diff --git a/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf index 10c9bc10..bcbabc09 100644 Binary files a/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf and b/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf differ diff --git a/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html b/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html index 59271cf1..9b6e52ba 100644 --- a/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html +++ b/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html @@ -266,7 +266,7 @@

Hydrogen bonds\(r_{DA}\)) must be less than a specified cutoff, typically 3 Å

  • the donor-hydrogen-acceptor angle (\(\theta_{DHA}\)) must be greater than a specified cutoff, typically 150°

    • -

    1c37bc925dd34d599e8c5cabee545af8

    +

    aad739c9004745b7a67e00909bc8e815

    Find water-water hydrogen bonds

    diff --git a/2.8.0-dev0/examples/constructing_universe.html b/2.8.0-dev0/examples/constructing_universe.html index bc7b55f1..aad4b968 100644 --- a/2.8.0-dev0/examples/constructing_universe.html +++ b/2.8.0-dev0/examples/constructing_universe.html @@ -715,7 +715,7 @@

    Adding a new segment

    NMP: residues 30-59 (blue)

  • LID: residues 122-159 (yellow)

    • -

    4f7b2b34b974484084c4c4e05b3d23be

    +

    fb480fdfc4f94e57ab15bd11c67a653e

    [26]:
    diff --git a/2.8.0-dev0/formats/auxiliary.html b/2.8.0-dev0/formats/auxiliary.html index c3c3b9d4..b15de9ed 100644 --- a/2.8.0-dev0/formats/auxiliary.html +++ b/2.8.0-dev0/formats/auxiliary.html @@ -261,7 +261,7 @@

    Reading data directlyIn [3]: aux = mda.auxiliary.core.auxreader(XVG_BZ2) In [4]: aux -Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f3006abf340> +Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7ffbb2284c70>

    In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.

    @@ -460,7 +460,7 @@

    Recreating auxiliariesIn [30]: del aux In [31]: mda.auxiliary.core.auxreader(**description) -Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f300cf8d210> +Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7ffbb1e508b0>

    The ‘description’ of any or all the auxiliaries added to a trajectory can be @@ -575,7 +575,7 @@

    Standalone Usage
    In [45]: import matplotlib.pyplot as plt
 
 In [46]: plt.plot(temp["Time"], temp["Temperature"])
-Out[46]: [<matplotlib.lines.Line2D at 0x7f3006abf310>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7ffbb2006650>]
 
 In [47]: plt.ylabel("Temperature [K]")
 Out[47]: Text(0, 0.5, 'Temperature [K]')
diff --git a/2.8.0-dev0/index.html b/2.8.0-dev0/index.html
index 98158853..114896f2 100644
--- a/2.8.0-dev0/index.html
+++ b/2.8.0-dev0/index.html
@@ -192,7 +192,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.8.0-dev0
    
-
    Last updated: Nov 05, 2024
    
+
    Last updated: Nov 08, 2024
    
 
    MDAnalysis (www.mdanalysis.org) is a Python
 toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write
 most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs.
diff --git a/2.8.0-dev0/reading_and_writing.html b/2.8.0-dev0/reading_and_writing.html
index 1c27a43e..58241710 100644
--- a/2.8.0-dev0/reading_and_writing.html
+++ b/2.8.0-dev0/reading_and_writing.html
@@ -320,13 +320,13 @@ 
    Building trajectories in memoryIn [16]: universe.atoms.positions
 Out[16]: 
-array([[0.35116178, 0.81360424, 0.00479816],
-       [0.86135435, 0.34042415, 0.5056929 ],
-       [0.47003326, 0.88686156, 0.90016526],
+array([[0.22084172, 0.69380623, 0.6204634 ],
+       [0.32873678, 0.3500816 , 0.8036403 ],
+       [0.8358787 , 0.2957448 , 0.07027348],
        ...,
-       [0.14932597, 0.07840037, 0.8601466 ],
-       [0.18089604, 0.6468601 , 0.36272588],
-       [0.77760845, 0.9033261 , 0.27372673]], dtype=float32)
+       [0.16618489, 0.35975078, 0.5305598 ],
+       [0.47995117, 0.5262336 , 0.41377455],
+       [0.38143802, 0.57584035, 0.6608682 ]], dtype=float32)

    or they can be directly passed in when creating a Universe.

