diff --git a/2.8.0-dev0/_modules/MDAnalysis/topology/tables.html b/2.8.0-dev0/_modules/MDAnalysis/topology/tables.html index 35afc29ea5..b6da1ca80f 100644 --- a/2.8.0-dev0/_modules/MDAnalysis/topology/tables.html +++ b/2.8.0-dev0/_modules/MDAnalysis/topology/tables.html @@ -189,10 +189,12 @@

Source code for MDAnalysis.topology.tables

 .. autodata:: TABLE_VDWRADII
 """
 
+from typing import Any
+
 
 

 [docs]
-def kv2dict(s, convertor=str):
+def kv2dict(s, convertor: Any = str):
     """Primitive ad-hoc parser of a key-value record list.
 
     * The string *s* should contain each key-value pair on a separate
@@ -318,10 +320,12 @@ 
Source code for MDAnalysis.topology.tables
 #: with :func:`MDAnalysis.topology.core.guess_atom_type`.
 atomelements = kv2dict(TABLE_ATOMELEMENTS)
 
+# fmt: off
 elements = ['H',
             'LI', 'BE', 'B', 'C', 'N', 'O', 'F',
             'NA', 'MG', 'AL', 'P', 'SI', 'S', 'CL',
             'K']
+# fmt: on
 
 #: Plain-text table with atomic masses in u.
 TABLE_MASSES = """
@@ -522,28 +526,31 @@ 
Source code for MDAnalysis.topology.tables
 #: .. SeeAlso:: :func:`MDAnalysis.topology.core.guess_bonds`
 vdwradii = kv2dict(TABLE_VDWRADII, convertor=float)
 
-Z2SYMB = {1: 'H',                                                                2: 'He', 
-          3: 'Li',   4: 'Be',  5: 'B',   6: 'C',   7: 'N',   8: 'O',   9: 'F',  10: 'Ne', 
-          11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P',  16: 'S',  17: 'Cl', 18: 'Ar', 
-          19: 'K',  20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V',  24: 'Cr', 25: 'Mn', 26: 'Fe', 
-          27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se', 
-          35: 'Br', 36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y',  40: 'Zr', 41: 'Nb', 42: 'Mo', 
-          43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In', 50: 'Sn', 
-          51: 'Sb', 52: 'Te', 53: 'I',  54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce', 
-          59: 'Pr', 60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy', 
-          67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta', 74: 'W', 
-          75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb', 
-          83: 'Bi', 84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th', 
-          91: 'Pa', 92: 'U',  93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk', 98: 'Cf', 
-          99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No', 103: 'Lr', 104: 'Rf', 105: 'Db', 
-          106: 'Sg', 107: 'Bh', 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn', 
+# fmt: off
+Z2SYMB = {1: 'H',                                                                2: 'He',
+          3: 'Li',   4: 'Be',  5: 'B',   6: 'C',   7: 'N',   8: 'O',   9: 'F',  10: 'Ne',
+          11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P',  16: 'S',  17: 'Cl', 18: 'Ar',
+          19: 'K',  20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V',  24: 'Cr', 25: 'Mn', 26: 'Fe',
+          27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se',
+          35: 'Br', 36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y',  40: 'Zr', 41: 'Nb', 42: 'Mo',
+          43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In', 50: 'Sn',
+          51: 'Sb', 52: 'Te', 53: 'I',  54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce',
+          59: 'Pr', 60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy',
+          67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta', 74: 'W',
+          75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb',
+          83: 'Bi', 84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th',
+          91: 'Pa', 92: 'U',  93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk', 98: 'Cf',
+          99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No', 103: 'Lr', 104: 'Rf', 105: 'Db',
+          106: 'Sg', 107: 'Bh', 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn',
           113: 'Nh', 114: 'Fl', 115: 'Mc', 116: 'Lv', 117: 'Ts', 118: 'Og'}
+# fmt: on
 
-SYMB2Z = {v:k for k, v in Z2SYMB.items()}
+SYMB2Z = {v: k for k, v in Z2SYMB.items()}
 
 # Conversion between SYBYL atom types and corresponding elements
 # Tripos MOL2 file format:
 #   https://web.archive.org/web/*/http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
+# fmt: off
 SYBYL2SYMB = {
     "H": "H", "H.spc": "H", "H.t3p": "H",
     "C.3": "C", "C.2": "C", "C.1": "C", "C.ar": "C", "C.cat": "C",
@@ -575,6 +582,7 @@ 
Source code for MDAnalysis.topology.tables
     "Mo": "Mo",
     "Sn": "Sn",
 }
+# fmt: on
 

 
            

diff --git a/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html b/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html
index 9034f1b151..ab8f98ce93 100644
--- a/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html
+++ b/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html
@@ -1049,7 +1049,7 @@ 
4.4.3.8. Classes
 

-DEFAULT_ACCEPTORS = {'CHARMM27': ('ND1', 'OG1', 'OD2', 'NE2', 'OD1', 'O', 'OC1', 'SD', 'OW', 'OE1', 'OC2', 'SG', 'OH2', 'OG', 'OE2', 'OH'), 'GLYCAM06': ('O', 'O2', 'SM', 'OW', 'OS', 'N', 'NT', 'OH', 'OY'), 'other': ()}

+DEFAULT_ACCEPTORS = {'CHARMM27': ('OG1', 'OW', 'OH2', 'ND1', 'OG', 'OE2', 'SD', 'OD2', 'OH', 'OC1', 'OD1', 'OE1', 'OC2', 'SG', 'O', 'NE2'), 'GLYCAM06': ('OW', 'SM', 'OS', 'NT', 'O2', 'N', 'OY', 'OH', 'O'), 'other': ()}
 
default atom names that are treated as hydrogen acceptors
 (see Default heavy atom names for CHARMM27 force field.);
 use the keyword acceptors to add a list of additional acceptor names.

@@ -1057,7 +1057,7 @@ 
4.4.3.8. Classes
 

-DEFAULT_DONORS = {'CHARMM27': ('NZ', 'ND2', 'ND1', 'NH1', 'OG1', 'OW', 'NE1', 'NE2', 'SG', 'NH2', 'N', 'OH2', 'OG', 'OH', 'NE'), 'GLYCAM06': ('N3', 'N', 'NT', 'OW', 'OH'), 'other': ()}

+DEFAULT_DONORS = {'CHARMM27': ('ND2', 'OG1', 'OW', 'SG', 'NH2', 'NE1', 'OH2', 'NE', 'ND1', 'OG', 'N', 'NH1', 'OH', 'NZ', 'NE2'), 'GLYCAM06': ('N3', 'N', 'OW', 'OH', 'NT'), 'other': ()}
 
default heavy atom names whose hydrogens are treated as donors
 (see Default heavy atom names for CHARMM27 force field.);
 use the keyword donors to add a list of additional donor names.

diff --git a/2.8.0-dev0/documentation_pages/topology/tables.html b/2.8.0-dev0/documentation_pages/topology/tables.html
index d001006064..b49454bae3 100644
--- a/2.8.0-dev0/documentation_pages/topology/tables.html
+++ b/2.8.0-dev0/documentation_pages/topology/tables.html
@@ -206,7 +206,7 @@
 kv2dict() for explanation of the file format.

 

 

-MDAnalysis.topology.tables.kv2dict(s, convertor=<class 'str'>)[source]

+MDAnalysis.topology.tables.kv2dict(s, convertor: ~typing.Any = <class 'str'>)[source]
 
Primitive ad-hoc parser of a key-value record list.

 
    
 
  • The string s should contain each key-value pair on a separate
diff --git a/2.8.0-dev0/index.html b/2.8.0-dev0/index.html
index f6c46b9955..625722330a 100644
--- a/2.8.0-dev0/index.html
+++ b/2.8.0-dev0/index.html
@@ -150,7 +150,7 @@ 
    MDAnalysis documentation
    2.8.0-dev0
    
 

 
Date:

-
Oct 13, 2024

+
Oct 15, 2024

 

 

