diffusionmap": [[8, "module-MDAnalysis.analysis.diffusionmap"]], "atoms (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.atoms"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix"]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues"]], "run() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.run"]], "transform() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.transform"]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral"]], "janin (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Janin"]], "mdanalysis.analysis.dihedrals": [[9, "module-MDAnalysis.analysis.dihedrals"]], "ramachandran (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran"]], "angles (mdanalysis.analysis.dihedrals.dihedral attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.angles"]], "angles (mdanalysis.analysis.dihedrals.dihedral.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.results.angles"]], "angles (mdanalysis.analysis.dihedrals.janin attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.angles"]], "angles (mdanalysis.analysis.dihedrals.janin.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.results.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.results.angles"]], "plot() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.plot"]], "plot() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.plot"]], "run() (mdanalysis.analysis.dihedrals.dihedral method)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.run"]], "run() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.run"]], "run() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.run"]], "mdanalysis.analysis.distances": [[10, "module-MDAnalysis.analysis.distances"]], "between() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.between"]], "contact_matrix() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.contact_matrix"]], "dist() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.dist"]], "distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.distance_array"]], "self_distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.self_distance_array"]], "mdanalysis.analysis.encore.bootstrap": [[12, "module-MDAnalysis.analysis.encore.bootstrap"]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix"]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples"]], "get_ensemble_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples"]], "affinitypropagation (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagation"]], "affinitypropagation() (in module mdanalysis.analysis.encore.clustering.affinityprop)": [[13, "MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation"]], "affinitypropagationnative (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagationNative"]], "cluster (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster"]], "clustercollection (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection"]], "clusteringmethod (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.ClusteringMethod"]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN"]], "kmeans (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans"]], "mdanalysis.analysis.encore.clustering.clustercollection": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"]], "mdanalysis.analysis.encore.clustering.clusteringmethod": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"]], "mdanalysis.analysis.encore.clustering.affinityprop": [[13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"]], "mdanalysis.analysis.encore.clustering.cluster": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "accepts_distance_matrix (mdanalysis.analysis.encore.clustering.clusteringmethod.kmeans attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans.accepts_distance_matrix"]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid"]], "cluster() (in module mdanalysis.analysis.encore.clustering.cluster)": [[13, "MDAnalysis.analysis.encore.clustering.cluster.cluster"]], "clusters (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.clusters"]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements"]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info"]], "get_centroids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_centroids"]], "get_ids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_ids"]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id"]], "metadata (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.metadata"]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size"]], "mdanalysis.analysis.encore.confdistmatrix": [[14, "module-MDAnalysis.analysis.encore.confdistmatrix"]], "conformational_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.conformational_distance_matrix"]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix"]], "set_rmsd_matrix_elements() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.set_rmsd_matrix_elements"]], "mdanalysis.analysis.encore.covariance": [[15, "module-MDAnalysis.analysis.encore.covariance"]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.covariance_matrix"]], "ml_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.ml_covariance_estimator"]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator"]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"]], "principalcomponentanalysis (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.PrincipalComponentAnalysis"]], "stochasticproximityembedding() (in module mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed.StochasticProximityEmbedding"]], "stochasticproximityembeddingnative (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.StochasticProximityEmbeddingNative"]], "reduce_dimensionality() (in module mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality.reduce_dimensionality"]], "mdanalysis.analysis.encore.similarity": [[17, "module-MDAnalysis.analysis.encore.similarity"]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces"]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces_convergence"]], "clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.clustering_ensemble_similarity"]], "cumulative_clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity"]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs"]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity"]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence"]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence"]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres"]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres_convergence"]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs"]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity"]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.hes"]], "prepare_ensembles_for_convergence_increasing_window() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.prepare_ensembles_for_convergence_increasing_window"]], "write_output() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.write_output"]], "mdanalysis.analysis.encore.utils": [[18, "module-MDAnalysis.analysis.encore.utils"]], "parallelcalculation (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation"]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[18, "MDAnalysis.analysis.encore.cutils.PureRMSD"]], "triangularmatrix (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix"]], "args (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.args"]], "as_array() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.as_array"]], "function (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.function"]], "kwargs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.kwargs"]], "loadz() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.loadz"]], "merge_universes() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.merge_universes"]], "n_jobs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.n_jobs"]], "nruns (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.nruns"]], "run() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.run"]], "savez() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.savez"]], "trm_indices() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices"]], "trm_indices_diag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_diag"]], "trm_indices_nodiag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_nodiag"]], "worker() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.worker"]], "gnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis"]], "mdanalysis.analysis.gnm": [[19, "module-MDAnalysis.analysis.gnm"]], "closecontactgnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis"]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues"]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues"]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors"]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors"]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.generate_grid"]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff"]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff"]], "order_list() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.order_list"]], "times (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.times"]], "times (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.times"]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel"]], "mdanalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors"]], "run() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run"]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve"]], "mdanalysis.analysis.hbonds.hbond_autocorrel": [[21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"]], "mdanalysis.analysis.helix_analysis": [[22, "module-MDAnalysis.analysis.helix_analysis"]], "holeanalysis (class in mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis"]], "mdanalysis.analysis.hole2": [[23, "module-MDAnalysis.analysis.hole2"]], "mdanalysis.analysis.hole2.templates": [[23, "module-MDAnalysis.analysis.hole2.templates"]], "mdanalysis.analysis.hole2.utils": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "path": [[23, "index-0"], [23, "index-1"], [110, "index-0"]], "simple2_rad (in module mdanalysis.analysis.hole2.templates)": [[23, "MDAnalysis.analysis.hole2.templates.SIMPLE2_RAD"]], "bin_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.bin_radii"]], "check_and_fix_long_filename() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.check_and_fix_long_filename"]], "collect_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.collect_hole"]], "create_vmd_surface() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.create_vmd_surface"]], "create_vmd_surface() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.create_vmd_surface"]], "delete_temporary_files() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.delete_temporary_files"]], "environment variable": [[23, "index-0"], [23, "index-1"], [69, "index-0"], [69, "index-1"], [110, "index-0"], [110, "index-1"], [113, "index-0"], [153, "index-0"]], "gather() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.gather"]], "guess_cpoint() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.guess_cpoint"]], "histogram_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.histogram_radii"]], "hole() (in module mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.hole"]], "min_radius() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.min_radius"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.outfiles"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.outfiles"]], "over_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.over_order_parameters"]], "plot() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot"]], "plot3d() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D"]], "plot3d_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D_order_parameters"]], "plot_mean_profile() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_mean_profile"]], "plot_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_order_parameters"]], "profiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.profiles"]], "profiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.profiles"]], "run() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.run"]], "run_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.run_hole"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.sphpdbs"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.sphpdbs"]], "write_simplerad2() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.write_simplerad2"]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis"]], "mdanalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"]], "count_by_ids() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_ids"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type"]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors"]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors"]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds"]], "lifetime() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime"]], "leafletfinder (class in mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder"]], "mdanalysis.analysis.leaflet": [[25, "module-MDAnalysis.analysis.leaflet"]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.group"]], "groups() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups"]], "groups_iter() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"]], "optimize_cutoff() (in module mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.optimize_cutoff"]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes"]], "update() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.update"]], "write_selection() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.write_selection"]], "applicationerror": [[26, "MDAnalysis.analysis.legacy.x3dna.ApplicationError"], [95, "MDAnalysis.exceptions.ApplicationError"]], "mdanalysis.analysis.legacy.x3dna": [[26, "module-MDAnalysis.analysis.legacy.x3dna"]], "x3dna (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA"]], "x3dnatraj (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj"]], "collect() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.collect"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean"]], "mean_std() 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"dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim"]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges"]], "mass_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density"]], "mass_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density_stddev"]], "pos (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos"]], "pos_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos_std"]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume"]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD"]], "mdanalysis.analysis.msd": [[29, "module-MDAnalysis.analysis.msd"]], "ag (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.ag"]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac"]], "msds_by_particle (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.msds_by_particle"]], "n_frames (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_frames"]], "n_particles (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_particles"]], "run() (mdanalysis.analysis.msd.einsteinmsd method)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.run"]], "timeseries (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.timeseries"]], "mdanalysis.analysis.nucleicacids": [[30, "module-MDAnalysis.analysis.nucleicacids"]], "nucpairdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist"]], "watsoncrickdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist"]], "pair_distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.pair_distances"]], "pair_distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.pair_distances"]], "run() (mdanalysis.analysis.nucleicacids.nucpairdist method)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.run"]], "run() (mdanalysis.analysis.nucleicacids.watsoncrickdist method)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.run"]], "times (mdanalysis.analysis.nucleicacids.nucpairdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.times"]], "times (mdanalysis.analysis.nucleicacids.watsoncrickdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.times"]], "mdanalysis.analysis.nuclinfo": [[31, "module-MDAnalysis.analysis.nuclinfo"]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.hydroxyl"]], "major_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.major_pair"]], "minor_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.minor_pair"]], "phase_as() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_as"]], "phase_cp() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_cp"]], "pseudo_dihe_baseflip() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip"]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors"]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_alpha"]], "tors_beta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_beta"]], "tors_chi() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_chi"]], "tors_delta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_delta"]], "tors_eps() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_eps"]], "tors_gamma() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_gamma"]], "tors_zeta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_zeta"]], "wc_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.wc_pair"]], "mdanalysis.analysis.pca": [[32, "module-MDAnalysis.analysis.pca"]], "pca (class in mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.PCA"]], "cosine_content() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cosine_content"]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.cumulated_variance"]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance"]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.cumulative_overlap"]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cumulative_overlap"]], "p_components (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.p_components"]], "p_components (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.p_components"]], "project_single_frame() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.project_single_frame"]], "rmsip() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.rmsip"]], "rmsip() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.rmsip"]], "run() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.run"]], "transform() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.transform"]], "variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.variance"]], "variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.variance"]], "mdanalysis.analysis.polymer": [[33, "module-MDAnalysis.analysis.polymer"]], "persistencelength (class in mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength"]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation"]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.fit"]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit"]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.fit_exponential_decay"]], "lb (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lb"]], "lb (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lb"]], "lp (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lp"]], "lp (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lp"]], "plot() (mdanalysis.analysis.polymer.persistencelength method)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.plot"]], "sort_backbone() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.sort_backbone"]], "x (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.x"]], "d (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.D"]], "mdanalysis.analysis.psa": [[34, "module-MDAnalysis.analysis.psa"]], "psapair (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAPair"]], "psanalysis (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAnalysis"]], "path (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.Path"]], "cluster() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.cluster"]], "discrete_frechet() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.discrete_frechet"]], "dist_mat_to_vec() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.dist_mat_to_vec"]], "fit_to_reference() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.fit_to_reference"]], "generate_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.generate_paths"]], "get_coord_axes() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_coord_axes"]], "get_msd_matrix() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_msd_matrix"]], "get_num_atoms() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_atoms"]], "get_num_atoms() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.get_num_atoms"]], "get_num_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_paths"]], "get_pairwise_distances() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_pairwise_distances"]], "get_path_metric_func() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_path_metric_func"]], "get_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_paths"]], "hausdorff() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff"]], "hausdorff_avg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_avg"]], "hausdorff_neighbors() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_neighbors"]], "hausdorff_pair (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.hausdorff_pair"]], "hausdorff_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.hausdorff_pairs"]], "hausdorff_wavg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_wavg"]], "load() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.load"]], "matrix_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.matrix_id"]], "nearest_neighbors (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.nearest_neighbors"]], "nearest_neighbors (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.nearest_neighbors"]], "npaths (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.npaths"]], "pair_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.pair_id"]], "path (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path"]], "path_select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.path_select"]], "path_select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path_select"]], "paths (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.paths"]], "plot() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot"]], "plot_annotated_heatmap() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_annotated_heatmap"]], "plot_nearest_neighbors() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_nearest_neighbors"]], "psa_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.psa_pairs"]], "ref_frame (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.ref_frame"]], "ref_frame (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.ref_frame"]], "run() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run"]], "run() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.run"]], "run_pairs_analysis() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run_pairs_analysis"]], "save_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.save_paths"]], "select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.select"]], "select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.select"]], "sqnorm() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.sqnorm"]], "to_path() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.to_path"]], "u_fitted (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_fitted"]], "u_original (mdanalysis.analysis.psa.path attribute)": 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mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.ByNumSelection"]], "byresselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.ByResSelection"]], "float_pattern (in module mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.FLOAT_PATTERN"]], "floatrangeselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.FloatRangeSelection"]], "int_pattern (in module mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.INT_PATTERN"]], "mdanalysis.core.selection": [[89, "module-MDAnalysis.core.selection"]], "nucleicbackboneselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.NucleicBackboneSelection"]], "nucleicselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.NucleicSelection"]], "nucleicsugarselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.NucleicSugarSelection"]], "propertyselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.PropertySelection"]], "proteinselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.ProteinSelection"]], "range_pattern (in module mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.RANGE_PATTERN"]], "rangeselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.RangeSelection"]], "residselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.ResidSelection"]], "sameselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.SameSelection"]], "selectionparser (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.SelectionParser"]], "singlecharselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.SingleCharSelection"]], "smartsselection (class in mdanalysis.core.selection)": [[89, "MDAnalysis.core.selection.SmartsSelection"]], "dtype 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"find_fragments() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.find_fragments"]], "make_whole() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.make_whole"]], "norm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.norm"]], "normal() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.normal"]], "pdot() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pdot"]], "pnorm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pnorm"]], "sarrus_det() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.sarrus_det"]], "stp() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.stp"]], "triclinic_box() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_box"]], "triclinic_vectors() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_vectors"]], "fastns (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.FastNS"]], "mdanalysis.lib.nsgrid": [[105, "module-MDAnalysis.lib.nsgrid"]], "nsresults (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.NSResults"]], "get_pair_distances() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pair_distances"]], "get_pairs() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pairs"]], "search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.search"]], "self_search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.self_search"]], "bz2picklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BZ2Picklable"]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable"]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.FileIOPicklable"]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.GzipPicklable"]], "mdanalysis.lib.picklable_file_io": [[106, "module-MDAnalysis.lib.picklable_file_io"]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.TextIOPicklable"]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open"]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open"]], "pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.pickle_open"]], "mdanalysis.lib.pkdtree": [[107, "module-MDAnalysis.lib.pkdtree"]], "periodickdtree (class in mdanalysis.lib.pkdtree)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree"]], "get_indices() (mdanalysis.lib.pkdtree.periodickdtree method)": 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"MDAnalysis.lib.qcprot.InnerProduct"]], "mdanalysis.lib.qcprot": [[108, "module-MDAnalysis.lib.qcprot"]], "arcball (class in mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.Arcball"]], "mdanalysis.lib.transformations": [[109, "module-MDAnalysis.lib.transformations"]], "arcball_nearest_axis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.arcball_nearest_axis"]], "compose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.compose_matrix"]], "concatenate_matrices() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.concatenate_matrices"]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.decompose_matrix"]], "down() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.down"]], "drag() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.drag"]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.euler_from_quaternion"]], "getconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.getconstrain"]], "matrix() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.matrix"]], "next() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.next"]], "place() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.place"]], "projection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.projection_from_matrix"]], "quaternion_imag() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_imag"]], "quaternion_real() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_real"]], "reflection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.reflection_from_matrix"]], "rotation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotation_from_matrix"]], "rotaxis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotaxis"]], "scale_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.scale_from_matrix"]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setaxes"]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setconstrain"]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.shear_from_matrix"]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.translation_from_matrix"]], "$home": [[110, "index-1"]], "fortranreader (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRANReader"]], "fortran_format_regex (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRAN_format_regex"]], "mdanalysis.lib.util": [[110, "module-MDAnalysis.lib.util"]], "namedstream (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.NamedStream"]], "namespace (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.Namespace"]], "_deprecate (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util._Deprecate"]], "anyopen() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.anyopen"]], "asiterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.asiterable"]], "blocks_of() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.blocks_of"]], "cached() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.cached"]], "check_atomgroup_not_empty() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_atomgroup_not_empty"]], "check_box() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_box"]], "check_compressed_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_compressed_format"]], "check_coords() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_coords"]], "close() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.close"]], "closed (mdanalysis.lib.util.namedstream property)": [[110, "MDAnalysis.lib.util.NamedStream.closed"]], "conv_float() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.conv_float"]], "convert_aa_code() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.convert_aa_code"]], "dedent_docstring() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.dedent_docstring"]], "deprecate() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.deprecate"]], "filename() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.filename"]], "fileno() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.fileno"]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.fixedwidth_bins"]], "flatten_dict() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.flatten_dict"]], "flush() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.flush"]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.format_from_filename_extension"]], "get_ext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_ext"]], "get_weights() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_weights"]], "greedy_splitext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.greedy_splitext"]], "group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.group_same_or_consecutive_integers"]], "guess_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.guess_format"]], "hasmethod() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.hasmethod"]], "isstream() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.isstream"]], "iterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.iterable"]], "ltruncate_int() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.ltruncate_int"]], "number_of_matches() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.number_of_matches"]], "openany() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.openany"]], "parse_fortran_format() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format"]], "parse_residue() (in module mdanalysis.lib.util)": 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(mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.tell"]], "truncate() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.truncate"]], "unique_int_1d() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.unique_int_1d"]], "unique_rows() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.unique_rows"]], "warn_if_not_unique() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.warn_if_not_unique"]], "which() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.which"]], "writable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.writable"]], "mdanalysis.lib": [[111, "module-MDAnalysis.lib"]], "duecredit_enable": [[113, "index-0"]], "mdanalysis.selections.base": [[115, "module-MDAnalysis.selections.base"]], "selectionwriterbase (class in mdanalysis.selections.base)": [[115, "MDAnalysis.selections.base.SelectionWriterBase"]], "__init__() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase.__init__"]], "_translate() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase._translate"]], "_write_head() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase._write_head"]], "_write_tail() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase._write_tail"]], "comment() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase.comment"]], "join() (in module mdanalysis.selections.base)": [[115, "MDAnalysis.selections.base.join"]], "write() (mdanalysis.selections.base.selectionwriterbase method)": [[115, "MDAnalysis.selections.base.SelectionWriterBase.write"]], "mdanalysis.selections.charmm": [[116, "module-MDAnalysis.selections.charmm"]], "selectionwriter (class in mdanalysis.selections.charmm)": [[116, "MDAnalysis.selections.charmm.SelectionWriter"]], "close() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.close"]], "comment() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.continuation"]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.ext"]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.format"]], "write() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.write"]], "write_preamble() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.write_preamble"]], "mdanalysis.selections.gromacs": [[117, "module-MDAnalysis.selections.gromacs"]], "selectionwriter (class in mdanalysis.selections.gromacs)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter"]], "close() (mdanalysis.selections.gromacs.selectionwriter method)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.close"]], "comment() (mdanalysis.selections.gromacs.selectionwriter method)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.gromacs.selectionwriter attribute)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.gromacs.selectionwriter attribute)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.continuation"]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.ext"]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.format"]], "write() (mdanalysis.selections.gromacs.selectionwriter method)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.write"]], "write_preamble() (mdanalysis.selections.gromacs.selectionwriter method)": [[117, "MDAnalysis.selections.gromacs.SelectionWriter.write_preamble"]], "mdanalysis.selections.jmol": [[118, "module-MDAnalysis.selections.jmol"]], "selectionwriter (class in mdanalysis.selections.jmol)": [[118, "MDAnalysis.selections.jmol.SelectionWriter"]], "close() (mdanalysis.selections.jmol.selectionwriter method)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.close"]], "comment() (mdanalysis.selections.jmol.selectionwriter method)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.jmol.selectionwriter attribute)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.jmol.selectionwriter attribute)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.continuation"]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms"]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.ext"]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.format"]], "write() (mdanalysis.selections.jmol.selectionwriter method)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.write"]], "write_preamble() (mdanalysis.selections.jmol.selectionwriter method)": [[118, "MDAnalysis.selections.jmol.SelectionWriter.write_preamble"]], "mdanalysis.selections.pymol": [[119, "module-MDAnalysis.selections.pymol"]], "selectionwriter (class in mdanalysis.selections.pymol)": [[119, "MDAnalysis.selections.pymol.SelectionWriter"]], "close() (mdanalysis.selections.pymol.selectionwriter method)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.close"]], "comment() (mdanalysis.selections.pymol.selectionwriter method)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.pymol.selectionwriter attribute)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.pymol.selectionwriter attribute)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.continuation"]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.ext"]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.format"]], "write() (mdanalysis.selections.pymol.selectionwriter method)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.write"]], "write_preamble() (mdanalysis.selections.pymol.selectionwriter method)": [[119, "MDAnalysis.selections.pymol.SelectionWriter.write_preamble"]], "mdanalysis.selections.vmd": [[120, "module-MDAnalysis.selections.vmd"]], "selectionwriter (class in mdanalysis.selections.vmd)": [[120, "MDAnalysis.selections.vmd.SelectionWriter"]], "close() (mdanalysis.selections.vmd.selectionwriter method)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.close"]], "comment() (mdanalysis.selections.vmd.selectionwriter method)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.vmd.selectionwriter attribute)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.vmd.selectionwriter attribute)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.continuation"]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.ext"]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.format"]], "write() (mdanalysis.selections.vmd.selectionwriter method)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.write"]], "write_preamble() (mdanalysis.selections.vmd.selectionwriter method)": [[120, "MDAnalysis.selections.vmd.SelectionWriter.write_preamble"]], "get_writer() (in module mdanalysis.selections)": [[121, "MDAnalysis.selections.get_writer"]], "crdparser (class in mdanalysis.topology.crdparser)": [[123, "MDAnalysis.topology.CRDParser.CRDParser"]], "mdanalysis.topology.crdparser": [[123, "module-MDAnalysis.topology.CRDParser"]], "close() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.close"]], "convert_forces_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_forces_from_native"]], "convert_forces_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_forces_to_native"]], "convert_pos_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_pos_from_native"]], "convert_pos_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_pos_to_native"]], "convert_time_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_time_from_native"]], "convert_time_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_from_native"]], "convert_velocities_to_native() 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mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGLES"]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRES"]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRESZ"]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL"]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM"]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM_LR"]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BONDS"]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CBTDIHS"]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CMAP"]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COM_PULL"]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONNBONDS"]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTR"]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTRNC"]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL14"]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_LR"]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP"]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_SR"]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES"]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS"]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS"]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING"]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DHDL_CON"]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRES"]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL"]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISPCORR"]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRES"]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL"]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DKDL"]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DPD"]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL"]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED"]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL"]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT"]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE"]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW"]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ECONSERVED"]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EKIN"]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EPOT"]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EQM"]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ETOT"]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FBPOSRES"]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FENEBONDS"]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FOURDIHS"]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96ANGLES"]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96BONDS"]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB12"]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB13"]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB14"]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GBPOL"]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_HARMONIC"]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_IDIHS"]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES"]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ"]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ14"]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC14_Q"]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB"]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_LR"]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP"]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_MORSE"]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION"]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NRE"]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRES"]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV"]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDIHS"]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDISPCORR"]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PIDIHS"]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POLARIZATION"]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POSRES"]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PRES"]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES"]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RBDIHS"]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES"]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS"]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS"]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RF_EXCL"]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_SETTLE"]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABANGLES"]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDS"]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC"]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABDIHS"]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TEMP"]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_THOLE_POL"]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY"]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE1"]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2"]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2FD"]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3"]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD"]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FD"]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT"]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FD"]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN"]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITEN"]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED"]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_WATER_POL"]], "ilist (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Ilist"]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.InteractionKind"]], "mdanalysis.topology.tpr": [[150, "module-MDAnalysis.topology.tpr"]], "mdanalysis.topology.tpr.obj": [[150, "module-MDAnalysis.topology.tpr.obj"]], "mdanalysis.topology.tpr.setting": [[150, "module-MDAnalysis.topology.tpr.setting"]], "mdanalysis.topology.tpr.utils": [[150, "module-MDAnalysis.topology.tpr.utils"]], "molblock (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Molblock"]], "moleculekind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind"]], "mtop (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Mtop"]], "params (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Params"]], "supported_versions (in module mdanalysis.topology.tpr)": [[150, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS"]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS"]], "tpxunpacker (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker"]], "tpxunpacker2020 (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020"]], "tpxheader (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader"]], "atnr (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.atnr"]], "atomnames (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atomnames"]], "atomnumber (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.atomnumber"]], "atoms (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atoms"]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox"]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bF"]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr"]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop"]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bV"]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bX"]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.define_unpack_real"]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atom"]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atoms"]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_block"]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_blocka"]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ffparams"]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_harm"]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ilists"]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_iparams"]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_molblock"]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_moltype"]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_mtop"]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_resinfo"]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_rvec"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string"]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symstr"]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symtab"]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[150, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol"]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.extract_box_info"]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state"]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen"]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.fileVersion_err"]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag"]], "from_unpacker() (mdanalysis.topology.tpr.utils.tpxunpacker2020 class method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.from_unpacker"]], "ftupd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.ftupd"]], "fudgeqq (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.fudgeQQ"]], "functype (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.functype"]], "fver (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fver"]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.iatoms"]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.ik"]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.interaction_types"]], "lamb (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.lamb"]], "m (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.m"]], "mb (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.mB"]], "molb_natoms_mol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol"]], "molb_nmol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nmol"]], "molb_nposres_xa (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA"]], "molb_nposres_xb (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB"]], "molb_type (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_type"]], "moltypes (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.moltypes"]], "natoms (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.natoms"]], "ndo_int() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_int"]], "ndo_ivec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_ivec"]], "ndo_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_real"]], "ndo_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_rvec"]], "ngtc (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.ngtc"]], "nmolblock (mdanalysis.topology.tpr.obj.mtop 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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.2.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.1.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.2.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.2.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.11.1. Analysis data files", "4.8.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.8.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.9.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.7.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.2.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.2.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.2.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.2.7.1.2. Clustering", "4.2.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.2.7.1.5. Covariance calculation \u2014 encore.covariance", "4.2.7.1.3. Dimensionality reduction", "4.2.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.2.7.1.7. Utility functions for ENCORE", "4.7.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.3.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.3.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.7.1.2. HELANAL \u2014 analysis of protein helices", "4.4.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.3.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.4.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.10.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.10.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.8.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.7.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.5.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.5.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.9.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.6.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.2.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.7.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.8.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.3.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "10.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "10.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "10.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "10.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "10.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "10. Auxiliary modules", "7. Converter modules", "7.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "7.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "7.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "7.8. Base classes \u2014 MDAnalysis.converters.base", "6.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "6.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "6.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "6.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "6.25. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "6.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "6.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "6.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "6.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "6.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "6.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "6.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "6.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "6.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "6.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "6.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "6.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "6.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "6.19. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.20. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.21. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "6.22. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.34. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.23. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.24. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.30. Base classes \u2014 MDAnalysis.coordinates.base", "6.33. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.27. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.31. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "6.26. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.28. Null output \u2014 MDAnalysis.coordinates.null", "6.32. Serialization of Coordinate Readers", "6.29. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "6. Coordinates modules", "7.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "11.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "11.1. Core functions of MDAnalysis", "11.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "11.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "11.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "11.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "11.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "11. Core modules", "16. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "13.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "13.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "13.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "13.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "13.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "13.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "13.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "13.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "13.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "13.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "13.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "13.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "13.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "13.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "13.2.10. Helper functions \u2014 MDAnalysis.lib.util", "13. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "17. References", "3. Selection commands", "9.2.6. Base classes for the selection writers", "9.2.4. CHARMM selections", "9.2.3. Gromacs selections", "9.2.5. Jmol selections", "9.2.2. PyMOL selections", "9.2.1. VMD selections", "9. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.26. Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.27. MDAnalysis topology tables", "5.28. Utility functions for the TPR topology parser", "5. Topology modules", "8. Trajectory transformations (\u201con-the-fly\u201d transformations)", "8.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "8.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "8.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "8.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "8.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "8.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "8.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "8.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "15. Constants and unit conversion \u2014 MDAnalysis.units", "14. Version information for MDAnalysis - MDAnalysis.version", "12.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "12.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "12. 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159, 160, 161, 162, 163, 164, 166], "do": [0, 1, 4, 6, 9, 10, 14, 17, 23, 34, 36, 38, 40, 44, 59, 65, 68, 71, 75, 76, 77, 80, 82, 83, 85, 87, 103, 110, 111, 112, 135, 148, 151, 153, 155, 156], "individu": [0, 10, 11, 17, 19, 23, 26, 29, 34, 35, 39, 42, 44, 59, 77, 80, 87, 93, 110, 112, 115, 116, 117, 118, 119, 120, 121, 134, 165, 166], "respect": [0, 4, 6, 29, 34, 36, 37, 84, 87, 89, 100, 109, 155], "show": [0, 2, 4, 6, 7, 8, 9, 17, 19, 20, 23, 26, 28, 29, 32, 33, 35, 36, 37, 103, 112, 114, 135], "how": [0, 2, 8, 10, 12, 13, 16, 17, 23, 25, 32, 37, 39, 42, 49, 52, 59, 61, 63, 68, 69, 75, 76, 80, 87, 88, 101, 102, 103, 110, 112, 114, 161, 166], "step": [0, 1, 2, 3, 4, 6, 8, 9, 16, 23, 24, 25, 26, 28, 29, 30, 32, 34, 35, 36, 37, 39, 40, 41, 42, 44, 48, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 79, 80, 81, 84, 87, 93, 99, 100, 101, 102, 148, 152, 156, 161], "manual": [0, 6, 17, 23, 69, 78, 89, 103, 112, 142, 152, 157], "explain": [0, 32, 40], "intermedi": [0, 23, 36, 103, 110, 161], "comput": [0, 1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 17, 22, 24, 28, 30, 31, 32, 34, 35, 36, 37, 38, 55, 59, 68, 80, 87, 88, 91, 99, 104, 105, 108, 110, 111, 113, 156, 157, 161], "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 50, 51, 55, 56, 57, 58, 59, 62, 63, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 165, 166], "requir": [0, 2, 3, 7, 8, 13, 14, 15, 17, 20, 23, 24, 29, 32, 33, 34, 36, 39, 41, 44, 49, 51, 52, 55, 57, 59, 61, 63, 65, 67, 69, 70, 73, 74, 75, 76, 79, 80, 81, 84, 86, 87, 92, 93, 95, 99, 100, 104, 107, 110, 114, 136, 138, 141, 150, 152, 153, 165], "lib": [0, 1, 2, 3, 6, 8, 9, 10, 24, 29, 30, 32, 36, 37, 58, 59, 69, 73, 78, 83, 84, 87, 89, 92], "qcprot": [0, 8, 36, 111, 112, 113], "implement": [0, 2, 4, 6, 8, 11, 13, 15, 16, 17, 25, 28, 29, 34, 36, 42, 51, 52, 55, 58, 59, 61, 65, 66, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 80, 81, 85, 87, 92, 99, 100, 103, 105, 106, 107, 108, 109, 110, 111, 113, 121, 142, 147, 148, 150, 151, 166], "exampl": [0, 1, 5, 6, 7, 8, 11, 13, 14, 16, 17, 19, 23, 25, 27, 28, 29, 32, 33, 34, 35, 38, 39, 40, 44, 46, 47, 48, 49, 52, 55, 57, 58, 67, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 83, 84, 86, 87, 89, 90, 91, 92, 93, 99, 101, 102, 103, 104, 106, 109, 110, 111, 113, 114, 120, 121, 130, 132, 133, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 166], "file": [0, 1, 3, 6, 8, 9, 13, 14, 16, 17, 18, 20, 24, 26, 29, 32, 34, 36, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 52, 53, 56, 58, 69, 71, 76, 77, 78, 79, 80, 81, 82, 85, 87, 91, 93, 95, 101, 102, 103, 105, 106, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148, 149, 150, 151, 152, 163, 164, 166], "provid": [0, 1, 2, 4, 6, 7, 8, 9, 10, 13, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 87, 89, 90, 93, 99, 100, 102, 104, 105, 106, 107, 110, 111, 112, 113, 114, 121, 135, 139, 148, 155, 158, 166], "part": [0, 5, 8, 13, 20, 23, 26, 29, 32, 34, 38, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 91, 109, 112, 114, 121, 141], "test": [0, 1, 3, 4, 8, 9, 13, 16, 17, 20, 22, 23, 26, 27, 29, 32, 33, 34, 36, 38, 39, 47, 48, 49, 52, 55, 59, 61, 69, 70, 73, 74, 76, 78, 80, 81, 82, 85, 86, 87, 92, 93, 100, 110, 112, 122, 132, 141, 163, 164], "suit": [0, 1, 8, 13, 16, 17, 23, 29, 32, 39, 112], "variabl": [0, 1, 5, 8, 13, 16, 29, 32, 40, 59, 68, 69, 75, 80, 99, 110, 113, 153], "psf": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 24, 26, 32, 34, 36, 49, 65, 66, 81, 87, 93, 110, 112, 114, 122, 148, 151], "dcd": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 26, 32, 34, 36, 49, 59, 74, 80, 81, 85, 87, 93, 110, 111, 112], "pdb_small": [0, 87], "For": [0, 1, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 37, 38, 39, 44, 46, 48, 49, 52, 55, 57, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 78, 80, 81, 83, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 105, 107, 110, 111, 112, 113, 114, 121, 132, 133, 141, 142, 147, 148, 152, 153, 157, 161], "all": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 18, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 110, 112, 113, 114, 115, 130, 131, 133, 135, 141, 142, 143, 144, 145, 147, 148, 152, 153, 154, 156, 158, 159, 160, 161, 163, 164, 166], "further": [0, 4, 19, 20, 24, 25, 26, 27, 31, 34, 36, 38, 40, 42, 48, 49, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 103, 106, 114, 121, 142, 143], "execut": [0, 1, 3, 7, 23, 26, 38, 48, 77, 110], "first": [0, 2, 3, 4, 6, 8, 9, 13, 17, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 87, 91, 92, 93, 101, 102, 104, 105, 109, 110, 114, 121, 132, 147, 148, 149, 152, 157, 162, 163, 164, 166], "import": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 16, 17, 20, 22, 23, 24, 26, 27, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 59, 61, 63, 65, 67, 69, 78, 79, 81, 86, 87, 90, 91, 92, 93, 101, 102, 103, 104, 109, 110, 111, 112, 122, 130, 132, 133, 142, 147, 152, 158, 163, 164, 165], "mda": [0, 1, 2, 3, 4, 7, 8, 9, 20, 22, 23, 25, 29, 32, 33, 34, 35, 36, 37, 40, 46, 47, 48, 49, 57, 59, 61, 78, 80, 81, 86, 87, 90, 93, 104, 110, 112, 121, 130, 132, 133, 147, 154, 155, 160], "from": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 52, 55, 56, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165, 166], "datafil": [0, 1, 2, 3, 4, 7, 8, 9, 13, 16, 17, 20, 22, 23, 26, 29, 32, 33, 34, 35, 36, 40, 47, 48, 49, 78, 81, 86, 87, 93, 110, 112, 122, 132, 147], "In": [0, 2, 3, 6, 8, 13, 14, 17, 20, 23, 24, 29, 36, 37, 38, 40, 44, 47, 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153, 156, 160], "translat": [0, 3, 6, 32, 36, 59, 61, 77, 87, 90, 91, 100, 109, 115, 149, 152, 155, 160], "have": [0, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 20, 23, 24, 26, 27, 29, 32, 34, 35, 36, 37, 38, 40, 42, 44, 46, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 85, 86, 87, 88, 89, 91, 92, 93, 99, 100, 101, 104, 110, 111, 113, 114, 121, 124, 126, 132, 135, 137, 139, 141, 142, 147, 148, 152, 153, 157, 160, 162, 166], "been": [0, 2, 3, 4, 6, 7, 8, 13, 16, 17, 19, 20, 23, 28, 32, 33, 34, 35, 36, 38, 39, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 73, 74, 75, 76, 79, 80, 81, 87, 89, 93, 102, 103, 104, 110, 113, 114, 133, 147, 160, 166], "remov": [0, 2, 4, 6, 8, 9, 10, 19, 20, 21, 23, 24, 28, 30, 32, 33, 34, 35, 36, 37, 38, 41, 52, 55, 57, 59, 61, 63, 65, 69, 70, 73, 74, 75, 76, 79, 81, 84, 87, 89, 90, 91, 92, 93, 99, 100, 103, 110, 114, 115, 133, 134, 137, 149, 155, 157], "order": [0, 2, 3, 4, 6, 8, 10, 12, 13, 14, 17, 18, 19, 23, 24, 26, 32, 33, 34, 36, 37, 38, 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157, 158, 159, 160, 161, 162, 165, 166], "optim": [0, 13, 20, 34, 36, 100, 108, 109, 110, 113, 152], "whole": [0, 3, 6, 7, 9, 17, 26, 32, 36, 38, 65, 69, 80, 81, 84, 87, 88, 104, 149, 152, 155, 156, 166], "1ake": [0, 36], "trj": [0, 34, 61, 80, 83, 85], "4ake": [0, 36, 67, 87, 112, 114], "filenam": [0, 3, 5, 6, 14, 17, 19, 23, 25, 26, 34, 36, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 87, 93, 95, 101, 102, 106, 110, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148], "rmsfit": 0, "run": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 48, 56, 59, 81, 87, 89, 110, 112, 114, 148, 151, 153, 166], "object": [0, 2, 8, 12, 13, 14, 15, 16, 17, 18, 20, 23, 24, 25, 28, 30, 34, 35, 37, 38, 40, 42, 44, 47, 48, 49, 52, 55, 56, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 89, 96, 101, 102, 103, 105, 106, 107, 109, 110, 111, 112, 114, 115, 122, 123, 125, 126, 127, 129, 132, 133, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 147, 150, 152, 154, 159, 163, 164, 166], "It": [0, 2, 3, 6, 8, 9, 13, 15, 17, 18, 20, 22, 23, 24, 25, 26, 28, 29, 32, 36, 37, 38, 39, 40, 44, 48, 49, 51, 58, 59, 63, 65, 66, 69, 70, 73, 76, 78, 80, 82, 83, 84, 86, 87, 91, 99, 101, 106, 110, 112, 113, 114, 140, 147, 151, 152, 163, 164, 166], "possibl": [0, 2, 4, 6, 8, 9, 10, 17, 20, 23, 24, 25, 29, 38, 40, 49, 57, 58, 59, 65, 66, 68, 69, 77, 78, 80, 81, 87, 89, 91, 93, 95, 100, 101, 103, 110, 113, 114, 147, 148, 149, 152, 158, 161], "arbitrari": [0, 2, 3, 6, 9, 10, 18, 23, 25, 26, 29, 30, 32, 34, 36, 59, 68, 84, 87, 89, 100, 101, 102, 110], "map": [0, 12, 13, 14, 23, 32, 34, 39, 40, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 89, 90, 91, 92, 93, 100, 107, 110], "base": [0, 3, 4, 6, 8, 9, 11, 13, 14, 15, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 51, 52, 54, 55, 56, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 74, 75, 77, 78, 79, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 100, 101, 104, 105, 106, 108, 110, 111, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 147, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160], "sequenc": [0, 17, 23, 26, 34, 36, 38, 65, 66, 76, 77, 80, 87, 91, 93, 104, 109, 110, 115, 126, 150, 152], "allow": [0, 2, 3, 5, 6, 9, 13, 16, 17, 20, 23, 24, 28, 29, 30, 32, 35, 36, 37, 40, 41, 42, 44, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 75, 76, 77, 80, 81, 82, 83, 87, 88, 89, 92, 93, 95, 96, 99, 103, 105, 106, 107, 110, 111, 112, 114, 121, 130, 135, 142, 149, 166], "homolog": 0, "wild": 0, "type": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 48, 49, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 114, 121, 123, 126, 127, 128, 129, 131, 132, 133, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 149, 150, 154, 155, 156, 157, 158, 159, 160, 161], "mutant": 0, "wa": [0, 3, 9, 20, 21, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 42, 48, 49, 52, 55, 56, 58, 59, 61, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 105, 110, 114, 115, 147, 148, 155, 157, 158, 159, 160], "aln": 0, "would": [0, 6, 20, 23, 32, 38, 40, 49, 52, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 87, 93, 111, 114, 147, 152, 156, 157, 161, 166], "produc": [0, 10, 23, 26, 33, 34, 36, 37, 41, 44, 52, 59, 87, 91, 101, 103, 106, 133, 136, 163, 164], "appropri": [0, 6, 8, 25, 29, 35, 36, 38, 40, 42, 43, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 78, 79, 80, 81, 87, 89, 91, 92, 93, 104, 110, 114, 115, 121, 161], "fasta2select": [0, 34, 36], "feed": [0, 23, 26], "result": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 91, 92, 93, 99, 100, 104, 105, 107, 108, 109, 110, 112, 114, 147, 148, 152, 155], "dictionari": [0, 2, 4, 6, 17, 18, 19, 20, 23, 26, 28, 34, 36, 38, 40, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 70, 71, 72, 73, 74, 76, 80, 81, 89, 92, 110, 148, 149], "seldict": 0, "see": [0, 1, 2, 3, 6, 7, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 36, 37, 38, 39, 42, 44, 47, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 83, 87, 89, 91, 93, 95, 99, 100, 102, 103, 104, 110, 114, 121, 133, 137, 141, 142, 147, 149, 150, 151, 152, 153, 