    @@ -334,13 +334,13 @@

    Building trajectories in memoryIn [18]: universe2.atoms.positions Out[18]: -array([[0.35116178, 0.81360424, 0.00479816], - [0.86135435, 0.34042415, 0.5056929 ], - [0.47003326, 0.88686156, 0.90016526], +array([[0.22084172, 0.69380623, 0.6204634 ], + [0.32873678, 0.3500816 , 0.8036403 ], + [0.8358787 , 0.2957448 , 0.07027348], ..., - [0.14932597, 0.07840037, 0.8601466 ], - [0.18089604, 0.6468601 , 0.36272588], - [0.77760845, 0.9033261 , 0.27372673]], dtype=float32) + [0.16618489, 0.35975078, 0.5305598 ], + [0.47995117, 0.5262336 , 0.41377455], + [0.38143802, 0.57584035, 0.6608682 ]], dtype=float32) diff --git a/2.8.0-dev0/searchindex.js b/2.8.0-dev0/searchindex.js index 87e5d1d5..0126d8a7 100644 --- a/2.8.0-dev0/searchindex.js +++ b/2.8.0-dev0/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Define __init__": [[16, "1.-Define-__init__"]], "2. Define your analysis in _single_frame() and other methods": [[16, "2.-Define-your-analysis-in-_single_frame()-and-other-methods"]], "2D averaging": [[48, "2D-averaging"]], "AMBER specification": [[86, "amber-specification"]], "ATOM/HETATM fields": [[81, "id2"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Accessing the results": [[26, "Accessing-the-results"]], "Acknowledgments": [[50, "Acknowledgments"]], "Adding TopologyAttrs": [[109, "adding-topologyattrs"]], "Adding a Residue or Segment to a Universe": [[0, "adding-a-residue-or-segment-to-a-universe"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Adding bonds": [[50, "Adding-bonds"]], "Adding changes to the UserGuide": [[4, "adding-changes-to-the-userguide"]], "Adding custom TopologyAttrs": [[0, "adding-custom-topologyattrs"]], "Adding new documentation": [[4, "adding-new-documentation"]], "Adding positions": [[50, "Adding-positions"]], "Adding to a Universe": [[109, "adding-to-a-universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding your code to MDAnalysis": [[3, "adding-your-code-to-mdanalysis"]], "Adding your documentation to MDAnalysis": [[3, "adding-your-documentation-to-mdanalysis"]], "Additional datasets": [[100, "additional-datasets"]], "Advanced preview with gh-pages": [[4, "advanced-preview-with-gh-pages"]], "Advanced topology concepts": [[0, null]], "Aligning a structure to another": [[9, null]], "Aligning a structure with align.alignto": [[9, "Aligning-a-structure-with-align.alignto"]], "Aligning a trajectory to a reference": [[10, null]], "Aligning a trajectory to itself": [[11, null]], "Aligning a trajectory to the first frame": [[11, "Aligning-a-trajectory-to-the-first-frame"]], "Aligning a trajectory to the third frame": [[11, "Aligning-a-trajectory-to-the-third-frame"]], "Aligning a trajectory with AlignTraj": [[10, "Aligning-a-trajectory-with-AlignTraj"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Alignments and RMS fitting": [[7, "alignments-and-rms-fitting"], [8, null]], "All distances between two selections": [[23, null]], "All distances within a selection": [[24, null]], "Analysing pore dimensions with HOLE2": [[30, null]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Analysis": [[6, null], [7, null], [53, "Analysis"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Assertions": [[108, "assertions"]], "Atom selection language": [[1, "atom-selection-language"], [106, null]], "Atom-wise distances between matching AtomGroups": [[22, null]], "AtomGroup": [[1, null]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Automatically building documentation": [[4, "automatically-building-documentation"]], "Auxiliary files": [[57, null]], "Average radial distribution functions": [[36, null]], "Azure": [[108, "azure"]], "Background": [[12, "Background"], [13, "Background"], [14, "Background"], [15, "Background"], [18, "Background"], [19, "Background"], [20, "Background"], [21, "Background"], [30, "Background"]], "Base units in MDAnalysis": [[113, "id1"]], "Before transformation": [[55, "Before-transformation"]], "Block analysis function": [[15, "Block-analysis-function"]], "Bonds": [[87, "bonds"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Boolean": [[106, "boolean"]], "Branches in MDAnalysis": [[3, "branches-in-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id12"], [105, "id13"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "Building MDAnalysis": [[3, "building-mdanalysis"]], "Building the documentation": [[3, "building-the-documentation"]], "Building the user guide": [[4, "building-the-user-guide"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "CONFIG (DL_Poly Config)": [[63, null]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, null]], "CRD (CHARMM CARD files)": [[65, null]], "CRYST1 fields": [[81, "id1"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Calculating hydrogen bond lifetimes": [[27, null]], "Calculating hydrogen bonds: advanced selections": [[28, null]], "Calculating hydrogen bonds: the basics": [[26, null]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, null]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, null]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, null]], "Calculating the RDF atom-to-atom": [[40, null]], "Calculating the average radial distribution function for a group of atoms to itself": [[36, "Calculating-the-average-radial-distribution-function-for-a-group-of-atoms-to-itself"]], "Calculating the average radial distribution function for two groups of atoms": [[36, "Calculating-the-average-radial-distribution-function-for-two-groups-of-atoms"]], "Calculating the distance between CA atoms": [[22, "Calculating-the-distance-between-CA-atoms"]], "Calculating the distance with periodic boundary conditions": [[22, "Calculating-the-distance-with-periodic-boundary-conditions"]], "Calculating the pairwise RMSD of a trajectory": [[12, null]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Calculating the root mean square deviation of atomic structures": [[13, null]], "Calculating the root mean square fluctuation over a trajectory": [[14, null]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "Calculating the solvent density around a protein": [[48, null]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Canonical attributes": [[109, "canonical-attributes"]], "Centering a trajectory in the box": [[55, null]], "Centering in the box": [[55, "Centering-in-the-box"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Changes:": [[105, "changes"], [105, "id5"], [105, "id10"], [105, "id17"], [105, "id23"], [105, "id28"], [105, "id33"], [105, "id39"]], "Charge": [[113, "charge"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Cirrus CI": [[108, "cirrus-ci"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Code formatting in Python": [[3, "code-formatting-in-python"]], "Codecov": [[108, "codecov"]], "Combine the results": [[15, "Combine-the-results"]], "Committing your code": [[3, "committing-your-code"]], "Communications": [[99, "communications"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Comparing different dimensionality reduction methods": [[43, "Comparing-different-dimensionality-reduction-methods"]], "Comparing the geometric similarity of trajectories": [[46, null]], "Completing the release": [[102, "completing-the-release"]], "Computing mass and charge density on each axis": [[49, null]], "Connectivity information": [[109, "connectivity-information"]], "Constants": [[113, "constants"]], "Constructing from AtomGroups": [[114, "constructing-from-atomgroups"]], "Constructing from Atoms": [[1, "constructing-from-atoms"]], "Constructing from scratch": [[114, "constructing-from-scratch"]], "Constructing, modifying, and adding to a Universe": [[50, null]], "Contact analysis: number of contacts within a cutoff": [[21, null]], "Continuous Integration tools": [[108, "continuous-integration-tools"]], "Contributing to MDAnalysis": [[2, null], [16, "Contributing-to-MDAnalysis"]], "Contributing to the main codebase": [[3, null]], "Contributing to the user guide": [[4, null]], "Coordinates": [[58, null], [61, "coordinates"]], "Copying coordinates into a new Universe": [[10, "Copying-coordinates-into-a-new-Universe"]], "Create a blog post outlining the release": [[102, "create-a-blog-post-outlining-the-release"]], "Create a release of the UserGuide": [[102, "create-a-release-of-the-userguide"]], "Creating a Universe": [[114, "creating-a-universe"]], "Creating a blank Universe": [[50, "Creating-a-blank-Universe"]], "Creating a branch": [[3, "creating-a-branch"]], "Creating a development environment": [[3, "creating-a-development-environment"], [4, "creating-a-development-environment"]], "Creating a pull request": [[3, "creating-a-pull-request"]], "Creating an AtomGroup": [[1, "creating-an-atomgroup"]], "Creating an analysis from a function": [[16, "Creating-an-analysis-from-a-function"]], "Creating an average structure": [[14, "Creating-an-average-structure"]], "Creating and populating a Universe with