diff --git a/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/2.8.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf index 23d7d246..07d408b3 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 bd1bf306..f3c0cf6b 100644 --- a/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html +++ b/2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html @@ -268,7 +268,7 @@

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°

    • -

    7bb880c9747b467eb68710bd0cae04ab

    +

    34a4a4f410194e59a30c1ba4168cfc14

    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 3b7455b0..7c332d27 100644 --- a/2.8.0-dev0/examples/constructing_universe.html +++ b/2.8.0-dev0/examples/constructing_universe.html @@ -717,7 +717,7 @@

    Adding a new segment

    NMP: residues 30-59 (blue)

  • LID: residues 122-159 (yellow)

    • -

    4adf27c13f3642c1afb1dc989f1dfb68

    +

    813f3c045dab4abe852f234784e358fb

    [26]:
    diff --git a/2.8.0-dev0/formats/auxiliary.html b/2.8.0-dev0/formats/auxiliary.html index 599e0eb4..4758621d 100644 --- a/2.8.0-dev0/formats/auxiliary.html +++ b/2.8.0-dev0/formats/auxiliary.html @@ -263,7 +263,7 @@

    Reading data directlyIn [3]: aux = mda.auxiliary.core.auxreader(XVG_BZ2) In [4]: aux -Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44aeb1960> +Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3dfc1120>

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

    @@ -462,7 +462,7 @@

    Recreating auxiliariesIn [30]: del aux In [31]: mda.auxiliary.core.auxreader(**description) -Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44bfef0d0> +Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3f38bf10>

    The ‘description’ of any or all the auxiliaries added to a trajectory can be @@ -577,7 +577,7 @@

    Standalone Usage
    In [45]: import matplotlib.pyplot as plt
 
 In [46]: plt.plot(temp["Time"], temp["Temperature"])
-Out[46]: [<matplotlib.lines.Line2D at 0x7fe44a69edd0>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7f9f3d955180>]
 
 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 735b5e76..90e38a4c 100644
--- a/2.8.0-dev0/index.html
+++ b/2.8.0-dev0/index.html
@@ -194,7 +194,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.8.0-dev0
    
-
    Last updated: Oct 11, 2024
    
+
    Last updated: Oct 13, 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 c963b800..2f84b2e1 100644
--- a/2.8.0-dev0/reading_and_writing.html
+++ b/2.8.0-dev0/reading_and_writing.html
@@ -322,13 +322,13 @@ 
    Building trajectories in memoryIn [16]: universe.atoms.positions
 Out[16]: 
-array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],
-       [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],
-       [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],
+array([[0.5946307 , 0.18919976, 0.44233742],
+       [0.5949025 , 0.9947764 , 0.6217801 ],
+       [0.9149371 , 0.6625653 , 0.798835  ],
        ...,
-       [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],
-       [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],
-       [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)
+       [0.7360544 , 0.5006215 , 0.67056286],
+       [0.7761591 , 0.55651474, 0.64369595],
+       [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)

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

    @@ -336,13 +336,13 @@

    Building trajectories in memoryIn [18]: universe2.atoms.positions Out[18]: -array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01], - [4.0881673e-01, 9.6393579e-01, 3.1211577e-02], - [3.5682514e-01, 3.8312599e-01, 2.8178158e-01], +array([[0.5946307 , 0.18919976, 0.44233742], + [0.5949025 , 0.9947764 , 0.6217801 ], + [0.9149371 , 0.6625653 , 0.798835 ], ..., - [8.6615133e-01, 3.7646204e-01, 1.2250387e-02], - [1.4942519e-01, 9.2269385e-01, 8.5091987e-04], - [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32) + [0.7360544 , 0.5006215 , 0.67056286], + [0.7761591 , 0.55651474, 0.64369595], + [0.45982844, 0.9889626 , 0.06811332]], dtype=float32) diff --git a/2.8.0-dev0/searchindex.js b/2.8.0-dev0/searchindex.js index 66437c3f..9e861583 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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[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 5d0cb963..b91cb683 100644 --- a/2.8.0-dev0/standard_selections.html +++ b/2.8.0-dev0/standard_selections.html @@ -334,10 +334,10 @@