 
MDAnalysis (www.mdanalysis.org) is an object-oriented python
diff --git a/2.8.0-dev0/searchindex.js b/2.8.0-dev0/searchindex.js
index 77ad7c33ec..836bb97403 100644
--- a/2.8.0-dev0/searchindex.js
+++ b/2.8.0-dev0/searchindex.js
@@ -1 +1 @@
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"covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.covariance_matrix", false]], "crdparser (class in mdanalysis.topology.crdparser)": [[128, "MDAnalysis.topology.CRDParser.CRDParser", false]], "crdreader (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDReader", false]], "crdwriter (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDWriter", false]], "create() (in module mdanalysis.lib.log)": [[108, "MDAnalysis.lib.log.create", false]], "cryst1() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.CRYST1", false]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[35, "MDAnalysis.analysis.pca.PCA.cumulated_variance", false]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[35, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance", false]], "cumulative_clustering_ensemble_similarity() (in 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"MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, 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[[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[118, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[155, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[108, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [115, "index-0", false], [115, "index-1", false], [118, "index-0", false], [158, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[131, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[110, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[132, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.frame", false]], "frame (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.frame", false]], "frame (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.frame", false]], "frame (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.frame", false]], "frame (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.frame", false]], "frame (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.frame", false]], "frame (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.frame", false]], "frame (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.frame", false]], "frame (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.frame", false]], "frame (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.frame", false]], "frame (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.frame", false]], "frame (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.frame", false]], "frame (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.frame", false]], "frame (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.frame", false]], "frame_data (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_data", false]], "frame_rep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_rep", false]], "frameiteratorall (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorAll", false]], "frameiteratorbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorBase", false]], "frameiteratorindices (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorIndices", false]], "frameiteratorsliced (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorSliced", false]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[3, "MDAnalysis.analysis.base.AnalysisBase.frames", false]], "frames 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false]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[21, "MDAnalysis.analysis.gnm.generate_grid", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff", false]], "generate_streamlines() (in module mdanalysis.visualization.streamlines)": [[168, "MDAnalysis.visualization.streamlines.generate_streamlines", false]], "generate_streamlines_3d() (in module mdanalysis.visualization.streamlines_3d)": [[169, "MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d", false]], "generate_table() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.generate_table", false]], "get_array() (mdanalysis.coordinates.memory.memoryreader 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false]], "get_atoms() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.get_atoms", false]], "get_aux_attribute() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.get_aux_attribute", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, 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false]], "get_aux_descriptions() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.get_aux_descriptions", false]], "get_aux_descriptions() 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(mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.get_connections", false]], "get_connections() (mdanalysis.core.groups.segment method)": [[92, "MDAnalysis.core.groups.Segment.get_connections", false]], "get_connections() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.get_connections", false]], "get_conversion_factor() (in module mdanalysis.units)": [[166, "MDAnalysis.units.get_conversion_factor", false]], "get_data() (mdanalysis.auxiliary.edr.edrreader method)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.get_data", false]], "get_description() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.get_description", false]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[16, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix", false]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": 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"MDAnalysis.analysis.base.AnalysisFromFunction.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.bat.bat class method)": [[4, "MDAnalysis.analysis.bat.BAT.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.density.densityanalysis class method)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.dihedrals.dihedral class method)": [[10, "MDAnalysis.analysis.dihedrals.Dihedral.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.dihedrals.janin class method)": [[10, "MDAnalysis.analysis.dihedrals.Janin.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.dihedrals.ramachandran class method)": [[10, "MDAnalysis.analysis.dihedrals.Ramachandran.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.dssp.dssp.dssp class method)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.gnm.gnmanalysis class method)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis class method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.msd.einsteinmsd class method)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.nucleicacids.majorpairdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.nucleicacids.minorpairdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.nucleicacids.nucpairdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.nucleicacids.watsoncrickdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.pca.pca class method)": [[35, "MDAnalysis.analysis.pca.PCA.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.rms.rmsd class method)": [[40, "MDAnalysis.analysis.rms.RMSD.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.rms.rmsf class method)": [[40, "MDAnalysis.analysis.rms.RMSF.get_supported_backends", false]], "get_weights() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.get_weights", false]], "get_writer() (in module mdanalysis.selections)": [[126, "MDAnalysis.selections.get_writer", false]], "get_writer_for() (in module 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"MDAnalysis.topology.LAMMPSParser.DATAParser.grab_datafile", false]], "grab_not_keywords() (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.grab_not_keywords", false]], "greedy_splitext() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.greedy_splitext", false]], "grid (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.grid", false]], "groparser (class in mdanalysis.topology.groparser)": [[134, "MDAnalysis.topology.GROParser.GROParser", false]], "groreader (class in mdanalysis.coordinates.gro)": [[61, "MDAnalysis.coordinates.GRO.GROReader", false]], "group (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.group", false]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.group", false]], "group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.group_same_or_consecutive_integers", false]], "groupby() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.groupby", false]], "groupby() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.groupby", false]], "groupby() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.groupby", false]], "groups() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.groups", false]], "groups_iter() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter", false]], "growriter (class in mdanalysis.coordinates.gro)": [[61, "MDAnalysis.coordinates.GRO.GROWriter", false]], "gsd_pickle_open() (in module mdanalysis.coordinates.gsd)": [[62, "MDAnalysis.coordinates.GSD.gsd_pickle_open", false]], "gsdparser (class in mdanalysis.topology.gsdparser)": [[135, "MDAnalysis.topology.GSDParser.GSDParser", false]], "gsdpicklable (class in mdanalysis.coordinates.gsd)": [[62, "MDAnalysis.coordinates.GSD.GSDPicklable", false]], "gsdreader (class in mdanalysis.coordinates.gsd)": [[62, "MDAnalysis.coordinates.GSD.GSDReader", false]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors", false]], "guess_angles() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_angles", false]], "guess_aromaticities() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_aromaticities", false]], "guess_atom_charge() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_charge", false]], "guess_atom_element() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_element", false]], "guess_atom_mass() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_mass", false]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_type", false]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_bonds", false]], "guess_bonds() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.guess_bonds", false]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_dihedrals", false]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[144, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module 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method)": [[92, "MDAnalysis.core.groups.AtomGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.gyration_moments", false]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open", false]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.GzipPicklable", false]], "h5md_version (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.H5MD_VERSION", false]], "h5mdreader (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader", false]], "h5mdwriter (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter", false]], "h5pypicklable (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5PYPicklable", false]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.hard_cut_q", false]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_forces", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_forces", false]], "has_forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_forces", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_positions", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_positions", false]], "has_positions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_positions", false]], "has_valid_coordinates() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_valid_coordinates", false]], "has_valid_coordinates() 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"MDAnalysis.coordinates.H5MD.H5MDWriter.has_velocities", false]], "has_velocities (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_velocities", false]], "hasmethod() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.hasmethod", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds", false]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[106, "MDAnalysis.lib.formats.libdcd.DCDFile.header", false]], "header() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.HEADER", false]], "helanal (class in mdanalysis.analysis.helix_analysis)": 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(mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.improper", false]], "improper() (mdanalysis.core.topologyobjects.improperdihedral method)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral.improper", false]], "improperdihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral", false]], "impropers (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Impropers", false]], "impropers (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.impropers", false]], "indices (mdanalysis.core.topologyobjects.topologygroup property)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.indices", false]], "indices (mdanalysis.core.topologyobjects.topologyobject property)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject.indices", false]], "initial_time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.initial_time", false]], "innerproduct() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.InnerProduct", false]], "inpreader (class in mdanalysis.coordinates.inpcrd)": [[64, "MDAnalysis.coordinates.INPCRD.INPReader", false]], "int_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.INT_PATTERN", false]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.interaction_types", false]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.InteractionKind", false]], "interpolated (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolated", false]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolation_spline_order", false]], "interrdf (class in mdanalysis.analysis.rdf)": [[38, 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"MDAnalysis.core.groups.ResidueGroup.sequence", false]], "sequence() (mdanalysis.core.topologyattrs.resnames method)": [[96, "MDAnalysis.core.topologyattrs.Resnames.sequence", false]], "sequence_alignment() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.sequence_alignment", false]], "set_array() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.set_array", false]], "set_atoms() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.atomindices method)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.atomstringattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomStringAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.set_atoms", false]], 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"set_residues() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.set_residues", false]], "set_rmsd_matrix_elements() (in module mdanalysis.analysis.encore.confdistmatrix)": [[16, "MDAnalysis.analysis.encore.confdistmatrix.set_rmsd_matrix_elements", false]], "set_segments() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentstringattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentStringAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.set_segments", false]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.setaxes", false]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.setconstrain", false]], "shape_parameter() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.shape_parameter", false]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.shear_from_matrix", false]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator", false]], "singlecharselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[155, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], "skip_timestep (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep", false]], "skipper() (mdanalysis.topology.topparser.topparser method)": [[146, "MDAnalysis.topology.TOPParser.TOPParser.skipper", false]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume", false]], "smartsselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SmartsSelection", false]], "soft_cut_q() (in 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"MDAnalysis.coordinates.TNG.TNGReader", false]], "to_indices() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.to_indices", false]], "top (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.top", false]], "topdict (mdanalysis.core.topologyobjects.topologygroup property)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.topDict", false]], "topology (class in mdanalysis.core.topology)": [[95, "MDAnalysis.core.topology.Topology", false]], "topologyattr (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr", false]], "topologydict (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyDict", false]], "topologygroup (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup", false]], "topologyobject (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject", false]], "topologyreaderbase (class in mdanalysis.topology.base)": [[150, "MDAnalysis.topology.base.TopologyReaderBase", false]], "topparser (class in mdanalysis.topology.topparser)": [[146, "MDAnalysis.topology.TOPParser.TOPParser", false]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors", false]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_alpha", false]], "tors_beta() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_beta", false]], "tors_chi() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_chi", false]], "tors_delta() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_delta", false]], "tors_eps() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_eps", false]], "tors_gamma() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_gamma", false]], "tors_zeta() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_zeta", false]], "total_charge() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.total_charge", false]], "total_charge() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.total_charge", false]], "total_charge() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.total_charge", false]], "total_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.total_charge", false]], "total_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.total_mass", false]], "total_mass() 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"MDAnalysis.coordinates.GSD.GSDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.totaltime", false]], "totaltime (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.totaltime", false]], "totaltime (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.totaltime", false]], "totaltime (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.totaltime", false]], "totaltime (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.totaltime", false]], "tp (mdanalysis.topology.tpr.obj.atom attribute)": [[155, "MDAnalysis.topology.tpr.obj.Atom.tp", false]], "tprparser (class in mdanalysis.topology.tprparser)": [[147, "MDAnalysis.topology.TPRParser.TPRParser", false]], "tpxheader (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader", false]], "tpxunpacker (class in mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker", false]], "tpxunpacker2020 (class in mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020", false]], "trajectory 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(in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.transform_StoR", false]], "transformationbase (class in mdanalysis.transformations.base)": [[158, "MDAnalysis.transformations.base.TransformationBase", false]], "transformations (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.transformations", false]], "transformations (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.transformations", false]], "transformations (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.transformations", false]], "transformations (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.transformations", false]], "transformations (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.transformations", false]], "transformations (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.transformations", false]], "transformations (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.transformations", false]], "transformations (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.transformations", false]], "transformations (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.transformations", false]], "transformations (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.transformations", false]], "transformations (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.transformations", false]], "transformations (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.transformations", false]], "translate (class in mdanalysis.transformations.translate)": [[164, "MDAnalysis.transformations.translate.translate", false]], "translate() (in module mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.translate", false]], "translate() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.translate", false]], "translate() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.translate", false]], "translate() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.translate", false]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.translation_from_matrix", false]], "transtable (class in mdanalysis.core.topology)": [[95, "MDAnalysis.core.topology.TransTable", false]], "trcreader (class in mdanalysis.coordinates.trc)": [[73, "MDAnalysis.coordinates.TRC.TRCReader", false]], "triangularmatrix (class in mdanalysis.analysis.encore.utils)": [[20, "MDAnalysis.analysis.encore.utils.TriangularMatrix", false]], "triclinic_box() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.triclinic_box", false]], "triclinic_dimensions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.triclinic_dimensions", false]], "triclinic_vectors() (in module mdanalysis.lib.mdamath)": 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false]], "trzreader (class in mdanalysis.coordinates.trz)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader", false]], "trzwriter (class in mdanalysis.coordinates.trz)": [[76, "MDAnalysis.coordinates.TRZ.TRZWriter", false]], "ts (mdanalysis.coordinates.trz.trzreader attribute)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.ts", false]], "ts (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.ts", false]], "txyzparser (class in mdanalysis.topology.txyzparser)": [[148, "MDAnalysis.topology.TXYZParser.TXYZParser", false]], "txyzreader (class in mdanalysis.coordinates.txyz)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader", false]], "type (mdanalysis.core.topologyobjects.topologyobject property)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject.type", false]], "type (mdanalysis.topology.tpr.obj.atoms attribute)": [[155, "MDAnalysis.topology.tpr.obj.Atoms.type", false]], "typeb (mdanalysis.topology.tpr.obj.atom attribute)": [[155, "MDAnalysis.topology.tpr.obj.Atom.typeB", false]], "typeb (mdanalysis.topology.tpr.obj.atoms attribute)": [[155, "MDAnalysis.topology.tpr.obj.Atoms.typeB", false]], "types() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.types", false]], "uncomment() (in module mdanalysis.auxiliary.xvg)": [[45, "MDAnalysis.auxiliary.XVG.uncomment", false]], "undo_augment() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.undo_augment", false]], "union() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.union", false]], "union() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.union", false]], "union() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.union", false]], "unique (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.unique", false]], "unique 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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. 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", "6.26. 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. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "6.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.22. TRZ trajectory I/O  \u2014 MDAnalysis.coordinates.TRZ", "6.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.31. Base classes \u2014 MDAnalysis.coordinates.base", "6.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers  \u2014 MDAnalysis.coordinates", "6.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.29. Null output \u2014 MDAnalysis.coordinates.null", "6.33. Serialization of Coordinate Readers", "6.30. 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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\ No newline at end of file