water": [[50, "Creating-and-populating-a-Universe-with-water"]], "Creating with an AtomGroup": [[109, "creating-with-an-atomgroup"]], "Creating your own class": [[16, "Creating-your-own-class"]], "Custom compiler flags and optimised installations": [[100, "custom-compiler-flags-and-optimised-installations"]], "Custom transformations": [[112, "custom-transformations"]], "Custom weights": [[13, "Custom-weights"]], "DATA (LAMMPS)": [[66, null]], "DCD (CHARMM, NAMD, or LAMMPS trajectory)": [[67, null]], "DCD (Flexible LAMMPS trajectory)": [[68, null]], "DMS (Desmond Molecular Structure files)": [[69, null]], "Default values and attribute levels": [[109, "default-values-and-attribute-levels"]], "Define your own function": [[18, "Define-your-own-function"]], "Defining salt bridges": [[18, "Defining-salt-bridges"]], "Defining the groups for contact analysis": [[19, "Defining-the-groups-for-contact-analysis"], [21, "Defining-the-groups-for-contact-analysis"]], "Deleting HOLE files": [[30, "Deleting-HOLE-files"]], "Deleting from a Universe": [[109, "deleting-from-a-universe"]], "Density": [[113, "density"]], "Deprecations:": [[105, "deprecations"], [105, "id6"], [105, "id18"], [105, "id24"], [105, "id29"], [105, "id34"], [105, "id40"]], "Determining the persistence length of a polymer": [[31, null]], "Developer notes": [[86, "developer-notes"], [87, "developer-notes"], [89, "developer-notes"], [91, "developer-notes"]], "Developing in Cython": [[3, "developing-in-cython"]], "Development versions": [[100, "development-versions"]], "Diffusion maps": [[33, "Diffusion-maps"]], "Dimension reduction": [[7, "dimension-reduction"], [32, null]], "Discrete Fr\u00e9chet distances": [[46, "Discrete-Fr\u00e9chet-distances"]], "Distances and contacts": [[7, "distances-and-contacts"], [17, null]], "Documenting changes": [[3, "documenting-changes"]], "Documenting your code": [[3, "documenting-your-code"]], "Doing all this on-the-fly": [[55, "Doing-all-this-on-the-fly"]], "Dynamic selection": [[53, "Dynamic-selection"]], "Dynamic selections": [[106, "dynamic-selections"]], "Dynamically updating AtomGroups": [[1, "dynamically-updating-atomgroups"]], "EDR Files": [[57, "edr-files"]], "Elastic network analysis": [[38, null]], "Empty AtomGroups": [[1, "empty-atomgroups"]], "Enchancements:": [[105, "enchancements"], [105, "id16"]], "Energy": [[113, "energy"]], "Enhancements:": [[105, "enhancements"], [105, "id4"], [105, "id22"], [105, "id26"], [105, "id31"], [105, "id37"]], "Ensure PEP8 compliance (mandatory) and format your code with Darker (optional)": [[3, "ensure-pep8-compliance-mandatory-and-format-your-code-with-darker-optional"]], "Estimating the error in a clustering ensemble similarity analysis": [[42, "Estimating-the-error-in-a-clustering-ensemble-similarity-analysis"]], "Estimating the error in a dimension reduction ensemble similarity analysis": [[44, "Estimating-the-error-in-a-dimension-reduction-ensemble-similarity-analysis"]], "Evaluating convergence": [[43, null]], "Evaluating convergence with similarity measures": [[43, "Evaluating-convergence-with-similarity-measures"]], "Example data": [[5, null]], "Example workflows": [[112, "example-workflows"]], "Examples": [[6, null]], "Failing tests": [[108, "failing-tests"]], "Find all hydrogen bonds": [[27, "Find-all-hydrogen-bonds"], [28, "Find-all-hydrogen-bonds"]], "Find water-water hydrogen bonds": [[26, "Find-water-water-hydrogen-bonds"]], "Fixes:": [[105, "fixes"], [105, "id3"], [105, "id9"], [105, "id15"], [105, "id21"], [105, "id27"], [105, "id32"], [105, "id38"]], "Fixtures": [[108, "fixtures"]], "Force": [[113, "force"]], "Forking": [[3, "forking"]], "Forking and cloning the User Guide": [[4, "forking-and-cloning-the-user-guide"]], "Format overview": [[61, null]], "Format reference": [[59, null]], "Format-specific attributes": [[109, "format-specific-attributes"]], "Fraction of native contacts over a trajectory": [[19, null]], "Fragments": [[98, "fragments"]], "Frame-wise form of the function": [[15, "Frame-wise-form-of-the-function"]], "Frames and trajectories": [[103, "frames-and-trajectories"]], "Frequently asked questions": [[56, null]], "Further analysis": [[26, "Further-analysis"]], "GMS (Gamess trajectory)": [[70, null]], "GRO (GROMACS structure file)": [[71, null]], "GROMACS entries used to create angles.": [[87, "id3"]], "GROMACS entries used to create bonds.": [[87, "id2"]], "GROMACS entries used to create dihedrals.": [[87, "id4"]], "GROMACS entries used to create improper dihedrals.": [[87, "id5"]], "GSD (HOOMD GSD file)": [[72, null]], "General": [[6, null]], "General conventions": [[108, "general-conventions"]], "General rules for importing": [[101, "general-rules-for-importing"]], "Generating paths": [[46, "Generating-paths"]], "Geometric": [[106, "geometric"]], "Getting atom information from AtomGroups": [[53, "Getting-atom-information-from-AtomGroups"]], "Getting started with Git": [[2, "getting-started-with-git"]], "Getting the develop branch ready for a release": [[102, "getting-the-develop-branch-ready-for-a-release"]], "GitHub Actions": [[108, "github-actions"]], "Group operators and set methods": [[1, "group-operators-and-set-methods"]], "Groupby and split": [[1, "groupby-and-split"]], "Groups of atoms": [[98, null]], "Guessing": [[60, null]], "Guessing topology attributes": [[114, "guessing-topology-attributes"]], "Guidelines for writing docstrings": [[3, "guidelines-for-writing-docstrings"]], "HISTORY (DL_Poly Config)": [[63, "history-dl-poly-config"]], "Hard cutoff with a single reference": [[19, "Hard-cutoff-with-a-single-reference"]], "Hausdorff method": [[46, "Hausdorff-method"]], "Helix analysis": [[39, null], [39, "id6"]], "Helper functions": [[26, "Helper-functions"]], "Hydrogen Bond Analysis": [[7, "hydrogen-bond-analysis"], [25, null]], "Hydrogen bond lifetime of individual hydrogen bonds": [[27, "Hydrogen-bond-lifetime-of-individual-hydrogen-bonds"]], "Hydrogen bonds": [[26, "Hydrogen-bonds"]], "Hydrogen bonds between specific 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46, 48, 49, 50, 52, 53, 55, 59, 104], "releas": [102, 105], "request": 3, "residu": [0, 23, 24, 98, 107], "restart": [64, 74], "restrt": 74, "restructuredtext": 4, "result": [15, 26], "rm": [7, 8], "rmsd": [12, 13, 53], "rmsf": 14, "root": [13, 14], "rule": 101, "run": [39, 87, 108], "salt": 18, "same": 108, "sanit": 4, "scikit": 48, "scratch": 114, "see": 15, "segid": 87, "segment": [0, 50, 98], "select": [1, 13, 23, 24, 28, 37, 52, 53, 57, 96, 103, 106, 107], "sequenc": 98, "serial": 15, "set": [1, 13, 42, 44], "similar": [7, 41, 42, 43, 44, 45, 46, 106], "simpl": [15, 106], "simul": 52, "singl": [19, 53, 96], "site": 40, "skip": 108, "slice": [1, 110], "soft": 19, "solvent": [48, 55], "space": 34, "specif": [28, 40, 78, 81, 82, 83, 84, 86, 87, 95, 109], "speed": 113, "split": [1, 15], "squar": [13, 14], "standalon": 57, "standard": [81, 107], "start": [2, 53], "static": 48, "step": 4, "store": 26, "structur": [7, 9, 13, 14, 35, 53, 69, 71, 78, 80, 82, 84], "sugar": 107, "suit": [101, 108], "summari": 102, "support": [57, 58, 61, 87, 96, 97], "surfac": [30, 48], "system": [52, 109], "tabl": [58, 61, 97], "task": 102, "temporari": [102, 108], "test": [3, 4, 100, 101, 105, 108], "thi": 55, "third": 11, "tile": 50, "time": [27, 113], "tinker": 91, "tip": 4, "tng": 85, "tool": 108, "top": 86, "topologi": [0, 50, 61, 75, 86, 87, 97, 109, 114], "topologyattr": [0, 109], "tpr": 87, "tprparser": 87, "trajectori": [7, 10, 11, 12, 13, 14, 15, 16, 19, 30, 34, 41, 46, 53, 55, 56, 57, 62, 67, 68, 70, 79, 85, 88, 89, 90, 94, 95, 103, 110, 111], "transfer": 103, "transform": [16, 48, 54, 55, 112], "transmiss": 77, "triangul": 48, "tripo": 78, "trj": 88, "trr": 89, "try": [42, 44], "trz": 90, "two": [12, 13, 23, 36], "txyz": 91, "type": 60, "typic": 102, "uniqu": 1, "unit": [57, 113], "univers": [0, 10, 13, 50, 57, 109, 114], "unwrap": 55, "up": 102, "updat": [1, 102], "upload": 102, "us": [4, 28, 30, 38, 43, 52, 57, 87, 98, 104, 108], "usag": 57, "user": [4, 99], "userguid": [4, 102], "v": 20, "valu": 109, "version": [2, 87, 100, 102], "view": 3, "virtualenv": 3, "visual": [101, 108], "visualis": [14, 30, 34, 48], "vmd": 30, "volumetr": [7, 47], "warn": 108, "water": [26, 48, 50], "weight": 13, "welcom": 99, "what": 4, "wheel": 102, "where": [2, 3], "whole": 48, "why": [56, 99], "wise": [15, 22, 24], "within": [21, 24], "without": 40, "work": [3, 30, 53], "workflow": [102, 112], "wrap": 55, "write": [3, 10, 16, 18, 53, 65, 66, 67, 71, 79, 81, 82, 83, 89, 96, 103, 108], "xml": 92, "xpdb": 93, "xplor": 84, "xtc": 94, "xvg": 57, "xyz": 95, "yasp": 90, "your": [3, 16, 18]}}) \ No newline at end of file diff --git a/2.8.0-dev0/standard_selections.html b/2.8.0-dev0/standard_selections.html index 3636adee..497b485c 100644 --- a/2.8.0-dev0/standard_selections.html +++ b/2.8.0-dev0/standard_selections.html @@ -332,10 +332,10 @@