161, 163, 164, 165, 166], "document": [0, 2, 5, 6, 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110, 133, 134, 137], "favor": [0, 36, 87], "17": [0, 5, 22, 26, 34, 36, 37, 38, 52, 58, 61, 65, 66, 69, 87, 92, 93, 113, 130, 142, 143, 149, 150], "none": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 100, 101, 102, 103, 104, 106, 107, 109, 110, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 150, 153, 154, 155, 156, 157, 158, 159, 160], "subselect": [0, 9, 87, 114], "tol_mass": [0, 34, 36], "1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 48, 49, 51, 52, 54, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 112, 113, 114, 128, 132, 133, 135, 137, 139, 141, 142, 144, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164], "strict": [0, 67, 87, 91, 92, 99], "fals": [0, 1, 2, 4, 6, 8, 9, 13, 14, 17, 20, 23, 25, 26, 32, 34, 35, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 99, 103, 105, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 150, 153, 156, 157, 158, 159, 164], "match_atom": 0, "sourc": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 86, 87, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 149, 150, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164], "perform": [0, 2, 3, 4, 6, 8, 9, 11, 14, 17, 18, 19, 20, 23, 24, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 89, 99, 100, 103, 104, 107, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 153, 155, 158, 163, 164], "spatial": [0, 34, 35, 59, 107, 155], "follow": [0, 2, 3, 6, 13, 16, 17, 19, 20, 24, 29, 34, 38, 39, 40, 42, 44, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 91, 100, 101, 103, 104, 105, 109, 110, 112, 114, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 152, 157, 161, 166], "wai": [0, 2, 4, 6, 8, 9, 13, 14, 19, 23, 24, 25, 29, 37, 40, 42, 49, 69, 76, 77, 80, 83, 86, 93, 109, 111, 112, 114, 115, 116, 117, 118, 119, 120, 136, 152, 155], "A": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 19, 22, 23, 24, 25, 28, 29, 30, 32, 34, 35, 36, 37, 38, 40, 44, 52, 54, 55, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 79, 80, 81, 82, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 104, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 132, 135, 139, 141, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161], "sel1": [0, 34, 36], "sel2": [0, 34, 36], "befor": [0, 2, 3, 4, 6, 10, 13, 14, 17, 24, 32, 36, 38, 39, 42, 44, 59, 65, 66, 69, 75, 76, 80, 87, 90, 91, 93, 99, 101, 102, 107, 108, 110, 114, 115, 139, 150, 152, 157, 158, 159], "its": [0, 3, 4, 8, 12, 13, 19, 23, 29, 32, 34, 37, 38, 40, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 79, 80, 82, 83, 86, 87, 89, 91, 93, 100, 104, 105, 106, 110, 113, 114, 121, 149, 152, 155], "coincid": [0, 100], "below": [0, 4, 5, 10, 17, 23, 29, 31, 32, 34, 36, 40, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 79, 80, 81, 86, 87, 103, 114, 121, 132], "explan": [0, 29, 59, 110, 149], "deriv": [0, 2, 6, 7, 11, 17, 38, 42, 44, 76, 80, 84, 93, 103, 110, 115, 145, 148], "shift": [0, 26, 87, 100, 105, 160], "behavior": [0, 34, 38, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 110, 114], "through": [0, 4, 6, 10, 11, 17, 20, 21, 23, 24, 25, 35, 38, 40, 41, 44, 49, 52, 55, 56, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 80, 81, 84, 86, 87, 89, 93, 100, 110, 112, 114, 123, 148, 160, 166], "construct": [0, 6, 8, 13, 19, 20, 34, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 86, 89, 93, 100, 105, 107, 110, 122, 148, 152], "alreadi": [0, 6, 7, 8, 23, 32, 42, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 83, 87, 93, 107, 114], "match": [0, 13, 16, 20, 23, 30, 34, 36, 49, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 78, 81, 87, 89, 91, 92, 155], "should": [0, 2, 3, 4, 6, 8, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 33, 34, 35, 36, 37, 38, 42, 44, 49, 52, 57, 59, 61, 62, 63, 65, 67, 75, 76, 80, 83, 85, 87, 89, 90, 91, 92, 96, 100, 103, 105, 106, 107, 110, 116, 117, 118, 119, 120, 131, 133, 134, 141, 142, 147, 148, 149, 156], "therefor": [0, 2, 6, 14, 17, 26, 27, 59, 65, 69, 75, 87, 104, 110, 141, 147], "preserv": [0, 8, 32, 34, 57, 61, 63, 65, 87], "exact": [0, 4, 17, 23, 29, 34, 69, 87], "either": [0, 4, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 28, 34, 36, 38, 40, 42, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 87, 92, 93, 99, 100, 101, 102, 104, 106, 107, 110, 111, 112, 114, 123, 133, 141, 148, 152, 159, 160, 166], "ani": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 16, 17, 23, 24, 25, 26, 28, 29, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 103, 104, 105, 106, 107, 110, 111, 113, 114, 121, 127, 128, 130, 132, 133, 137, 147, 148, 152, 153, 161, 166], "other": [0, 2, 3, 4, 6, 8, 9, 13, 16, 17, 19, 23, 25, 26, 28, 29, 30, 32, 34, 37, 38, 39, 40, 41, 42, 46, 47, 49, 50, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 104, 106, 110, 111, 114, 132, 133, 141, 147, 148, 149, 152, 153, 157, 161, 164, 166], "new": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 44, 46, 47, 48, 49, 50, 51, 52, 53, 55, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 104, 105, 106, 109, 110, 112, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 153, 161, 166], "made": [0, 4, 5, 6, 8, 9, 15, 17, 19, 25, 32, 49, 79, 80, 81, 87, 89, 92, 93, 99, 110, 114, 148, 152], "sort": [0, 23, 24, 26, 32, 33, 38, 45, 87, 89, 90, 91, 92, 110, 114], "index": [0, 2, 6, 8, 23, 24, 25, 26, 28, 29, 30, 32, 34, 36, 37, 38, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 90, 91, 92, 100, 102, 110, 115, 116, 117, 118, 119, 120, 121, 130, 141, 142, 148, 149, 166], "destroi": 0, "correspond": [0, 3, 6, 8, 9, 12, 13, 18, 23, 25, 32, 34, 36, 37, 38, 39, 42, 43, 49, 52, 55, 58, 59, 61, 62, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 99, 100, 103, 105, 107, 110, 113, 114, 130, 150, 155, 157, 158], "safest": 0, "mix": [0, 38], "string": [0, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 29, 32, 34, 36, 37, 38, 40, 42, 48, 58, 59, 62, 63, 65, 67, 69, 78, 79, 80, 81, 86, 87, 89, 91, 93, 101, 103, 106, 109, 111, 114, 115, 116, 117, 118, 119, 120, 121, 133, 135, 141, 142, 149, 150, 155, 162, 163, 164], "paramet": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "str": [0, 2, 3, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 51, 52, 55, 57, 58, 59, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 86, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 106, 107, 110, 113, 114, 116, 118, 121, 132, 139, 145, 149, 155, 159, 163, 164], "dict": [0, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 25, 26, 29, 30, 32, 34, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 81, 82, 84, 87, 89, 90, 92, 93, 101, 103, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 161], "tupl": [0, 4, 6, 10, 18, 19, 20, 26, 32, 34, 35, 36, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 79, 81, 87, 90, 91, 92, 93, 99, 103, 104, 109, 110, 141, 147, 148, 150, 152], "option": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "oper": [0, 2, 6, 18, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 81, 87, 89, 92, 100, 101, 104, 105, 107, 110, 111, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 160], "valid": [0, 8, 9, 32, 34, 35, 36, 42, 44, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 81, 105, 110, 137, 142, 143, 149], "ident": [0, 17, 20, 32, 34, 36, 57, 58, 87, 92, 93, 109, 110, 130, 148], "where": [0, 1, 5, 6, 7, 8, 15, 17, 18, 19, 20, 23, 29, 32, 33, 34, 35, 36, 37, 38, 40, 44, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 110, 112, 114, 133, 141, 147, 152, 155, 156, 158, 161], "return": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "clustalw": [0, 34, 36], "stamp": [0, 2, 23, 34, 36], "2": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 46, 47, 48, 49, 51, 52, 53, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 106, 109, 110, 113, 114, 132, 133, 134, 135, 137, 141, 142, 143, 145, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164, 166], "3": [0, 2, 3, 4, 6, 7, 8, 9, 10, 13, 15, 16, 17, 18, 20, 21, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 81, 84, 87, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 113, 114, 132, 133, 134, 137, 141, 142, 147, 148, 149, 150, 152, 157, 158, 159, 160, 161, 163, 164, 166], "gener": [0, 1, 5, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 32, 34, 35, 36, 38, 39, 40, 44, 47, 52, 58, 59, 61, 62, 63, 65, 70, 73, 74, 76, 78, 80, 81, 82, 87, 89, 91, 92, 93, 100, 102, 105, 107, 109, 110, 112, 113, 114, 130, 131, 134, 139, 141, 147, 148, 156, 161, 163, 164, 166], "equival": [0, 6, 18, 22, 24, 29, 36, 37, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 82, 87, 106, 107, 114, 142], "each": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 70, 72, 73, 74, 75, 76, 77, 80, 81, 86, 87, 89, 90, 91, 92, 93, 99, 100, 103, 104, 105, 108, 110, 112, 115, 121, 132, 141, 147, 148, 149, 155, 158, 160], "list": [0, 2, 3, 4, 6, 9, 12, 13, 14, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 109, 112, 113, 114, 115, 121, 123, 126, 127, 128, 129, 131, 137, 138, 141, 142, 143, 144, 147, 148, 149, 152, 158, 161, 166], "defin": [0, 2, 3, 4, 6, 13, 16, 17, 20, 23, 24, 25, 28, 34, 36, 37, 38, 40, 44, 52, 57, 59, 61, 65, 66, 69, 75, 76, 79, 80, 87, 91, 92, 93, 100, 101, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 132, 141, 145, 147, 148, 150, 152, 153, 155, 158, 159, 161], "describ": [0, 2, 3, 11, 13, 15, 16, 17, 18, 23, 25, 29, 31, 34, 36, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 103, 104, 105, 110, 112, 113, 114, 121, 139, 142, 151, 152, 162], "under": [0, 17, 23, 25, 26, 34, 36, 37, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 81, 87, 93, 99, 100, 103, 105, 110, 120, 148, 152, 166], "bool": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 96, 100, 101, 103, 104, 107, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 153, 154, 155, 156, 157, 158, 159, 160], "whether": [0, 9, 13, 14, 16, 17, 20, 23, 24, 26, 34, 40, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 89, 91, 103, 106, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152], "default": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 26, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 44, 47, 48, 49, 50, 51, 52, 53, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 103, 104, 106, 107, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 149, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "array_lik": [0, 2, 3, 6, 9, 10, 14, 15, 17, 18, 23, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 92, 100, 101, 102, 104, 107, 109, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 155, 158], "choos": [0, 6, 8, 20, 23, 32, 34, 77, 80, 87, 89, 91, 155, 159], "With": [0, 6, 15, 20, 26, 34, 36, 37, 40, 46, 77, 99, 155, 158], "weigh": [0, 34, 36, 155, 158], "equal": [0, 1, 8, 13, 18, 23, 32, 34, 36, 37, 38, 44, 59, 89, 92, 99, 100, 103, 110, 155, 158, 163], "float": [0, 4, 6, 7, 8, 10, 13, 15, 16, 17, 19, 20, 23, 24, 25, 28, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 44, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 81, 84, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 114, 147, 149, 150, 154, 155, 158, 161, 163, 164], "same": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 16, 17, 20, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 44, 48, 49, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 92, 93, 99, 100, 101, 104, 105, 109, 110, 114, 121, 130, 147, 148, 150, 155, 157, 158, 160], "length": [0, 2, 3, 6, 8, 10, 13, 14, 17, 19, 20, 22, 23, 24, 29, 30, 32, 33, 34, 36, 38, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 84, 87, 90, 91, 92, 93, 100, 101, 104, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 158, 161], "element": [0, 3, 6, 12, 13, 14, 16, 17, 18, 23, 32, 34, 36, 37, 38, 48, 49, 59, 65, 75, 87, 90, 91, 99, 105, 110, 114, 115, 123, 126, 128, 135, 137, 138, 141, 142, 143, 149, 150, 155, 158], "reject": [0, 25, 34, 36], "differ": [0, 1, 2, 3, 4, 6, 8, 11, 13, 16, 17, 19, 20, 23, 24, 25, 32, 34, 36, 37, 38, 42, 44, 49, 52, 55, 56, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 83, 84, 86, 87, 91, 92, 93, 101, 109, 110, 112, 113, 114, 121, 126, 137, 142, 148, 152, 161], "more": [0, 1, 2, 3, 4, 8, 9, 10, 11, 13, 16, 17, 23, 24, 25, 32, 34, 36, 37, 38, 39, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 88, 91, 93, 100, 101, 102, 103, 105, 106, 109, 110, 111, 112, 114, 141, 142, 147, 148, 152, 156, 164, 166], "than": [0, 3, 4, 6, 8, 9, 10, 15, 17, 19, 20, 23, 24, 32, 34, 36, 37, 38, 41, 42, 51, 57, 59, 65, 67, 69, 75, 77, 81, 87, 91, 92, 93, 99, 100, 104, 105, 106, 110, 114, 147, 150, 156], "Will": [0, 4, 6, 8, 9, 17, 18, 20, 24, 28, 32, 33, 35, 36, 38, 44, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 93, 104], "rais": [0, 2, 3, 6, 9, 23, 26, 29, 30, 32, 36, 40, 42, 43, 44, 49, 52, 55, 57, 58, 59, 60, 61, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 93, 95, 102, 103, 104, 106, 109, 110, 114, 121, 135, 137, 145, 147, 157, 161], "selectionerror": [0, 36, 89, 95], "doe": [0, 3, 6, 13, 14, 23, 24, 29, 32, 34, 36, 37, 59, 61, 64, 65, 67, 69, 70, 77, 78, 80, 82, 84, 87, 91, 93, 95, 100, 101, 103, 104, 110, 114, 121, 131, 138, 141, 151, 153, 156], "try": [0, 20, 23, 42, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 79, 81, 83, 85, 110, 131, 133, 142, 147, 162], "prepar": [0, 93], "drop": [0, 17, 58, 87, 110], "residu": [0, 3, 6, 9, 10, 19, 23, 25, 28, 30, 31, 32, 35, 36, 37, 38, 48, 65, 66, 67, 80, 86, 87, 89, 90, 91, 93, 95, 96, 110, 112, 114, 123, 125, 126, 127, 128, 130, 131, 132, 134, 137, 139, 140, 141, 142, 144, 148, 159, 160], "non": [0, 2, 3, 6, 8, 9, 17, 23, 24, 25, 29, 30, 32, 33, 36, 38, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 89, 103, 104, 105, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 126, 141, 156, 157], "get_matching_atom": 0, "detail": [0, 4, 6, 7, 8, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 49, 52, 59, 61, 65, 75, 79, 80, 90, 102, 103, 110, 111, 114, 141, 142, 148, 152, 166], "e": [0, 2, 4, 6, 9, 13, 17, 18, 23, 24, 25, 26, 28, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 86, 87, 89, 91, 92, 93, 99, 100, 101, 103, 104, 105, 109, 110, 111, 112, 113, 114, 115, 137, 141, 147, 148, 149, 150, 152, 153, 154, 157, 158, 161, 162, 163, 164, 166], "context": [0, 23, 44, 48, 58, 59, 65, 69, 76, 78, 80, 101, 102, 106, 110, 121, 153], "rest": [0, 3, 6, 150], "ligand": [0, 3, 6, 19, 35, 38, 78, 93], "surround": 0, "water": [0, 6, 7, 8, 10, 20, 23, 24, 39, 87, 88, 93, 99, 112, 113, 114, 132, 150, 161], "old_rmsd": 0, "new_rmsd": 0, "after": [0, 1, 2, 3, 6, 8, 10, 17, 18, 20, 23, 24, 26, 32, 34, 35, 36, 37, 38, 42, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 86, 87, 91, 93, 103, 106, 107, 110, 114, 141, 147, 149, 152, 157, 158, 162], "effici": [0, 1, 10, 18, 34, 65, 68, 69, 73, 103, 113, 148], "method": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 16, 17, 19, 20, 22, 23, 25, 26, 28, 29, 31, 32, 33, 35, 36, 37, 38, 40, 42, 46, 49, 52, 55, 56, 57, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 77, 81, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 100, 101, 102, 103, 105, 107, 108, 109, 110, 112, 113, 114, 115, 121, 136, 145, 147, 148, 150, 152, 156, 159], "ad": [0, 1, 2, 3, 4, 6, 9, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 30, 32, 36, 37, 42, 49, 52, 55, 56, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 87, 89, 90, 91, 92, 93, 99, 100, 102, 103, 104, 110, 132, 133, 135, 137, 138, 139, 141, 142, 143, 145, 147, 149, 152], "toggl": [0, 38, 93, 142], "8": [0, 2, 4, 9, 26, 31, 34, 36, 37, 40, 48, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 70, 72, 73, 74, 76, 78, 81, 84, 87, 89, 91, 92, 93, 100, 104, 110, 114, 115, 116, 117, 118, 119, 120, 126, 137, 142, 148, 149, 150, 160, 161, 163, 164], "check": [0, 4, 6, 9, 10, 13, 19, 20, 23, 31, 32, 33, 34, 36, 38, 42, 44, 52, 55, 58, 59, 61, 65, 70, 71, 72, 73, 74, 76, 77, 78, 81, 87, 92, 100, 105, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160], "includ": [0, 1, 3, 5, 9, 11, 13, 17, 23, 24, 25, 29, 32, 34, 36, 38, 42, 44, 48, 52, 55, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 89, 90, 93, 99, 100, 103, 106, 109, 110, 114, 121, 132, 138, 142, 148, 150, 152, 166], "work": [0, 2, 4, 6, 8, 9, 10, 11, 13, 16, 17, 18, 23, 28, 31, 36, 37, 38, 39, 40, 49, 52, 55, 58, 59, 61, 68, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 95, 100, 103, 104, 105, 106, 110, 112, 113, 114, 115, 121, 132, 142, 147, 152, 155, 160, 166], "incomplet": [0, 9, 27], "lenient": 0, "wherea": [0, 8, 32, 34, 87, 110, 111], "old": [0, 52, 80, 86, 87, 93, 110, 148], "kwarg": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 18, 23, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 86, 87, 91, 92, 93, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 147, 153], "replac": [0, 6, 12, 23, 58, 87, 93, 99, 100, 106, 110, 147, 148], "mass_weight": [0, 34, 36], "sinc": [0, 4, 6, 8, 9, 14, 17, 19, 21, 23, 24, 28, 32, 33, 34, 35, 36, 38, 39, 49, 52, 65, 69, 75, 76, 81, 87, 91, 114, 141, 156], "instead": [0, 2, 3, 4, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 42, 49, 51, 52, 53, 54, 55, 56, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 80, 81, 87, 89, 91, 92, 93, 96, 99, 100, 101, 102, 104, 105, 110, 114, 115, 116, 117, 118, 119, 120, 121, 126, 137, 148, 152, 159], "prefix": [0, 23, 34, 87, 103, 114], "rmsfit_": 0, "forc": [0, 20, 30, 31, 39, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 82, 84, 85, 87, 89, 92, 93, 100, 102, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 161], "in_memori": [0, 17, 36, 37, 81, 93], "both": [0, 2, 3, 4, 6, 9, 10, 14, 17, 23, 24, 26, 29, 30, 32, 34, 36, 38, 40, 49, 54, 56, 58, 61, 65, 69, 72, 80, 87, 92, 99, 102, 103, 112, 113, 114, 130, 133, 140, 141, 164], "must": [0, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 18, 20, 23, 24, 26, 29, 32, 34, 36, 38, 40, 42, 44, 49, 52, 55, 59, 61, 65, 67, 68, 69, 70, 71, 73, 74, 76, 77, 80, 81, 84, 87, 90, 91, 93, 99, 100, 104, 105, 106, 107, 108, 110, 114, 115, 141, 145, 147, 152, 155, 157, 161], "instanc": [0, 2, 3, 4, 6, 7, 8, 9, 13, 16, 17, 18, 23, 25, 28, 29, 32, 33, 34, 35, 36, 39, 40, 42, 43, 44, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 84, 86, 87, 88, 91, 92, 93, 100, 101, 103, 105, 106, 110, 112, 114, 115, 141, 145, 148, 150, 152, 159, 163, 164, 165, 166], "output": [0, 2, 6, 13, 14, 17, 18, 19, 23, 26, 32, 34, 35, 36, 40, 49, 50, 51, 52, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 86, 87, 89, 91, 100, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 128, 148, 157], "format": [0, 3, 4, 6, 10, 13, 14, 15, 16, 17, 18, 23, 25, 26, 34, 37, 38, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 56, 58, 59, 60, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 77, 78, 79, 81, 82, 84, 85, 87, 91, 92, 93, 95, 100, 103, 104, 105, 109, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 143, 145, 147, 149, 150, 151, 162, 166], "determin": [0, 3, 4, 6, 8, 9, 10, 13, 18, 22, 23, 24, 25, 26, 29, 32, 33, 34, 38, 42, 44, 59, 65, 79, 80, 87, 91, 93, 100, 104, 108, 110, 113, 147, 157], "extens": [0, 4, 6, 17, 23, 25, 34, 44, 51, 59, 65, 66, 67, 68, 69, 77, 78, 79, 80, 85, 87, 93, 110, 111, 116, 117, 118, 119, 120, 132, 148, 151, 162], "One": [0, 2, 3, 6, 13, 16, 23, 24, 25, 26, 34, 37, 38, 48, 87, 93, 101, 114, 152, 161], "save": [0, 3, 4, 6, 7, 8, 10, 14, 17, 18, 20, 26, 28, 29, 32, 34, 36, 37, 52, 58, 59, 61, 63, 65, 69, 73, 74, 78, 83, 100, 101, 102, 106], "an": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 52, 55, 56, 57, 58, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "altern": [0, 6, 9, 17, 19, 22, 23, 24, 28, 32, 41, 44, 49, 62, 65, 66, 87, 92, 93, 104, 110, 114, 121, 134, 152], "np": [0, 2, 3, 4, 5, 6, 8, 17, 20, 23, 24, 26, 28, 29, 32, 34, 36, 37, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 93, 100, 101, 102, 104, 108, 109, 110, 114, 147, 149, 152, 163, 164], "savetxt": [0, 4, 28, 36], "subdomain": [0, 105], "against": [0, 17, 69, 92, 105], "written": [0, 2, 6, 14, 17, 19, 23, 34, 38, 40, 48, 51, 52, 55, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 80, 83, 84, 87, 91, 93, 101, 102, 103, 104, 106, 110, 115, 116, 117, 118, 119, 120, 121, 139, 142, 148, 152, 166], "prepend": [0, 34], "toler": [0, 4, 87, 89, 163, 164], "given": [0, 3, 4, 5, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 29, 30, 32, 34, 35, 36, 37, 38, 40, 42, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 101, 102, 106, 110, 114, 132, 136, 141, 147, 150, 152, 155, 156, 157, 158, 159, 160, 162], "find": [0, 9, 10, 13, 19, 20, 23, 24, 25, 32, 34, 38, 40, 42, 43, 46, 52, 61, 77, 83, 87, 90, 96, 101, 110, 111, 114, 131, 141, 147], "fail": [0, 6, 26, 28, 38, 49, 59, 65, 67, 69, 73, 83, 85, 87, 95, 104, 110, 145], "t": [0, 2, 4, 7, 17, 20, 22, 24, 29, 30, 32, 34, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 52, 55, 56, 58, 59, 60, 61, 64, 65, 66, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 90, 91, 99, 100, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 152, 153, 156, 157, 158, 159, 160, 161], "found": [0, 2, 9, 19, 20, 23, 24, 25, 34, 38, 40, 42, 43, 49, 59, 65, 70, 77, 78, 79, 86, 87, 89, 91, 93, 108, 110, 111, 132, 147, 148, 166], "overwrit": [0, 20, 35, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "perman": [0, 37, 93], "switch": [0, 4, 9, 24, 38, 40, 105], "memori": [0, 8, 10, 13, 14, 18, 29, 36, 37, 40, 41, 42, 44, 53, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 85, 87, 90, 93, 110, 147, 157], "place": [0, 6, 9, 14, 17, 23, 38, 40, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 90, 93, 100, 102, 104, 108, 109, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 154, 160], "which": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 23, 24, 25, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 46, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 165, 166], "improv": [0, 15, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 89, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "substanti": [0, 81], "some": [0, 4, 8, 9, 17, 20, 23, 26, 28, 32, 37, 38, 39, 40, 42, 47, 48, 49, 59, 61, 65, 68, 69, 76, 78, 79, 80, 83, 87, 89, 91, 104, 109, 110, 111, 135, 146, 147, 148, 150, 152, 161, 165, 166], "out": [0, 4, 17, 22, 23, 32, 36, 37, 38, 39, 40, 42, 44, 45, 52, 55, 56, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 80, 81, 87, 93, 103, 109, 115, 141, 148, 161, 162, 165, 166], "ignor": [0, 6, 13, 16, 18, 23, 42, 44, 59, 63, 65, 66, 75, 80, 81, 82, 84, 87, 91, 92, 93, 103, 104, 114, 126, 132, 133, 135, 137, 141, 147, 149], "verbos": [0, 2, 3, 4, 6, 7, 8, 9, 13, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 81, 93, 103], "logger": [0, 38, 103], "inform": [0, 8, 9, 13, 16, 17, 20, 23, 24, 25, 33, 34, 37, 38, 42, 49, 50, 52, 55, 57, 59, 61, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 80, 83, 84, 87, 90, 91, 93, 100, 101, 102, 104, 110, 114, 122, 123, 126, 127, 128, 130, 132, 133, 137, 138, 139, 140, 141, 142, 143, 144, 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28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 44, 52, 53, 55, 59, 61, 70, 73, 74, 76, 79, 80, 84, 87, 88, 89, 90, 91, 92, 93, 100, 104, 105, 109, 110, 112, 147, 152, 153, 164, 166], "ndarrai": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 19, 20, 23, 24, 28, 29, 30, 33, 34, 35, 36, 40, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 84, 87, 91, 92, 93, 100, 102, 104, 105, 107, 108, 109, 110, 112, 147], "alia": [0, 4, 6, 9, 23, 24, 28, 30, 32, 33, 35, 36, 38, 87, 89, 91, 150], "attribut": [0, 2, 3, 4, 6, 7, 9, 18, 19, 20, 23, 24, 26, 28, 30, 32, 33, 34, 35, 36, 38, 39, 40, 42, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 81, 83, 84, 87, 89, 90, 92, 93, 94, 100, 101, 102, 107, 110, 112, 114, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 152, 153, 161], "reflect": [0, 32, 77, 79, 84, 87, 105, 109, 110, 114], "upon": [0, 20, 59, 61, 75, 76, 77, 78, 92, 93, 103, 145, 147, 152], "recommend": [0, 2, 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"index": 114, "preexist": 114, "modifi": 114, "order": 114, "charmm": 116, "jmol": 118, "pymol": 119, "export": 121, "recogn": 121, "extens": 121, "todo": [123, 141], "dl": 124, "poli": 124, "dlpolypars": 124, "molecular": 125, "extend": 126, "topolgi": 127, "fhiaimspars": 127, "hoomd": 131, "xml": 131, "itp": 132, "preprocessor": 132, "lammpspars": 133, "style": 133, "minim": 136, "psf": 140, "prmtop": 141, "portabl": 142, "run": 142, "tpr": [142, 150], "version": [142, 162], "tprparser": [142, 150], "guess": 147, "unknown": 147, "inform": [147, 162], "guesser": 147, "element": 147, "bondord": 148, "improp": 148, "definit": 150, "fly": 152, "workflow": 152, "complex": 152, "closur": 152, "box": 154, "dimens": 154, "boxdimens": 154, "No": 156, "jump": 156, "unwrap": [156, 160], "nojump": 156, "averag": 157, "positionaverag": 157, "rotat": 158, "translat": 159, "wrap": 160, "constant": 161, "convers": 161, "encod": 161, "mdanalysis_base_unit": 161, "footnot": 161, "streamplot": [163, 164], "2d": 163, "visual": [163, 164, 165], "streamlin": 163, "3d": 164, "streamlines_3d": 164, "lipid": 165, "flow": 165, "document": 166, "get": 166, "involv": 166, "guid": 166, "instal": 166, "conda": 166, "pip": 166, "sourc": 166, "indic": 166}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx.ext.todo": 2, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align": [[0, "coordinate-fitting-and-alignment-mdanalysis-analysis-align"]], "RMS-fitting tutorial": [[0, "rms-fitting-tutorial"]], "Common usage": [[0, "common-usage"]], "Functions and Classes": [[0, "functions-and-classes"], [20, "functions-and-classes"]], "Helper functions": [[0, "helper-functions"], [78, "helper-functions"], [90, "helper-functions"]], "Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances": [[1, "simple-atomic-distance-analysis-mdanalysis-analysis-atomicdistances"]], "Basic usage": [[1, "basic-usage"]], "Analysis building blocks \u2014 MDAnalysis.analysis.base": [[2, "analysis-building-blocks-mdanalysis-analysis-base"]], "Example of using a standard analysis tool": [[2, "example-of-using-a-standard-analysis-tool"]], "Writing new analysis tools": [[2, "writing-new-analysis-tools"]], "Classes": [[2, "classes"], [4, "classes"], [8, "classes"], [29, "classes"], [37, "classes"], [38, "classes"], [40, "classes"], [47, "classes"], [47, "id5"], [48, "classes"], [48, "id2"], [49, "classes"], [49, "id1"], [52, "classes"], [55, "classes"], [57, "classes"], [58, "classes"], [59, "classes"], [60, "classes"], [61, "classes"], [62, "classes"], [63, "classes"], [64, "classes"], [65, "classes"], [71, "classes"], [72, "classes"], [75, "classes"], [78, "classes"], [81, "classes"], [82, "classes"], [86, "classes"], [87, "classes"], [90, "classes"], [93, "classes"], [105, "classes"], [123, "classes"], [125, "classes"], [126, "classes"], [127, "classes"], [128, "classes"], [129, "classes"], [130, "classes"], [131, "classes"], [132, "classes"], [133, "classes"], [134, "classes"], [135, "classes"], [136, "classes"], [137, "classes"], [138, "classes"], [139, "classes"], [140, "classes"], [141, "classes"], [142, "classes"], [143, "classes"], [144, "classes"], [145, "classes"]], "Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat": [[3, "bond-angle-torsion-coordinates-analysis-mdanalysis-analysis-bat"]], "Example applications": [[3, "example-applications"], [9, "example-applications"], [26, "example-applications"], [36, "example-applications"]], "Analysis classes": [[3, "analysis-classes"], [26, "analysis-classes"], [36, "analysis-classes"]], "Native contacts analysis \u2014 MDAnalysis.analysis.contacts": [[4, "native-contacts-analysis-mdanalysis-analysis-contacts"]], "Examples for contact analysis": [[4, "examples-for-contact-analysis"]], "One-dimensional contact analysis": [[4, "one-dimensional-contact-analysis"]], "Two-dimensional contact analysis (q1-q2)": [[4, "two-dimensional-contact-analysis-q1-q2"]], "Writing your own contact analysis": [[4, "writing-your-own-contact-analysis"]], "Functions": [[4, "functions"], [36, "functions"], [93, "functions"], [100, "functions"], [108, "functions"], [109, "functions"], [161, "functions"]], "Analysis data files": [[5, "analysis-data-files"]], "Data files": [[5, "data-files"]], "Generating densities from trajectories \u2014 MDAnalysis.analysis.density": [[6, "generating-densities-from-trajectories-mdanalysis-analysis-density"]], "Generating a density from a MD trajectory": [[6, "generating-a-density-from-a-md-trajectory"]], "Creating densities": [[6, "creating-densities"]], "Density object": [[6, "density-object"]], "Dielectric \u2014 MDAnalysis.analysis.dielectric": [[7, "dielectric-mdanalysis-analysis-dielectric"]], "Diffusion map \u2014 MDAnalysis.analysis.diffusionmap": [[8, "diffusion-map-mdanalysis-analysis-diffusionmap"]], "Diffusion Map tutorial": [[8, "diffusion-map-tutorial"]], "Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals": [[9, "dihedral-angles-analysis-mdanalysis-analysis-dihedrals"]], "General dihedral analysis": [[9, "general-dihedral-analysis"]], "Ramachandran analysis": [[9, "ramachandran-analysis"]], "Janin analysis": [[9, "janin-analysis"]], "Reference plots": [[9, "reference-plots"]], "Analysis Classes": [[9, "analysis-classes"]], "Distance analysis \u2014 MDAnalysis.analysis.distances": [[10, "distance-analysis-mdanalysis-analysis-distances"]], "ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore": [[11, "encore-ensemble-similarity-calculations-mdanalysis-analysis-encore"]], "Modules": [[11, "modules"]], "References": [[11, "references"], [113, "references"]], "bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap": [[12, "bootstrap-procedures-mdanalysis-analysis-ensemble-bootstrap"]], "Clustering": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "clustering frontend \u2014 MDAnalysis.analysis.encore.clustering.cluster": [[13, "clustering-frontend-mdanalysis-analysis-encore-clustering-cluster"]], "Cluster representation \u2014 MDAnalysis.analysis.encore.clustering.ClusterCollection": [[13, "cluster-representation-mdanalysis-analysis-encore-clustering-clustercollection"]], "clustering frontend \u2014 MDAnalysis.analysis.encore.clustering.ClusteringMethod": [[13, "clustering-frontend-mdanalysis-analysis-encore-clustering-clusteringmethod"]], "Clustering algorithms": [[13, "clustering-algorithms"]], "Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix": [[14, "distance-matrix-calculation-mdanalysis-analysis-ensemble-confdistmatrix"]], "Covariance calculation \u2014 encore.covariance": [[15, "covariance-calculation-encore-covariance"]], "Dimensionality reduction": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "dimensionality reduction frontend \u2014 MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "dimensionality-reduction-frontend-mdanalysis-analysis-encore-dimensionality-reduction-reduce-dimensionality"]], "dimensionality reduction frontend \u2014 MDAnalysis.analysis.encore.clustering.DimensionalityReductionMethod": [[16, "dimensionality-reduction-frontend-mdanalysis-analysis-encore-clustering-dimensionalityreductionmethod"]], "Dimensionality reduction algorithms": [[16, "dimensionality-reduction-algorithms"]], "Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity": [[17, "ensemble-similarity-calculations-mdanalysis-analysis-encore-similarity"]], "Functions for ensemble comparisons": [[17, "functions-for-ensemble-comparisons"]], "Function reference": [[17, "function-reference"]], "Utility functions for ENCORE": [[18, "module-MDAnalysis.analysis.encore.utils"]], "Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm": [[19, "elastic-network-analysis-of-md-trajectories-mdanalysis-analysis-gnm"]], "Analysis tasks": [[19, "analysis-tasks"]], "Utility functions": [[19, "utility-functions"]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "hydrogen-bond-autocorrelation-mdanalysis-analysis-hydrogenbonds-hbond-autocorrel"]], "Description": [[20, "description"]], "Input": [[20, "input"], [24, "input"]], "Output": [[20, "output"], [24, "output"], [37, "output"]], "Worked Example for Polyamide": [[20, "worked-example-for-polyamide"]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)": [[21, "hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel-deprecated"]], "HELANAL \u2014 analysis of protein helices": [[22, "helanal-analysis-of-protein-helices"]], "Example use": [[22, "example-use"]], "HOLE analysis \u2014 MDAnalysis.analysis.hole2": [[23, "hole-analysis-mdanalysis-analysis-hole2"]], "Module": [[23, "module-MDAnalysis.analysis.hole2"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2": [[23, "id3"]], "Using HOLE on a PDB file": [[23, "using-hole-on-a-pdb-file"]], "Using HOLE on a trajectory": [[23, "using-hole-on-a-trajectory"]], "Using HOLE with VMD": [[23, "using-hole-with-vmd"]], "Analyzing a full trajectory": [[23, "analyzing-a-full-trajectory"]], "Creating subsampled HOLE surface": [[23, "creating-subsampled-hole-surface"]], "Loading a trajectory into VMD with subsampling": [[23, "loading-a-trajectory-into-vmd-with-subsampling"]], "Creating a subsampled trajectory": [[23, "creating-a-subsampled-trajectory"]], "Functions and classes": [[23, "functions-and-classes"]], "Utility functions and templates": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.helper": [[23, "hole-analysis-mdanalysis-analysis-hole2-helper"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.templates": [[23, "hole-analysis-mdanalysis-analysis-hole2-templates"]], "Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "hydrogen-bond-analysis-mdanalysis-analysis-hydrogenbonds-hbond-analysis"]], "Example use of HydrogenBondAnalysis": [[24, "example-use-of-hydrogenbondanalysis"]], "The class and its methods": [[24, "the-class-and-its-methods"]], "Leaflet identification \u2014 MDAnalysis.analysis.leaflet": [[25, "leaflet-identification-mdanalysis-analysis-leaflet"]], "Algorithm": [[25, "algorithm"]], "Classes and Functions": [[25, "classes-and-functions"], [32, "classes-and-functions"]], "Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna": [[26, "generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-legacy-x3dna"]], "Single structure": [[26, "single-structure"]], "Trajectory": [[26, "trajectory"]], "Utilities": [[26, "utilities"]], "MDAnalysis.analysis.legacy \u2014 Legacy analysis code": [[27, "mdanalysis-analysis-legacy-legacy-analysis-code"]], "Legacy modules": [[27, "legacy-modules"]], "Linear Density \u2014 MDAnalysis.analysis.lineardensity": [[28, "linear-density-mdanalysis-analysis-lineardensity"]], "Mean Squared Displacement \u2014 MDAnalysis.analysis.msd": [[29, "mean-squared-displacement-mdanalysis-analysis-msd"]], "Computing an MSD": [[29, "computing-an-msd"]], "Computing Self-Diffusivity": [[29, "computing-self-diffusivity"]], "Combining Multiple Replicates": [[29, "combining-multiple-replicates"]], "Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids": [[30, "updated-nucleic-acid-analysis-mdanalysis-analysis-nucleicacids"]], "Distances": [[30, "distances"], [31, "distances"]], "Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo": [[31, "nucleic-acid-analysis-mdanalysis-analysis-nuclinfo"]], "Phases": [[31, "phases"]], "Dihedral angles": [[31, "dihedral-angles"]], "Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca": [[32, "principal-component-analysis-pca-mdanalysis-analysis-pca"]], "PCA Tutorial": [[32, "pca-tutorial"]], "Polymer analysis \u2014 MDAnalysis.analysis.polymer": [[33, "polymer-analysis-mdanalysis-analysis-polymer"]], "Calculating path similarity \u2014 MDAnalysis.analysis.psa": [[34, "calculating-path-similarity-mdanalysis-analysis-psa"]], "Helper functions and variables": [[34, "helper-functions-and-variables"]], "Classes, methods, and functions": [[34, "classes-methods-and-functions"]], "Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf": [[35, "radial-distribution-functions-mdanalysis-analysis-rdf"]], "Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms": [[36, "calculating-root-mean-square-quantities-mdanalysis-analysis-rms"]], "Calculating RMSD for multiple domains": [[36, "calculating-rmsd-for-multiple-domains"]], "Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics": [[37, "water-dynamics-analysis-mdanalysis-analysis-waterdynamics"]], "Example use of the analysis classes": [[37, "example-use-of-the-analysis-classes"]], "HydrogenBondLifetimes": [[37, "hydrogenbondlifetimes"]], "WaterOrientationalRelaxation": [[37, "waterorientationalrelaxation"], [37, "id76"]], "AngularDistribution": [[37, "angulardistribution"], [37, "id77"]], "MeanSquareDisplacement": [[37, "meansquaredisplacement"], [37, "id78"]], "SurvivalProbability": [[37, "survivalprobability"], [37, "id79"]], "Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis": [[38, "water-bridge-analysis-mdanalysis-analysis-hydrogenbonds-waterbridgeanalysis"]], "Theory": [[38, "theory"]], "Output as Network": [[38, "output-as-network"]], "Output as Timeseries": [[38, "output-as-timeseries"]], "Detection of water bridges": [[38, "detection-of-water-bridges"]], "Default heavy atom names for CHARMM27 force field.": [[38, "id69"]], "Heavy atom types for GLYCAM06 force field.": [[38, "id70"]], "How to perform WaterBridgeAnalysis": [[38, "how-to-perform-waterbridgeanalysis"]], "Use count_by_type": [[38, "use-count-by-type"]], "Use count_by_time": [[38, "use-count-by-time"]], "Analysis modules": [[39, "analysis-modules"]], "Building blocks for Analysis": [[39, "building-blocks-for-analysis"]], "Distances and contacts": [[39, "distances-and-contacts"]], "Hydrogen bonding": [[39, "hydrogen-bonding"]], "Membranes and membrane proteins": [[39, "membranes-and-membrane-proteins"]], "Nucleic acids": [[39, "nucleic-acids"]], "Polymers": [[39, "polymers"]], "Structure": [[39, "structure"]], "Macromolecules": [[39, "macromolecules"]], "Liquids": [[39, "liquids"]], "Volumetric analysis": [[39, "volumetric-analysis"]], "Dimensionality Reduction": [[39, "dimensionality-reduction"]], "Legacy analysis modules": [[39, "legacy-analysis-modules"]], "Data": [[39, "data"], [161, "data"], [162, "data"]], "EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR": [[40, "edr-auxiliary-reader-mdanalysis-auxiliary-edr"]], "Background": [[40, "background"]], "Standalone Usage of the EDRReader": [[40, "standalone-usage-of-the-edrreader"]], "Adding EDR data to trajectories": [[40, "adding-edr-data-to-trajectories"]], "XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG": [[41, "xvg-auxiliary-reader-mdanalysis-auxiliary-xvg"]], "XVG Readers": [[41, "xvg-readers"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary.base": [[42, "auxiliary-readers-mdanalysis-auxiliary-base"]], "Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core": [[43, "common-functions-for-auxiliary-reading-mdanalysis-auxiliary-core"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary": [[44, "auxiliary-readers-mdanalysis-auxiliary"]], "Supported formats": [[44, "supported-formats"]], "Auxiliary API": [[44, "auxiliary-api"]], "Auxiliaries and trajectories": [[44, "auxiliaries-and-trajectories"]], "Adding an auxiliary to a trajectory": [[44, "adding-an-auxiliary-to-a-trajectory"]], "Iterating by an auxiliary": [[44, "iterating-by-an-auxiliary"]], "Accessing auxiliary attributes": [[44, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[44, "recreating-auxiliaries"]], "AuxStep class": [[44, "auxstep-class"]], "Attributes": [[44, "attributes"], [44, "id2"], [80, "attributes"], [80, "id19"], [80, "id21"]], "Methods": [[44, "methods"], [44, "id3"], [80, "methods"], [80, "id18"], [80, "id20"], [80, "id22"]], "AuxReader class": [[44, "auxreader-class"]], "Registry": [[44, "registry"], [80, "registry"]], "Replicating auxiliaries": [[44, "replicating-auxiliaries"]], "Auxiliary modules": [[45, "auxiliary-modules"]], "Converter modules": [[46, "converter-modules"]], "OpenMM topology parser MDAnalysis.converters.OpenMMParser": [[47, "openmm-topology-parser-mdanalysis-converters-openmmparser"]], "OpenMM structure I/O \u2014 MDAnalysis.converters.OpenMM": [[47, "openmm-structure-i-o-mdanalysis-converters-openmm"]], "ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser": [[48, "parmed-topology-parser-mdanalysis-converters-parmedparser"]], "ParmEd structure I/O \u2014 MDAnalysis.converters.ParmEd": [[48, "parmed-structure-i-o-mdanalysis-converters-parmed"]], "RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser": [[49, "rdkit-topology-parser-mdanalysis-converters-rdkitparser"]], "RDKit molecule I/O \u2014 MDAnalysis.converters.RDKit": [[49, "rdkit-molecule-i-o-mdanalysis-converters-rdkit"]], "Base classes \u2014 MDAnalysis.converters.base": [[50, "base-classes-mdanalysis-converters-base"]], "CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD": [[51, "crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd"]], "DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD": [[52, "dcd-trajectory-i-o-mdanalysis-coordinates-dcd"]], "DL_Poly format reader MDAnalysis.coordinates.DLPoly": [[53, "dl-poly-format-reader-mdanalysis-coordinates-dlpoly"]], "DESRES file format \u2014 MDAnalysis.coordinates.DMS": [[54, "desres-file-format-mdanalysis-coordinates-dms"]], "FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS": [[55, "fhi-aims-file-format-mdanalysis-coordinates-fhiaims"]], "Developer notes: FHIAIMSWriter format strings": [[55, "developer-notes-fhiaimswriter-format-strings"]], "GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS": [[56, "gamess-trajectory-reader-mdanalysis-coordinates-gms"]], "GRO file format \u2014 MDAnalysis.coordinates.GRO": [[57, "gro-file-format-mdanalysis-coordinates-gro"]], "Writing GRO files": [[57, "writing-gro-files"]], "Developer notes: GROWriter format strings": [[57, "developer-notes-growriter-format-strings"]], "GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD": [[58, "gsd-trajectory-reader-mdanalysis-coordinates-gsd"]], "H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD": [[59, "h5md-trajectories-mdanalysis-coordinates-h5md"]], "Units": [[59, "units"]], "Example: Loading an H5MD simulation": [[59, "example-loading-an-h5md-simulation"]], "Example: Writing an H5MD file": [[59, "example-writing-an-h5md-file"]], "Example: Opening an H5MD file in parallel": [[59, "example-opening-an-h5md-file-in-parallel"]], "Building parallel h5py and HDF5 on Linux": [[59, "building-parallel-h5py-and-hdf5-on-linux"]], "INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD": [[60, "inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd"]], "LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS": [[61, "lammps-dcd-trajectory-and-data-i-o-mdanalysis-coordinates-lammps"]], "Data file formats": [[61, "data-file-formats"]], "Dump files": [[61, "dump-files"]], "Example: Loading a LAMMPS simulation": [[61, "example-loading-a-lammps-simulation"]], "MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF": [[62, "mmtf-trajectory-reader-mdanalysis-coordinates-mmtf"]], "MOL2 file format \u2014 MDAnalysis.coordinates.MOL2": [[63, "mol2-file-format-mdanalysis-coordinates-mol2"], [135, "mol2-file-format-mdanalysis-coordinates-mol2"]], "Example for working with mol2 files": [[63, "example-for-working-with-mol2-files"]], "MOL2 format notes": [[63, "mol2-format-notes"]], "NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN": [[64, "namdbin-files-format-mdanalysis-coordinates-namdbin"]], "PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB": [[65, "pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb"]], "Capabilities": [[65, "capabilities"]], "Examples for working with PDB files": [[65, "examples-for-working-with-pdb-files"]], "PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT": [[66, "pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt"]], "PQR file format \u2014 MDAnalysis.coordinates.PQR": [[67, "pqr-file-format-mdanalysis-coordinates-pqr"]], "TNG trajectory files \u2014 MDAnalysis.coordinates.TNG": [[68, "tng-trajectory-files-mdanalysis-coordinates-tng"]], "Current Limitations": [[68, "current-limitations"]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[69, "amber-trajectories-mdanalysis-coordinates-trj"]], "Binary NetCDF trajectories": [[69, "binary-netcdf-trajectories"]], "ASCII TRAJ trajectories": [[69, "ascii-traj-trajectories"]], "TRR trajectory files \u2014 MDAnalysis.coordinates.TRR": [[70, "trr-trajectory-files-mdanalysis-coordinates-trr"]], "TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ": [[71, "trz-trajectory-i-o-mdanalysis-coordinates-trz"]], "TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ": [[72, "txyz-file-format-mdanalysis-coordinates-txyz"]], "XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR": [[73, "xdr-based-trajectory-files-mdanalysis-coordinates-xdr"]], "XTC trajectory files \u2014 MDAnalysis.coordinates.XTC": [[74, "xtc-trajectory-files-mdanalysis-coordinates-xtc"]], "XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ": [[75, "xyz-trajectory-reader-mdanalysis-coordinates-xyz"]], "XYZ File format": [[75, "xyz-file-format"]], "Base classes \u2014 MDAnalysis.coordinates.base": [[76, "base-classes-mdanalysis-coordinates-base"]], "FrameIterators": [[76, "frameiterators"]], "Readers": [[76, "readers"], [80, "readers"]], "Writers": [[76, "writers"], [80, "writers"]], "Converters": [[76, "converters"]], "Helper classes": [[76, "helper-classes"]], "ChainReader \u2014 MDAnalysis.coordinates.chain": [[77, "chainreader-mdanalysis-coordinates-chain"]], "Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles": [[78, "reading-trajectories-with-chemfiles-mdanalysis-coordinates-chemfiles"]], "Using the CHEMFILES reader": [[78, "using-the-chemfiles-reader"]], "Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core": [[79, "common-functions-for-coordinate-reading-mdanalysis-coordinates-core"]], "Trajectory Readers and Writers \u2014 MDAnalysis.coordinates": [[80, "trajectory-readers-and-writers-mdanalysis-coordinates"]], "Timesteps": [[80, "timesteps"]], "Supported coordinate formats": [[80, "supported-coordinate-formats"]], "Table of supported coordinate formats": [[80, "id23"]], "Trajectory API": [[80, "trajectory-api"]], "Timestep class": [[80, "timestep-class"]], "Private attributes": [[80, "private-attributes"]], "Trajectory Reader class": [[80, "trajectory-reader-class"]], "Trajectory Writer class": [[80, "trajectory-writer-class"]], "Single Frame Writer class": [[80, "single-frame-writer-class"]], "Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory": [[81, "reading-trajectories-from-memory-mdanalysis-coordinates-memory"]], "How to use the MemoryReader": [[81, "how-to-use-the-memoryreader"]], "In-memory representation of arbitrary trajectories": [[81, "in-memory-representation-of-arbitrary-trajectories"]], "Switching a trajectory to an in-memory representation": [[81, "switching-a-trajectory-to-an-in-memory-representation"]], "Constructing a Reader from a numpy array": [[81, "constructing-a-reader-from-a-numpy-array"]], "Creating an in-memory trajectory of a sub-system": [[81, "creating-an-in-memory-trajectory-of-a-sub-system"]], "Null output \u2014 MDAnalysis.coordinates.null": [[82, "null-output-mdanalysis-coordinates-null"]], "Serialization of Coordinate Readers": [[83, "serialization-of-coordinate-readers"]], "How to serialize a new reader": [[83, "how-to-serialize-a-new-reader"]], "File Access": [[83, "file-access"]], "To seek or not to seek": [[83, "to-seek-or-not-to-seek"]], "Miscellaneous": [[83, "miscellaneous"]], "Tests": [[83, "tests"], [166, "tests"]], "_SingleFrameReader Test": [[83, "singleframereader-test"]], "BaseReaderTest and MultiframeReaderTest": [[83, "basereadertest-and-multiframereadertest"]], "File handler Test": [[83, "file-handler-test"]], "Currently implemented picklable IO Formats": [[83, "currently-implemented-picklable-io-formats"]], "Timestep Class \u2014 MDAnalysis.coordinates.timestep": [[84, "timestep-class-mdanalysis-coordinates-timestep"]], "Timestep": [[84, "timestep"]], "Coordinates modules": [[85, "coordinates-modules"]], "AtomGroup accessors \u2014 MDAnalysis.core.accessors": [[86, "atomgroup-accessors-mdanalysis-core-accessors"]], "Core objects: Containers \u2014 MDAnalysis.core.groups": [[87, "core-objects-containers-mdanalysis-core-groups"]], "Collections": [[87, "collections"]], "Chemical units": [[87, "chemical-units"]], "Levels": [[87, "levels"]], "Core functions of MDAnalysis": [[88, "core-functions-of-mdanalysis"]], "Atom selection Hierarchy \u2014 MDAnalysis.core.selection": [[89, "atom-selection-hierarchy-mdanalysis-core-selection"]], "Core Topology object \u2014 MDAnalysis.core.topology": [[90, "core-topology-object-mdanalysis-core-topology"]], "Topology attribute objects \u2014 MDAnalysis.core.topologyattrs": [[91, "topology-attribute-objects-mdanalysis-core-topologyattrs"]], "Core Topology Objects \u2014 MDAnalysis.core.topologyobjects": [[92, "core-topology-objects-mdanalysis-core-topologyobjects"]], "Core object: Universe \u2014 MDAnalysis.core.universe": [[93, "core-object-universe-mdanalysis-core-universe"]], "Core modules": [[94, "core-modules"]], "Important objects for users": [[94, "important-objects-for-users"]], "Topology system": [[94, "topology-system"]], "Selection system": [[94, "selection-system"]], "Custom exceptions and warnings \u2014 MDAnalysis.exceptions": [[95, "custom-exceptions-and-warnings-mdanalysis-exceptions"]], "Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch": [[96, "neighbor-search-wrapper-for-mdanalysis-mdanalysis-lib-neighborsearch"]], "Distance calculation library \u2014 MDAnalysis.lib.c_distances": [[97, "distance-calculation-library-mdanalysis-lib-c-distances"]], "Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp": [[98, "parallel-distance-calculation-library-mdanalysis-lib-c-distances-openmp"]], "Correlations utilities \u2014 MDAnalysis.lib.correlations": [[99, "correlations-utilities-mdanalysis-lib-correlations"]], "Autocorrelation Function": [[99, "autocorrelation-function"]], "Intermittency Function": [[99, "intermittency-function"]], "Fast distance array computation \u2014 MDAnalysis.lib.distances": [[100, "fast-distance-array-computation-mdanalysis-lib-distances"]], "Selection of acceleration (\u201cbackend\u201d)": [[100, "selection-of-acceleration-backend"]], "Available backends for accelerated distance functions.": [[100, "id1"]], "Use of the distopia library": [[100, "use-of-the-distopia-library"]], "Functions available using the distopia backend.": [[100, "id2"]], "Low-level modules for MDAnalysis.lib.distances": [[100, "low-level-modules-for-mdanalysis-lib-distances"]], "Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd": [[101, "low-level-dcd-trajectory-reading-mdanalysis-lib-formats-libdcd"]], "Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr": [[102, "low-level-gromacs-xdr-trajectory-reading-mdanalysis-lib-formats-libmdaxdr"]], "Setting up logging \u2014 MDAnalysis.lib.log": [[103, "setting-up-logging-mdanalysis-lib-log"]], "Convenience functions": [[103, "convenience-functions"]], "Other functions and classes for logging purposes": [[103, "other-functions-and-classes-for-logging-purposes"]], "Mathematical helper functions \u2014 MDAnalysis.lib.mdamath": [[104, "mathematical-helper-functions-mdanalysis-lib-mdamath"]], "Linear algebra": [[104, "linear-algebra"]], "Connectivity": [[104, "connectivity"]], "Neighbor search library \u2014 MDAnalysis.lib.nsgrid": [[105, "neighbor-search-library-mdanalysis-lib-nsgrid"]], "About the code": [[105, "about-the-code"]], "About the algorithm": [[105, "about-the-algorithm"]], "Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io": [[106, "picklable-read-only-i-o-classes-mdanalysis-lib-picklable-file-io"]], "PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree": [[107, "periodickdtree-mdanalysis-lib-pkdtree"]], "Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot": [[108, "fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot"]], "Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations": [[109, "homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations"]], "Requirements": [[109, "requirements"]], "Helper functions \u2014 MDAnalysis.lib.util": [[110, "helper-functions-mdanalysis-lib-util"]], "Files and directories": [[110, "files-and-directories"]], "Streams": [[110, "streams"]], "Containers and lists": [[110, "containers-and-lists"]], "Arrays": [[110, "arrays"]], "File parsing": [[110, "file-parsing"]], "Data manipulation and handling": [[110, "data-manipulation-and-handling"]], "Strings": [[110, "strings"]], "Class decorators": [[110, "class-decorators"]], "Function decorators": [[110, "function-decorators"]], "Code management": [[110, "code-management"]], "Data format checks": [[110, "data-format-checks"]], "Library functions \u2014 MDAnalysis.lib": [[111, "module-MDAnalysis.lib"]], "Overview": [[111, "overview"]], "List of modules": [[111, "list-of-modules"]], "Low level file formats": [[111, "low-level-file-formats"]], "Libmdanalysis": [[111, "libmdanalysis"]], "Overview over MDAnalysis": [[112, "overview-over-mdanalysis"]], "Using MDAnalysis in python": [[112, "using-mdanalysis-in-python"]], "Examples": [[112, "examples"]], "Included trajectories": [[112, "included-trajectories"]], "Code snippets": [[112, "code-snippets"]], "Citations for the whole MDAnalysis library": [[113, "citations-for-the-whole-mdanalysis-library"]], "Citations for included algorithms and modules": [[113, "citations-for-included-algorithms-and-modules"]], "Citations using Duecredit": [[113, "citations-using-duecredit"]], "Selection commands": [[114, "selection-commands"]], "Selection Keywords": [[114, "selection-keywords"]], "Simple selections": [[114, "simple-selections"]], "Pattern matching": [[114, "pattern-matching"]], "Boolean": [[114, "boolean"]], "Geometric": [[114, "geometric"]], "Similarity and connectivity": [[114, "similarity-and-connectivity"]], "Index": [[114, "index"]], "Preexisting selections and modifiers": [[114, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[114, "dynamic-selections"]], "Ordered selections": [[114, "ordered-selections"]], "Base classes for the selection writers": [[115, "base-classes-for-the-selection-writers"]], "CHARMM selections": [[116, "charmm-selections"]], "Gromacs selections": [[117, "gromacs-selections"]], "Jmol selections": [[118, "jmol-selections"]], "PyMOL selections": [[119, "pymol-selections"]], "VMD selections": [[120, "vmd-selections"]], "Selection exporters": [[121, "selection-exporters"]], "Table of supported exporters and recognized file name extensions.": [[121, "id2"]], "How to write selections": [[121, "how-to-write-selections"]], "Single AtomGroup": [[121, "single-atomgroup"]], "Multiple selections": [[121, "multiple-selections"]], "Selection writers": [[121, "selection-writers"]], "The topology system": [[122, "the-topology-system"]], "CRD topology parser": [[123, "crd-topology-parser"]], "Todo": [[123, "id1"], [141, "id1"]], "DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser": [[124, "dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser"]], "DESRES Molecular Structure file format topology parser": [[125, "desres-molecular-structure-file-format-topology-parser"]], "Extended PDB topology parser": [[126, "extended-pdb-topology-parser"]], "FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser": [[127, "fhi-aims-topology-parser-mdanalysis-topolgy-fhiaimsparser"]], "GAMESS Topology Parser": [[128, "gamess-topology-parser"]], "GRO topology parser": [[129, "gro-topology-parser"]], "GSD topology parser": [[130, "gsd-topology-parser"]], "HOOMD XML topology parser": [[131, "hoomd-xml-topology-parser"]], "ITP topology parser": [[132, "itp-topology-parser"]], "Preprocessor variables": [[132, "preprocessor-variables"]], "LAMMPSParser": [[133, "lammpsparser"]], "Atom styles": [[133, "atom-styles"]], "MMTF Topology Parser": [[134, "mmtf-topology-parser"]], "Minimal topology parser": [[136, "minimal-topology-parser"]], "PDB Topology Parser": [[137, "pdb-topology-parser"]], "PDBQT topology parser": [[138, "pdbqt-topology-parser"]], "PQR topology parser": [[139, "pqr-topology-parser"]], "PSF topology parser": [[140, "psf-topology-parser"]], "AMBER PRMTOP topology parser": [[141, "amber-prmtop-topology-parser"]], "Gromacs portable run input TPR format parser": [[142, "gromacs-portable-run-input-tpr-format-parser"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[142, "id4"]], "Development notes": [[142, "development-notes"]], "TXYZ topology parser": [[143, "txyz-topology-parser"]], "XYZ Topology Parser": [[144, "xyz-topology-parser"]], "Base topology reader classes \u2014 MDAnalysis.topology.base": [[145, "base-topology-reader-classes-mdanalysis-topology-base"]], "Common functions for topology building \u2014 MDAnalysis.topology.core": [[146, "common-functions-for-topology-building-mdanalysis-topology-core"]], "Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers": [[147, "guessing-unknown-topology-information-mdanalysis-topology-guessers"]], "Example uses of guessers": [[147, "example-uses-of-guessers"]], "Guessing elements from atom names": [[147, "guessing-elements-from-atom-names"]], "Topology readers \u2014 MDAnalysis.topology": [[148, "topology-readers-mdanalysis-topology"]], "Table of Supported Topology Formats": [[148, "id19"]], "Developer Notes": [[148, "developer-notes"]], "atoms": [[148, "atoms"]], "bonds": [[148, "bonds"]], "bondorder": [[148, "bondorder"]], "angles": [[148, "angles"]], "dihedrals": [[148, "dihedrals"]], "impropers": [[148, "impropers"]], "MDAnalysis topology tables": [[149, "mdanalysis-topology-tables"]], "Utility functions for the TPR topology parser": [[150, "utility-functions-for-the-tpr-topology-parser"]], "TPR support": [[150, "tpr-support"]], "TPRParser settings": [[150, "tprparser-settings"]], "Class definitions for the TPRParser": [[150, "class-definitions-for-the-tprparser"]], "Utilities for the TPRParser": [[150, "utilities-for-the-tprparser"]], "Topology modules": [[151, "topology-modules"]], "Trajectory transformations (\u201con-the-fly\u201d transformations)": [[152, "module-MDAnalysis.transformations"]], "Workflows": [[152, "workflows"]], "Creating transformations": [[152, "creating-transformations"]], "Creating complex transformation classes": [[152, "creating-complex-transformation-classes"]], "Creating complex transformation closure functions": [[152, "creating-complex-transformation-closure-functions"]], "Transformations in MDAnalysis": [[152, "transformations-in-mdanalysis"]], "How to transformations": [[152, "how-to-transformations"]], "Building blocks for Transformation Classes": [[152, "building-blocks-for-transformation-classes"]], "Currently implemented transformations": [[152, "currently-implemented-transformations"]], "Transformations Base Class \u2014 MDAnalysis.transformations.base": [[153, "transformations-base-class-mdanalysis-transformations-base"]], "Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions": [[154, "set-box-dimensions-mdanalysis-transformations-boxdimensions"]], "Fitting transformations \u2014 MDAnalysis.transformations.fit": [[155, "fitting-transformations-mdanalysis-transformations-fit"]], "No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump": [[156, "no-jump-trajectory-unwrapping-mdanalysis-transformations-nojump"]], "Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging": [[157, "trajectory-coordinate-averaging-mdanalysis-transformations-positionaveraging"]], "Trajectory rotation \u2014 MDAnalysis.transformations.rotate": [[158, "trajectory-rotation-mdanalysis-transformations-rotate"]], "Trajectory translation \u2014 MDAnalysis.transformations.translate": [[159, "trajectory-translation-mdanalysis-transformations-translate"]], "Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap": [[160, "wrap-unwrap-transformations-mdanalysis-transformations-wrap"]], "Constants and unit conversion \u2014 MDAnalysis.units": [[161, "constants-and-unit-conversion-mdanalysis-units"]], "Base units in MDAnalysis as encoded in MDANALYSIS_BASE_UNITS": [[161, "id71"]], "Implementation notes": [[161, "implementation-notes"]], "Conversions": [[161, "conversions"]], "References and footnotes": [[161, "references-and-footnotes"]], "Version information for MDAnalysis - MDAnalysis.version": [[162, "version-information-for-mdanalysis-mdanalysis-version"]], "Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines": [[163, "streamplots-2d-mdanalysis-visualization-streamlines"]], "Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D": [[164, "streamplots-3d-mdanalysis-visualization-streamlines-3d"]], "Visualization modules": [[165, "visualization-modules"]], "Visualization of Lipid Flow": [[165, "visualization-of-lipid-flow"]], "MDAnalysis documentation": [[166, "mdanalysis-documentation"]], "Getting involved": [[166, "getting-involved"]], "User Guide": [[166, "user-guide"]], "Installing MDAnalysis": [[166, "installing-mdanalysis"]], "conda": [[166, "conda"]], "pip": [[166, "pip"]], "Source Code": [[166, "source-code"]], "Citation": [[166, "citation"]], "Indices and tables": [[166, "indices-and-tables"]]}, "indexentries": {"aligntraj (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AlignTraj"]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure"]], "mdanalysis.analysis.align": [[0, "module-MDAnalysis.analysis.align"]], "_fit_to() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align._fit_to"]], "alignto() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.alignto"]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select"]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename"]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename"]], "get_matching_atoms() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.get_matching_atoms"]], "mobile_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.mobile_atoms"]], "mobile_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.mobile_atoms"]], "module": [[0, "module-MDAnalysis.analysis.align"], [1, "module-MDAnalysis.analysis.atomicdistances"], [2, "module-MDAnalysis.analysis.base"], [3, "module-MDAnalysis.analysis.bat"], [4, "module-MDAnalysis.analysis.contacts"], [5, "module-MDAnalysis.analysis.data.filenames"], [6, "module-MDAnalysis.analysis.density"], [7, "module-MDAnalysis.analysis.dielectric"], [8, "module-MDAnalysis.analysis.diffusionmap"], [9, "module-MDAnalysis.analysis.dihedrals"], [10, "module-MDAnalysis.analysis.distances"], [12, "module-MDAnalysis.analysis.encore.bootstrap"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"], [13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"], [13, "module-MDAnalysis.analysis.encore.clustering.cluster"], [14, "module-MDAnalysis.analysis.encore.confdistmatrix"], [15, "module-MDAnalysis.analysis.encore.covariance"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"], [17, "module-MDAnalysis.analysis.encore.similarity"], [18, "module-MDAnalysis.analysis.encore.utils"], [19, "module-MDAnalysis.analysis.gnm"], [20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"], [21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"], [22, "module-MDAnalysis.analysis.helix_analysis"], [23, "module-MDAnalysis.analysis.hole2"], [23, "module-MDAnalysis.analysis.hole2.templates"], [23, "module-MDAnalysis.analysis.hole2.utils"], [24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"], [25, "module-MDAnalysis.analysis.leaflet"], [26, "module-MDAnalysis.analysis.legacy.x3dna"], [28, "module-MDAnalysis.analysis.lineardensity"], [29, "module-MDAnalysis.analysis.msd"], [30, "module-MDAnalysis.analysis.nucleicacids"], [31, "module-MDAnalysis.analysis.nuclinfo"], [32, "module-MDAnalysis.analysis.pca"], [33, "module-MDAnalysis.analysis.polymer"], [34, "module-MDAnalysis.analysis.psa"], [35, "module-MDAnalysis.analysis.rdf"], [36, "module-MDAnalysis.analysis.rms"], [37, "module-MDAnalysis.analysis.waterdynamics"], [38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"], [40, "module-MDAnalysis.auxiliary.EDR"], [41, "module-MDAnalysis.auxiliary.XVG"], [42, "module-MDAnalysis.auxiliary.base"], [43, "module-MDAnalysis.auxiliary.core"], [44, "module-MDAnalysis.auxiliary.__init__"], [46, "module-MDAnalysis.converters"], [47, "module-MDAnalysis.converters.OpenMM"], [47, "module-MDAnalysis.converters.OpenMMParser"], [48, "module-MDAnalysis.converters.ParmEd"], [48, "module-MDAnalysis.converters.ParmEdParser"], [49, "module-MDAnalysis.converters.RDKit"], [49, "module-MDAnalysis.converters.RDKitParser"], [50, "module-MDAnalysis.converters.base"], [51, "module-MDAnalysis.coordinates.CRD"], [52, "module-MDAnalysis.coordinates.DCD"], [53, "module-MDAnalysis.coordinates.DLPoly"], [54, "module-MDAnalysis.coordinates.DMS"], [55, "module-MDAnalysis.coordinates.FHIAIMS"], [56, "module-MDAnalysis.coordinates.GMS"], [57, "module-MDAnalysis.coordinates.GRO"], [58, "module-MDAnalysis.coordinates.GSD"], [59, "module-MDAnalysis.coordinates.H5MD"], [60, "module-MDAnalysis.coordinates.INPCRD"], [61, "module-MDAnalysis.coordinates.LAMMPS"], [62, "module-MDAnalysis.coordinates.MMTF"], [63, "module-MDAnalysis.coordinates.MOL2"], [64, "module-MDAnalysis.coordinates.NAMDBIN"], [65, "module-MDAnalysis.coordinates.PDB"], [66, "module-MDAnalysis.coordinates.PDBQT"], [67, "module-MDAnalysis.coordinates.PQR"], [68, "module-MDAnalysis.coordinates.TNG"], [69, "module-MDAnalysis.coordinates.TRJ"], [70, "module-MDAnalysis.coordinates.TRR"], [71, "module-MDAnalysis.coordinates.TRZ"], [72, "module-MDAnalysis.coordinates.TXYZ"], [73, "module-MDAnalysis.coordinates.XDR"], [74, "module-MDAnalysis.coordinates.XTC"], [75, "module-MDAnalysis.coordinates.XYZ"], [76, "module-MDAnalysis.coordinates.base"], [77, "module-MDAnalysis.coordinates.chain"], [78, "module-MDAnalysis.coordinates.chemfiles"], [79, "module-MDAnalysis.coordinates.core"], [80, "module-MDAnalysis.coordinates.__init__"], [81, "module-MDAnalysis.coordinates.memory"], [82, "module-MDAnalysis.coordinates.null"], [84, "module-MDAnalysis.coordinates.timestep"], [86, "module-MDAnalysis.core.accessors"], [87, "module-MDAnalysis.core.groups"], [88, "module-MDAnalysis.core.__init__"], [89, "module-MDAnalysis.core.selection"], [90, "module-MDAnalysis.core.topology"], [91, "module-MDAnalysis.core.topologyattrs"], [92, "module-MDAnalysis.core.topologyobjects"], [93, "module-MDAnalysis.core.universe"], [95, "module-MDAnalysis.exceptions"], [96, "module-MDAnalysis.lib.NeighborSearch"], [97, "module-MDAnalysis.lib.c_distances"], [98, "module-MDAnalysis.lib.c_distances_openmp"], [99, "module-MDAnalysis.lib.correlations"], [100, "module-MDAnalysis.lib.distances"], [101, "module-MDAnalysis.lib.formats.libdcd"], [102, "module-MDAnalysis.lib.formats.libmdaxdr"], [103, "module-MDAnalysis.lib.log"], [104, "module-MDAnalysis.lib.mdamath"], [105, "module-MDAnalysis.lib.nsgrid"], [106, "module-MDAnalysis.lib.picklable_file_io"], [107, "module-MDAnalysis.lib.pkdtree"], [108, "module-MDAnalysis.lib.qcprot"], [109, "module-MDAnalysis.lib.transformations"], [110, "module-MDAnalysis.lib.util"], [111, "module-MDAnalysis.lib"], [115, "module-MDAnalysis.selections.base"], [116, "module-MDAnalysis.selections.charmm"], [117, "module-MDAnalysis.selections.gromacs"], [118, "module-MDAnalysis.selections.jmol"], [119, "module-MDAnalysis.selections.pymol"], [120, "module-MDAnalysis.selections.vmd"], [123, "module-MDAnalysis.topology.CRDParser"], [124, "module-MDAnalysis.topology.DLPolyParser"], [125, "module-MDAnalysis.topology.DMSParser"], [126, "module-MDAnalysis.topology.ExtendedPDBParser"], [127, "module-MDAnalysis.topology.FHIAIMSParser"], [128, "module-MDAnalysis.topology.GMSParser"], [129, "module-MDAnalysis.topology.GROParser"], [130, "module-MDAnalysis.topology.GSDParser"], [131, "module-MDAnalysis.topology.HoomdXMLParser"], [132, "module-MDAnalysis.topology.ITPParser"], [133, "module-MDAnalysis.topology.LAMMPSParser"], [134, "module-MDAnalysis.topology.MMTFParser"], [135, "module-MDAnalysis.topology.MOL2Parser"], [136, "module-MDAnalysis.topology.MinimalParser"], [137, "module-MDAnalysis.topology.PDBParser"], [138, "module-MDAnalysis.topology.PDBQTParser"], [139, "module-MDAnalysis.topology.PQRParser"], [140, "module-MDAnalysis.topology.PSFParser"], [141, "module-MDAnalysis.topology.TOPParser"], [142, "module-MDAnalysis.topology.TPRParser"], [143, "module-MDAnalysis.topology.TXYZParser"], [144, "module-MDAnalysis.topology.XYZParser"], [145, "module-MDAnalysis.topology.base"], [146, "module-MDAnalysis.topology.core"], [147, "module-MDAnalysis.topology.guessers"], [148, "module-MDAnalysis.topology.