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"MDAnalysis.lib.distances.augment_coordinates", false]], "autocorrelation() (in module mdanalysis.lib.correlations)": [[104, "MDAnalysis.lib.correlations.autocorrelation", false]], "aux_list (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.aux_list", false]], "aux_list (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.aux_list", false]], "aux_list (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.aux_list", false]], "aux_list (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.aux_list", false]], "aux_list (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.aux_list", false]], "aux_list (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.aux_list", false]], "aux_list (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.aux_list", false]], "aux_list (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.aux_list", false]], "aux_list (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.aux_list", false]], "aux_list (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.aux_list", false]], "aux_list (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.aux_list", false]], "aux_list (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.aux_list", false]], "aux_list (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.aux_list", false]], "aux_list (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.aux_list", false]], "auxfile (mdanalysis.auxiliary.base.auxfilereader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader.auxfile", false]], "auxfilereader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader", false]], "auxreader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxReader", false]], "auxreader() (in module mdanalysis.auxiliary.core)": [[47, "MDAnalysis.auxiliary.core.auxreader", false]], "auxstep (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxStep", false]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.auxstep", false]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure", false]], "backboneselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BackboneSelection", false]], "backendbase (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendBase", false]], "backenddask (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendDask", false]], "backendmultiprocessing (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendMultiprocessing", false]], "backendserial (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendSerial", false]], "baseselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BaseSelection", false]], "bat (class in mdanalysis.analysis.bat)": [[4, "MDAnalysis.analysis.bat.BAT", false]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[4, "MDAnalysis.analysis.bat.BAT.results.bat", false]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox", false]], "bbox() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bbox", false]], "bbox() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bbox", false]], "bbox() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bbox", false]], "between() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.between", false]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bF", false]], "bfactor (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bfactor", false]], "bfactor() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor", false]], "bfactor_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor_setter", false]], "bfactors (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.bfactors", false]], "bfactors (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.segment property)": [[92, "MDAnalysis.core.groups.Segment.bfactors", false]], "bfactors (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.bfactors", false]], "bfactors() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors", false]], "bfactors_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors_setter", false]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins", false]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr", false]], "blocks (mdanalysis.coordinates.tng.tngreader property)": [[72, "MDAnalysis.coordinates.TNG.TNGReader.blocks", false]], "blocks_of() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.blocks_of", false]], "bond (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Bond", false]], "bond (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bond", false]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation", false]], "bonded_atoms (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bonded_atoms", false]], "bonded_atoms() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.bonded_atoms", false]], "bonds (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Bonds", false]], "bonds (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.bonds", false]], "bonds() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.bonds", false]], "boolselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BoolSelection", false]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[14, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix", false]], "box (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.Box", false]], "box_volume() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.box_volume", false]], "bsphere() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bsphere", false]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop", false]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable", false]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bV", false]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bX", false]], "bynumselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByNumSelection", false]], "byresselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByResSelection", false]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open", false]], "bz2picklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.BZ2Picklable", false]], "cached() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.cached", false]], "calc_angles() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.calc_angles", false]], "calc_bonds() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.calc_bonds", false]], "calc_dihedrals() (in module 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"MDAnalysis.core.groups.SegmentGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.center_of_charge", false]], "center_of_geometry() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_geometry", false]], "center_of_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.center_of_mass", false]], "centers() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.centers", false]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid", false]], "centroid() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.centroid", false]], "centroid() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.centroid", false]], "centroid() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.centroid", false]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.ces", false]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.ces_convergence", false]], "chainids (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs", false]], "chainreader (class in mdanalysis.coordinates.chain)": [[82, "MDAnalysis.coordinates.chain.ChainReader", false]], "char (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char", false]], "char_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char_std", false]], "charge_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density", false]], "charge_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, 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false]], "close() (mdanalysis.converters.openmmparser.openmmapptopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser.close", false]], "close() (mdanalysis.converters.openmmparser.openmmtopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser.close", false]], "close() (mdanalysis.converters.parmedparser.parmedparser method)": [[52, "MDAnalysis.converters.ParmEdParser.ParmEdParser.close", false]], "close() (mdanalysis.converters.rdkitparser.rdkitparser method)": [[53, "MDAnalysis.converters.RDKitParser.RDKitParser.close", false]], "close() (mdanalysis.coordinates.base.converterbase method)": [[81, "MDAnalysis.coordinates.base.ConverterBase.close", false]], "close() (mdanalysis.coordinates.base.iobase method)": [[81, "MDAnalysis.coordinates.base.IOBase.close", false]], "close() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.close", false]], "close() 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module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity", false]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs", false]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.cumulative_overlap", false]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[35, "MDAnalysis.analysis.pca.PCA.cumulative_overlap", false]], "data (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.data", false]], "data (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.data", false]], "data_blacklist (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.data_blacklist", false]], "data_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.data_dict", false]], "data_selector (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.data_selector", false]], "dataparser (class in mdanalysis.topology.lammpsparser)": [[138, "MDAnalysis.topology.LAMMPSParser.DATAParser", false]], "datareader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader", false]], "datawriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter", false]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN", false]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[106, "MDAnalysis.lib.formats.libdcd.DCDFile", false]], "dcdreader (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDReader", false]], "dcdreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader", false]], "dcdwriter (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter", false]], "dcdwriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter", false]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.decompose_matrix", false]], "dedent_docstring() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.dedent_docstring", false]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS", false]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS", false]], "default_format (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.default_format", false]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms", false]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.define_unpack_real", false]], "del_topologyattr() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.del_TopologyAttr", false]], "del_topologyattr() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.del_TopologyAttr", false]], "delete_angles() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_angles", false]], "delete_bonds() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_bonds", false]], "delete_dihedrals() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_dihedrals", false]], "delete_impropers() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_impropers", false]], "delta (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.delta", false]], "delta (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.delta", false]], "density (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.Density", false]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.density", false]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.results.density", false]], "densityanalysis (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.DensityAnalysis", false]], "densityunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.densityUnit_factor", false]], "deprecate() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.deprecate", false]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant", false]], "difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.difference", false]], "difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.difference", false]], "difference() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.difference", false]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap", false]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[10, "MDAnalysis.analysis.dihedrals.Dihedral", false]], "dihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Dihedral", false]], "dihedral (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dihedral", false]], "dihedral() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.dihedral", false]], "dihedral() (mdanalysis.core.topologyobjects.dihedral method)": [[97, "MDAnalysis.core.topologyobjects.Dihedral.dihedral", false]], "dihedrals (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Dihedrals", false]], "dihedrals (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dihedrals", false]], "dihedrals() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dihedrals", false]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim", false]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac", false]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[18, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod", false]], "dimensions (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dimensions", false]], "dimensions (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.dimensions", false]], "dimensions (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dimensions", false]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity", false]], "dipole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_moment", false]], "dipole_vector() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_vector", false]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence", false]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence", false]], "dist() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.dist", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix", false]], "distance() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.distance", false]], "distance_array() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.distance_array", false]], "distance_array() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.distance_array", false]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix", false]], "distances (mdanalysis.analysis.nucleicacids.majorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.minorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.distances", false]], "dmsparser (class in mdanalysis.topology.dmsparser)": [[130, "MDAnalysis.topology.DMSParser.DMSParser", false]], "dmsreader (class in mdanalysis.coordinates.dms)": [[58, "MDAnalysis.coordinates.DMS.DMSReader", false]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atom", false]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atoms", false]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_block", false]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_blocka", false]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ffparams", false]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_harm", false]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ilists", false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp_ndarray", false]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.dt", false]], "dt (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.dt", false]], "dt (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.dt", false]], "dt (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.dt", false]], "dt (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dt", false]], "dt (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.dt", false]], "dt (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.dt", false]], "dt (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.dt", false]], "dt (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.dt", false]], "dt (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.dt", false]], "dt (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dt", false]], "dt (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.dt", false]], "dt (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.dt", false]], "dt (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.dt", false]], "dt (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.dt", false]], "dtype (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dtype", false]], "dtype (mdanalysis.core.selection.floatrangeselection attribute)": [[94, "MDAnalysis.core.selection.FloatRangeSelection.dtype", false]], "dtype (mdanalysis.core.selection.rangeselection attribute)": [[94, "MDAnalysis.core.selection.RangeSelection.dtype", false]], "dtype (mdanalysis.core.topologyattrs.altlocs attribute)": [[96, "MDAnalysis.core.topologyattrs.AltLocs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.aromaticities attribute)": [[96, "MDAnalysis.core.topologyattrs.Aromaticities.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomids attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Molnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.moltypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Moltypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.nonbondedindices attribute)": [[96, "MDAnalysis.core.topologyattrs.NonbondedIndices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[118, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[155, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[108, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [115, "index-0", false], [115, "index-1", false], [118, "index-0", false], [158, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[131, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[110, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[132, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, 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"MDAnalysis.topology.GSDParser.GSDParser", false]], "gsdpicklable (class in mdanalysis.coordinates.gsd)": [[62, "MDAnalysis.coordinates.GSD.GSDPicklable", false]], "gsdreader (class in mdanalysis.coordinates.gsd)": [[62, "MDAnalysis.coordinates.GSD.GSDReader", false]], "guess_acceptors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_acceptors", false]], "guess_angles() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_angles", false]], "guess_aromaticities() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_aromaticities", false]], "guess_atom_charge() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_charge", false]], "guess_atom_element() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_element", false]], "guess_atom_mass() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_mass", false]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_type", false]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_bonds", false]], "guess_bonds() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.guess_bonds", false]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_dihedrals", false]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[144, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.guess_format", false]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_gasteiger_charges", false]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens", false]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_improper_dihedrals", false]], "guess_masses() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_masses", false]], "guess_types() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_types", false]], "guessed_attributes (mdanalysis.core.topology.topology property)": [[95, "MDAnalysis.core.topology.Topology.guessed_attributes", false]], "gyration_moments() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.gyration_moments", false]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open", false]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.GzipPicklable", false]], "h5md_version (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.H5MD_VERSION", false]], "h5mdreader (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader", false]], "h5mdwriter (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter", false]], "h5pypicklable (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5PYPicklable", false]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.hard_cut_q", false]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_forces", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_forces", false]], "has_forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_forces", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_positions", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_positions", false]], "has_positions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_positions", false]], "has_valid_coordinates() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.datawriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.dcdwriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.trr.trrwriter