    Protein backbone -

    C

    -

    N

    -

    CA

    +

    CA

    O

    +

    C

    +

    N

    @@ -347,44 +347,44 @@

    Protein backbone -

    THY

    -

    RG

    +

    RC5

    +

    A

    +

    DC3

    +

    THY

    +

    DA5

    +

    DT3

    +

    RU5

    +

    ADE

    + +

    DG3

    RU3

    -

    DA3

    G

    -

    RC5

    -

    DT3

    +

    DC

    +

    RA5

    RC

    +

    DA3

    +

    U

    -

    RU

    -

    RA

    +

    DA

    DC5

    -

    URA

    -

    RG3

    -

    RG5

    -

    RA5

    -

    DG5

    - -

    T

    +

    RC3

    +

    RA

    C

    -

    A

    -

    RA3

    -

    DC3

    -

    RU5

    -

    DT5

    -

    DT

    +

    RG

    +

    URA

    +

    DG

    -

    GUA

    -

    U

    -

    RC3

    +

    RA3

    CYT

    -

    DA

    -

    DG3

    -

    DC

    -

    ADE

    +

    DG5

    +

    DT

    +

    GUA

    +

    RU

    +

    RG3

    +

    DT5

    -

    DG

    -

    DA5

    +

    RG5

    +

    T

    @@ -399,11 +399,11 @@

    Nucleic backbone -

    O3’