__init__"], [149, "module-MDAnalysis.topology.tables"], [150, "module-MDAnalysis.topology.tpr"], [150, "module-MDAnalysis.topology.tpr.obj"], [150, "module-MDAnalysis.topology.tpr.setting"], [150, "module-MDAnalysis.topology.tpr.utils"], [152, "module-MDAnalysis.transformations"], [153, "module-MDAnalysis.transformations.base"], [154, "module-MDAnalysis.transformations.boxdimensions"], [155, "module-MDAnalysis.transformations.fit"], [156, "module-MDAnalysis.transformations.nojump"], [157, "module-MDAnalysis.transformations.positionaveraging"], [158, "module-MDAnalysis.transformations.rotate"], [159, "module-MDAnalysis.transformations.translate"], [160, "module-MDAnalysis.transformations.wrap"], [161, "module-MDAnalysis.units"], [162, "module-MDAnalysis.version"], [163, "module-MDAnalysis.visualization.streamlines"], [164, "module-MDAnalysis.visualization.streamlines_3D"]], "positions (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.positions"]], "positions (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.positions"]], "reference_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.reference_atoms"]], "reference_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.reference_atoms"]], "rmsd (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.rmsd"]], "rmsd (mdanalysis.analysis.align.aligntraj.results attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.results.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.rmsd"]], "rotation_matrix() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.rotation_matrix"]], "sequence_alignment() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.sequence_alignment"]], "universe (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.universe"]], "universe (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.universe"]], "atomicdistances (class in mdanalysis.analysis.atomicdistances)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances"]], "mdanalysis.analysis.atomicdistances": [[1, "module-MDAnalysis.analysis.atomicdistances"]], "n_atoms (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_atoms"]], "n_frames (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_frames"]], "results (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.results"]], "analysisbase (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisBase"]], "analysisfromfunction (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction"]], "mdanalysis.analysis.base": [[2, "module-MDAnalysis.analysis.base"]], "results (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.Results"]], "analysis_class() (in module mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.analysis_class"]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.frames"]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames"]], "frames (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.frames"]], "results (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.results"]], "run() (mdanalysis.analysis.base.analysisbase method)": [[2, "MDAnalysis.analysis.base.AnalysisBase.run"]], "times (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.times"]], "times (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.times"]], "times (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.times"]], "timeseries (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.timeseries"]], "timeseries (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.timeseries"]], "bat (class in mdanalysis.analysis.bat)": [[3, "MDAnalysis.analysis.bat.BAT"]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.Cartesian"]], "mdanalysis.analysis.bat": [[3, "module-MDAnalysis.analysis.bat"]], "atoms (mdanalysis.analysis.bat.bat property)": [[3, "MDAnalysis.analysis.bat.BAT.atoms"]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[3, "MDAnalysis.analysis.bat.BAT.results.bat"]], "load() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.load"]], "run() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.run"]], "save() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.save"]], "contacts (class in mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.Contacts"]], "mdanalysis.analysis.contacts": [[4, "module-MDAnalysis.analysis.contacts"]], "contact_matrix() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.contact_matrix"]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.hard_cut_q"]], "q1q2() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.q1q2"]], "radius_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.radius_cut_q"]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.soft_cut_q"]], "timeseries (mdanalysis.analysis.contacts.contacts attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.timeseries"]], "timeseries (mdanalysis.analysis.contacts.contacts.results attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.results.timeseries"]], "janin_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Janin_ref"]], "mdanalysis.analysis.data.filenames": [[5, "module-MDAnalysis.analysis.data.filenames"]], "rama_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Rama_ref"]], "density (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.Density"]], "densityanalysis (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.DensityAnalysis"]], "mdanalysis.analysis.density": [[6, "module-MDAnalysis.analysis.density"]], "_set_user_grid() (mdanalysis.analysis.density.densityanalysis static method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis._set_user_grid"]], "centers() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.centers"]], "check_compatible() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.check_compatible"]], "convert_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_density"]], "convert_length() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_length"]], "default_format (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.default_format"]], "delta (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.delta"]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.density"]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.results.density"]], "edges (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.edges"]], "export() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.export"]], "grid (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.grid"]], "interpolated (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolated"]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolation_spline_order"]], "load() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.load"]], "make_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.make_density"]], "origin (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.origin"]], "resample() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample"]], "resample_factor() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample_factor"]], "run() (mdanalysis.analysis.density.densityanalysis method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.run"]], "save() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.save"]], "units (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.units"]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant"]], "m (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M"]], "m2 (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M2"]], "mdanalysis.analysis.dielectric": [[7, "module-MDAnalysis.analysis.dielectric"]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps"]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean"]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct"]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap"]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix"]], "mdanalysis.analysis.diffusionmap": [[8, "module-MDAnalysis.analysis.diffusionmap"]], "atoms (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.atoms"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix"]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues"]], "run() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.run"]], "transform() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.transform"]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral"]], "janin (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Janin"]], "mdanalysis.analysis.dihedrals": [[9, "module-MDAnalysis.analysis.dihedrals"]], "ramachandran (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran"]], "angles (mdanalysis.analysis.dihedrals.dihedral attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.angles"]], "angles (mdanalysis.analysis.dihedrals.dihedral.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.results.angles"]], "angles (mdanalysis.analysis.dihedrals.janin attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.angles"]], "angles (mdanalysis.analysis.dihedrals.janin.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.results.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.results.angles"]], "plot() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.plot"]], "plot() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.plot"]], "run() (mdanalysis.analysis.dihedrals.dihedral method)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.run"]], "run() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.run"]], "run() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.run"]], "mdanalysis.analysis.distances": [[10, "module-MDAnalysis.analysis.distances"]], "between() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.between"]], "contact_matrix() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.contact_matrix"]], "dist() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.dist"]], "distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.distance_array"]], "self_distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.self_distance_array"]], "mdanalysis.analysis.encore.bootstrap": [[12, "module-MDAnalysis.analysis.encore.bootstrap"]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix"]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples"]], "get_ensemble_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples"]], "affinitypropagation (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagation"]], "affinitypropagation() (in module mdanalysis.analysis.encore.clustering.affinityprop)": [[13, "MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation"]], "affinitypropagationnative (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagationNative"]], "cluster (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster"]], "clustercollection (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection"]], "clusteringmethod (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.ClusteringMethod"]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN"]], "kmeans (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans"]], "mdanalysis.analysis.encore.clustering.clustercollection": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"]], "mdanalysis.analysis.encore.clustering.clusteringmethod": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"]], "mdanalysis.analysis.encore.clustering.affinityprop": [[13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"]], "mdanalysis.analysis.encore.clustering.cluster": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "accepts_distance_matrix (mdanalysis.analysis.encore.clustering.clusteringmethod.kmeans attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans.accepts_distance_matrix"]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid"]], "cluster() (in module mdanalysis.analysis.encore.clustering.cluster)": [[13, "MDAnalysis.analysis.encore.clustering.cluster.cluster"]], "clusters (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.clusters"]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements"]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info"]], "get_centroids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_centroids"]], "get_ids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_ids"]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id"]], "metadata (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.metadata"]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size"]], "mdanalysis.analysis.encore.confdistmatrix": [[14, "module-MDAnalysis.analysis.encore.confdistmatrix"]], "conformational_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.conformational_distance_matrix"]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix"]], "set_rmsd_matrix_elements() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.set_rmsd_matrix_elements"]], "mdanalysis.analysis.encore.covariance": [[15, "module-MDAnalysis.analysis.encore.covariance"]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.covariance_matrix"]], "ml_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.ml_covariance_estimator"]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator"]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"]], "principalcomponentanalysis (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.PrincipalComponentAnalysis"]], "stochasticproximityembedding() (in module mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed.StochasticProximityEmbedding"]], "stochasticproximityembeddingnative (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.StochasticProximityEmbeddingNative"]], "reduce_dimensionality() (in module mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality.reduce_dimensionality"]], "mdanalysis.analysis.encore.similarity": [[17, "module-MDAnalysis.analysis.encore.similarity"]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces"]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces_convergence"]], "clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.clustering_ensemble_similarity"]], "cumulative_clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity"]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs"]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity"]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence"]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence"]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres"]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres_convergence"]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs"]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity"]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.hes"]], "prepare_ensembles_for_convergence_increasing_window() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.prepare_ensembles_for_convergence_increasing_window"]], "write_output() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.write_output"]], "mdanalysis.analysis.encore.utils": [[18, "module-MDAnalysis.analysis.encore.utils"]], "parallelcalculation (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation"]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[18, "MDAnalysis.analysis.encore.cutils.PureRMSD"]], "triangularmatrix (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix"]], "args (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.args"]], "as_array() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.as_array"]], "function (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.function"]], "kwargs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.kwargs"]], "loadz() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.loadz"]], "merge_universes() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.merge_universes"]], "n_jobs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.n_jobs"]], "nruns (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.nruns"]], "run() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.run"]], "savez() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.savez"]], "trm_indices() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices"]], "trm_indices_diag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_diag"]], "trm_indices_nodiag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_nodiag"]], "worker() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.worker"]], "gnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis"]], "mdanalysis.analysis.gnm": [[19, "module-MDAnalysis.analysis.gnm"]], "closecontactgnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis"]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues"]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues"]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors"]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors"]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.generate_grid"]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff"]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff"]], "order_list() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.order_list"]], "times (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.times"]], "times (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.times"]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel"]], "mdanalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors"]], "run() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run"]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve"]], "mdanalysis.analysis.hbonds.hbond_autocorrel": [[21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"]], "mdanalysis.analysis.helix_analysis": [[22, "module-MDAnalysis.analysis.helix_analysis"]], "holeanalysis (class in mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis"]], "mdanalysis.analysis.hole2": [[23, "module-MDAnalysis.analysis.hole2"]], "mdanalysis.analysis.hole2.templates": [[23, "module-MDAnalysis.analysis.hole2.templates"]], "mdanalysis.analysis.hole2.utils": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "path": [[23, "index-0"], [23, "index-1"], [110, "index-0"]], "simple2_rad (in module mdanalysis.analysis.hole2.templates)": [[23, "MDAnalysis.analysis.hole2.templates.SIMPLE2_RAD"]], "bin_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.bin_radii"]], "check_and_fix_long_filename() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.check_and_fix_long_filename"]], "collect_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.collect_hole"]], "create_vmd_surface() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.create_vmd_surface"]], "create_vmd_surface() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.create_vmd_surface"]], "delete_temporary_files() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.delete_temporary_files"]], "environment variable": [[23, "index-0"], [23, "index-1"], [69, "index-0"], [69, "index-1"], [110, "index-0"], [110, "index-1"], [113, "index-0"], [153, "index-0"]], "gather() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.gather"]], "guess_cpoint() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.guess_cpoint"]], "histogram_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.histogram_radii"]], "hole() (in module mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.hole"]], "min_radius() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.min_radius"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.outfiles"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.outfiles"]], "over_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.over_order_parameters"]], "plot() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot"]], "plot3d() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D"]], "plot3d_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D_order_parameters"]], "plot_mean_profile() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_mean_profile"]], "plot_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_order_parameters"]], "profiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.profiles"]], "profiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.profiles"]], "run() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.run"]], "run_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.run_hole"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.sphpdbs"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.sphpdbs"]], "write_simplerad2() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.write_simplerad2"]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis"]], "mdanalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"]], "count_by_ids() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_ids"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type"]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors"]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors"]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds"]], "lifetime() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime"]], "leafletfinder (class in mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder"]], "mdanalysis.analysis.leaflet": [[25, "module-MDAnalysis.analysis.leaflet"]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.group"]], "groups() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups"]], "groups_iter() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"]], "optimize_cutoff() (in module mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.optimize_cutoff"]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes"]], "update() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.update"]], "write_selection() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.write_selection"]], "applicationerror": [[26, "MDAnalysis.analysis.legacy.x3dna.ApplicationError"], [95, "MDAnalysis.exceptions.ApplicationError"]], "mdanalysis.analysis.legacy.x3dna": [[26, "module-MDAnalysis.analysis.legacy.x3dna"]], "x3dna (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA"]], "x3dnatraj (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj"]], "collect() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.collect"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean"]], "mean_std() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean_std"]], "mean_std() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean_std"]], "plot() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.plot"]], "plot() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.plot"]], "profiles (mdanalysis.analysis.legacy.x3dna.x3dna attribute)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.profiles"]], "profiles (mdanalysis.analysis.legacy.x3dna.x3dnatraj attribute)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.profiles"]], "run() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.run"]], "run() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.run"]], "run_x3dna() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.run_x3dna"]], "save() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.save"]], "save() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.save"]], "sorted_profiles_iter() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.sorted_profiles_iter"]], "sorted_profiles_iter() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.sorted_profiles_iter"]], "std() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.std"]], "std() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.std"]], "lineardensity (class in mdanalysis.analysis.lineardensity)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity"]], "mdanalysis.analysis.lineardensity": [[28, "module-MDAnalysis.analysis.lineardensity"]], "note (mdanalysis.analysis.lineardensity.lineardensity attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.Note"]], "results (class in mdanalysis.analysis.lineardensity)": [[28, "MDAnalysis.analysis.lineardensity.Results"]], "char (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char"]], "char_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char_std"]], "charge_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density"]], "charge_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density_stddev"]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim"]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges"]], "mass_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density"]], "mass_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density_stddev"]], "pos (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos"]], "pos_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos_std"]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume"]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD"]], "mdanalysis.analysis.msd": [[29, "module-MDAnalysis.analysis.msd"]], "ag (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.ag"]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac"]], "msds_by_particle (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.msds_by_particle"]], "n_frames (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_frames"]], "n_particles (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_particles"]], "run() (mdanalysis.analysis.msd.einsteinmsd method)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.run"]], "timeseries (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.timeseries"]], "mdanalysis.analysis.nucleicacids": [[30, "module-MDAnalysis.analysis.nucleicacids"]], "nucpairdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist"]], "watsoncrickdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist"]], "pair_distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.pair_distances"]], "pair_distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.pair_distances"]], "run() (mdanalysis.analysis.nucleicacids.nucpairdist method)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.run"]], "run() (mdanalysis.analysis.nucleicacids.watsoncrickdist method)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.run"]], "times (mdanalysis.analysis.nucleicacids.nucpairdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.times"]], "times (mdanalysis.analysis.nucleicacids.watsoncrickdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.times"]], "mdanalysis.analysis.nuclinfo": [[31, "module-MDAnalysis.analysis.nuclinfo"]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.hydroxyl"]], "major_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.major_pair"]], "minor_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.minor_pair"]], "phase_as() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_as"]], "phase_cp() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_cp"]], "pseudo_dihe_baseflip() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip"]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors"]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_alpha"]], "tors_beta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_beta"]], "tors_chi() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_chi"]], "tors_delta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_delta"]], "tors_eps() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_eps"]], "tors_gamma() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_gamma"]], "tors_zeta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_zeta"]], "wc_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.wc_pair"]], "mdanalysis.analysis.pca": [[32, "module-MDAnalysis.analysis.pca"]], "pca (class in mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.PCA"]], "cosine_content() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cosine_content"]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.cumulated_variance"]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance"]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.cumulative_overlap"]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cumulative_overlap"]], "p_components (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.p_components"]], "p_components (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.p_components"]], "project_single_frame() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.project_single_frame"]], "rmsip() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.rmsip"]], "rmsip() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.rmsip"]], "run() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.run"]], "transform() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.transform"]], "variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.variance"]], "variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.variance"]], "mdanalysis.analysis.polymer": [[33, "module-MDAnalysis.analysis.polymer"]], "persistencelength (class in mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength"]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation"]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.fit"]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit"]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.fit_exponential_decay"]], "lb (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lb"]], "lb (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lb"]], "lp (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lp"]], "lp (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lp"]], "plot() (mdanalysis.analysis.polymer.persistencelength method)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.plot"]], "sort_backbone() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.sort_backbone"]], "x (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.x"]], "d (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.D"]], "mdanalysis.analysis.psa": [[34, "module-MDAnalysis.analysis.psa"]], "psapair (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAPair"]], "psanalysis (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAnalysis"]], "path (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.Path"]], "cluster() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.cluster"]], "discrete_frechet() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.discrete_frechet"]], "dist_mat_to_vec() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.dist_mat_to_vec"]], "fit_to_reference() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.fit_to_reference"]], "generate_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.generate_paths"]], "get_coord_axes() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_coord_axes"]], "get_msd_matrix() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_msd_matrix"]], "get_num_atoms() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_atoms"]], "get_num_atoms() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.get_num_atoms"]], "get_num_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_paths"]], "get_pairwise_distances() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_pairwise_distances"]], "get_path_metric_func() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_path_metric_func"]], "get_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_paths"]], "hausdorff() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff"]], "hausdorff_avg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_avg"]], "hausdorff_neighbors() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_neighbors"]], "hausdorff_pair (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.hausdorff_pair"]], "hausdorff_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.hausdorff_pairs"]], "hausdorff_wavg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_wavg"]], "load() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.load"]], "matrix_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.matrix_id"]], "nearest_neighbors (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.nearest_neighbors"]], "nearest_neighbors (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.nearest_neighbors"]], "npaths (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.npaths"]], "pair_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.pair_id"]], "path (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path"]], "path_select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.path_select"]], "path_select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path_select"]], "paths (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.paths"]], "plot() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot"]], "plot_annotated_heatmap() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_annotated_heatmap"]], "plot_nearest_neighbors() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_nearest_neighbors"]], "psa_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.psa_pairs"]], "ref_frame (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.ref_frame"]], "ref_frame (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.ref_frame"]], "run() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run"]], "run() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.run"]], "run_pairs_analysis() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run_pairs_analysis"]], "save_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.save_paths"]], "select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.select"]], "select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.select"]], "sqnorm() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.sqnorm"]], "to_path() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.to_path"]], "u_fitted (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_fitted"]], "u_original (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_original"]], "u_reference (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.u_reference"]], "u_reference (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_reference"]], "universes (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.universes"]], "interrdf (class in mdanalysis.analysis.rdf)": [[35, "MDAnalysis.analysis.rdf.InterRDF"]], "interrdf_s (class in mdanalysis.analysis.rdf)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s"]], "mdanalysis.analysis.rdf": [[35, "module-MDAnalysis.analysis.rdf"]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.bins"]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.bins"]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.bins"]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins"]], "cdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.cdf"]], "cdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.cdf"]], "count (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.count"]], "count (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.count"]], "count (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.count"]], "count (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.count"]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.edges"]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.edges"]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.edges"]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges"]], "get_cdf() (mdanalysis.analysis.rdf.interrdf_s method)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.get_cdf"]], "rdf (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.rdf"]], "mdanalysis.analysis.rms": [[36, "module-MDAnalysis.analysis.rms"]], "rmsd (class in mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.RMSD"]], "rmsf (class in mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.RMSF"]], "rmsd (mdanalysis.analysis.rms.rmsd attribute)": [[36, "MDAnalysis.analysis.rms.RMSD.rmsd"]], "rmsd (mdanalysis.analysis.rms.rmsd.results attribute)": [[36, "MDAnalysis.analysis.rms.RMSD.results.rmsd"]], "rmsd() (in module mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.rmsd"]], "rmsf (mdanalysis.analysis.rms.rmsf attribute)": [[36, "MDAnalysis.analysis.rms.RMSF.rmsf"]], "rmsf (mdanalysis.analysis.rms.rmsf.results attribute)": [[36, "MDAnalysis.analysis.rms.RMSF.results.rmsf"]], "run() (mdanalysis.analysis.rms.rmsd method)": [[36, "MDAnalysis.analysis.rms.RMSD.run"]], "run() (mdanalysis.analysis.rms.rmsf method)": [[36, "MDAnalysis.analysis.rms.RMSF.run"]], "angulardistribution (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.AngularDistribution"]], "mdanalysis.analysis.waterdynamics": [[37, "module-MDAnalysis.analysis.waterdynamics"]], "meansquaredisplacement (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement"]], "survivalprobability (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.SurvivalProbability"]], "waterorientationalrelaxation (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation"]], "lg2() (mdanalysis.analysis.waterdynamics.waterorientationalrelaxation static method)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.lg2"]], "run() (mdanalysis.analysis.waterdynamics.angulardistribution method)": [[37, "MDAnalysis.analysis.waterdynamics.AngularDistribution.run"]], "run() (mdanalysis.analysis.waterdynamics.meansquaredisplacement method)": [[37, "MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement.run"]], "run() (mdanalysis.analysis.waterdynamics.survivalprobability method)": [[37, "MDAnalysis.analysis.waterdynamics.SurvivalProbability.run"]], "run() (mdanalysis.analysis.waterdynamics.waterorientationalrelaxation method)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.run"]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"]], "mdanalysis.analysis.hydrogenbonds.wbridge_analysis": [[38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"]], "waterbridgeanalysis (class in mdanalysis.analysis.hydrogenbonds.wbridge_analysis)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_type"]], "generate_table() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.generate_table"]], "network (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.network"]], "network (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis.results attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.network"]], "r_cov (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.r_cov"]], "table (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.table"]], "timeseries (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timeseries"]], "timeseries (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis.results attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps"]], "timesteps_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps_by_type"]], "edrreader (class in mdanalysis.auxiliary.edr)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader"]], "edrstep (class in mdanalysis.auxiliary.edr)": [[40, "MDAnalysis.auxiliary.EDR.EDRStep"]], "mdanalysis.auxiliary.edr": [[40, "module-MDAnalysis.auxiliary.EDR"]], "_auxdata (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader._auxdata"]], "_n_steps (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader._n_steps"]], "data_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.data_dict"]], "get_data() (mdanalysis.auxiliary.edr.edrreader method)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.get_data"]], "read_all_times() (mdanalysis.auxiliary.edr.edrreader method)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.read_all_times"]], "terms (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.terms"]], "unit_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.unit_dict"]], "mdanalysis.auxiliary.xvg": [[41, "module-MDAnalysis.auxiliary.XVG"]], "xvgfilereader (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGFileReader"]], "xvgreader (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGReader"]], "xvgstep (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGStep"]], "read_all_times() (mdanalysis.auxiliary.xvg.xvgfilereader method)": [[41, "MDAnalysis.auxiliary.XVG.XVGFileReader.read_all_times"]], "read_all_times() (mdanalysis.auxiliary.xvg.xvgreader method)": [[41, "MDAnalysis.auxiliary.XVG.XVGReader.read_all_times"]], "uncomment() (in module mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.uncomment"]], "auxfilereader (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader"]], "auxreader (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxReader"]], "auxstep (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxStep"]], "mdanalysis.auxiliary.base": [[42, "module-MDAnalysis.auxiliary.base"]], "attach_auxiliary() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.attach_auxiliary"]], "auxfile (mdanalysis.auxiliary.base.auxfilereader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader.auxfile"]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.auxstep"]], "calc_representative() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.calc_representative"]], "close() (mdanalysis.auxiliary.base.auxfilereader method)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader.close"]], "constant_dt (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.constant_dt"]], "copy() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.copy"]], "data (mdanalysis.auxiliary.base.auxstep property)": [[42, "MDAnalysis.auxiliary.base.AuxStep.data"]], "data_selector (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.data_selector"]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.dt"]], "frame_data (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.frame_data"]], "frame_rep (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.frame_rep"]], "get_description() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.get_description"]], "initial_time (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.initial_time"]], "move_to_ts() (mdanalysis.auxiliary.base.auxreader method)": [[42, 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"MDAnalysis.exceptions.SelectionError"]], "selectionwarning": [[95, "MDAnalysis.exceptions.SelectionWarning"]], "streamwarning": [[95, "MDAnalysis.exceptions.StreamWarning"]], "atomneighborsearch (class in mdanalysis.lib.neighborsearch)": [[96, "MDAnalysis.lib.NeighborSearch.AtomNeighborSearch"]], "mdanalysis.lib.neighborsearch": [[96, "module-MDAnalysis.lib.NeighborSearch"]], "search() (mdanalysis.lib.neighborsearch.atomneighborsearch method)": [[96, "MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search"]], "mdanalysis.lib.c_distances": [[97, "module-MDAnalysis.lib.c_distances"]], "mdanalysis.lib.c_distances_openmp": [[98, "module-MDAnalysis.lib.c_distances_openmp"]], "mdanalysis.lib.correlations": [[99, "module-MDAnalysis.lib.correlations"]], "autocorrelation() (in module mdanalysis.lib.correlations)": [[99, "MDAnalysis.lib.correlations.autocorrelation"]], "correct_intermittency() (in module mdanalysis.lib.correlations)": [[99, "MDAnalysis.lib.correlations.correct_intermittency"]], "mdanalysis.lib.distances": [[100, "module-MDAnalysis.lib.distances"]], "apply_pbc() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.apply_PBC"]], "augment_coordinates() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.augment_coordinates"]], "calc_angles() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_angles"]], "calc_bonds() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_bonds"]], "calc_dihedrals() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_dihedrals"]], "capped_distance() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.capped_distance"]], "distance_array() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.distance_array"]], "minimize_vectors() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.minimize_vectors"]], "self_capped_distance() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.self_capped_distance"]], "self_distance_array() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.self_distance_array"]], "transform_rtos() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.transform_RtoS"]], "transform_stor() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.transform_StoR"]], "undo_augment() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.undo_augment"]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile"]], "mdanalysis.lib.formats.libdcd": [[101, "module-MDAnalysis.lib.formats.libdcd"]], "charmm_bitfield (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.charmm_bitfield"]], "close() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.close"]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.header"]], "open() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.open"]], "read() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.read"]], "readframes() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.readframes"]], "seek() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.seek"]], "tell() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.tell"]], "write() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.write"]], "write_header() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.write_header"]], "mdanalysis.lib.formats.libmdaxdr": [[102, "module-MDAnalysis.lib.formats.libmdaxdr"]], "trrfile (class in mdanalysis.lib.formats.libmdaxdr)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile"]], "xtcfile (class in mdanalysis.lib.formats.libmdaxdr)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile"]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.calc_offsets"]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.calc_offsets"]], "close() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.close"]], "close() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.close"]], "offsets (mdanalysis.lib.formats.libmdaxdr.trrfile attribute)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.offsets"]], "offsets (mdanalysis.lib.formats.libmdaxdr.xtcfile attribute)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.offsets"]], "open() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.open"]], "open() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.open"]], "read() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.read"]], "read() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.read"]], "read_direct_x() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.read_direct_x"]], "read_direct_xvf() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.read_direct_xvf"]], "seek() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.seek"]], "seek() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.seek"]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.set_offsets"]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.set_offsets"]], "tell() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.tell"]], "tell() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.tell"]], "write() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.write"]], "write() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.write"]], "mdanalysis.lib.log": [[103, "module-MDAnalysis.lib.log"]], "nullhandler (class in mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.NullHandler"]], "progressbar (class in mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.ProgressBar"]], "clear_handlers() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.clear_handlers"]], "create() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.create"]], "emit() (mdanalysis.lib.log.nullhandler method)": [[103, "MDAnalysis.lib.log.NullHandler.emit"]], "start_logging() (in module mdanalysis)": [[103, "MDAnalysis.start_logging"]], "start_logging() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.start_logging"]], "stop_logging() (in module mdanalysis)": [[103, "MDAnalysis.stop_logging"]], "stop_logging() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.stop_logging"]], "mdanalysis.lib.mdamath": [[104, "module-MDAnalysis.lib.mdamath"]], "angle() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.angle"]], "box_volume() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.box_volume"]], "dihedral() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.dihedral"]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.find_fragments"]], "make_whole() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.make_whole"]], "norm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.norm"]], "normal() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.normal"]], "pdot() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pdot"]], "pnorm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pnorm"]], "sarrus_det() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.sarrus_det"]], "stp() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.stp"]], "triclinic_box() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_box"]], "triclinic_vectors() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_vectors"]], "fastns (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.FastNS"]], "mdanalysis.lib.nsgrid": [[105, "module-MDAnalysis.lib.nsgrid"]], "nsresults (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.NSResults"]], "get_pair_distances() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pair_distances"]], "get_pairs() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pairs"]], "search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.search"]], "self_search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.self_search"]], "bz2picklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BZ2Picklable"]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable"]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.FileIOPicklable"]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.GzipPicklable"]], "mdanalysis.lib.picklable_file_io": [[106, "module-MDAnalysis.lib.picklable_file_io"]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.TextIOPicklable"]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open"]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open"]], "pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.pickle_open"]], "mdanalysis.lib.pkdtree": [[107, "module-MDAnalysis.lib.pkdtree"]], "periodickdtree (class in mdanalysis.lib.pkdtree)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree"]], "get_indices() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.get_indices"]], "pbc (mdanalysis.lib.pkdtree.periodickdtree property)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.pbc"]], "search() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search"]], "search_pairs() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search_pairs"]], "search_tree() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search_tree"]], "set_coords() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.set_coords"]], "calcrmsdrotationalmatrix() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation"]], "innerproduct() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.InnerProduct"]], "mdanalysis.lib.qcprot": [[108, "module-MDAnalysis.lib.qcprot"]], "arcball (class in mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.Arcball"]], "mdanalysis.lib.transformations": [[109, "module-MDAnalysis.lib.transformations"]], "arcball_nearest_axis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.arcball_nearest_axis"]], "compose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.compose_matrix"]], "concatenate_matrices() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.concatenate_matrices"]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.decompose_matrix"]], "down() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.down"]], "drag() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.drag"]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.euler_from_quaternion"]], "getconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.getconstrain"]], "matrix() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.matrix"]], "next() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.next"]], "place() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.place"]], "projection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.projection_from_matrix"]], "quaternion_imag() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_imag"]], "quaternion_real() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_real"]], "reflection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.reflection_from_matrix"]], "rotation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotation_from_matrix"]], "rotaxis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotaxis"]], "scale_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.scale_from_matrix"]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setaxes"]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setconstrain"]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.shear_from_matrix"]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.translation_from_matrix"]], "$home": [[110, "index-1"]], "fortranreader (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRANReader"]], "fortran_format_regex (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRAN_format_regex"]], "mdanalysis.lib.util": [[110, "module-MDAnalysis.lib.util"]], "namedstream (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.NamedStream"]], "namespace (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.Namespace"]], "_deprecate (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util._Deprecate"]], "anyopen() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.anyopen"]], "asiterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.asiterable"]], "blocks_of() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.blocks_of"]], "cached() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.cached"]], "check_atomgroup_not_empty() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_atomgroup_not_empty"]], "check_box() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_box"]], "check_compressed_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_compressed_format"]], "check_coords() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_coords"]], "close() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.close"]], "closed (mdanalysis.lib.util.namedstream property)": [[110, "MDAnalysis.lib.util.NamedStream.closed"]], "conv_float() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.conv_float"]], "convert_aa_code() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.convert_aa_code"]], "dedent_docstring() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.dedent_docstring"]], "deprecate() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.deprecate"]], "filename() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.filename"]], "fileno() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.fileno"]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.fixedwidth_bins"]], "flatten_dict() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.flatten_dict"]], "flush() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.flush"]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.format_from_filename_extension"]], "get_ext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_ext"]], "get_weights() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_weights"]], "greedy_splitext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.greedy_splitext"]], "group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.group_same_or_consecutive_integers"]], "guess_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.guess_format"]], "hasmethod() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.hasmethod"]], "isstream() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.isstream"]], "iterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.iterable"]], "ltruncate_int() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.ltruncate_int"]], "number_of_matches() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.number_of_matches"]], "openany() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.openany"]], "parse_fortran_format() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format"]], "parse_residue() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.parse_residue"]], "read() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.read"]], "readable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.readable"]], "readline() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.readline"]], "realpath() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.realpath"]], "reset() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.reset"]], "seek() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.seek"]], "seekable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.seekable"]], "static_variables() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.static_variables"]], "store_init_arguments() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.store_init_arguments"]], "tell() 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"MDAnalysis.topology.TXYZParser.TXYZParser.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.convert_velocities_from_native"]], "convert_velocities_to_native() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.convert_velocities_to_native"]], "parse() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.parse"]], "units (mdanalysis.topology.txyzparser.txyzparser attribute)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.units"]], "mdanalysis.topology.xyzparser": [[144, "module-MDAnalysis.topology.XYZParser"]], "xyzparser (class in mdanalysis.topology.xyzparser)": [[144, "MDAnalysis.topology.XYZParser.XYZParser"]], "parse() (mdanalysis.topology.xyzparser.xyzparser method)": [[144, "MDAnalysis.topology.XYZParser.XYZParser.parse"]], "mdanalysis.topology.base": [[145, "module-MDAnalysis.topology.base"]], "topologyreaderbase (class in mdanalysis.topology.base)": [[145, "MDAnalysis.topology.base.TopologyReaderBase"]], "close() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.close"]], "convert_forces_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_forces_from_native"]], "convert_forces_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_forces_to_native"]], "convert_pos_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_pos_from_native"]], "convert_pos_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_pos_to_native"]], "convert_time_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_time_from_native"]], "convert_time_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_velocities_from_native"]], "convert_velocities_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_velocities_to_native"]], "units (mdanalysis.topology.base.topologyreaderbase attribute)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.units"]], "mdanalysis.topology.core": [[146, "module-MDAnalysis.topology.core"]], "mdanalysis.topology.guessers": [[147, "module-MDAnalysis.topology.guessers"]], "get_atom_mass() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.get_atom_mass"]], "guess_angles() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_angles"]], "guess_aromaticities() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_aromaticities"]], "guess_atom_charge() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_charge"]], "guess_atom_element() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_element"]], "guess_atom_mass() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_mass"]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_type"]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_bonds"]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_dihedrals"]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_gasteiger_charges"]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_improper_dihedrals"]], "guess_masses() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_masses"]], "guess_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_types"]], "validate_atom_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.validate_atom_types"]], "mdanalysis.topology.__init__": [[148, "module-MDAnalysis.topology.__init__"]], "mdanalysis.topology.tables": [[149, "module-MDAnalysis.topology.tables"]], "table_atomelements (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_ATOMELEMENTS"]], "table_masses (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_MASSES"]], "table_vdwradii (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_VDWRADII"]], "atomelements (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.atomelements"]], "kv2dict() (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.kv2dict"]], "masses (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.masses"]], "vdwradii (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.vdwradii"]], "atom (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Atom"]], "atomkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.AtomKind"]], "atoms (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Atoms"]], "box (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Box"]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGLES"]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRES"]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRESZ"]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL"]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM"]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM_LR"]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BONDS"]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CBTDIHS"]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CMAP"]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COM_PULL"]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONNBONDS"]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTR"]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTRNC"]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL14"]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_LR"]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP"]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_SR"]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES"]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS"]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS"]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING"]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DHDL_CON"]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRES"]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL"]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISPCORR"]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRES"]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL"]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DKDL"]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DPD"]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL"]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED"]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL"]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT"]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE"]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW"]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ECONSERVED"]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EKIN"]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EPOT"]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EQM"]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ETOT"]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FBPOSRES"]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FENEBONDS"]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FOURDIHS"]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96ANGLES"]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96BONDS"]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB12"]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB13"]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB14"]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GBPOL"]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_HARMONIC"]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_IDIHS"]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES"]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ"]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ14"]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC14_Q"]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB"]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_LR"]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP"]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_MORSE"]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION"]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NRE"]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRES"]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV"]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDIHS"]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDISPCORR"]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PIDIHS"]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POLARIZATION"]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POSRES"]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PRES"]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES"]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RBDIHS"]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES"]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS"]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS"]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RF_EXCL"]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_SETTLE"]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABANGLES"]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDS"]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC"]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABDIHS"]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TEMP"]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_THOLE_POL"]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY"]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE1"]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2"]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2FD"]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3"]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD"]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FD"]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT"]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FD"]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN"]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITEN"]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED"]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_WATER_POL"]], "ilist (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Ilist"]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.InteractionKind"]], "mdanalysis.topology.tpr": [[150, "module-MDAnalysis.topology.tpr"]], "mdanalysis.topology.tpr.obj": [[150, "module-MDAnalysis.topology.tpr.obj"]], "mdanalysis.topology.tpr.setting": [[150, "module-MDAnalysis.topology.tpr.setting"]], "mdanalysis.topology.tpr.utils": [[150, "module-MDAnalysis.topology.tpr.utils"]], "molblock (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Molblock"]], "moleculekind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind"]], "mtop (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Mtop"]], "params (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Params"]], "supported_versions (in module mdanalysis.topology.tpr)": [[150, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS"]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[150, 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"module-MDAnalysis.version"]], "__version__ (in module mdanalysis.version)": [[162, "MDAnalysis.version.__version__"]], "mdanalysis.visualization.streamlines": [[163, "module-MDAnalysis.visualization.streamlines"]], "generate_streamlines() (in module mdanalysis.visualization.streamlines)": [[163, "MDAnalysis.visualization.streamlines.generate_streamlines"]], "mdanalysis.visualization.streamlines_3d": [[164, "module-MDAnalysis.visualization.streamlines_3D"]], "generate_streamlines_3d() (in module mdanalysis.visualization.streamlines_3d)": [[164, "MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d"]]}}) \ No newline at end of file diff --git a/dev/_modules/MDAnalysis/analysis/dielectric.html b/dev/_modules/MDAnalysis/analysis/dielectric.html index 39d8cccbc2..c5cc48733c 100644 --- a/dev/_modules/MDAnalysis/analysis/dielectric.html +++ b/dev/_modules/MDAnalysis/analysis/dielectric.html @@ -162,6 +162,10 @@

Source code for MDAnalysis.analysis.dielectric

the usual case if electrostatics are handled with a Ewald summation technique. See [Neumann1983]_ for details on the derivation. + .. warning:: + Applying this class requires that no free charges, such as ions or + charged fragments, are present in the simulation. + Parameters ---------- atomgroup : MDAnalysis.core.groups.AtomGroup diff --git a/dev/documentation_pages/analysis/dielectric.html b/dev/documentation_pages/analysis/dielectric.html index 5e74a3ed7b..16da310be1 100644 --- a/dev/documentation_pages/analysis/dielectric.html +++ b/dev/documentation_pages/analysis/dielectric.html @@ -147,6 +147,11 @@

4.8.4. Dielectric — [Neumann1983] for details on the derivation.

+
+

Warning

+

Applying this class requires that no free charges, such as ions or +charged fragments, are present in the simulation.

