From 816f202aac5212d8612b2d9575167bfd97cef847 Mon Sep 17 00:00:00 2001 From: github-actions Date: Fri, 24 Nov 2023 03:07:08 +0000 Subject: [PATCH] rebuilt html docs for version 2.7.0-dev0 from branch develop with sphinx at a6fd626 --- .../auxiliary-1.pdf | Bin 10152 -> 10152 bytes .../analysis/hydrogen_bonds/hbonds.html | 2 +- .../examples/constructing_universe.html | 2 +- 2.7.0-dev0/formats/auxiliary.html | 6 +- 2.7.0-dev0/index.html | 2 +- 2.7.0-dev0/reading_and_writing.html | 24 ++--- 2.7.0-dev0/searchindex.js | 2 +- 2.7.0-dev0/standard_selections.html | 90 +++++++++--------- 2.7.0-dev0/testing.html | 10 +- .../auxiliary-1.pdf | Bin 10152 -> 10152 bytes .../analysis/hydrogen_bonds/hbonds.html | 2 +- dev/examples/constructing_universe.html | 2 +- dev/formats/auxiliary.html | 6 +- dev/index.html | 2 +- dev/reading_and_writing.html | 24 ++--- dev/searchindex.js | 2 +- dev/standard_selections.html | 90 +++++++++--------- dev/testing.html | 10 +- 18 files changed, 138 insertions(+), 138 deletions(-) diff --git a/2.7.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/2.7.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf index d1544b2f65facafeda6fd227240a076221c3e256..f09507d2fca4be01eb9bbdf876112f436ba09fb5 100644 GIT binary patch delta 19 acmZ4CzrufmpbDFbfw6(9$!2ktiOc{$2?dM* delta 19 acmZ4CzrufmpbDFzfw6&^!DexliOc{#*9C?E diff --git a/2.7.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html b/2.7.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html index 349e37d30..1cf94294d 100644 --- a/2.7.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html +++ b/2.7.0-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°

    • -

    0071495ab8c44bf497b9222ecc6dbaad

    +

    2910b68d2c0d4d05b79dde26aca48e0a

    Find water-water hydrogen bonds

    diff --git a/2.7.0-dev0/examples/constructing_universe.html b/2.7.0-dev0/examples/constructing_universe.html index 41f20b514..752646443 100644 --- a/2.7.0-dev0/examples/constructing_universe.html +++ b/2.7.0-dev0/examples/constructing_universe.html @@ -715,7 +715,7 @@

    Adding a new segment

    NMP: residues 30-59 (blue)

  • LID: residues 122-159 (yellow)

    • -

    f3284674c13f481fb3bdefdeddca6b44

    +

    1cc00375615b413d878cc6f95e7cfcda

    [26]:
    diff --git a/2.7.0-dev0/formats/auxiliary.html b/2.7.0-dev0/formats/auxiliary.html index eba683e3e..cc928d8a4 100644 --- a/2.7.0-dev0/formats/auxiliary.html +++ b/2.7.0-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 0x7f23e7d58fd0> +Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fd021ce3070>

    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 0x7f23b3eedcd0> +Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fd022ba1b50>

    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 0x7f23b3a92910>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7fd022280670>]
 
 In [47]: plt.ylabel("Temperature [K]")
 Out[47]: Text(0, 0.5, 'Temperature [K]')
diff --git a/2.7.0-dev0/index.html b/2.7.0-dev0/index.html
index 4f43b01e2..b00df45a3 100644
--- a/2.7.0-dev0/index.html
+++ b/2.7.0-dev0/index.html
@@ -190,7 +190,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.7.0-dev0
    