method)": [[75, "MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xdr.xdrbasewriter method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xtc.xtcwriter method)": [[79, "MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_velocities", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_velocities", false]], "has_velocities (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_velocities", false]], "hasmethod() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.hasmethod", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds", false]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[106, "MDAnalysis.lib.formats.libdcd.DCDFile.header", false]], "header() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.HEADER", false]], "helanal (class in mdanalysis.analysis.helix_analysis)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL", false]], "helix_analysis() (in module mdanalysis.analysis.helix_analysis)": [[24, "MDAnalysis.analysis.helix_analysis.helix_analysis", false]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.hes", false]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges", false]], "historyparser (class in mdanalysis.topology.dlpolyparser)": [[129, "MDAnalysis.topology.DLPolyParser.HistoryParser", false]], "historyreader (class in mdanalysis.coordinates.dlpoly)": [[57, "MDAnalysis.coordinates.DLPoly.HistoryReader", false]], "hoomdxmlparser (class in mdanalysis.topology.hoomdxmlparser)": [[136, "MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser", false]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis", false]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel", false]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.hydroxyl", false]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[155, "MDAnalysis.topology.tpr.obj.Ilist.iatoms", false]], "icodes (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.ICodes", false]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id", false]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[155, "MDAnalysis.topology.tpr.obj.Ilist.ik", false]], "ilist (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.Ilist", false]], "improper (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.improper", false]], "improper() (mdanalysis.core.topologyobjects.improperdihedral method)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral.improper", false]], "improperdihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral", false]], "impropers (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Impropers", false]], "impropers (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.impropers", false]], "indices (mdanalysis.core.topologyobjects.topologygroup property)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.indices", false]], "indices (mdanalysis.core.topologyobjects.topologyobject property)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject.indices", false]], "initial_time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.initial_time", false]], "innerproduct() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.InnerProduct", false]], "inpreader (class in mdanalysis.coordinates.inpcrd)": [[64, "MDAnalysis.coordinates.INPCRD.INPReader", false]], "int_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.INT_PATTERN", false]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.interaction_types", false]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.InteractionKind", false]], "interpolated (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolated", false]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolation_spline_order", false]], "interrdf (class in mdanalysis.analysis.rdf)": [[38, 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property)": [[92, "MDAnalysis.core.groups.UpdatingAtomGroup.is_uptodate", false]], "isdisjoint() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.isdisjoint", false]], "isdisjoint() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.isdisjoint", false]], "isdisjoint() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.isdisjoint", false]], "isstream() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.isstream", false]], "issubset() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.issubset", false]], "issubset() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.issubset", false]], "issubset() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.issubset", false]], "issuperset() (mdanalysis.core.groups.atomgroup method)": [[92, 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"iter_auxiliary() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.iter_auxiliary", false]], "iterable() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.iterable", false]], "iterative_average() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.iterative_average", false]], "itpparser (class in mdanalysis.topology.itpparser)": [[137, "MDAnalysis.topology.ITPParser.ITPParser", false]], "ix (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.ix", false]], "ix (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.ix", false]], "ix (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.ix", false]], "ix (mdanalysis.core.groups.residuegroup property)": [[92, 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"MDAnalysis.core.topologyattrs.Masses.shape_parameter", false]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.shear_from_matrix", false]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator", false]], "singlecharselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[155, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], "skip_timestep (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep", false]], "skipper() (mdanalysis.topology.topparser.topparser method)": [[146, "MDAnalysis.topology.TOPParser.TOPParser.skipper", false]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume", false]], "smartsselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SmartsSelection", false]], "soft_cut_q() (in 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109, 112, 115, 171], "complic": [0, 92, 93, 119], "compnd": [69, 70], "compon": [7, 18, 19, 27, 43, 72, 75, 92, 95, 96, 109, 113, 118, 153, 168, 169, 171], "component_index": 27, "componentbas": 92, "compos": [18, 155], "compose_matrix": 114, "composit": [111, 117], "compound": [7, 69, 92, 96, 165], "comprehens": [115, 118, 171], "compress": [20, 55, 60, 63, 68, 69, 70, 71, 72, 74, 79, 80, 82, 85, 107, 111, 115, 117], "compression_opt": 63, "compresslevel": 111, "compris": 19, "comput": [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 15, 16, 19, 21, 24, 26, 30, 32, 33, 34, 35, 38, 40, 42, 59, 63, 72, 85, 92, 93, 96, 104, 109, 110, 113, 115, 116, 118, 161, 162, 166], "computation": [19, 31], "computation_group": 3, "concaten": [19, 31, 82, 92, 95, 105, 111, 114, 119], "concatenate_matric": 114, "concatent": 119, "concentr": 166, "concern": [90, 115, 116, 156], "conclus": 35, "conda": [43, 74], "condid": 113, "condit": [1, 2, 5, 7, 8, 11, 22, 27, 31, 38, 40, 63, 85, 92, 94, 97, 101, 110, 112, 137, 152], "condtion": 112, "conduct": 171, "conect": [69, 92, 142], "conf": 113, "conf_dist_arg": 16, "conf_dist_funct": 16, "conf_dist_kwarg": 16, "conf_dist_matrix": 16, "confdistmatrix": [13, 14], "confer": 118, "config": [57, 85, 129, 153, 171], "configpars": 129, "configread": 57, "configur": [4, 10, 11, 34, 40, 56, 63, 105, 108, 110], "confin": 69, "confirm": 31, "conflict": 74, "conform": [5, 10, 14, 15, 16, 18, 19, 21, 32, 33, 53, 61, 69, 71, 98, 118], "conformational_distance_matrix": 16, "confus": 115, "conjug": 53, "conjunct": 63, "conn": 155, "connbond": 155, "connect": [22, 27, 38, 42, 69, 70, 77, 92, 96, 97, 98, 105, 115, 117, 143, 144, 147, 148, 153, 155], "consant": 46, "consecut": [15, 24, 26, 27, 53, 69, 92, 104, 115, 119], "consequ": [80, 98, 106, 161, 162], "conserv": [92, 155], "consid": [0, 1, 3, 7, 9, 11, 15, 19, 21, 22, 26, 28, 40, 42, 46, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 92, 94, 97, 98, 104, 108, 110, 115, 119, 152, 166], "consider": [22, 26, 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81, 82, 86, 105, 115, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "conversion_factor": 166, "conversionwarn": 100, "convert": [7, 11, 28, 31, 44, 56, 59, 61, 62, 63, 65, 67, 69, 71, 72, 74, 75, 76, 77, 78, 79, 80, 82, 85, 86, 91, 92, 94, 98, 100, 105, 107, 109, 114, 115, 117, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150, 153, 154, 166], "convert_aa_cod": [94, 115], "convert_dens": 7, "convert_dimensions_to_unitcel": [56, 59, 61, 63, 65, 75, 78, 79, 81, 85], "convert_forces_from_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_forces_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_length": 7, "convert_pos_from_n": 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69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_velocities_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "converterbas": [54, 81], "converterwrapp": [91, 92], "convertor": 154, "cookbook": 21, "coontain": 110, "coor": [68, 85], "coord": [11, 12, 16, 80, 92, 93, 98, 105, 109, 110, 112, 152, 153], "coord1": 105, "coord2": 105, "coord_nam": 115, "coord_par": 46, "coordiant": [17, 71, 105], "coordin": [3, 7, 9, 11, 12, 16, 17, 18, 19, 21, 24, 28, 31, 35, 38, 40, 43, 44, 46, 48, 51, 52, 53, 54, 92, 93, 96, 98, 105, 106, 107, 109, 110, 112, 113, 114, 115, 116, 117, 118, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 141, 142, 143, 144, 145, 146, 147, 148, 150, 152, 153, 156, 157, 160, 161, 163, 164, 165, 168, 169, 171], "coordinat": 40, "coordinate_arrai": 86, "coords1": 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63, 69, 80, 92, 96, 98, 100, 105, 106, 107, 108, 109, 115, 136, 146], "zeta": 33, "zheng": 9, "zhiyi": 42, "zhou": [104, 118], "zink": 154, "ziolek": 118, "zip": [21, 105, 117], "zmax": [92, 110, 119, 169], "zmin": [92, 110, 119, 169], "zn": 154, "znd": 38, "zone": [92, 119], "zr": 154, "zsu": 65, "zu": 65, "zvalu": 69, "zz": 7, "\u00e1": 104, "\u00e5": [3, 5, 7, 22, 26, 42, 56, 59, 65, 69, 71, 74, 86, 89, 92, 96, 104, 159, 166], "\u00e5ngstrom": 63, "\u00e5ngstr\u00f6m": [7, 59, 65, 74, 166], "\u00ed": 104, "\u03b1": 12, "\u03bc": 166, "\u03c0": [12, 109], "\u03c6": 10, "\u03c8": 10}, "titles": ["4.3.1. Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. 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", "6.26. 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. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "6.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.22. TRZ trajectory I/O  \u2014 MDAnalysis.coordinates.TRZ", "6.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.31. Base classes \u2014 MDAnalysis.coordinates.base", "6.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers  \u2014 MDAnalysis.coordinates", "6.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.29. Null output \u2014 MDAnalysis.coordinates.null", "6.33. Serialization of Coordinate Readers", "6.30. 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. Visualization modules", "MDAnalysis documentation"], "titleterms": {"2d": 168, "3d": 169, "For": 34, "In": 86, "No": 161, "One": 5, "The": [26, 127], "To": 88, "_single_fram": 34, "_singleframeread": 88, "about": 110, "acceler": 105, "access": [48, 88], "accessor": 91, "acid": [32, 33, 43], "ad": [34, 44, 48], "addit": 43, "aggreg": 39, "aim": [59, 132], "algebra": 109, "algorithm": [15, 18, 27, 110, 118], "align": [0, 113], "also": 25, "amber": [74, 146], "an": [31, 48, 63, 86], "analysi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], "analysisbas": 34, "angl": [4, 10, 33, 153], "api": [48, 85], "appli": 34, "applic": [4, 10, 12, 28, 40], "arbitrari": 86, "arrai": [86, 105, 115], "ascii": 74, "assign": 12, "atom": [1, 42, 94, 138, 152, 153], "atomgroup": [91, 126], "atomicdist": 1, "attribut": [48, 85, 96], "autocorrel": [22, 23, 104], "auxiliari": [44, 45, 46, 47, 48, 49], "auxread": 48, "auxstep": 48, "avail": 105, "averag": [12, 162], "backend": [2, 34, 105], "backendbas": 34, "background": 44, "bar": 34, "base": [3, 46, 54, 78, 81, 120, 150, 158, 166], "basereadertest": 88, "basic": 1, "bat": 4, "binari": 74, "block": [3, 43, 157], "bond": [4, 22, 23, 26, 43, 153], "bondord": 153, "boolean": 119, "bootstrap": 14, "box": 159, "boxdimens": 159, "bridg": 42, "build": [3, 43, 63, 151, 157], "built": 43, "c_distanc": 102, "c_distances_openmp": 103, "calcul": [12, 13, 16, 17, 19, 37, 40, 102, 103], "capabl": 69, "chain": 82, "chainread": 82, "charmm": 121, "charmm27": 42, "check": 115, "chemfil": 83, "chemic": 92, "citat": [118, 171], "class": [0, 2, 3, 4, 5, 9, 10, 12, 22, 24, 26, 27, 28, 31, 34, 35, 39, 40, 42, 43, 44, 48, 51, 52, 53, 54, 56, 59, 61, 62, 63, 64, 65, 66, 67, 68, 69, 73, 76, 77, 80, 81, 83, 85, 86, 87, 89, 91, 92, 95, 98, 108, 110, 111, 115, 120, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 155, 157, 158], "closur": 157, "cluster": [15, 18], "clustercollect": 15, "clusteringmethod": 15, "code": [29, 110, 115, 117, 171], "collect": 92, "combin": [31, 34], "command": 119, "common": [0, 47, 84, 151], "compar": 34, "comparison": 19, "complex": 157, "compon": 35, "comput": [31, 105], "conda": 171, "confdistmatrix": 16, "connect": [109, 119], "constant": 166, "construct": 86, "contact": [5, 43], "contain": [92, 115], "conveni": 108, "convers": 166, "convert": [50, 51, 52, 53, 54, 81], "coordin": [0, 4, 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, 83, 84, 85, 86, 87, 88, 89, 90, 140, 162], "core": [47, 84, 91, 92, 93, 94, 95, 96, 97, 98, 99, 151], "correl": 104, "count_by_tim": 42, "count_by_typ": 42, "covari": 17, "crd": [55, 128], "creat": [7, 86, 157], "current": [72, 88, 157], "custom": [34, 100], "data": [6, 43, 44, 65, 115, 166, 167], "dcd": [56, 65, 106], "decor": 115, "default": 42, "definit": 155, "densiti": [7, 30], "depend": 43, "deprec": 23, "descript": 22, "desr": [58, 130], "detect": 42, "develop": [34, 59, 61, 147, 153], "dielectr": 8, "diffus": [9, 31], "diffusionmap": 9, "dihedr": [10, 33, 153], "dimens": 159, "dimension": [5, 18, 43], "dimensionality_reduct": 18, "dimensionalityreductionmethod": 18, "directori": 115, "disk": 34, "displac": 31, "distanc": [1, 11, 16, 32, 33, 43, 102, 103, 105], "distopia": 105, "distribut": 38, "dl": 129, "dl_poli": 57, "dlpoli": 57, "dlpolypars": 129, "dm": 58, "document": 171, "doe": 34, "domain": 40, "dssp": 12, "duecredit": 118, "dump": 65, "dure": 12, "dynam": [41, 119], "edr": 44, "edrread": 44, "elast": 21, "element": 152, "encod": 166, "encor": [13, 15, 17, 18, 19, 20], "ensembl": [13, 14, 16, 19], "exampl": [3, 4, 5, 10, 12, 22, 24, 26, 28, 40, 63, 65, 67, 69, 117, 152], "except": 100, "export": 126, "extend": 131, "extens": 126, "fast": [34, 105, 113], "fhi": [59, 132], "fhiaim": 59, "fhiaimspars": 132, "fhiaimswrit": 59, "field": 42, "file": [6, 12, 55, 58, 59, 61, 63, 64, 65, 67, 68, 69, 70, 71, 72, 75, 77, 78, 79, 80, 88, 115, 116, 126, 130, 140], "find": 12, "fit": [0, 160], "flow": 170, "fly": 157, "footnot": 166, "forc": 42, "format": [48, 57, 58, 59, 61, 65, 67, 68, 71, 77, 80, 85, 88, 106, 107, 115, 116, 129, 130, 140, 147, 153], "frame": 85, "frameiter": 81, "from": [7, 34, 86, 152], "frontend": [15, 18], "function": [0, 5, 12, 19, 20, 21, 22, 24, 25, 27, 35, 38, 40, 47, 83, 84, 93, 95, 98, 104, 105, 108, 109, 113, 114, 115, 116, 151, 155, 157, 166], "gamess": [60, 133], "gener": [7, 10, 28, 147], "geometr": 119, "get": [43, 171], "glycam06": 42, "gm": 60, "gnm": 21, "gro": [61, 134], "gromac": [107, 122, 147], "gromos11": 73, "group": 92, "growrit": 61, "gsd": [62, 135], "guess": 152, "guesser": 152, "guid": 171, "h5md": 63, "h5py": 63, "handl": 115, "handler": 88, "hbond": 23, "hbond_analysi": 26, "hbond_autocorrel": [22, 23], "hdf5": 63, "heavi": 42, "helan": 24, "helic": 24, "helicoid": 28, "helix": 12, "helper": [0, 34, 81, 83, 95, 109, 115], "hierarchi": 94, "hole": 25, "hole2": 25, "homogen": 114, "hoomd": 136, "how": [34, 42, 86, 88, 126, 157], "hydrogen": [22, 23, 26, 43], "hydrogenbond": [22, 26, 42], "hydrogenbondanalysi": 26, "i": [34, 51, 52, 53, 56, 65, 76, 111], "identif": 27, "implement": [88, 157, 166], "import": 99, "improp": 153, "includ": [117, 118], "index": 119, "indic": 171, "inform": [152, 167], "inpcrd": 64, "input": [22, 26, 147], "instal": 171, "intermitt": 104, "involv": 171, "io": 88, "issu": 34, "iter": 48, "itp": 137, "its": 26, "janin": 10, "jmol": 123, "jump": 161, "keyword": 119, "known": 34, "lammp": 65, "lammpspars": 138, "leaflet": 27, "legaci": [28, 29, 43], "level": [92, 105, 106, 107, 116], "lib": [101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116], "libdcd": 106, "libmdanalysi": 116, "libmdaxdr": 107, "librari": [102, 103, 105, 110, 116, 118], "limit": [34, 72], "linear": [30, 109], "lineardens": 30, "linux": 63, "lipid": 170, "liquid": 43, "list": [115, 116], "load": [63, 65], "log": 108, "loop": 12, "low": [105, 106, 107, 116], "macromolecul": 43, "maintain": 12, "manag": 115, "manipul": 115, "map": 9, "match": 119, "mathemat": 109, "matric": 114, "matrix": 16, "md": [7, 21], "mdahole2": 25, "mdamath": 109, "mdanalysi": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 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, 83, 84, 85, 86, 87, 89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 129, 132, 140, 147, 150, 151, 152, 153, 154, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 171], "mdanalysis_base_unit": 166, "mean": [31, 40], "membran": 43, "memori": [34, 86], "memoryread": 86, "method": [26, 34, 48, 85], "minim": 141, "miscellan": 88, "miss": 34, "mmtf": [66, 139], "modifi": 119, "modul": [13, 25, 29, 43, 49, 50, 90, 99, 105, 115, 116, 118, 156, 170], "mol2": [67, 140], "molecul": 53, "molecular": 130, "msd": 31, "multiframereadertest": 88, "multipl": [31, 40, 126], "namdbin": 68, "name": [42, 126, 152], "nativ": 5, "neighbor": [101, 110], "neighborsearch": 101, "netcdf": 74, "network": [21, 42], "new": [3, 34, 88], "nojump": 161, "note": [59, 61, 67, 147, 153, 166], "nsgrid": 110, "nucleic": [32, 33, 43], "nucleicacid": 32, "nuclinfo": 33, "null": 87, "numpi": 86, "o": [51, 52, 53, 56, 65, 76, 111], "object": [7, 92, 95, 96, 97, 98, 99], "onli": 111, "open": 63, "openmm": 51, "openmmpars": 51, "order": 119, "other": 108, "out": 34, "output": [22, 26, 42, 87], "over": 117, "overview": [116, 117], "own": [5, 34], "packag": 115, "parallel": [34, 43, 63, 103], "paramet": 28, "parm": 52, "parmedpars": 52, "pars": [115, 147], "parser": [51, 52, 53, 128, 130, 131, 132, 133, 134, 135, 136, 137, 139, 141, 142, 143, 144, 145, 146, 147, 148, 149, 155], "part": 12, "path": 37, "pattern": 119, "pca": 35, "pdb": [12, 69, 131, 142], "pdbqt": [70, 143], "perform": 42, "periodickdtre": 112, "phase": 33, "picklabl": [88, 111], "picklable_file_io": 111, "pip": 171, "pkdtree": 112, "plot": 10, "poli": 129, "polyamid": 22, "polym": [36, 43], "portabl": 147, "positionaverag": 162, "pqr": [71, 144], "preexist": 119, "preprocessor": 137, "princip": 35, "privat": 85, "prmtop": 146, "procedur": 14, "profil": 28, "progress": 34, "protein": [12, 24, 43], "psa": 37, "psf": 145, "purpos": 108, "pymol": 124, "python": 117, "q1": 5, "q2": 5, "qcp": 113, "qcprot": 113, "quantiti": 40, "quaternion": 114, "radial": 38, "ramachandran": 10, "rdf": 38, "rdkit": 53, "rdkitpars": 53, "read": [34, 47, 83, 84, 86, 106, 107, 111, 147], "reader": [44, 45, 46, 48, 57, 60, 62, 66, 73, 80, 81, 83, 85, 86, 88, 129, 150, 153], "recogn": 126, "recreat": 48, "reduce_dimension": 18, "reduct": [18, 43], "refer": [10, 13, 19, 118, 166], "registri": [48, 85], "replic": [31, 48], "represent": [15, 86], "requir": 114, "result": 39, "resultsgroup": 34, "rm": [0, 40], "rmsd": [40, 113], "root": 40, "rotat": 163, "run": [43, 147], "search": [101, 110], "secondari": 12, "see": 25, "seek": 88, "select": [94, 99, 105, 119, 120, 121, 122, 123, 124, 125, 126], "self": 31, "serial": [34, 88], "set": [108, 155, 159], "sheet": 12, "similar": [13, 19, 37, 119], "simpl": [1, 119], "simul": [12, 63, 65], "singl": [28, 85, 126], "snippet": 117, "sourc": 171, "split": 34, "squar": [31, 40], "standalon": 44, "standard": 3, "start": 43, "stream": 115, "streamlin": 168, "streamlines_3d": 169, "streamplot": [168, 169], "string": [59, 61, 115], "structur": [12, 28, 43, 51, 52, 55, 64, 69, 70, 113, 130], "style": 138, "sub": 86, "support": [48, 85, 126, 153, 155], "switch": 86, "system": [86, 99, 127], "tabl": [85, 126, 153, 154, 171], "task": 21, "templat": 25, "test": [88, 171], "theori": 42, "timeseri": 42, "timestep": [85, 89], "tng": 72, "todo": [128, 146], "tool": [3, 34], "topolgi": 132, "topologi": [51, 52, 53, 95, 96, 97, 99, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156], "topologyattr": 96, "topologyobject": 97, "torsion": 4, "tpr": [147, 155], "tprparser": [147, 155], "traj": 74, "trajectori": [7, 12, 21, 28, 44, 48, 56, 60, 62, 63, 65, 66, 72, 73, 74, 75, 76, 78, 79, 80, 83, 85, 86, 106, 107, 117, 157, 161, 162, 163, 164], "transform": [114, 157, 158, 159, 160, 161, 162, 163, 164, 165], "translat": 164, "trc": 73, "trj": 74, "trr": 75, "trz": 76, "tutori": [0, 9, 35], "two": 5, "txyz": [77, 148], "type": 42, "unit": [63, 92, 166], "univers": 98, "unknown": 152, "unwrap": [161, 165], "up": 108, "updat": 32, "us": [3, 24, 26, 34, 42, 43, 83, 86, 105, 117, 118, 152], "usag": [0, 1, 44], "user": [99, 171], "util": [20, 21, 25, 28, 104, 115, 155], "variabl": 137, "version": [147, 167], "visual": [168, 169, 170], "vmd": 125, "volumetr": 43, "warn": 100, "water": [41, 42], "waterbridgeanalysi": 42, "waterdynam": 41, "when": 34, "whole": 118, "work": [22, 34, 67, 69], "workflow": 157, "wrap": 165, "wrapper": 101, "write": [3, 5, 34, 61, 63, 126], "writer": [81, 85, 120, 126], "x3dna": 28, "xdr": [78, 107], "xml": 136, "xtc": 79, "xvg": 45, "xyz": [80, 149], "your": [5, 34]}})
\ No newline at end of file
diff --git a/dev/_modules/MDAnalysis/topology/tables.html b/dev/_modules/MDAnalysis/topology/tables.html
index 35afc29ea5..b6da1ca80f 100644
--- a/dev/_modules/MDAnalysis/topology/tables.html
+++ b/dev/_modules/MDAnalysis/topology/tables.html
@@ -189,10 +189,12 @@ 
Source code for MDAnalysis.topology.tables
 .. autodata:: TABLE_VDWRADII
 """
 