    +

    O5’

    +

    P

    +

    O3’

    C3’

    C5’

    -

    P

    -

    O5’

    @@ -413,22 +413,22 @@

    Nucleic backbone -

    O2

    -

    N4

    -

    C2

    -

    N9

    -

    N2

    -

    O4

    -

    O6

    +

    C5

    +

    C4

    +

    O2

    N1

    - -

    N3

    -

    N7

    -

    C5

    +

    C2

    C6

    -

    C4

    N6

    +

    N7

    + +

    N3

    C8

    +

    N2

    +

    N9

    +

    O6

    +

    N4

    +

    O4

    C5M

    @@ -439,11 +439,11 @@

    Nucleic sugars -

    C3’

    +

    C1’

    +

    O4’

    C2’

    +

    C3’

    C4’

    -

    C1’

    -

    O4’

    diff --git a/2.8.0-dev0/testing.html b/2.8.0-dev0/testing.html index 04043c75..ecf34d3a 100644 --- a/2.8.0-dev0/testing.html +++ b/2.8.0-dev0/testing.html @@ -433,13 +433,13 @@

    Testing exceptions and warnings

    Failing tests

    -

    To mark an expected failure, use pytest.mark.xfail() decorator:

    +

    To mark an expected failure, use pytest.mark.xfail() decorator:

    @pytest.mark.xfail
 def tested_expected_failure():
     assert 1 == 2
    -

    To manually fail a test, make a call to pytest.fail():

    +

    To manually fail a test, make a call to pytest.fail():

    def test_open(self, tmpdir):
     outfile = str(tmpdir.join('lammps-writer-test.dcd'))
     try:
@@ -452,7 +452,7 @@ 
    Failing tests
 
    Skipping tests
    
-
    To skip tests based on a condition, use pytest.mark.skipif(condition) decorator:
    
+
    To skip tests based on a condition, use pytest.mark.skipif(condition) decorator:
    
 
    import numpy as np
 try:
     from numpy import shares_memory
@@ -467,7 +467,7 @@ 
    Skipping testsassert not np.shares_memory(original.ts.positions, copy.ts.positions)
 
    
 
    
-
    To skip a test if a module is not available for importing, use pytest.importorskip('module_name')
    
+
    To skip a test if a module is not available for importing, use pytest.importorskip('module_name')
    
 
    def test_write_trajectory_netCDF4(self, universe, outfile):
     pytest.importorskip("netCDF4")
     return self._test_write_trajectory(universe, outfile)
@@ -477,7 +477,7 @@ 
    Skipping tests
 
    Fixtures
    
-
    Use fixtures as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the pytest.fixture() decorator, over a function that returns the object you need:
    
+
    Use fixtures as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the pytest.fixture() decorator, over a function that returns the object you need:
    
 
    @pytest.fixture
 def universe(self):
     return mda.Universe(self.ref_filename)
diff --git a/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf
index 10c9bc10..bcbabc09 100644
Binary files a/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf and b/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf differ
diff --git a/dev/examples/analysis/hydrogen_bonds/hbonds.html b/dev/examples/analysis/hydrogen_bonds/hbonds.html
index 59271cf1..9b6e52ba 100644
--- a/dev/examples/analysis/hydrogen_bonds/hbonds.html
+++ b/dev/examples/analysis/hydrogen_bonds/hbonds.html
@@ -266,7 +266,7 @@ 
    Hydrogen bonds\(r_{DA}\)) must be less than a specified cutoff, typically 3 Å
    
 
  • the donor-hydrogen-acceptor angle (\(\theta_{DHA}\)) must be greater than a specified cutoff, typically 150°
    • 
 
-
    
 
    
 
    In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.
    
@@ -460,7 +460,7 @@ 
    Recreating auxiliariesIn [30]: del aux
 
 In [31]: mda.auxiliary.core.auxreader(**description)
-Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f300cf8d210>
+Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7ffbb1e508b0>
 
    
 
    
 
    The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -575,7 +575,7 @@ 
    Standalone Usage
    In [45]: import matplotlib.pyplot as plt
 
 In [46]: plt.plot(temp["Time"], temp["Temperature"])
-Out[46]: [<matplotlib.lines.Line2D at 0x7f3006abf310>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7ffbb2006650>]
 
 In [47]: plt.ylabel("Temperature [K]")
 Out[47]: Text(0, 0.5, 'Temperature [K]')
diff --git a/dev/index.html b/dev/index.html
index 98158853..114896f2 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -192,7 +192,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.8.0-dev0
    
-
    Last updated: Nov 05, 2024
    
+
    Last updated: Nov 08, 2024
    
 
    MDAnalysis (www.mdanalysis.org) is a Python
 toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write
 most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs.
diff --git a/dev/reading_and_writing.html b/dev/reading_and_writing.html
index 1c27a43e..58241710 100644
--- a/dev/reading_and_writing.html
+++ b/dev/reading_and_writing.html
@@ -320,13 +320,13 @@ 
    Building trajectories in memoryIn [16]: universe.atoms.positions
 Out[16]: 
-array([[0.35116178, 0.81360424, 0.00479816],
-       [0.86135435, 0.34042415, 0.5056929 ],
-       [0.47003326, 0.88686156, 0.90016526],
+array([[0.22084172, 0.69380623, 0.6204634 ],
+       [0.32873678, 0.3500816 , 0.8036403 ],
+       [0.8358787 , 0.2957448 , 0.07027348],
        ...,
-       [0.14932597, 0.07840037, 0.8601466 ],
-       [0.18089604, 0.6468601 , 0.36272588],
-       [0.77760845, 0.9033261 , 0.27372673]], dtype=float32)
+       [0.16618489, 0.35975078, 0.5305598 ],
+       [0.47995117, 0.5262336 , 0.41377455],
+       [0.38143802, 0.57584035, 0.6608682 ]], dtype=float32)

    or they can be directly passed in when creating a Universe.