-
    Last updated: Nov 21, 2023
    
+
    Last updated: Nov 24, 2023
    
 
    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/2.7.0-dev0/reading_and_writing.html b/2.7.0-dev0/reading_and_writing.html
index 23f89d779..ae930de7f 100644
--- a/2.7.0-dev0/reading_and_writing.html
+++ b/2.7.0-dev0/reading_and_writing.html
@@ -320,13 +320,13 @@ 
    Building trajectories in memoryIn [16]: universe.atoms.positions
 Out[16]: 
-array([[0.95849204, 0.7487938 , 0.9704986 ],
-       [0.42354256, 0.2889326 , 0.06184179],
-       [0.5241738 , 0.642687  , 0.6946113 ],
+array([[0.01341493, 0.8954516 , 0.48900408],
+       [0.0416302 , 0.81844276, 0.6713378 ],
+       [0.32844332, 0.8965664 , 0.8370764 ],
        ...,
-       [0.7527609 , 0.1350824 , 0.80041414],
-       [0.1707926 , 0.5413459 , 0.8568687 ],
-       [0.0265642 , 0.16363254, 0.5556602 ]], dtype=float32)
+       [0.04501093, 0.29551986, 0.05062775],
+       [0.6661255 , 0.7034433 , 0.08090701],
+       [0.52956533, 0.7413073 , 0.81429756]], 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([[0.95849204, 0.7487938 , 0.9704986 ], - [0.42354256, 0.2889326 , 0.06184179], - [0.5241738 , 0.642687 , 0.6946113 ], +array([[0.01341493, 0.8954516 , 0.48900408], + [0.0416302 , 0.81844276, 0.6713378 ], + [0.32844332, 0.8965664 , 0.8370764 ], ..., - [0.7527609 , 0.1350824 , 0.80041414], - [0.1707926 , 0.5413459 , 0.8568687 ], - [0.0265642 , 0.16363254, 0.5556602 ]], dtype=float32) + [0.04501093, 0.29551986, 0.05062775], + [0.6661255 , 0.7034433 , 0.08090701], + [0.52956533, 0.7413073 , 0.81429756]], dtype=float32) diff --git a/2.7.0-dev0/searchindex.js b/2.7.0-dev0/searchindex.js index 3fc79fdd6..0c212c24c 100644 --- a/2.7.0-dev0/searchindex.js +++ b/2.7.0-dev0/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["advanced_topology", "atomgroup", "contributing", "contributing_code", "contributing_docs", "datasets", "examples/README", "examples/analysis/README", "examples/analysis/alignment_and_rms/README", "examples/analysis/alignment_and_rms/aligning_structure_to_another", "examples/analysis/alignment_and_rms/aligning_trajectory", "examples/analysis/alignment_and_rms/aligning_trajectory_to_frame", "examples/analysis/alignment_and_rms/pairwise_rmsd", "examples/analysis/alignment_and_rms/rmsd", "examples/analysis/alignment_and_rms/rmsf", "examples/analysis/custom_parallel_analysis", "examples/analysis/custom_trajectory_analysis", "examples/analysis/distances_and_contacts/README", "examples/analysis/distances_and_contacts/contacts_custom", "examples/analysis/distances_and_contacts/contacts_native_fraction", "examples/analysis/distances_and_contacts/contacts_q1q2", "examples/analysis/distances_and_contacts/contacts_within_cutoff", "examples/analysis/distances_and_contacts/distances_between_atomgroups", "examples/analysis/distances_and_contacts/distances_between_selections", "examples/analysis/distances_and_contacts/distances_within_selection", "examples/analysis/hydrogen_bonds/README", "examples/analysis/hydrogen_bonds/hbonds", "examples/analysis/hydrogen_bonds/hbonds-lifetimes", "examples/analysis/hydrogen_bonds/hbonds-selections", "examples/analysis/polymers_and_membranes/README", "examples/analysis/polymers_and_membranes/hole2", "examples/analysis/polymers_and_membranes/polymer", "examples/analysis/reduced_dimensions/README", "examples/analysis/reduced_dimensions/diffusion_map", "examples/analysis/reduced_dimensions/pca", "examples/analysis/structure/README", "examples/analysis/structure/average_rdf", "examples/analysis/structure/dihedrals", "examples/analysis/structure/elastic_network", "examples/analysis/structure/helanal", "examples/analysis/structure/site_specific_rdf", "examples/analysis/trajectory_similarity/README", "examples/analysis/trajectory_similarity/clustering_ensemble_similarity", "examples/analysis/trajectory_similarity/convergence", "examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity", "examples/analysis/trajectory_similarity/harmonic_ensemble_similarity", "examples/analysis/trajectory_similarity/psa", "examples/analysis/volumetric/README", "examples/analysis/volumetric/density_analysis", "examples/analysis/volumetric/linear_density", "examples/constructing_universe", "examples/other/README", "examples/other/parmed_sim", "examples/quickstart", "examples/transformations/README", "examples/transformations/center_protein_in_box", "faq", "formats/auxiliary", "formats/coordinates", "formats/format_reference", "formats/guessing", "formats/index", "formats/reference/chemfiles", "formats/reference/config", "formats/reference/coor", "formats/reference/crd", "formats/reference/data", "formats/reference/dcd", "formats/reference/dcd_lammps", "formats/reference/dms", "formats/reference/gms", "formats/reference/gro", "formats/reference/gsd", "formats/reference/in", "formats/reference/inpcrd", 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106, 108, 109, 110, 111, 112, 113, 114], "through": [1, 2, 3, 7, 12, 14, 15, 32, 41, 49, 53, 57, 98, 103, 105, 106, 109, 111, 114], "instanc": [1, 36, 50, 53, 57, 78, 106, 114], "typic": [1, 3, 7, 8, 13, 14, 26, 50, 52, 53, 96, 98, 99, 108, 109, 111, 112, 114], "select_atom": [1, 9, 11, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 26, 31, 34, 36, 37, 40, 48, 50, 52, 53, 55, 96, 98, 103, 105, 106, 110, 111, 112, 114], "manipul": [1, 53, 80, 99], "test": [1, 2, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 70, 93, 96, 98, 102, 103, 106, 109, 110, 111, 112, 114], "datafil": [1, 5, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 93, 96, 98, 101, 103, 106, 108, 109, 110, 111, 112, 114], "pdb": [1, 9, 10, 13, 14, 22, 23, 24, 34, 37, 46, 50, 52, 53, 57, 58, 59, 61, 77, 78, 83, 96, 97, 98, 103, 105, 108, 109, 114], "3": [1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 81, 82, 83, 84, 87, 93, 94, 95, 96, 98, 103, 104, 106, 108, 109, 110, 111, 112, 113, 114], "4": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 82, 83, 87, 88, 93, 96, 98, 100, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "resnam": [1, 18, 19, 21, 26, 27, 28, 36, 37, 40, 48, 50, 53, 55, 61, 65, 72, 81, 82, 86, 87, 96, 97, 98, 105, 106, 109, 112], "arg": [1, 15, 18, 19, 21, 27, 28, 53, 83, 98, 106, 107, 109], "out": [1, 3, 4, 9, 10, 11, 12, 14, 19, 30, 34, 39, 48, 50, 52, 55, 57, 61, 70, 78, 93, 98, 102, 103, 105, 106, 109, 110, 111, 113, 114], "312": [1, 98, 104, 108], "see": [1, 2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 26, 27, 28, 30, 32, 33, 34, 37, 38, 40, 42, 43, 44, 46, 48, 50, 52, 53, 55, 56, 57, 60, 61, 63, 66, 67, 69, 76, 81, 84, 87, 94, 96, 98, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "more": [1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 33, 34, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 53, 56, 57, 60, 61, 65, 69, 87, 98, 101, 103, 105, 106, 108, 109, 112, 114], "inform": [1, 3, 4, 7, 10, 12, 14, 15, 16, 19, 22, 26, 28, 30, 32, 33, 34, 37, 40, 42, 43, 44, 46, 50, 52, 56, 57, 60, 62, 63, 66, 69, 70, 71, 72, 80, 81, 82, 84, 87, 88, 94, 95, 98, 101, 103, 105, 106, 108, 111, 112, 114], "like": [1, 3, 4, 5, 13, 16, 19, 26, 30, 34, 39, 40, 43, 48, 53, 55, 57, 60, 83, 100, 106, 108], "list": [1, 2, 3, 5, 13, 15, 16, 19, 26, 30, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 57, 61, 65, 67, 82, 87, 96, 99, 100, 102, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114], "5": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 67, 71, 78, 82, 87, 93, 98, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "print": [1, 5, 9, 10, 11, 13, 14, 15, 19, 23, 26, 27, 28, 30, 31, 34, 36, 37, 39, 40, 42, 43, 44, 45, 46, 49, 50, 53, 57, 101, 103, 108, 109, 110, 111, 114], "n": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 83, 95, 96, 98, 104, 105, 106, 107, 113], "type": [1, 3, 26, 42, 50, 52, 53, 58, 61, 65, 66, 72, 80, 81, 82, 83, 84, 85, 86, 87, 91, 92, 96, 97, 98, 104, 105, 106, 109, 113], "met": [1, 53, 83, 107, 109], "resid": [1, 13, 14, 23, 24, 26, 27, 36, 40, 46, 50, 53, 61, 65, 66, 69, 72, 75, 81, 82, 87, 89, 98, 105, 106, 109], "altloc": [1, 14, 61, 81, 82, 97, 106, 109], "return": [1, 3, 4, 9, 10, 13, 15, 16, 18, 19, 20, 21, 22, 24, 27, 30, 33, 34, 37, 40, 42, 44, 50, 53, 57, 98, 102, 105, 106, 108, 110, 111, 112], "below": [1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 61, 98, 103, 106, 107, 108, 109, 112, 113, 114], "code": [1, 2, 4, 5, 6, 7, 11, 13, 14, 15, 16, 30, 36, 48, 50, 57, 67, 78, 81, 82, 84, 93, 98, 99, 102, 103, 104, 105, 106, 108, 109, 112, 114], "everi": [1, 3, 4, 10, 14, 15, 16, 24, 27, 30, 31, 34, 37, 39, 42, 44, 48, 50, 52, 53, 57, 60, 61, 98, 103, 105, 106, 108, 109, 111, 114], "second": [1, 10, 12, 18, 19, 21, 40, 44, 53, 113], "element": [1, 42, 50, 53, 60, 61, 65, 66, 70, 81, 82, 86, 97, 105, 109, 114], "first": [1, 3, 4, 7, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 49, 50, 53, 55, 57, 61, 69, 72, 81, 83, 89, 94, 98, 100, 101, 105, 106, 108, 110, 111, 114], "6th": [1, 106], "correspond": [1, 3, 12, 13, 14, 16, 24, 26, 27, 40, 55, 71, 98, 108, 109], "indic": [1, 3, 12, 13, 14, 19, 24, 26, 27, 30, 33, 34, 38, 40, 43, 50, 53, 81, 82, 84, 87, 91, 96, 101, 105, 106, 108, 109, 110], "6": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 66, 69, 78, 81, 82, 83, 84, 87, 91, 93, 98, 102, 103, 104, 106, 109, 110, 111, 112, 114], "ag": [1, 10, 13, 40, 96, 98, 103], "also": [1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 32, 34, 37, 39, 40, 41, 42, 44, 48, 53, 55, 57, 61, 62, 81, 82, 87, 89, 98, 100, 101, 102, 103, 105, 106, 108, 109, 110, 111, 112, 113, 114], "support": [1, 3, 13, 19, 30, 46, 53, 66, 71, 72, 82, 84, 85, 88, 100, 103, 105, 106, 109, 111, 114], "fanci": [1, 53, 110], "pass": [1, 3, 4, 13, 16, 18, 19, 22, 23, 24, 26, 28, 30, 31, 34, 36, 37, 39, 42, 43, 44, 45, 49, 50, 53, 55, 60, 61, 62, 66, 80, 81, 93, 95, 96, 100, 102, 103, 105, 106, 108, 110, 112, 114], "ndarrai": [1, 53, 110], "8": [1, 4, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 87, 98, 103, 105, 106, 109, 110, 111, 112, 114], "10": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 71, 78, 82, 83, 87, 98, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "9": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 84, 87, 98, 102, 103, 105, 106, 108, 109, 110, 111, 112, 114], "47680": 1, "boolean": [1, 53, 108, 110], "allow": [1, 2, 3, 10, 13, 14, 19, 27, 28, 30, 36, 37, 40, 42, 43, 44, 52, 53, 56, 57, 60, 96, 99, 100, 103, 105, 106, 108, 110, 114], "you": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 61, 62, 64, 67, 78, 79, 80, 89, 96, 98, 99, 100, 101, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "true": [1, 3, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 30, 34, 37, 38, 40, 42, 44, 45, 46, 48, 50, 52, 53, 55, 66, 68, 89, 94, 103, 105, 106, 108, 110, 114], "fals": [1, 4, 9, 11, 14, 19, 20, 26, 27, 30, 40, 44, 46, 48, 50, 53, 57, 78, 103, 105, 106, 108, 109, 110, 114], "valu": [1, 3, 7, 8, 11, 12, 13, 14, 15, 19, 24, 26, 27, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 57, 60, 65, 66, 67, 76, 81, 82, 83, 89, 92, 105, 106, 108, 110, 114], "must": [1, 2, 3, 4, 11, 12, 13, 16, 18, 22, 23, 26, 27, 30, 31, 34, 42, 43, 46, 48, 50, 53, 60, 66, 79, 83, 84, 100, 101, 108, 109, 112, 114], "same": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 24, 26, 28, 30, 31, 33, 34, 36, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 67, 93, 95, 96, 98, 102, 103, 105, 106, 109, 110, 114], "length": [1, 3, 6, 7, 12, 13, 22, 24, 27, 29, 39, 40, 42, 44, 45, 46, 48, 50, 52, 53, 63, 66, 67, 68, 71, 79, 88, 99, 104, 105, 110, 111], "origin": [1, 3, 4, 7, 9, 13, 14, 23, 27, 32, 33, 34, 39, 50, 53, 55, 57, 67, 98, 102, 106, 108, 110, 113], "condit": [1, 15, 105, 106, 108, 110, 112], "arr": 1, "11": [1, 3, 9, 10, 13, 14, 15, 16, 19, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 83, 87, 98, 103, 104, 105, 106, 109, 110, 112, 113, 114], "len": [1, 12, 23, 24, 30, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 50, 53, 57, 98, 103, 108, 109, 111], "12": [1, 3, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 33, 34, 36, 37, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 82, 86, 98, 103, 104, 106, 109, 110, 111, 112, 113, 114], "13": [1, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 34, 36, 37, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 106, 109, 110, 112, 114], "number": [1, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 50, 52, 53, 57, 60, 65, 69, 71, 72, 75, 81, 82, 83, 84, 85, 87, 89, 91, 