    Protein backbone -

    N

    -

    CA

    +

    CA

    C

    O

    +

    N

    @@ -351,42 +351,42 @@

    Protein backbone

    RU

    RG3

    -

    GUA

    +

    RC5

    +

    RG

    RA

    -

    THY

    -

    DA5

    DC5

    -

    RC

    - -

    DC3

    -

    ADE

    -

    A

    -

    DT3

    -

    DA

    -

    C

    +

    CYT

    DG5

    -

    URA

    -

    DC

    -

    CYT

    +

    RA5

    RC3

    -

    RA3

    -

    T

    -

    RG

    +

    RC

    DA3

    -

    U

    - -

    RG5

    -

    RU5

    -

    DG3

    -

    DT

    DG

    -

    RC5

    -

    RA5

    -

    DT5

    +

    URA

    +

    DT

    +

    RG5

    -

    G

    +

    DG3

    +

    DT3

    +

    RA3

    +

    DC3

    RU3

    +

    DT5

    +

    A

    +

    DC

    + +

    DA5

    +

    ADE

    +

    DA

    +

    G

    +

    U

    +

    GUA

    +

    T

    +

    RU5

    + +

    C

    +

    THY

    @@ -401,11 +401,11 @@

    Nucleic backbone -

    O3’

    +

    O5’

    C5’

    C3’

    P

    -

    O5’

    +

    O3’

    @@ -415,23 +415,23 @@

    Nucleic backbone -

    N4

    +

    N1

    +

    O2

    N9

    -

    N3

    -

    C8

    +

    N6

    N7

    -

    N1

    -

    O2

    -

    C5

    - -

    C6

    N2

    -

    N6

    -

    O4

    -

    C4

    O6

    C2

    + +

    N4

    +

    C8

    +

    O4

    C5M

    +

    C6

    +

    C5

    +

    N3

    +

    C4

    @@ -443,9 +443,9 @@

    Nucleic sugars

    O4’

    C1’

    -

    C4’

    -

    C3’

    C2’

    +

    C3’

    +

    C4’

    diff --git a/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf index 23d7d246..07d408b3 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 bd1bf306..f3c0cf6b 100644 --- a/dev/examples/analysis/hydrogen_bonds/hbonds.html +++ b/dev/examples/analysis/hydrogen_bonds/hbonds.html @@ -268,7 +268,7 @@

    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°

    • -

    7bb880c9747b467eb68710bd0cae04ab

    +

    34a4a4f410194e59a30c1ba4168cfc14

    Find water-water hydrogen bonds

    diff --git a/dev/examples/constructing_universe.html b/dev/examples/constructing_universe.html index 3b7455b0..7c332d27 100644 --- a/dev/examples/constructing_universe.html +++ b/dev/examples/constructing_universe.html @@ -717,7 +717,7 @@

    Adding a new segment

    NMP: residues 30-59 (blue)

  • LID: residues 122-159 (yellow)

    • -

    4adf27c13f3642c1afb1dc989f1dfb68

    +

    813f3c045dab4abe852f234784e358fb

    [26]:
    diff --git a/dev/formats/auxiliary.html b/dev/formats/auxiliary.html index 599e0eb4..4758621d 100644 --- a/dev/formats/auxiliary.html +++ b/dev/formats/auxiliary.html @@ -263,7 +263,7 @@

    Reading data directlyIn [3]: aux = mda.auxiliary.core.auxreader(XVG_BZ2) In [4]: aux -Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44aeb1960> +Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3dfc1120>

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

    @@ -462,7 +462,7 @@

    Recreating auxiliariesIn [30]: del aux In [31]: mda.auxiliary.core.auxreader(**description) -Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44bfef0d0> +Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3f38bf10>

    The ‘description’ of any or all the auxiliaries added to a trajectory can be @@ -577,7 +577,7 @@

    Standalone Usage
    In [45]: import matplotlib.pyplot as plt
 
 In [46]: plt.plot(temp["Time"], temp["Temperature"])
-Out[46]: [<matplotlib.lines.Line2D at 0x7fe44a69edd0>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7f9f3d955180>]
 
 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 735b5e76..90e38a4c 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -194,7 +194,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.8.0-dev0
    