+
Parameters

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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.2.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.1.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.2.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.2.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.11.1. Analysis data files", "4.8.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.8.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.9.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.7.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.2.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.2.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.2.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.2.7.1.2. Clustering", "4.2.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.2.7.1.5. Covariance calculation \u2014 encore.covariance", "4.2.7.1.3. Dimensionality reduction", "4.2.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.2.7.1.7. Utility functions for ENCORE", "4.7.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.3.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.3.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.7.1.2. HELANAL \u2014 analysis of protein helices", "4.4.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.3.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.4.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.10.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.10.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.8.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.7.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.5.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.5.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.9.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.6.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.2.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.7.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.8.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.3.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "10.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "10.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "10.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "10.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "10.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "10. Auxiliary modules", "7. Converter modules", "7.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "7.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "7.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "7.8. Base classes \u2014 MDAnalysis.converters.base", "6.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "6.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "6.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "6.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "6.25. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "6.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "6.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "6.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "6.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "6.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "6.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "6.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "6.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "6.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "6.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "6.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "6.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "6.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "6.19. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.20. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.21. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "6.22. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.34. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.23. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.24. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.30. Base classes \u2014 MDAnalysis.coordinates.base", "6.33. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.27. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.31. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "6.26. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.28. Null output \u2014 MDAnalysis.coordinates.null", "6.32. Serialization of Coordinate Readers", "6.29. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "6. Coordinates modules", "7.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "11.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "11.1. Core functions of MDAnalysis", "11.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "11.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "11.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "11.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "11.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "11. Core modules", "16. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "13.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "13.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "13.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "13.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "13.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "13.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "13.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "13.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "13.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "13.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "13.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "13.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "13.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "13.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "13.2.10. Helper functions \u2014 MDAnalysis.lib.util", "13. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "17. References", "3. Selection commands", "9.2.6. Base classes for the selection writers", "9.2.4. CHARMM selections", "9.2.3. Gromacs selections", "9.2.5. Jmol selections", "9.2.2. PyMOL selections", "9.2.1. VMD selections", "9. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.26. Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.27. MDAnalysis topology tables", "5.28. Utility functions for the TPR topology parser", "5. Topology modules", "8. Trajectory transformations (\u201con-the-fly\u201d transformations)", "8.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "8.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "8.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "8.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "8.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "8.6.2. 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14, 16, 17, 34, 39, 40, 111, 112, 113, 150, 155], "between": [0, 1, 2, 3, 4, 6, 8, 9, 10, 11, 13, 14, 17, 18, 19, 20, 22, 23, 24, 29, 30, 32, 34, 35, 36, 38, 40, 42, 44, 45, 49, 52, 55, 58, 59, 61, 65, 66, 67, 70, 71, 72, 73, 74, 76, 77, 79, 80, 81, 84, 86, 87, 91, 92, 93, 95, 100, 101, 104, 105, 106, 107, 108, 109, 110, 112, 113, 115, 116, 117, 118, 119, 120, 147, 148, 151, 152, 156, 161, 163, 164], "two": [0, 1, 2, 8, 10, 11, 13, 16, 17, 23, 24, 25, 26, 30, 32, 33, 34, 35, 36, 37, 38, 40, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 79, 81, 86, 87, 90, 91, 92, 94, 99, 100, 103, 104, 105, 108, 109, 113, 114, 136, 147, 148, 152, 156], "set": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 91, 92, 93, 99, 100, 102, 105, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 151, 152, 153, 155, 156, 157, 158, 159, 160, 163, 164, 166], "theobald2005": [0, 8, 36, 108], "rotat": [0, 3, 6, 14, 22, 34, 36, 37, 87, 93, 104, 108, 109, 113, 152, 155], "matrix": [0, 4, 8, 10, 11, 12, 13, 15, 16, 17, 18, 19, 25, 32, 34, 87, 104, 108, 109, 110, 111, 113], "r": [0, 3, 4, 8, 9, 22, 23, 29, 32, 35, 36, 37, 38, 49, 58, 59, 69, 78, 80, 87, 91, 96, 100, 101, 102, 106, 108, 109, 110, 112, 113, 114, 150], "minim": [0, 3, 25, 36, 48, 80, 100, 111, 148, 151, 155, 166], "liu2010": [0, 108], "pleas": [0, 1, 4, 6, 8, 9, 11, 14, 17, 23, 24, 25, 27, 28, 29, 30, 32, 33, 36, 37, 38, 39, 49, 59, 69, 75, 76, 100, 102, 108, 110, 113, 114, 141, 142, 152, 165, 166], "cite": [0, 8, 11, 17, 29, 32, 36, 39, 113, 166], "when": [0, 2, 4, 6, 8, 10, 11, 13, 17, 23, 24, 26, 29, 32, 34, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 57, 58, 59, 60, 61, 64, 65, 67, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 83, 84, 86, 87, 89, 90, 91, 92, 93, 95, 96, 100, 101, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 119, 120, 122, 135, 137, 142, 148, 152, 153, 156, 157, 158, 160, 161, 162, 166], "thi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 46, 48, 49, 52, 55, 57, 58, 59, 61, 62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 86, 87, 89, 90, 91, 92, 93, 94, 95, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 126, 129, 130, 132, 133, 134, 136, 137, 139, 141, 142, 145, 146, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 166], "typic": [0, 6, 9, 10, 19, 23, 25, 26, 34, 35, 39, 46, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 84, 85, 87, 91, 92, 93, 100, 101, 107, 108, 110, 112, 114, 121, 148, 151, 156, 157], "one": [0, 2, 3, 4, 6, 8, 9, 10, 12, 13, 16, 17, 18, 23, 24, 26, 29, 30, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 87, 89, 90, 91, 93, 99, 100, 101, 102, 105, 106, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 131, 132, 136, 141, 142, 147, 148, 152, 156, 157, 161, 165, 166], "select": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 48, 49, 51, 52, 55, 57, 58, 59, 61, 65, 66, 67, 70, 72, 73, 74, 76, 79, 80, 81, 84, 87, 88, 91, 92, 93, 95, 101, 110, 111, 112, 163, 164, 166], "group": [0, 1, 3, 4, 6, 7, 8, 10, 13, 14, 17, 19, 20, 24, 25, 28, 32, 34, 35, 36, 37, 38, 49, 51, 59, 65, 67, 80, 81, 84, 89, 91, 92, 93, 94, 96, 99, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 147, 149, 152, 155, 159, 160, 163, 164], "atom": [0, 3, 4, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 46, 47, 48, 49, 51, 52, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 90, 91, 92, 93, 94, 95, 96, 99, 100, 101, 102, 104, 105, 107, 110, 112, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 149, 150, 151, 155, 156, 158, 159, 160, 166], "c": [0, 2, 3, 9, 13, 16, 19, 23, 30, 33, 35, 36, 37, 38, 40, 49, 52, 53, 55, 58, 59, 61, 63, 65, 66, 69, 70, 72, 73, 74, 76, 78, 80, 81, 84, 87, 89, 91, 92, 99, 100, 101, 104, 105, 108, 109, 110, 112, 113, 114, 142, 149, 150, 154, 161], "alpha": [0, 9, 10, 22, 23, 31, 36, 52, 55, 59, 61, 65, 66, 70, 73, 74, 76, 80, 81, 84, 87, 91, 100, 104, 105, 109, 110, 114, 154], "transform": [0, 2, 6, 8, 29, 32, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 87, 89, 93, 100, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "appli": [0, 2, 6, 8, 10, 13, 19, 23, 25, 32, 36, 37, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 87, 89, 92, 93, 100, 104, 109, 110, 114, 115, 152, 153, 154, 155, 156, 157, 158, 159, 160], "current": [0, 6, 8, 9, 13, 17, 23, 29, 32, 36, 37, 38, 40, 41, 42, 44, 48, 49, 51, 52, 55, 56, 57, 58, 59, 61, 63, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 84, 87, 93, 100, 101, 102, 103, 105, 106, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 132, 141, 142, 147, 148, 150, 157], "frame": [0, 1, 2, 3, 4, 6, 8, 9, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 26, 29, 30, 32, 34, 36, 37, 38, 40, 42, 44, 48, 49, 51, 52, 54, 55, 56, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 83, 84, 87, 93, 99, 101, 102, 103, 106, 109, 110, 112, 114, 115, 116, 117, 118, 119, 120, 151, 152, 156, 157, 163, 164], "trajectori": [0, 1, 2, 3, 4, 8, 9, 10, 11, 13, 16, 17, 20, 24, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 42, 45, 47, 48, 49, 50, 51, 53, 55, 57, 63, 65, 66, 67, 72, 76, 77, 79, 82, 83, 84, 85, 87, 93, 96, 103, 106, 107, 110, 111, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 148, 153, 154, 155, 160, 161, 163, 164, 166], "obtain": [0, 2, 6, 9, 13, 16, 17, 23, 25, 32, 36, 43, 44, 59, 65, 67, 69, 71, 80, 87, 88, 91, 104, 105, 113, 135, 137, 141, 166], "alignto": 0, "aligntraj": [0, 6, 17, 34, 36], "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 44, 46, 47, 48, 49, 50, 51, 52, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 89, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "do": [0, 1, 4, 6, 9, 10, 14, 17, 23, 34, 36, 38, 40, 44, 59, 65, 68, 71, 75, 76, 77, 80, 82, 83, 85, 87, 103, 110, 111, 112, 135, 148, 151, 153, 155, 156], "individu": [0, 10, 11, 17, 19, 23, 26, 29, 34, 35, 39, 42, 44, 59, 77, 80, 87, 93, 110, 112, 115, 116, 117, 118, 119, 120, 121, 134, 165, 166], "respect": [0, 4, 6, 29, 34, 36, 37, 84, 87, 89, 100, 109, 155], "show": [0, 2, 4, 6, 7, 8, 9, 17, 19, 20, 23, 26, 28, 29, 32, 33, 35, 36, 37, 103, 112, 114, 135], "how": [0, 2, 8, 10, 12, 13, 16, 17, 23, 25, 32, 37, 39, 42, 49, 52, 59, 61, 63, 68, 69, 75, 76, 80, 87, 88, 101, 102, 103, 110, 112, 114, 161, 166], "step": [0, 1, 2, 3, 4, 6, 8, 9, 16, 23, 24, 25, 26, 28, 29, 30, 32, 34, 35, 36, 37, 39, 40, 41, 42, 44, 48, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 79, 80, 81, 84, 87, 93, 99, 100, 101, 102, 148, 152, 156, 161], "manual": [0, 6, 17, 23, 69, 78, 89, 103, 112, 142, 152, 157], "explain": [0, 32, 40], "intermedi": [0, 23, 36, 103, 110, 161], "comput": [0, 1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 17, 22, 24, 28, 30, 31, 32, 34, 35, 36, 37, 38, 55, 59, 68, 80, 87, 88, 91, 99, 104, 105, 108, 110, 111, 113, 156, 157, 161], "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 50, 51, 55, 56, 57, 58, 59, 62, 63, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 165, 166], "requir": [0, 2, 3, 8, 13, 14, 15, 17, 20, 23, 24, 29, 32, 33, 34, 36, 39, 41, 44, 49, 51, 52, 55, 57, 59, 61, 63, 65, 67, 69, 70, 73, 74, 75, 76, 79, 80, 81, 84, 86, 87, 92, 93, 95, 99, 100, 104, 107, 110, 114, 136, 138, 141, 150, 152, 153, 165], "lib": [0, 1, 2, 3, 6, 8, 9, 10, 24, 29, 30, 32, 36, 37, 58, 59, 69, 73, 78, 83, 84, 87, 89, 92], "qcprot": [0, 8, 36, 111, 112, 113], "implement": [0, 2, 4, 6, 8, 11, 13, 15, 16, 17, 25, 28, 29, 34, 36, 42, 51, 52, 55, 58, 59, 61, 65, 66, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 80, 81, 85, 87, 92, 99, 100, 103, 105, 106, 107, 108, 109, 110, 111, 113, 121, 142, 147, 148, 150, 151, 166], "exampl": [0, 1, 5, 6, 7, 8, 11, 13, 14, 16, 17, 19, 23, 25, 27, 28, 29, 32, 33, 34, 35, 38, 39, 40, 44, 46, 47, 48, 49, 52, 55, 57, 58, 67, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 83, 84, 86, 87, 89, 90, 91, 92, 93, 99, 101, 102, 103, 104, 106, 109, 110, 111, 113, 114, 120, 121, 130, 132, 133, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 166], "file": [0, 1, 3, 6, 8, 9, 13, 14, 16, 17, 18, 20, 24, 26, 29, 32, 34, 36, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 52, 53, 56, 58, 69, 71, 76, 77, 78, 79, 80, 81, 82, 85, 87, 91, 93, 95, 101, 102, 103, 105, 106, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148, 149, 150, 151, 152, 163, 164, 166], "provid": [0, 1, 2, 4, 6, 7, 8, 9, 10, 13, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 87, 89, 90, 93, 99, 100, 102, 104, 105, 106, 107, 110, 111, 112, 113, 114, 121, 135, 139, 148, 155, 158, 166], "part": [0, 5, 8, 13, 20, 23, 26, 29, 32, 34, 38, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 91, 109, 112, 114, 121, 141], "test": [0, 1, 3, 4, 8, 9, 13, 16, 17, 20, 22, 23, 26, 27, 29, 32, 33, 34, 36, 38, 39, 47, 48, 49, 52, 55, 59, 61, 69, 70, 73, 74, 76, 78, 80, 81, 82, 85, 86, 87, 92, 93, 100, 110, 112, 122, 132, 141, 163, 164], "suit": [0, 1, 8, 13, 16, 17, 23, 29, 32, 39, 112], "variabl": [0, 1, 5, 8, 13, 16, 29, 32, 40, 59, 68, 69, 75, 80, 99, 110, 113, 153], "psf": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 24, 26, 32, 34, 36, 49, 65, 66, 81, 87, 93, 110, 112, 114, 122, 148, 151], "dcd": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 26, 32, 34, 36, 49, 59, 74, 80, 81, 85, 87, 93, 110, 111, 112], "pdb_small": [0, 87], "For": [0, 1, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 37, 38, 39, 44, 46, 48, 49, 52, 55, 57, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 78, 80, 81, 83, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 105, 107, 110, 111, 112, 113, 114, 121, 132, 133, 141, 142, 147, 148, 152, 153, 157, 161], "all": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 18, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 110, 112, 113, 114, 115, 130, 131, 133, 135, 141, 142, 143, 144, 145, 147, 148, 152, 153, 154, 156, 158, 159, 160, 161, 163, 164, 166], "further": [0, 4, 19, 20, 24, 25, 26, 27, 31, 34, 36, 38, 40, 42, 48, 49, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 103, 106, 114, 121, 142, 143], "execut": [0, 1, 3, 7, 23, 26, 38, 48, 77, 110], "first": [0, 2, 3, 4, 6, 8, 9, 13, 17, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 87, 91, 92, 93, 101, 102, 104, 105, 109, 110, 114, 121, 132, 147, 148, 149, 152, 157, 162, 163, 164, 166], "import": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 16, 17, 20, 22, 23, 24, 26, 27, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 59, 61, 63, 65, 67, 69, 78, 79, 81, 86, 87, 90, 91, 92, 93, 101, 102, 103, 104, 109, 110, 111, 112, 122, 130, 132, 133, 142, 147, 152, 158, 163, 164, 165], "mda": [0, 1, 2, 3, 4, 7, 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33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 48, 49, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 114, 121, 123, 126, 127, 128, 129, 131, 132, 133, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 149, 150, 154, 155, 156, 157, 158, 159, 160, 161], "mutant": 0, "wa": [0, 3, 9, 20, 21, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 42, 48, 49, 52, 55, 56, 58, 59, 61, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 105, 110, 114, 115, 147, 148, 155, 157, 158, 159, 160], "aln": 0, "would": [0, 6, 20, 23, 32, 38, 40, 49, 52, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 87, 93, 111, 114, 147, 152, 156, 157, 161, 166], "produc": [0, 10, 23, 26, 33, 34, 36, 37, 41, 44, 52, 59, 87, 91, 101, 103, 106, 133, 136, 163, 164], "appropri": [0, 6, 8, 25, 29, 35, 36, 38, 40, 42, 43, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 78, 79, 80, 81, 87, 89, 91, 92, 93, 104, 110, 114, 115, 121, 161], "fasta2select": [0, 34, 36], "feed": [0, 23, 26], "result": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 91, 92, 93, 99, 100, 104, 105, 107, 108, 109, 110, 112, 114, 147, 148, 152, 155], "dictionari": [0, 2, 4, 6, 17, 18, 19, 20, 23, 26, 28, 34, 36, 38, 40, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 70, 71, 72, 73, 74, 76, 80, 81, 89, 92, 110, 148, 149], "seldict": 0, "see": [0, 1, 2, 3, 6, 7, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 36, 37, 38, 39, 42, 44, 47, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 83, 87, 89, 91, 93, 95, 99, 100, 102, 103, 104, 110, 114, 121, 133, 137, 141, 142, 147, 149, 150, 151, 152, 153, 161, 163, 164, 165, 166], "document": [0, 2, 5, 6, 13, 14, 26, 31, 34, 35, 39, 42, 59, 61, 65, 66, 68, 69, 77, 78, 79, 83, 100, 103, 109, 143, 152, 165], "advanc": [0, 44, 80, 87, 93, 111], "version": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 84, 86, 87, 89, 90, 91, 92, 93, 95, 96, 97, 98, 99, 100, 102, 103, 104, 105, 106, 108, 109, 110, 111, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 147, 148, 150, 153, 155, 157, 158, 159, 160, 161, 166], "10": [0, 2, 3, 4, 8, 9, 11, 13, 15, 17, 19, 23, 24, 25, 26, 29, 30, 31, 32, 34, 36, 37, 38, 44, 48, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 72, 73, 74, 76, 78, 81, 84, 87, 89, 92, 93, 99, 103, 104, 105, 107, 109, 110, 112, 113, 114, 137, 142, 149, 150, 156, 161, 163, 164], "now": [0, 2, 4, 6, 8, 9, 10, 19, 20, 23, 28, 29, 30, 32, 33, 34, 36, 37, 42, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 61, 62, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 79, 81, 84, 86, 87, 89, 91, 92, 93, 95, 96, 100, 103, 104, 110, 114, 115, 133, 134, 135, 137, 139, 141, 142, 147, 150], "exclus": [0, 20, 23, 35, 37, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 105, 106, 142], "access": [0, 1, 2, 3, 5, 6, 9, 18, 21, 23, 24, 25, 28, 29, 30, 34, 38, 39, 40, 42, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 86, 87, 89, 91, 92, 93, 95, 100, 105, 106, 110, 111, 112, 114, 136, 148, 166], "16": [0, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 32, 34, 36, 57, 59, 62, 65, 66, 79, 81, 84, 87, 90, 93, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 134, 139, 148, 149, 150, 163], "rms_fit_trj": 0, "deprec": [0, 4, 6, 8, 9, 19, 23, 24, 28, 30, 32, 33, 34, 35, 36, 37, 38, 39, 52, 55, 57, 59, 61, 70, 73, 74, 75, 76, 81, 87, 91, 92, 103, 110, 133, 134, 137], "favor": [0, 36, 87], "17": [0, 5, 22, 26, 34, 36, 37, 38, 52, 58, 61, 65, 66, 69, 87, 92, 93, 113, 130, 142, 143, 149, 150], "none": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 100, 101, 102, 103, 104, 106, 107, 109, 110, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 150, 153, 154, 155, 156, 157, 158, 159, 160], "subselect": [0, 9, 87, 114], "tol_mass": [0, 34, 36], "1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 48, 49, 51, 52, 54, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 103, 104, 105, 106, 109, 110, 112, 113, 114, 128, 132, 133, 135, 137, 139, 141, 142, 144, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164], "strict": [0, 67, 87, 91, 92, 99], "fals": [0, 1, 2, 4, 6, 8, 9, 13, 14, 17, 20, 23, 25, 26, 32, 34, 35, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 99, 103, 105, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 150, 153, 156, 157, 158, 159, 164], "match_atom": 0, "sourc": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 86, 87, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 106, 107, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 149, 150, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164], "perform": [0, 2, 3, 4, 6, 8, 9, 11, 14, 17, 18, 19, 20, 23, 24, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 89, 99, 100, 103, 104, 107, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 153, 155, 158, 163, 164], "spatial": [0, 34, 35, 59, 107, 155], "follow": [0, 2, 3, 6, 13, 16, 17, 19, 20, 24, 29, 34, 38, 39, 40, 42, 44, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 91, 100, 101, 103, 104, 105, 109, 110, 112, 114, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 152, 157, 161, 166], "wai": [0, 2, 4, 6, 8, 9, 13, 14, 19, 23, 24, 25, 29, 37, 40, 42, 49, 69, 76, 77, 80, 83, 86, 93, 109, 111, 112, 114, 115, 116, 117, 118, 119, 120, 136, 152, 155], "A": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 19, 22, 23, 24, 25, 28, 29, 30, 32, 34, 35, 36, 37, 38, 40, 44, 52, 54, 55, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 79, 80, 81, 82, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 104, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 132, 135, 139, 141, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161], "sel1": [0, 34, 36], "sel2": [0, 34, 36], "befor": [0, 2, 3, 4, 6, 10, 13, 14, 17, 24, 32, 36, 38, 39, 42, 44, 59, 65, 66, 69, 75, 76, 80, 87, 90, 91, 93, 99, 101, 102, 107, 108, 110, 114, 115, 139, 150, 152, 157, 158, 159], "its": [0, 3, 4, 8, 12, 13, 19, 23, 29, 32, 34, 37, 38, 40, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 79, 80, 82, 83, 86, 87, 89, 91, 93, 100, 104, 105, 106, 110, 113, 114, 121, 149, 152, 155], "coincid": [0, 100], "below": [0, 4, 5, 10, 17, 23, 29, 31, 32, 34, 36, 40, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 79, 80, 81, 86, 87, 103, 114, 121, 132], "explan": [0, 29, 59, 110, 149], "deriv": [0, 2, 6, 7, 11, 17, 38, 42, 44, 76, 80, 84, 93, 103, 110, 115, 145, 148], "shift": [0, 26, 87, 100, 105, 160], "behavior": [0, 34, 38, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 110, 114], "through": [0, 4, 6, 10, 11, 17, 20, 21, 23, 24, 25, 35, 38, 40, 41, 44, 49, 52, 55, 56, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 80, 81, 84, 86, 87, 89, 93, 100, 110, 112, 114, 123, 148, 160, 166], "construct": [0, 6, 8, 13, 19, 20, 34, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 86, 89, 93, 100, 105, 107, 110, 122, 148, 152], "alreadi": [0, 6, 7, 8, 23, 32, 42, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 83, 87, 93, 107, 114], "match": [0, 13, 16, 20, 23, 30, 34, 36, 49, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 78, 81, 87, 89, 91, 92, 155], "should": [0, 2, 3, 4, 6, 8, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 33, 34, 35, 36, 37, 38, 42, 44, 49, 52, 57, 59, 61, 62, 63, 65, 67, 75, 76, 80, 83, 85, 87, 89, 90, 91, 92, 96, 100, 103, 105, 106, 107, 110, 116, 117, 118, 119, 120, 131, 133, 134, 141, 142, 147, 148, 149, 156], "therefor": [0, 2, 6, 14, 17, 26, 27, 59, 65, 69, 75, 87, 104, 110, 141, 147], "preserv": [0, 8, 32, 34, 57, 61, 63, 65, 87], "exact": [0, 4, 17, 23, 29, 34, 69, 87], "either": [0, 4, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 28, 34, 36, 38, 40, 42, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 87, 92, 93, 99, 100, 101, 102, 104, 106, 107, 110, 111, 112, 114, 123, 133, 141, 148, 152, 159, 160, 166], "ani": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 16, 17, 23, 24, 25, 26, 28, 29, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 103, 104, 105, 106, 107, 110, 111, 113, 114, 121, 127, 128, 130, 132, 133, 137, 147, 148, 152, 153, 161, 166], "other": [0, 2, 3, 4, 6, 8, 9, 13, 16, 17, 19, 23, 25, 26, 28, 29, 30, 32, 34, 37, 38, 39, 40, 41, 42, 46, 47, 49, 50, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 104, 106, 110, 111, 114, 132, 133, 141, 147, 148, 149, 152, 153, 157, 161, 164, 166], "new": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 44, 46, 47, 48, 49, 50, 51, 52, 53, 55, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 104, 105, 106, 109, 110, 112, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 153, 161, 166], "made": [0, 4, 5, 6, 8, 9, 15, 17, 19, 25, 32, 49, 79, 80, 81, 87, 89, 92, 93, 99, 110, 114, 148, 152], "sort": [0, 23, 24, 26, 32, 33, 38, 45, 87, 89, 90, 91, 92, 110, 114], "index": [0, 2, 6, 8, 23, 24, 25, 26, 28, 29, 30, 32, 34, 36, 37, 38, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 90, 91, 92, 100, 102, 110, 115, 116, 117, 118, 119, 120, 121, 130, 141, 142, 148, 149, 166], "destroi": 0, "correspond": [0, 3, 6, 8, 9, 12, 13, 18, 23, 25, 32, 34, 36, 37, 38, 39, 42, 43, 49, 52, 55, 58, 59, 61, 62, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 99, 100, 103, 105, 107, 110, 113, 114, 130, 150, 155, 157, 158], "safest": 0, "mix": [0, 38], "string": [0, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 29, 32, 34, 36, 37, 38, 40, 42, 48, 58, 59, 62, 63, 65, 67, 69, 78, 79, 80, 81, 86, 87, 89, 91, 93, 101, 103, 106, 109, 111, 114, 115, 116, 117, 118, 119, 120, 121, 133, 135, 141, 142, 149, 150, 155, 162, 163, 164], "paramet": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "str": [0, 2, 3, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 51, 52, 55, 57, 58, 59, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 86, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 106, 107, 110, 113, 114, 116, 118, 121, 132, 139, 145, 149, 155, 159, 163, 164], "dict": [0, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 25, 26, 29, 30, 32, 34, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 81, 82, 84, 87, 89, 90, 92, 93, 101, 103, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 161], "tupl": [0, 4, 6, 10, 18, 19, 20, 26, 32, 34, 35, 36, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 79, 81, 87, 90, 91, 92, 93, 99, 103, 104, 109, 110, 141, 147, 148, 150, 152], "option": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "oper": [0, 2, 6, 18, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 81, 87, 89, 92, 100, 101, 104, 105, 107, 110, 111, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 160], "valid": [0, 8, 9, 32, 34, 35, 36, 42, 44, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 81, 105, 110, 137, 142, 143, 149], "ident": [0, 17, 20, 32, 34, 36, 57, 58, 87, 92, 93, 109, 110, 130, 148], "where": [0, 1, 5, 6, 7, 8, 15, 17, 18, 19, 20, 23, 29, 32, 33, 34, 35, 36, 37, 38, 40, 44, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 110, 112, 114, 133, 141, 147, 152, 155, 156, 158, 161], "return": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "clustalw": [0, 34, 36], "stamp": [0, 2, 23, 34, 36], "2": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 46, 47, 48, 49, 51, 52, 53, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 106, 109, 110, 113, 114, 132, 133, 134, 135, 137, 141, 142, 143, 145, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164, 166], "3": [0, 2, 3, 4, 6, 7, 8, 9, 10, 13, 15, 16, 17, 18, 20, 21, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 81, 84, 87, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 113, 114, 132, 133, 134, 137, 141, 142, 147, 148, 149, 150, 152, 157, 158, 159, 160, 161, 163, 164, 166], "gener": [0, 1, 5, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 32, 34, 35, 36, 38, 39, 40, 44, 47, 52, 58, 59, 61, 62, 63, 65, 70, 73, 74, 76, 78, 80, 81, 82, 87, 89, 91, 92, 93, 100, 102, 105, 107, 109, 110, 112, 113, 114, 130, 131, 134, 139, 141, 147, 148, 156, 161, 163, 164, 166], "equival": [0, 6, 18, 22, 24, 29, 36, 37, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 82, 87, 106, 107, 114, 142], "each": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 70, 72, 73, 74, 75, 76, 77, 80, 81, 86, 87, 89, 90, 91, 92, 93, 99, 100, 103, 104, 105, 108, 110, 112, 115, 121, 132, 141, 147, 148, 149, 155, 158, 160], "list": [0, 2, 3, 4, 6, 9, 12, 13, 14, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 109, 112, 113, 114, 115, 121, 123, 126, 127, 128, 129, 131, 137, 138, 141, 142, 143, 144, 147, 148, 149, 152, 158, 161, 166], "defin": [0, 2, 3, 4, 6, 13, 16, 17, 20, 23, 24, 25, 28, 34, 36, 37, 38, 40, 44, 52, 57, 59, 61, 65, 66, 69, 75, 76, 79, 80, 87, 91, 92, 93, 100, 101, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 132, 141, 145, 147, 148, 150, 152, 153, 155, 158, 159, 161], "describ": [0, 2, 3, 11, 13, 15, 16, 17, 18, 23, 25, 29, 31, 34, 36, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 103, 104, 105, 110, 112, 113, 114, 121, 139, 142, 151, 152, 162], "under": [0, 17, 23, 25, 26, 34, 36, 37, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 81, 87, 93, 99, 100, 103, 105, 110, 120, 148, 152, 166], "bool": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 96, 100, 101, 103, 104, 107, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 153, 154, 155, 156, 157, 158, 159, 160], "whether": [0, 9, 13, 14, 16, 17, 20, 23, 24, 26, 34, 40, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 89, 91, 103, 106, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152], "default": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 26, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 44, 47, 48, 49, 50, 51, 52, 53, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 103, 104, 106, 107, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 149, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "array_lik": [0, 2, 3, 6, 9, 10, 14, 15, 17, 18, 23, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 92, 100, 101, 102, 104, 107, 109, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 155, 158], "choos": [0, 6, 8, 20, 23, 32, 34, 77, 80, 87, 89, 91, 155, 159], "With": [0, 6, 15, 20, 26, 34, 36, 37, 40, 46, 77, 99, 155, 158], "weigh": [0, 34, 36, 155, 158], "equal": [0, 1, 8, 13, 18, 23, 32, 34, 36, 37, 38, 44, 59, 89, 92, 99, 100, 103, 110, 155, 158, 163], "float": [0, 4, 6, 7, 8, 10, 13, 15, 16, 17, 19, 20, 23, 24, 25, 28, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 44, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 81, 84, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 114, 147, 149, 150, 154, 155, 158, 161, 163, 164], "same": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 16, 17, 20, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 44, 48, 49, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 92, 93, 99, 100, 101, 104, 105, 109, 110, 114, 121, 130, 147, 148, 150, 155, 157, 158, 160], "length": [0, 2, 3, 6, 8, 10, 13, 14, 17, 19, 20, 22, 23, 24, 29, 30, 32, 33, 34, 36, 38, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 84, 87, 90, 91, 92, 93, 100, 101, 104, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 158, 161], "element": [0, 3, 6, 12, 13, 14, 16, 17, 18, 23, 32, 34, 36, 37, 38, 48, 49, 59, 65, 75, 87, 90, 91, 99, 105, 110, 114, 115, 123, 126, 128, 135, 137, 138, 141, 142, 143, 149, 150, 155, 158], "reject": [0, 25, 34, 36], "differ": [0, 1, 2, 3, 4, 6, 8, 11, 13, 16, 17, 19, 20, 23, 24, 25, 32, 34, 36, 37, 38, 42, 44, 49, 52, 55, 56, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 83, 84, 86, 87, 91, 92, 93, 101, 109, 110, 112, 113, 114, 121, 126, 137, 142, 148, 152, 161], "more": [0, 1, 2, 3, 4, 8, 9, 10, 11, 13, 16, 17, 23, 24, 25, 32, 34, 36, 37, 38, 39, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 88, 91, 93, 100, 101, 102, 103, 105, 106, 109, 110, 111, 112, 114, 141, 142, 147, 148, 152, 156, 164, 166], "than": [0, 3, 4, 6, 8, 9, 10, 15, 17, 19, 20, 23, 24, 32, 34, 36, 37, 38, 41, 42, 51, 57, 59, 65, 67, 69, 75, 77, 81, 87, 91, 92, 93, 99, 100, 104, 105, 106, 110, 114, 147, 150, 156], "Will": [0, 4, 6, 8, 9, 17, 18, 20, 24, 28, 32, 33, 35, 36, 38, 44, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 93, 104], "rais": [0, 2, 3, 6, 9, 23, 26, 29, 30, 32, 36, 40, 42, 43, 44, 49, 52, 55, 57, 58, 59, 60, 61, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 93, 95, 102, 103, 104, 106, 109, 110, 114, 121, 135, 137, 145, 147, 157, 161], "selectionerror": [0, 36, 89, 95], "doe": [0, 3, 6, 13, 14, 23, 24, 29, 32, 34, 36, 37, 59, 61, 64, 65, 67, 69, 70, 77, 78, 80, 82, 84, 87, 91, 93, 95, 100, 101, 103, 104, 110, 114, 121, 131, 138, 141, 151, 153, 156], "try": [0, 20, 23, 42, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 79, 81, 83, 85, 110, 131, 133, 142, 147, 162], "prepar": [0, 93], "drop": [0, 17, 58, 87, 110], "residu": [0, 3, 6, 9, 10, 19, 23, 25, 28, 30, 31, 32, 35, 36, 37, 38, 48, 65, 66, 67, 80, 86, 87, 89, 90, 91, 93, 95, 96, 110, 112, 114, 123, 125, 126, 127, 128, 130, 131, 132, 134, 137, 139, 140, 141, 142, 144, 148, 159, 160], "non": [0, 2, 3, 6, 8, 9, 17, 23, 24, 25, 29, 30, 32, 33, 36, 38, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 89, 103, 104, 105, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 126, 141, 156, 157], "get_matching_atom": 0, "detail": [0, 4, 6, 7, 8, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 49, 52, 59, 61, 65, 75, 79, 80, 90, 102, 103, 110, 111, 114, 141, 142, 148, 152, 166], "e": [0, 2, 4, 6, 9, 13, 17, 18, 23, 24, 25, 26, 28, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 86, 87, 89, 91, 92, 93, 99, 100, 101, 103, 104, 105, 109, 110, 111, 112, 113, 114, 115, 137, 141, 147, 148, 149, 150, 152, 153, 154, 157, 158, 161, 162, 163, 164, 166], "context": [0, 23, 44, 48, 58, 59, 65, 69, 76, 78, 80, 101, 102, 106, 110, 121, 153], "rest": [0, 3, 6, 150], "ligand": [0, 3, 6, 19, 35, 38, 78, 93], "surround": 0, "water": [0, 6, 7, 8, 10, 20, 23, 24, 39, 87, 88, 93, 99, 112, 113, 114, 132, 150, 161], "old_rmsd": 0, "new_rmsd": 0, "after": [0, 1, 2, 3, 6, 8, 10, 17, 18, 20, 23, 24, 26, 32, 34, 35, 36, 37, 38, 42, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 86, 87, 91, 93, 103, 106, 107, 110, 114, 141, 147, 149, 152, 157, 158, 162], "effici": [0, 1, 10, 18, 34, 65, 68, 69, 73, 103, 113, 148], "method": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 16, 17, 19, 20, 22, 23, 25, 26, 28, 29, 31, 32, 33, 35, 36, 37, 38, 40, 42, 46, 49, 52, 55, 56, 57, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 77, 81, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 100, 101, 102, 103, 105, 107, 108, 109, 110, 112, 113, 114, 115, 121, 136, 145, 147, 148, 150, 152, 156, 159], "ad": [0, 1, 2, 3, 4, 6, 9, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 30, 32, 36, 37, 42, 49, 52, 55, 56, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 87, 89, 90, 91, 92, 93, 99, 100, 102, 103, 104, 110, 132, 133, 135, 137, 138, 139, 141, 142, 143, 145, 147, 149, 152], "toggl": [0, 38, 93, 142], "8": [0, 2, 4, 9, 26, 31, 34, 36, 37, 40, 48, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 70, 72, 73, 74, 76, 78, 81, 84, 87, 89, 91, 92, 93, 100, 104, 110, 114, 115, 116, 117, 118, 119, 120, 126, 137, 142, 148, 149, 150, 160, 161, 163, 164], "check": [0, 4, 6, 9, 10, 13, 19, 20, 23, 31, 32, 33, 34, 36, 38, 42, 44, 52, 55, 58, 59, 61, 65, 70, 71, 72, 73, 74, 76, 77, 78, 81, 87, 92, 100, 105, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160], "includ": [0, 1, 3, 5, 9, 11, 13, 17, 23, 24, 25, 29, 32, 34, 36, 38, 42, 44, 48, 52, 55, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 89, 90, 93, 99, 100, 103, 106, 109, 110, 114, 121, 132, 138, 142, 148, 150, 152, 166], "work": [0, 2, 4, 6, 8, 9, 10, 11, 13, 16, 17, 18, 23, 28, 31, 36, 37, 38, 39, 40, 49, 52, 55, 58, 59, 61, 68, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 95, 100, 103, 104, 105, 106, 110, 112, 113, 114, 115, 121, 132, 142, 147, 152, 155, 160, 166], "incomplet": [0, 9, 27], "lenient": 0, "wherea": [0, 8, 32, 34, 87, 110, 111], "old": [0, 52, 80, 86, 87, 93, 110, 148], "kwarg": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 18, 23, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 86, 87, 91, 92, 93, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 147, 153], "replac": [0, 6, 12, 23, 58, 87, 93, 99, 100, 106, 110, 147, 148], "mass_weight": [0, 34, 36], "sinc": [0, 4, 6, 8, 9, 14, 17, 19, 21, 23, 24, 28, 32, 33, 34, 35, 36, 38, 39, 49, 52, 65, 69, 75, 76, 81, 87, 91, 114, 141, 156], "instead": [0, 2, 3, 4, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 42, 49, 51, 52, 53, 54, 55, 56, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 80, 81, 87, 89, 91, 92, 93, 96, 99, 100, 101, 102, 104, 105, 110, 114, 115, 116, 117, 118, 119, 120, 121, 126, 137, 148, 152, 159], "prefix": [0, 23, 34, 87, 103, 114], "rmsfit_": 0, "forc": [0, 20, 30, 31, 39, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 82, 84, 85, 87, 89, 92, 93, 100, 102, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 161], "in_memori": [0, 17, 36, 37, 81, 93], "both": [0, 2, 3, 4, 6, 9, 10, 14, 17, 23, 24, 26, 29, 30, 32, 34, 36, 38, 40, 49, 54, 56, 58, 61, 65, 69, 72, 80, 87, 92, 99, 102, 103, 112, 113, 114, 130, 133, 140, 141, 164], "must": [0, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 18, 20, 23, 24, 26, 29, 32, 34, 36, 38, 40, 42, 44, 49, 52, 55, 59, 61, 65, 67, 68, 69, 70, 71, 73, 74, 76, 77, 80, 81, 84, 87, 90, 91, 93, 99, 100, 104, 105, 106, 107, 108, 110, 114, 115, 141, 145, 147, 152, 155, 157, 161], "instanc": [0, 2, 3, 4, 6, 7, 8, 9, 13, 16, 17, 18, 23, 25, 28, 29, 32, 33, 34, 35, 36, 39, 40, 42, 43, 44, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 84, 86, 87, 88, 91, 92, 93, 100, 101, 103, 105, 106, 110, 112, 114, 115, 141, 145, 148, 150, 152, 159, 163, 164, 165, 166], "output": [0, 2, 6, 13, 14, 17, 18, 19, 23, 26, 32, 34, 35, 36, 40, 49, 50, 51, 52, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 86, 87, 89, 91, 100, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 128, 148, 157], "format": [0, 3, 4, 6, 10, 13, 14, 15, 16, 17, 18, 23, 25, 26, 34, 37, 38, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 56, 58, 59, 60, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 77, 78, 79, 81, 82, 84, 85, 87, 91, 92, 93, 95, 100, 103, 104, 105, 109, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 143, 145, 147, 149, 150, 151, 162, 166], "determin": [0, 3, 4, 6, 8, 9, 10, 13, 18, 22, 23, 24, 25, 26, 29, 32, 33, 34, 38, 42, 44, 59, 65, 79, 80, 87, 91, 93, 100, 104, 108, 110, 113, 147, 157], "extens": [0, 4, 6, 17, 23, 25, 34, 44, 51, 59, 65, 66, 67, 68, 69, 77, 78, 79, 80, 85, 87, 93, 110, 111, 116, 117, 118, 119, 120, 132, 148, 151, 162], "One": [0, 2, 3, 6, 13, 16, 23, 24, 25, 26, 34, 37, 38, 48, 87, 93, 101, 114, 152, 161], "save": [0, 3, 4, 6, 7, 8, 10, 14, 17, 18, 20, 26, 28, 29, 32, 34, 36, 37, 52, 58, 59, 61, 63, 65, 69, 73, 74, 78, 83, 100, 101, 102, 106], "an": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 52, 55, 56, 57, 58, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "altern": [0, 6, 9, 17, 19, 22, 23, 24, 28, 32, 41, 44, 49, 62, 65, 66, 87, 92, 93, 104, 110, 114, 121, 134, 152], "np": 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110, 111, 114, 131, 141, 147], "fail": [0, 6, 26, 28, 38, 49, 59, 65, 67, 69, 73, 83, 85, 87, 95, 104, 110, 145], "t": [0, 2, 4, 7, 17, 20, 22, 24, 29, 30, 32, 34, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 52, 55, 56, 58, 59, 60, 61, 64, 65, 66, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 90, 91, 99, 100, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 152, 153, 156, 157, 158, 159, 160, 161], "found": [0, 2, 9, 19, 20, 23, 24, 25, 34, 38, 40, 42, 43, 49, 59, 65, 70, 77, 78, 79, 86, 87, 89, 91, 93, 108, 110, 111, 132, 147, 148, 166], "overwrit": [0, 20, 35, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "perman": [0, 37, 93], "switch": [0, 4, 9, 24, 38, 40, 105], "memori": [0, 8, 10, 13, 14, 18, 29, 36, 37, 40, 41, 42, 44, 53, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 85, 87, 90, 93, 110, 147, 157], "place": [0, 6, 9, 14, 17, 23, 38, 40, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 90, 93, 100, 102, 104, 108, 109, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 154, 160], "which": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 23, 24, 25, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 46, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 165, 166], "improv": [0, 15, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 89, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "substanti": [0, 81], "some": [0, 4, 8, 9, 17, 20, 23, 26, 28, 32, 37, 38, 39, 40, 42, 47, 48, 49, 59, 61, 65, 68, 69, 76, 78, 79, 80, 83, 87, 89, 91, 104, 109, 110, 111, 135, 146, 147, 148, 150, 152, 161, 165, 166], "out": [0, 4, 17, 22, 23, 32, 36, 37, 38, 39, 40, 42, 44, 45, 52, 55, 56, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 80, 81, 87, 93, 103, 109, 115, 141, 148, 161, 162, 165, 166], "ignor": [0, 6, 13, 16, 18, 23, 42, 44, 59, 63, 65, 66, 75, 80, 81, 82, 84, 87, 91, 92, 93, 103, 104, 114, 126, 132, 133, 135, 137, 141, 147, 149], "verbos": [0, 2, 3, 4, 6, 7, 8, 9, 13, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 81, 93, 103], "logger": [0, 38, 103], "inform": [0, 8, 9, 13, 16, 17, 20, 23, 24, 25, 33, 34, 37, 38, 42, 49, 50, 52, 55, 57, 59, 61, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 80, 83, 84, 87, 90, 91, 93, 100, 101, 102, 104, 110, 114, 122, 123, 126, 127, 128, 130, 132, 133, 137, 138, 139, 140, 141, 142, 143, 144, 146, 148, 151, 165, 166], "progress": [0, 2, 3, 4, 6, 7, 8, 9, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 93, 103], "reference_atom": [0, 104], "mobile_atom": 0, "insid": [0, 2, 5, 20, 23, 37, 80, 83, 87, 89, 92, 99, 105, 111, 113, 121, 152, 160], "rmsd_align": 0, "valu": [0, 2, 3, 4, 6, 8, 9, 13, 14, 16, 17, 20, 23, 24, 26, 29, 30, 32, 34, 35, 36, 37, 38, 40, 41, 42, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 149, 150, 153, 161, 163, 164], "least": [0, 2, 3, 4, 6, 8, 9, 13, 15, 19, 23, 25, 29, 30, 32, 36, 44, 52, 55, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 77, 81, 106, 108, 110, 126, 137, 142], "minimim": 0, "numpi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 44, 52, 53, 55, 59, 61, 70, 73, 74, 76, 79, 80, 84, 87, 88, 89, 90, 91, 92, 93, 100, 104, 105, 109, 110, 112, 147, 152, 153, 164, 166], "ndarrai": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 19, 20, 23, 24, 28, 29, 30, 33, 34, 35, 36, 40, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 84, 87, 91, 92, 93, 100, 102, 104, 105, 107, 108, 109, 110, 112, 147], "alia": [0, 4, 6, 9, 23, 24, 28, 30, 32, 33, 35, 36, 38, 87, 89, 91, 150], "attribut": [0, 2, 3, 4, 6, 7, 9, 18, 19, 20, 23, 24, 26, 28, 30, 32, 33, 34, 35, 36, 38, 39, 40, 42, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 81, 83, 84, 87, 89, 90, 92, 93, 94, 100, 101, 102, 107, 110, 112, 114, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 152, 153, 161], "reflect": [0, 32, 77, 79, 84, 87, 105, 109, 110, 114], "upon": [0, 20, 59, 61, 75, 76, 77, 78, 92, 93, 103, 145, 147, 152], "recommend": [0, 2, 24, 38, 59, 65, 110, 111, 112, 114, 147, 166], "wrap": [0, 2, 3, 6, 13, 16, 18, 29, 36, 61, 65, 87, 91, 106, 107, 110, 152, 156, 158, 159], "statement": [0, 32, 80, 110, 115], "final": [0, 4, 6, 9, 13, 16, 17, 18, 20, 28, 32, 37, 38, 49, 57, 65, 75, 87, 90, 92, 107, 112, 114], "guarante": [0, 6, 24, 67, 104, 110], "restor": [0, 6], "log": [0, 2, 3, 6, 9, 17, 29, 30, 32, 36, 38, 80, 111, 148], "level": [0, 5, 23, 59, 73, 76, 78, 89, 90, 96, 103, 106, 110], "except": [0, 23, 26, 35, 38, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 81, 84, 87, 89, 91, 93, 110, 111, 148, 152], "represent": [0, 14, 18, 23, 34, 38, 52, 55, 57, 61, 71, 80, 92, 93, 104, 120, 121, 126, 137, 138], "remaind": [0, 112], "python": [0, 2, 6, 17, 23, 26, 39, 40, 46, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 83, 84, 86, 87, 88, 89, 91, 101, 102, 103, 106, 108, 109, 110, 111, 113, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 149, 150, 152, 165, 166], "session": [0, 69, 112], "memoryread": [0, 36, 79, 80, 93], "alwai": [0, 2, 4, 6, 13, 16, 17, 26, 32, 33, 36, 40, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 76, 80, 81, 87, 91, 93, 109, 110, 112, 114, 139, 147, 148, 152, 161], "treat": [0, 6, 19, 22, 24, 37, 38, 42, 59, 62, 77, 87, 92, 93, 104, 112, 132, 141, 148, 163, 164], "had": [0, 35, 156], "directori": [0, 23, 26, 34, 73, 106, 112, 113, 132], "19": [0, 9, 10, 32, 35, 61, 65, 66, 69, 76, 77, 81, 87, 91, 92, 93, 95, 99, 100, 104, 105, 110, 133, 141, 149, 150, 161], "support": [0, 2, 4, 6, 10, 17, 18, 23, 26, 28, 35, 36, 37, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 83, 85, 87, 89, 93, 100, 101, 102, 106, 110, 111, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 151, 155, 161, 166], "start": [0, 1, 2, 3, 4, 6, 8, 9, 16, 18, 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MDAnalysis.analysis.legacy.x3dna": [[26, "generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-legacy-x3dna"]], "Single structure": [[26, "single-structure"]], "Trajectory": [[26, "trajectory"]], "Utilities": [[26, "utilities"]], "MDAnalysis.analysis.legacy \u2014 Legacy analysis code": [[27, "mdanalysis-analysis-legacy-legacy-analysis-code"]], "Legacy modules": [[27, "legacy-modules"]], "Linear Density \u2014 MDAnalysis.analysis.lineardensity": [[28, "linear-density-mdanalysis-analysis-lineardensity"]], "Mean Squared Displacement \u2014 MDAnalysis.analysis.msd": [[29, "mean-squared-displacement-mdanalysis-analysis-msd"]], "Computing an MSD": [[29, "computing-an-msd"]], "Computing Self-Diffusivity": [[29, "computing-self-diffusivity"]], "Combining Multiple Replicates": [[29, "combining-multiple-replicates"]], "Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids": [[30, "updated-nucleic-acid-analysis-mdanalysis-analysis-nucleicacids"]], "Distances": [[30, "distances"], [31, "distances"]], "Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo": [[31, "nucleic-acid-analysis-mdanalysis-analysis-nuclinfo"]], "Phases": [[31, "phases"]], "Dihedral angles": [[31, "dihedral-angles"]], "Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca": [[32, "principal-component-analysis-pca-mdanalysis-analysis-pca"]], "PCA Tutorial": [[32, "pca-tutorial"]], "Polymer analysis \u2014 MDAnalysis.analysis.polymer": [[33, "polymer-analysis-mdanalysis-analysis-polymer"]], "Calculating path similarity \u2014 MDAnalysis.analysis.psa": [[34, "calculating-path-similarity-mdanalysis-analysis-psa"]], "Helper functions and variables": [[34, "helper-functions-and-variables"]], "Classes, methods, and functions": [[34, "classes-methods-and-functions"]], "Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf": [[35, "radial-distribution-functions-mdanalysis-analysis-rdf"]], "Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms": [[36, "calculating-root-mean-square-quantities-mdanalysis-analysis-rms"]], "Calculating RMSD for multiple domains": [[36, "calculating-rmsd-for-multiple-domains"]], "Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics": [[37, "water-dynamics-analysis-mdanalysis-analysis-waterdynamics"]], "Example use of the analysis classes": [[37, "example-use-of-the-analysis-classes"]], "HydrogenBondLifetimes": [[37, "hydrogenbondlifetimes"]], "WaterOrientationalRelaxation": [[37, "waterorientationalrelaxation"], [37, "id76"]], "AngularDistribution": [[37, "angulardistribution"], [37, "id77"]], "MeanSquareDisplacement": [[37, "meansquaredisplacement"], [37, "id78"]], "SurvivalProbability": [[37, "survivalprobability"], [37, "id79"]], "Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis": [[38, "water-bridge-analysis-mdanalysis-analysis-hydrogenbonds-waterbridgeanalysis"]], "Theory": [[38, "theory"]], "Output as Network": [[38, "output-as-network"]], "Output as Timeseries": [[38, "output-as-timeseries"]], "Detection of water bridges": [[38, "detection-of-water-bridges"]], "Default heavy atom names for CHARMM27 force field.": [[38, "id69"]], "Heavy atom types for GLYCAM06 force field.": [[38, "id70"]], "How to perform WaterBridgeAnalysis": [[38, "how-to-perform-waterbridgeanalysis"]], "Use count_by_type": [[38, "use-count-by-type"]], "Use count_by_time": [[38, "use-count-by-time"]], "Analysis modules": [[39, "analysis-modules"]], "Building blocks for Analysis": [[39, "building-blocks-for-analysis"]], "Distances and contacts": [[39, "distances-and-contacts"]], "Hydrogen bonding": [[39, "hydrogen-bonding"]], "Membranes and membrane proteins": [[39, "membranes-and-membrane-proteins"]], "Nucleic acids": [[39, "nucleic-acids"]], "Polymers": [[39, "polymers"]], "Structure": [[39, "structure"]], "Macromolecules": [[39, "macromolecules"]], "Liquids": [[39, "liquids"]], "Volumetric analysis": [[39, "volumetric-analysis"]], "Dimensionality Reduction": [[39, "dimensionality-reduction"]], "Legacy analysis modules": [[39, "legacy-analysis-modules"]], "Data": [[39, "data"], [161, "data"], [162, "data"]], "EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR": [[40, "edr-auxiliary-reader-mdanalysis-auxiliary-edr"]], "Background": [[40, "background"]], "Standalone Usage of the EDRReader": [[40, "standalone-usage-of-the-edrreader"]], "Adding EDR data to trajectories": [[40, "adding-edr-data-to-trajectories"]], "XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG": [[41, "xvg-auxiliary-reader-mdanalysis-auxiliary-xvg"]], "XVG Readers": [[41, "xvg-readers"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary.base": [[42, "auxiliary-readers-mdanalysis-auxiliary-base"]], "Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core": [[43, "common-functions-for-auxiliary-reading-mdanalysis-auxiliary-core"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary": [[44, "auxiliary-readers-mdanalysis-auxiliary"]], "Supported formats": [[44, "supported-formats"]], "Auxiliary API": [[44, "auxiliary-api"]], "Auxiliaries and trajectories": [[44, "auxiliaries-and-trajectories"]], "Adding an auxiliary to a trajectory": [[44, "adding-an-auxiliary-to-a-trajectory"]], "Iterating by an auxiliary": [[44, "iterating-by-an-auxiliary"]], "Accessing auxiliary attributes": [[44, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[44, "recreating-auxiliaries"]], "AuxStep class": [[44, "auxstep-class"]], "Attributes": [[44, "attributes"], [44, "id2"], [80, "attributes"], [80, "id19"], [80, "id21"]], "Methods": [[44, "methods"], [44, "id3"], [80, "methods"], [80, "id18"], [80, "id20"], [80, "id22"]], "AuxReader class": [[44, "auxreader-class"]], "Registry": [[44, "registry"], [80, "registry"]], "Replicating auxiliaries": [[44, "replicating-auxiliaries"]], "Auxiliary modules": [[45, "auxiliary-modules"]], "Converter modules": [[46, "converter-modules"]], "OpenMM topology parser MDAnalysis.converters.OpenMMParser": [[47, "openmm-topology-parser-mdanalysis-converters-openmmparser"]], "OpenMM structure I/O \u2014 MDAnalysis.converters.OpenMM": [[47, "openmm-structure-i-o-mdanalysis-converters-openmm"]], "ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser": [[48, "parmed-topology-parser-mdanalysis-converters-parmedparser"]], "ParmEd structure I/O \u2014 MDAnalysis.converters.ParmEd": [[48, "parmed-structure-i-o-mdanalysis-converters-parmed"]], "RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser": [[49, "rdkit-topology-parser-mdanalysis-converters-rdkitparser"]], "RDKit molecule I/O \u2014 MDAnalysis.converters.RDKit": [[49, "rdkit-molecule-i-o-mdanalysis-converters-rdkit"]], "Base classes \u2014 MDAnalysis.converters.base": [[50, "base-classes-mdanalysis-converters-base"]], "CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD": [[51, "crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd"]], "DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD": [[52, "dcd-trajectory-i-o-mdanalysis-coordinates-dcd"]], "DL_Poly format reader MDAnalysis.coordinates.DLPoly": [[53, "dl-poly-format-reader-mdanalysis-coordinates-dlpoly"]], "DESRES file format \u2014 MDAnalysis.coordinates.DMS": [[54, "desres-file-format-mdanalysis-coordinates-dms"]], "FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS": [[55, "fhi-aims-file-format-mdanalysis-coordinates-fhiaims"]], "Developer notes: FHIAIMSWriter format strings": [[55, "developer-notes-fhiaimswriter-format-strings"]], "GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS": [[56, "gamess-trajectory-reader-mdanalysis-coordinates-gms"]], "GRO file format \u2014 MDAnalysis.coordinates.GRO": [[57, "gro-file-format-mdanalysis-coordinates-gro"]], "Writing GRO files": [[57, "writing-gro-files"]], "Developer notes: GROWriter format strings": [[57, "developer-notes-growriter-format-strings"]], "GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD": [[58, "gsd-trajectory-reader-mdanalysis-coordinates-gsd"]], "H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD": [[59, "h5md-trajectories-mdanalysis-coordinates-h5md"]], "Units": [[59, "units"]], "Example: Loading an H5MD simulation": [[59, "example-loading-an-h5md-simulation"]], "Example: Writing an H5MD file": [[59, "example-writing-an-h5md-file"]], "Example: Opening an H5MD file in parallel": [[59, "example-opening-an-h5md-file-in-parallel"]], "Building parallel h5py and HDF5 on Linux": [[59, "building-parallel-h5py-and-hdf5-on-linux"]], "INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD": [[60, "inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd"]], "LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS": [[61, "lammps-dcd-trajectory-and-data-i-o-mdanalysis-coordinates-lammps"]], "Data file formats": [[61, "data-file-formats"]], "Dump files": [[61, "dump-files"]], "Example: Loading a LAMMPS simulation": [[61, "example-loading-a-lammps-simulation"]], "MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF": [[62, "mmtf-trajectory-reader-mdanalysis-coordinates-mmtf"]], "MOL2 file format \u2014 MDAnalysis.coordinates.MOL2": [[63, "mol2-file-format-mdanalysis-coordinates-mol2"], [135, "mol2-file-format-mdanalysis-coordinates-mol2"]], "Example for working with mol2 files": [[63, "example-for-working-with-mol2-files"]], "MOL2 format notes": [[63, "mol2-format-notes"]], "NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN": [[64, "namdbin-files-format-mdanalysis-coordinates-namdbin"]], "PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB": [[65, "pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb"]], "Capabilities": [[65, "capabilities"]], "Examples for working with PDB files": [[65, "examples-for-working-with-pdb-files"]], "PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT": [[66, "pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt"]], "PQR file format \u2014 MDAnalysis.coordinates.PQR": [[67, "pqr-file-format-mdanalysis-coordinates-pqr"]], "TNG trajectory files \u2014 MDAnalysis.coordinates.TNG": [[68, "tng-trajectory-files-mdanalysis-coordinates-tng"]], "Current Limitations": [[68, "current-limitations"]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[69, "amber-trajectories-mdanalysis-coordinates-trj"]], "Binary NetCDF trajectories": [[69, "binary-netcdf-trajectories"]], "ASCII TRAJ trajectories": [[69, "ascii-traj-trajectories"]], "TRR trajectory files \u2014 MDAnalysis.coordinates.TRR": [[70, "trr-trajectory-files-mdanalysis-coordinates-trr"]], "TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ": [[71, "trz-trajectory-i-o-mdanalysis-coordinates-trz"]], "TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ": [[72, "txyz-file-format-mdanalysis-coordinates-txyz"]], "XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR": [[73, "xdr-based-trajectory-files-mdanalysis-coordinates-xdr"]], "XTC trajectory files \u2014 MDAnalysis.coordinates.XTC": [[74, "xtc-trajectory-files-mdanalysis-coordinates-xtc"]], "XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ": [[75, "xyz-trajectory-reader-mdanalysis-coordinates-xyz"]], "XYZ File format": [[75, "xyz-file-format"]], "Base classes \u2014 MDAnalysis.coordinates.base": [[76, "base-classes-mdanalysis-coordinates-base"]], "FrameIterators": [[76, "frameiterators"]], "Readers": [[76, "readers"], [80, "readers"]], "Writers": [[76, "writers"], [80, "writers"]], "Converters": [[76, "converters"]], "Helper classes": [[76, "helper-classes"]], "ChainReader \u2014 MDAnalysis.coordinates.chain": [[77, "chainreader-mdanalysis-coordinates-chain"]], "Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles": [[78, "reading-trajectories-with-chemfiles-mdanalysis-coordinates-chemfiles"]], "Using the CHEMFILES reader": [[78, "using-the-chemfiles-reader"]], "Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core": [[79, "common-functions-for-coordinate-reading-mdanalysis-coordinates-core"]], "Trajectory Readers and Writers \u2014 MDAnalysis.coordinates": [[80, "trajectory-readers-and-writers-mdanalysis-coordinates"]], "Timesteps": [[80, "timesteps"]], "Supported coordinate formats": [[80, "supported-coordinate-formats"]], "Table of supported coordinate formats": [[80, "id23"]], "Trajectory API": [[80, "trajectory-api"]], "Timestep class": [[80, "timestep-class"]], "Private attributes": [[80, "private-attributes"]], "Trajectory Reader class": [[80, "trajectory-reader-class"]], "Trajectory Writer class": [[80, "trajectory-writer-class"]], "Single Frame Writer class": [[80, "single-frame-writer-class"]], "Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory": [[81, "reading-trajectories-from-memory-mdanalysis-coordinates-memory"]], "How to use the MemoryReader": [[81, "how-to-use-the-memoryreader"]], "In-memory representation of arbitrary trajectories": [[81, "in-memory-representation-of-arbitrary-trajectories"]], "Switching a trajectory to an in-memory representation": [[81, "switching-a-trajectory-to-an-in-memory-representation"]], "Constructing a Reader from a numpy array": [[81, "constructing-a-reader-from-a-numpy-array"]], "Creating an in-memory trajectory of a sub-system": [[81, "creating-an-in-memory-trajectory-of-a-sub-system"]], "Null output \u2014 MDAnalysis.coordinates.null": [[82, "null-output-mdanalysis-coordinates-null"]], "Serialization of Coordinate Readers": [[83, "serialization-of-coordinate-readers"]], "How to serialize a new reader": [[83, "how-to-serialize-a-new-reader"]], "File Access": [[83, "file-access"]], "To seek or not to seek": [[83, "to-seek-or-not-to-seek"]], "Miscellaneous": [[83, "miscellaneous"]], "Tests": [[83, "tests"], [166, "tests"]], "_SingleFrameReader Test": [[83, "singleframereader-test"]], "BaseReaderTest and MultiframeReaderTest": [[83, "basereadertest-and-multiframereadertest"]], "File handler Test": [[83, "file-handler-test"]], "Currently implemented picklable IO Formats": [[83, "currently-implemented-picklable-io-formats"]], "Timestep Class \u2014 MDAnalysis.coordinates.timestep": [[84, "timestep-class-mdanalysis-coordinates-timestep"]], "Timestep": [[84, "timestep"]], "Coordinates modules": [[85, "coordinates-modules"]], "AtomGroup accessors \u2014 MDAnalysis.core.accessors": [[86, "atomgroup-accessors-mdanalysis-core-accessors"]], "Core objects: Containers \u2014 MDAnalysis.core.groups": [[87, "core-objects-containers-mdanalysis-core-groups"]], "Collections": [[87, "collections"]], "Chemical units": [[87, "chemical-units"]], "Levels": [[87, "levels"]], "Core functions of MDAnalysis": [[88, "core-functions-of-mdanalysis"]], "Atom selection Hierarchy \u2014 MDAnalysis.core.selection": [[89, "atom-selection-hierarchy-mdanalysis-core-selection"]], "Core Topology object \u2014 MDAnalysis.core.topology": [[90, "core-topology-object-mdanalysis-core-topology"]], "Topology attribute objects \u2014 MDAnalysis.core.topologyattrs": [[91, "topology-attribute-objects-mdanalysis-core-topologyattrs"]], "Core Topology Objects \u2014 MDAnalysis.core.topologyobjects": [[92, "core-topology-objects-mdanalysis-core-topologyobjects"]], "Core