92, 93, 96, 103, 105, 106, 108, 109, 114], "wai": [1, 3, 4, 7, 10, 12, 13, 14, 15, 16, 18, 19, 26, 27, 30, 33, 34, 48, 52, 53, 79, 98, 99, 103, 105, 106, 108, 109, 111, 114], "compar": [1, 6, 7, 9, 10, 11, 12, 14, 15, 17, 19, 22, 32, 34, 40, 41, 42, 44, 45, 108], "one": [1, 2, 3, 4, 10, 11, 12, 13, 15, 19, 27, 28, 30, 31, 39, 46, 50, 53, 56, 57, 83, 87, 88, 91, 92, 96, 98, 99, 100, 103, 104, 105, 106, 108, 109, 114], "concaten": [1, 15, 53, 103, 106, 114], "subtract": [1, 13, 84], "union": [1, 106], "differ": [1, 3, 4, 7, 9, 10, 12, 13, 15, 16, 19, 26, 28, 34, 36, 38, 40, 41, 45, 46, 48, 50, 53, 55, 60, 66, 67, 70, 71, 75, 82, 87, 91, 93, 95, 96, 98, 99, 100, 102, 103, 104, 105, 106, 112, 114], "achiev": [1, 15], "similar": [1, 3, 4, 6, 12, 15, 19, 23, 24, 30, 32, 33, 34, 37, 38, 53, 73, 82, 83, 87, 92, 93, 98, 104], "outcom": [1, 105], "kei": [1, 2, 30, 38, 39, 49, 53, 57, 98, 99, 114], "preserv": [1, 4, 19, 66, 105], "ani": [1, 2, 3, 4, 11, 15, 16, 18, 27, 28, 30, 31, 37, 42, 43, 44, 46, 49, 50, 53, 56, 57, 61, 67, 89, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 112], "duplic": [1, 30, 53, 103, 106], "where": [1, 4, 5, 7, 9, 14, 15, 16, 19, 20, 21, 22, 27, 31, 32, 33, 36, 37, 38, 40, 43, 44, 46, 48, 50, 53, 57, 60, 61, 66, 71, 89, 98, 100, 102, 105, 106, 108, 109], "its": [1, 2, 3, 4, 7, 9, 13, 15, 18, 19, 20, 22, 30, 32, 33, 44, 46, 49, 52, 53, 98, 99, 100, 101, 103, 106, 108, 109, 111, 112], "topologi": [1, 5, 14, 15, 26, 28, 52, 53, 59, 63, 65, 66, 69, 70, 71, 72, 73, 76, 77, 78, 80, 81, 82, 83, 84, 91, 92, 93, 95, 98, 99, 103, 105, 106, 108, 111], "14": [1, 9, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 82, 98, 100, 103, 104, 105, 106, 109, 110, 112, 114], "ag1": [1, 40], "15": [1, 7, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 41, 42, 43, 44, 45, 48, 49, 50, 52, 53, 57, 81, 82, 98, 103, 104, 106, 109, 110, 112, 114], "ag2": [1, 40], "16": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 104, 105, 106, 109, 110, 111, 112], "concat": 1, "17": [1, 12, 15, 16, 19, 20, 21, 26, 27, 30, 33, 34, 36, 39, 42, 44, 48, 49, 50, 52, 53, 57, 69, 81, 82, 87, 98, 103, 104, 106, 109, 110, 111, 112], "18": [1, 9, 15, 16, 19, 26, 27, 30, 42, 44, 46, 48, 49, 50, 52, 53, 57, 78, 81, 82, 86, 98, 103, 105, 106, 109, 110, 112, 113], "19": [1, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 37, 40, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 104, 105, 106, 109, 112, 113], "avail": [1, 2, 3, 7, 15, 16, 19, 32, 33, 36, 40, 42, 43, 44, 53, 56, 57, 60, 66, 73, 77, 79, 82, 87, 96, 98, 99, 100, 102, 105, 106, 108, 109, 114], "keep": [1, 2, 3, 10, 14, 30, 34, 39, 43, 44, 48, 55, 72, 96, 99, 101, 102, 108], "well": [1, 2, 4, 7, 15, 32, 33, 44, 48, 61, 67, 99, 101, 105, 108], "equival": [1, 27, 48, 87], "result": [1, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 24, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 52, 53, 61, 89, 94, 105, 106, 108, 110], "t": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 48, 49, 50, 52, 53, 55, 56, 57, 66, 82, 92, 96, 98, 100, 103, 104, 105, 106, 107, 108, 110, 111, 112, 114], "sort": [1, 26, 27, 30, 34, 53, 105, 106], "isdisjoint": 1, "do": [1, 3, 4, 6, 10, 11, 12, 13, 15, 16, 19, 22, 26, 27, 28, 30, 34, 37, 42, 44, 45, 46, 48, 50, 52, 53, 95, 99, 101, 102, 103, 105, 108, 114], "share": [1, 3, 105], "issubset": 1, "part": [1, 2, 3, 4, 15, 30, 48, 57, 101, 103, 105, 106, 108, 111], "is_strict_subset": 1, "issuperset": 1, "is_strict_superset": 1, "both": [1, 3, 4, 13, 15, 16, 22, 30, 38, 48, 50, 52, 53, 60, 63, 72, 81, 85, 87, 91, 98, 100, 102, 103, 105, 108, 109, 114], "intersect": [1, 106], "common": [1, 3, 7, 12, 13, 14, 15, 22, 26, 31, 32, 34, 53, 55, 68, 70, 104, 106, 108], "symmetric_differ": 1, "separ": [1, 5, 7, 15, 16, 19, 30, 31, 36, 40, 42, 43, 81, 83, 84, 100, 102, 106, 108, 114], "properti": [1, 16, 30, 39, 53, 60, 98, 105, 106, 109, 111, 112], "level": [1, 3, 4, 15, 48, 85, 98, 101, 108, 114], "connect": [1, 3, 4, 33, 50, 52, 53, 60, 61, 82, 87, 91, 105, 114], "residu": [1, 3, 7, 13, 14, 17, 19, 21, 22, 26, 28, 30, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 55, 61, 65, 69, 70, 71, 72, 75, 81, 82, 83, 86, 87, 92, 93, 95, 96, 99, 105, 106, 109, 112, 114], "molecul": [1, 4, 10, 13, 26, 31, 38, 50, 55, 58, 61, 66, 78, 87, 92, 95, 98, 105, 106, 108, 109, 112], "segment": [1, 10, 49, 53, 61, 65, 70, 81, 87, 95, 99, 103, 105, 106, 109, 114], "20": [1, 15, 16, 19, 26, 30, 31, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 105, 106, 110, 111, 112, 113], "21": [1, 3, 9, 15, 16, 26, 27, 28, 30, 31, 33, 42, 44, 48, 49, 50, 52, 53, 57, 71, 81, 82, 98, 99, 103, 104, 105, 106, 109, 112, 113, 114], "24": [1, 15, 16, 26, 27, 30, 34, 39, 44, 49, 50, 53, 57, 81, 82, 87, 98, 103, 105, 112], "accord": [1, 13, 14, 87, 91, 106, 109], "produc": [1, 23, 27, 34, 53, 57, 67, 105, 108], "dictionari": [1, 18, 30, 57, 60, 89, 105, 108, 114], "22": [1, 15, 16, 26, 30, 44, 46, 48, 49, 50, 53, 57, 81, 82, 98, 103, 105, 106, 112], "mass": [1, 6, 7, 9, 10, 15, 16, 23, 24, 28, 30, 36, 40, 45, 46, 47, 48, 53, 55, 61, 63, 65, 66, 86, 87, 92, 97, 106, 109, 112, 113, 114], "32": [1, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 50, 52, 53, 55, 57, 98, 104, 105], "06": [1, 38, 104, 113], "008": [1, 53], "23853": 1, "11084": 1, "011": [1, 39, 53], "1040": [1, 98], "007": [1, 53, 82], "289": 1, "999": [1, 53, 65, 93], "11404": 1, "98977": 1, "multipl": [1, 3, 27, 39, 48, 53, 57, 62, 89, 94, 98, 100, 105, 106, 112, 114], "them": [1, 3, 4, 7, 9, 10, 13, 15, 18, 19, 22, 34, 38, 39, 42, 43, 44, 45, 46, 50, 52, 53, 55, 60, 61, 66, 68, 79, 81, 82, 89, 95, 101, 102, 103, 104, 105, 106, 108, 109, 112], "23": [1, 15, 16, 26, 30, 34, 44, 48, 49, 50, 53, 57, 81, 82, 87, 93, 98, 103, 106, 112], "sol": [1, 30, 36, 37, 40, 48, 50, 55, 87, 112], "22168": 1, "iter": [1, 12, 14, 15, 16, 30, 44, 49, 53, 103, 105, 108, 109, 110, 111], "atom1": [1, 95], "25": [1, 15, 26, 27, 30, 34, 46, 49, 50, 53, 57, 81, 82, 83, 98, 103, 105], "atom2": [1, 95], "26": [1, 15, 26, 30, 34, 49, 50, 53, 57, 81, 82, 83, 87, 93, 98, 103], "atom3": 1, "27": [1, 15, 26, 30, 49, 50, 53, 57, 81, 82, 93, 98, 103, 104, 107, 113], "28": [1, 3, 15, 30, 49, 50, 53, 57, 78, 98, 103], "ca": [1, 9, 10, 11, 12, 13, 14, 16, 18, 20, 21, 23, 24, 36, 37, 38, 39, 40, 42, 43, 44, 46, 53, 60, 98, 103, 106, 107], "c": [1, 3, 13, 27, 30, 31, 34, 36, 37, 38, 39, 46, 48, 50, 52, 53, 62, 67, 78, 81, 82, 85, 87, 88, 98, 100, 102, 103, 104, 105, 106, 107, 113], "cb": [1, 36, 53, 98], "h2": [1, 26, 28, 50, 78], "h": [1, 3, 27, 31, 36, 39, 45, 50, 52, 53, 78, 87, 96, 98, 103, 106], "neat": [1, 4], "shortcut": [1, 106], "simpli": [1, 3, 12, 13, 15, 21, 24, 26, 34, 40, 50, 52, 53, 60, 79, 84, 88, 101, 104, 105, 106, 109, 113], "29": [1, 13, 15, 30, 34, 46, 49, 50, 53, 57, 98, 103, 113], "30": [1, 13, 14, 15, 22, 23, 30, 33, 42, 49, 50, 53, 57, 78, 98, 103, 104, 110, 112, 113], "31": [1, 15, 16, 19, 30, 48, 49, 50, 53, 57, 81, 82, 98, 103], "altern": [1, 3, 13, 20, 30, 48, 57, 77, 81, 82, 96, 103, 106, 108, 109, 112], "provid": [1, 3, 4, 7, 12, 13, 15, 16, 17, 25, 26, 30, 31, 34, 37, 38, 43, 44, 46, 52, 53, 55, 57, 60, 61, 62, 65, 71, 81, 82, 83, 88, 94, 96, 99, 100, 103, 105, 106, 108, 109, 114], "belong": [1, 28, 50, 53, 61, 98, 106, 107], "33": [1, 15, 49, 50, 53, 57, 81, 82], "34": [1, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 37, 38, 39, 40, 42, 43, 44, 45, 49, 50, 52, 53, 55, 57, 81, 82, 98, 104], "These": [1, 3, 4, 5, 7, 8, 17, 24, 37, 43, 48, 53, 57, 72, 81, 82, 89, 94, 98, 106, 108, 109], "user": [1, 2, 3, 6, 7, 15, 19, 26, 28, 39, 42, 43, 44, 45, 49, 53, 60, 61, 66, 68, 69, 72, 78, 79, 87, 88, 100, 101, 102, 103, 105, 106, 108, 109, 114], "work": [1, 2, 4, 7, 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, 55, 56, 57, 62, 67, 79, 96, 99, 100, 102, 104, 105, 106, 108, 111], "35": [1, 19, 20, 30, 49, 50, 53, 57, 98, 103, 104], "null": 1, "36": [1, 49, 50, 53, 57, 83], "abov": [1, 3, 10, 13, 16, 23, 24, 26, 27, 28, 39, 48, 53, 55, 57, 83, 102, 103, 105, 106, 108, 109, 111], "37": [1, 38, 49, 50, 53, 57, 83, 98, 104], "For": [1, 2, 3, 4, 7, 9, 12, 13, 15, 16, 19, 26, 28, 30, 32, 33, 34, 37, 39, 40, 42, 43, 44, 46, 50, 52, 53, 55, 57, 60, 61, 66, 78, 83, 87, 89, 96, 98, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 114], "38": [1, 16, 23, 49, 52, 53, 57, 81, 82], "does_not_exist": 1, "39": [1, 13, 15, 16, 18, 20, 21, 23, 24, 26, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 50, 52, 53, 57, 81, 82], "40": [1, 19, 30, 49, 53, 57, 81, 82, 98, 103, 110], "have": [1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 18, 19, 22, 24, 26, 27, 30, 31, 33, 34, 36, 37, 40, 42, 44, 45, 46, 48, 50, 53, 55, 57, 60, 63, 66, 67, 69, 71, 75, 79, 81, 82, 84, 87, 89, 95, 98, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 114], "evalu": [1, 6, 7, 34, 41, 49, 106], "context": [1, 15, 30, 52, 53, 96, 108], "41": [1, 30, 49, 57, 81, 82, 98], "bool": [1, 3, 18, 50, 109, 110], "skip": [1, 3, 16, 46, 57, 100], "over": [1, 6, 7, 8, 12, 15, 16, 17, 18, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 53, 55, 72, 102, 103, 105, 108, 110, 111, 112], "instead": [1, 3, 4, 9, 10, 12, 14, 15, 16, 19, 23, 24, 30, 34, 37, 39, 43, 44, 48, 50, 55, 61, 81, 82, 88, 92, 93, 100, 105, 106, 108, 111, 114], "rais": [1, 3, 33, 49, 53, 65, 79, 81, 82, 83, 99, 100, 101, 105, 108], "error": [1, 3, 4, 9, 49, 53, 72, 79, 89, 94, 100, 101, 105, 108], "which": [1, 3, 4, 10, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 30, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 55, 57, 60, 61, 67, 68, 83, 87, 89, 91, 94, 96, 98, 99, 100, 102, 103, 105, 106, 108, 109, 112, 114], "help": [1, 2, 3, 4, 13, 16, 22, 96, 99, 100, 106, 108], "occasion": [1, 89, 94], "aris": [1, 4], "logic": 1, "too": [1, 16, 42, 44, 48, 53, 55, 56, 99, 108], "restrict": [1, 13, 14, 87], "geometr": [1, 6, 7, 26, 41, 52], "normal": [1, 3, 15, 30, 38, 39, 43, 44, 84, 91, 96, 102, 104, 105, 108], "static": [1, 10, 15, 53, 106, 109, 111, 114], "within": [1, 6, 7, 16, 17, 18, 19, 20, 22, 26, 28, 30, 36, 38, 40, 42, 43, 44, 45, 50, 53, 57, 60, 67, 77, 105, 106, 111, 112], "chang": [1, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 49, 53, 55, 57, 61, 71, 72, 81, 87, 89, 100, 102, 103, 106, 108, 111], "trajectori": [1, 5, 6, 8, 9, 17, 18, 20, 21, 26, 27, 32, 33, 36, 37, 38, 40, 42, 43, 44, 45, 48, 49, 50, 52, 54, 58, 59, 61, 66, 71, 72, 81, 82, 91, 93, 99, 104, 105, 106, 108, 112, 113, 114], "frame": [1, 7, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 26, 27, 30, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 46, 48, 49, 52, 55, 56, 61, 66, 71, 81, 82, 89, 94, 99, 105, 106, 108, 110, 111, 112, 114], "sever": [1, 3, 7, 16, 29, 30, 33, 34, 53, 82, 101, 105, 108, 114], "requir": [1, 3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 65, 66, 79, 81, 82, 83, 95, 96, 98, 100, 103, 105, 106, 108, 109], "function": [1, 2, 3, 4, 6, 7, 8, 13, 17, 19, 20, 21, 27, 30, 33, 34, 35, 37, 41, 42, 43, 44, 45, 46, 52, 53, 55, 56, 57, 85, 87, 98, 100, 101, 102, 104, 105, 106, 109, 111, 112, 114], "implement": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 39, 53, 57, 62, 66, 76, 82, 87, 95, 106, 112], "mani": [1, 2, 3, 4, 13, 15, 16, 21, 26, 30, 34, 39, 40, 42, 43, 44, 53, 99, 100, 108, 109, 111, 114], "interest": [1, 19, 30, 48, 53, 100], "bond": [1, 13, 31, 49, 52, 53, 55, 57, 61, 66, 78, 80, 81, 82, 84, 86, 91, 92, 97, 98, 99, 104, 105, 106, 109, 114], "angl": [1, 6, 7, 22, 26, 27, 28, 35, 39, 50, 53, 57, 61, 66, 67, 84, 86, 92, 97, 99, 104, 105, 106, 109, 113, 114], "dihedr": [1, 6, 7, 35, 53, 61, 66, 84, 86, 97, 105, 106, 109, 114], "improperdihedr": [1, 109], "present": [1, 3, 19, 21, 26, 27, 40, 52, 65, 68, 81, 92, 95, 98, 105], "residuegroup": [1, 53, 98, 105, 109], "free": [2, 3, 101], "open": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 87, 89, 94, 104, 108], "sourc": [2, 3, 4, 16, 30, 53, 57, 84, 96, 100, 102, 105, 108], "project": [2, 3, 4, 7, 32, 37, 39, 43, 44, 48, 99, 105], "It": [2, 3, 4, 7, 9, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 32, 33, 34, 36, 37, 40, 45, 48, 49, 50, 53, 57, 60, 61, 67, 76, 78, 82, 85, 87, 89, 99, 104, 106, 108, 110, 112, 114], "evolv": 2, "grow": [2, 5, 108], "demand": 2, "base": [2, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 19, 28, 33, 39, 42, 44, 46, 50, 52, 53, 60, 61, 65, 79, 87, 89, 94, 102, 103, 104, 105, 106, 107, 108, 109], "develop": [2, 15, 52, 72, 101, 108], "team": 2, "veri": [2, 