-
    Last updated: Oct 11, 2024
    
+
    Last updated: Oct 13, 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 c963b800..2f84b2e1 100644
--- a/dev/reading_and_writing.html
+++ b/dev/reading_and_writing.html
@@ -322,13 +322,13 @@ 
    Building trajectories in memoryIn [16]: universe.atoms.positions
 Out[16]: 
-array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],
-       [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],
-       [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],
+array([[0.5946307 , 0.18919976, 0.44233742],
+       [0.5949025 , 0.9947764 , 0.6217801 ],
+       [0.9149371 , 0.6625653 , 0.798835  ],
        ...,
-       [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],
-       [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],
-       [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)
+       [0.7360544 , 0.5006215 , 0.67056286],
+       [0.7761591 , 0.55651474, 0.64369595],
+       [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)

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

    @@ -336,13 +336,13 @@

    Building trajectories in memoryIn [18]: universe2.atoms.positions Out[18]: -array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01], - [4.0881673e-01, 9.6393579e-01, 3.1211577e-02], - [3.5682514e-01, 3.8312599e-01, 2.8178158e-01], +array([[0.5946307 , 0.18919976, 0.44233742], + [0.5949025 , 0.9947764 , 0.6217801 ], + [0.9149371 , 0.6625653 , 0.798835 ], ..., - [8.6615133e-01, 3.7646204e-01, 1.2250387e-02], - [1.4942519e-01, 9.2269385e-01, 8.5091987e-04], - [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32) + [0.7360544 , 0.5006215 , 0.67056286], + [0.7761591 , 0.55651474, 0.64369595], + [0.45982844, 0.9889626 , 0.06811332]], dtype=float32) diff --git a/dev/searchindex.js b/dev/searchindex.js index 66437c3f..9e861583 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 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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, 58, 61], "copi": 10, "core": 101, "cosin": 34, "coverag": 108, "crd": 65, "crdbox": 88, "creat": [1, 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"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 5d0cb963..b91cb683 100644 --- a/dev/standard_selections.html +++ b/dev/standard_selections.html @@ -334,10 +334,10 @@

    Protein backbone -

    N

    -

    CA

    +

    CA

    C

    O

    +

    N

    @@ -351,42 +351,42 @@

    Protein backbone

    RU

    RG3

    -

    GUA

    +

    RC5

    +

    RG

    RA

    -

    THY

    -

    DA5

    DC5

    -

    RC

    - -

    DC3

    -

    ADE

    -

    A

    -

    DT3

    -

    DA

    -

    C

    +

    CYT

    DG5

    -

    URA

    -

    DC

    -

    CYT

    +

    RA5

    RC3

    -

    RA3

    -

    T

    -

    RG

    +

    RC

    DA3

    -

    U

    - -

    RG5

    -

    RU5

    -

    DG3

    -

    DT

    DG

    -

    RC5

    -

    RA5

    -

    DT5

    +

    URA

    +

    DT

    +

    RG5

    -

    G

    +

    DG3

    +

    DT3

    +

    RA3

    +

    DC3

    RU3

    +

    DT5

    +

    A

    +

    DC

    + +

    DA5

    +

    ADE

    +

    DA

    +

    G

    +

    U

    +

    GUA

    +

    T

    +

    RU5

    + +

    C

    +

    THY

    @@ -401,11 +401,11 @@

    Nucleic backbone -

    O3’

    +

    O5’

    C5’

    C3’

    P

    -

    O5’

    +

    O3’

    @@ -415,23 +415,23 @@

    Nucleic backbone -

    N4

    +

    N1

    +

    O2

    N9

    -

    N3

    -

    C8

    +

    N6

    N7

    -

    N1

    -

    O2

    -

    C5

    - -

    C6

    N2

    -

    N6

    -

    O4

    -

    C4

    O6

    C2

    + +

    N4

    +

    C8

    +

    O4

    C5M

    +

    C6

    +

    C5

    +

    N3

    +

    C4

    @@ -443,9 +443,9 @@

    Nucleic sugars

    O4’

    C1’

    -

    C4’

    -

    C3’

    C2’

    +

    C3’

    +

    C4’