object: Universe \u2014 MDAnalysis.core.universe": [[93, "core-object-universe-mdanalysis-core-universe"]], "Core modules": [[94, "core-modules"]], "Important objects for users": [[94, "important-objects-for-users"]], "Topology system": [[94, "topology-system"]], "Selection system": [[94, "selection-system"]], "Custom exceptions and warnings \u2014 MDAnalysis.exceptions": [[95, "custom-exceptions-and-warnings-mdanalysis-exceptions"]], "Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch": [[96, "neighbor-search-wrapper-for-mdanalysis-mdanalysis-lib-neighborsearch"]], "Distance calculation library \u2014 MDAnalysis.lib.c_distances": [[97, "distance-calculation-library-mdanalysis-lib-c-distances"]], "Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp": [[98, "parallel-distance-calculation-library-mdanalysis-lib-c-distances-openmp"]], "Correlations utilities \u2014 MDAnalysis.lib.correlations": [[99, "correlations-utilities-mdanalysis-lib-correlations"]], "Autocorrelation Function": [[99, "autocorrelation-function"]], "Intermittency Function": [[99, "intermittency-function"]], "Fast distance array computation \u2014 MDAnalysis.lib.distances": [[100, "fast-distance-array-computation-mdanalysis-lib-distances"]], "Selection of acceleration (\u201cbackend\u201d)": [[100, "selection-of-acceleration-backend"]], "Available backends for accelerated distance functions.": [[100, "id1"]], "Use of the distopia library": [[100, "use-of-the-distopia-library"]], "Functions available using the distopia backend.": [[100, "id2"]], "Low-level modules for MDAnalysis.lib.distances": [[100, "low-level-modules-for-mdanalysis-lib-distances"]], "Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd": [[101, "low-level-dcd-trajectory-reading-mdanalysis-lib-formats-libdcd"]], "Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr": [[102, "low-level-gromacs-xdr-trajectory-reading-mdanalysis-lib-formats-libmdaxdr"]], "Setting up logging \u2014 MDAnalysis.lib.log": [[103, "setting-up-logging-mdanalysis-lib-log"]], "Convenience functions": [[103, "convenience-functions"]], "Other functions and classes for logging purposes": [[103, "other-functions-and-classes-for-logging-purposes"]], "Mathematical helper functions \u2014 MDAnalysis.lib.mdamath": [[104, "mathematical-helper-functions-mdanalysis-lib-mdamath"]], "Linear algebra": [[104, "linear-algebra"]], "Connectivity": [[104, "connectivity"]], "Neighbor search library \u2014 MDAnalysis.lib.nsgrid": [[105, "neighbor-search-library-mdanalysis-lib-nsgrid"]], "About the code": [[105, "about-the-code"]], "About the algorithm": [[105, "about-the-algorithm"]], "Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io": [[106, "picklable-read-only-i-o-classes-mdanalysis-lib-picklable-file-io"]], "PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree": [[107, "periodickdtree-mdanalysis-lib-pkdtree"]], "Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot": [[108, "fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot"]], "Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations": [[109, "homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations"]], "Requirements": [[109, "requirements"]], "Helper functions \u2014 MDAnalysis.lib.util": [[110, "helper-functions-mdanalysis-lib-util"]], "Files and directories": [[110, "files-and-directories"]], "Streams": [[110, "streams"]], "Containers and lists": [[110, "containers-and-lists"]], "Arrays": [[110, "arrays"]], "File parsing": [[110, "file-parsing"]], "Data manipulation and handling": [[110, "data-manipulation-and-handling"]], "Strings": [[110, "strings"]], "Class decorators": [[110, "class-decorators"]], "Function decorators": [[110, "function-decorators"]], "Code management": [[110, "code-management"]], "Data format checks": [[110, "data-format-checks"]], "Library functions \u2014 MDAnalysis.lib": [[111, "module-MDAnalysis.lib"]], "Overview": [[111, "overview"]], "List of modules": [[111, "list-of-modules"]], "Low level file formats": [[111, "low-level-file-formats"]], "Libmdanalysis": [[111, "libmdanalysis"]], "Overview over MDAnalysis": [[112, "overview-over-mdanalysis"]], "Using MDAnalysis in python": [[112, "using-mdanalysis-in-python"]], "Examples": [[112, "examples"]], "Included trajectories": [[112, "included-trajectories"]], "Code snippets": [[112, "code-snippets"]], "Citations for the whole MDAnalysis library": [[113, "citations-for-the-whole-mdanalysis-library"]], "Citations for included algorithms and modules": [[113, "citations-for-included-algorithms-and-modules"]], "Citations using Duecredit": [[113, "citations-using-duecredit"]], "Selection commands": [[114, "selection-commands"]], "Selection Keywords": [[114, "selection-keywords"]], "Simple selections": [[114, "simple-selections"]], "Pattern matching": [[114, "pattern-matching"]], "Boolean": [[114, "boolean"]], "Geometric": [[114, "geometric"]], "Similarity and connectivity": [[114, "similarity-and-connectivity"]], "Index": [[114, "index"]], "Preexisting selections and modifiers": [[114, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[114, "dynamic-selections"]], "Ordered selections": [[114, "ordered-selections"]], "Base classes for the selection writers": [[115, "base-classes-for-the-selection-writers"]], "CHARMM selections": [[116, "charmm-selections"]], "Gromacs selections": [[117, "gromacs-selections"]], "Jmol selections": [[118, "jmol-selections"]], "PyMOL selections": [[119, "pymol-selections"]], "VMD selections": [[120, "vmd-selections"]], "Selection exporters": [[121, "selection-exporters"]], "Table of supported exporters and recognized file name extensions.": [[121, "id2"]], "How to write selections": [[121, "how-to-write-selections"]], "Single AtomGroup": [[121, "single-atomgroup"]], "Multiple selections": [[121, "multiple-selections"]], "Selection writers": [[121, "selection-writers"]], "The topology system": [[122, "the-topology-system"]], "CRD topology parser": [[123, "crd-topology-parser"]], "Todo": [[123, "id1"], [141, "id1"]], "DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser": [[124, "dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser"]], "DESRES Molecular Structure file format topology parser": [[125, "desres-molecular-structure-file-format-topology-parser"]], "Extended PDB topology parser": [[126, "extended-pdb-topology-parser"]], "FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser": [[127, "fhi-aims-topology-parser-mdanalysis-topolgy-fhiaimsparser"]], "GAMESS Topology Parser": [[128, "gamess-topology-parser"]], "GRO topology parser": [[129, "gro-topology-parser"]], "GSD topology parser": [[130, "gsd-topology-parser"]], "HOOMD XML topology parser": [[131, "hoomd-xml-topology-parser"]], "ITP topology parser": [[132, "itp-topology-parser"]], "Preprocessor variables": [[132, "preprocessor-variables"]], "LAMMPSParser": [[133, "lammpsparser"]], "Atom styles": [[133, "atom-styles"]], "MMTF Topology Parser": [[134, "mmtf-topology-parser"]], "Minimal topology parser": [[136, "minimal-topology-parser"]], "PDB Topology Parser": [[137, "pdb-topology-parser"]], "PDBQT topology parser": [[138, "pdbqt-topology-parser"]], "PQR topology parser": [[139, "pqr-topology-parser"]], "PSF topology parser": [[140, "psf-topology-parser"]], "AMBER PRMTOP topology parser": [[141, "amber-prmtop-topology-parser"]], "Gromacs portable run input TPR format parser": [[142, "gromacs-portable-run-input-tpr-format-parser"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[142, "id4"]], "Development notes": [[142, "development-notes"]], "TXYZ topology parser": [[143, "txyz-topology-parser"]], "XYZ Topology Parser": [[144, "xyz-topology-parser"]], "Base topology reader classes \u2014 MDAnalysis.topology.base": [[145, "base-topology-reader-classes-mdanalysis-topology-base"]], "Common functions for topology building \u2014 MDAnalysis.topology.core": [[146, "common-functions-for-topology-building-mdanalysis-topology-core"]], "Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers": [[147, "guessing-unknown-topology-information-mdanalysis-topology-guessers"]], "Example uses of guessers": [[147, "example-uses-of-guessers"]], "Guessing elements from atom names": [[147, "guessing-elements-from-atom-names"]], "Topology readers \u2014 MDAnalysis.topology": [[148, "topology-readers-mdanalysis-topology"]], "Table of Supported Topology Formats": [[148, "id19"]], "Developer Notes": [[148, "developer-notes"]], "atoms": [[148, "atoms"]], "bonds": [[148, "bonds"]], "bondorder": [[148, "bondorder"]], "angles": [[148, "angles"]], "dihedrals": [[148, "dihedrals"]], "impropers": [[148, "impropers"]], "MDAnalysis topology tables": [[149, "mdanalysis-topology-tables"]], "Utility functions for the TPR topology parser": [[150, "utility-functions-for-the-tpr-topology-parser"]], "TPR support": [[150, "tpr-support"]], "TPRParser settings": [[150, "tprparser-settings"]], "Class definitions for the TPRParser": [[150, "class-definitions-for-the-tprparser"]], "Utilities for the TPRParser": [[150, "utilities-for-the-tprparser"]], "Topology modules": [[151, "topology-modules"]], "Trajectory transformations (\u201con-the-fly\u201d transformations)": [[152, "module-MDAnalysis.transformations"]], "Workflows": [[152, "workflows"]], "Creating transformations": [[152, "creating-transformations"]], "Creating complex transformation classes": [[152, "creating-complex-transformation-classes"]], "Creating complex transformation closure functions": [[152, "creating-complex-transformation-closure-functions"]], "Transformations in MDAnalysis": [[152, "transformations-in-mdanalysis"]], "How to transformations": [[152, "how-to-transformations"]], "Building blocks for Transformation Classes": [[152, "building-blocks-for-transformation-classes"]], "Currently implemented transformations": [[152, "currently-implemented-transformations"]], "Transformations Base Class \u2014 MDAnalysis.transformations.base": [[153, "transformations-base-class-mdanalysis-transformations-base"]], "Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions": [[154, "set-box-dimensions-mdanalysis-transformations-boxdimensions"]], "Fitting transformations \u2014 MDAnalysis.transformations.fit": [[155, "fitting-transformations-mdanalysis-transformations-fit"]], "No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump": [[156, "no-jump-trajectory-unwrapping-mdanalysis-transformations-nojump"]], "Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging": [[157, "trajectory-coordinate-averaging-mdanalysis-transformations-positionaveraging"]], "Trajectory rotation \u2014 MDAnalysis.transformations.rotate": [[158, "trajectory-rotation-mdanalysis-transformations-rotate"]], "Trajectory translation \u2014 MDAnalysis.transformations.translate": [[159, "trajectory-translation-mdanalysis-transformations-translate"]], "Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap": [[160, "wrap-unwrap-transformations-mdanalysis-transformations-wrap"]], "Constants and unit conversion \u2014 MDAnalysis.units": [[161, "constants-and-unit-conversion-mdanalysis-units"]], "Base units in MDAnalysis as encoded in MDANALYSIS_BASE_UNITS": [[161, "id71"]], "Implementation notes": [[161, "implementation-notes"]], "Conversions": [[161, "conversions"]], "References and footnotes": [[161, "references-and-footnotes"]], "Version information for MDAnalysis - MDAnalysis.version": [[162, "version-information-for-mdanalysis-mdanalysis-version"]], "Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines": [[163, "streamplots-2d-mdanalysis-visualization-streamlines"]], "Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D": [[164, "streamplots-3d-mdanalysis-visualization-streamlines-3d"]], "Visualization modules": [[165, "visualization-modules"]], "Visualization of Lipid Flow": [[165, "visualization-of-lipid-flow"]], "MDAnalysis documentation": [[166, "mdanalysis-documentation"]], "Getting involved": [[166, "getting-involved"]], "User Guide": [[166, "user-guide"]], "Installing MDAnalysis": [[166, "installing-mdanalysis"]], "conda": [[166, "conda"]], "pip": [[166, "pip"]], "Source Code": [[166, "source-code"]], "Citation": [[166, "citation"]], "Indices and tables": [[166, "indices-and-tables"]]}, "indexentries": {"aligntraj (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AlignTraj"]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure"]], "mdanalysis.analysis.align": [[0, "module-MDAnalysis.analysis.align"]], "_fit_to() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align._fit_to"]], "alignto() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.alignto"]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select"]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename"]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename"]], "get_matching_atoms() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.get_matching_atoms"]], "mobile_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.mobile_atoms"]], "mobile_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.mobile_atoms"]], "module": [[0, "module-MDAnalysis.analysis.align"], [1, "module-MDAnalysis.analysis.atomicdistances"], [2, "module-MDAnalysis.analysis.base"], [3, "module-MDAnalysis.analysis.bat"], [4, "module-MDAnalysis.analysis.contacts"], [5, "module-MDAnalysis.analysis.data.filenames"], [6, "module-MDAnalysis.analysis.density"], [7, "module-MDAnalysis.analysis.dielectric"], [8, "module-MDAnalysis.analysis.diffusionmap"], [9, "module-MDAnalysis.analysis.dihedrals"], [10, "module-MDAnalysis.analysis.distances"], [12, "module-MDAnalysis.analysis.encore.bootstrap"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"], [13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"], [13, "module-MDAnalysis.analysis.encore.clustering.cluster"], [14, "module-MDAnalysis.analysis.encore.confdistmatrix"], [15, "module-MDAnalysis.analysis.encore.covariance"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"], [17, "module-MDAnalysis.analysis.encore.similarity"], [18, "module-MDAnalysis.analysis.encore.utils"], [19, "module-MDAnalysis.analysis.gnm"], [20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"], [21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"], [22, "module-MDAnalysis.analysis.helix_analysis"], [23, "module-MDAnalysis.analysis.hole2"], [23, "module-MDAnalysis.analysis.hole2.templates"], [23, "module-MDAnalysis.analysis.hole2.utils"], [24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"], [25, "module-MDAnalysis.analysis.leaflet"], [26, "module-MDAnalysis.analysis.legacy.x3dna"], [28, "module-MDAnalysis.analysis.lineardensity"], [29, "module-MDAnalysis.analysis.msd"], [30, "module-MDAnalysis.analysis.nucleicacids"], [31, "module-MDAnalysis.analysis.nuclinfo"], [32, "module-MDAnalysis.analysis.pca"], [33, "module-MDAnalysis.analysis.polymer"], [34, "module-MDAnalysis.analysis.psa"], [35, "module-MDAnalysis.analysis.rdf"], [36, "module-MDAnalysis.analysis.rms"], [37, "module-MDAnalysis.analysis.waterdynamics"], [38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"], [40, "module-MDAnalysis.auxiliary.EDR"], [41, "module-MDAnalysis.auxiliary.XVG"], [42, "module-MDAnalysis.auxiliary.base"], [43, "module-MDAnalysis.auxiliary.core"], [44, "module-MDAnalysis.auxiliary.__init__"], [46, "module-MDAnalysis.converters"], [47, "module-MDAnalysis.converters.OpenMM"], [47, "module-MDAnalysis.converters.OpenMMParser"], [48, "module-MDAnalysis.converters.ParmEd"], [48, "module-MDAnalysis.converters.ParmEdParser"], [49, "module-MDAnalysis.converters.RDKit"], [49, "module-MDAnalysis.converters.RDKitParser"], [50, "module-MDAnalysis.converters.base"], [51, "module-MDAnalysis.coordinates.CRD"], [52, "module-MDAnalysis.coordinates.DCD"], [53, "module-MDAnalysis.coordinates.DLPoly"], [54, "module-MDAnalysis.coordinates.DMS"], [55, "module-MDAnalysis.coordinates.FHIAIMS"], [56, "module-MDAnalysis.coordinates.GMS"], [57, "module-MDAnalysis.coordinates.GRO"], [58, "module-MDAnalysis.coordinates.GSD"], [59, "module-MDAnalysis.coordinates.H5MD"], [60, "module-MDAnalysis.coordinates.INPCRD"], [61, "module-MDAnalysis.coordinates.LAMMPS"], [62, "module-MDAnalysis.coordinates.MMTF"], [63, "module-MDAnalysis.coordinates.MOL2"], [64, "module-MDAnalysis.coordinates.NAMDBIN"], [65, "module-MDAnalysis.coordinates.PDB"], [66, "module-MDAnalysis.coordinates.PDBQT"], [67, "module-MDAnalysis.coordinates.PQR"], [68, "module-MDAnalysis.coordinates.TNG"], [69, "module-MDAnalysis.coordinates.TRJ"], [70, "module-MDAnalysis.coordinates.TRR"], [71, "module-MDAnalysis.coordinates.TRZ"], [72, "module-MDAnalysis.coordinates.TXYZ"], [73, "module-MDAnalysis.coordinates.XDR"], [74, "module-MDAnalysis.coordinates.XTC"], [75, "module-MDAnalysis.coordinates.XYZ"], [76, "module-MDAnalysis.coordinates.base"], [77, "module-MDAnalysis.coordinates.chain"], [78, "module-MDAnalysis.coordinates.chemfiles"], [79, "module-MDAnalysis.coordinates.core"], [80, "module-MDAnalysis.coordinates.__init__"], [81, "module-MDAnalysis.coordinates.memory"], [82, "module-MDAnalysis.coordinates.null"], [84, "module-MDAnalysis.coordinates.timestep"], [86, "module-MDAnalysis.core.accessors"], [87, "module-MDAnalysis.core.groups"], [88, "module-MDAnalysis.core.__init__"], [89, "module-MDAnalysis.core.selection"], [90, "module-MDAnalysis.core.topology"], [91, "module-MDAnalysis.core.topologyattrs"], [92, "module-MDAnalysis.core.topologyobjects"], [93, "module-MDAnalysis.core.universe"], [95, "module-MDAnalysis.exceptions"], [96, "module-MDAnalysis.lib.NeighborSearch"], [97, "module-MDAnalysis.lib.c_distances"], [98, "module-MDAnalysis.lib.c_distances_openmp"], [99, "module-MDAnalysis.lib.correlations"], [100, "module-MDAnalysis.lib.distances"], [101, "module-MDAnalysis.lib.formats.libdcd"], [102, "module-MDAnalysis.lib.formats.libmdaxdr"], [103, "module-MDAnalysis.lib.log"], [104, "module-MDAnalysis.lib.mdamath"], [105, "module-MDAnalysis.lib.nsgrid"], [106, "module-MDAnalysis.lib.picklable_file_io"], [107, "module-MDAnalysis.lib.pkdtree"], [108, "module-MDAnalysis.lib.qcprot"], [109, "module-MDAnalysis.lib.transformations"], [110, "module-MDAnalysis.lib.util"], [111, "module-MDAnalysis.lib"], [115, "module-MDAnalysis.selections.base"], [116, "module-MDAnalysis.selections.charmm"], [117, "module-MDAnalysis.selections.gromacs"], [118, "module-MDAnalysis.selections.jmol"], [119, "module-MDAnalysis.selections.pymol"], [120, "module-MDAnalysis.selections.vmd"], [123, "module-MDAnalysis.topology.CRDParser"], [124, "module-MDAnalysis.topology.DLPolyParser"], [125, "module-MDAnalysis.topology.DMSParser"], [126, "module-MDAnalysis.topology.ExtendedPDBParser"], [127, "module-MDAnalysis.topology.FHIAIMSParser"], [128, "module-MDAnalysis.topology.GMSParser"], [129, "module-MDAnalysis.topology.GROParser"], [130, "module-MDAnalysis.topology.GSDParser"], [131, "module-MDAnalysis.topology.HoomdXMLParser"], [132, "module-MDAnalysis.topology.ITPParser"], [133, "module-MDAnalysis.topology.LAMMPSParser"], [134, "module-MDAnalysis.topology.MMTFParser"], [135, "module-MDAnalysis.topology.MOL2Parser"], [136, "module-MDAnalysis.topology.MinimalParser"], [137, "module-MDAnalysis.topology.PDBParser"], [138, "module-MDAnalysis.topology.PDBQTParser"], [139, "module-MDAnalysis.topology.PQRParser"], [140, "module-MDAnalysis.topology.PSFParser"], [141, "module-MDAnalysis.topology.TOPParser"], [142, "module-MDAnalysis.topology.TPRParser"], [143, "module-MDAnalysis.topology.TXYZParser"], [144, "module-MDAnalysis.topology.XYZParser"], [145, "module-MDAnalysis.topology.base"], [146, "module-MDAnalysis.topology.core"], [147, "module-MDAnalysis.topology.guessers"], [148, "module-MDAnalysis.topology.__init__"], [149, "module-MDAnalysis.topology.tables"], [150, "module-MDAnalysis.topology.tpr"], [150, "module-MDAnalysis.topology.tpr.obj"], [150, "module-MDAnalysis.topology.tpr.setting"], [150, "module-MDAnalysis.topology.tpr.utils"], [152, "module-MDAnalysis.transformations"], [153, "module-MDAnalysis.transformations.base"], [154, "module-MDAnalysis.transformations.boxdimensions"], [155, "module-MDAnalysis.transformations.fit"], [156, "module-MDAnalysis.transformations.nojump"], [157, "module-MDAnalysis.transformations.positionaveraging"], [158, "module-MDAnalysis.transformations.rotate"], [159, "module-MDAnalysis.transformations.translate"], [160, "module-MDAnalysis.transformations.wrap"], [161, "module-MDAnalysis.units"], [162, "module-MDAnalysis.version"], [163, "module-MDAnalysis.visualization.streamlines"], [164, "module-MDAnalysis.visualization.streamlines_3D"]], "positions (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.positions"]], "positions (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.positions"]], "reference_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.reference_atoms"]], "reference_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.reference_atoms"]], "rmsd (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.rmsd"]], "rmsd (mdanalysis.analysis.align.aligntraj.results attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.results.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.rmsd"]], "rotation_matrix() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.rotation_matrix"]], "sequence_alignment() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.sequence_alignment"]], "universe (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.universe"]], "universe (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.universe"]], "atomicdistances (class in mdanalysis.analysis.atomicdistances)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances"]], "mdanalysis.analysis.atomicdistances": [[1, "module-MDAnalysis.analysis.atomicdistances"]], "n_atoms (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_atoms"]], "n_frames (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_frames"]], "results (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.results"]], "analysisbase (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisBase"]], "analysisfromfunction (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction"]], "mdanalysis.analysis.base": [[2, "module-MDAnalysis.analysis.base"]], "results (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.Results"]], "analysis_class() (in module mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.analysis_class"]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.frames"]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames"]], "frames (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.frames"]], "results (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.results"]], "run() (mdanalysis.analysis.base.analysisbase method)": [[2, "MDAnalysis.analysis.base.AnalysisBase.run"]], "times (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.times"]], "times (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.times"]], "times (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.times"]], "timeseries (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.timeseries"]], "timeseries (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.timeseries"]], "bat (class in mdanalysis.analysis.bat)": [[3, "MDAnalysis.analysis.bat.BAT"]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.Cartesian"]], "mdanalysis.analysis.bat": [[3, "module-MDAnalysis.analysis.bat"]], "atoms (mdanalysis.analysis.bat.bat property)": [[3, "MDAnalysis.analysis.bat.BAT.atoms"]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[3, "MDAnalysis.analysis.bat.BAT.results.bat"]], "load() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.load"]], "run() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.run"]], "save() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.save"]], "contacts (class in mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.Contacts"]], "mdanalysis.analysis.contacts": [[4, "module-MDAnalysis.analysis.contacts"]], "contact_matrix() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.contact_matrix"]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.hard_cut_q"]], "q1q2() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.q1q2"]], "radius_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.radius_cut_q"]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.soft_cut_q"]], "timeseries (mdanalysis.analysis.contacts.contacts attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.timeseries"]], "timeseries (mdanalysis.analysis.contacts.contacts.results attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.results.timeseries"]], "janin_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Janin_ref"]], "mdanalysis.analysis.data.filenames": [[5, "module-MDAnalysis.analysis.data.filenames"]], "rama_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Rama_ref"]], "density (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.Density"]], "densityanalysis (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.DensityAnalysis"]], "mdanalysis.analysis.density": [[6, "module-MDAnalysis.analysis.density"]], "_set_user_grid() (mdanalysis.analysis.density.densityanalysis static method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis._set_user_grid"]], "centers() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.centers"]], "check_compatible() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.check_compatible"]], "convert_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_density"]], "convert_length() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_length"]], "default_format (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.default_format"]], "delta (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.delta"]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.density"]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.results.density"]], "edges (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.edges"]], "export() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.export"]], "grid (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.grid"]], "interpolated (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolated"]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolation_spline_order"]], "load() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.load"]], "make_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.make_density"]], "origin (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.origin"]], "resample() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample"]], "resample_factor() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample_factor"]], "run() (mdanalysis.analysis.density.densityanalysis method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.run"]], "save() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.save"]], "units (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.units"]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant"]], "m (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M"]], "m2 (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M2"]], "mdanalysis.analysis.dielectric": [[7, "module-MDAnalysis.analysis.dielectric"]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps"]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean"]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct"]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap"]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix"]], "mdanalysis.analysis.diffusionmap": [[8, "module-MDAnalysis.analysis.diffusionmap"]], "atoms (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.atoms"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix"]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues"]], "run() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.run"]], "transform() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.transform"]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral"]], "janin (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Janin"]], "mdanalysis.analysis.dihedrals": [[9, "module-MDAnalysis.analysis.dihedrals"]], "ramachandran (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran"]], "angles (mdanalysis.analysis.dihedrals.dihedral attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.angles"]], "angles (mdanalysis.analysis.dihedrals.dihedral.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.results.angles"]], "angles (mdanalysis.analysis.dihedrals.janin attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.angles"]], "angles (mdanalysis.analysis.dihedrals.janin.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.results.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.results.angles"]], "plot() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.plot"]], "plot() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.plot"]], "run() (mdanalysis.analysis.dihedrals.dihedral method)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.run"]], "run() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.run"]], "run() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.run"]], "mdanalysis.analysis.distances": [[10, "module-MDAnalysis.analysis.distances"]], "between() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.between"]], "contact_matrix() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.contact_matrix"]], "dist() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.dist"]], "distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.distance_array"]], "self_distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.self_distance_array"]], "mdanalysis.analysis.encore.bootstrap": [[12, "module-MDAnalysis.analysis.encore.bootstrap"]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix"]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples"]], "get_ensemble_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples"]], "affinitypropagation (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagation"]], "affinitypropagation() (in module mdanalysis.analysis.encore.clustering.affinityprop)": [[13, "MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation"]], "affinitypropagationnative (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagationNative"]], "cluster (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster"]], "clustercollection (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection"]], "clusteringmethod (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.ClusteringMethod"]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN"]], "kmeans (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans"]], "mdanalysis.analysis.encore.clustering.clustercollection": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"]], "mdanalysis.analysis.encore.clustering.clusteringmethod": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"]], "mdanalysis.analysis.encore.clustering.affinityprop": [[13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"]], "mdanalysis.analysis.encore.clustering.cluster": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "accepts_distance_matrix (mdanalysis.analysis.encore.clustering.clusteringmethod.kmeans attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans.accepts_distance_matrix"]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid"]], "cluster() (in module mdanalysis.analysis.encore.clustering.cluster)": [[13, "MDAnalysis.analysis.encore.clustering.cluster.cluster"]], "clusters (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.clusters"]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements"]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info"]], "get_centroids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_centroids"]], "get_ids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_ids"]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id"]], "metadata (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.metadata"]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size"]], "mdanalysis.analysis.encore.confdistmatrix": [[14, "module-MDAnalysis.analysis.encore.confdistmatrix"]], "conformational_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.conformational_distance_matrix"]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix"]], "set_rmsd_matrix_elements() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.set_rmsd_matrix_elements"]], "mdanalysis.analysis.encore.covariance": [[15, "module-MDAnalysis.analysis.encore.covariance"]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.covariance_matrix"]], "ml_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.ml_covariance_estimator"]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator"]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"]], "principalcomponentanalysis (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.PrincipalComponentAnalysis"]], "stochasticproximityembedding() (in module mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed.StochasticProximityEmbedding"]], "stochasticproximityembeddingnative (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.StochasticProximityEmbeddingNative"]], "reduce_dimensionality() (in module mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality.reduce_dimensionality"]], "mdanalysis.analysis.encore.similarity": [[17, "module-MDAnalysis.analysis.encore.similarity"]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces"]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces_convergence"]], "clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.clustering_ensemble_similarity"]], "cumulative_clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity"]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs"]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity"]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence"]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence"]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres"]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres_convergence"]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs"]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity"]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.hes"]], "prepare_ensembles_for_convergence_increasing_window() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.prepare_ensembles_for_convergence_increasing_window"]], "write_output() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.write_output"]], "mdanalysis.analysis.encore.utils": [[18, "module-MDAnalysis.analysis.encore.utils"]], "parallelcalculation (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation"]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[18, "MDAnalysis.analysis.encore.cutils.PureRMSD"]], "triangularmatrix (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix"]], "args (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.args"]], "as_array() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.as_array"]], "function (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.function"]], "kwargs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.kwargs"]], "loadz() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.loadz"]], "merge_universes() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.merge_universes"]], "n_jobs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.n_jobs"]], "nruns (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.nruns"]], "run() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.run"]], "savez() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.savez"]], "trm_indices() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices"]], "trm_indices_diag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_diag"]], "trm_indices_nodiag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_nodiag"]], "worker() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.worker"]], "gnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis"]], "mdanalysis.analysis.gnm": [[19, "module-MDAnalysis.analysis.gnm"]], "closecontactgnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis"]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues"]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues"]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors"]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors"]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.generate_grid"]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff"]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff"]], "order_list() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.order_list"]], "times (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.times"]], "times (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.times"]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel"]], "mdanalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors"]], "run() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run"]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve"]], "mdanalysis.analysis.hbonds.hbond_autocorrel": [[21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"]], "mdanalysis.analysis.helix_analysis": [[22, "module-MDAnalysis.analysis.helix_analysis"]], "holeanalysis (class in mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis"]], "mdanalysis.analysis.hole2": [[23, "module-MDAnalysis.analysis.hole2"]], "mdanalysis.analysis.hole2.templates": [[23, "module-MDAnalysis.analysis.hole2.templates"]], "mdanalysis.analysis.hole2.utils": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "path": [[23, "index-0"], [23, "index-1"], [110, "index-0"]], "simple2_rad (in module mdanalysis.analysis.hole2.templates)": [[23, "MDAnalysis.analysis.hole2.templates.SIMPLE2_RAD"]], "bin_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.bin_radii"]], "check_and_fix_long_filename() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.check_and_fix_long_filename"]], "collect_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.collect_hole"]], "create_vmd_surface() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.create_vmd_surface"]], "create_vmd_surface() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.create_vmd_surface"]], "delete_temporary_files() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.delete_temporary_files"]], "environment variable": [[23, "index-0"], [23, "index-1"], [69, "index-0"], [69, "index-1"], [110, "index-0"], [110, "index-1"], [113, "index-0"], [153, "index-0"]], "gather() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.gather"]], "guess_cpoint() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.guess_cpoint"]], "histogram_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.histogram_radii"]], "hole() (in module mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.hole"]], "min_radius() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.min_radius"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.outfiles"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.outfiles"]], "over_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.over_order_parameters"]], "plot() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot"]], "plot3d() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D"]], "plot3d_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D_order_parameters"]], "plot_mean_profile() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_mean_profile"]], "plot_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_order_parameters"]], "profiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.profiles"]], "profiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.profiles"]], "run() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.run"]], "run_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.run_hole"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.sphpdbs"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.sphpdbs"]], "write_simplerad2() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.write_simplerad2"]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis"]], "mdanalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"]], "count_by_ids() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_ids"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type"]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors"]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors"]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds"]], "lifetime() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime"]], "leafletfinder (class in mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder"]], "mdanalysis.analysis.leaflet": [[25, "module-MDAnalysis.analysis.leaflet"]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.group"]], "groups() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups"]], "groups_iter() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"]], "optimize_cutoff() (in module mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.optimize_cutoff"]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes"]], "update() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.update"]], "write_selection() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.write_selection"]], "applicationerror": [[26, "MDAnalysis.analysis.legacy.x3dna.ApplicationError"], [95, "MDAnalysis.exceptions.ApplicationError"]], "mdanalysis.analysis.legacy.x3dna": [[26, "module-MDAnalysis.analysis.legacy.x3dna"]], "x3dna (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA"]], "x3dnatraj (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj"]], "collect() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.collect"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean"]], "mean_std() 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"dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim"]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges"]], "mass_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density"]], "mass_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density_stddev"]], "pos (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos"]], "pos_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos_std"]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume"]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD"]], "mdanalysis.analysis.msd": [[29, "module-MDAnalysis.analysis.msd"]], "ag (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.ag"]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac"]], "msds_by_particle (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.msds_by_particle"]], "n_frames (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_frames"]], "n_particles (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_particles"]], "run() (mdanalysis.analysis.msd.einsteinmsd method)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.run"]], "timeseries (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.timeseries"]], "mdanalysis.analysis.nucleicacids": [[30, "module-MDAnalysis.analysis.nucleicacids"]], "nucpairdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist"]], "watsoncrickdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist"]], "pair_distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.pair_distances"]], "pair_distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.pair_distances"]], "run() (mdanalysis.analysis.nucleicacids.nucpairdist method)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.run"]], "run() (mdanalysis.analysis.nucleicacids.watsoncrickdist method)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.run"]], "times (mdanalysis.analysis.nucleicacids.nucpairdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.times"]], "times (mdanalysis.analysis.nucleicacids.watsoncrickdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.times"]], "mdanalysis.analysis.nuclinfo": [[31, "module-MDAnalysis.analysis.nuclinfo"]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.hydroxyl"]], "major_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.major_pair"]], "minor_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.minor_pair"]], "phase_as() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_as"]], "phase_cp() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_cp"]], "pseudo_dihe_baseflip() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip"]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors"]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_alpha"]], "tors_beta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_beta"]], "tors_chi() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_chi"]], "tors_delta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_delta"]], "tors_eps() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_eps"]], "tors_gamma() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_gamma"]], "tors_zeta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_zeta"]], "wc_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.wc_pair"]], "mdanalysis.analysis.pca": [[32, "module-MDAnalysis.analysis.pca"]], "pca (class in mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.PCA"]], "cosine_content() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cosine_content"]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.cumulated_variance"]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance"]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.cumulative_overlap"]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cumulative_overlap"]], "p_components (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.p_components"]], "p_components (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.p_components"]], "project_single_frame() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.project_single_frame"]], "rmsip() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.rmsip"]], "rmsip() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.rmsip"]], "run() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.run"]], "transform() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.transform"]], "variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.variance"]], "variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.variance"]], "mdanalysis.analysis.polymer": [[33, "module-MDAnalysis.analysis.polymer"]], "persistencelength (class in mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength"]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation"]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.fit"]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit"]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.fit_exponential_decay"]], "lb (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lb"]], "lb (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lb"]], "lp (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lp"]], "lp (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lp"]], "plot() (mdanalysis.analysis.polymer.persistencelength method)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.plot"]], "sort_backbone() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.sort_backbone"]], "x (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.x"]], "d (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.D"]], "mdanalysis.analysis.psa": [[34, "module-MDAnalysis.analysis.psa"]], "psapair (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAPair"]], "psanalysis (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAnalysis"]], "path (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.Path"]], "cluster() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.cluster"]], "discrete_frechet() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.discrete_frechet"]], "dist_mat_to_vec() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.dist_mat_to_vec"]], "fit_to_reference() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.fit_to_reference"]], "generate_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.generate_paths"]], "get_coord_axes() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_coord_axes"]], "get_msd_matrix() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_msd_matrix"]], "get_num_atoms() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_atoms"]], "get_num_atoms() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.get_num_atoms"]], "get_num_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_paths"]], "get_pairwise_distances() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_pairwise_distances"]], "get_path_metric_func() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_path_metric_func"]], "get_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_paths"]], "hausdorff() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff"]], "hausdorff_avg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_avg"]], "hausdorff_neighbors() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_neighbors"]], "hausdorff_pair (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.hausdorff_pair"]], "hausdorff_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.hausdorff_pairs"]], "hausdorff_wavg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_wavg"]], "load() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.load"]], "matrix_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.matrix_id"]], "nearest_neighbors (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.nearest_neighbors"]], "nearest_neighbors (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.nearest_neighbors"]], "npaths (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.npaths"]], "pair_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.pair_id"]], "path (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path"]], "path_select (mdanalysis.analysis.psa.psanalysis attribute)": 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(mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins"]], "cdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.cdf"]], "cdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.cdf"]], "count (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.count"]], "count (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.count"]], "count (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.count"]], "count (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.count"]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.edges"]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, 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"MDAnalysis.lib.picklable_file_io.FileIOPicklable"]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.GzipPicklable"]], "mdanalysis.lib.picklable_file_io": [[106, "module-MDAnalysis.lib.picklable_file_io"]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.TextIOPicklable"]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open"]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open"]], "pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.pickle_open"]], "mdanalysis.lib.pkdtree": [[107, "module-MDAnalysis.lib.pkdtree"]], "periodickdtree (class in mdanalysis.lib.pkdtree)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree"]], "get_indices() (mdanalysis.lib.pkdtree.periodickdtree method)": 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"MDAnalysis.lib.transformations.Arcball.drag"]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.euler_from_quaternion"]], "getconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.getconstrain"]], "matrix() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.matrix"]], "next() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.next"]], "place() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.place"]], "projection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.projection_from_matrix"]], "quaternion_imag() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_imag"]], "quaternion_real() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_real"]], "reflection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.reflection_from_matrix"]], "rotation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotation_from_matrix"]], "rotaxis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotaxis"]], "scale_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.scale_from_matrix"]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setaxes"]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setconstrain"]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.shear_from_matrix"]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.translation_from_matrix"]], "$home": [[110, "index-1"]], "fortranreader (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRANReader"]], "fortran_format_regex (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRAN_format_regex"]], "mdanalysis.lib.util": [[110, "module-MDAnalysis.lib.util"]], "namedstream (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.NamedStream"]], "namespace (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.Namespace"]], "_deprecate (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util._Deprecate"]], "anyopen() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.anyopen"]], "asiterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.asiterable"]], "blocks_of() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.blocks_of"]], "cached() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.cached"]], "check_atomgroup_not_empty() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_atomgroup_not_empty"]], "check_box() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_box"]], "check_compressed_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_compressed_format"]], "check_coords() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_coords"]], "close() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.close"]], "closed (mdanalysis.lib.util.namedstream property)": [[110, "MDAnalysis.lib.util.NamedStream.closed"]], "conv_float() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.conv_float"]], "convert_aa_code() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.convert_aa_code"]], "dedent_docstring() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.dedent_docstring"]], "deprecate() (in module 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"group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.group_same_or_consecutive_integers"]], "guess_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.guess_format"]], "hasmethod() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.hasmethod"]], "isstream() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.isstream"]], "iterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.iterable"]], "ltruncate_int() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.ltruncate_int"]], "number_of_matches() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.number_of_matches"]], "openany() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.openany"]], "parse_fortran_format() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format"]], "parse_residue() (in module mdanalysis.lib.util)": 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(mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.tell"]], "truncate() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.truncate"]], "unique_int_1d() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.unique_int_1d"]], "unique_rows() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.unique_rows"]], "warn_if_not_unique() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.warn_if_not_unique"]], "which() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.which"]], "writable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.writable"]], "mdanalysis.lib": [[111, "module-MDAnalysis.lib"]], "duecredit_enable": [[113, "index-0"]], "mdanalysis.selections.base": [[115, "module-MDAnalysis.selections.base"]], "selectionwriterbase (class in mdanalysis.selections.base)": [[115, "MDAnalysis.selections.base.SelectionWriterBase"]], "__init__() 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"selectionwriter (class in mdanalysis.selections.charmm)": [[116, "MDAnalysis.selections.charmm.SelectionWriter"]], "close() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.close"]], "comment() (mdanalysis.selections.charmm.selectionwriter method)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.comment"]], "commentfmt (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.commentfmt"]], "continuation (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.continuation"]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.ext"]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[116, "MDAnalysis.selections.charmm.SelectionWriter.format"]], "write() (mdanalysis.selections.charmm.selectionwriter method)": [[116, 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"convert_forces_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_forces_to_native"]], "convert_pos_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_pos_from_native"]], "convert_pos_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_pos_to_native"]], "convert_time_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_time_from_native"]], "convert_time_to_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.crdparser.crdparser method)": [[123, "MDAnalysis.topology.CRDParser.CRDParser.convert_velocities_from_native"]], "convert_velocities_to_native() 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"MDAnalysis.topology.guessers.guess_dihedrals"]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_gasteiger_charges"]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_improper_dihedrals"]], "guess_masses() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_masses"]], "guess_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_types"]], "validate_atom_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.validate_atom_types"]], "mdanalysis.topology.__init__": [[148, "module-MDAnalysis.topology.