3, 12, 13, 15, 19, 23, 24, 27, 44, 45, 48, 79, 93, 103, 108], "much": [2, 3, 10, 11, 12, 13, 14, 16, 19, 30, 34, 42, 43, 48, 50, 60, 105, 108], "welcom": 2, "take": [2, 3, 4, 7, 14, 15, 16, 17, 23, 26, 30, 33, 42, 44, 48, 93, 96, 99, 100, 103, 106, 108, 109, 112, 114], "form": [2, 13, 19, 26, 42, 53, 55, 60], "bug": [2, 3, 16, 88, 102], "report": [2, 52, 99, 108], "enhanc": [2, 3], "request": [2, 4, 101, 102, 108], "issu": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 50, 57, 61, 63, 67, 79, 84, 87, 89, 94, 99, 100, 101, 102, 106, 108], "tracker": [2, 87, 99, 108], "fix": [2, 3, 4, 48, 49, 68, 72, 102], "improv": [2, 27, 99, 108], "speed": [2, 105, 108], "clariti": [2, 26], "modernis": 2, "featur": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 83, 99, 100, 102, 114], "addit": [2, 3, 7, 44, 57, 61, 82, 96, 98, 101, 102, 103, 105, 106, 108, 109], "document": [2, 5, 7, 15, 19, 22, 26, 30, 43, 48, 53, 66, 76, 89, 94, 105, 106, 108, 113], "includ": [2, 3, 4, 7, 9, 10, 13, 14, 15, 16, 19, 34, 36, 37, 39, 43, 48, 50, 52, 53, 55, 57, 84, 85, 87, 95, 96, 98, 99, 100, 102, 104, 105, 106, 108, 109, 111, 112, 114], "typo": [2, 3], "build": [2, 15, 16, 50, 53, 65, 87, 99, 100, 105], "question": [2, 3, 99], "discuss": [2, 3, 15, 27, 60, 63, 79, 87, 99, 101, 108], "mdnalysi": [2, 99, 108], "mail": [2, 99, 100, 101, 102, 108], "commun": [2, 3, 88], "subscrib": [2, 99], "conduct": [2, 99], "member": 2, "agre": [2, 99], "adher": [2, 102], "pleas": [2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 61, 87, 99, 100, 102, 104, 105, 112], "read": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 30, 33, 38, 39, 43, 44, 49, 50, 52, 60, 62, 63, 64, 74, 80, 90, 91, 92, 99, 105, 106, 109, 110, 111, 113, 114], "mdanalysistest": [2, 3, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 55, 57, 100, 101, 102, 103, 105, 108], "packag": [2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 79, 86, 96, 100, 101, 104, 105, 106, 108], "distribut": [2, 3, 6, 7, 15, 30, 35, 38, 41, 42, 44, 45, 70, 100, 102], "under": [2, 3, 15, 19, 53, 87, 101, 105, 108, 110], "gnu": [2, 108], "gener": [2, 3, 4, 7, 8, 9, 10, 14, 15, 18, 19, 20, 28, 30, 34, 37, 38, 39, 48, 50, 53, 55, 58, 59, 61, 67, 77, 80, 89, 94, 99, 102, 103, 104, 105, 113, 114], "public": [2, 3, 16, 30, 99, 102, 104, 108], "licens": [2, 15, 105, 108], "later": [2, 4, 13, 15, 102, 105, 106], "copyleft": 2, "deriv": [2, 3, 84, 87, 98, 105, 109], "made": [2, 3, 4, 26, 48, 71, 103, 105, 106, 109], "Be": [2, 15, 100], "sure": [2, 3, 4, 18, 100, 102, 106, 108], "comfort": 2, "befor": [2, 3, 4, 13, 16, 30, 36, 45, 48, 60, 89, 100, 101, 102, 105, 106, 108, 111], "push": [2, 4, 15, 102, 108], "page": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 102, 104, 106, 108], "came": [2, 108], "panda": [2, 13, 15, 16, 18, 19, 20, 21, 26, 33, 34, 49, 53, 108], "guid": [2, 3, 6, 7, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 69, 100, 108], "idea": [2, 3, 53, 102], "If": [2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 16, 23, 26, 27, 30, 34, 36, 37, 38, 40, 42, 44, 46, 50, 52, 53, 55, 57, 61, 65, 66, 67, 68, 79, 81, 82, 83, 84, 88, 89, 92, 96, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "look": [2, 3, 4, 10, 12, 13, 15, 19, 23, 24, 26, 28, 36, 37, 39, 48, 55, 61, 83, 86, 92, 96, 98, 108, 111], "brand": 2, "we": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 68, 82, 88, 96, 98, 99, 100, 101, 102, 105, 108, 109], "recommend": [2, 3, 21, 26, 45, 61, 100, 101, 102, 108], "go": [2, 3, 4, 15, 16, 96, 102, 106], "main": [2, 4, 100], "codebas": [2, 16, 105], "your": [2, 4, 5, 6, 7, 10, 13, 15, 17, 19, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 61, 67, 75, 84, 87, 99, 100, 103, 104, 105, 108, 111, 112], "own": [2, 3, 4, 6, 7, 13, 15, 17, 19, 20, 21, 30, 42, 52, 53, 66, 99, 101, 108, 112], "encourag": [2, 108], "an": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 57, 60, 62, 66, 67, 69, 71, 72, 78, 80, 83, 84, 85, 87, 88, 89, 94, 96, 98, 99, 100, 101, 102, 104, 105, 106, 108, 110, 112, 114], "toolkit": [2, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 52, 53, 55, 99, 104], "mdakit": [2, 105], "standalon": [2, 16, 108], "solv": [2, 87], "specif": [2, 3, 4, 7, 14, 16, 26, 27, 29, 30, 36, 53, 56, 60, 66, 73, 98, 100, 101, 103, 104, 105, 108, 110, 114], "scientif": [2, 3, 15, 85, 104, 105], "technic": [2, 3, 4, 88], "problem": [2, 3, 4, 13, 61, 68, 87, 99], "option": [2, 9, 10, 14, 16, 19, 22, 23, 24, 30, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 57, 61, 66, 67, 82, 83, 95, 100, 103, 104, 105, 108, 109, 114], "regist": [2, 44], "registri": 2, "advertis": [2, 105], "broader": 2, "continu": [2, 3, 19, 27, 48, 89, 94, 102, 103, 105, 109, 114], "against": [2, 4, 102, 105], "latest": [2, 3, 15, 100, 108], "make": [2, 3, 4, 7, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 28, 33, 34, 38, 39, 40, 42, 43, 44, 45, 49, 53, 55, 56, 98, 100, 102, 103, 106, 108, 109, 111, 112, 114], "peopl": [2, 3, 102], "togeth": [2, 53, 99, 103, 112], "daunt": 2, "aspect": 2, "stick": [2, 50], "guidelin": [2, 105], "process": [2, 3, 7, 15, 17, 18, 19, 23, 24, 26, 27, 48, 67, 102, 105, 108, 114], "straightforward": [2, 53, 103, 106], "mostli": [2, 15], "troubl": [2, 40], "As": [2, 3, 4, 10, 12, 13, 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10, 11, 16, 18, 19, 25, 33, 34, 35, 39, 41, 46, 47, 53, 55, 57, 61, 100, 104, 105, 109], "squar": [6, 7, 8, 9, 11, 12, 15, 16, 24, 38, 104, 105], "deviat": [6, 7, 8, 9, 11, 30, 37, 39, 42, 44, 83, 104], "pairwis": [6, 7, 8, 13, 14, 19, 39, 40], "rmsd": [6, 7, 8, 9, 10, 11, 14, 30, 33, 41, 46, 57, 104, 110], "fluctuat": [6, 7, 8, 13, 19, 27, 34], "contact": [6, 99, 104], "wise": [6, 7, 17, 23, 53], "fraction": [6, 7, 17, 18, 20, 21, 76], "nativ": [6, 7, 15, 17, 20, 21, 63, 100, 104], "q1": [6, 7, 17, 18, 19, 21], "q2": [6, 7, 17, 18, 19, 21], "cutoff": [6, 7, 17, 18, 20, 26, 38, 57, 106], "write": [6, 7, 9, 11, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 30, 34, 46, 48, 50, 52, 61, 62, 64, 68, 78, 90, 99, 105, 111, 113, 114], "harmon": [6, 7, 19, 20, 33, 41, 87, 104], "ensembl": [6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 41, 46, 48, 49, 50, 55, 104], "cluster": [6, 7, 15, 41, 44, 46], "dimens": [6, 22, 23, 26, 29, 37, 41, 49, 50, 55, 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57, 98, 104], "motion": [7, 32, 34, 38], "physic": [7, 32, 33, 34, 104], "state": [7, 12, 13, 14, 15, 19, 32, 33, 34, 38, 53, 102, 103, 104, 111], "represent": [7, 32, 48, 67, 76, 96, 105, 112, 114], "explor": [7, 15, 32], "techniqu": [7, 32, 33, 34], "varianc": [7, 32, 34, 42, 43], "largest": [7, 32, 34, 46, 108], "uncorrel": [7, 27, 32, 34], "success": [7, 32, 34, 46], "essenti": [7, 32, 33, 34, 104, 108], "subspac": [7, 32, 34, 43], "visualis": [7, 9, 10, 19, 22, 23, 24, 32, 33, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 50, 55, 99], "repres": [7, 12, 13, 15, 20, 27, 32, 33, 34, 38, 39, 40, 42, 43, 44, 48, 50, 53, 57, 60, 67, 103, 109], "neighour": [7, 32, 33], "geometri": [7, 13, 23, 30, 32, 33, 37, 39, 48, 50, 53, 104, 106, 109, 112], "intrins": [7, 32, 33], "manifold": [7, 32, 33], "suitabl": [7, 16, 32, 33, 49], "sampl": [7, 9, 10, 11, 12, 13, 18, 19, 20, 21, 30, 32, 33, 34, 39, 42, 43, 44, 53, 104], "replica": [7, 32, 33], "exchang": [7, 32, 33], "simul": [7, 9, 10, 11, 12, 13, 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101, "visual": [101, 108], "prepar": 102, "releas": [102, 105], "polici": 102, "typic": 102, "workflow": [102, 112], "summari": 102, "task": 102, "readi": 102, "packag": 102, "complet": 102, "manual": 102, "upload": 102, "cirru": [102, 108], "ci": [102, 108], "wheel": 102, "temporari": [102, 108], "forg": 102, "blog": 102, "post": 102, "outlin": 102, "increment": 102, "clean": 102, "up": 102, "old": 102, "In": 103, "transfer": 103, "output": 103, "pickl": 103, "6": 105, "bug": 105, "fix": 105, "contributor": 105, "0": 105, "major": 105, "enhanc": 105, "deprec": 105, "5": 105, "enchanc": 105, "4": 105, "3": 105, "czi": 105, "eoss": 105, "perform": 105, "improv": 105, "known": 105, "failur": 105, "issu": 105, "boolean": 106, "connect": [106, 109], "preexist": 106, "nucleic": 107, "acid": 107, "nucleobas": 107, "sugar": 107, "coverag": 108, "continu": 108, "integr": 108, "tool": 108, "action": 108, "azur": 108, "codecov": 108, "convent": 108, "assert": 108, "except": 108, "warn": 108, "fail": 108, "skip": 108, "fixtur": 108, "same": 108, "directori": 108, "canon": 109, "valu": 109, "level": 109, "object": 109, "convers": 113, "speed": 113, "forc": 113, "energi": 113, "scratch": 114, "properti": 114}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "nbsphinx": 4, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Advanced topology concepts": [[0, "advanced-topology-concepts"]], "Adding a Residue or Segment to a Universe": [[0, "adding-a-residue-or-segment-to-a-universe"]], "Molecules": [[0, "molecules"]], "Adding custom TopologyAttrs": [[0, "adding-custom-topologyattrs"]], "AtomGroup": [[1, "atomgroup"]], "Creating an AtomGroup": [[1, "creating-an-atomgroup"]], "Atom selection language": [[1, "atom-selection-language"], [106, "atom-selection-language"]], "Indexing and slicing": [[1, "indexing-and-slicing"]], "Group operators and set methods": [[1, "group-operators-and-set-methods"]], "Groupby and split": [[1, "groupby-and-split"]], "Constructing from Atoms": [[1, "constructing-from-atoms"]], "Order and uniqueness": [[1, "order-and-uniqueness"]], "Empty AtomGroups": [[1, "empty-atomgroups"]], "Dynamically updating AtomGroups": [[1, "dynamically-updating-atomgroups"]], "Methods": [[1, "methods"]], "Contributing to MDAnalysis": [[2, "contributing-to-mdanalysis"], [16, "Contributing-to-MDAnalysis"]], "Where to start?": [[2, "where-to-start"]], "Version control, Git, and GitHub": [[2, "version-control-git-and-github"]], "Getting started with Git": [[2, "getting-started-with-git"]], "Contributing to the main codebase": [[3, "contributing-to-the-main-codebase"]], "Working with the code": [[3, "working-with-the-code"]], "Forking": [[3, "forking"]], "Creating a development environment": [[3, "creating-a-development-environment"], [4, "creating-a-development-environment"]], "With conda": [[3, "with-conda"], [3, "id1"]], "With pip and virtualenv": [[3, "with-pip-and-virtualenv"], [3, "id2"]], "On a Mac": [[3, "on-a-mac"]], "Building MDAnalysis": [[3, "building-mdanalysis"]], "Branches in MDAnalysis": [[3, "branches-in-mdanalysis"]], "Creating a branch": [[3, "creating-a-branch"]], "Writing new code": [[3, "writing-new-code"]], "Code formatting in Python": [[3, "code-formatting-in-python"]], "Modules and dependencies": [[3, "modules-and-dependencies"]], "Developing in Cython": [[3, "developing-in-cython"]], "Testing your code": [[3, "testing-your-code"]], "Documenting your code": [[3, "documenting-your-code"]], "Ensure PEP8 compliance (mandatory) and format your code with Darker (optional)": [[3, "ensure-pep8-compliance-mandatory-and-format-your-code-with-darker-optional"]], "Adding your code to MDAnalysis": [[3, "adding-your-code-to-mdanalysis"]], "Committing your code": [[3, "committing-your-code"]], "Pushing your code to GitHub": [[3, "pushing-your-code-to-github"]], "Rebasing your code": [[3, "rebasing-your-code"]], "Creating a pull request": [[3, "creating-a-pull-request"]], "Working with the code documentation": [[3, "working-with-the-code-documentation"]], "Building the documentation": [[3, "building-the-documentation"]], "Where to write docstrings": [[3, "where-to-write-docstrings"]], "Guidelines for writing docstrings": [[3, "guidelines-for-writing-docstrings"]], "Documenting changes": [[3, "documenting-changes"]], "Writing docs for abstract base classes": [[3, "writing-docs-for-abstract-base-classes"]], "Adding your documentation to MDAnalysis": [[3, "adding-your-documentation-to-mdanalysis"]], "Viewing the documentation interactively": [[3, "viewing-the-documentation-interactively"]], "Contributing to the user guide": [[4, "contributing-to-the-user-guide"]], "Forking and cloning the User Guide": [[4, "forking-and-cloning-the-user-guide"]], "Building the user guide": [[4, "building-the-user-guide"]], "Saving state in Jupyter notebooks": [[4, "saving-state-in-jupyter-notebooks"]], "Test with pytest and nbval": [[4, "test-with-pytest-and-nbval"]], "Sanitization": [[4, "sanitization"]], "On the hole2 notebook": [[4, "on-the-hole2-notebook"]], "Adding changes to the