    @@ -334,13 +334,13 @@

    Building trajectories in memoryIn [18]: universe2.atoms.positions Out[18]: -array([[0.35116178, 0.81360424, 0.00479816], - [0.86135435, 0.34042415, 0.5056929 ], - [0.47003326, 0.88686156, 0.90016526], +array([[0.22084172, 0.69380623, 0.6204634 ], + [0.32873678, 0.3500816 , 0.8036403 ], + [0.8358787 , 0.2957448 , 0.07027348], ..., - [0.14932597, 0.07840037, 0.8601466 ], - [0.18089604, 0.6468601 , 0.36272588], - [0.77760845, 0.9033261 , 0.27372673]], dtype=float32) + [0.16618489, 0.35975078, 0.5305598 ], + [0.47995117, 0.5262336 , 0.41377455], + [0.38143802, 0.57584035, 0.6608682 ]], dtype=float32)

    diff --git a/dev/searchindex.js b/dev/searchindex.js index 87e5d1d5..0126d8a7 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Define __init__": [[16, "1.-Define-__init__"]], "2. Define your analysis in _single_frame() and other methods": [[16, "2.-Define-your-analysis-in-_single_frame()-and-other-methods"]], "2D averaging": [[48, "2D-averaging"]], "AMBER specification": [[86, "amber-specification"]], "ATOM/HETATM fields": [[81, "id2"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Accessing the results": [[26, "Accessing-the-results"]], "Acknowledgments": [[50, "Acknowledgments"]], "Adding TopologyAttrs": [[109, "adding-topologyattrs"]], "Adding a Residue or Segment to a Universe": [[0, "adding-a-residue-or-segment-to-a-universe"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Adding bonds": [[50, "Adding-bonds"]], "Adding changes to the UserGuide": [[4, "adding-changes-to-the-userguide"]], "Adding custom TopologyAttrs": [[0, "adding-custom-topologyattrs"]], "Adding new documentation": [[4, "adding-new-documentation"]], "Adding positions": [[50, "Adding-positions"]], "Adding to a Universe": [[109, "adding-to-a-universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding your code to MDAnalysis": [[3, "adding-your-code-to-mdanalysis"]], "Adding your documentation to MDAnalysis": [[3, "adding-your-documentation-to-mdanalysis"]], "Additional datasets": [[100, "additional-datasets"]], "Advanced preview with gh-pages": [[4, "advanced-preview-with-gh-pages"]], "Advanced topology concepts": [[0, null]], "Aligning a structure to another": [[9, null]], "Aligning a structure with align.alignto": [[9, "Aligning-a-structure-with-align.alignto"]], "Aligning a trajectory to a reference": [[10, null]], "Aligning a trajectory to itself": [[11, null]], "Aligning a trajectory to the first frame": [[11, "Aligning-a-trajectory-to-the-first-frame"]], "Aligning a trajectory to the third frame": [[11, "Aligning-a-trajectory-to-the-third-frame"]], "Aligning a trajectory with AlignTraj": [[10, "Aligning-a-trajectory-with-AlignTraj"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Alignments and RMS fitting": [[7, "alignments-and-rms-fitting"], [8, null]], "All distances between two selections": [[23, null]], "All distances within a selection": [[24, null]], "Analysing pore dimensions with HOLE2": [[30, null]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Analysis": [[6, null], [7, null], [53, "Analysis"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Assertions": [[108, "assertions"]], "Atom selection language": [[1, "atom-selection-language"], [106, null]], "Atom-wise distances between matching AtomGroups": [[22, null]], "AtomGroup": [[1, null]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Automatically building documentation": [[4, "automatically-building-documentation"]], "Auxiliary files": [[57, null]], "Average radial distribution functions": [[36, null]], "Azure": [[108, "azure"]], "Background": [[12, "Background"], [13, "Background"], [14, "Background"], [15, "Background"], [18, "Background"], [19, "Background"], [20, "Background"], [21, "Background"], [30, "Background"]], "Base units in MDAnalysis": [[113, "id1"]], "Before transformation": [[55, "Before-transformation"]], "Block analysis function": [[15, "Block-analysis-function"]], "Bonds": [[87, "bonds"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Boolean": [[106, "boolean"]], "Branches in MDAnalysis": [[3, "branches-in-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id12"], [105, "id13"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "Building MDAnalysis": [[3, "building-mdanalysis"]], "Building the documentation": [[3, "building-the-documentation"]], "Building the user guide": [[4, "building-the-user-guide"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "CONFIG (DL_Poly Config)": [[63, null]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, null]], "CRD (CHARMM CARD files)": [[65, null]], "CRYST1 fields": [[81, "id1"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Calculating hydrogen bond lifetimes": [[27, null]], "Calculating hydrogen bonds: advanced selections": [[28, null]], "Calculating hydrogen bonds: the basics": [[26, null]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, null]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, null]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, null]], "Calculating the RDF atom-to-atom": [[40, null]], "Calculating the average radial distribution function for a group of atoms to itself": [[36, "Calculating-the-average-radial-distribution-function-for-a-group-of-atoms-to-itself"]], "Calculating the average radial distribution function for two groups of atoms": [[36, "Calculating-the-average-radial-distribution-function-for-two-groups-of-atoms"]], "Calculating the distance between CA atoms": [[22, "Calculating-the-distance-between-CA-atoms"]], "Calculating the distance with periodic boundary conditions": [[22, "Calculating-the-distance-with-periodic-boundary-conditions"]], "Calculating the pairwise RMSD of a trajectory": [[12, null]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Calculating the root mean square deviation of atomic structures": [[13, null]], "Calculating the root mean square fluctuation over a trajectory": [[14, null]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "Calculating the solvent density around a protein": [[48, null]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Canonical attributes": [[109, "canonical-attributes"]], "Centering a trajectory in the box": [[55, null]], "Centering in the box": [[55, "Centering-in-the-box"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Changes:": [[105, "changes"], [105, "id5"], [105, "id10"], [105, "id17"], [105, "id23"], [105, "id28"], [105, "id33"], [105, "id39"]], "Charge": [[113, "charge"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Cirrus