+from typing import Any
+
 
 

 [docs]
-def kv2dict(s, convertor=str):
+def kv2dict(s, convertor: Any = str):
     """Primitive ad-hoc parser of a key-value record list.
 
     * The string *s* should contain each key-value pair on a separate
@@ -318,10 +320,12 @@ 
Source code for MDAnalysis.topology.tables
 #: with :func:`MDAnalysis.topology.core.guess_atom_type`.
 atomelements = kv2dict(TABLE_ATOMELEMENTS)
 
+# fmt: off
 elements = ['H',
             'LI', 'BE', 'B', 'C', 'N', 'O', 'F',
             'NA', 'MG', 'AL', 'P', 'SI', 'S', 'CL',
             'K']
+# fmt: on
 
 #: Plain-text table with atomic masses in u.
 TABLE_MASSES = """
@@ -522,28 +526,31 @@ 
Source code for MDAnalysis.topology.tables
 #: .. SeeAlso:: :func:`MDAnalysis.topology.core.guess_bonds`
 vdwradii = kv2dict(TABLE_VDWRADII, convertor=float)
 
-Z2SYMB = {1: 'H',                                                                2: 'He', 
-          3: 'Li',   4: 'Be',  5: 'B',   6: 'C',   7: 'N',   8: 'O',   9: 'F',  10: 'Ne', 
-          11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P',  16: 'S',  17: 'Cl', 18: 'Ar', 
-          19: 'K',  20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V',  24: 'Cr', 25: 'Mn', 26: 'Fe', 
-          27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se', 
-          35: 'Br', 36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y',  40: 'Zr', 41: 'Nb', 42: 'Mo', 
-          43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In', 50: 'Sn', 
-          51: 'Sb', 52: 'Te', 53: 'I',  54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce', 
-          59: 'Pr', 60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy', 
-          67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta', 74: 'W', 
-          75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb', 
-          83: 'Bi', 84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th', 
-          91: 'Pa', 92: 'U',  93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk', 98: 'Cf', 
-          99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No', 103: 'Lr', 104: 'Rf', 105: 'Db', 
-          106: 'Sg', 107: 'Bh', 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn', 
+# fmt: off
+Z2SYMB = {1: 'H',                                                                2: 'He',
+          3: 'Li',   4: 'Be',  5: 'B',   6: 'C',   7: 'N',   8: 'O',   9: 'F',  10: 'Ne',
+          11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P',  16: 'S',  17: 'Cl', 18: 'Ar',
+          19: 'K',  20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V',  24: 'Cr', 25: 'Mn', 26: 'Fe',
+          27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se',
+          35: 'Br', 36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y',  40: 'Zr', 41: 'Nb', 42: 'Mo',
+          43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In', 50: 'Sn',
+          51: 'Sb', 52: 'Te', 53: 'I',  54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce',
+          59: 'Pr', 60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy',
+          67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta', 74: 'W',
+          75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb',
+          83: 'Bi', 84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th',
+          91: 'Pa', 92: 'U',  93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk', 98: 'Cf',
+          99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No', 103: 'Lr', 104: 'Rf', 105: 'Db',
+          106: 'Sg', 107: 'Bh', 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn',
           113: 'Nh', 114: 'Fl', 115: 'Mc', 116: 'Lv', 117: 'Ts', 118: 'Og'}
+# fmt: on
 
-SYMB2Z = {v:k for k, v in Z2SYMB.items()}
+SYMB2Z = {v: k for k, v in Z2SYMB.items()}
 
 # Conversion between SYBYL atom types and corresponding elements
 # Tripos MOL2 file format:
 #   https://web.archive.org/web/*/http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
+# fmt: off
 SYBYL2SYMB = {
     "H": "H", "H.spc": "H", "H.t3p": "H",
     "C.3": "C", "C.2": "C", "C.1": "C", "C.ar": "C", "C.cat": "C",
@@ -575,6 +582,7 @@ 
Source code for MDAnalysis.topology.tables
     "Mo": "Mo",
     "Sn": "Sn",
 }
+# fmt: on
 

 
            

diff --git a/dev/documentation_pages/analysis/wbridge_analysis.html b/dev/documentation_pages/analysis/wbridge_analysis.html
index 9034f1b151..ab8f98ce93 100644
--- a/dev/documentation_pages/analysis/wbridge_analysis.html
+++ b/dev/documentation_pages/analysis/wbridge_analysis.html
@@ -1049,7 +1049,7 @@ 
4.4.3.8. Classes
 

-DEFAULT_ACCEPTORS = {'CHARMM27': ('ND1', 'OG1', 'OD2', 'NE2', 'OD1', 'O', 'OC1', 'SD', 'OW', 'OE1', 'OC2', 'SG', 'OH2', 'OG', 'OE2', 'OH'), 'GLYCAM06': ('O', 'O2', 'SM', 'OW', 'OS', 'N', 'NT', 'OH', 'OY'), 'other': ()}

+DEFAULT_ACCEPTORS = {'CHARMM27': ('OG1', 'OW', 'OH2', 'ND1', 'OG', 'OE2', 'SD', 'OD2', 'OH', 'OC1', 'OD1', 'OE1', 'OC2', 'SG', 'O', 'NE2'), 'GLYCAM06': ('OW', 'SM', 'OS', 'NT', 'O2', 'N', 'OY', 'OH', 'O'), 'other': ()}
 
default atom names that are treated as hydrogen acceptors
 (see Default heavy atom names for CHARMM27 force field.);
 use the keyword acceptors to add a list of additional acceptor names.

@@ -1057,7 +1057,7 @@ 
4.4.3.8. Classes
 

-DEFAULT_DONORS = {'CHARMM27': ('NZ', 'ND2', 'ND1', 'NH1', 'OG1', 'OW', 'NE1', 'NE2', 'SG', 'NH2', 'N', 'OH2', 'OG', 'OH', 'NE'), 'GLYCAM06': ('N3', 'N', 'NT', 'OW', 'OH'), 'other': ()}

+DEFAULT_DONORS = {'CHARMM27': ('ND2', 'OG1', 'OW', 'SG', 'NH2', 'NE1', 'OH2', 'NE', 'ND1', 'OG', 'N', 'NH1', 'OH', 'NZ', 'NE2'), 'GLYCAM06': ('N3', 'N', 'OW', 'OH', 'NT'), 'other': ()}
 
default heavy atom names whose hydrogens are treated as donors
 (see Default heavy atom names for CHARMM27 force field.);
 use the keyword donors to add a list of additional donor names.

diff --git a/dev/documentation_pages/topology/tables.html b/dev/documentation_pages/topology/tables.html
index d001006064..b49454bae3 100644
--- a/dev/documentation_pages/topology/tables.html
+++ b/dev/documentation_pages/topology/tables.html
@@ -206,7 +206,7 @@
 kv2dict() for explanation of the file format.

 

 

-MDAnalysis.topology.tables.kv2dict(s, convertor=<class 'str'>)[source]

+MDAnalysis.topology.tables.kv2dict(s, convertor: ~typing.Any = <class 'str'>)[source]
 
Primitive ad-hoc parser of a key-value record list.