UserGuide": [[4, "adding-changes-to-the-userguide"]], "Automatically building documentation": [[4, "automatically-building-documentation"]], "Using pre-commit hooks": [[4, "using-pre-commit-hooks"]], "Example data": [[5, "example-data"]], "MDAnalysisTests": [[5, "mdanalysistests"]], "MDAnalysisData": [[5, "mdanalysisdata"]], "Examples": [[6, "examples"]], "General": [[6, null]], "Analysis": [[6, null], [7, "analysis"], [53, "Analysis"]], "Imports and dependencies": [[7, "imports-and-dependencies"]], "Alignments and RMS fitting": [[7, "alignments-and-rms-fitting"], [8, "alignments-and-rms-fitting"]], "Distances and contacts": [[7, "distances-and-contacts"], [17, "distances-and-contacts"]], "Trajectory similarity": [[7, "trajectory-similarity"], [41, "trajectory-similarity"]], "Structure": [[7, "structure"], [35, "structure"]], "Volumetric analyses": [[7, "volumetric-analyses"], [47, "volumetric-analyses"]], "Dimension reduction": [[7, "dimension-reduction"], [32, "dimension-reduction"]], "Polymers and membranes": [[7, "polymers-and-membranes"], [29, "polymers-and-membranes"]], "Hydrogen Bond Analysis": [[7, "hydrogen-bond-analysis"], [25, "hydrogen-bond-analysis"]], "Aligning a structure to another": [[9, "Aligning-a-structure-to-another"]], "Loading files": [[9, "Loading-files"], [10, "Loading-files"], [11, "Loading-files"], [12, "Loading-files"], [13, "Loading-files"], [14, "Loading-files"], [15, "Loading-files"], [16, "Loading-files"], [18, "Loading-files"], [19, "Loading-files"], [20, "Loading-files"], [21, "Loading-files"], [22, "Loading-files"], [23, "Loading-files"], [24, "Loading-files"], [26, "Loading-files"], [27, "Loading-files"], [28, "Loading-files"], [31, "Loading-files"], [33, "Loading-files"], [34, "Loading-files"], [36, "Loading-files"], [37, "Loading-files"], [38, "Loading-files"], [39, "Loading-files"], [40, "Loading-files"], [42, "Loading-files"], [43, "Loading-files"], [44, "Loading-files"], [45, "Loading-files"], [46, "Loading-files"], [48, "Loading-files"], [49, "Loading-files"], [55, "Loading-files"]], "Aligning a structure with align.alignto": [[9, "Aligning-a-structure-with-align.alignto"]], "References": [[9, "References"], [10, "References"], [11, "References"], [12, "References"], [13, "References"], [14, "References"], [15, "References"], [16, "References"], [18, "References"], [19, "References"], [20, "References"], [21, "References"], [22, "References"], [23, "References"], [24, "References"], [26, "References"], [27, "References"], [28, "References"], [30, "References"], [31, "References"], [33, "References"], [34, "References"], [36, "References"], [37, "References"], [38, "References"], [39, "References"], [40, "References"], [42, "References"], [43, "References"], [44, "References"], [45, "References"], [45, "id5"], [46, "References"], [48, "References"], [49, "References"], [50, "References"], [52, "References"], [53, "References"], [55, "References"], [104, "references"]], "Aligning a trajectory to a reference": [[10, "Aligning-a-trajectory-to-a-reference"]], "Aligning a trajectory with AlignTraj": [[10, "Aligning-a-trajectory-with-AlignTraj"]], "Copying coordinates into a new Universe": [[10, "Copying-coordinates-into-a-new-Universe"]], "Writing trajectories to a file": [[10, "Writing-trajectories-to-a-file"]], "Aligning a trajectory to itself": [[11, "Aligning-a-trajectory-to-itself"]], "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"]], "Calculating the pairwise RMSD of a trajectory": [[12, "Calculating-the-pairwise-RMSD-of-a-trajectory"]], "Background": [[12, "Background"], [13, "Background"], [14, "Background"], [15, "Background"], [18, "Background"], [19, "Background"], [20, "Background"], [21, "Background"], [30, "Background"]], "Pairwise RMSD of a trajectory to itself": [[12, "Pairwise-RMSD-of-a-trajectory-to-itself"]], "Pairwise RMSD between two trajectories": [[12, "Pairwise-RMSD-between-two-trajectories"]], "Calculating the root mean square deviation of atomic structures": [[13, "Calculating-the-root-mean-square-deviation-of-atomic-structures"]], "RMSD between two sets of coordinates": [[13, "RMSD-between-two-sets-of-coordinates"]], "RMSD of a Universe with multiple selections": [[13, "RMSD-of-a-Universe-with-multiple-selections"]], "Plotting the data": [[13, "Plotting-the-data"]], "RMSD of an AtomGroup with multiple selections": [[13, "RMSD-of-an-AtomGroup-with-multiple-selections"]], "Weighted RMSD of a trajectory": [[13, "Weighted-RMSD-of-a-trajectory"]], "Mass": [[13, "Mass"]], "Custom weights": [[13, "Custom-weights"]], "Calculating the root mean square fluctuation over a trajectory": [[14, "Calculating-the-root-mean-square-fluctuation-over-a-trajectory"]], "Creating an average structure": [[14, "Creating-an-average-structure"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Plotting RMSF": [[14, "Plotting-RMSF"]], "Visualising RMSF as B-factors": [[14, "Visualising-RMSF-as-B-factors"]], "Parallelizing analysis": [[15, "Parallelizing-analysis"]], "Radius of gyration": [[15, "Radius-of-gyration"], [16, "Radius-of-gyration"]], "Serial Analysis": [[15, "Serial-Analysis"]], "Parallelization in a simple per-frame fashion": [[15, "Parallelization-in-a-simple-per-frame-fashion"]], "Frame-wise form of the function": [[15, "Frame-wise-form-of-the-function"]], "Parallelization with multiprocessing": [[15, "Parallelization-with-multiprocessing"]], "Parallelization with dask": [[15, "Parallelization-with-dask"]], "Parallelization in a split-apply-combine fashion": [[15, "Parallelization-in-a-split-apply-combine-fashion"]], "Block analysis function": [[15, "Block-analysis-function"]], "Split the trajectory": [[15, "Split-the-trajectory"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Combine the results": [[15, "Combine-the-results"]], "Other possible parallelism approaches for multiple analyses": [[15, "Other-possible-parallelism-approaches-for-multiple-analyses"]], "See Also": [[15, "See-Also"]], "Writing your own trajectory analysis": [[16, "Writing-your-own-trajectory-analysis"]], "Creating an analysis from a function": [[16, "Creating-an-analysis-from-a-function"]], "Transforming a function into a class": [[16, "Transforming-a-function-into-a-class"]], "Creating your own class": [[16, "Creating-your-own-class"]], "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"]], "Write your own native contacts analysis method": [[18, "Write-your-own-native-contacts-analysis-method"]], "Defining salt bridges": [[18, "Defining-salt-bridges"]], "Define your own function": [[18, "Define-your-own-function"]], "Plotting": [[18, "Plotting"], [19, "Plotting"], [19, "id6"], [19, "id7"], [20, "Plotting"], [21, "Plotting"], [22, "Plotting"], [22, "id4"], [23, "Plotting"], [24, "Plotting"], [24, "id4"], [30, "Plotting"], [30, "id8"], [37, "Plotting"], [42, "Plotting"], [42, "id5"], [42, "id6"], [44, "Plotting"], [44, "id5"], [44, "id6"], [45, "Plotting"], [46, "Plotting"], [46, "id5"]], "Fraction of native contacts over a trajectory": [[19, "Fraction-of-native-contacts-over-a-trajectory"]], "Defining the groups for contact analysis": [[19, "Defining-the-groups-for-contact-analysis"], [21, "Defining-the-groups-for-contact-analysis"]], "Hard cutoff with a single reference": [[19, "Hard-cutoff-with-a-single-reference"]], "Radius cutoff": [[19, "Radius-cutoff"]], "Soft cutoff and multiple references": [[19, "Soft-cutoff-and-multiple-references"]], "Multiple references": [[19, "Multiple-references"]], "Soft cutoff": [[19, "Soft-cutoff"]], "Q1 vs Q2 contact analysis": [[20, "Q1-vs-Q2-contact-analysis"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Contact analysis: number of contacts within a cutoff": [[21, "Contact-analysis:-number-of-contacts-within-a-cutoff"]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Atom-wise distances between matching AtomGroups": [[22, "Atom-wise-distances-between-matching-AtomGroups"]], "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"]], "All distances between two selections": [[23, "All-distances-between-two-selections"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Plotting distance as a heatmap": [[23, "Plotting-distance-as-a-heatmap"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "All distances within a selection": [[24, "All-distances-within-a-selection"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating hydrogen bonds: the basics": [[26, "Calculating-hydrogen-bonds:-the-basics"]], "Hydrogen bonds": [[26, "Hydrogen-bonds"]], "Find water-water hydrogen bonds": [[26, "Find-water-water-hydrogen-bonds"]], "Accessing the results": [[26, "Accessing-the-results"]], "Helper functions": [[26, "Helper-functions"]], "Further analysis": [[26, "Further-analysis"]], "Store data": [[26, "Store-data"]], "Calculating hydrogen bond lifetimes": [[27, "Calculating-hydrogen-bond-lifetimes"]], "Find all hydrogen bonds": [[27, "Find-all-hydrogen-bonds"], [28, "Find-all-hydrogen-bonds"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Intermittent lifetime": [[27, "Intermittent-lifetime"]], "Hydrogen bond lifetime of individual hydrogen bonds": [[27, "Hydrogen-bond-lifetime-of-individual-hydrogen-bonds"]], "Calculating hydrogen bonds: advanced selections": [[28, "Calculating-hydrogen-bonds:-advanced-selections"]], "Use guess_acceptors and guess_hydrogens to create atom selections": [[28, "Use-guess_acceptors-and-guess_hydrogens-to-create-atom-selections"]], "More advanced selections": [[28, "More-advanced-selections"]], "Hydrogen bonds between specific groups": [[28, "Hydrogen-bonds-between-specific-groups"]], "Analysing pore dimensions with HOLE2": [[30, "Analysing-pore-dimensions-with-HOLE2"]], "Using HOLE with a PDB file": [[30, "Using-HOLE-with-a-PDB-file"]], "Using HOLE with a trajectory": [[30, "Using-HOLE-with-a-trajectory"]], "Working with the data": [[30, "Working-with-the-data"]], "Visualising the VMD surface": [[30, "Visualising-the-VMD-surface"]], "Ordering HOLE profiles with an order parameter": [[30, "Ordering-HOLE-profiles-with-an-order-parameter"]], "Deleting HOLE files": [[30, "Deleting-HOLE-files"]], "Determining the persistence length of a polymer": [[31, "Determining-the-persistence-length-of-a-polymer"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Non-linear dimension reduction to diffusion maps": [[33, "Non-linear-dimension-reduction-to-diffusion-maps"]], "Diffusion maps": [[33, "Diffusion-maps"]], "Principal component analysis of a trajectory": [[34, "Principal-component-analysis-of-a-trajectory"]], "Principal component analysis": [[34, "Principal-component-analysis"]], "Visualising projections into a reduced dimensional space": [[34, "Visualising-projections-into-a-reduced-dimensional-space"]], "Measuring convergence with cosine content": [[34, "Measuring-convergence-with-cosine-content"]], "Average radial distribution functions": [[36, "Average-radial-distribution-functions"]], "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 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"]], "Protein dihedral angle analysis": [[37, "Protein-dihedral-angle-analysis"]], "Selecting dihedral atom groups": [[37, "Selecting-dihedral-atom-groups"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Ramachandran analysis": [[37, "Ramachandran-analysis"]], "Janin analysis": [[37, "Janin-analysis"]], "Elastic network analysis": [[38, "Elastic-network-analysis"]], "Using a Gaussian network model": [[38, "Using-a-Gaussian-network-model"]], "Using a Gaussian network model with only close contacts": [[38, "Using-a-Gaussian-network-model-with-only-close-contacts"]], "Helix analysis": [[39, "Helix-analysis"], [39, "id6"]], "Running the analysis": [[39, "Running-the-analysis"]], "Calculating the RDF atom-to-atom": [[40, "Calculating-the-RDF-atom-to-atom"]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "The site-specific RDF without densities": [[40, "The-site-specific-RDF-without-densities"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, "Calculating-the-Clustering-Ensemble-Similarity-between-ensembles"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Trying out different clustering parameters": [[42, "Trying-out-different-clustering-parameters"]], "Estimating the error in a clustering ensemble similarity analysis": [[42, "Estimating-the-error-in-a-clustering-ensemble-similarity-analysis"]], "Evaluating convergence": [[43, "Evaluating-convergence"]], "Evaluating convergence with similarity measures": [[43, "Evaluating-convergence-with-similarity-measures"]], "Using