CI": [[108, "cirrus-ci"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Code formatting in Python": [[3, "code-formatting-in-python"]], "Codecov": [[108, "codecov"]], "Combine the results": [[15, "Combine-the-results"]], "Committing your code": [[3, "committing-your-code"]], "Communications": [[99, "communications"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Comparing different dimensionality 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exporters", "Topology", "Groups of atoms", "Welcome to MDAnalysis User Guide\u2019s documentation!", "Installation", "Module imports in MDAnalysis", "Preparing a release", "Reading and writing files", "References", "MDAnalysis Release Notes", "Atom selection language", "Standard residues in MDAnalysis selections", "Tests in MDAnalysis", "The topology system", "Slicing trajectories", "Trajectories", "On-the-fly transformations", "Units and constants", "Universe"], "titleterms": {"": 99, "0": 105, "1": [16, 105], "2": [16, 105], "2d": 48, "3": 105, "3d": 48, "4": 105, "5": 105, "6": 105, "7": 105, "IN": 73, "In": 103, "On": [3, 4, 112], "The": [40, 109], "With": 3, "__init__": 16, "_single_fram": 16, "abstract": 3, "access": [26, 57], "acid": 107, "acknowledg": 50, "action": 108, "ad": [0, 3, 4, 50, 109], "addit": 100, "advanc": [0, 4, 28], "aim": 73, "align": [7, 8, 9, 10, 11, 14, 46, 48], "alignto": 9, "aligntraj": 10, "all": [23, 24, 27, 28, 55, 61], "also": 15, "amber": [74, 79, 86, 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102, 103], "ca": 22, "calcul": [12, 13, 14, 20, 21, 22, 23, 24, 26, 27, 28, 31, 36, 37, 40, 42, 44, 45, 48], "canon": 109, "card": 65, "case": 98, "center": [48, 55], "chain": 31, "chainid": 87, "chang": [3, 4, 56, 105], "charg": [49, 113], "charmm": [65, 67, 84], "chemfil": 62, "choos": 31, "ci": [102, 108], "cirru": [102, 108], "citat": [53, 104], "class": [3, 16], "clean": 102, "clone": 4, "close": 38, "cluster": [42, 43], "code": [3, 101], "codebas": 3, "codecov": 108, "combin": 15, "commit": [3, 4], "commun": 99, "compar": [43, 46], "compil": 100, "complet": 102, "complianc": 3, "compon": 34, "compress": 94, "comput": 49, "concept": 0, "conda": [3, 100, 102], "condit": 22, "config": 63, "connect": [106, 109], "constant": [27, 113], "construct": [1, 50, 114], "contact": [7, 17, 18, 19, 20, 21, 38], "content": 34, "continu": 108, "contribut": [2, 3, 4, 16], "contributor": 105, "control": 2, "convent": 108, "converg": [34, 43], "convers": 113, "coor": 64, "coordin": [10, 13, 23, 53, 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109, 114], "fr\u00e9chet": 46, "function": [15, 16, 18, 26, 36, 40, 108], "further": 26, "gamess": 70, "gaussian": 38, "gener": [6, 46, 85, 87, 101, 108], "geometr": [46, 106], "get": [2, 53, 102], "gh": 4, "git": 2, "github": [2, 3, 108], "gm": 70, "gro": 71, "gromac": [71, 75, 87, 89, 94], "group": [1, 19, 21, 28, 36, 37, 53, 98], "groupbi": 1, "gsd": 72, "guess": [60, 114], "guess_acceptor": 28, "guess_hydrogen": 28, "guid": [4, 53, 99], "guidelin": 3, "gyrat": [15, 16], "handl": 57, "hard": 19, "harmon": 45, "hausdorff": 46, "heatmap": 23, "helix": 39, "helper": 26, "hetatm": 81, "histori": 63, "hole": 30, "hole2": [4, 30], "hook": 4, "hoomd": [72, 92], "hydrogen": [7, 25, 26, 27, 28], "ibisco": 90, "imag": 48, "import": [7, 101, 108], "improp": [60, 87], "improv": 105, "increment": 102, "index": [1, 106], "individu": 27, "inform": [53, 58, 61, 109], "inpcrd": 74, "input": [73, 103, 108], "instal": 100, "integr": 108, "interact": [3, 48], "intermitt": 27, "issu": 105, "iter": 57, "itp": 75, "itself": [11, 12, 36], "janin": 37, "jupyt": 4, "keyword": [86, 106], "known": 105, "lammp": [66, 67, 68, 76], "lammpsdump": 76, "languag": [1, 106], "larger": 50, "length": [31, 113], "level": 109, "lifetim": 27, "linear": 33, "list": [98, 101], "load": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 57, 114], "lossless": 89, "mac": 3, "macromolecular": 77, "main": 3, "major": 105, "make": 48, "mamba": 3, "mandatori": 3, "manual": 102, "map": 33, "mass": [13, 49, 60], "match": [22, 23], "matplotlib": 48, "mdanalysi": [2, 3, 16, 52, 61, 87, 99, 101, 105, 107, 108, 113], "mdanalysisdata": 5, "mdanalysistest": 5, "mdcrd": 88, "mean": [13, 14], "measur": [34, 43], "membran": [7, 29], "memori": [57, 103], "merg": 50, "method": [1, 16, 18, 42, 43, 44, 46, 53, 109, 114], "mmtf": 77, "model": 38, "modifi": [50, 106, 109], "modul": [3, 101, 108], "mol2": 78, "molecul": [0, 48], "molecular": 69, "more": 28, "multipl": [13, 15, 19, 42, 44, 96, 103], "multiprocess": 15, "nambdin": 64, "namd": [64, 67, 84], "nativ": [18, 19], "nbval": 4, "nc": 79, "ncdf": 79, "netcdf": 79, "network": 38, "new": [3, 4, 10, 50, 105, 108], "next": [85, 102], "nglview": 48, "non": [23, 33], "note": [86, 87, 89, 91, 95, 105], "notebook": 4, "nucleic": 107, "nucleobas": 107, "number": [21, 102], "object": 109, "old": 102, "one": [42, 44], "onli": 38, "openmm": 52, "oper": 1, "optimis": 100, "option": [3, 4, 101], "order": [1, 30, 106], "other": [15, 16, 51], "out": [42, 44, 53, 65, 66, 67, 71, 79, 81, 82, 83, 89], "outlin": 102, "output": 103, "over": [14, 19, 56, 57], "overview": [4, 53, 61], "own": [16, 18], "packag": [3, 102], "page": 4, "pairwis": 12, "parallel": [15, 108], "paramet": [30, 42, 44], "parm": [52, 80], "parm7": 86, "pars": [86, 87], "parser": [61, 97], "particip": 99, "pass": 57, "path": 46, "pdb": [30, 81, 82, 93], "pdb2pqr": 83, "pdbqt": 82, "pep8": 3, "per": 15, 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[4, 102], "v": 20, "valu": 109, "version": [2, 87, 100, 102], "view": 3, "virtualenv": 3, "visual": [101, 108], "visualis": [14, 30, 34, 48], "vmd": 30, "volumetr": [7, 47], "warn": 108, "water": [26, 48, 50], "weight": 13, "welcom": 99, "what": 4, "wheel": 102, "where": [2, 3], "whole": 48, "why": [56, 99], "wise": [15, 22, 24], "within": [21, 24], "without": 40, "work": [3, 30, 53], "workflow": [102, 112], "wrap": 55, "write": [3, 10, 16, 18, 53, 65, 66, 67, 71, 79, 81, 82, 83, 89, 96, 103, 108], "xml": 92, "xpdb": 93, "xplor": 84, "xtc": 94, "xvg": 57, "xyz": 95, "yasp": 90, "your": [3, 16, 18]}}) \ No newline at end of file diff --git a/dev/standard_selections.html b/dev/standard_selections.html index 3636adee..497b485c 100644 --- a/dev/standard_selections.html +++ b/dev/standard_selections.html @@ -332,10 +332,10 @@