 
    
 
  • The string s should contain each key-value pair on a separate
diff --git a/dev/index.html b/dev/index.html
index f6c46b9955..625722330a 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -150,7 +150,7 @@ 
    MDAnalysis documentation
    2.8.0-dev0
    
 

 
Date:

-
Oct 13, 2024

+
Oct 15, 2024

 

 

 
MDAnalysis (www.mdanalysis.org) is an object-oriented python
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 77ad7c33ec..836bb97403 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
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"MDAnalysis.coordinates.TXYZ.TXYZReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.aux_list", false]], "auxfile (mdanalysis.auxiliary.base.auxfilereader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader.auxfile", false]], "auxfilereader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader", false]], "auxreader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxReader", false]], "auxreader() (in module mdanalysis.auxiliary.core)": [[47, "MDAnalysis.auxiliary.core.auxreader", false]], "auxstep (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxStep", false]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.auxstep", false]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure", false]], "backboneselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BackboneSelection", false]], "backendbase (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendBase", false]], "backenddask (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendDask", false]], "backendmultiprocessing (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendMultiprocessing", false]], "backendserial (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendSerial", false]], "baseselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BaseSelection", false]], "bat (class in mdanalysis.analysis.bat)": [[4, "MDAnalysis.analysis.bat.BAT", false]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[4, "MDAnalysis.analysis.bat.BAT.results.bat", false]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox", false]], "bbox() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bbox", false]], "bbox() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bbox", false]], "bbox() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bbox", false]], "between() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.between", false]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bF", false]], "bfactor (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bfactor", false]], "bfactor() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor", false]], "bfactor_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor_setter", false]], "bfactors (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.bfactors", false]], "bfactors (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.segment property)": [[92, "MDAnalysis.core.groups.Segment.bfactors", false]], "bfactors (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.bfactors", false]], "bfactors() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors", false]], "bfactors_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors_setter", false]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins", false]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr", false]], "blocks (mdanalysis.coordinates.tng.tngreader property)": [[72, "MDAnalysis.coordinates.TNG.TNGReader.blocks", false]], "blocks_of() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.blocks_of", false]], "bond (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Bond", false]], "bond (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bond", false]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation", false]], "bonded_atoms (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bonded_atoms", false]], "bonded_atoms() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.bonded_atoms", false]], "bonds (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Bonds", false]], "bonds (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.bonds", false]], "bonds() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.bonds", false]], "boolselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BoolSelection", false]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[14, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix", false]], "box (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.Box", false]], "box_volume() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.box_volume", false]], "bsphere() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bsphere", false]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop", false]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable", false]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bV", false]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.bX", false]], "bynumselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByNumSelection", false]], "byresselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByResSelection", false]], "bz2_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.bz2_pickle_open", false]], "bz2picklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.BZ2Picklable", false]], "cached() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.cached", false]], "calc_angles() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.calc_angles", false]], "calc_bonds() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.calc_bonds", false]], "calc_dihedrals() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.calc_dihedrals", false]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[107, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.calc_offsets", false]], "calc_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[107, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.calc_offsets", false]], "calc_representative() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.calc_representative", false]], "calcrmsdrotationalmatrix() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix", false]], "capped_distance() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.capped_distance", false]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[4, "MDAnalysis.analysis.bat.BAT.Cartesian", false]], "cdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.cdf", false]], "cdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.cdf", false]], "center() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center", false]], "center() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center", false]], "center() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center", false]], "center_in_box (class in mdanalysis.transformations.translate)": [[164, "MDAnalysis.transformations.translate.center_in_box", false]], "center_of_charge() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.center_of_charge", false]], "center_of_geometry() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_geometry", false]], "center_of_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.center_of_mass", false]], "centers() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.centers", false]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.centroid", false]], "centroid() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.centroid", false]], "centroid() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.centroid", false]], "centroid() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.centroid", false]], "ces() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.ces", false]], "ces_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.ces_convergence", false]], "chainids (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs", false]], "chainreader (class in mdanalysis.coordinates.chain)": [[82, "MDAnalysis.coordinates.chain.ChainReader", false]], "char (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char", false]], "char_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char_std", false]], "charge_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density", false]], "charge_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, 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(mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.check_slice_indices", false]], "chemfilespicklable (class in mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.ChemfilesPicklable", false]], "chemfilesreader (class in mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.ChemfilesReader", false]], "chemfileswriter (class in 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false]], "close() (mdanalysis.converters.openmmparser.openmmapptopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser.close", false]], "close() (mdanalysis.converters.openmmparser.openmmtopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser.close", false]], "close() (mdanalysis.converters.parmedparser.parmedparser method)": [[52, "MDAnalysis.converters.ParmEdParser.ParmEdParser.close", false]], "close() (mdanalysis.converters.rdkitparser.rdkitparser method)": [[53, "MDAnalysis.converters.RDKitParser.RDKitParser.close", false]], "close() (mdanalysis.coordinates.base.converterbase method)": [[81, "MDAnalysis.coordinates.base.ConverterBase.close", false]], "close() (mdanalysis.coordinates.base.iobase method)": [[81, "MDAnalysis.coordinates.base.IOBase.close", false]], "close() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.close", false]], "close() 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"MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.close", false]], "close() (mdanalysis.coordinates.gms.gmsreader method)": [[60, "MDAnalysis.coordinates.GMS.GMSReader.close", false]], "close() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.close", false]], "close() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.close", false]], "close() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.close", false]], "close() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.close", false]], "close() (mdanalysis.coordinates.lammps.datawriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter.close", false]], "close() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.close", false]], "close() (mdanalysis.coordinates.lammps.dcdwriter method)": [[65, 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"MDAnalysis.coordinates.LAMMPS.DCDReader", false]], "dcdwriter (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter", false]], "dcdwriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter", false]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.decompose_matrix", false]], "dedent_docstring() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.dedent_docstring", false]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS", false]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS", false]], "default_format (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.default_format", false]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms", false]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.define_unpack_real", false]], "del_topologyattr() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.del_TopologyAttr", false]], "del_topologyattr() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.del_TopologyAttr", false]], "delete_angles() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_angles", false]], "delete_bonds() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_bonds", false]], "delete_dihedrals() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_dihedrals", false]], "delete_impropers() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_impropers", false]], "delta (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.delta", false]], "delta (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.delta", false]], "density (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.Density", false]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.density", false]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.results.density", false]], "densityanalysis (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.DensityAnalysis", false]], "densityunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.densityUnit_factor", false]], "deprecate() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.deprecate", false]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant", false]], "difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.difference", false]], "difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.difference", false]], "difference() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.difference", false]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap", false]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[10, "MDAnalysis.analysis.dihedrals.Dihedral", false]], "dihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Dihedral", false]], "dihedral (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dihedral", false]], "dihedral() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.dihedral", false]], "dihedral() (mdanalysis.core.topologyobjects.dihedral method)": [[97, "MDAnalysis.core.topologyobjects.Dihedral.dihedral", false]], "dihedrals (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Dihedrals", false]], "dihedrals (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dihedrals", false]], "dihedrals() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dihedrals", false]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim", false]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac", false]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[18, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod", false]], "dimensions (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dimensions", false]], "dimensions (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.dimensions", false]], "dimensions (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dimensions", false]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity", false]], "dipole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_moment", false]], "dipole_vector() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_vector", false]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence", false]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence", false]], "dist() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.dist", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix", false]], "distance() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.distance", false]], "distance_array() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.distance_array", false]], "distance_array() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.distance_array", false]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix", false]], "distances (mdanalysis.analysis.nucleicacids.majorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.minorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.distances", false]], "dmsparser (class in mdanalysis.topology.dmsparser)": [[130, "MDAnalysis.topology.DMSParser.DMSParser", false]], "dmsreader (class in mdanalysis.coordinates.dms)": [[58, "MDAnalysis.coordinates.DMS.DMSReader", false]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atom", false]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atoms", false]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_block", false]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_blocka", false]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ffparams", false]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_harm", false]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ilists", false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp_ndarray", false]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.dt", false]], "dt (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.dt", false]], "dt (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.dt", false]], "dt (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.dt", false]], "dt (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dt", false]], "dt (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.dt", false]], "dt (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.dt", false]], "dt (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.dt", false]], "dt (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.dt", false]], "dt (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.dt", false]], "dt (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dt", false]], "dt (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.dt", false]], "dt (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.dt", false]], "dt (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.dt", false]], "dt (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.dt", false]], "dtype (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dtype", false]], "dtype (mdanalysis.core.selection.floatrangeselection attribute)": [[94, "MDAnalysis.core.selection.FloatRangeSelection.dtype", false]], "dtype (mdanalysis.core.selection.rangeselection attribute)": [[94, "MDAnalysis.core.selection.RangeSelection.dtype", false]], "dtype (mdanalysis.core.topologyattrs.altlocs attribute)": [[96, "MDAnalysis.core.topologyattrs.AltLocs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.aromaticities attribute)": [[96, "MDAnalysis.core.topologyattrs.Aromaticities.