default arguments with clustering ensemble similarity": [[43, "Using-default-arguments-with-clustering-ensemble-similarity"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Using default arguments with dimension reduction ensemble similarity": [[43, "Using-default-arguments-with-dimension-reduction-ensemble-similarity"]], "Comparing different dimensionality reduction methods": [[43, "Comparing-different-dimensionality-reduction-methods"]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, "Calculating-the-Dimension-Reduction-Ensemble-Similarity-between-ensembles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Trying out different dimension reduction parameters": [[44, "Trying-out-different-dimension-reduction-parameters"]], "Estimating the error in a dimension reduction ensemble similarity analysis": [[44, "Estimating-the-error-in-a-dimension-reduction-ensemble-similarity-analysis"]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, "Calculating-the-Harmonic-Ensemble-Similarity-between-ensembles"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Comparing the geometric similarity of trajectories": [[46, "Comparing-the-geometric-similarity-of-trajectories"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Generating paths": [[46, "Generating-paths"]], "Hausdorff method": [[46, "Hausdorff-method"]], "Discrete Fr\u00e9chet distances": [[46, "Discrete-Fr\u00e9chet-distances"]], "Calculating the solvent density around a protein": [[48, "Calculating-the-solvent-density-around-a-protein"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Visualisation": [[48, "Visualisation"]], "matplotlib (3D static plot)": [[48, "matplotlib-(3D-static-plot)"]], "nglview (interactive)": [[48, "nglview-(interactive)"]], "scikit-image (triangulated surface)": [[48, "scikit-image-(triangulated-surface)"]], "pyvista (3D surface)": [[48, "pyvista-(3D-surface)"]], "2D averaging": [[48, "2D-averaging"]], "Computing mass and charge density on each axis": [[49, "Computing-mass-and-charge-density-on-each-axis"]], "Constructing, modifying, and adding to a Universe": [[50, "Constructing,-modifying,-and-adding-to-a-Universe"]], "Creating and populating a Universe with water": [[50, "Creating-and-populating-a-Universe-with-water"]], "Creating a blank Universe": [[50, "Creating-a-blank-Universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding positions": [[50, "Adding-positions"]], "Adding bonds": [[50, "Adding-bonds"]], "Merging with a protein": [[50, "Merging-with-a-protein"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Tiling into a larger Universe": [[50, "Tiling-into-a-larger-Universe"]], "Acknowledgments": [[50, "Acknowledgments"]], "Other": [[51, "other"]], "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms": [[52, "Using-ParmEd-with-MDAnalysis-and-OpenMM-to-simulate-a-selection-of-atoms"]], "Loading files: the difference between ParmEd and MDAnalysis": [[52, "Loading-files:-the-difference-between-ParmEd-and-MDAnalysis"]], "Using MDAnalysis to select atoms": [[52, "Using-MDAnalysis-to-select-atoms"]], "Using ParmEd and OpenMM to create a simulation system": [[52, "Using-ParmEd-and-OpenMM-to-create-a-simulation-system"]], "Quick start guide": [[53, "Quick-start-guide"]], "Overview": [[53, "Overview"]], "Loading a structure or trajectory": [[53, "Loading-a-structure-or-trajectory"]], "Working with groups of atoms": [[53, "Working-with-groups-of-atoms"]], "Selecting atoms": [[53, "Selecting-atoms"]], "Getting atom information from AtomGroups": [[53, "Getting-atom-information-from-AtomGroups"]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Working with trajectories": [[53, "Working-with-trajectories"]], "Dynamic selection": [[53, "Dynamic-selection"]], "Writing out coordinates": [[53, "Writing-out-coordinates"]], "Single frame": [[53, "Single-frame"]], "Trajectories": [[53, "Trajectories"], [56, "trajectories"], [111, "trajectories"]], "RMSD": [[53, "RMSD"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Transformations": [[54, "transformations"]], "Centering a trajectory in the box": [[55, "Centering-a-trajectory-in-the-box"]], "Before transformation": [[55, "Before-transformation"]], "Unwrapping the protein": [[55, "Unwrapping-the-protein"]], "Centering in the box": [[55, "Centering-in-the-box"]], "Wrapping the solvent back into the box": [[55, "Wrapping-the-solvent-back-into-the-box"]], "Doing all this on-the-fly": [[55, "Doing-all-this-on-the-fly"]], "Frequently asked questions": [[56, "frequently-asked-questions"]], "Why do the atom positions change over trajectories?": [[56, "why-do-the-atom-positions-change-over-trajectories"]], "Auxiliary files": [[57, "auxiliary-files"]], "Supported formats": [[57, "supported-formats"]], "XVG Files": [[57, "xvg-files"]], "Reading data directly": [[57, "reading-data-directly"]], "Loading data into a Universe": [[57, "loading-data-into-a-universe"]], "Passing arguments to auxiliary data": [[57, "passing-arguments-to-auxiliary-data"]], "Iterating over auxiliary data": [[57, "iterating-over-auxiliary-data"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[57, "recreating-auxiliaries"]], "EDR Files": [[57, "edr-files"]], "Standalone Usage": [[57, "standalone-usage"]], "Unit Handling": [[57, "unit-handling"]], "Use with Trajectories": [[57, "use-with-trajectories"]], "Selecting Trajectory Frames Based on Auxiliary Data": [[57, "selecting-trajectory-frames-based-on-auxiliary-data"]], "Memory Usage": [[57, "memory-usage"]], "Coordinates": [[58, "coordinates"], [61, "coordinates"]], "Table of supported coordinate readers and the information read": [[58, "id2"], [61, "id12"]], "Format reference": [[59, "format-reference"]], "Guessing": [[60, "guessing"]], "Masses": [[60, "masses"]], "Types": [[60, "types"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Format overview": [[61, "format-overview"]], "Table of all supported formats in MDAnalysis": [[61, "id10"]], "Topology": [[61, "topology"], [97, "topology"]], "Table of supported topology parsers and the attributes read": [[61, "id11"], [97, "id1"]], "chemfiles (chemfiles Trajectory or file)": [[62, "chemfiles-chemfiles-trajectory-or-file"]], "CONFIG (DL_Poly Config)": [[63, "config-dl-poly-config"]], "HISTORY (DL_Poly Config)": [[63, "history-dl-poly-config"]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, "coor-nambdin-namd-binary-restart-files"]], "CRD (CHARMM CARD files)": [[65, "crd-charmm-card-files"]], "Reading in": [[65, "reading-in"], [66, "reading-in"], [67, "reading-in"], [70, "reading-in"], [71, "reading-in"], [72, "reading-in"], [76, "reading-in"], [79, "reading-in"], [81, "reading-in"], [82, "reading-in"], [83, "reading-in"], [84, "reading-in"], [85, "reading-in"], [88, "reading-in"], [89, "reading-in"], [94, "reading-in"], [95, "reading-in"]], "Writing out": [[65, "writing-out"], [66, "writing-out"], [67, "writing-out"], [71, "writing-out"], [79, "writing-out"], [81, "writing-out"], [82, "writing-out"], [83, "writing-out"], [89, "writing-out"]], "DATA (LAMMPS)": [[66, "data-lammps"]], "DCD (CHARMM, NAMD, or LAMMPS trajectory)": [[67, "dcd-charmm-namd-or-lammps-trajectory"]], "DCD (Flexible LAMMPS trajectory)": [[68, "dcd-flexible-lammps-trajectory"]], "DMS (Desmond Molecular Structure files)": [[69, "dms-desmond-molecular-structure-files"]], "GMS (Gamess trajectory)": [[70, "gms-gamess-trajectory"]], "GRO (GROMACS structure file)": [[71, "gro-gromacs-structure-file"]], "GSD (HOOMD GSD file)": [[72, "gsd-hoomd-gsd-file"]], "IN, FHIAIMS (FHI-aims input files)": [[73, "in-fhiaims-fhi-aims-input-files"]], "INPCRD, RESTRT (AMBER restart files)": [[74, "inpcrd-restrt-amber-restart-files"]], "ITP (GROMACS portable topology files)": [[75, "itp-gromacs-portable-topology-files"]], "LAMMPSDUMP (LAMMPS ascii dump file)": [[76, "lammpsdump-lammps-ascii-dump-file"]], "MMTF (Macromolecular Transmission Format)": [[77, "mmtf-macromolecular-transmission-format"]], "MOL2 (Tripos structure)": [[78, "mol2-tripos-structure"]], "MOL2 specification": [[78, "mol2-specification"]], "NCDF, NC (AMBER NetCDF trajectory)": [[79, "ncdf-nc-amber-netcdf-trajectory"]], "ParmEd (ParmEd Structure)": [[80, "parmed-parmed-structure"]], "PDB, ENT (Standard PDB file)": [[81, "pdb-ent-standard-pdb-file"]], "PDB specification": [[81, "pdb-specification"]], "CRYST1 fields": [[81, "id1"]], "ATOM/HETATM fields": [[81, "id2"]], "PDBQT (Autodock structure)": [[82, "pdbqt-autodock-structure"]], "PDBQT specification": [[82, "pdbqt-specification"]], "PDB format with AutoDOCK extensions for the PDBQT format.": [[82, "id1"]], "PQR file (PDB2PQR / APBS)": [[83, "pqr-file-pdb2pqr-apbs"]], "PQR specification": [[83, "pqr-specification"]], "PSF (CHARMM, NAMD, or XPLOR protein structure file)": [[84, "psf-charmm-namd-or-xplor-protein-structure-file"]], "PSF specification": [[84, "psf-specification"]], "TNG (Trajectory Next Generation)": [[85, "tng-trajectory-next-generation"]], "TOP, PRMTOP, PARM7 (AMBER topology)": [[86, "top-prmtop-parm7-amber-topology"]], "AMBER specification": [[86, "amber-specification"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Developer notes": [[86, "developer-notes"], [87, "developer-notes"], [89, "developer-notes"], [91, "developer-notes"]], "TPR (GROMACS run topology files)": [[87, "tpr-gromacs-run-topology-files"]], "Supported versions": [[87, "supported-versions"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[87, "id1"]], "TPR specification": [[87, "tpr-specification"]], "segid and chainID": [[87, "segid-and-chainid"]], "Bonds": [[87, "bonds"]], "GROMACS entries used to create bonds.": [[87, "id2"]], "GROMACS entries used to create angles.": [[87, "id3"]], "GROMACS entries used to create dihedrals.": [[87, "id4"]], "GROMACS entries used to create improper dihedrals.": [[87, "id5"]], "TRJ, MDCRD, CRDBOX (AMBER ASCII trajectory)": [[88, "trj-mdcrd-crdbox-amber-ascii-trajectory"]], "TRR (GROMACS lossless trajectory file)": [[89, "trr-gromacs-lossless-trajectory-file"]], "TRZ (IBIsCO and YASP trajectory)": [[90, "trz-ibisco-and-yasp-trajectory"]], "TXYZ, ARC (Tinker)": [[91, "txyz-arc-tinker"]], "XML (HOOMD)": [[92, "xml-hoomd"]], "XPDB (Extended PDB file)": [[93, "xpdb-extended-pdb-file"]], "XTC (GROMACS compressed trajectory file)": [[94, "xtc-gromacs-compressed-trajectory-file"]], "XYZ trajectory": [[95, "xyz-trajectory"]], "XYZ specification": [[95, "xyz-specification"]], "Note": [[95, "note"]], "Selection exporters": [[96, "selection-exporters"]], "Supported selection exporters": [[96, "id2"]], "Writing selections": [[96, "writing-selections"]], "Single AtomGroup": [[96, "single-atomgroup"]], "Multiple selections": [[96, "multiple-selections"]], "Reading in selections": [[96, "reading-in-selections"]], "Groups of atoms": [[98, "groups-of-atoms"]], "Residues and Segments": [[98, "residues-and-segments"]], "Use case: Sequence of residues by segment": [[98, "use-case-sequence-of-residues-by-segment"]], "Use case: Atoms list grouped by residues": [[98, "use-case-atoms-list-grouped-by-residues"]], "Fragments": [[98, "fragments"]], "Welcome to MDAnalysis User Guide\u2019s documentation!": [[99, "welcome-to-mdanalysis-user-guide-s-documentation"]], "Why MDAnalysis?": [[99, "why-mdanalysis"]], "Participating": [[99, "participating"]], "Communications": [[99, "communications"]], "Installation": [[100, "installation"]], "conda": [[100, "conda"]], "pip": [[100, "pip"]], "Development versions": [[100, "development-versions"]], "Testing": [[100, "testing"]], "Custom compiler flags and optimised installations": [[100, "custom-compiler-flags-and-optimised-installations"]], "Additional datasets": [[100, "additional-datasets"]], "Module imports in MDAnalysis": [[101, "module-imports-in-mdanalysis"]], "General rules for importing": [[101, "general-rules-for-importing"]], "Module imports in MDAnalysis.analysis": [[101, "module-imports-in-mdanalysis-analysis"]], "Module imports in the test suite": [[101, "module-imports-in-the-test-suite"]], "Module dependencies in the code": [[101, "module-dependencies-in-the-code"]], "List of core module dependencies": [[101, "list-of-core-module-dependencies"]], "Modules in the \u201ccore\u201d": [[101, "modules-in-the-core"]], "Optional modules in MDAnalysis.analysis and MDAnalysis.visualization": [[101, "optional-modules-in-mdanalysis-analysis-and-mdanalysis-visualization"]], "Preparing a release": [[102, "preparing-a-release"]], "Release policy and release