    Protein backbone -

    C

    -

    N

    -

    CA

    +

    CA

    O

    +

    C

    +

    N

    @@ -347,44 +347,44 @@

    Protein backbone -

    THY

    -

    RG

    +

    RC5

    +

    A

    +

    DC3

    +

    THY

    +

    DA5

    +

    DT3

    +

    RU5

    +

    ADE

    + +

    DG3

    RU3

    -

    DA3

    G

    -

    RC5

    -

    DT3

    +

    DC

    +

    RA5

    RC

    +

    DA3

    +

    U

    -

    RU

    -

    RA

    +

    DA

    DC5

    -

    URA

    -

    RG3

    -

    RG5

    -

    RA5

    -

    DG5

    - -

    T

    +

    RC3

    +

    RA

    C

    -

    A

    -

    RA3

    -

    DC3

    -

    RU5

    -

    DT5

    -

    DT

    +

    RG

    +

    URA

    +

    DG

    -

    GUA

    -

    U

    -

    RC3

    +

    RA3

    CYT

    -

    DA

    -

    DG3

    -

    DC

    -

    ADE

    +

    DG5

    +

    DT

    +

    GUA

    +

    RU

    +

    RG3

    +

    DT5

    -

    DG

    -

    DA5

    +

    RG5

    +

    T

    @@ -399,11 +399,11 @@

    Nucleic backbone -

    O3’

    +

    O5’

    +

    P

    +

    O3’

    C3’

    C5’

    -

    P

    -

    O5’

    @@ -413,22 +413,22 @@

    Nucleic backbone -

    O2

    -

    N4

    -

    C2

    -

    N9

    -

    N2

    -

    O4

    -

    O6

    +

    C5

    +

    C4

    +

    O2

    N1

    - -

    N3

    -

    N7

    -

    C5

    +

    C2

    C6

    -

    C4

    N6

    +

    N7

    + +

    N3

    C8

    +

    N2

    +

    N9

    +

    O6

    +

    N4

    +

    O4

    C5M

    @@ -439,11 +439,11 @@

    Nucleic sugars -

    C3’

    +

    C1’

    +

    O4’

    C2’

    +

    C3’

    C4’

    -

    C1’

    -

    O4’

    diff --git a/dev/testing.html b/dev/testing.html index 04043c75..ecf34d3a 100644 --- a/dev/testing.html +++ b/dev/testing.html @@ -433,13 +433,13 @@

    Testing exceptions and warnings

    Failing tests

    -

    To mark an expected failure, use pytest.mark.xfail() decorator:

    +

    To mark an expected failure, use pytest.mark.xfail() decorator:

    @pytest.mark.xfail
 def tested_expected_failure():
     assert 1 == 2
    -

    To manually fail a test, make a call to pytest.fail():

    +

    To manually fail a test, make a call to pytest.fail():

    def test_open(self, tmpdir):
     outfile = str(tmpdir.join('lammps-writer-test.dcd'))
     try:
@@ -452,7 +452,7 @@ 
    Failing tests
 
    Skipping tests
    
-
    To skip tests based on a condition, use pytest.mark.skipif(condition) decorator:
    
+
    To skip tests based on a condition, use pytest.mark.skipif(condition) decorator:
    
 
    import numpy as np
 try:
     from numpy import shares_memory
@@ -467,7 +467,7 @@ 
    Skipping testsassert not np.shares_memory(original.ts.positions, copy.ts.positions)
 
    
 
    
-
    To skip a test if a module is not available for importing, use pytest.importorskip('module_name')
    
+
    To skip a test if a module is not available for importing, use pytest.importorskip('module_name')
    
 
    def test_write_trajectory_netCDF4(self, universe, outfile):
     pytest.importorskip("netCDF4")
     return self._test_write_trajectory(universe, outfile)
@@ -477,7 +477,7 @@ 
    Skipping tests
 
    Fixtures
    
-
    Use fixtures as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the pytest.fixture() decorator, over a function that returns the object you need:
    
+
    Use fixtures as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the pytest.fixture() decorator, over a function that returns the object you need:
    
 
    @pytest.fixture
 def universe(self):
     return mda.Universe(self.ref_filename)