__init__"]], "mdanalysis.topology.tables": [[149, "module-MDAnalysis.topology.tables"]], "table_atomelements (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_ATOMELEMENTS"]], "table_masses (in module 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mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGLES"]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRES"]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRESZ"]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL"]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM"]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM_LR"]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BONDS"]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CBTDIHS"]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CMAP"]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COM_PULL"]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONNBONDS"]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTR"]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTRNC"]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL14"]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_LR"]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP"]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_SR"]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES"]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS"]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS"]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING"]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DHDL_CON"]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRES"]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL"]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISPCORR"]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRES"]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL"]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DKDL"]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DPD"]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL"]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED"]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL"]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT"]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE"]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW"]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ECONSERVED"]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EKIN"]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EPOT"]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EQM"]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ETOT"]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FBPOSRES"]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FENEBONDS"]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FOURDIHS"]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96ANGLES"]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96BONDS"]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB12"]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB13"]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB14"]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GBPOL"]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_HARMONIC"]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_IDIHS"]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES"]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ"]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ14"]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC14_Q"]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB"]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_LR"]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP"]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_MORSE"]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION"]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NRE"]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRES"]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV"]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDIHS"]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDISPCORR"]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PIDIHS"]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POLARIZATION"]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POSRES"]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PRES"]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES"]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RBDIHS"]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES"]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS"]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS"]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RF_EXCL"]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_SETTLE"]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABANGLES"]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDS"]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC"]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABDIHS"]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TEMP"]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_THOLE_POL"]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY"]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE1"]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2"]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2FD"]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3"]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD"]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FD"]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT"]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FD"]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN"]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITEN"]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED"]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_WATER_POL"]], "ilist (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Ilist"]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.InteractionKind"]], "mdanalysis.topology.tpr": [[150, "module-MDAnalysis.topology.tpr"]], "mdanalysis.topology.tpr.obj": [[150, "module-MDAnalysis.topology.tpr.obj"]], "mdanalysis.topology.tpr.setting": [[150, "module-MDAnalysis.topology.tpr.setting"]], "mdanalysis.topology.tpr.utils": [[150, "module-MDAnalysis.topology.tpr.utils"]], "molblock (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Molblock"]], "moleculekind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind"]], "mtop (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Mtop"]], "params (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Params"]], "supported_versions (in module mdanalysis.topology.tpr)": [[150, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS"]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS"]], "tpxunpacker (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker"]], "tpxunpacker2020 (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020"]], "tpxheader (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader"]], "atnr (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.atnr"]], "atomnames (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atomnames"]], "atomnumber (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.atomnumber"]], "atoms (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atoms"]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox"]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bF"]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr"]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop"]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bV"]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bX"]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.define_unpack_real"]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atom"]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atoms"]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_block"]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_blocka"]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ffparams"]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_harm"]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ilists"]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_iparams"]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_molblock"]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_moltype"]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_mtop"]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_resinfo"]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_rvec"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string"]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symstr"]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symtab"]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[150, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol"]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.extract_box_info"]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state"]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen"]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.fileVersion_err"]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag"]], "from_unpacker() (mdanalysis.topology.tpr.utils.tpxunpacker2020 class method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.from_unpacker"]], "ftupd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.ftupd"]], "fudgeqq (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.fudgeQQ"]], "functype (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.functype"]], "fver (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fver"]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.iatoms"]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.ik"]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.interaction_types"]], "lamb (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.lamb"]], "m (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.m"]], "mb (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.mB"]], "molb_natoms_mol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol"]], "molb_nmol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nmol"]], "molb_nposres_xa (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA"]], "molb_nposres_xb (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB"]], "molb_type (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_type"]], "moltypes (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.moltypes"]], "natoms (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.natoms"]], "ndo_int() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_int"]], "ndo_ivec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_ivec"]], "ndo_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_real"]], "ndo_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_rvec"]], "ngtc (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.ngtc"]], "nmolblock (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.nmolblock"]], "nmoltype (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.nmoltype"]], "nr (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.nr"]], "nr (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.nr"]], "nres (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.nres"]], "ntypes (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.ntypes"]], "number_of_atoms() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_atoms"]], "number_of_residues() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_residues"]], "precision (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, 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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.2.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.1.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.2.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.2.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.11.1. Analysis data files", "4.8.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.8.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.9.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.7.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.2.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.2.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.2.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.2.7.1.2. Clustering", "4.2.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.2.7.1.5. Covariance calculation \u2014 encore.covariance", "4.2.7.1.3. Dimensionality reduction", "4.2.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.2.7.1.7. Utility functions for ENCORE", "4.7.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.3.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.3.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.7.1.2. HELANAL \u2014 analysis of protein helices", "4.4.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.3.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.4.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.10.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.10.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.8.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.7.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.5.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.5.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.9.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.6.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.2.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.7.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.8.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.3.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "10.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "10.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "10.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "10.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "10.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "10. Auxiliary modules", "7. Converter modules", "7.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "7.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "7.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "7.8. Base classes \u2014 MDAnalysis.converters.base", "6.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "6.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "6.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "6.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "6.25. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "6.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "6.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "6.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "6.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "6.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "6.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "6.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "6.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "6.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "6.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "6.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "6.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "6.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "6.19. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.20. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.21. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "6.22. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.34. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.23. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.24. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.30. Base classes \u2014 MDAnalysis.coordinates.base", "6.33. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.27. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.31. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "6.26. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.28. Null output \u2014 MDAnalysis.coordinates.null", "6.32. Serialization of Coordinate Readers", "6.29. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "6. Coordinates modules", "7.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "11.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "11.1. Core functions of MDAnalysis", "11.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "11.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "11.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "11.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "11.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "11. Core modules", "16. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "13.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "13.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "13.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "13.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "13.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "13.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "13.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "13.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "13.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "13.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "13.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "13.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "13.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "13.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "13.2.10. Helper functions \u2014 MDAnalysis.lib.util", "13. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "17. References", "3. Selection commands", "9.2.6. Base classes for the selection writers", "9.2.4. CHARMM selections", "9.2.3. Gromacs selections", "9.2.5. Jmol selections", "9.2.2. PyMOL selections", "9.2.1. VMD selections", "9. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.26. Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.27. MDAnalysis topology tables", "5.28. Utility functions for the TPR topology parser", "5. Topology modules", "8. Trajectory transformations (\u201con-the-fly\u201d transformations)", "8.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "8.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "8.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "8.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "8.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "8.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "8.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "8.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "15. Constants and unit conversion \u2014 MDAnalysis.units", "14. Version information for MDAnalysis - MDAnalysis.version", "12.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "12.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "12. 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159, 160, 161, 162, 163, 164, 166], "do": [0, 1, 4, 6, 9, 10, 14, 17, 23, 34, 36, 38, 40, 44, 59, 65, 68, 71, 75, 76, 77, 80, 82, 83, 85, 87, 103, 110, 111, 112, 135, 148, 151, 153, 155, 156], "individu": [0, 10, 11, 17, 19, 23, 26, 29, 34, 35, 39, 42, 44, 59, 77, 80, 87, 93, 110, 112, 115, 116, 117, 118, 119, 120, 121, 134, 165, 166], "respect": [0, 4, 6, 29, 34, 36, 37, 84, 87, 89, 100, 109, 155], "show": [0, 2, 4, 6, 7, 8, 9, 17, 19, 20, 23, 26, 28, 29, 32, 33, 35, 36, 37, 103, 112, 114, 135], "how": [0, 2, 8, 10, 12, 13, 16, 17, 23, 25, 32, 37, 39, 42, 49, 52, 59, 61, 63, 68, 69, 75, 76, 80, 87, 88, 101, 102, 103, 110, 112, 114, 161, 166], "step": [0, 1, 2, 3, 4, 6, 8, 9, 16, 23, 24, 25, 26, 28, 29, 30, 32, 34, 35, 36, 37, 39, 40, 41, 42, 44, 48, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 79, 80, 81, 84, 87, 93, 99, 100, 101, 102, 148, 152, 156, 161], "manual": [0, 6, 17, 23, 69, 78, 89, 103, 112, 142, 152, 157], "explain": [0, 32, 40], "intermedi": [0, 23, 36, 103, 110, 161], "comput": [0, 1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 17, 22, 24, 28, 30, 31, 32, 34, 35, 36, 37, 38, 55, 59, 68, 80, 87, 88, 91, 99, 104, 105, 108, 110, 111, 113, 156, 157, 161], "i": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 50, 51, 55, 56, 57, 58, 59, 62, 63, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 165, 166], "requir": [0, 2, 3, 7, 8, 13, 14, 15, 17, 20, 23, 24, 29, 32, 33, 34, 36, 39, 41, 44, 49, 51, 52, 55, 57, 59, 61, 63, 65, 67, 69, 70, 73, 74, 75, 76, 79, 80, 81, 84, 86, 87, 92, 93, 95, 99, 100, 104, 107, 110, 114, 136, 138, 141, 150, 152, 153, 165], "lib": [0, 1, 2, 3, 6, 8, 9, 10, 24, 29, 30, 32, 36, 37, 58, 59, 69, 73, 78, 83, 84, 87, 89, 92], "qcprot": [0, 8, 36, 111, 112, 113], "implement": [0, 2, 4, 6, 8, 11, 13, 15, 16, 17, 25, 28, 29, 34, 36, 42, 51, 52, 55, 58, 59, 61, 65, 66, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 80, 81, 85, 87, 92, 99, 100, 103, 105, 106, 107, 108, 109, 110, 111, 113, 121, 142, 147, 148, 150, 151, 166], "exampl": [0, 1, 5, 6, 7, 8, 11, 13, 14, 16, 17, 19, 23, 25, 27, 28, 29, 32, 33, 34, 35, 38, 39, 40, 44, 46, 47, 48, 49, 52, 55, 57, 58, 67, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 83, 84, 86, 87, 89, 90, 91, 92, 93, 99, 101, 102, 103, 104, 106, 109, 110, 111, 113, 114, 120, 121, 130, 132, 133, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 166], "file": [0, 1, 3, 6, 8, 9, 13, 14, 16, 17, 18, 20, 24, 26, 29, 32, 34, 36, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 52, 53, 56, 58, 69, 71, 76, 77, 78, 79, 80, 81, 82, 85, 87, 91, 93, 95, 101, 102, 103, 105, 106, 112, 113, 114, 115, 116, 117, 118, 119, 120, 122, 123, 124, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148, 149, 150, 151, 152, 163, 164, 166], "provid": [0, 1, 2, 4, 6, 7, 8, 9, 10, 13, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 87, 89, 90, 93, 99, 100, 102, 104, 105, 106, 107, 110, 111, 112, 113, 114, 121, 135, 139, 148, 155, 158, 166], "part": [0, 5, 8, 13, 20, 23, 26, 29, 32, 34, 38, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 91, 109, 112, 114, 121, 141], "test": [0, 1, 3, 4, 8, 9, 13, 16, 17, 20, 22, 23, 26, 27, 29, 32, 33, 34, 36, 38, 39, 47, 48, 49, 52, 55, 59, 61, 69, 70, 73, 74, 76, 78, 80, 81, 82, 85, 86, 87, 92, 93, 100, 110, 112, 122, 132, 141, 163, 164], "suit": [0, 1, 8, 13, 16, 17, 23, 29, 32, 39, 112], "variabl": [0, 1, 5, 8, 13, 16, 29, 32, 40, 59, 68, 69, 75, 80, 99, 110, 113, 153], "psf": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 24, 26, 32, 34, 36, 49, 65, 66, 81, 87, 93, 110, 112, 114, 122, 148, 151], "dcd": [0, 2, 3, 4, 8, 13, 16, 17, 19, 22, 23, 26, 32, 34, 36, 49, 59, 74, 80, 81, 85, 87, 93, 110, 111, 112], "pdb_small": [0, 87], "For": [0, 1, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 37, 38, 39, 44, 46, 48, 49, 52, 55, 57, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 78, 80, 81, 83, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 105, 107, 110, 111, 112, 113, 114, 121, 132, 133, 141, 142, 147, 148, 152, 153, 157, 161], "all": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 18, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 110, 112, 113, 114, 115, 130, 131, 133, 135, 141, 142, 143, 144, 145, 147, 148, 152, 153, 154, 156, 158, 159, 160, 161, 163, 164, 166], "further": [0, 4, 19, 20, 24, 25, 26, 27, 31, 34, 36, 38, 40, 42, 48, 49, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 103, 106, 114, 121, 142, 143], "execut": [0, 1, 3, 7, 23, 26, 38, 48, 77, 110], "first": [0, 2, 3, 4, 6, 8, 9, 13, 17, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 87, 91, 92, 93, 101, 102, 104, 105, 109, 110, 114, 121, 132, 147, 148, 149, 152, 157, 162, 163, 164, 166], "import": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 16, 17, 20, 22, 23, 24, 26, 27, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 59, 61, 63, 65, 67, 69, 78, 79, 81, 86, 87, 90, 91, 92, 93, 101, 102, 103, 104, 109, 110, 111, 112, 122, 130, 132, 133, 142, 147, 152, 158, 163, 164, 165], "mda": [0, 1, 2, 3, 4, 7, 8, 9, 20, 22, 23, 25, 29, 32, 33, 34, 35, 36, 37, 40, 46, 47, 48, 49, 57, 59, 61, 78, 80, 81, 86, 87, 90, 93, 104, 110, 112, 121, 130, 132, 133, 147, 154, 155, 160], "from": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 52, 55, 56, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 122, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165, 166], "datafil": [0, 1, 2, 3, 4, 7, 8, 9, 13, 16, 17, 20, 22, 23, 26, 29, 32, 33, 34, 35, 36, 40, 47, 48, 49, 78, 81, 86, 87, 93, 110, 112, 122, 132, 147], "In": [0, 2, 3, 6, 8, 13, 14, 17, 20, 23, 24, 29, 36, 37, 38, 40, 44, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 85, 87, 89, 90, 91, 93, 99, 100, 101, 103, 105, 106, 109, 110, 112, 113, 114, 115, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 149, 151, 152, 156, 157, 161, 162], "simplest": [0, 17, 24, 93], "case": [0, 1, 6, 7, 8, 10, 14, 17, 23, 24, 28, 29, 34, 37, 38, 40, 42, 44, 46, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 86, 87, 89, 91, 93, 99, 100, 103, 105, 106, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152, 153, 156, 157, 161], "we": [0, 1, 2, 3, 4, 6, 8, 9, 13, 16, 17, 20, 23, 29, 32, 33, 34, 35, 36, 37, 38, 48, 49, 52, 55, 58, 59, 61, 65, 66, 68, 69, 70, 72, 73, 74, 75, 76, 80, 81, 83, 89, 92, 101, 103, 110, 111, 112, 113, 114, 139, 141, 147, 149, 152, 161, 162, 166], "simpli": [0, 6, 13, 16, 17, 23, 25, 38, 69, 80, 81, 87, 89, 93, 110, 113, 147, 148, 157], "ref": [0, 2, 9, 32, 36, 108, 155], "univers": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 46, 47, 48, 49, 52, 55, 57, 58, 59, 61, 62, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 78, 80, 81, 85, 86, 87, 88, 91, 92, 94, 104, 106, 108, 109, 110, 112, 114, 122, 126, 130, 132, 133, 134, 137, 145, 147, 148, 150, 151, 152, 155], "mobil": [0, 2, 34, 36, 38], "select_atom": [0, 2, 3, 4, 6, 8, 9, 20, 25, 32, 33, 34, 35, 36, 37, 48, 49, 59, 63, 65, 80, 81, 87, 88, 89, 91, 93, 110, 112, 114, 121, 155], "name": [0, 2, 3, 4, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42, 44, 46, 49, 51, 52, 55, 57, 58, 59, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 86, 87, 88, 89, 91, 93, 94, 103, 106, 110, 112, 114, 115, 116, 117, 118, 119, 120, 123, 126, 127, 128, 130, 131, 132, 133, 134, 137, 138, 140, 141, 142, 143, 144, 145, 148, 149, 150, 163, 164], "ca": [0, 2, 4, 9, 10, 13, 14, 15, 16, 17, 19, 22, 23, 32, 34, 36, 59, 65, 87, 89, 91, 112, 114, 149], "posit": [0, 2, 3, 6, 7, 8, 9, 10, 13, 19, 22, 23, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 42, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 68, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 86, 87, 88, 91, 93, 96, 100, 101, 102, 103, 104, 105, 106, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 150, 152, 153, 156, 157, 159, 160, 161], "28": [0, 63, 113, 142, 149, 150], "20178579474479": 0, "note": [0, 4, 6, 10, 13, 16, 17, 19, 20, 23, 24, 26, 28, 29, 31, 32, 33, 34, 36, 37, 38, 47, 48, 49, 50, 51, 52, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 81, 87, 90, 91, 92, 93, 94, 100, 101, 102, 103, 104, 106, 108, 109, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 143, 145, 147, 149, 152, 153, 156, 160], "translat": [0, 3, 6, 32, 36, 59, 61, 77, 87, 90, 91, 100, 109, 115, 149, 152, 155, 160], "have": [0, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 20, 23, 24, 26, 27, 29, 32, 34, 35, 36, 37, 38, 40, 42, 44, 46, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 85, 86, 87, 88, 89, 91, 92, 93, 99, 100, 101, 104, 110, 111, 113, 114, 121, 124, 126, 132, 135, 137, 139, 141, 142, 147, 148, 152, 153, 157, 160, 162, 166], "been": [0, 2, 3, 4, 6, 7, 8, 13, 16, 17, 19, 20, 23, 28, 32, 33, 34, 35, 36, 38, 39, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 73, 74, 75, 76, 79, 80, 81, 87, 89, 93, 102, 103, 104, 110, 113, 114, 133, 147, 160, 166], "remov": [0, 2, 4, 6, 8, 9, 10, 19, 20, 21, 23, 24, 28, 30, 32, 33, 34, 35, 36, 37, 38, 41, 52, 55, 57, 59, 61, 63, 65, 69, 70, 73, 74, 75, 76, 79, 81, 84, 87, 89, 90, 91, 92, 93, 99, 100, 103, 110, 114, 115, 133, 134, 137, 149, 155, 157], "order": [0, 2, 3, 4, 6, 8, 10, 12, 13, 14, 17, 18, 19, 23, 24, 26, 32, 33, 34, 36, 37, 38, 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157, 158, 159, 160, 161, 162, 165, 166], "optim": [0, 13, 20, 34, 36, 100, 108, 109, 110, 113, 152], "whole": [0, 3, 6, 7, 9, 17, 26, 32, 36, 38, 65, 69, 80, 81, 84, 87, 88, 104, 149, 152, 155, 156, 166], "1ake": [0, 36], "trj": [0, 34, 61, 80, 83, 85], "4ake": [0, 36, 67, 87, 112, 114], "filenam": [0, 3, 5, 6, 14, 17, 19, 23, 25, 26, 34, 36, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 87, 93, 95, 101, 102, 106, 110, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 148], "rmsfit": 0, "run": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 48, 56, 59, 81, 87, 89, 110, 112, 114, 148, 151, 153, 166], "object": [0, 2, 8, 12, 13, 14, 15, 16, 17, 18, 20, 23, 24, 25, 28, 30, 34, 35, 37, 38, 40, 42, 44, 47, 48, 49, 52, 55, 56, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 89, 96, 101, 102, 103, 105, 106, 107, 109, 110, 111, 112, 114, 115, 122, 123, 125, 126, 127, 129, 132, 133, 135, 136, 137, 138, 139, 140, 141, 143, 144, 145, 147, 150, 152, 154, 159, 163, 164, 166], "It": [0, 2, 3, 6, 8, 9, 13, 15, 17, 18, 20, 22, 23, 24, 25, 26, 28, 29, 32, 36, 37, 38, 39, 40, 44, 48, 49, 51, 58, 59, 63, 65, 66, 69, 70, 73, 76, 78, 80, 82, 83, 84, 86, 87, 91, 99, 101, 106, 110, 112, 113, 114, 140, 147, 151, 152, 163, 164, 166], "possibl": [0, 2, 4, 6, 8, 9, 10, 17, 20, 23, 24, 25, 29, 38, 40, 49, 57, 58, 59, 65, 66, 68, 69, 77, 78, 80, 81, 87, 89, 91, 93, 95, 100, 101, 103, 110, 113, 114, 147, 148, 149, 152, 158, 161], "arbitrari": [0, 2, 3, 6, 9, 10, 18, 23, 25, 26, 29, 30, 32, 34, 36, 59, 68, 84, 87, 89, 100, 101, 102, 110], "map": [0, 12, 13, 14, 23, 32, 34, 39, 40, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 89, 90, 91, 92, 93, 100, 107, 110], "base": [0, 3, 4, 6, 8, 9, 11, 13, 14, 15, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 51, 52, 54, 55, 56, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 74, 75, 77, 78, 79, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 100, 101, 104, 105, 106, 108, 110, 111, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 147, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160], "sequenc": [0, 17, 23, 26, 34, 36, 38, 65, 66, 76, 77, 80, 87, 91, 93, 104, 109, 110, 115, 126, 150, 152], "allow": [0, 2, 3, 5, 6, 9, 13, 16, 17, 20, 23, 24, 28, 29, 30, 32, 35, 36, 37, 40, 41, 42, 44, 49, 51, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 75, 76, 77, 80, 81, 82, 83, 87, 88, 89, 92, 93, 95, 96, 99, 103, 105, 106, 107, 110, 111, 112, 114, 121, 130, 135, 142, 149, 166], "homolog": 0, "wild": 0, "type": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 48, 49, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 114, 121, 123, 126, 127, 128, 129, 131, 132, 133, 134, 135, 137, 138, 139, 140, 141, 142, 143, 144, 147, 148, 149, 150, 154, 155, 156, 157, 158, 159, 160, 161], "mutant": 0, "wa": [0, 3, 9, 20, 21, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 42, 48, 49, 52, 55, 56, 58, 59, 61, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 105, 110, 114, 115, 147, 148, 155, 157, 158, 159, 160], "aln": 0, "would": [0, 6, 20, 23, 32, 38, 40, 49, 52, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 87, 93, 111, 114, 147, 152, 156, 157, 161, 166], "produc": [0, 10, 23, 26, 33, 34, 36, 37, 41, 44, 52, 59, 87, 91, 101, 103, 106, 133, 136, 163, 164], "appropri": [0, 6, 8, 25, 29, 35, 36, 38, 40, 42, 43, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 78, 79, 80, 81, 87, 89, 91, 92, 93, 104, 110, 114, 115, 121, 161], "fasta2select": [0, 34, 36], "feed": [0, 23, 26], "result": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 91, 92, 93, 99, 100, 104, 105, 107, 108, 109, 110, 112, 114, 147, 148, 152, 155], "dictionari": [0, 2, 4, 6, 17, 18, 19, 20, 23, 26, 28, 34, 36, 38, 40, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 70, 71, 72, 73, 74, 76, 80, 81, 89, 92, 110, 148, 149], "seldict": 0, "see": [0, 1, 2, 3, 6, 7, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 36, 37, 38, 39, 42, 44, 47, 49, 52, 55, 57, 58, 59, 61, 63, 65, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 83, 87, 89, 91, 93, 95, 99, 100, 102, 103, 104, 110, 114, 121, 133, 137, 141, 142, 147, 149, 150, 151, 152, 153, 161, 163, 164, 165, 166], "document": [0, 2, 5, 6, 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157, 161, 166], "wai": [0, 2, 4, 6, 8, 9, 13, 14, 19, 23, 24, 25, 29, 37, 40, 42, 49, 69, 76, 77, 80, 83, 86, 93, 109, 111, 112, 114, 115, 116, 117, 118, 119, 120, 136, 152, 155], "A": [0, 2, 3, 4, 6, 8, 9, 10, 13, 14, 16, 17, 19, 22, 23, 24, 25, 28, 29, 30, 32, 34, 35, 36, 37, 38, 40, 44, 52, 54, 55, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 79, 80, 81, 82, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 104, 106, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 132, 135, 139, 141, 147, 148, 149, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161], "sel1": [0, 34, 36], "sel2": [0, 34, 36], "befor": [0, 2, 3, 4, 6, 10, 13, 14, 17, 24, 32, 36, 38, 39, 42, 44, 59, 65, 66, 69, 75, 76, 80, 87, 90, 91, 93, 99, 101, 102, 107, 108, 110, 114, 115, 139, 150, 152, 157, 158, 159], "its": [0, 3, 4, 8, 12, 13, 19, 23, 29, 32, 34, 37, 38, 40, 49, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 79, 80, 82, 83, 86, 87, 89, 91, 93, 100, 104, 105, 106, 110, 113, 114, 121, 149, 152, 155], "coincid": [0, 100], "below": [0, 4, 5, 10, 17, 23, 29, 31, 32, 34, 36, 40, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 79, 80, 81, 86, 87, 103, 114, 121, 132], "explan": [0, 29, 59, 110, 149], "deriv": [0, 2, 6, 7, 11, 17, 38, 42, 44, 76, 80, 84, 93, 103, 110, 115, 145, 148], "shift": [0, 26, 87, 100, 105, 160], "behavior": [0, 34, 38, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 81, 87, 91, 93, 110, 114], "through": [0, 4, 6, 10, 11, 17, 20, 21, 23, 24, 25, 35, 38, 40, 41, 44, 49, 52, 55, 56, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 80, 81, 84, 86, 87, 89, 93, 100, 110, 112, 114, 123, 148, 160, 166], "construct": [0, 6, 8, 13, 19, 20, 34, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 86, 89, 93, 100, 105, 107, 110, 122, 148, 152], "alreadi": [0, 6, 7, 8, 23, 32, 42, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 83, 87, 93, 107, 114], "match": [0, 13, 16, 20, 23, 30, 34, 36, 49, 52, 55, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 76, 78, 81, 87, 89, 91, 92, 155], "should": [0, 2, 3, 4, 6, 8, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 33, 34, 35, 36, 37, 38, 42, 44, 49, 52, 57, 59, 61, 62, 63, 65, 67, 75, 76, 80, 83, 85, 87, 89, 90, 91, 92, 96, 100, 103, 105, 106, 107, 110, 116, 117, 118, 119, 120, 131, 133, 134, 141, 142, 147, 148, 149, 156], "therefor": [0, 2, 6, 14, 17, 26, 27, 59, 65, 69, 75, 87, 104, 110, 141, 147], "preserv": [0, 8, 32, 34, 57, 61, 63, 65, 87], "exact": [0, 4, 17, 23, 29, 34, 69, 87], "either": [0, 4, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 28, 34, 36, 38, 40, 42, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 84, 87, 92, 93, 99, 100, 101, 102, 104, 106, 107, 110, 111, 112, 114, 123, 133, 141, 148, 152, 159, 160, 166], "ani": [0, 1, 2, 3, 4, 6, 8, 9, 10, 13, 16, 17, 23, 24, 25, 26, 28, 29, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 82, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 103, 104, 105, 106, 107, 110, 111, 113, 114, 121, 127, 128, 130, 132, 133, 137, 147, 148, 152, 153, 161, 166], "other": [0, 2, 3, 4, 6, 8, 9, 13, 16, 17, 19, 23, 25, 26, 28, 29, 30, 32, 34, 37, 38, 39, 40, 41, 42, 46, 47, 49, 50, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 104, 106, 110, 111, 114, 132, 133, 141, 147, 148, 149, 152, 153, 157, 161, 164, 166], "new": [0, 1, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 44, 46, 47, 48, 49, 50, 51, 52, 53, 55, 58, 59, 61, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 80, 81, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 99, 100, 101, 102, 104, 105, 106, 109, 110, 112, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 153, 161, 166], "made": [0, 4, 5, 6, 8, 9, 15, 17, 19, 25, 32, 49, 79, 80, 81, 87, 89, 92, 93, 99, 110, 114, 148, 152], "sort": [0, 23, 24, 26, 32, 33, 38, 45, 87, 89, 90, 91, 92, 110, 114], "index": [0, 2, 6, 8, 23, 24, 25, 26, 28, 29, 30, 32, 34, 36, 37, 38, 41, 42, 44, 49, 52, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 90, 91, 92, 100, 102, 110, 115, 116, 117, 118, 119, 120, 121, 130, 141, 142, 148, 149, 166], "destroi": 0, "correspond": [0, 3, 6, 8, 9, 12, 13, 18, 23, 25, 32, 34, 36, 37, 38, 39, 42, 43, 49, 52, 55, 58, 59, 61, 62, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 99, 100, 103, 105, 107, 110, 113, 114, 130, 150, 155, 157, 158], "safest": 0, "mix": [0, 38], "string": [0, 4, 6, 8, 9, 10, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 29, 32, 34, 36, 37, 38, 40, 42, 48, 58, 59, 62, 63, 65, 67, 69, 78, 79, 80, 81, 86, 87, 89, 91, 93, 101, 103, 106, 109, 111, 114, 115, 116, 117, 118, 119, 120, 121, 133, 135, 141, 142, 149, 150, 155, 162, 163, 164], "paramet": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "str": [0, 2, 3, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 40, 41, 42, 51, 52, 55, 57, 58, 59, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 81, 86, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 106, 107, 110, 113, 114, 116, 118, 121, 132, 139, 145, 149, 155, 159, 163, 164], "dict": [0, 2, 3, 4, 6, 9, 13, 17, 18, 20, 23, 25, 26, 29, 30, 32, 34, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 81, 82, 84, 87, 89, 90, 92, 93, 101, 103, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 161], "tupl": [0, 4, 6, 10, 18, 19, 20, 26, 32, 34, 35, 36, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 79, 81, 87, 90, 91, 92, 93, 99, 103, 104, 109, 110, 141, 147, 148, 150, 152], "option": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 153, 154, 155, 156, 157, 158, 159, 160, 163, 164], "oper": [0, 2, 6, 18, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 81, 87, 89, 92, 100, 101, 104, 105, 107, 110, 111, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 160], "valid": [0, 8, 9, 32, 34, 35, 36, 42, 44, 52, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 78, 81, 105, 110, 137, 142, 143, 149], "ident": [0, 17, 20, 32, 34, 36, 57, 58, 87, 92, 93, 109, 110, 130, 148], "where": [0, 1, 5, 6, 7, 8, 15, 17, 18, 19, 20, 23, 29, 32, 33, 34, 35, 36, 37, 38, 40, 44, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 89, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 110, 112, 114, 133, 141, 147, 152, 155, 156, 158, 161], "return": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 86, 87, 88, 89, 90, 91, 92, 93, 96, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "clustalw": [0, 34, 36], "stamp": [0, 2, 23, 34, 36], "2": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 42, 44, 46, 47, 48, 49, 51, 52, 53, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 106, 109, 110, 113, 114, 132, 133, 134, 135, 137, 141, 142, 143, 145, 147, 148, 149, 150, 152, 153, 154, 155, 157, 158, 159, 160, 161, 162, 163, 164, 166], "3": [0, 2, 3, 4, 6, 7, 8, 9, 10, 13, 15, 16, 17, 18, 20, 21, 23, 24, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 81, 84, 87, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 113, 114, 132, 133, 134, 137, 141, 142, 147, 148, 149, 150, 152, 157, 158, 159, 160, 161, 163, 164, 166], "gener": [0, 1, 5, 12, 13, 14, 17, 18, 19, 20, 22, 23, 24, 27, 32, 34, 35, 36, 38, 39, 40, 44, 47, 52, 58, 59, 61, 62, 63, 65, 70, 73, 74, 76, 78, 80, 81, 82, 87, 89, 91, 92, 93, 100, 102, 105, 107, 109, 110, 112, 113, 114, 130, 131, 134, 139, 141, 147, 148, 156, 161, 163, 164, 166], "equival": [0, 6, 18, 22, 24, 29, 36, 37, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 82, 87, 106, 107, 114, 142], "each": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 70, 72, 73, 74, 75, 76, 77, 80, 81, 86, 87, 89, 90, 91, 92, 93, 99, 100, 103, 104, 105, 108, 110, 112, 115, 121, 132, 141, 147, 148, 149, 155, 158, 160], "list": [0, 2, 3, 4, 6, 9, 12, 13, 14, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 49, 52, 55, 58, 59, 61, 63, 65, 66, 67, 68, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 102, 103, 104, 105, 109, 112, 113, 114, 115, 121, 123, 126, 127, 128, 129, 131, 137, 138, 141, 142, 143, 144, 147, 148, 149, 152, 158, 161, 166], "defin": [0, 2, 3, 4, 6, 13, 16, 17, 20, 23, 24, 25, 28, 34, 36, 37, 38, 40, 44, 52, 57, 59, 61, 65, 66, 69, 75, 76, 79, 80, 87, 91, 92, 93, 100, 101, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 132, 141, 145, 147, 148, 150, 152, 153, 155, 158, 159, 161], "describ": [0, 2, 3, 11, 13, 15, 16, 17, 18, 23, 25, 29, 31, 34, 36, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 84, 85, 87, 89, 90, 91, 92, 93, 103, 104, 105, 110, 112, 113, 114, 121, 139, 142, 151, 152, 162], "under": [0, 17, 23, 25, 26, 34, 36, 37, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 65, 66, 67, 68, 69, 70, 72, 73, 74, 75, 76, 81, 87, 93, 99, 100, 103, 105, 110, 120, 148, 152, 166], "bool": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 38, 40, 42, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 91, 92, 93, 96, 100, 101, 103, 104, 107, 110, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 153, 154, 155, 156, 157, 158, 159, 160], "whether": [0, 9, 13, 14, 16, 17, 20, 23, 24, 26, 34, 40, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 87, 89, 91, 103, 106, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 152], "default": [0, 1, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 16, 17, 19, 20, 23, 24, 26, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 44, 47, 48, 49, 50, 51, 52, 53, 55, 57, 58, 59, 61, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 100, 101, 103, 104, 106, 107, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 149, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165], "array_lik": [0, 2, 3, 6, 9, 10, 14, 15, 17, 18, 23, 29, 30, 32, 33, 34, 36, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 84, 87, 90, 91, 92, 100, 101, 102, 104, 107, 109, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 155, 158], "choos": [0, 6, 8, 20, 23, 32, 34, 77, 80, 87, 89, 91, 155, 159], "With": [0, 6, 15, 20, 26, 34, 36, 37, 40, 46, 77, 99, 155, 158], "weigh": [0, 34, 36, 155, 158], "equal": [0, 1, 8, 13, 18, 23, 32, 34, 36, 37, 38, 44, 59, 89, 92, 99, 100, 103, 110, 155, 158, 163], "float": [0, 4, 6, 7, 8, 10, 13, 15, 16, 17, 19, 20, 23, 24, 25, 28, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42, 44, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 76, 77, 81, 84, 87, 89, 91, 93, 96, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 114, 147, 149, 150, 154, 155, 158, 161, 163, 164], "same": [0, 1, 2, 3, 4, 6, 9, 10, 12, 13, 14, 16, 17, 20, 23, 24, 25, 26, 29, 30, 31, 32, 34, 35, 36, 38, 39, 40, 44, 48, 49, 52, 55, 58, 59, 61, 63, 65, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 92, 93, 99, 100, 101, 104, 105, 109, 110, 114, 121, 130, 147, 148, 150, 155, 157, 158, 160], "length": [0, 2, 3, 6, 8, 10, 13, 14, 17, 19, 20, 22, 23, 24, 29, 30, 32, 33, 34, 36, 38, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 79, 80, 81, 82, 84, 87, 90, 91, 92, 93, 100, 101, 104, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 158, 161], "element": [0, 3, 6, 12, 13, 14, 16, 17, 18, 23, 32, 34, 36, 37, 38, 48, 49, 59, 65, 75, 87, 90, 91, 99, 105, 110, 114, 115, 123, 126, 128, 135, 137, 138, 141, 142, 143, 149, 150, 155, 158], "reject": [0, 25, 34, 36], "differ": [0, 1, 2, 3, 4, 6, 8, 11, 13, 16, 17, 19, 20, 23, 24, 25, 32, 34, 36, 37, 38, 42, 44, 49, 52, 55, 56, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 83, 84, 86, 87, 91, 92, 93, 101, 109, 110, 112, 113, 114, 121, 126, 137, 142, 148, 152, 161], "more": [0, 1, 2, 3, 4, 8, 9, 10, 11, 13, 16, 17, 23, 24, 25, 32, 34, 36, 37, 38, 39, 40, 42, 44, 49, 51, 52, 55, 58, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 88, 91, 93, 100, 101, 102, 103, 105, 106, 109, 110, 111, 112, 114, 141, 142, 147, 148, 152, 156, 164, 166], "than": [0, 3, 4, 6, 8, 9, 10, 15, 17, 19, 20, 23, 24, 32, 34, 36, 37, 38, 41, 42, 51, 57, 59, 65, 67, 69, 75, 77, 81, 87, 91, 92, 93, 99, 100, 104, 105, 106, 110, 114, 147, 150, 156], "Will": [0, 4, 6, 8, 9, 17, 18, 20, 24, 28, 32, 33, 35, 36, 38, 44, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 93, 104], "rais": [0, 2, 3, 6, 9, 23, 26, 29, 30, 32, 36, 40, 42, 43, 44, 49, 52, 55, 57, 58, 59, 60, 61, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 93, 95, 102, 103, 104, 106, 109, 110, 114, 121, 135, 137, 145, 147, 157, 161], "selectionerror": [0, 36, 89, 95], "doe": [0, 3, 6, 13, 14, 23, 24, 29, 32, 34, 36, 37, 59, 61, 64, 65, 67, 69, 70, 77, 78, 80, 82, 84, 87, 91, 93, 95, 100, 101, 103, 104, 110, 114, 121, 131, 138, 141, 151, 153, 156], "try": [0, 20, 23, 42, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 79, 81, 83, 85, 110, 131, 133, 142, 147, 162], "prepar": [0, 93], "drop": [0, 17, 58, 87, 110], "residu": [0, 3, 6, 9, 10, 19, 23, 25, 28, 30, 31, 32, 35, 36, 37, 38, 48, 65, 66, 67, 80, 86, 87, 89, 90, 91, 93, 95, 96, 110, 112, 114, 123, 125, 126, 127, 128, 130, 131, 132, 134, 137, 139, 140, 141, 142, 144, 148, 159, 160], "non": [0, 2, 3, 6, 8, 9, 17, 23, 24, 25, 29, 30, 32, 33, 36, 38, 40, 41, 42, 44, 52, 55, 57, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 76, 81, 87, 89, 103, 104, 105, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 126, 141, 156, 157], "get_matching_atom": 0, "detail": [0, 4, 6, 7, 8, 13, 14, 16, 17, 20, 23, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 49, 52, 59, 61, 65, 75, 79, 80, 90, 102, 103, 110, 111, 114, 141, 142, 148, 152, 166], "e": [0, 2, 4, 6, 9, 13, 17, 18, 23, 24, 25, 26, 28, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 77, 80, 81, 83, 84, 86, 87, 89, 91, 92, 93, 99, 100, 101, 103, 104, 105, 109, 110, 111, 112, 113, 114, 115, 137, 141, 147, 148, 149, 150, 152, 153, 154, 157, 158, 161, 162, 163, 164, 166], "context": [0, 23, 44, 48, 58, 59, 65, 69, 76, 78, 80, 101, 102, 106, 110, 121, 153], "rest": [0, 3, 6, 150], "ligand": [0, 3, 6, 19, 35, 38, 78, 93], "surround": 0, "water": [0, 6, 7, 8, 10, 20, 23, 24, 39, 87, 88, 93, 99, 112, 113, 114, 132, 150, 161], "old_rmsd": 0, "new_rmsd": 0, "after": [0, 1, 2, 3, 6, 8, 10, 17, 18, 20, 23, 24, 26, 32, 34, 35, 36, 37, 38, 42, 44, 49, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 80, 81, 86, 87, 91, 93, 103, 106, 107, 110, 114, 141, 147, 149, 152, 157, 158, 162], "effici": [0, 1, 10, 18, 34, 65, 68, 69, 73, 103, 113, 148], "method": [0, 2, 3, 4, 6, 7, 8, 9, 11, 13, 15, 16, 17, 19, 20, 22, 23, 25, 26, 28, 29, 31, 32, 33, 35, 36, 37, 38, 40, 42, 46, 49, 52, 55, 56, 57, 58, 59, 61, 65, 70, 72, 73, 74, 75, 76, 77, 81, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 100, 101, 102, 103, 105, 107, 108, 109, 110, 112, 113, 114, 115, 121, 136, 145, 147, 148, 150, 152, 156, 159], "ad": [0, 1, 2, 3, 4, 6, 9, 10, 13, 16, 17, 19, 23, 24, 26, 28, 29, 30, 32, 36, 37, 42, 49, 52, 55, 56, 57, 58, 59, 61, 63, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 83, 84, 87, 89, 90, 91, 92, 93, 99, 100, 102, 103, 104, 110, 132, 133, 135, 137, 138, 139, 141, 142, 143, 145, 147, 149, 152], "toggl": [0, 38, 93, 142], "8": [0, 2, 4, 9, 26, 31, 34, 36, 37, 40, 48, 49, 52, 55, 57, 58, 59, 61, 63, 65, 66, 70, 72, 73, 74, 76, 78, 81, 84, 87, 89, 91, 92, 93, 100, 104, 110, 114, 115, 116, 117, 118, 119, 120, 126, 137, 142, 148, 149, 150, 160, 161, 163, 164], "check": [0, 4, 6, 9, 10, 13, 19, 20, 23, 31, 32, 33, 34, 36, 38, 42, 44, 52, 55, 58, 59, 61, 65, 70, 71, 72, 73, 74, 76, 77, 78, 81, 87, 92, 100, 105, 147, 152, 153, 154, 155, 156, 157, 158, 159, 160], "includ": [0, 1, 3, 5, 9, 11, 13, 17, 23, 24, 25, 29, 32, 34, 36, 38, 42, 44, 48, 52, 55, 57, 58, 59, 61, 65, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 87, 89, 90, 93, 99, 100, 103, 106, 109, 110, 114, 121, 132, 138, 142, 148, 150, 152, 166], "work": [0, 2, 4, 6, 8, 9, 10, 11, 13, 16, 17, 18, 23, 28, 31, 36, 37, 38, 39, 40, 49, 52, 55, 58, 59, 61, 68, 69, 70, 72, 73, 74, 76, 80, 81, 83, 84, 87, 95, 100, 103, 104, 105, 106, 110, 112, 113, 114, 115, 121, 132, 142, 147, 152, 155, 160, 166], "incomplet": [0, 9, 27], "lenient": 0, "wherea": [0, 8, 32, 34, 87, 110, 111], "old": [0, 52, 80, 86, 87, 93, 110, 148], "kwarg": [0, 1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 16, 18, 23, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 86, 87, 91, 92, 93, 110, 114, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 147, 153], "replac": [0, 6, 12, 23, 58, 87, 93, 99, 100, 106, 110, 147, 148], "mass_weight": [0, 34, 36], "sinc": [0, 4, 6, 8, 9, 14, 17, 19, 21, 23, 24, 28, 32, 33, 34, 35, 36, 38, 39, 49, 52, 65, 69, 75, 76, 81, 87, 91, 114, 141, 156], "instead": [0, 2, 3, 4, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 42, 49, 51, 52, 53, 54, 55, 56, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 77, 78, 80, 81, 87, 89, 91, 92, 93, 96, 99, 100, 101, 102, 104, 105, 110, 114, 115, 116, 117, 118, 119, 120, 121, 126, 137, 148, 152, 159], "prefix": [0, 23, 34, 87, 103, 114], "rmsfit_": 0, "forc": [0, 20, 30, 31, 39, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 80, 81, 82, 84, 85, 87, 89, 92, 93, 100, 102, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 161], "in_memori": [0, 17, 36, 37, 81, 93], "both": [0, 2, 3, 4, 6, 9, 10, 14, 17, 23, 24, 26, 29, 30, 32, 34, 36, 38, 40, 49, 54, 56, 58, 61, 65, 69, 72, 80, 87, 92, 99, 102, 103, 112, 113, 114, 130, 133, 140, 141, 164], "must": [0, 2, 3, 4, 6, 8, 9, 10, 12, 13, 14, 17, 18, 20, 23, 24, 26, 29, 32, 34, 36, 38, 40, 42, 44, 49, 52, 55, 59, 61, 65, 67, 68, 69, 70, 71, 73, 74, 76, 77, 80, 81, 84, 87, 90, 91, 93, 99, 100, 104, 105, 106, 107, 108, 110, 114, 115, 141, 145, 147, 152, 155, 157, 161], "instanc": [0, 2, 3, 4, 6, 7, 8, 9, 13, 16, 17, 18, 23, 25, 28, 29, 32, 33, 34, 35, 36, 39, 40, 42, 43, 44, 52, 55, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 75, 76, 77, 79, 80, 81, 82, 84, 86, 87, 88, 91, 92, 93, 100, 101, 103, 105, 106, 110, 112, 114, 115, 141, 145, 148, 150, 152, 159, 163, 164, 165, 166], "output": [0, 2, 6, 13, 14, 17, 18, 19, 23, 26, 32, 34, 35, 36, 40, 49, 50, 51, 52, 55, 56, 57, 58, 59, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 79, 80, 81, 85, 86, 87, 89, 91, 100, 103, 104, 105, 110, 112, 114, 115, 116, 117, 118, 119, 120, 121, 128, 148, 157], "format": [0, 3, 4, 6, 10, 13, 14, 15, 16, 17, 18, 23, 25, 26, 34, 37, 38, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 56, 58, 59, 60, 62, 65, 66, 68, 69, 70, 71, 73, 74, 76, 77, 78, 79, 81, 82, 84, 85, 87, 91, 92, 93, 95, 100, 103, 104, 105, 109, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 136, 137, 138, 139, 140, 141, 143, 145, 147, 149, 150, 151, 162, 166], "determin": [0, 3, 4, 6, 8, 9, 10, 13, 18, 22, 23, 24, 25, 26, 29, 32, 33, 34, 38, 42, 44, 59, 65, 79, 80, 87, 91, 93, 100, 104, 108, 110, 113, 147, 157], "extens": [0, 4, 6, 17, 23, 25, 34, 44, 51, 59, 65, 66, 67, 68, 69, 77, 78, 79, 80, 85, 87, 93, 110, 111, 116, 117, 118, 119, 120, 132, 148, 151, 162], "One": [0, 2, 3, 6, 13, 16, 23, 24, 25, 26, 34, 37, 38, 48, 87, 93, 101, 114, 152, 161], "save": [0, 3, 4, 6, 7, 8, 10, 14, 17, 18, 20, 26, 28, 29, 32, 34, 36, 37, 52, 58, 59, 61, 63, 65, 69, 73, 74, 78, 83, 100, 101, 102, 106], "an": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 52, 55, 56, 57, 58, 61, 63, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 99, 100, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 115, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 147, 148, 150, 152, 156, 157, 158, 159, 160, 161, 162, 163, 164, 166], "altern": [0, 6, 9, 17, 19, 22, 23, 24, 28, 32, 41, 44, 49, 62, 65, 66, 87, 92, 93, 104, 110, 114, 121, 134, 152], "np": [0, 2, 3, 4, 5, 6, 8, 17, 20, 23, 24, 26, 28, 29, 32, 34, 36, 37, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 87, 89, 90, 93, 100, 101, 102, 104, 108, 109, 110, 114, 147, 149, 152, 163, 164], "savetxt": [0, 4, 28, 36], "subdomain": [0, 105], "against": [0, 17, 69, 92, 105], "written": [0, 2, 6, 14, 17, 19, 23, 34, 38, 40, 48, 51, 52, 55, 57, 59, 61, 63, 65, 66, 67, 69, 70, 71, 73, 74, 75, 76, 80, 83, 84, 87, 91, 93, 101, 102, 103, 104, 106, 110, 115, 116, 117, 118, 119, 120, 121, 139, 142, 148, 152, 166], "prepend": [0, 34], "toler": [0, 4, 87, 89, 163, 164], "given": [0, 3, 4, 5, 6, 7, 8, 9, 13, 14, 16, 17, 20, 23, 24, 29, 30, 32, 34, 35, 36, 37, 38, 40, 42, 44, 48, 49, 52, 55, 57, 58, 59, 61, 65, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 84, 87, 89, 90, 91, 92, 93, 96, 99, 101, 102, 106, 110, 114, 132, 136, 141, 147, 150, 152, 155, 156, 157, 158, 159, 160, 162], "find": [0, 9, 10, 13, 19, 20, 23, 24, 25, 32, 34, 38, 40, 42, 43, 46, 52, 61, 77, 83, 87, 90, 96, 101, 110, 111, 114, 131, 141, 147], "fail": [0, 6, 26, 28, 38, 49, 59, 65, 67, 69, 73, 83, 85, 87, 95, 104, 110, 145], "t": [0, 2, 4, 7, 17, 20, 22, 24, 29, 30, 32, 34, 36, 37, 38, 40, 42, 44, 47, 48, 49, 50, 52, 55, 56, 58, 59, 60, 61, 64, 65, 66, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 80, 81, 84, 87, 89, 90, 91, 99, 100, 102, 103, 104, 105, 106, 109, 110, 111, 112, 113, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 152, 153, 156, 157, 158, 159, 160, 161], "found": [0, 2, 9, 19, 20, 23, 24, 25, 34, 38, 40, 42, 43, 49, 59, 65, 70, 77, 78, 79, 86, 87, 89, 91, 93, 108, 110, 111, 132, 147, 148, 166], "overwrit": [0, 20, 35, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "perman": [0, 37, 93], "switch": [0, 4, 9, 24, 38, 40, 105], "memori": [0, 8, 10, 13, 14, 18, 29, 36, 37, 40, 41, 42, 44, 53, 55, 58, 59, 61, 65, 69, 70, 72, 73, 74, 76, 80, 85, 87, 90, 93, 110, 147, 157], "place": [0, 6, 9, 14, 17, 23, 38, 40, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 80, 81, 87, 90, 93, 100, 102, 104, 108, 109, 110, 111, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 152, 154, 160], "which": [0, 2, 3, 4, 6, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 23, 24, 25, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 46, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 67, 68, 69, 70, 72, 73, 74, 76, 77, 78, 79, 80, 81, 84, 86, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 112, 113, 114, 121, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 165, 166], "improv": [0, 15, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 89, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "substanti": [0, 81], "some": [0, 4, 8, 9, 17, 20, 23, 26, 28, 32, 37, 38, 39, 40, 42, 47, 48, 49, 59, 61, 65, 68, 69, 76, 78, 79, 80, 83, 87, 89, 91, 104, 109, 110, 111, 135, 146, 147, 148, 150, 152, 161, 165, 166], "out": [0, 4, 17, 22, 23, 32, 36, 37, 38, 39, 40, 42, 44, 45, 52, 55, 56, 57, 58, 59, 61, 63, 65, 69, 70, 72, 73, 74, 76, 80, 81, 87, 93, 103, 109, 115, 141, 148, 161, 162, 165, 166], "ignor": [0, 6, 13, 16, 18, 23, 42, 44, 59, 63, 65, 66, 75, 80, 81, 82, 84, 87, 91, 92, 93, 103, 104, 114, 126, 132, 133, 135, 137, 141, 147, 149], "verbos": [0, 2, 3, 4, 6, 7, 8, 9, 13, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 81, 93, 103], "logger": [0, 38, 103], "inform": [0, 8, 9, 13, 16, 17, 20, 23, 24, 25, 33, 34, 37, 38, 42, 49, 50, 52, 55, 57, 59, 61, 65, 66, 67, 68, 69, 70, 73, 74, 75, 76, 80, 83, 84, 87, 90, 91, 93, 100, 101, 102, 104, 110, 114, 122, 123, 126, 127, 128, 130, 132, 133, 137, 138, 139, 140, 141, 142, 143, 144, 146, 148, 151, 165, 166], "progress": [0, 2, 3, 4, 6, 7, 8, 9, 14, 23, 28, 29, 30, 32, 33, 35, 36, 37, 38, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 81, 93, 103], "reference_atom": [0, 104], "mobile_atom": 0, "insid": [0, 2, 5, 20, 23, 37, 80, 83, 87, 89, 92, 99, 105, 111, 113, 121, 152, 160], "rmsd_align": 0, "valu": [0, 2, 3, 4, 6, 8, 9, 13, 14, 16, 17, 20, 23, 24, 26, 29, 30, 32, 34, 35, 36, 37, 38, 40, 41, 42, 44, 47, 48, 49, 50, 52, 55, 58, 59, 61, 65, 67, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 87, 89, 90, 91, 92, 93, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 112, 114, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147, 149, 150, 153, 161, 163, 164], "least": [0, 2, 3, 4, 6, 8, 9, 13, 15, 19, 23, 25, 29, 30, 32, 36, 44, 52, 55, 58, 59, 61, 65, 67, 70, 72, 73, 74, 76, 77, 81, 106, 108, 110, 126, 137, 142], "minimim": 0, "numpi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 26, 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17, 19, 23, 26, 29, 32, 36, 38, 42, 44, 47, 48, 49, 50, 52, 53, 55, 56, 58, 59, 61, 63, 65, 66, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 80, 81, 87, 92, 100, 101, 102, 106, 109, 110, 112, 113, 115, 116, 117, 118, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 147], "allclos": [3, 109], "atol": [3, 87, 89], "1e": [3, 13, 87, 89, 161], "pi": [3, 35, 100, 104, 109], "12": [3, 8, 23, 34, 37, 48, 55, 59, 63, 65, 66, 87, 110, 113, 115, 141, 149, 150, 161, 163, 164], "good": [3, 37, 68, 103], "disk": [3, 17, 23, 36, 59, 69, 73, 74, 110], "load": [3, 5, 6, 7, 8, 14, 17, 18, 20, 26, 29, 32, 34, 36, 40, 44, 58, 63, 65, 69, 70, 73, 74, 80, 81, 84, 87, 88, 93, 106, 112, 122, 130], "again": [3, 20, 23, 73, 100, 148, 156], "npy": 3, "rnew": 3, "o": [3, 8, 9, 15, 20, 23, 33, 38, 39, 46, 55, 59, 76, 78, 80, 83, 85, 87, 89, 92, 100, 105, 110, 111, 112, 113, 114, 147, 149], "ag": [3, 9, 29, 35, 49, 59, 65, 81, 86, 87, 91, 92, 93, 114, 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38, 39, 44, 52, 55, 58, 59, 61, 65, 68, 69, 70, 72, 73, 74, 75, 76, 79, 80, 81, 87, 91, 93, 100, 103, 105, 107, 109, 110, 115, 148, 150, 157], "next": [3, 4, 24, 26, 29, 37, 41, 42, 44, 52, 55, 58, 59, 61, 65, 70, 72, 73, 74, 76, 80, 81, 83, 101, 102, 109, 114, 121, 141], "r_": [3, 29], "01": [3, 11, 17, 48, 89, 113, 133], "a_": [3, 33], "012": [3, 66], "bat_fram": 3, "convers": [3, 6, 10, 40, 47, 48, 49, 50, 52, 55, 57, 58, 59, 61, 65, 70, 72, 73, 74, 76, 77, 81, 100, 109, 110, 123, 125, 126, 127, 128, 129, 130, 131, 132, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145], "dimens": [3, 6, 8, 10, 16, 17, 23, 29, 30, 32, 34, 52, 55, 57, 59, 61, 63, 65, 67, 69, 70, 73, 74, 76, 80, 81, 84, 87, 91, 93, 96, 100, 104, 105, 107, 110, 152, 156, 159], "proper": [3, 34, 76, 110, 142, 148, 150], "oppos": [3, 34], "around": [3, 6, 10, 13, 24, 29, 35, 37, 59, 65, 87, 88, 89, 92, 96, 99, 100, 104, 107, 110, 114, 139], "properti": [3, 6, 22, 29, 30, 31, 34, 42, 49, 52, 55, 56, 58, 59, 61, 65, 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61, 68, 71, 73, 80, 101], "journal": [3, 8, 9, 11, 15, 16, 17, 19, 23, 29, 30, 31, 34, 37, 68, 99, 109, 113, 156, 161], "physic": [3, 6, 8, 29, 37, 59, 99, 113, 161], "chemistri": [3, 29, 30, 31, 37, 68, 91, 161], "107": [3, 38, 99, 113, 149], "1048": 3, "1055": 3, "2003": [3, 9, 15, 16, 26], "doi": [3, 4, 8, 9, 11, 17, 19, 23, 26, 29, 30, 31, 32, 34, 36, 37, 38, 68, 99, 109, 112, 113, 149, 156, 161, 163, 164], "1021": [3, 19, 29, 30, 31, 37, 99, 113, 149, 156], "jp027149c": 3, "simon": [3, 9], "hikiri": 3, "takashi": 3, "yoshidom": 3, "mitsunori": 3, "ikeguchi": 3, "entropi": 3, "chemic": [3, 8, 19, 29, 30, 31, 37, 99, 147, 156], "theori": [3, 29, 91, 99, 156], "5990": 3, "6000": 3, "2016": [3, 8, 32, 36, 81, 108, 113, 142, 150], "pmid": [3, 19, 30, 31], "27951672": 3, "ac": [3, 19, 38, 99, 149, 156], "jctc": [3, 99, 156], "6b00563": 3, "l": [3, 6, 8, 19, 25, 29, 34, 36, 87, 100, 108, 110, 113, 161], "alchem": 3, "grid": [3, 6, 19, 23, 100, 105, 111, 163, 164], "dock": [3, 63, 135], 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164], "2d": 163, "visual": [163, 164, 165], "streamlin": 163, "3d": 164, "streamlines_3d": 164, "lipid": 165, "flow": 165, "document": 166, "get": 166, "involv": 166, "guid": 166, "instal": 166, "conda": 166, "pip": 166, "sourc": 166, "indic": 166}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx.ext.todo": 2, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align": [[0, "coordinate-fitting-and-alignment-mdanalysis-analysis-align"]], "RMS-fitting tutorial": [[0, "rms-fitting-tutorial"]], "Common usage": [[0, "common-usage"]], "Functions and Classes": [[0, "functions-and-classes"], [20, "functions-and-classes"]], "Helper functions": [[0, "helper-functions"], [78, "helper-functions"], [90, "helper-functions"]], "Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances": [[1, "simple-atomic-distance-analysis-mdanalysis-analysis-atomicdistances"]], "Basic usage": [[1, "basic-usage"]], "Analysis building blocks \u2014 MDAnalysis.analysis.base": [[2, "analysis-building-blocks-mdanalysis-analysis-base"]], "Example of using a standard analysis tool": [[2, "example-of-using-a-standard-analysis-tool"]], "Writing new analysis tools": [[2, "writing-new-analysis-tools"]], "Classes": [[2, "classes"], [4, "classes"], [8, "classes"], [29, "classes"], [37, "classes"], [38, "classes"], [40, "classes"], [47, "classes"], [47, "id5"], [48, "classes"], [48, "id2"], [49, "classes"], [49, "id1"], [52, "classes"], [55, "classes"], [57, "classes"], [58, "classes"], [59, "classes"], [60, "classes"], [61, "classes"], [62, "classes"], [63, "classes"], [64, "classes"], [65, "classes"], [71, "classes"], [72, "classes"], [75, "classes"], [78, "classes"], [81, "classes"], [82, "classes"], [86, "classes"], [87, "classes"], [90, "classes"], [93, "classes"], [105, "classes"], [123, "classes"], [125, "classes"], [126, "classes"], [127, "classes"], [128, "classes"], [129, "classes"], [130, "classes"], [131, "classes"], [132, "classes"], [133, "classes"], [134, "classes"], [135, "classes"], [136, "classes"], [137, "classes"], [138, "classes"], [139, "classes"], [140, "classes"], [141, "classes"], [142, "classes"], [143, "classes"], [144, "classes"], [145, "classes"]], "Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat": [[3, "bond-angle-torsion-coordinates-analysis-mdanalysis-analysis-bat"]], "Example applications": [[3, "example-applications"], [9, "example-applications"], [26, "example-applications"], [36, "example-applications"]], "Analysis classes": [[3, "analysis-classes"], [26, "analysis-classes"], [36, "analysis-classes"]], "Native contacts analysis \u2014 MDAnalysis.analysis.contacts": [[4, "native-contacts-analysis-mdanalysis-analysis-contacts"]], "Examples for contact analysis": [[4, "examples-for-contact-analysis"]], "One-dimensional contact analysis": [[4, "one-dimensional-contact-analysis"]], "Two-dimensional contact analysis (q1-q2)": [[4, "two-dimensional-contact-analysis-q1-q2"]], "Writing your own contact analysis": [[4, "writing-your-own-contact-analysis"]], "Functions": [[4, "functions"], [36, "functions"], [93, "functions"], [100, "functions"], [108, "functions"], [109, "functions"], [161, "functions"]], "Analysis data files": [[5, "analysis-data-files"]], "Data files": [[5, "data-files"]], "Generating densities from trajectories \u2014 MDAnalysis.analysis.density": [[6, "generating-densities-from-trajectories-mdanalysis-analysis-density"]], "Generating a density from a MD trajectory": [[6, "generating-a-density-from-a-md-trajectory"]], "Creating densities": [[6, "creating-densities"]], "Density object": [[6, "density-object"]], "Dielectric \u2014 MDAnalysis.analysis.dielectric": [[7, "dielectric-mdanalysis-analysis-dielectric"]], "Diffusion map \u2014 MDAnalysis.analysis.diffusionmap": [[8, "diffusion-map-mdanalysis-analysis-diffusionmap"]], "Diffusion Map tutorial": [[8, "diffusion-map-tutorial"]], "Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals": [[9, "dihedral-angles-analysis-mdanalysis-analysis-dihedrals"]], "General dihedral analysis": [[9, "general-dihedral-analysis"]], "Ramachandran analysis": [[9, "ramachandran-analysis"]], "Janin analysis": [[9, "janin-analysis"]], "Reference plots": [[9, "reference-plots"]], "Analysis Classes": [[9, "analysis-classes"]], "Distance analysis \u2014 MDAnalysis.analysis.distances": [[10, "distance-analysis-mdanalysis-analysis-distances"]], "ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore": [[11, "encore-ensemble-similarity-calculations-mdanalysis-analysis-encore"]], "Modules": [[11, "modules"]], "References": [[11, "references"], [113, "references"]], "bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap": [[12, "bootstrap-procedures-mdanalysis-analysis-ensemble-bootstrap"]], "Clustering": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "clustering frontend \u2014 MDAnalysis.analysis.encore.clustering.cluster": [[13, "clustering-frontend-mdanalysis-analysis-encore-clustering-cluster"]], "Cluster representation \u2014 MDAnalysis.analysis.encore.clustering.ClusterCollection": [[13, "cluster-representation-mdanalysis-analysis-encore-clustering-clustercollection"]], "clustering frontend \u2014 MDAnalysis.analysis.encore.clustering.ClusteringMethod": [[13, "clustering-frontend-mdanalysis-analysis-encore-clustering-clusteringmethod"]], "Clustering algorithms": [[13, "clustering-algorithms"]], "Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix": [[14, "distance-matrix-calculation-mdanalysis-analysis-ensemble-confdistmatrix"]], "Covariance calculation \u2014 encore.covariance": [[15, "covariance-calculation-encore-covariance"]], "Dimensionality