numbering": [[102, "release-policy-and-release-numbering"]], "Typical workflow for preparing a release": [[102, "typical-workflow-for-preparing-a-release"]], "Summary of tasks": [[102, "summary-of-tasks"]], "Getting the develop branch ready for a release": [[102, "getting-the-develop-branch-ready-for-a-release"]], "Packaging the release": [[102, "packaging-the-release"]], "Completing the release": [[102, "completing-the-release"]], "Manually upload Cirrus CI wheels (temporary)": [[102, "manually-upload-cirrus-ci-wheels-temporary"]], "Update conda-forge packages": [[102, "update-conda-forge-packages"]], "Create a release of the UserGuide": [[102, "create-a-release-of-the-userguide"]], "Create a blog post outlining the release": [[102, "create-a-blog-post-outlining-the-release"]], "Increment develop branch files ready for the next version": [[102, "increment-develop-branch-files-ready-for-the-next-version"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Reading and writing files": [[103, "reading-and-writing-files"]], "Input": [[103, "input"]], "Reading multiple trajectories": [[103, "reading-multiple-trajectories"]], "Trajectory formats": [[103, "trajectory-formats"]], "In-memory trajectories": [[103, "in-memory-trajectories"]], "Reading trajectories into memory": [[103, "reading-trajectories-into-memory"]], "Transferring trajectories into memory": [[103, "transferring-trajectories-into-memory"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "In-memory trajectories of an atom selection": [[103, "in-memory-trajectories-of-an-atom-selection"]], "Output": [[103, "output"]], "Frames and trajectories": [[103, "frames-and-trajectories"]], "Pickling": [[103, "pickling"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "MDAnalysis Release Notes": [[105, "mdanalysis-release-notes"]], "Release 2.6.1 of MDAnalysis": [[105, "release-2-6-1-of-mdanalysis"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "New Contributors": [[105, "new-contributors"], [105, "id1"], [105, "id5"], [105, "id13"]], "Release 2.6.0 of MDAnalysis": [[105, "release-2-6-0-of-mdanalysis"]], "Major changes:": [[105, "major-changes"], [105, "id2"], [105, "id8"], [105, "id14"], [105, "id19"], [105, "id24"], [105, "id30"]], "Fixes:": [[105, "fixes"], [105, "id3"], [105, "id9"], [105, "id15"], [105, "id21"], [105, "id26"], [105, "id32"]], "Enhancements:": [[105, "enhancements"], [105, "id16"], [105, "id20"], [105, "id25"], [105, "id31"]], "Changes:": [[105, "changes"], [105, "id4"], [105, "id11"], [105, "id17"], [105, "id22"], [105, "id27"], [105, "id33"]], "Deprecations:": [[105, "deprecations"], [105, "id12"], [105, "id18"], [105, "id23"], [105, "id28"], [105, "id34"]], "Release 2.5.0 of MDAnalysis": [[105, "release-2-5-0-of-mdanalysis"]], "Enchancements:": [[105, "enchancements"], [105, "id10"]], "Release 2.4.3 of MDAnalysis": [[105, "release-2-4-3-of-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id6"], [105, "id7"]], "Release 2.4.2 of MDAnalysis": [[105, "release-2-4-2-of-mdanalysis"]], "Release 2.4.1 of MDAnalysis": [[105, "release-2-4-1-of-mdanalysis"]], "Release 2.4.0 of MDAnalysis": [[105, "release-2-4-0-of-mdanalysis"]], "Release 2.3.0 of MDAnalysis": [[105, "release-2-3-0-of-mdanalysis"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Release 2.2.0 of MDAnalysis": [[105, "release-2-2-0-of-mdanalysis"]], "Known test failures:": [[105, "known-test-failures"], [105, "id29"]], "Release 2.1.0 of MDAnalysis": [[105, "release-2-1-0-of-mdanalysis"]], "Release 2.0.0 of MDAnalysis": [[105, "release-2-0-0-of-mdanalysis"]], "Notes:": [[105, "notes"]], "Known issues:": [[105, "known-issues"]], "Selection Keywords": [[106, "selection-keywords"]], "Simple selections": [[106, "simple-selections"]], "Boolean": [[106, "boolean"]], "Geometric": [[106, "geometric"]], "Similarity and connectivity": [[106, "similarity-and-connectivity"]], "Index": [[106, "index"]], "Preexisting selections and modifiers": [[106, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[106, "dynamic-selections"]], "Ordered selections": [[106, "ordered-selections"]], "Standard residues in MDAnalysis selections": [[107, "standard-residues-in-mdanalysis-selections"]], "Proteins": [[107, "proteins"]], "Protein backbone": [[107, "protein-backbone"]], "Nucleic acids": [[107, "nucleic-acids"]], "Nucleic backbone": [[107, "nucleic-backbone"]], "Nucleobases": [[107, "nucleobases"]], "Nucleic sugars": [[107, "nucleic-sugars"]], "Tests in MDAnalysis": [[108, "tests-in-mdanalysis"]], "Running the test suite": [[108, "running-the-test-suite"]], "Testing in parallel": [[108, "testing-in-parallel"]], "Test coverage": [[108, "test-coverage"]], "Continuous Integration tools": [[108, "continuous-integration-tools"]], "GitHub Actions": [[108, "github-actions"]], "Azure": [[108, "azure"]], "Cirrus CI": [[108, "cirrus-ci"]], "Codecov": [[108, "codecov"]], "Writing new tests": [[108, "writing-new-tests"]], "General conventions": [[108, "general-conventions"]], "Assertions": [[108, "assertions"]], "Testing exceptions and warnings": [[108, "testing-exceptions-and-warnings"]], "Failing tests": [[108, "failing-tests"]], "Skipping tests": [[108, "skipping-tests"]], "Fixtures": [[108, "fixtures"]], "Testing the same function with different inputs": [[108, "testing-the-same-function-with-different-inputs"]], "Temporary files and directories": [[108, "temporary-files-and-directories"]], "Module imports": [[108, "module-imports"]], "Tests for analysis and visualization modules": [[108, "tests-for-analysis-and-visualization-modules"]], "Using test data files": [[108, "using-test-data-files"]], "The topology system": [[109, "the-topology-system"]], "Topology attributes": [[109, "topology-attributes"]], "Canonical attributes": [[109, "canonical-attributes"]], "Format-specific attributes": [[109, "format-specific-attributes"]], "Connectivity information": [[109, "connectivity-information"]], "Adding TopologyAttrs": [[109, "adding-topologyattrs"]], "Modifying TopologyAttrs": [[109, "modifying-topologyattrs"]], "Default values and attribute levels": [[109, "default-values-and-attribute-levels"]], "Topology objects": [[109, "topology-objects"]], "Adding to a Universe": [[109, "adding-to-a-universe"]], "Creating with an AtomGroup": [[109, "creating-with-an-atomgroup"]], "Deleting from a Universe": [[109, "deleting-from-a-universe"]], "Topology-specific methods": [[109, "topology-specific-methods"]], "Slicing trajectories": [[110, "slicing-trajectories"]], "On-the-fly transformations": [[112, "on-the-fly-transformations"]], "Example workflows": [[112, "example-workflows"]], "Custom transformations": [[112, "custom-transformations"]], "Units and constants": [[113, "units-and-constants"]], "Base units in MDAnalysis": [[113, "id1"]], "Unit conversion": [[113, "unit-conversion"]], "Constants": [[113, "constants"]], "Length": [[113, "length"]], "Density": [[113, "density"]], "Time": [[113, "time"]], "Charge": [[113, "charge"]], "Speed": [[113, "speed"]], "Force": [[113, "force"]], "Energy": [[113, "energy"]], "Universe": [[114, "universe"]], "Creating a Universe": [[114, "creating-a-universe"]], "Loading from files": [[114, "loading-from-files"]], "Constructing from AtomGroups": [[114, "constructing-from-atomgroups"]], "Constructing from scratch": [[114, "constructing-from-scratch"]], "Guessing topology attributes": [[114, "guessing-topology-attributes"]], "Universe properties and methods": [[114, "universe-properties-and-methods"]]}, "indexentries": {"x y z": [[83, "term-X-Y-Z"]], "atomname": [[83, "term-atomName"]], "chainid": [[83, "term-chainID"]], "charge": [[83, "term-charge"]], "radius": [[83, "term-radius"]], "recordname": [[83, "term-recordName"]], "residuename": [[83, "term-residueName"]], "residuenumber": [[83, "term-residueNumber"]], "serial": [[83, "term-serial"]], "duecredit_enable": [[104, "index-0"]], "environment variable": [[104, "index-0"]]}}) \ No newline at end of file +Search.setIndex({"docnames": ["advanced_topology", "atomgroup", "contributing", "contributing_code", "contributing_docs", "datasets", "examples/README", "examples/analysis/README", "examples/analysis/alignment_and_rms/README", "examples/analysis/alignment_and_rms/aligning_structure_to_another", "examples/analysis/alignment_and_rms/aligning_trajectory", "examples/analysis/alignment_and_rms/aligning_trajectory_to_frame", "examples/analysis/alignment_and_rms/pairwise_rmsd", "examples/analysis/alignment_and_rms/rmsd", "examples/analysis/alignment_and_rms/rmsf", "examples/analysis/custom_parallel_analysis", "examples/analysis/custom_trajectory_analysis", "examples/analysis/distances_and_contacts/README", "examples/analysis/distances_and_contacts/contacts_custom", "examples/analysis/distances_and_contacts/contacts_native_fraction", "examples/analysis/distances_and_contacts/contacts_q1q2", "examples/analysis/distances_and_contacts/contacts_within_cutoff", "examples/analysis/distances_and_contacts/distances_between_atomgroups", "examples/analysis/distances_and_contacts/distances_between_selections", "examples/analysis/distances_and_contacts/distances_within_selection", "examples/analysis/hydrogen_bonds/README", "examples/analysis/hydrogen_bonds/hbonds", "examples/analysis/hydrogen_bonds/hbonds-lifetimes", "examples/analysis/hydrogen_bonds/hbonds-selections", "examples/analysis/polymers_and_membranes/README", "examples/analysis/polymers_and_membranes/hole2", "examples/analysis/polymers_and_membranes/polymer", "examples/analysis/reduced_dimensions/README", "examples/analysis/reduced_dimensions/diffusion_map", "examples/analysis/reduced_dimensions/pca", "examples/analysis/structure/README", "examples/analysis/structure/average_rdf", "examples/analysis/structure/dihedrals", "examples/analysis/structure/elastic_network", "examples/analysis/structure/helanal", "examples/analysis/structure/site_specific_rdf", "examples/analysis/trajectory_similarity/README", "examples/analysis/trajectory_similarity/clustering_ensemble_similarity", "examples/analysis/trajectory_similarity/convergence", "examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity", "examples/analysis/trajectory_similarity/harmonic_ensemble_similarity", "examples/analysis/trajectory_similarity/psa", "examples/analysis/volumetric/README", "examples/analysis/volumetric/density_analysis", "examples/analysis/volumetric/linear_density", 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of contacts within a cutoff", "Atom-wise distances between matching AtomGroups", "All distances between two selections", "All distances within a selection", "Hydrogen Bond Analysis", "Calculating hydrogen bonds: the basics", "Calculating hydrogen bond lifetimes", "Calculating hydrogen bonds: advanced selections", "Polymers and membranes", "Analysing pore dimensions with HOLE2", "Determining the persistence length of a polymer", "Dimension reduction", "Non-linear dimension reduction to diffusion maps", "Principal component analysis of a trajectory", "Structure", "Average radial distribution functions", "Protein dihedral angle analysis", "Elastic network analysis", "Helix analysis", "Calculating the RDF atom-to-atom", "Trajectory similarity", "Calculating the Clustering Ensemble Similarity between ensembles", "Evaluating convergence", "Calculating the Dimension Reduction Ensemble Similarity between ensembles", "Calculating the Harmonic Ensemble Similarity between ensembles", "Comparing the geometric similarity of trajectories", "Volumetric analyses", "Calculating the solvent density around a protein", "Computing mass and charge density on each axis", "Constructing, modifying, and adding to a Universe", "Other", "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms", "Quick start guide", "Transformations", "Centering a trajectory in the box", "Frequently asked questions", "Auxiliary files", "Coordinates", "Format reference", "Guessing", "Format overview", "chemfiles (chemfiles Trajectory or file)", "CONFIG (DL_Poly Config)", "COOR, NAMBDIN (NAMD binary restart files)", "CRD (CHARMM CARD files)", "DATA (LAMMPS)", "DCD (CHARMM, NAMD, or LAMMPS trajectory)", "DCD (Flexible LAMMPS trajectory)", "DMS (Desmond Molecular Structure files)", "GMS (Gamess trajectory)", "GRO (GROMACS structure file)", "GSD (HOOMD GSD file)", "IN, FHIAIMS (FHI-aims input files)", "INPCRD, RESTRT (AMBER restart files)", "ITP (GROMACS portable topology files)", "LAMMPSDUMP 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48, 52, 53, 99, 102, 