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomids attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Molnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.moltypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Moltypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.nonbondedindices attribute)": [[96, "MDAnalysis.core.topologyattrs.NonbondedIndices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[118, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[155, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[108, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [115, "index-0", false], [115, "index-1", false], [118, "index-0", false], [158, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[131, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[110, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[132, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.frame", false]], "frame (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.frame", false]], "frame (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.frame", false]], "frame (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.frame", false]], "frame (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.frame", false]], "frame (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.frame", false]], "frame (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.frame", false]], "frame (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.frame", false]], "frame (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.frame", false]], "frame (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.frame", false]], "frame (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.frame", false]], "frame (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.frame", false]], "frame (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.frame", false]], "frame 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"guess_atom_mass() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_mass", false]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_type", false]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_bonds", false]], "guess_bonds() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.guess_bonds", false]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_dihedrals", false]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[144, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.guess_format", false]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_gasteiger_charges", false]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens", false]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_improper_dihedrals", false]], "guess_masses() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_masses", false]], "guess_types() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_types", false]], "guessed_attributes (mdanalysis.core.topology.topology property)": [[95, "MDAnalysis.core.topology.Topology.guessed_attributes", false]], "gyration_moments() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.gyration_moments", false]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open", false]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.GzipPicklable", false]], "h5md_version (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.H5MD_VERSION", false]], "h5mdreader (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader", false]], "h5mdwriter (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter", false]], "h5pypicklable (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5PYPicklable", false]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.hard_cut_q", false]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_forces", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_forces", false]], "has_forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_forces", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_positions", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_positions", false]], "has_positions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_positions", false]], "has_valid_coordinates() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.datawriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.dcdwriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.trr.trrwriter method)": [[75, "MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xdr.xdrbasewriter method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xtc.xtcwriter method)": [[79, "MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_velocities", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_velocities", false]], "has_velocities (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_velocities", false]], "hasmethod() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.hasmethod", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds", false]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[106, "MDAnalysis.lib.formats.libdcd.DCDFile.header", false]], "header() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.HEADER", false]], "helanal (class in mdanalysis.analysis.helix_analysis)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL", false]], "helix_analysis() (in module mdanalysis.analysis.helix_analysis)": [[24, "MDAnalysis.analysis.helix_analysis.helix_analysis", false]], "hes() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.hes", false]], "hist_bin_edges (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.hist_bin_edges", false]], "historyparser (class in mdanalysis.topology.dlpolyparser)": [[129, "MDAnalysis.topology.DLPolyParser.HistoryParser", false]], "historyreader (class in mdanalysis.coordinates.dlpoly)": [[57, "MDAnalysis.coordinates.DLPoly.HistoryReader", false]], "hoomdxmlparser (class in mdanalysis.topology.hoomdxmlparser)": [[136, "MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser", false]], "hydrogenbondanalysis (class in mdanalysis.analysis.hydrogenbonds.hbond_analysis)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis", false]], "hydrogenbondautocorrel (class in mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel", false]], "hydroxyl() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.hydroxyl", false]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[155, "MDAnalysis.topology.tpr.obj.Ilist.iatoms", false]], "icodes (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.ICodes", false]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id", false]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[155, "MDAnalysis.topology.tpr.obj.Ilist.ik", false]], "ilist (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.Ilist", false]], "improper (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.improper", false]], "improper() (mdanalysis.core.topologyobjects.improperdihedral method)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral.improper", false]], "improperdihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral", false]], "impropers (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Impropers", false]], "impropers (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.impropers", false]], "indices (mdanalysis.core.topologyobjects.topologygroup property)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.indices", false]], "indices (mdanalysis.core.topologyobjects.topologyobject property)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject.indices", false]], "initial_time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.initial_time", false]], "innerproduct() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.InnerProduct", false]], "inpreader (class in mdanalysis.coordinates.inpcrd)": [[64, "MDAnalysis.coordinates.INPCRD.INPReader", false]], "int_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.INT_PATTERN", false]], "interaction_types (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.interaction_types", false]], "interactionkind (class in mdanalysis.topology.tpr.obj)": [[155, "MDAnalysis.topology.tpr.obj.InteractionKind", false]], "interpolated (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolated", false]], "interpolation_spline_order (mdanalysis.analysis.density.density property)": [[7, "MDAnalysis.analysis.density.Density.interpolation_spline_order", false]], "interrdf (class in mdanalysis.analysis.rdf)": [[38, 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false]], "iter_auxiliary() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.iter_auxiliary", false]], "iter_auxiliary() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.iter_auxiliary", false]], "iterable() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.iterable", false]], "iterative_average() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.iterative_average", false]], "itpparser (class in mdanalysis.topology.itpparser)": [[137, "MDAnalysis.topology.ITPParser.ITPParser", false]], "ix (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.ix", false]], "ix (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.ix", false]], "ix (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.ix", false]], "ix (mdanalysis.core.groups.residuegroup property)": [[92, 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"MDAnalysis.core.topologyattrs.Masses.shape_parameter", false]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.shear_from_matrix", false]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator", false]], "singlecharselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[155, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], "skip_timestep (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep", false]], "skipper() (mdanalysis.topology.topparser.topparser method)": [[146, "MDAnalysis.topology.TOPParser.TOPParser.skipper", false]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume", false]], "smartsselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SmartsSelection", false]], "soft_cut_q() (in 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109, 112, 115, 171], "complic": [0, 92, 93, 119], "compnd": [69, 70], "compon": [7, 18, 19, 27, 43, 72, 75, 92, 95, 96, 109, 113, 118, 153, 168, 169, 171], "component_index": 27, "componentbas": 92, "compos": [18, 155], "compose_matrix": 114, "composit": [111, 117], "compound": [7, 69, 92, 96, 165], "comprehens": [115, 118, 171], "compress": [20, 55, 60, 63, 68, 69, 70, 71, 72, 74, 79, 80, 82, 85, 107, 111, 115, 117], "compression_opt": 63, "compresslevel": 111, "compris": 19, "comput": [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 15, 16, 19, 21, 24, 26, 30, 32, 33, 34, 35, 38, 40, 42, 59, 63, 72, 85, 92, 93, 96, 104, 109, 110, 113, 115, 116, 118, 161, 162, 166], "computation": [19, 31], "computation_group": 3, "concaten": [19, 31, 82, 92, 95, 105, 111, 114, 119], "concatenate_matric": 114, "concatent": 119, "concentr": 166, "concern": [90, 115, 116, 156], "conclus": 35, "conda": [43, 74], "condid": 113, "condit": [1, 2, 5, 7, 8, 11, 22, 27, 31, 38, 40, 63, 85, 92, 94, 97, 101, 110, 112, 137, 152], "condtion": 112, "conduct": 171, "conect": [69, 92, 142], "conf": 113, "conf_dist_arg": 16, "conf_dist_funct": 16, "conf_dist_kwarg": 16, "conf_dist_matrix": 16, "confdistmatrix": [13, 14], "confer": 118, "config": [57, 85, 129, 153, 171], "configpars": 129, "configread": 57, "configur": [4, 10, 11, 34, 40, 56, 63, 105, 108, 110], "confin": 69, "confirm": 31, "conflict": 74, "conform": [5, 10, 14, 15, 16, 18, 19, 21, 32, 33, 53, 61, 69, 71, 98, 118], "conformational_distance_matrix": 16, "confus": 115, "conjug": 53, "conjunct": 63, "conn": 155, "connbond": 155, "connect": [22, 27, 38, 42, 69, 70, 77, 92, 96, 97, 98, 105, 115, 117, 143, 144, 147, 148, 153, 155], "consant": 46, "consecut": [15, 24, 26, 27, 53, 69, 92, 104, 115, 119], "consequ": [80, 98, 106, 161, 162], "conserv": [92, 155], "consid": [0, 1, 3, 7, 9, 11, 15, 19, 21, 22, 26, 28, 40, 42, 46, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 92, 94, 97, 98, 104, 108, 110, 115, 119, 152, 166], "consider": [22, 26, 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81, 82, 86, 105, 115, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "conversion_factor": 166, "conversionwarn": 100, "convert": [7, 11, 28, 31, 44, 56, 59, 61, 62, 63, 65, 67, 69, 71, 72, 74, 75, 76, 77, 78, 79, 80, 82, 85, 86, 91, 92, 94, 98, 100, 105, 107, 109, 114, 115, 117, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150, 153, 154, 166], "convert_aa_cod": [94, 115], "convert_dens": 7, "convert_dimensions_to_unitcel": [56, 59, 61, 63, 65, 75, 78, 79, 81, 85], "convert_forces_from_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_forces_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_length": 7, "convert_pos_from_n": 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69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_velocities_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "converterbas": [54, 81], "converterwrapp": [91, 92], "convertor": 154, "cookbook": 21, "coontain": 110, "coor": [68, 85], "coord": [11, 12, 16, 80, 92, 93, 98, 105, 109, 110, 112, 152, 153], "coord1": 105, "coord2": 105, "coord_nam": 115, "coord_par": 46, "coordiant": [17, 71, 105], "coordin": [3, 7, 9, 11, 12, 16, 17, 18, 19, 21, 24, 28, 31, 35, 38, 40, 43, 44, 46, 48, 51, 52, 53, 54, 92, 93, 96, 98, 105, 106, 107, 109, 110, 112, 113, 114, 115, 116, 117, 118, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 141, 142, 143, 144, 145, 146, 147, 148, 150, 152, 153, 156, 157, 160, 161, 163, 164, 165, 168, 169, 171], "coordinat": 40, "coordinate_arrai": 86, "coords1": 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63, 69, 80, 92, 96, 98, 100, 105, 106, 107, 108, 109, 115, 136, 146], "zeta": 33, "zheng": 9, "zhiyi": 42, "zhou": [104, 118], "zink": 154, "ziolek": 118, "zip": [21, 105, 117], "zmax": [92, 110, 119, 169], "zmin": [92, 110, 119, 169], "zn": 154, "znd": 38, "zone": [92, 119], "zr": 154, "zsu": 65, "zu": 65, "zvalu": 69, "zz": 7, "\u00e1": 104, "\u00e5": [3, 5, 7, 22, 26, 42, 56, 59, 65, 69, 71, 74, 86, 89, 92, 96, 104, 159, 166], "\u00e5ngstrom": 63, "\u00e5ngstr\u00f6m": [7, 59, 65, 74, 166], "\u00ed": 104, "\u03b1": 12, "\u03bc": 166, "\u03c0": [12, 109], "\u03c6": 10, "\u03c8": 10}, "titles": ["4.3.1. Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. 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", "6.26. 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. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "6.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.22. TRZ trajectory I/O  \u2014 MDAnalysis.coordinates.TRZ", "6.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.31. Base classes \u2014 MDAnalysis.coordinates.base", "6.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers  \u2014 MDAnalysis.coordinates", "6.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.29. Null output \u2014 MDAnalysis.coordinates.null", "6.33. Serialization of Coordinate Readers", "6.30. 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. 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(mdanalysis.topology.gsdparser.gsdparser method)": [[135, "MDAnalysis.topology.GSDParser.GSDParser.close", false]], "close() (mdanalysis.topology.hoomdxmlparser.hoomdxmlparser method)": [[136, "MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser.close", false]], "close() (mdanalysis.topology.itpparser.itpparser method)": [[137, "MDAnalysis.topology.ITPParser.ITPParser.close", false]], "close() (mdanalysis.topology.lammpsparser.dataparser method)": [[138, "MDAnalysis.topology.LAMMPSParser.DATAParser.close", false]], "close() (mdanalysis.topology.minimalparser.minimalparser method)": [[141, "MDAnalysis.topology.MinimalParser.MinimalParser.close", false]], "close() (mdanalysis.topology.mol2parser.mol2parser method)": [[140, "MDAnalysis.topology.MOL2Parser.MOL2Parser.close", false]], "close() (mdanalysis.topology.pdbparser.pdbparser method)": [[142, "MDAnalysis.topology.PDBParser.PDBParser.close", false]], "close() (mdanalysis.topology.pdbqtparser.pdbqtparser method)": [[143, 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(mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dimensions", false]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity", false]], "dipole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_moment", false]], "dipole_vector() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_vector", false]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence", false]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence", false]], "dist() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.dist", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix", false]], "distance() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.distance", false]], "distance_array() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.distance_array", false]], "distance_array() (in module mdanalysis.lib.distances)": [[105, "MDAnalysis.lib.distances.distance_array", false]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix", false]], "distances (mdanalysis.analysis.nucleicacids.majorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.minorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.distances", false]], "dmsparser (class in mdanalysis.topology.dmsparser)": [[130, "MDAnalysis.topology.DMSParser.DMSParser", false]], "dmsreader (class in mdanalysis.coordinates.dms)": [[58, "MDAnalysis.coordinates.DMS.DMSReader", false]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atom", false]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_atoms", false]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_block", false]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_blocka", false]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ffparams", false]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_harm", false]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_ilists", false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp_ndarray", false]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.dt", false]], "dt (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.dt", false]], "dt (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.dt", false]], "dt (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.dt", false]], "dt (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dt", false]], "dt (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.dt", false]], "dt (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.dt", false]], "dt (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.dt", false]], "dt (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.dt", false]], "dt (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.dt", false]], "dt (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dt", false]], "dt (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.dt", false]], "dt (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.dt", false]], "dt (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.dt", false]], "dt (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.dt", false]], "dtype (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dtype", false]], "dtype (mdanalysis.core.selection.floatrangeselection attribute)": [[94, "MDAnalysis.core.selection.FloatRangeSelection.dtype", false]], "dtype (mdanalysis.core.selection.rangeselection attribute)": [[94, "MDAnalysis.core.selection.RangeSelection.dtype", false]], "dtype (mdanalysis.core.topologyattrs.altlocs attribute)": [[96, "MDAnalysis.core.topologyattrs.AltLocs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.aromaticities attribute)": [[96, "MDAnalysis.core.topologyattrs.Aromaticities.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomids attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Molnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.moltypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Moltypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.nonbondedindices attribute)": [[96, "MDAnalysis.core.topologyattrs.NonbondedIndices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[118, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[155, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[108, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [115, "index-0", false], [115, "index-1", false], [118, "index-0", false], [158, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[114, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[131, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[113, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[110, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[132, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[155, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[109, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[160, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[115, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[166, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[121, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[122, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[123, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[124, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[125, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.frame", false]], "frame (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.frame", false]], "frame (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.frame", false]], "frame (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.frame", false]], "frame (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.frame", false]], "frame (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.frame", false]], "frame (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.frame", false]], "frame (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.frame", false]], "frame (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.frame", false]], "frame (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.frame", false]], "frame (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.frame", false]], "frame (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.frame", false]], "frame (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.frame", false]], "frame (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.frame", false]], "frame_data (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_data", false]], "frame_rep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_rep", false]], "frameiteratorall (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorAll", false]], "frameiteratorbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorBase", false]], "frameiteratorindices (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorIndices", false]], "frameiteratorsliced (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorSliced", false]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[3, "MDAnalysis.analysis.base.AnalysisBase.frames", false]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[3, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames", false]], "frames (mdanalysis.analysis.base.results attribute)": [[3, "MDAnalysis.analysis.base.results.frames", false]], "from_blank() (mdanalysis.core.topologyattrs.topologyattr class method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.from_blank", false]], "from_coordinates() (mdanalysis.coordinates.timestep.timestep class method)": [[89, "MDAnalysis.coordinates.timestep.Timestep.from_coordinates", false]], "from_smiles() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.from_smiles", false]], "from_timestep() (mdanalysis.coordinates.timestep.timestep class method)": [[89, "MDAnalysis.coordinates.timestep.Timestep.from_timestep", false]], "from_unpacker() (mdanalysis.topology.tpr.utils.tpxunpacker2020 class method)": [[155, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.from_unpacker", false]], "ftupd (in module mdanalysis.topology.tpr.setting)": [[155, "MDAnalysis.topology.tpr.setting.ftupd", false]], "fudgeqq (mdanalysis.topology.tpr.obj.params attribute)": [[155, "MDAnalysis.topology.tpr.obj.Params.fudgeQQ", false]], "function (mdanalysis.analysis.encore.utils.parallelcalculation attribute)": [[20, "MDAnalysis.analysis.encore.utils.ParallelCalculation.function", false]], "functype (mdanalysis.topology.tpr.obj.params attribute)": [[155, "MDAnalysis.topology.tpr.obj.Params.functype", false]], "fver (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[155, "MDAnalysis.topology.tpr.obj.TpxHeader.fver", false]], "gbscreens (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.GBScreens", false]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs", false]], "gen_selection_class() (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.gen_selection_class", false]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[21, "MDAnalysis.analysis.gnm.generate_grid", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff", false]], "generate_streamlines() (in module mdanalysis.visualization.streamlines)": [[168, "MDAnalysis.visualization.streamlines.generate_streamlines", false]], "generate_streamlines_3d() (in module mdanalysis.visualization.streamlines_3d)": [[169, "MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d", false]], "generate_table() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.generate_table", false]], "get_array() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_array", false]], "get_atom_mass() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.get_atom_mass", false]], "get_atoms() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.atomindices method)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.resindices method)": [[96, "MDAnalysis.core.topologyattrs.Resindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.get_atoms", false]], "get_aux_attribute() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.get_aux_attribute", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, 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false]], "get_aux_descriptions() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.get_aux_descriptions", false]], "get_auxreader_for() (in module mdanalysis.auxiliary.core)": [[47, "MDAnalysis.auxiliary.core.get_auxreader_for", false]], "get_cdf() (mdanalysis.analysis.rdf.interrdf_s method)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.get_cdf", false]], "get_centroids() (mdanalysis.analysis.encore.clustering.clustercollection.clustercollection method)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection.get_centroids", false]], "get_connections() (mdanalysis.core.groups.atom method)": [[92, "MDAnalysis.core.groups.Atom.get_connections", false]], "get_connections() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.get_connections", false]], "get_connections() (mdanalysis.core.groups.residue method)": [[92, "MDAnalysis.core.groups.Residue.get_connections", false]], "get_connections() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.get_connections", false]], "get_connections() (mdanalysis.core.groups.segment method)": [[92, "MDAnalysis.core.groups.Segment.get_connections", false]], "get_connections() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.get_connections", false]], "get_conversion_factor() (in module mdanalysis.units)": [[166, "MDAnalysis.units.get_conversion_factor", false]], "get_data() (mdanalysis.auxiliary.edr.edrreader method)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.get_data", false]], "get_description() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.get_description", false]], "get_distance_matrix() (in module mdanalysis.analysis.encore.confdistmatrix)": [[16, "MDAnalysis.analysis.encore.confdistmatrix.get_distance_matrix", false]], "get_distance_matrix_bootstrap_samples() (in module mdanalysis.analysis.encore.bootstrap)": 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false]], "get_residues() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.get_residues", false]], "get_residues() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.get_residues", false]], "get_residues() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.get_residues", false]], "get_segments() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.get_segments", false]], "get_segments() (mdanalysis.core.topologyattrs.atomindices method)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.get_segments", false]], "get_segments() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.get_segments", false]], "get_segments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.get_segments", false]], "get_segments() 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(mdanalysis.analysis.nucleicacids.nucpairdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.nucleicacids.watsoncrickdist class method)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.pca.pca class method)": [[35, "MDAnalysis.analysis.pca.PCA.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.rms.rmsd class method)": [[40, "MDAnalysis.analysis.rms.RMSD.get_supported_backends", false]], "get_supported_backends() (mdanalysis.analysis.rms.rmsf class method)": [[40, "MDAnalysis.analysis.rms.RMSF.get_supported_backends", false]], "get_weights() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.get_weights", false]], "get_writer() (in module mdanalysis.selections)": [[126, "MDAnalysis.selections.get_writer", false]], "get_writer_for() (in module mdanalysis.coordinates.core)": [[84, "MDAnalysis.coordinates.core.get_writer_for", false]], "getconstrain() (mdanalysis.lib.transformations.arcball method)": [[114, "MDAnalysis.lib.transformations.Arcball.getconstrain", false]], "global_axis (mdanalysis.analysis.helix_analysis.helanal.results attribute)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL.results.global_axis", false]], "global_tilts (mdanalysis.analysis.helix_analysis.helanal.results attribute)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL.results.global_tilts", false]], "gmsparser (class in mdanalysis.topology.gmsparser)": [[133, "MDAnalysis.topology.GMSParser.GMSParser", false]], "gmsreader (class in mdanalysis.coordinates.gms)": [[60, "MDAnalysis.coordinates.GMS.GMSReader", false]], "gnmanalysis (class in mdanalysis.analysis.gnm)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis", false]], "grab_datafile() (mdanalysis.topology.lammpsparser.dataparser method)": [[138, "MDAnalysis.topology.LAMMPSParser.DATAParser.grab_datafile", false]], "grab_not_keywords() (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.grab_not_keywords", false]], "greedy_splitext() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.greedy_splitext", false]], "grid (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.grid", false]], "groparser (class in mdanalysis.topology.groparser)": [[134, "MDAnalysis.topology.GROParser.GROParser", false]], "groreader (class in mdanalysis.coordinates.gro)": [[61, "MDAnalysis.coordinates.GRO.GROReader", false]], "group (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.group", false]], "group() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.group", false]], "group_same_or_consecutive_integers() (in module mdanalysis.lib.util)": [[115, 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"guess_atom_mass() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_mass", false]], "guess_atom_type() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_atom_type", false]], "guess_bonds() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_bonds", false]], "guess_bonds() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.guess_bonds", false]], "guess_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_dihedrals", false]], "guess_donors() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[144, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.guess_format", false]], "guess_gasteiger_charges() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_gasteiger_charges", false]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens", false]], "guess_improper_dihedrals() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_improper_dihedrals", false]], "guess_masses() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_masses", false]], "guess_types() (in module mdanalysis.topology.guessers)": [[152, "MDAnalysis.topology.guessers.guess_types", false]], "guessed_attributes (mdanalysis.core.topology.topology property)": [[95, "MDAnalysis.core.topology.Topology.guessed_attributes", false]], "gyration_moments() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.gyration_moments", false]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open", false]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[111, "MDAnalysis.lib.picklable_file_io.GzipPicklable", false]], "h5md_version (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.H5MD_VERSION", false]], "h5mdreader (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader", false]], "h5mdwriter (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter", false]], "h5pypicklable (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5PYPicklable", false]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.hard_cut_q", false]], "harmonic_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.harmonic_ensemble_similarity", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_forces", false]], "has_forces (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_forces", false]], "has_forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_forces", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_positions", false]], "has_positions (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_positions", false]], "has_positions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_positions", false]], "has_valid_coordinates() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_valid_coordinates", false]], "has_valid_coordinates() 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"MDAnalysis.coordinates.H5MD.H5MDWriter.has_velocities", false]], "has_velocities (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_velocities", false]], "hasmethod() (in module mdanalysis.lib.util)": [[115, "MDAnalysis.lib.util.hasmethod", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.hbonds", false]], "hbonds (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis.results attribute)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results.hbonds", false]], "header (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[106, "MDAnalysis.lib.formats.libdcd.DCDFile.header", false]], "header() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.HEADER", false]], "helanal (class in mdanalysis.analysis.helix_analysis)": 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"mdanalysis.analysis.nuclinfo": [[33, "module-MDAnalysis.analysis.nuclinfo", false]], "mdanalysis.analysis.pca": [[35, "module-MDAnalysis.analysis.pca", false]], "mdanalysis.analysis.polymer": [[36, "module-MDAnalysis.analysis.polymer", false]], "mdanalysis.analysis.psa": [[37, "module-MDAnalysis.analysis.psa", false]], "mdanalysis.analysis.rdf": [[38, "module-MDAnalysis.analysis.rdf", false]], "mdanalysis.analysis.results": [[39, "module-MDAnalysis.analysis.results", false]], "mdanalysis.analysis.rms": [[40, "module-MDAnalysis.analysis.rms", false]], "mdanalysis.analysis.waterdynamics": [[41, "module-MDAnalysis.analysis.waterdynamics", false]], "mdanalysis.auxiliary.__init__": [[48, "module-MDAnalysis.auxiliary.__init__", false]], "mdanalysis.auxiliary.base": [[46, "module-MDAnalysis.auxiliary.base", false]], "mdanalysis.auxiliary.core": [[47, "module-MDAnalysis.auxiliary.core", false]], "mdanalysis.auxiliary.edr": [[44, "module-MDAnalysis.auxiliary.EDR", false]], "mdanalysis.auxiliary.xvg": [[45, "module-MDAnalysis.auxiliary.XVG", false]], "mdanalysis.converters": [[50, "module-MDAnalysis.converters", false]], "mdanalysis.converters.base": [[54, "module-MDAnalysis.converters.base", false]], "mdanalysis.converters.openmm": [[51, "module-MDAnalysis.converters.OpenMM", false]], "mdanalysis.converters.openmmparser": [[51, "module-MDAnalysis.converters.OpenMMParser", false]], "mdanalysis.converters.parmed": [[52, "module-MDAnalysis.converters.ParmEd", false]], "mdanalysis.converters.parmedparser": [[52, "module-MDAnalysis.converters.ParmEdParser", false]], "mdanalysis.converters.rdkit": [[53, "module-MDAnalysis.converters.RDKit", false]], "mdanalysis.converters.rdkitparser": [[53, "module-MDAnalysis.converters.RDKitParser", false]], "mdanalysis.coordinates.__init__": [[85, "module-MDAnalysis.coordinates.__init__", false]], "mdanalysis.coordinates.base": [[81, "module-MDAnalysis.coordinates.base", false]], "mdanalysis.coordinates.chain": [[82, 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"mdanalysis.coordinates.inpcrd": [[64, "module-MDAnalysis.coordinates.INPCRD", false]], "mdanalysis.coordinates.lammps": [[65, "module-MDAnalysis.coordinates.LAMMPS", false]], "mdanalysis.coordinates.memory": [[86, "module-MDAnalysis.coordinates.memory", false]], "mdanalysis.coordinates.mmtf": [[66, "module-MDAnalysis.coordinates.MMTF", false]], "mdanalysis.coordinates.mol2": [[67, "module-MDAnalysis.coordinates.MOL2", false]], "mdanalysis.coordinates.namdbin": [[68, "module-MDAnalysis.coordinates.NAMDBIN", false]], "mdanalysis.coordinates.null": [[87, "module-MDAnalysis.coordinates.null", false]], "mdanalysis.coordinates.pdb": [[69, "module-MDAnalysis.coordinates.PDB", false]], "mdanalysis.coordinates.pdbqt": [[70, "module-MDAnalysis.coordinates.PDBQT", false]], "mdanalysis.coordinates.pqr": [[71, "module-MDAnalysis.coordinates.PQR", false]], "mdanalysis.coordinates.timestep": [[89, "module-MDAnalysis.coordinates.timestep", false]], "mdanalysis.coordinates.tng": [[72, 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(mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.mobile_atoms", false]], "model() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.MODEL", false]], "models (mdanalysis.core.universe.universe property)": [[98, "MDAnalysis.core.universe.Universe.models", false]], "module": [[0, "module-MDAnalysis.analysis.align", false], [1, "module-MDAnalysis.analysis.atomicdistances", false], [2, "module-MDAnalysis.analysis.backends", false], [3, "module-MDAnalysis.analysis.base", false], [4, "module-MDAnalysis.analysis.bat", false], [5, "module-MDAnalysis.analysis.contacts", false], [6, "module-MDAnalysis.analysis.data.filenames", false], [7, "module-MDAnalysis.analysis.density", false], [8, "module-MDAnalysis.analysis.dielectric", false], [9, "module-MDAnalysis.analysis.diffusionmap", false], [10, "module-MDAnalysis.analysis.dihedrals", false], [11, "module-MDAnalysis.analysis.distances", false], [12, 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false]], "transformations (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.transformations", false]], "transformations (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.transformations", false]], "transformations (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.transformations", false]], "transformations (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.transformations", false]], "translate (class in mdanalysis.transformations.translate)": [[164, "MDAnalysis.transformations.translate.translate", false]], "translate() (in module mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.translate", false]], "translate() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.translate", false]], "translate() (mdanalysis.core.groups.residuegroup method)": [[92, 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81, 82, 86, 105, 115, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "conversion_factor": 166, "conversionwarn": 100, "convert": [7, 11, 28, 31, 44, 56, 59, 61, 62, 63, 65, 67, 69, 71, 72, 74, 75, 76, 77, 78, 79, 80, 82, 85, 86, 91, 92, 94, 98, 100, 105, 107, 109, 114, 115, 117, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150, 153, 154, 166], "convert_aa_cod": [94, 115], "convert_dens": 7, "convert_dimensions_to_unitcel": [56, 59, 61, 63, 65, 75, 78, 79, 81, 85], "convert_forces_from_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_forces_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_length": 7, "convert_pos_from_n": 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69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "convert_velocities_to_n": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 140, 141, 142, 143, 144, 145, 146, 147, 148, 150], "converterbas": [54, 81], "converterwrapp": [91, 92], "convertor": 154, "cookbook": 21, "coontain": 110, "coor": [68, 85], "coord": [11, 12, 16, 80, 92, 93, 98, 105, 109, 110, 112, 152, 153], "coord1": 105, "coord2": 105, "coord_nam": 115, "coord_par": 46, "coordiant": [17, 71, 105], "coordin": [3, 7, 9, 11, 12, 16, 17, 18, 19, 21, 24, 28, 31, 35, 38, 40, 43, 44, 46, 48, 51, 52, 53, 54, 92, 93, 96, 98, 105, 106, 107, 109, 110, 112, 113, 114, 115, 116, 117, 118, 119, 128, 130, 131, 132, 133, 134, 135, 136, 137, 138, 141, 142, 143, 144, 145, 146, 147, 148, 150, 152, 153, 156, 157, 160, 161, 163, 164, 165, 168, 169, 171], "coordinat": 40, "coordinate_arrai": 86, "coords1": 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63, 69, 80, 92, 96, 98, 100, 105, 106, 107, 108, 109, 115, 136, 146], "zeta": 33, "zheng": 9, "zhiyi": 42, "zhou": [104, 118], "zink": 154, "ziolek": 118, "zip": [21, 105, 117], "zmax": [92, 110, 119, 169], "zmin": [92, 110, 119, 169], "zn": 154, "znd": 38, "zone": [92, 119], "zr": 154, "zsu": 65, "zu": 65, "zvalu": 69, "zz": 7, "\u00e1": 104, "\u00e5": [3, 5, 7, 22, 26, 42, 56, 59, 65, 69, 71, 74, 86, 89, 92, 96, 104, 159, 166], "\u00e5ngstrom": 63, "\u00e5ngstr\u00f6m": [7, 59, 65, 74, 166], "\u00ed": 104, "\u03b1": 12, "\u03bc": 166, "\u03c0": [12, 109], "\u03c6": 10, "\u03c8": 10}, "titles": ["4.3.1. Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. 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", "6.26. 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. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "6.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "6.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "6.22. TRZ trajectory I/O  \u2014 MDAnalysis.coordinates.TRZ", "6.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "6.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "6.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "6.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "6.31. Base classes \u2014 MDAnalysis.coordinates.base", "6.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "6.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "6.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "6.1. Trajectory Readers and Writers  \u2014 MDAnalysis.coordinates", "6.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "6.29. Null output \u2014 MDAnalysis.coordinates.null", "6.33. Serialization of Coordinate Readers", "6.30. 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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