reduction": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "dimensionality reduction frontend \u2014 MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "dimensionality-reduction-frontend-mdanalysis-analysis-encore-dimensionality-reduction-reduce-dimensionality"]], "dimensionality reduction frontend \u2014 MDAnalysis.analysis.encore.clustering.DimensionalityReductionMethod": [[16, "dimensionality-reduction-frontend-mdanalysis-analysis-encore-clustering-dimensionalityreductionmethod"]], "Dimensionality reduction algorithms": [[16, "dimensionality-reduction-algorithms"]], "Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity": [[17, "ensemble-similarity-calculations-mdanalysis-analysis-encore-similarity"]], "Functions for ensemble comparisons": [[17, "functions-for-ensemble-comparisons"]], "Function reference": [[17, "function-reference"]], "Utility functions for ENCORE": [[18, "module-MDAnalysis.analysis.encore.utils"]], "Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm": [[19, "elastic-network-analysis-of-md-trajectories-mdanalysis-analysis-gnm"]], "Analysis tasks": [[19, "analysis-tasks"]], "Utility functions": [[19, "utility-functions"]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "hydrogen-bond-autocorrelation-mdanalysis-analysis-hydrogenbonds-hbond-autocorrel"]], "Description": [[20, "description"]], "Input": [[20, "input"], [24, "input"]], "Output": [[20, "output"], [24, "output"], [37, "output"]], "Worked Example for Polyamide": [[20, "worked-example-for-polyamide"]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)": [[21, "hydrogen-bond-autocorrelation-mdanalysis-analysis-hbonds-hbond-autocorrel-deprecated"]], "HELANAL \u2014 analysis of protein helices": [[22, "helanal-analysis-of-protein-helices"]], "Example use": [[22, "example-use"]], "HOLE analysis \u2014 MDAnalysis.analysis.hole2": [[23, "hole-analysis-mdanalysis-analysis-hole2"]], "Module": [[23, "module-MDAnalysis.analysis.hole2"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2": [[23, "id3"]], "Using HOLE on a PDB file": [[23, "using-hole-on-a-pdb-file"]], "Using HOLE on a trajectory": [[23, "using-hole-on-a-trajectory"]], "Using HOLE with VMD": [[23, "using-hole-with-vmd"]], "Analyzing a full trajectory": [[23, "analyzing-a-full-trajectory"]], "Creating subsampled HOLE surface": [[23, "creating-subsampled-hole-surface"]], "Loading a trajectory into VMD with subsampling": [[23, "loading-a-trajectory-into-vmd-with-subsampling"]], "Creating a subsampled trajectory": [[23, "creating-a-subsampled-trajectory"]], "Functions and classes": [[23, "functions-and-classes"]], "Utility functions and templates": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.helper": [[23, "hole-analysis-mdanalysis-analysis-hole2-helper"]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2.templates": [[23, "hole-analysis-mdanalysis-analysis-hole2-templates"]], "Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "hydrogen-bond-analysis-mdanalysis-analysis-hydrogenbonds-hbond-analysis"]], "Example use of HydrogenBondAnalysis": [[24, "example-use-of-hydrogenbondanalysis"]], "The class and its methods": [[24, "the-class-and-its-methods"]], "Leaflet identification \u2014 MDAnalysis.analysis.leaflet": [[25, "leaflet-identification-mdanalysis-analysis-leaflet"]], "Algorithm": [[25, "algorithm"]], "Classes and Functions": [[25, "classes-and-functions"], [32, "classes-and-functions"]], "Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna": [[26, "generation-and-analysis-of-x3dna-helicoidal-parameter-profiles-mdanalysis-analysis-legacy-x3dna"]], "Single structure": [[26, "single-structure"]], "Trajectory": [[26, "trajectory"]], "Utilities": [[26, "utilities"]], "MDAnalysis.analysis.legacy \u2014 Legacy analysis code": [[27, "mdanalysis-analysis-legacy-legacy-analysis-code"]], "Legacy modules": [[27, "legacy-modules"]], "Linear Density \u2014 MDAnalysis.analysis.lineardensity": [[28, "linear-density-mdanalysis-analysis-lineardensity"]], "Mean Squared Displacement \u2014 MDAnalysis.analysis.msd": [[29, "mean-squared-displacement-mdanalysis-analysis-msd"]], "Computing an MSD": [[29, "computing-an-msd"]], "Computing Self-Diffusivity": [[29, "computing-self-diffusivity"]], "Combining Multiple Replicates": [[29, "combining-multiple-replicates"]], "Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids": [[30, "updated-nucleic-acid-analysis-mdanalysis-analysis-nucleicacids"]], "Distances": [[30, "distances"], [31, "distances"]], "Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo": [[31, "nucleic-acid-analysis-mdanalysis-analysis-nuclinfo"]], "Phases": [[31, "phases"]], "Dihedral angles": [[31, "dihedral-angles"]], "Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca": [[32, "principal-component-analysis-pca-mdanalysis-analysis-pca"]], "PCA Tutorial": [[32, "pca-tutorial"]], "Polymer analysis \u2014 MDAnalysis.analysis.polymer": [[33, "polymer-analysis-mdanalysis-analysis-polymer"]], "Calculating path similarity \u2014 MDAnalysis.analysis.psa": [[34, "calculating-path-similarity-mdanalysis-analysis-psa"]], "Helper functions and variables": [[34, "helper-functions-and-variables"]], "Classes, methods, and functions": [[34, "classes-methods-and-functions"]], "Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf": [[35, "radial-distribution-functions-mdanalysis-analysis-rdf"]], "Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms": [[36, "calculating-root-mean-square-quantities-mdanalysis-analysis-rms"]], "Calculating RMSD for multiple domains": [[36, "calculating-rmsd-for-multiple-domains"]], "Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics": [[37, "water-dynamics-analysis-mdanalysis-analysis-waterdynamics"]], "Example use of the analysis classes": [[37, "example-use-of-the-analysis-classes"]], "HydrogenBondLifetimes": [[37, "hydrogenbondlifetimes"]], "WaterOrientationalRelaxation": [[37, "waterorientationalrelaxation"], [37, "id76"]], "AngularDistribution": [[37, "angulardistribution"], [37, "id77"]], "MeanSquareDisplacement": [[37, "meansquaredisplacement"], [37, "id78"]], "SurvivalProbability": [[37, "survivalprobability"], [37, "id79"]], "Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis": [[38, "water-bridge-analysis-mdanalysis-analysis-hydrogenbonds-waterbridgeanalysis"]], "Theory": [[38, "theory"]], "Output as Network": [[38, "output-as-network"]], "Output as Timeseries": [[38, "output-as-timeseries"]], "Detection of water bridges": [[38, "detection-of-water-bridges"]], "Default heavy atom names for CHARMM27 force field.": [[38, "id69"]], "Heavy atom types for GLYCAM06 force field.": [[38, "id70"]], "How to perform WaterBridgeAnalysis": [[38, "how-to-perform-waterbridgeanalysis"]], "Use count_by_type": [[38, "use-count-by-type"]], "Use count_by_time": [[38, "use-count-by-time"]], "Analysis modules": [[39, "analysis-modules"]], "Building blocks for Analysis": [[39, "building-blocks-for-analysis"]], "Distances and contacts": [[39, "distances-and-contacts"]], "Hydrogen bonding": [[39, "hydrogen-bonding"]], "Membranes and membrane proteins": [[39, "membranes-and-membrane-proteins"]], "Nucleic acids": [[39, "nucleic-acids"]], "Polymers": [[39, "polymers"]], "Structure": [[39, "structure"]], "Macromolecules": [[39, "macromolecules"]], "Liquids": [[39, "liquids"]], "Volumetric analysis": [[39, "volumetric-analysis"]], "Dimensionality Reduction": [[39, "dimensionality-reduction"]], "Legacy analysis modules": [[39, "legacy-analysis-modules"]], "Data": [[39, "data"], [161, "data"], [162, "data"]], "EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR": [[40, "edr-auxiliary-reader-mdanalysis-auxiliary-edr"]], "Background": [[40, "background"]], "Standalone Usage of the EDRReader": [[40, "standalone-usage-of-the-edrreader"]], "Adding EDR data to trajectories": [[40, "adding-edr-data-to-trajectories"]], "XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG": [[41, "xvg-auxiliary-reader-mdanalysis-auxiliary-xvg"]], "XVG Readers": [[41, "xvg-readers"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary.base": [[42, "auxiliary-readers-mdanalysis-auxiliary-base"]], "Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core": [[43, "common-functions-for-auxiliary-reading-mdanalysis-auxiliary-core"]], "Auxiliary Readers \u2014 MDAnalysis.auxiliary": [[44, "auxiliary-readers-mdanalysis-auxiliary"]], "Supported formats": [[44, "supported-formats"]], "Auxiliary API": [[44, "auxiliary-api"]], "Auxiliaries and trajectories": [[44, "auxiliaries-and-trajectories"]], "Adding an auxiliary to a trajectory": [[44, "adding-an-auxiliary-to-a-trajectory"]], "Iterating by an auxiliary": [[44, "iterating-by-an-auxiliary"]], "Accessing auxiliary attributes": [[44, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[44, "recreating-auxiliaries"]], "AuxStep class": [[44, "auxstep-class"]], "Attributes": [[44, "attributes"], [44, "id2"], [80, "attributes"], [80, "id19"], [80, "id21"]], "Methods": [[44, "methods"], [44, "id3"], [80, "methods"], [80, "id18"], [80, "id20"], [80, "id22"]], "AuxReader class": [[44, "auxreader-class"]], "Registry": [[44, "registry"], [80, "registry"]], "Replicating auxiliaries": [[44, "replicating-auxiliaries"]], "Auxiliary modules": [[45, "auxiliary-modules"]], "Converter modules": [[46, "converter-modules"]], "OpenMM topology parser MDAnalysis.converters.OpenMMParser": [[47, "openmm-topology-parser-mdanalysis-converters-openmmparser"]], "OpenMM structure I/O \u2014 MDAnalysis.converters.OpenMM": [[47, "openmm-structure-i-o-mdanalysis-converters-openmm"]], "ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser": [[48, "parmed-topology-parser-mdanalysis-converters-parmedparser"]], "ParmEd structure I/O \u2014 MDAnalysis.converters.ParmEd": [[48, "parmed-structure-i-o-mdanalysis-converters-parmed"]], "RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser": [[49, "rdkit-topology-parser-mdanalysis-converters-rdkitparser"]], "RDKit molecule I/O \u2014 MDAnalysis.converters.RDKit": [[49, "rdkit-molecule-i-o-mdanalysis-converters-rdkit"]], "Base classes \u2014 MDAnalysis.converters.base": [[50, "base-classes-mdanalysis-converters-base"]], "CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD": [[51, "crd-structure-files-in-mdanalysis-mdanalysis-coordinates-crd"]], "DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD": [[52, "dcd-trajectory-i-o-mdanalysis-coordinates-dcd"]], "DL_Poly format reader MDAnalysis.coordinates.DLPoly": [[53, "dl-poly-format-reader-mdanalysis-coordinates-dlpoly"]], "DESRES file format \u2014 MDAnalysis.coordinates.DMS": [[54, "desres-file-format-mdanalysis-coordinates-dms"]], "FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS": [[55, "fhi-aims-file-format-mdanalysis-coordinates-fhiaims"]], "Developer notes: FHIAIMSWriter format strings": [[55, "developer-notes-fhiaimswriter-format-strings"]], "GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS": [[56, "gamess-trajectory-reader-mdanalysis-coordinates-gms"]], "GRO file format \u2014 MDAnalysis.coordinates.GRO": [[57, "gro-file-format-mdanalysis-coordinates-gro"]], "Writing GRO files": [[57, "writing-gro-files"]], "Developer notes: GROWriter format strings": [[57, "developer-notes-growriter-format-strings"]], "GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD": [[58, "gsd-trajectory-reader-mdanalysis-coordinates-gsd"]], "H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD": [[59, "h5md-trajectories-mdanalysis-coordinates-h5md"]], "Units": [[59, "units"]], "Example: Loading an H5MD simulation": [[59, "example-loading-an-h5md-simulation"]], "Example: Writing an H5MD file": [[59, "example-writing-an-h5md-file"]], "Example: Opening an H5MD file in parallel": [[59, "example-opening-an-h5md-file-in-parallel"]], "Building parallel h5py and HDF5 on Linux": [[59, "building-parallel-h5py-and-hdf5-on-linux"]], "INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD": [[60, "inpcrd-structure-files-in-mdanalysis-mdanalysis-coordinates-inpcrd"]], "LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS": [[61, "lammps-dcd-trajectory-and-data-i-o-mdanalysis-coordinates-lammps"]], "Data file formats": [[61, "data-file-formats"]], "Dump files": [[61, "dump-files"]], "Example: Loading a LAMMPS simulation": [[61, "example-loading-a-lammps-simulation"]], "MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF": [[62, "mmtf-trajectory-reader-mdanalysis-coordinates-mmtf"]], "MOL2 file format \u2014 MDAnalysis.coordinates.MOL2": [[63, "mol2-file-format-mdanalysis-coordinates-mol2"], [135, "mol2-file-format-mdanalysis-coordinates-mol2"]], "Example for working with mol2 files": [[63, "example-for-working-with-mol2-files"]], "MOL2 format notes": [[63, "mol2-format-notes"]], "NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN": [[64, "namdbin-files-format-mdanalysis-coordinates-namdbin"]], "PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB": [[65, "pdb-structure-files-in-mdanalysis-mdanalysis-coordinates-pdb"]], "Capabilities": [[65, "capabilities"]], "Examples for working with PDB files": [[65, "examples-for-working-with-pdb-files"]], "PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT": [[66, "pdbqt-structure-files-in-mdanalysis-mdanalysis-coordinates-pdbqt"]], "PQR file format \u2014 MDAnalysis.coordinates.PQR": [[67, "pqr-file-format-mdanalysis-coordinates-pqr"]], "TNG trajectory files \u2014 MDAnalysis.coordinates.TNG": [[68, "tng-trajectory-files-mdanalysis-coordinates-tng"]], "Current Limitations": [[68, "current-limitations"]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[69, "amber-trajectories-mdanalysis-coordinates-trj"]], "Binary NetCDF trajectories": [[69, "binary-netcdf-trajectories"]], "ASCII TRAJ trajectories": [[69, "ascii-traj-trajectories"]], "TRR trajectory files \u2014 MDAnalysis.coordinates.TRR": [[70, "trr-trajectory-files-mdanalysis-coordinates-trr"]], "TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ": [[71, "trz-trajectory-i-o-mdanalysis-coordinates-trz"]], "TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ": [[72, "txyz-file-format-mdanalysis-coordinates-txyz"]], "XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR": [[73, "xdr-based-trajectory-files-mdanalysis-coordinates-xdr"]], "XTC trajectory files \u2014 MDAnalysis.coordinates.XTC": [[74, "xtc-trajectory-files-mdanalysis-coordinates-xtc"]], "XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ": [[75, "xyz-trajectory-reader-mdanalysis-coordinates-xyz"]], "XYZ File format": [[75, "xyz-file-format"]], "Base classes \u2014 MDAnalysis.coordinates.base": [[76, "base-classes-mdanalysis-coordinates-base"]], "FrameIterators": [[76, "frameiterators"]], "Readers": [[76, "readers"], [80, "readers"]], "Writers": [[76, "writers"], [80, "writers"]], "Converters": [[76, "converters"]], "Helper classes": [[76, "helper-classes"]], "ChainReader \u2014 MDAnalysis.coordinates.chain": [[77, "chainreader-mdanalysis-coordinates-chain"]], "Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles": [[78, "reading-trajectories-with-chemfiles-mdanalysis-coordinates-chemfiles"]], "Using the CHEMFILES reader": [[78, "using-the-chemfiles-reader"]], "Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core": [[79, "common-functions-for-coordinate-reading-mdanalysis-coordinates-core"]], "Trajectory Readers and Writers \u2014 MDAnalysis.coordinates": [[80, "trajectory-readers-and-writers-mdanalysis-coordinates"]], "Timesteps": [[80, "timesteps"]], "Supported coordinate formats": [[80, "supported-coordinate-formats"]], "Table of supported coordinate formats": [[80, "id23"]], "Trajectory API": [[80, "trajectory-api"]], "Timestep class": [[80, "timestep-class"]], "Private attributes": [[80, "private-attributes"]], "Trajectory Reader class": [[80, "trajectory-reader-class"]], "Trajectory Writer class": [[80, "trajectory-writer-class"]], "Single Frame Writer class": [[80, "single-frame-writer-class"]], "Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory": [[81, "reading-trajectories-from-memory-mdanalysis-coordinates-memory"]], "How to use the MemoryReader": [[81, "how-to-use-the-memoryreader"]], "In-memory representation of arbitrary trajectories": [[81, "in-memory-representation-of-arbitrary-trajectories"]], "Switching a trajectory to an in-memory representation": [[81, "switching-a-trajectory-to-an-in-memory-representation"]], "Constructing a Reader from a numpy array": [[81, "constructing-a-reader-from-a-numpy-array"]], "Creating an in-memory trajectory of a sub-system": [[81, "creating-an-in-memory-trajectory-of-a-sub-system"]], "Null output \u2014 MDAnalysis.coordinates.null": [[82, "null-output-mdanalysis-coordinates-null"]], "Serialization of Coordinate Readers": [[83, "serialization-of-coordinate-readers"]], "How to serialize a new reader": [[83, "how-to-serialize-a-new-reader"]], "File Access": [[83, "file-access"]], "To seek or not to seek": [[83, "to-seek-or-not-to-seek"]], "Miscellaneous": [[83, "miscellaneous"]], "Tests": [[83, "tests"], [166, "tests"]], "_SingleFrameReader Test": [[83, "singleframereader-test"]], "BaseReaderTest and MultiframeReaderTest": [[83, "basereadertest-and-multiframereadertest"]], "File handler Test": [[83, "file-handler-test"]], "Currently implemented picklable IO Formats": [[83, "currently-implemented-picklable-io-formats"]], "Timestep Class \u2014 MDAnalysis.coordinates.timestep": [[84, "timestep-class-mdanalysis-coordinates-timestep"]], "Timestep": [[84, "timestep"]], "Coordinates modules": [[85, "coordinates-modules"]], "AtomGroup accessors \u2014 MDAnalysis.core.accessors": [[86, "atomgroup-accessors-mdanalysis-core-accessors"]], "Core objects: Containers \u2014 MDAnalysis.core.groups": [[87, "core-objects-containers-mdanalysis-core-groups"]], "Collections": [[87, "collections"]], "Chemical units": [[87, "chemical-units"]], "Levels": [[87, "levels"]], "Core functions of MDAnalysis": [[88, "core-functions-of-mdanalysis"]], "Atom selection Hierarchy \u2014 MDAnalysis.core.selection": [[89, "atom-selection-hierarchy-mdanalysis-core-selection"]], "Core Topology object \u2014 MDAnalysis.core.topology": [[90, "core-topology-object-mdanalysis-core-topology"]], "Topology attribute objects \u2014 MDAnalysis.core.topologyattrs": [[91, "topology-attribute-objects-mdanalysis-core-topologyattrs"]], "Core Topology Objects \u2014 MDAnalysis.core.topologyobjects": [[92, "core-topology-objects-mdanalysis-core-topologyobjects"]], "Core object: Universe \u2014 MDAnalysis.core.universe": [[93, "core-object-universe-mdanalysis-core-universe"]], "Core modules": [[94, "core-modules"]], "Important objects for users": [[94, "important-objects-for-users"]], "Topology system": [[94, "topology-system"]], "Selection system": [[94, "selection-system"]], "Custom exceptions and warnings \u2014 MDAnalysis.exceptions": [[95, "custom-exceptions-and-warnings-mdanalysis-exceptions"]], "Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch": [[96, "neighbor-search-wrapper-for-mdanalysis-mdanalysis-lib-neighborsearch"]], "Distance calculation library \u2014 MDAnalysis.lib.c_distances": [[97, "distance-calculation-library-mdanalysis-lib-c-distances"]], "Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp": [[98, "parallel-distance-calculation-library-mdanalysis-lib-c-distances-openmp"]], "Correlations utilities \u2014 MDAnalysis.lib.correlations": [[99, "correlations-utilities-mdanalysis-lib-correlations"]], "Autocorrelation Function": [[99, "autocorrelation-function"]], "Intermittency Function": [[99, "intermittency-function"]], "Fast distance array computation \u2014 MDAnalysis.lib.distances": [[100, "fast-distance-array-computation-mdanalysis-lib-distances"]], "Selection of acceleration (\u201cbackend\u201d)": [[100, "selection-of-acceleration-backend"]], "Available backends for accelerated distance functions.": [[100, "id1"]], "Use of the distopia library": [[100, "use-of-the-distopia-library"]], "Functions available using the distopia backend.": [[100, "id2"]], "Low-level modules for MDAnalysis.lib.distances": [[100, "low-level-modules-for-mdanalysis-lib-distances"]], "Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd": [[101, "low-level-dcd-trajectory-reading-mdanalysis-lib-formats-libdcd"]], "Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr": [[102, "low-level-gromacs-xdr-trajectory-reading-mdanalysis-lib-formats-libmdaxdr"]], "Setting up logging \u2014 MDAnalysis.lib.log": [[103, "setting-up-logging-mdanalysis-lib-log"]], "Convenience functions": [[103, "convenience-functions"]], "Other functions and classes for logging purposes": [[103, "other-functions-and-classes-for-logging-purposes"]], "Mathematical helper functions \u2014 MDAnalysis.lib.mdamath": [[104, "mathematical-helper-functions-mdanalysis-lib-mdamath"]], "Linear algebra": [[104, "linear-algebra"]], "Connectivity": [[104, "connectivity"]], "Neighbor search library \u2014 MDAnalysis.lib.nsgrid": [[105, "neighbor-search-library-mdanalysis-lib-nsgrid"]], "About the code": [[105, "about-the-code"]], "About the algorithm": [[105, "about-the-algorithm"]], "Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io": [[106, "picklable-read-only-i-o-classes-mdanalysis-lib-picklable-file-io"]], "PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree": [[107, "periodickdtree-mdanalysis-lib-pkdtree"]], "Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot": [[108, "fast-qcp-rmsd-structure-alignment-mdanalysis-lib-qcprot"]], "Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations": [[109, "homogeneous-transformation-matrices-and-quaternions-mdanalysis-lib-transformations"]], "Requirements": [[109, "requirements"]], "Helper functions \u2014 MDAnalysis.lib.util": [[110, "helper-functions-mdanalysis-lib-util"]], "Files and directories": [[110, "files-and-directories"]], "Streams": [[110, "streams"]], "Containers and lists": [[110, "containers-and-lists"]], "Arrays": [[110, "arrays"]], "File parsing": [[110, "file-parsing"]], "Data manipulation and handling": [[110, "data-manipulation-and-handling"]], "Strings": [[110, "strings"]], "Class decorators": [[110, "class-decorators"]], "Function decorators": [[110, "function-decorators"]], "Code management": [[110, "code-management"]], "Data format checks": [[110, "data-format-checks"]], "Library functions \u2014 MDAnalysis.lib": [[111, "module-MDAnalysis.lib"]], "Overview": [[111, "overview"]], "List of modules": [[111, "list-of-modules"]], "Low level file formats": [[111, "low-level-file-formats"]], "Libmdanalysis": [[111, "libmdanalysis"]], "Overview over MDAnalysis": [[112, "overview-over-mdanalysis"]], "Using MDAnalysis in python": [[112, "using-mdanalysis-in-python"]], "Examples": [[112, "examples"]], "Included trajectories": [[112, "included-trajectories"]], "Code snippets": [[112, "code-snippets"]], "Citations for the whole MDAnalysis library": [[113, "citations-for-the-whole-mdanalysis-library"]], "Citations for included algorithms and modules": [[113, "citations-for-included-algorithms-and-modules"]], "Citations using Duecredit": [[113, "citations-using-duecredit"]], "Selection commands": [[114, "selection-commands"]], "Selection Keywords": [[114, "selection-keywords"]], "Simple selections": [[114, "simple-selections"]], "Pattern matching": [[114, "pattern-matching"]], "Boolean": [[114, "boolean"]], "Geometric": [[114, "geometric"]], "Similarity and connectivity": [[114, "similarity-and-connectivity"]], "Index": [[114, "index"]], "Preexisting selections and modifiers": [[114, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[114, "dynamic-selections"]], "Ordered selections": [[114, "ordered-selections"]], "Base classes for the selection writers": [[115, "base-classes-for-the-selection-writers"]], "CHARMM selections": [[116, "charmm-selections"]], "Gromacs selections": [[117, "gromacs-selections"]], "Jmol selections": [[118, "jmol-selections"]], "PyMOL selections": [[119, "pymol-selections"]], "VMD selections": [[120, "vmd-selections"]], "Selection exporters": [[121, "selection-exporters"]], "Table of supported exporters and recognized file name extensions.": [[121, "id2"]], "How to write selections": [[121, "how-to-write-selections"]], "Single AtomGroup": [[121, "single-atomgroup"]], "Multiple selections": [[121, "multiple-selections"]], "Selection writers": [[121, "selection-writers"]], "The topology system": [[122, "the-topology-system"]], "CRD topology parser": [[123, "crd-topology-parser"]], "Todo": [[123, "id1"], [141, "id1"]], "DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser": [[124, "dl-poly-format-topology-readers-mdanalysis-topology-dlpolyparser"]], "DESRES Molecular Structure file format topology parser": [[125, "desres-molecular-structure-file-format-topology-parser"]], "Extended PDB topology parser": [[126, "extended-pdb-topology-parser"]], "FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser": [[127, "fhi-aims-topology-parser-mdanalysis-topolgy-fhiaimsparser"]], "GAMESS Topology Parser": [[128, "gamess-topology-parser"]], "GRO topology parser": [[129, "gro-topology-parser"]], "GSD topology parser": [[130, "gsd-topology-parser"]], "HOOMD XML topology parser": [[131, "hoomd-xml-topology-parser"]], "ITP topology parser": [[132, "itp-topology-parser"]], "Preprocessor variables": [[132, "preprocessor-variables"]], "LAMMPSParser": [[133, "lammpsparser"]], "Atom styles": [[133, "atom-styles"]], "MMTF Topology Parser": [[134, "mmtf-topology-parser"]], "Minimal topology parser": [[136, "minimal-topology-parser"]], "PDB Topology Parser": [[137, "pdb-topology-parser"]], "PDBQT topology parser": [[138, "pdbqt-topology-parser"]], "PQR topology parser": [[139, "pqr-topology-parser"]], "PSF topology parser": [[140, "psf-topology-parser"]], "AMBER PRMTOP topology parser": [[141, "amber-prmtop-topology-parser"]], "Gromacs portable run input TPR format parser": [[142, "gromacs-portable-run-input-tpr-format-parser"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[142, "id4"]], "Development notes": [[142, "development-notes"]], "TXYZ topology parser": [[143, "txyz-topology-parser"]], "XYZ Topology Parser": [[144, "xyz-topology-parser"]], "Base topology reader classes \u2014 MDAnalysis.topology.base": [[145, "base-topology-reader-classes-mdanalysis-topology-base"]], "Common functions for topology building \u2014 MDAnalysis.topology.core": [[146, "common-functions-for-topology-building-mdanalysis-topology-core"]], "Guessing unknown Topology information \u2014 MDAnalysis.topology.guessers": [[147, "guessing-unknown-topology-information-mdanalysis-topology-guessers"]], "Example uses of guessers": [[147, "example-uses-of-guessers"]], "Guessing elements from atom names": [[147, "guessing-elements-from-atom-names"]], "Topology readers \u2014 MDAnalysis.topology": [[148, "topology-readers-mdanalysis-topology"]], "Table of Supported Topology Formats": [[148, "id19"]], "Developer Notes": [[148, "developer-notes"]], "atoms": [[148, "atoms"]], "bonds": [[148, "bonds"]], "bondorder": [[148, "bondorder"]], "angles": [[148, "angles"]], "dihedrals": [[148, "dihedrals"]], "impropers": [[148, "impropers"]], "MDAnalysis topology tables": [[149, "mdanalysis-topology-tables"]], "Utility functions for the TPR topology parser": [[150, "utility-functions-for-the-tpr-topology-parser"]], "TPR support": [[150, "tpr-support"]], "TPRParser settings": [[150, "tprparser-settings"]], "Class definitions for the TPRParser": [[150, "class-definitions-for-the-tprparser"]], "Utilities for the TPRParser": [[150, "utilities-for-the-tprparser"]], "Topology modules": [[151, "topology-modules"]], "Trajectory transformations (\u201con-the-fly\u201d transformations)": [[152, "module-MDAnalysis.transformations"]], "Workflows": [[152, "workflows"]], "Creating transformations": [[152, "creating-transformations"]], "Creating complex transformation classes": [[152, "creating-complex-transformation-classes"]], "Creating complex transformation closure functions": [[152, "creating-complex-transformation-closure-functions"]], "Transformations in MDAnalysis": [[152, "transformations-in-mdanalysis"]], "How to transformations": [[152, "how-to-transformations"]], "Building blocks for Transformation Classes": [[152, "building-blocks-for-transformation-classes"]], "Currently implemented transformations": [[152, "currently-implemented-transformations"]], "Transformations Base Class \u2014 MDAnalysis.transformations.base": [[153, "transformations-base-class-mdanalysis-transformations-base"]], "Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions": [[154, "set-box-dimensions-mdanalysis-transformations-boxdimensions"]], "Fitting transformations \u2014 MDAnalysis.transformations.fit": [[155, "fitting-transformations-mdanalysis-transformations-fit"]], "No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump": [[156, "no-jump-trajectory-unwrapping-mdanalysis-transformations-nojump"]], "Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging": [[157, "trajectory-coordinate-averaging-mdanalysis-transformations-positionaveraging"]], "Trajectory rotation \u2014 MDAnalysis.transformations.rotate": [[158, "trajectory-rotation-mdanalysis-transformations-rotate"]], "Trajectory translation \u2014 MDAnalysis.transformations.translate": [[159, "trajectory-translation-mdanalysis-transformations-translate"]], "Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap": [[160, "wrap-unwrap-transformations-mdanalysis-transformations-wrap"]], "Constants and unit conversion \u2014 MDAnalysis.units": [[161, "constants-and-unit-conversion-mdanalysis-units"]], "Base units in MDAnalysis as encoded in MDANALYSIS_BASE_UNITS": [[161, "id71"]], "Implementation notes": [[161, "implementation-notes"]], "Conversions": [[161, "conversions"]], "References and footnotes": [[161, "references-and-footnotes"]], "Version information for MDAnalysis - MDAnalysis.version": [[162, "version-information-for-mdanalysis-mdanalysis-version"]], "Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines": [[163, "streamplots-2d-mdanalysis-visualization-streamlines"]], "Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D": [[164, "streamplots-3d-mdanalysis-visualization-streamlines-3d"]], "Visualization modules": [[165, "visualization-modules"]], "Visualization of Lipid Flow": [[165, "visualization-of-lipid-flow"]], "MDAnalysis documentation": [[166, "mdanalysis-documentation"]], "Getting involved": [[166, "getting-involved"]], "User Guide": [[166, "user-guide"]], "Installing MDAnalysis": [[166, "installing-mdanalysis"]], "conda": [[166, "conda"]], "pip": [[166, "pip"]], "Source Code": [[166, "source-code"]], "Citation": [[166, "citation"]], "Indices and tables": [[166, "indices-and-tables"]]}, "indexentries": {"aligntraj (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AlignTraj"]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure"]], "mdanalysis.analysis.align": [[0, "module-MDAnalysis.analysis.align"]], "_fit_to() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align._fit_to"]], "alignto() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.alignto"]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select"]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename"]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename"]], "get_matching_atoms() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.get_matching_atoms"]], "mobile_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.mobile_atoms"]], "mobile_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.mobile_atoms"]], "module": [[0, "module-MDAnalysis.analysis.align"], [1, "module-MDAnalysis.analysis.atomicdistances"], [2, "module-MDAnalysis.analysis.base"], [3, "module-MDAnalysis.analysis.bat"], [4, "module-MDAnalysis.analysis.contacts"], [5, "module-MDAnalysis.analysis.data.filenames"], [6, "module-MDAnalysis.analysis.density"], [7, "module-MDAnalysis.analysis.dielectric"], [8, "module-MDAnalysis.analysis.diffusionmap"], [9, "module-MDAnalysis.analysis.dihedrals"], [10, "module-MDAnalysis.analysis.distances"], [12, "module-MDAnalysis.analysis.encore.bootstrap"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"], [13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"], [13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"], [13, "module-MDAnalysis.analysis.encore.clustering.cluster"], [14, "module-MDAnalysis.analysis.encore.confdistmatrix"], [15, "module-MDAnalysis.analysis.encore.covariance"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"], [16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"], [17, "module-MDAnalysis.analysis.encore.similarity"], [18, "module-MDAnalysis.analysis.encore.utils"], [19, "module-MDAnalysis.analysis.gnm"], [20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"], [21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"], [22, "module-MDAnalysis.analysis.helix_analysis"], [23, "module-MDAnalysis.analysis.hole2"], [23, "module-MDAnalysis.analysis.hole2.templates"], [23, "module-MDAnalysis.analysis.hole2.utils"], [24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"], [25, "module-MDAnalysis.analysis.leaflet"], [26, "module-MDAnalysis.analysis.legacy.x3dna"], [28, "module-MDAnalysis.analysis.lineardensity"], [29, "module-MDAnalysis.analysis.msd"], [30, "module-MDAnalysis.analysis.nucleicacids"], [31, "module-MDAnalysis.analysis.nuclinfo"], [32, "module-MDAnalysis.analysis.pca"], [33, "module-MDAnalysis.analysis.polymer"], [34, "module-MDAnalysis.analysis.psa"], [35, "module-MDAnalysis.analysis.rdf"], [36, "module-MDAnalysis.analysis.rms"], [37, "module-MDAnalysis.analysis.waterdynamics"], [38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"], [40, "module-MDAnalysis.auxiliary.EDR"], [41, "module-MDAnalysis.auxiliary.XVG"], [42, "module-MDAnalysis.auxiliary.base"], [43, "module-MDAnalysis.auxiliary.core"], [44, "module-MDAnalysis.auxiliary.__init__"], [46, "module-MDAnalysis.converters"], [47, "module-MDAnalysis.converters.OpenMM"], [47, "module-MDAnalysis.converters.OpenMMParser"], [48, "module-MDAnalysis.converters.ParmEd"], [48, "module-MDAnalysis.converters.ParmEdParser"], [49, "module-MDAnalysis.converters.RDKit"], [49, "module-MDAnalysis.converters.RDKitParser"], [50, "module-MDAnalysis.converters.base"], [51, "module-MDAnalysis.coordinates.CRD"], [52, "module-MDAnalysis.coordinates.DCD"], [53, "module-MDAnalysis.coordinates.DLPoly"], [54, "module-MDAnalysis.coordinates.DMS"], [55, "module-MDAnalysis.coordinates.FHIAIMS"], [56, "module-MDAnalysis.coordinates.GMS"], [57, "module-MDAnalysis.coordinates.GRO"], [58, "module-MDAnalysis.coordinates.GSD"], [59, "module-MDAnalysis.coordinates.H5MD"], [60, "module-MDAnalysis.coordinates.INPCRD"], [61, "module-MDAnalysis.coordinates.LAMMPS"], [62, "module-MDAnalysis.coordinates.MMTF"], [63, "module-MDAnalysis.coordinates.MOL2"], [64, "module-MDAnalysis.coordinates.NAMDBIN"], [65, "module-MDAnalysis.coordinates.PDB"], [66, "module-MDAnalysis.coordinates.PDBQT"], [67, "module-MDAnalysis.coordinates.PQR"], [68, "module-MDAnalysis.coordinates.TNG"], [69, "module-MDAnalysis.coordinates.TRJ"], [70, "module-MDAnalysis.coordinates.TRR"], [71, "module-MDAnalysis.coordinates.TRZ"], [72, "module-MDAnalysis.coordinates.TXYZ"], [73, "module-MDAnalysis.coordinates.XDR"], [74, "module-MDAnalysis.coordinates.XTC"], [75, "module-MDAnalysis.coordinates.XYZ"], [76, "module-MDAnalysis.coordinates.base"], [77, "module-MDAnalysis.coordinates.chain"], [78, "module-MDAnalysis.coordinates.chemfiles"], [79, "module-MDAnalysis.coordinates.core"], [80, "module-MDAnalysis.coordinates.__init__"], [81, "module-MDAnalysis.coordinates.memory"], [82, "module-MDAnalysis.coordinates.null"], [84, "module-MDAnalysis.coordinates.timestep"], [86, "module-MDAnalysis.core.accessors"], [87, "module-MDAnalysis.core.groups"], [88, "module-MDAnalysis.core.__init__"], [89, "module-MDAnalysis.core.selection"], [90, "module-MDAnalysis.core.topology"], [91, "module-MDAnalysis.core.topologyattrs"], [92, "module-MDAnalysis.core.topologyobjects"], [93, "module-MDAnalysis.core.universe"], [95, "module-MDAnalysis.exceptions"], [96, "module-MDAnalysis.lib.NeighborSearch"], [97, "module-MDAnalysis.lib.c_distances"], [98, "module-MDAnalysis.lib.c_distances_openmp"], [99, "module-MDAnalysis.lib.correlations"], [100, "module-MDAnalysis.lib.distances"], [101, "module-MDAnalysis.lib.formats.libdcd"], [102, "module-MDAnalysis.lib.formats.libmdaxdr"], [103, "module-MDAnalysis.lib.log"], [104, "module-MDAnalysis.lib.mdamath"], [105, "module-MDAnalysis.lib.nsgrid"], [106, "module-MDAnalysis.lib.picklable_file_io"], [107, "module-MDAnalysis.lib.pkdtree"], [108, "module-MDAnalysis.lib.qcprot"], [109, "module-MDAnalysis.lib.transformations"], [110, "module-MDAnalysis.lib.util"], [111, "module-MDAnalysis.lib"], [115, "module-MDAnalysis.selections.base"], [116, "module-MDAnalysis.selections.charmm"], [117, "module-MDAnalysis.selections.gromacs"], [118, "module-MDAnalysis.selections.jmol"], [119, "module-MDAnalysis.selections.pymol"], [120, "module-MDAnalysis.selections.vmd"], [123, "module-MDAnalysis.topology.CRDParser"], [124, "module-MDAnalysis.topology.DLPolyParser"], [125, "module-MDAnalysis.topology.DMSParser"], [126, "module-MDAnalysis.topology.ExtendedPDBParser"], [127, "module-MDAnalysis.topology.FHIAIMSParser"], [128, "module-MDAnalysis.topology.GMSParser"], [129, "module-MDAnalysis.topology.GROParser"], [130, "module-MDAnalysis.topology.GSDParser"], [131, "module-MDAnalysis.topology.HoomdXMLParser"], [132, "module-MDAnalysis.topology.ITPParser"], [133, "module-MDAnalysis.topology.LAMMPSParser"], [134, "module-MDAnalysis.topology.MMTFParser"], [135, "module-MDAnalysis.topology.MOL2Parser"], [136, "module-MDAnalysis.topology.MinimalParser"], [137, "module-MDAnalysis.topology.PDBParser"], [138, "module-MDAnalysis.topology.PDBQTParser"], [139, "module-MDAnalysis.topology.PQRParser"], [140, "module-MDAnalysis.topology.PSFParser"], [141, "module-MDAnalysis.topology.TOPParser"], [142, "module-MDAnalysis.topology.TPRParser"], [143, "module-MDAnalysis.topology.TXYZParser"], [144, "module-MDAnalysis.topology.XYZParser"], [145, "module-MDAnalysis.topology.base"], [146, "module-MDAnalysis.topology.core"], [147, "module-MDAnalysis.topology.guessers"], [148, "module-MDAnalysis.topology.__init__"], [149, "module-MDAnalysis.topology.tables"], [150, "module-MDAnalysis.topology.tpr"], [150, "module-MDAnalysis.topology.tpr.obj"], [150, "module-MDAnalysis.topology.tpr.setting"], [150, "module-MDAnalysis.topology.tpr.utils"], [152, "module-MDAnalysis.transformations"], [153, "module-MDAnalysis.transformations.base"], [154, "module-MDAnalysis.transformations.boxdimensions"], [155, "module-MDAnalysis.transformations.fit"], [156, "module-MDAnalysis.transformations.nojump"], [157, "module-MDAnalysis.transformations.positionaveraging"], [158, "module-MDAnalysis.transformations.rotate"], [159, "module-MDAnalysis.transformations.translate"], [160, "module-MDAnalysis.transformations.wrap"], [161, "module-MDAnalysis.units"], [162, "module-MDAnalysis.version"], [163, "module-MDAnalysis.visualization.streamlines"], [164, "module-MDAnalysis.visualization.streamlines_3D"]], "positions (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.positions"]], "positions (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.positions"]], "reference_atoms (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.reference_atoms"]], "reference_atoms (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.reference_atoms"]], "rmsd (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.rmsd"]], "rmsd (mdanalysis.analysis.align.aligntraj.results attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.results.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.rmsd"]], "rmsd (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.rmsd"]], "rotation_matrix() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.rotation_matrix"]], "sequence_alignment() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.sequence_alignment"]], "universe (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.universe"]], "universe (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.universe"]], "atomicdistances (class in mdanalysis.analysis.atomicdistances)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances"]], "mdanalysis.analysis.atomicdistances": [[1, "module-MDAnalysis.analysis.atomicdistances"]], "n_atoms (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_atoms"]], "n_frames (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.n_frames"]], "results (mdanalysis.analysis.atomicdistances.atomicdistances attribute)": [[1, "MDAnalysis.analysis.atomicdistances.AtomicDistances.results"]], "analysisbase (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisBase"]], "analysisfromfunction (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction"]], "mdanalysis.analysis.base": [[2, "module-MDAnalysis.analysis.base"]], "results (class in mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.Results"]], "analysis_class() (in module mdanalysis.analysis.base)": [[2, "MDAnalysis.analysis.base.analysis_class"]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.frames"]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames"]], "frames (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.frames"]], "results (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.results"]], "run() (mdanalysis.analysis.base.analysisbase method)": [[2, "MDAnalysis.analysis.base.AnalysisBase.run"]], "times (mdanalysis.analysis.base.analysisbase attribute)": [[2, "MDAnalysis.analysis.base.AnalysisBase.times"]], "times (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.times"]], "times (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.times"]], "timeseries (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[2, "MDAnalysis.analysis.base.AnalysisFromFunction.results.timeseries"]], "timeseries (mdanalysis.analysis.base.results attribute)": [[2, "MDAnalysis.analysis.base.results.timeseries"]], "bat (class in mdanalysis.analysis.bat)": [[3, "MDAnalysis.analysis.bat.BAT"]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.Cartesian"]], "mdanalysis.analysis.bat": [[3, "module-MDAnalysis.analysis.bat"]], "atoms (mdanalysis.analysis.bat.bat property)": [[3, "MDAnalysis.analysis.bat.BAT.atoms"]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[3, "MDAnalysis.analysis.bat.BAT.results.bat"]], "load() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.load"]], "run() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.run"]], "save() (mdanalysis.analysis.bat.bat method)": [[3, "MDAnalysis.analysis.bat.BAT.save"]], "contacts (class in mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.Contacts"]], "mdanalysis.analysis.contacts": [[4, "module-MDAnalysis.analysis.contacts"]], "contact_matrix() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.contact_matrix"]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.hard_cut_q"]], "q1q2() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.q1q2"]], "radius_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.radius_cut_q"]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[4, "MDAnalysis.analysis.contacts.soft_cut_q"]], "timeseries (mdanalysis.analysis.contacts.contacts attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.timeseries"]], "timeseries (mdanalysis.analysis.contacts.contacts.results attribute)": [[4, "MDAnalysis.analysis.contacts.Contacts.results.timeseries"]], "janin_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Janin_ref"]], "mdanalysis.analysis.data.filenames": [[5, "module-MDAnalysis.analysis.data.filenames"]], "rama_ref (in module mdanalysis.analysis.data.filenames)": [[5, "MDAnalysis.analysis.data.filenames.Rama_ref"]], "density (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.Density"]], "densityanalysis (class in mdanalysis.analysis.density)": [[6, "MDAnalysis.analysis.density.DensityAnalysis"]], "mdanalysis.analysis.density": [[6, "module-MDAnalysis.analysis.density"]], "_set_user_grid() (mdanalysis.analysis.density.densityanalysis static method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis._set_user_grid"]], "centers() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.centers"]], "check_compatible() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.check_compatible"]], "convert_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_density"]], "convert_length() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.convert_length"]], "default_format (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.default_format"]], "delta (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.delta"]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.density"]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.results.density"]], "edges (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.edges"]], "export() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.export"]], "grid (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.grid"]], "interpolated (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolated"]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[6, "MDAnalysis.analysis.density.Density.interpolation_spline_order"]], "load() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.load"]], "make_density() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.make_density"]], "origin (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.origin"]], "resample() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample"]], "resample_factor() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.resample_factor"]], "run() (mdanalysis.analysis.density.densityanalysis method)": [[6, "MDAnalysis.analysis.density.DensityAnalysis.run"]], "save() (mdanalysis.analysis.density.density method)": [[6, "MDAnalysis.analysis.density.Density.save"]], "units (mdanalysis.analysis.density.density attribute)": [[6, "MDAnalysis.analysis.density.Density.units"]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant"]], "m (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M"]], "m2 (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.M2"]], "mdanalysis.analysis.dielectric": [[7, "module-MDAnalysis.analysis.dielectric"]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps"]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean"]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[7, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct"]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap"]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix"]], "mdanalysis.analysis.diffusionmap": [[8, "module-MDAnalysis.analysis.diffusionmap"]], "atoms (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.atoms"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix"]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix"]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues"]], "run() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.run"]], "transform() (mdanalysis.analysis.diffusionmap.diffusionmap method)": [[8, "MDAnalysis.analysis.diffusionmap.DiffusionMap.transform"]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral"]], "janin (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Janin"]], "mdanalysis.analysis.dihedrals": [[9, "module-MDAnalysis.analysis.dihedrals"]], "ramachandran (class in mdanalysis.analysis.dihedrals)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran"]], "angles (mdanalysis.analysis.dihedrals.dihedral attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.angles"]], "angles (mdanalysis.analysis.dihedrals.dihedral.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.results.angles"]], "angles (mdanalysis.analysis.dihedrals.janin attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.angles"]], "angles (mdanalysis.analysis.dihedrals.janin.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Janin.results.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.angles"]], "angles (mdanalysis.analysis.dihedrals.ramachandran.results attribute)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.results.angles"]], "plot() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.plot"]], "plot() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.plot"]], "run() (mdanalysis.analysis.dihedrals.dihedral method)": [[9, "MDAnalysis.analysis.dihedrals.Dihedral.run"]], "run() (mdanalysis.analysis.dihedrals.janin method)": [[9, "MDAnalysis.analysis.dihedrals.Janin.run"]], "run() (mdanalysis.analysis.dihedrals.ramachandran method)": [[9, "MDAnalysis.analysis.dihedrals.Ramachandran.run"]], "mdanalysis.analysis.distances": [[10, "module-MDAnalysis.analysis.distances"]], "between() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.between"]], "contact_matrix() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.contact_matrix"]], "dist() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.dist"]], "distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.distance_array"]], "self_distance_array() (in module mdanalysis.analysis.distances)": [[10, "MDAnalysis.analysis.distances.self_distance_array"]], "mdanalysis.analysis.encore.bootstrap": [[12, "module-MDAnalysis.analysis.encore.bootstrap"]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix"]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_distance_matrix_bootstrap_samples"]], "get_ensemble_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": [[12, "MDAnalysis.analysis.encore.bootstrap.get_ensemble_bootstrap_samples"]], "affinitypropagation (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagation"]], "affinitypropagation() (in module mdanalysis.analysis.encore.clustering.affinityprop)": [[13, "MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation"]], "affinitypropagationnative (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.AffinityPropagationNative"]], "cluster (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster"]], "clustercollection (class in mdanalysis.analysis.encore.clustering.clustercollection)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection"]], "clusteringmethod (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.ClusteringMethod"]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN"]], "kmeans (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans"]], "mdanalysis.analysis.encore.clustering.clustercollection": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusterCollection"]], "mdanalysis.analysis.encore.clustering.clusteringmethod": [[13, "module-MDAnalysis.analysis.encore.clustering.ClusteringMethod"]], "mdanalysis.analysis.encore.clustering.affinityprop": [[13, "module-MDAnalysis.analysis.encore.clustering.affinityprop"]], "mdanalysis.analysis.encore.clustering.cluster": [[13, "module-MDAnalysis.analysis.encore.clustering.cluster"]], "accepts_distance_matrix (mdanalysis.analysis.encore.clustering.clusteringmethod.kmeans attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans.accepts_distance_matrix"]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid"]], "cluster() (in module mdanalysis.analysis.encore.clustering.cluster)": [[13, "MDAnalysis.analysis.encore.clustering.cluster.cluster"]], "clusters (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.clusters"]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements"]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[13, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info"]], "get_centroids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_centroids"]], "get_ids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_ids"]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id"]], "metadata (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.metadata"]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[13, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size"]], "mdanalysis.analysis.encore.confdistmatrix": [[14, "module-MDAnalysis.analysis.encore.confdistmatrix"]], "conformational_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.conformational_distance_matrix"]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix"]], "set_rmsd_matrix_elements() (in module mdanalysis.analysis.encore.confdistmatrix)": [[14, "MDAnalysis.analysis.encore.confdistmatrix.set_rmsd_matrix_elements"]], "mdanalysis.analysis.encore.covariance": [[15, "module-MDAnalysis.analysis.encore.covariance"]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.covariance_matrix"]], "ml_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.ml_covariance_estimator"]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[15, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator"]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod"]], "mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality"]], "mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed": [[16, "module-MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed"]], "principalcomponentanalysis (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.PrincipalComponentAnalysis"]], "stochasticproximityembedding() (in module mdanalysis.analysis.encore.dimensionality_reduction.stochasticproxembed)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed.StochasticProximityEmbedding"]], "stochasticproximityembeddingnative (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.StochasticProximityEmbeddingNative"]], "reduce_dimensionality() (in module mdanalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality)": [[16, "MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality.reduce_dimensionality"]], "mdanalysis.analysis.encore.similarity": [[17, "module-MDAnalysis.analysis.encore.similarity"]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces"]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.ces_convergence"]], "clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.clustering_ensemble_similarity"]], "cumulative_clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity"]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs"]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity"]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence"]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence"]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres"]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.dres_convergence"]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs"]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity"]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.hes"]], "prepare_ensembles_for_convergence_increasing_window() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.prepare_ensembles_for_convergence_increasing_window"]], "write_output() (in module mdanalysis.analysis.encore.similarity)": [[17, "MDAnalysis.analysis.encore.similarity.write_output"]], "mdanalysis.analysis.encore.utils": [[18, "module-MDAnalysis.analysis.encore.utils"]], "parallelcalculation (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation"]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[18, "MDAnalysis.analysis.encore.cutils.PureRMSD"]], "triangularmatrix (class in mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix"]], "args (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.args"]], "as_array() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.as_array"]], "function (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.function"]], "kwargs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.kwargs"]], "loadz() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.loadz"]], "merge_universes() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.merge_universes"]], "n_jobs (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.n_jobs"]], "nruns (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.nruns"]], "run() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.run"]], "savez() (mdanalysis.analysis.encore.utils.triangularmatrix method)": [[18, "MDAnalysis.analysis.encore.utils.TriangularMatrix.savez"]], "trm_indices() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices"]], "trm_indices_diag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_diag"]], "trm_indices_nodiag() (in module mdanalysis.analysis.encore.utils)": [[18, "MDAnalysis.analysis.encore.utils.trm_indices_nodiag"]], "worker() (mdanalysis.analysis.encore.utils.parallelcalculation method)": [[18, "MDAnalysis.analysis.encore.utils.ParallelCalculation.worker"]], "gnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis"]], "mdanalysis.analysis.gnm": [[19, "module-MDAnalysis.analysis.gnm"]], "closecontactgnmanalysis (class in mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis"]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues"]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues"]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors"]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors"]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.generate_grid"]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff"]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff"]], "order_list() (in module mdanalysis.analysis.gnm)": [[19, "MDAnalysis.analysis.gnm.order_list"]], "times (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.GNMAnalysis.results.times"]], "times (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[19, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.times"]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel"]], "mdanalysis.analysis.hydrogenbonds.hbond_autocorrel": [[20, "module-MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel"]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors"]], "run() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.run"]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[20, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve"]], "mdanalysis.analysis.hbonds.hbond_autocorrel": [[21, "module-MDAnalysis.analysis.hbonds.hbond_autocorrel"]], "mdanalysis.analysis.helix_analysis": [[22, "module-MDAnalysis.analysis.helix_analysis"]], "holeanalysis (class in mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis"]], "mdanalysis.analysis.hole2": [[23, "module-MDAnalysis.analysis.hole2"]], "mdanalysis.analysis.hole2.templates": [[23, "module-MDAnalysis.analysis.hole2.templates"]], "mdanalysis.analysis.hole2.utils": [[23, "module-MDAnalysis.analysis.hole2.utils"]], "path": [[23, "index-0"], [23, "index-1"], [110, "index-0"]], "simple2_rad (in module mdanalysis.analysis.hole2.templates)": [[23, "MDAnalysis.analysis.hole2.templates.SIMPLE2_RAD"]], "bin_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.bin_radii"]], "check_and_fix_long_filename() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.check_and_fix_long_filename"]], "collect_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.collect_hole"]], "create_vmd_surface() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.create_vmd_surface"]], "create_vmd_surface() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.create_vmd_surface"]], "delete_temporary_files() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.delete_temporary_files"]], "environment variable": [[23, "index-0"], [23, "index-1"], [69, "index-0"], [69, "index-1"], [110, "index-0"], [110, "index-1"], [113, "index-0"], [153, "index-0"]], "gather() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.gather"]], "guess_cpoint() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.guess_cpoint"]], "histogram_radii() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.histogram_radii"]], "hole() (in module mdanalysis.analysis.hole2)": [[23, "MDAnalysis.analysis.hole2.hole"]], "min_radius() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.min_radius"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.outfiles"]], "outfiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.outfiles"]], "over_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.over_order_parameters"]], "plot() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot"]], "plot3d() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D"]], "plot3d_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot3D_order_parameters"]], "plot_mean_profile() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_mean_profile"]], "plot_order_parameters() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.plot_order_parameters"]], "profiles (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.profiles"]], "profiles (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.profiles"]], "run() (mdanalysis.analysis.hole2.holeanalysis method)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.run"]], "run_hole() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.run_hole"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.sphpdbs"]], "sphpdbs (mdanalysis.analysis.hole2.holeanalysis.results attribute)": [[23, "MDAnalysis.analysis.hole2.HoleAnalysis.results.sphpdbs"]], "write_simplerad2() (in module mdanalysis.analysis.hole2.utils)": [[23, "MDAnalysis.analysis.hole2.utils.write_simplerad2"]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis"]], "mdanalysis.analysis.hydrogenbonds.hbond_analysis": [[24, "module-MDAnalysis.analysis.hydrogenbonds.hbond_analysis"]], "count_by_ids() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_ids"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type"]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors"]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors"]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds"]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds"]], "lifetime() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[24, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.lifetime"]], "leafletfinder (class in mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder"]], "mdanalysis.analysis.leaflet": [[25, "module-MDAnalysis.analysis.leaflet"]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.group"]], "groups() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups"]], "groups_iter() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter"]], "optimize_cutoff() (in module mdanalysis.analysis.leaflet)": [[25, "MDAnalysis.analysis.leaflet.optimize_cutoff"]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes"]], "update() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.update"]], "write_selection() (mdanalysis.analysis.leaflet.leafletfinder method)": [[25, "MDAnalysis.analysis.leaflet.LeafletFinder.write_selection"]], "applicationerror": [[26, "MDAnalysis.analysis.legacy.x3dna.ApplicationError"], [95, "MDAnalysis.exceptions.ApplicationError"]], "mdanalysis.analysis.legacy.x3dna": [[26, "module-MDAnalysis.analysis.legacy.x3dna"]], "x3dna (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA"]], "x3dnatraj (class in mdanalysis.analysis.legacy.x3dna)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj"]], "collect() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.collect"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean"]], "mean() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean"]], "mean_std() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.mean_std"]], "mean_std() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.mean_std"]], "plot() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.plot"]], "plot() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.plot"]], "profiles (mdanalysis.analysis.legacy.x3dna.x3dna attribute)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.profiles"]], "profiles (mdanalysis.analysis.legacy.x3dna.x3dnatraj attribute)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.profiles"]], "run() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.run"]], "run() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.run"]], "run_x3dna() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.run_x3dna"]], "save() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.save"]], "save() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.save"]], "sorted_profiles_iter() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.sorted_profiles_iter"]], "sorted_profiles_iter() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.sorted_profiles_iter"]], "std() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNA.std"]], "std() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[26, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.std"]], "lineardensity (class in mdanalysis.analysis.lineardensity)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity"]], "mdanalysis.analysis.lineardensity": [[28, "module-MDAnalysis.analysis.lineardensity"]], "note (mdanalysis.analysis.lineardensity.lineardensity attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.Note"]], "results (class in mdanalysis.analysis.lineardensity)": [[28, "MDAnalysis.analysis.lineardensity.Results"]], "char (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char"]], "char_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char_std"]], "charge_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density"]], "charge_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density_stddev"]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim"]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges"]], "mass_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density"]], "mass_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.mass_density_stddev"]], "pos (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos"]], "pos_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.pos_std"]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[28, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume"]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD"]], "mdanalysis.analysis.msd": [[29, "module-MDAnalysis.analysis.msd"]], "ag (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.ag"]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac"]], "msds_by_particle (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.msds_by_particle"]], "n_frames (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_frames"]], "n_particles (mdanalysis.analysis.msd.einsteinmsd attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.n_particles"]], "run() (mdanalysis.analysis.msd.einsteinmsd method)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.run"]], "timeseries (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[29, "MDAnalysis.analysis.msd.EinsteinMSD.results.timeseries"]], "mdanalysis.analysis.nucleicacids": [[30, "module-MDAnalysis.analysis.nucleicacids"]], "nucpairdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist"]], "watsoncrickdist (class in mdanalysis.analysis.nucleicacids)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist"]], "pair_distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.pair_distances"]], "pair_distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.pair_distances"]], "run() (mdanalysis.analysis.nucleicacids.nucpairdist method)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.run"]], "run() (mdanalysis.analysis.nucleicacids.watsoncrickdist method)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.run"]], "times (mdanalysis.analysis.nucleicacids.nucpairdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.NucPairDist.times"]], "times (mdanalysis.analysis.nucleicacids.watsoncrickdist attribute)": [[30, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.times"]], "mdanalysis.analysis.nuclinfo": [[31, "module-MDAnalysis.analysis.nuclinfo"]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.hydroxyl"]], "major_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.major_pair"]], "minor_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.minor_pair"]], "phase_as() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_as"]], "phase_cp() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.phase_cp"]], "pseudo_dihe_baseflip() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip"]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors"]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_alpha"]], "tors_beta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_beta"]], "tors_chi() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_chi"]], "tors_delta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_delta"]], "tors_eps() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_eps"]], "tors_gamma() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_gamma"]], "tors_zeta() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.tors_zeta"]], "wc_pair() (in module mdanalysis.analysis.nuclinfo)": [[31, "MDAnalysis.analysis.nuclinfo.wc_pair"]], "mdanalysis.analysis.pca": [[32, "module-MDAnalysis.analysis.pca"]], "pca (class in mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.PCA"]], "cosine_content() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cosine_content"]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.cumulated_variance"]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance"]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.cumulative_overlap"]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.cumulative_overlap"]], "p_components (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.p_components"]], "p_components (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.p_components"]], "project_single_frame() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.project_single_frame"]], "rmsip() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.rmsip"]], "rmsip() (in module mdanalysis.analysis.pca)": [[32, "MDAnalysis.analysis.pca.rmsip"]], "run() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.run"]], "transform() (mdanalysis.analysis.pca.pca method)": [[32, "MDAnalysis.analysis.pca.PCA.transform"]], "variance (mdanalysis.analysis.pca.pca attribute)": [[32, "MDAnalysis.analysis.pca.PCA.variance"]], "variance (mdanalysis.analysis.pca.pca.results attribute)": [[32, "MDAnalysis.analysis.pca.PCA.results.variance"]], "mdanalysis.analysis.polymer": [[33, "module-MDAnalysis.analysis.polymer"]], "persistencelength (class in mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength"]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation"]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.fit"]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit"]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.fit_exponential_decay"]], "lb (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lb"]], "lb (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lb"]], "lp (mdanalysis.analysis.polymer.persistencelength attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.lp"]], "lp (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.lp"]], "plot() (mdanalysis.analysis.polymer.persistencelength method)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.plot"]], "sort_backbone() (in module mdanalysis.analysis.polymer)": [[33, "MDAnalysis.analysis.polymer.sort_backbone"]], "x (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[33, "MDAnalysis.analysis.polymer.PersistenceLength.results.x"]], "d (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.D"]], "mdanalysis.analysis.psa": [[34, "module-MDAnalysis.analysis.psa"]], "psapair (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAPair"]], "psanalysis (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.PSAnalysis"]], "path (class in mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.Path"]], "cluster() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.cluster"]], "discrete_frechet() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.discrete_frechet"]], "dist_mat_to_vec() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.dist_mat_to_vec"]], "fit_to_reference() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.fit_to_reference"]], "generate_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.generate_paths"]], "get_coord_axes() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_coord_axes"]], "get_msd_matrix() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_msd_matrix"]], "get_num_atoms() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_atoms"]], "get_num_atoms() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.get_num_atoms"]], "get_num_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_num_paths"]], "get_pairwise_distances() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_pairwise_distances"]], "get_path_metric_func() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.get_path_metric_func"]], "get_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.get_paths"]], "hausdorff() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff"]], "hausdorff_avg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_avg"]], "hausdorff_neighbors() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_neighbors"]], "hausdorff_pair (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.hausdorff_pair"]], "hausdorff_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.hausdorff_pairs"]], "hausdorff_wavg() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.hausdorff_wavg"]], "load() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.load"]], "matrix_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.matrix_id"]], "nearest_neighbors (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.nearest_neighbors"]], "nearest_neighbors (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.nearest_neighbors"]], "npaths (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.npaths"]], "pair_id (mdanalysis.analysis.psa.psapair attribute)": [[34, "MDAnalysis.analysis.psa.PSAPair.pair_id"]], "path (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path"]], "path_select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.path_select"]], "path_select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.path_select"]], "paths (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.paths"]], "plot() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot"]], "plot_annotated_heatmap() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_annotated_heatmap"]], "plot_nearest_neighbors() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.plot_nearest_neighbors"]], "psa_pairs (mdanalysis.analysis.psa.psanalysis property)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.psa_pairs"]], "ref_frame (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.ref_frame"]], "ref_frame (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.ref_frame"]], "run() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run"]], "run() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.run"]], "run_pairs_analysis() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.run_pairs_analysis"]], "save_paths() (mdanalysis.analysis.psa.psanalysis method)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.save_paths"]], "select (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.select"]], "select (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.select"]], "sqnorm() (in module mdanalysis.analysis.psa)": [[34, "MDAnalysis.analysis.psa.sqnorm"]], "to_path() (mdanalysis.analysis.psa.path method)": [[34, "MDAnalysis.analysis.psa.Path.to_path"]], "u_fitted (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_fitted"]], "u_original (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_original"]], "u_reference (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.u_reference"]], "u_reference (mdanalysis.analysis.psa.path attribute)": [[34, "MDAnalysis.analysis.psa.Path.u_reference"]], "universes (mdanalysis.analysis.psa.psanalysis attribute)": [[34, "MDAnalysis.analysis.psa.PSAnalysis.universes"]], "interrdf (class in mdanalysis.analysis.rdf)": [[35, "MDAnalysis.analysis.rdf.InterRDF"]], "interrdf_s (class in mdanalysis.analysis.rdf)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s"]], "mdanalysis.analysis.rdf": [[35, "module-MDAnalysis.analysis.rdf"]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.bins"]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.bins"]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.bins"]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins"]], "cdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.cdf"]], "cdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.cdf"]], "count (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.count"]], "count (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.count"]], "count (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.count"]], "count (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.count"]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.edges"]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.edges"]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.edges"]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges"]], "get_cdf() (mdanalysis.analysis.rdf.interrdf_s method)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.get_cdf"]], "rdf (mdanalysis.analysis.rdf.interrdf attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF.results.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.rdf"]], "rdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[35, "MDAnalysis.analysis.rdf.InterRDF_s.results.rdf"]], "mdanalysis.analysis.rms": [[36, "module-MDAnalysis.analysis.rms"]], "rmsd (class in mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.RMSD"]], "rmsf (class in mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.RMSF"]], "rmsd (mdanalysis.analysis.rms.rmsd attribute)": [[36, "MDAnalysis.analysis.rms.RMSD.rmsd"]], "rmsd (mdanalysis.analysis.rms.rmsd.results attribute)": [[36, "MDAnalysis.analysis.rms.RMSD.results.rmsd"]], "rmsd() (in module mdanalysis.analysis.rms)": [[36, "MDAnalysis.analysis.rms.rmsd"]], "rmsf (mdanalysis.analysis.rms.rmsf attribute)": [[36, "MDAnalysis.analysis.rms.RMSF.rmsf"]], "rmsf (mdanalysis.analysis.rms.rmsf.results attribute)": [[36, "MDAnalysis.analysis.rms.RMSF.results.rmsf"]], "run() (mdanalysis.analysis.rms.rmsd method)": [[36, "MDAnalysis.analysis.rms.RMSD.run"]], "run() (mdanalysis.analysis.rms.rmsf method)": [[36, "MDAnalysis.analysis.rms.RMSF.run"]], "angulardistribution (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.AngularDistribution"]], "mdanalysis.analysis.waterdynamics": [[37, "module-MDAnalysis.analysis.waterdynamics"]], "meansquaredisplacement (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement"]], "survivalprobability (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.SurvivalProbability"]], "waterorientationalrelaxation (class in mdanalysis.analysis.waterdynamics)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation"]], "lg2() (mdanalysis.analysis.waterdynamics.waterorientationalrelaxation static method)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.lg2"]], "run() (mdanalysis.analysis.waterdynamics.angulardistribution method)": [[37, "MDAnalysis.analysis.waterdynamics.AngularDistribution.run"]], "run() (mdanalysis.analysis.waterdynamics.meansquaredisplacement method)": [[37, "MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement.run"]], "run() (mdanalysis.analysis.waterdynamics.survivalprobability method)": [[37, "MDAnalysis.analysis.waterdynamics.SurvivalProbability.run"]], "run() (mdanalysis.analysis.waterdynamics.waterorientationalrelaxation method)": [[37, "MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation.run"]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"]], "mdanalysis.analysis.hydrogenbonds.wbridge_analysis": [[38, "module-MDAnalysis.analysis.hydrogenbonds.wbridge_analysis"]], "waterbridgeanalysis (class in mdanalysis.analysis.hydrogenbonds.wbridge_analysis)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis"]], "count_by_time() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_type"]], "generate_table() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.generate_table"]], "network (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.network"]], "network (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis.results attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.network"]], "r_cov (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.r_cov"]], "table (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.table"]], "timeseries (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timeseries"]], "timeseries (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis.results attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps"]], "timesteps_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[38, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps_by_type"]], "edrreader (class in mdanalysis.auxiliary.edr)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader"]], "edrstep (class in mdanalysis.auxiliary.edr)": [[40, "MDAnalysis.auxiliary.EDR.EDRStep"]], "mdanalysis.auxiliary.edr": [[40, "module-MDAnalysis.auxiliary.EDR"]], "_auxdata (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader._auxdata"]], "_n_steps (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader._n_steps"]], "data_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.data_dict"]], "get_data() (mdanalysis.auxiliary.edr.edrreader method)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.get_data"]], "read_all_times() (mdanalysis.auxiliary.edr.edrreader method)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.read_all_times"]], "terms (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.terms"]], "unit_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[40, "MDAnalysis.auxiliary.EDR.EDRReader.unit_dict"]], "mdanalysis.auxiliary.xvg": [[41, "module-MDAnalysis.auxiliary.XVG"]], "xvgfilereader (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGFileReader"]], "xvgreader (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGReader"]], "xvgstep (class in mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.XVGStep"]], "read_all_times() (mdanalysis.auxiliary.xvg.xvgfilereader method)": [[41, "MDAnalysis.auxiliary.XVG.XVGFileReader.read_all_times"]], "read_all_times() (mdanalysis.auxiliary.xvg.xvgreader method)": [[41, "MDAnalysis.auxiliary.XVG.XVGReader.read_all_times"]], "uncomment() (in module mdanalysis.auxiliary.xvg)": [[41, "MDAnalysis.auxiliary.XVG.uncomment"]], "auxfilereader (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader"]], "auxreader (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxReader"]], "auxstep (class in mdanalysis.auxiliary.base)": [[42, "MDAnalysis.auxiliary.base.AuxStep"]], "mdanalysis.auxiliary.base": [[42, "module-MDAnalysis.auxiliary.base"]], "attach_auxiliary() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.attach_auxiliary"]], "auxfile (mdanalysis.auxiliary.base.auxfilereader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader.auxfile"]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.auxstep"]], "calc_representative() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.calc_representative"]], "close() (mdanalysis.auxiliary.base.auxfilereader method)": [[42, "MDAnalysis.auxiliary.base.AuxFileReader.close"]], "constant_dt (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.constant_dt"]], "copy() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.copy"]], "data (mdanalysis.auxiliary.base.auxstep property)": [[42, "MDAnalysis.auxiliary.base.AuxStep.data"]], "data_selector (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.data_selector"]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.dt"]], "frame_data (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.frame_data"]], "frame_rep (mdanalysis.auxiliary.base.auxreader attribute)": [[42, "MDAnalysis.auxiliary.base.AuxReader.frame_rep"]], "get_description() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.get_description"]], "initial_time (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.initial_time"]], "move_to_ts() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.move_to_ts"]], "n_steps (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.n_steps"]], "next() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.next"]], "next_nonempty_frame() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.next_nonempty_frame"]], "read_ts() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.read_ts"]], "represent_ts_as (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.represent_ts_as"]], "rewind() (mdanalysis.auxiliary.base.auxreader method)": [[42, "MDAnalysis.auxiliary.base.AuxReader.rewind"]], "step (mdanalysis.auxiliary.base.auxreader property)": [[42, "MDAnalysis.auxiliary.base.AuxReader.step"]], "step (mdanalysis.auxiliary.base.auxstep attribute)": [[42, "MDAnalysis.auxiliary.base.AuxStep.step"]], "step_to_frame() 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"MDAnalysis.exceptions.SelectionError"]], "selectionwarning": [[95, "MDAnalysis.exceptions.SelectionWarning"]], "streamwarning": [[95, "MDAnalysis.exceptions.StreamWarning"]], "atomneighborsearch (class in mdanalysis.lib.neighborsearch)": [[96, "MDAnalysis.lib.NeighborSearch.AtomNeighborSearch"]], "mdanalysis.lib.neighborsearch": [[96, "module-MDAnalysis.lib.NeighborSearch"]], "search() (mdanalysis.lib.neighborsearch.atomneighborsearch method)": [[96, "MDAnalysis.lib.NeighborSearch.AtomNeighborSearch.search"]], "mdanalysis.lib.c_distances": [[97, "module-MDAnalysis.lib.c_distances"]], "mdanalysis.lib.c_distances_openmp": [[98, "module-MDAnalysis.lib.c_distances_openmp"]], "mdanalysis.lib.correlations": [[99, "module-MDAnalysis.lib.correlations"]], "autocorrelation() (in module mdanalysis.lib.correlations)": [[99, "MDAnalysis.lib.correlations.autocorrelation"]], "correct_intermittency() (in module mdanalysis.lib.correlations)": [[99, "MDAnalysis.lib.correlations.correct_intermittency"]], "mdanalysis.lib.distances": [[100, "module-MDAnalysis.lib.distances"]], "apply_pbc() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.apply_PBC"]], "augment_coordinates() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.augment_coordinates"]], "calc_angles() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_angles"]], "calc_bonds() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_bonds"]], "calc_dihedrals() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.calc_dihedrals"]], "capped_distance() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.capped_distance"]], "distance_array() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.distance_array"]], "minimize_vectors() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.minimize_vectors"]], "self_capped_distance() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.self_capped_distance"]], "self_distance_array() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.self_distance_array"]], "transform_rtos() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.transform_RtoS"]], "transform_stor() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.transform_StoR"]], "undo_augment() (in module mdanalysis.lib.distances)": [[100, "MDAnalysis.lib.distances.undo_augment"]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile"]], "mdanalysis.lib.formats.libdcd": [[101, "module-MDAnalysis.lib.formats.libdcd"]], "charmm_bitfield (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.charmm_bitfield"]], "close() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.close"]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.header"]], "open() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.open"]], "read() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.read"]], "readframes() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.readframes"]], "seek() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.seek"]], "tell() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.tell"]], "write() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.write"]], "write_header() (mdanalysis.lib.formats.libdcd.dcdfile method)": [[101, "MDAnalysis.lib.formats.libdcd.DCDFile.write_header"]], "mdanalysis.lib.formats.libmdaxdr": [[102, "module-MDAnalysis.lib.formats.libmdaxdr"]], "trrfile (class in mdanalysis.lib.formats.libmdaxdr)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile"]], "xtcfile (class in mdanalysis.lib.formats.libmdaxdr)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile"]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.calc_offsets"]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.calc_offsets"]], "close() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.close"]], "close() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.close"]], "offsets (mdanalysis.lib.formats.libmdaxdr.trrfile attribute)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.offsets"]], "offsets (mdanalysis.lib.formats.libmdaxdr.xtcfile attribute)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.offsets"]], "open() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.open"]], "open() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.open"]], "read() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.read"]], "read() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.read"]], "read_direct_x() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.read_direct_x"]], "read_direct_xvf() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.read_direct_xvf"]], "seek() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.seek"]], "seek() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.seek"]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.set_offsets"]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.set_offsets"]], "tell() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.tell"]], "tell() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.tell"]], "write() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.write"]], "write() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[102, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.write"]], "mdanalysis.lib.log": [[103, "module-MDAnalysis.lib.log"]], "nullhandler (class in mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.NullHandler"]], "progressbar (class in mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.ProgressBar"]], "clear_handlers() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.clear_handlers"]], "create() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.create"]], "emit() (mdanalysis.lib.log.nullhandler method)": [[103, "MDAnalysis.lib.log.NullHandler.emit"]], "start_logging() (in module mdanalysis)": [[103, "MDAnalysis.start_logging"]], "start_logging() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.start_logging"]], "stop_logging() (in module mdanalysis)": [[103, "MDAnalysis.stop_logging"]], "stop_logging() (in module mdanalysis.lib.log)": [[103, "MDAnalysis.lib.log.stop_logging"]], "mdanalysis.lib.mdamath": [[104, "module-MDAnalysis.lib.mdamath"]], "angle() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.angle"]], "box_volume() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.box_volume"]], "dihedral() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.dihedral"]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.find_fragments"]], "make_whole() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.make_whole"]], "norm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.norm"]], "normal() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.normal"]], "pdot() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pdot"]], "pnorm() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.pnorm"]], "sarrus_det() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.sarrus_det"]], "stp() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.stp"]], "triclinic_box() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_box"]], "triclinic_vectors() (in module mdanalysis.lib.mdamath)": [[104, "MDAnalysis.lib.mdamath.triclinic_vectors"]], "fastns (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.FastNS"]], "mdanalysis.lib.nsgrid": [[105, "module-MDAnalysis.lib.nsgrid"]], "nsresults (class in mdanalysis.lib.nsgrid)": [[105, "MDAnalysis.lib.nsgrid.NSResults"]], "get_pair_distances() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pair_distances"]], "get_pairs() (mdanalysis.lib.nsgrid.nsresults method)": [[105, "MDAnalysis.lib.nsgrid.NSResults.get_pairs"]], "search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.search"]], "self_search() (mdanalysis.lib.nsgrid.fastns method)": [[105, "MDAnalysis.lib.nsgrid.FastNS.self_search"]], "bz2picklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BZ2Picklable"]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable"]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.FileIOPicklable"]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.GzipPicklable"]], "mdanalysis.lib.picklable_file_io": [[106, "module-MDAnalysis.lib.picklable_file_io"]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.TextIOPicklable"]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open"]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open"]], "pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[106, "MDAnalysis.lib.picklable_file_io.pickle_open"]], "mdanalysis.lib.pkdtree": [[107, "module-MDAnalysis.lib.pkdtree"]], "periodickdtree (class in mdanalysis.lib.pkdtree)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree"]], "get_indices() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.get_indices"]], "pbc (mdanalysis.lib.pkdtree.periodickdtree property)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.pbc"]], "search() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search"]], "search_pairs() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search_pairs"]], "search_tree() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.search_tree"]], "set_coords() (mdanalysis.lib.pkdtree.periodickdtree method)": [[107, "MDAnalysis.lib.pkdtree.PeriodicKDTree.set_coords"]], "calcrmsdrotationalmatrix() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix"]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation"]], "innerproduct() (in module mdanalysis.lib.qcprot)": [[108, "MDAnalysis.lib.qcprot.InnerProduct"]], "mdanalysis.lib.qcprot": [[108, "module-MDAnalysis.lib.qcprot"]], "arcball (class in mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.Arcball"]], "mdanalysis.lib.transformations": [[109, "module-MDAnalysis.lib.transformations"]], "arcball_nearest_axis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.arcball_nearest_axis"]], "compose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.compose_matrix"]], "concatenate_matrices() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.concatenate_matrices"]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.decompose_matrix"]], "down() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.down"]], "drag() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.drag"]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.euler_from_quaternion"]], "getconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.getconstrain"]], "matrix() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.matrix"]], "next() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.next"]], "place() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.place"]], "projection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.projection_from_matrix"]], "quaternion_imag() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_imag"]], "quaternion_real() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.quaternion_real"]], "reflection_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.reflection_from_matrix"]], "rotation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotation_from_matrix"]], "rotaxis() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.rotaxis"]], "scale_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.scale_from_matrix"]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setaxes"]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[109, "MDAnalysis.lib.transformations.Arcball.setconstrain"]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.shear_from_matrix"]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[109, "MDAnalysis.lib.transformations.translation_from_matrix"]], "$home": [[110, "index-1"]], "fortranreader (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRANReader"]], "fortran_format_regex (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.FORTRAN_format_regex"]], "mdanalysis.lib.util": [[110, "module-MDAnalysis.lib.util"]], "namedstream (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.NamedStream"]], "namespace (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.Namespace"]], "_deprecate (class in mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util._Deprecate"]], "anyopen() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.anyopen"]], "asiterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.asiterable"]], "blocks_of() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.blocks_of"]], "cached() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.cached"]], "check_atomgroup_not_empty() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_atomgroup_not_empty"]], "check_box() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_box"]], "check_compressed_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_compressed_format"]], "check_coords() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.check_coords"]], "close() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.close"]], "closed (mdanalysis.lib.util.namedstream property)": [[110, "MDAnalysis.lib.util.NamedStream.closed"]], "conv_float() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.conv_float"]], "convert_aa_code() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.convert_aa_code"]], "dedent_docstring() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.dedent_docstring"]], "deprecate() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.deprecate"]], "filename() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.filename"]], "fileno() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.fileno"]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.fixedwidth_bins"]], "flatten_dict() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.flatten_dict"]], "flush() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.flush"]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.format_from_filename_extension"]], "get_ext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_ext"]], "get_weights() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.get_weights"]], "greedy_splitext() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.greedy_splitext"]], "group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.group_same_or_consecutive_integers"]], "guess_format() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.guess_format"]], "hasmethod() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.hasmethod"]], "isstream() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.isstream"]], "iterable() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.iterable"]], "ltruncate_int() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.ltruncate_int"]], "number_of_matches() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.number_of_matches"]], "openany() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.openany"]], "parse_fortran_format() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.parse_FORTRAN_format"]], "parse_residue() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.parse_residue"]], "read() (mdanalysis.lib.util.fortranreader method)": [[110, "MDAnalysis.lib.util.FORTRANReader.read"]], "readable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.readable"]], "readline() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.readline"]], "realpath() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.realpath"]], "reset() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.reset"]], "seek() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.seek"]], "seekable() (mdanalysis.lib.util.namedstream method)": [[110, "MDAnalysis.lib.util.NamedStream.seekable"]], "static_variables() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.static_variables"]], "store_init_arguments() (in module mdanalysis.lib.util)": [[110, "MDAnalysis.lib.util.store_init_arguments"]], "tell() 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"MDAnalysis.topology.TXYZParser.TXYZParser.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.convert_velocities_from_native"]], "convert_velocities_to_native() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.convert_velocities_to_native"]], "parse() (mdanalysis.topology.txyzparser.txyzparser method)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.parse"]], "units (mdanalysis.topology.txyzparser.txyzparser attribute)": [[143, "MDAnalysis.topology.TXYZParser.TXYZParser.units"]], "mdanalysis.topology.xyzparser": [[144, "module-MDAnalysis.topology.XYZParser"]], "xyzparser (class in mdanalysis.topology.xyzparser)": [[144, "MDAnalysis.topology.XYZParser.XYZParser"]], "parse() (mdanalysis.topology.xyzparser.xyzparser method)": [[144, "MDAnalysis.topology.XYZParser.XYZParser.parse"]], "mdanalysis.topology.base": [[145, "module-MDAnalysis.topology.base"]], "topologyreaderbase (class in mdanalysis.topology.base)": [[145, "MDAnalysis.topology.base.TopologyReaderBase"]], "close() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.close"]], "convert_forces_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_forces_from_native"]], "convert_forces_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_forces_to_native"]], "convert_pos_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_pos_from_native"]], "convert_pos_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_pos_to_native"]], "convert_time_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_time_from_native"]], "convert_time_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_time_to_native"]], "convert_velocities_from_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_velocities_from_native"]], "convert_velocities_to_native() (mdanalysis.topology.base.topologyreaderbase method)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.convert_velocities_to_native"]], "units (mdanalysis.topology.base.topologyreaderbase attribute)": [[145, "MDAnalysis.topology.base.TopologyReaderBase.units"]], "mdanalysis.topology.core": [[146, "module-MDAnalysis.topology.core"]], "mdanalysis.topology.guessers": [[147, "module-MDAnalysis.topology.guessers"]], "get_atom_mass() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.get_atom_mass"]], "guess_angles() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_angles"]], "guess_aromaticities() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_aromaticities"]], "guess_atom_charge() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_charge"]], "guess_atom_element() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_element"]], "guess_atom_mass() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_mass"]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_atom_type"]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_bonds"]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_dihedrals"]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_gasteiger_charges"]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_improper_dihedrals"]], "guess_masses() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_masses"]], "guess_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.guess_types"]], "validate_atom_types() (in module mdanalysis.topology.guessers)": [[147, "MDAnalysis.topology.guessers.validate_atom_types"]], "mdanalysis.topology.__init__": [[148, "module-MDAnalysis.topology.__init__"]], "mdanalysis.topology.tables": [[149, "module-MDAnalysis.topology.tables"]], "table_atomelements (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_ATOMELEMENTS"]], "table_masses (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_MASSES"]], "table_vdwradii (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.TABLE_VDWRADII"]], "atomelements (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.atomelements"]], "kv2dict() (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.kv2dict"]], "masses (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.masses"]], "vdwradii (in module mdanalysis.topology.tables)": [[149, "MDAnalysis.topology.tables.vdwradii"]], "atom (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Atom"]], "atomkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.AtomKind"]], "atoms (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Atoms"]], "box (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Box"]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGLES"]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRES"]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANGRESZ"]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL"]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM"]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BHAM_LR"]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_BONDS"]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CBTDIHS"]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CMAP"]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COM_PULL"]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONNBONDS"]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTR"]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CONSTRNC"]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL14"]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_LR"]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP"]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_COUL_SR"]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES"]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS"]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS"]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING"]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DHDL_CON"]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRES"]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL"]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISPCORR"]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRES"]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL"]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DKDL"]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DPD"]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL"]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED"]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL"]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT"]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE"]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW"]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ECONSERVED"]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EKIN"]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EPOT"]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_EQM"]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ETOT"]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FBPOSRES"]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FENEBONDS"]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_FOURDIHS"]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96ANGLES"]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_G96BONDS"]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB12"]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB13"]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GB14"]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_GBPOL"]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_HARMONIC"]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_IDIHS"]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES"]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ"]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ14"]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC14_Q"]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB"]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_LR"]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP"]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_MORSE"]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION"]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_NRE"]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRES"]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV"]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDIHS"]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PDISPCORR"]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PIDIHS"]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POLARIZATION"]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_POSRES"]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_PRES"]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES"]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RBDIHS"]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES"]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS"]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS"]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_RF_EXCL"]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_SETTLE"]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABANGLES"]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDS"]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC"]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TABDIHS"]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_TEMP"]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_THOLE_POL"]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY"]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE1"]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2"]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE2FD"]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3"]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD"]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3FD"]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT"]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FD"]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN"]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VSITEN"]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED"]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.F_WATER_POL"]], "ilist (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Ilist"]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.InteractionKind"]], "mdanalysis.topology.tpr": [[150, "module-MDAnalysis.topology.tpr"]], "mdanalysis.topology.tpr.obj": [[150, "module-MDAnalysis.topology.tpr.obj"]], "mdanalysis.topology.tpr.setting": [[150, "module-MDAnalysis.topology.tpr.setting"]], "mdanalysis.topology.tpr.utils": [[150, "module-MDAnalysis.topology.tpr.utils"]], "molblock (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Molblock"]], "moleculekind (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind"]], "mtop (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Mtop"]], "params (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.Params"]], "supported_versions (in module mdanalysis.topology.tpr)": [[150, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS"]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS"]], "tpxunpacker (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker"]], "tpxunpacker2020 (class in mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020"]], "tpxheader (class in mdanalysis.topology.tpr.obj)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader"]], "atnr (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.atnr"]], "atomnames (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atomnames"]], "atomnumber (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.atomnumber"]], "atoms (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.atoms"]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox"]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bF"]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr"]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop"]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bV"]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.bX"]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.define_unpack_real"]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atom"]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_atoms"]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_block"]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_blocka"]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ffparams"]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_harm"]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_ilists"]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_iparams"]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_molblock"]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_moltype"]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_mtop"]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_resinfo"]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_rvec"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string"]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string"]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symstr"]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.do_symtab"]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[150, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol"]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.extract_box_info"]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state"]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen"]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.fileVersion_err"]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag"]], "from_unpacker() (mdanalysis.topology.tpr.utils.tpxunpacker2020 class method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.from_unpacker"]], "ftupd (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.ftupd"]], "fudgeqq (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.fudgeQQ"]], "functype (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.functype"]], "fver (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.fver"]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.iatoms"]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.ik"]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[150, "MDAnalysis.topology.tpr.setting.interaction_types"]], "lamb (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.lamb"]], "m (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.m"]], "mb (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.mB"]], "molb_natoms_mol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_natoms_mol"]], "molb_nmol (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nmol"]], "molb_nposres_xa (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xA"]], "molb_nposres_xb (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_nposres_xB"]], "molb_type (mdanalysis.topology.tpr.obj.molblock attribute)": [[150, "MDAnalysis.topology.tpr.obj.Molblock.molb_type"]], "moltypes (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.moltypes"]], "natoms (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.natoms"]], "ndo_int() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_int"]], "ndo_ivec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_ivec"]], "ndo_real() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_real"]], "ndo_rvec() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.ndo_rvec"]], "ngtc (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.ngtc"]], "nmolblock (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.nmolblock"]], "nmoltype (mdanalysis.topology.tpr.obj.mtop attribute)": [[150, "MDAnalysis.topology.tpr.obj.Mtop.nmoltype"]], "nr (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.nr"]], "nr (mdanalysis.topology.tpr.obj.ilist attribute)": [[150, "MDAnalysis.topology.tpr.obj.Ilist.nr"]], "nres (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.nres"]], "ntypes (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.ntypes"]], "number_of_atoms() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_atoms"]], "number_of_residues() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.number_of_residues"]], "precision (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.precision"]], "process() (mdanalysis.topology.tpr.obj.interactionkind method)": [[150, "MDAnalysis.topology.tpr.obj.InteractionKind.process"]], "ptype (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.ptype"]], "q (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.q"]], "qb (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.qB"]], "read_tpxheader() (in module mdanalysis.topology.tpr.utils)": [[150, "MDAnalysis.topology.tpr.utils.read_tpxheader"]], "rel (mdanalysis.topology.tpr.obj.box attribute)": [[150, "MDAnalysis.topology.tpr.obj.Box.rel"]], "remap_angles() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.remap_angles"]], "remap_bonds() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.remap_bonds"]], "remap_dihe() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.remap_dihe"]], "remap_impr() (mdanalysis.topology.tpr.obj.moleculekind method)": [[150, "MDAnalysis.topology.tpr.obj.MoleculeKind.remap_impr"]], "reppow (mdanalysis.topology.tpr.obj.params attribute)": [[150, "MDAnalysis.topology.tpr.obj.Params.reppow"]], "resind (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.resind"]], "resnames (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.resnames"]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[150, "MDAnalysis.topology.tpr.obj.Box.size"]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody"]], "tp (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.tp"]], "type (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.type"]], "typeb (mdanalysis.topology.tpr.obj.atom attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atom.typeB"]], "typeb (mdanalysis.topology.tpr.obj.atoms attribute)": [[150, "MDAnalysis.topology.tpr.obj.Atoms.typeB"]], "unpack_fstring() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.unpack_fstring"]], "unpack_int64() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.unpack_int64"]], "unpack_uchar() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.unpack_uchar"]], "unpack_uchar() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.unpack_uchar"]], "unpack_uint64() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.unpack_uint64"]], "unpack_ushort() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker.unpack_ushort"]], "unpack_ushort() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[150, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.unpack_ushort"]], "v (mdanalysis.topology.tpr.obj.box attribute)": [[150, "MDAnalysis.topology.tpr.obj.Box.v"]], "ver_str (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[150, "MDAnalysis.topology.tpr.obj.TpxHeader.ver_str"]], "mdanalysis.transformations": [[152, "module-MDAnalysis.transformations"]], "mdanalysis.transformations.base": [[153, "module-MDAnalysis.transformations.base"]], "omp_num_threads": [[153, "index-0"]], "transformationbase (class in mdanalysis.transformations.base)": [[153, "MDAnalysis.transformations.base.TransformationBase"]], "mdanalysis.transformations.boxdimensions": [[154, "module-MDAnalysis.transformations.boxdimensions"]], "set_dimensions (class in mdanalysis.transformations.boxdimensions)": [[154, "MDAnalysis.transformations.boxdimensions.set_dimensions"]], "mdanalysis.transformations.fit": [[155, "module-MDAnalysis.transformations.fit"]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[155, "MDAnalysis.transformations.fit.fit_rot_trans"]], "fit_translation (class in mdanalysis.transformations.fit)": [[155, "MDAnalysis.transformations.fit.fit_translation"]], "mdanalysis.transformations.nojump": [[156, "module-MDAnalysis.transformations.nojump"]], "nojump (class in mdanalysis.transformations.nojump)": [[156, "MDAnalysis.transformations.nojump.NoJump"]], "mdanalysis.transformations.positionaveraging": [[157, "module-MDAnalysis.transformations.positionaveraging"]], "positionaverager (class in mdanalysis.transformations.positionaveraging)": [[157, "MDAnalysis.transformations.positionaveraging.PositionAverager"]], "mdanalysis.transformations.rotate": [[158, "module-MDAnalysis.transformations.rotate"]], "rotateby (class in mdanalysis.transformations.rotate)": [[158, "MDAnalysis.transformations.rotate.rotateby"]], "mdanalysis.transformations.translate": [[159, "module-MDAnalysis.transformations.translate"]], "center_in_box (class in mdanalysis.transformations.translate)": [[159, "MDAnalysis.transformations.translate.center_in_box"]], "translate (class in mdanalysis.transformations.translate)": [[159, "MDAnalysis.transformations.translate.translate"]], "mdanalysis.transformations.wrap": [[160, "module-MDAnalysis.transformations.wrap"]], "unwrap (class in mdanalysis.transformations.wrap)": [[160, "MDAnalysis.transformations.wrap.unwrap"]], "wrap (class in mdanalysis.transformations.wrap)": [[160, "MDAnalysis.transformations.wrap.wrap"]], "mdanalysis_base_units (in module mdanalysis.units)": [[161, "MDAnalysis.units.MDANALYSIS_BASE_UNITS"]], "mdanalysis.units": [[161, "module-MDAnalysis.units"]], "chargeunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.chargeUnit_factor"]], "constants (in module mdanalysis.units)": [[161, "MDAnalysis.units.constants"]], "conversion_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.conversion_factor"]], "convert() (in module mdanalysis.units)": [[161, "MDAnalysis.units.convert"]], "densityunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.densityUnit_factor"]], "forceunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.forceUnit_factor"]], "get_conversion_factor() (in module mdanalysis.units)": [[161, "MDAnalysis.units.get_conversion_factor"]], "lengthunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.lengthUnit_factor"]], "speedunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.speedUnit_factor"]], "timeunit_factor (in module mdanalysis.units)": [[161, "MDAnalysis.units.timeUnit_factor"]], "unit_types (in module mdanalysis.units)": [[161, "MDAnalysis.units.unit_types"]], "water (in module mdanalysis.units)": [[161, "MDAnalysis.units.water"]], "mdanalysis.version": [[162, "module-MDAnalysis.version"]], "__version__ (in module mdanalysis.version)": [[162, "MDAnalysis.version.__version__"]], "mdanalysis.visualization.streamlines": [[163, "module-MDAnalysis.visualization.streamlines"]], "generate_streamlines() (in module mdanalysis.visualization.streamlines)": [[163, "MDAnalysis.visualization.streamlines.generate_streamlines"]], "mdanalysis.visualization.streamlines_3d": [[164, "module-MDAnalysis.visualization.streamlines_3D"]], "generate_streamlines_3d() (in module mdanalysis.visualization.streamlines_3d)": [[164, "MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d"]]}}) \ No newline at end of file