103, 106, 109, 111, 112], "traceback": [0, 108], "most": [0, 1, 3, 7, 10, 14, 15, 16, 26, 27, 32, 34, 39, 40, 41, 53, 60, 68, 69, 83, 87, 99, 100, 103, 105, 106, 108, 109, 114], "recent": [0, 3, 67, 87, 102, 108, 109], "call": [0, 1, 3, 4, 7, 12, 15, 16, 19, 28, 30, 32, 34, 37, 50, 53, 68, 98, 99, 105, 106, 108, 109, 112], "stdin": 0, "line": [0, 3, 12, 13, 26, 27, 30, 33, 43, 48, 49, 57, 81, 83, 91, 95, 96, 98, 100, 105, 108, 114], "modul": [0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 25, 30, 38, 39, 41, 42, 43, 44, 45, 46, 53, 55, 79, 100, 105, 109, 112], "core": [0, 2, 3, 13, 14, 15, 22, 23, 42, 44, 50, 53, 57, 83, 100, 102, 103, 105, 109, 112], "py": [0, 3, 4, 5, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 33, 37, 38, 39, 40, 42, 43, 44, 45, 49, 53, 101, 102, 104, 105, 108], "2278": 0, "__getattr__": 0, "cl": [0, 30], "self": [0, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 33, 38, 39, 42, 43, 44, 45, 49, 108], "__class__": 0, "__name__": 0, "attr": 0, "attributeerror": 0, "ha": [0, 2, 3, 7, 9, 10, 11, 13, 14, 15, 16, 18, 19, 22, 23, 24, 28, 29, 30, 34, 36, 40, 42, 43, 44, 45, 46, 48, 50, 52, 53, 55, 70, 87, 96, 98, 100, 102, 103, 105, 106, 108, 109, 111, 114], "attribut": [0, 1, 3, 14, 15, 26, 30, 39, 40, 53, 56, 60, 65, 66, 77, 81, 83, 87, 99, 103, 105, 106, 108], "howev": [0, 1, 3, 7, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 31, 32, 34, 39, 44, 48, 50, 52, 53, 55, 57, 67, 69, 71, 72, 84, 87, 89, 96, 98, 100, 101, 102, 103, 105, 108, 109, 114], "order": [0, 3, 7, 12, 13, 15, 16, 19, 26, 31, 32, 33, 34, 37, 42, 43, 44, 48, 52, 53, 57, 61, 66, 67, 82, 90, 98, 100, 101, 102, 103, 105, 109, 110, 111, 112, 114], "molnum": [0, 61, 87, 97, 108, 109], "name": [0, 3, 4, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 57, 60, 61, 65, 67, 70, 78, 81, 82, 83, 86, 87, 92, 95, 96, 97, 98, 100, 102, 103, 105, 106, 107, 108, 109, 114], "moltyp": [0, 61, 87, 97, 106, 109], "each": [0, 1, 3, 4, 6, 7, 9, 10, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 44, 45, 46, 47, 48, 50, 53, 55, 57, 60, 61, 66, 96, 98, 99, 101, 102, 103, 105, 108, 109, 111, 112, 113, 114], "11086": 0, "11087": 0, "11088": 0, "akeco": 0, "na": [0, 1, 30, 105], "2": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114], "7": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114], "dev0": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114], "univers": [1, 3, 5, 6, 7, 9, 11, 12, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 56, 60, 61, 62, 66, 68, 71, 77, 80, 81, 82, 88, 89, 93, 94, 95, 96, 98, 99, 103, 105, 106, 108, 110, 111, 112], "contain": [1, 3, 4, 7, 8, 12, 14, 15, 17, 26, 30, 34, 37, 39, 40, 41, 42, 44, 46, 48, 50, 53, 55, 57, 66, 72, 81, 84, 87, 88, 89, 91, 92, 93, 96, 98, 101, 102, 103, 104, 105, 106, 108, 109, 111, 112, 114], "all": [1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 26, 30, 33, 34, 37, 38, 44, 46, 48, 50, 53, 57, 66, 81, 83, 92, 95, 98, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "particl": [1, 9, 13, 14, 34, 36, 40, 50, 52, 53, 72, 105], "molecular": [1, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 58, 59, 61, 66, 80, 85, 97, 99, 104, 114], "system": [1, 2, 3, 4, 14, 15, 22, 26, 30, 36, 40, 50, 53, 57, 61, 80, 81, 83, 105, 108, 114], "regardless": [1, 3, 53, 113], "whether": [1, 3, 9, 10, 14, 16, 34, 50, 114], "realli": [1, 13, 15, 108], "g": [1, 3, 4, 5, 7, 14, 15, 19, 20, 26, 30, 32, 33, 34, 37, 53, 57, 67, 80, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 112, 113, 114], "mai": [1, 3, 4, 7, 9, 12, 14, 15, 16, 18, 19, 26, 27, 28, 30, 32, 33, 34, 36, 38, 42, 43, 44, 48, 50, 53, 57, 93, 100, 101, 102, 103, 105, 111], "unit": [1, 5, 26, 48, 49, 50, 52, 53, 63, 66, 67, 68, 76, 79, 81, 82, 88, 101, 103, 105, 106, 108, 112], "coars": [1, 9, 19, 20, 53, 104], "grain": [1, 9, 19, 20, 53, 104], "bead": [1, 9, 53], "": [1, 2, 3, 4, 9, 10, 13, 16, 19, 26, 27, 30, 33, 34, 37, 39, 40, 42, 44, 45, 48, 50, 52, 53, 55, 56, 57, 60, 67, 81, 87, 96, 98, 101, 102, 103, 104, 105, 109, 111, 113, 114], "master": [1, 3, 109, 114], "The": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 56, 57, 60, 61, 62, 66, 67, 68, 69, 70, 72, 73, 77, 78, 79, 80, 83, 84, 85, 86, 87, 88, 89, 92, 93, 94, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 110, 111, 112, 113, 114], "probabl": [1, 7, 15, 38, 41, 42, 44, 53, 88], "import": [1, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 56, 57, 60, 78, 83, 87, 93, 96, 98, 102, 103, 105, 106, 109, 110, 111, 112, 114], "virtual": [1, 3, 4, 93, 98], "everyth": [1, 3, 48, 53, 98, 101, 102], "can": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 61, 62, 63, 64, 66, 67, 68, 69, 70, 71, 72, 74, 78, 79, 80, 81, 83, 84, 89, 91, 92, 94, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "through": [1, 2, 3, 7, 12, 14, 15, 32, 41, 49, 53, 57, 98, 103, 105, 106, 109, 111, 114], "instanc": [1, 36, 50, 53, 57, 78, 106, 114], "typic": [1, 3, 7, 8, 13, 14, 26, 50, 52, 53, 96, 98, 99, 108, 109, 111, 112, 114], "select_atom": [1, 9, 11, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 26, 31, 34, 36, 37, 40, 48, 50, 52, 53, 55, 96, 98, 103, 105, 106, 110, 111, 112, 114], "manipul": [1, 53, 80, 99], "test": [1, 2, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 70, 93, 96, 98, 102, 103, 106, 109, 110, 111, 112, 114], "datafil": [1, 5, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 93, 96, 98, 101, 103, 106, 108, 109, 110, 111, 112, 114], "pdb": [1, 9, 10, 13, 14, 22, 23, 24, 34, 37, 46, 50, 52, 53, 57, 58, 59, 61, 77, 78, 83, 96, 97, 98, 103, 105, 108, 109, 114], "3": [1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 81, 82, 83, 84, 87, 93, 94, 95, 96, 98, 103, 104, 106, 108, 109, 110, 111, 112, 113, 114], "4": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 82, 83, 87, 88, 93, 96, 98, 100, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "resnam": [1, 18, 19, 21, 26, 27, 28, 36, 37, 40, 48, 50, 53, 55, 61, 65, 72, 81, 82, 86, 87, 96, 97, 98, 105, 106, 109, 112], "arg": [1, 15, 18, 19, 21, 27, 28, 53, 83, 98, 106, 107, 109], "out": [1, 3, 4, 9, 10, 11, 12, 14, 19, 30, 34, 39, 48, 50, 52, 55, 57, 61, 70, 78, 93, 98, 102, 103, 105, 106, 109, 110, 111, 113, 114], "312": [1, 98, 104, 108], "see": [1, 2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 26, 27, 28, 30, 32, 33, 34, 37, 38, 40, 42, 43, 44, 46, 48, 50, 52, 53, 55, 56, 57, 60, 61, 63, 66, 67, 69, 76, 81, 84, 87, 94, 96, 98, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "more": [1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 33, 34, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 53, 56, 57, 60, 61, 65, 69, 87, 98, 101, 103, 105, 106, 108, 109, 112, 114], "inform": [1, 3, 4, 7, 10, 12, 14, 15, 16, 19, 22, 26, 28, 30, 32, 33, 34, 37, 40, 42, 43, 44, 46, 50, 52, 56, 57, 60, 62, 63, 66, 69, 70, 71, 72, 80, 81, 82, 84, 87, 88, 94, 95, 98, 101, 103, 105, 106, 108, 111, 112, 114], "like": [1, 3, 4, 5, 13, 16, 19, 26, 30, 34, 39, 40, 43, 48, 53, 55, 57, 60, 83, 100, 106, 108], "list": [1, 2, 3, 5, 13, 15, 16, 19, 26, 30, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 57, 61, 65, 67, 82, 87, 96, 99, 100, 102, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114], "5": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 67, 71, 78, 82, 87, 93, 98, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "print": [1, 5, 9, 10, 11, 13, 14, 15, 19, 23, 26, 27, 28, 30, 31, 34, 36, 37, 39, 40, 42, 43, 44, 45, 46, 49, 50, 53, 57, 101, 103, 108, 109, 110, 111, 114], "n": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 83, 95, 96, 98, 104, 105, 106, 107, 113], "type": [1, 3, 26, 42, 50, 52, 53, 58, 61, 65, 66, 72, 80, 81, 82, 83, 84, 85, 86, 87, 91, 92, 96, 97, 98, 104, 105, 106, 109, 113], "met": [1, 53, 83, 107, 109], "resid": [1, 13, 14, 23, 24, 26, 27, 36, 40, 46, 50, 53, 61, 65, 66, 69, 72, 75, 81, 82, 87, 89, 98, 105, 106, 109], "altloc": [1, 14, 61, 81, 82, 97, 106, 109], "return": [1, 3, 4, 9, 10, 13, 15, 16, 18, 19, 20, 21, 22, 24, 27, 30, 33, 34, 37, 40, 42, 44, 50, 53, 57, 98, 102, 105, 106, 108, 110, 111, 112], "below": [1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 61, 98, 103, 106, 107, 108, 109, 112, 113, 114], "code": [1, 2, 4, 5, 6, 7, 11, 13, 14, 15, 16, 30, 36, 48, 50, 57, 67, 78, 81, 82, 84, 93, 98, 99, 102, 103, 104, 105, 106, 108, 109, 112, 114], "everi": [1, 3, 4, 10, 14, 15, 16, 24, 27, 30, 31, 34, 37, 39, 42, 44, 48, 50, 52, 53, 57, 60, 61, 98, 103, 105, 106, 108, 109, 111, 114], "second": [1, 10, 12, 18, 19, 21, 40, 44, 53, 113], "element": [1, 42, 50, 53, 60, 61, 65, 66, 70, 81, 82, 86, 97, 105, 109, 114], "first": [1, 3, 4, 7, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 49, 50, 53, 55, 57, 61, 69, 72, 81, 83, 89, 94, 98, 100, 101, 105, 106, 108, 110, 111, 114], "6th": [1, 106], "correspond": [1, 3, 12, 13, 14, 16, 24, 26, 27, 40, 55, 71, 98, 108, 109], "indic": [1, 3, 12, 13, 14, 19, 24, 26, 27, 30, 33, 34, 38, 40, 43, 50, 53, 81, 82, 84, 87, 91, 96, 101, 105, 106, 108, 109, 110], "6": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 66, 69, 78, 81, 82, 83, 84, 87, 91, 93, 98, 102, 103, 104, 106, 109, 110, 111, 112, 114], "ag": [1, 10, 13, 40, 96, 98, 103], "also": [1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 32, 34, 37, 39, 40, 41, 42, 44, 48, 53, 55, 57, 61, 62, 81, 82, 87, 89, 98, 100, 101, 102, 103, 105, 106, 108, 109, 110, 111, 112, 113, 114], "support": [1, 3, 13, 19, 30, 46, 53, 66, 71, 72, 82, 84, 85, 88, 100, 103, 105, 106, 109, 111, 114], "fanci": [1, 53, 110], "pass": [1, 3, 4, 13, 16, 18, 19, 22, 23, 24, 26, 28, 30, 31, 34, 36, 37, 39, 42, 43, 44, 45, 49, 50, 53, 55, 60, 61, 62, 66, 80, 81, 93, 95, 96, 100, 102, 103, 105, 106, 108, 110, 112, 114], "ndarrai": [1, 53, 110], "8": [1, 4, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 87, 98, 103, 105, 106, 109, 110, 111, 112, 114], "10": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 71, 78, 82, 83, 87, 98, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "9": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 84, 87, 98, 102, 103, 105, 106, 108, 109, 110, 111, 112, 114], "47680": 1, "boolean": [1, 53, 108, 110], "allow": [1, 2, 3, 10, 13, 14, 19, 27, 28, 30, 36, 37, 40, 42, 43, 44, 52, 53, 56, 57, 60, 96, 99, 100, 103, 105, 106, 108, 110, 114], "you": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 61, 62, 64, 67, 78, 79, 80, 89, 96, 98, 99, 100, 101, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "true": [1, 3, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 30, 34, 37, 38, 40, 42, 44, 45, 46, 48, 50, 52, 53, 55, 66, 68, 89, 94, 103, 105, 106, 108, 110, 114], "fals": [1, 4, 9, 11, 14, 19, 20, 26, 27, 30, 40, 44, 46, 48, 50, 53, 57, 78, 103, 105, 106, 108, 109, 110, 114], "valu": [1, 3, 7, 8, 11, 12, 13, 14, 15, 19, 24, 26, 27, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 57, 60, 65, 66, 67, 76, 81, 82, 83, 89, 92, 105, 106, 108, 110, 114], "must": [1, 2, 3, 4, 11, 12, 13, 16, 18, 22, 23, 26, 27, 30, 31, 34, 42, 43, 46, 48, 50, 53, 60, 66, 79, 83, 84, 100, 101, 108, 109, 112, 114], "same": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 24, 26, 28, 30, 31, 33, 34, 36, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 67, 93, 95, 96, 98, 102, 103, 105, 106, 109, 110, 114], "length": [1, 3, 6, 7, 12, 13, 22, 24, 27, 29, 39, 40, 42, 44, 45, 46, 48, 50, 52, 53, 63, 66, 67, 68, 71, 79, 88, 99, 104, 105, 110, 111], "origin": [1, 3, 4, 7, 9, 13, 14, 23, 27, 32, 33, 34, 39, 50, 53, 55, 57, 67, 98, 102, 106, 108, 110, 113], "condit": [1, 15, 105, 106, 108, 110, 112], "arr": 1, "11": [1, 3, 9, 10, 13, 14, 15, 16, 19, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 83, 87, 98, 103, 104, 105, 106, 109, 110, 112, 113, 114], "len": [1, 12, 23, 24, 30, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 50, 53, 57, 98, 103, 108, 109, 111], "12": [1, 3, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 33, 34, 36, 37, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 82, 86, 98, 103, 104, 106, 109, 110, 111, 112, 113, 114], "13": [1, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 34, 36, 37, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 106, 109, 110, 112, 114], "number": [1, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 50, 52, 53, 57, 60, 65, 69, 71, 72, 75, 81, 82, 83, 84, 85, 87, 89, 91, 92, 93, 96, 103, 105, 106, 108, 109, 114], "wai": [1, 3, 4, 7, 10, 12, 13, 14, 15, 16, 18, 19, 26, 27, 30, 33, 34, 48, 52, 53, 79, 98, 99, 103, 105, 106, 108, 109, 111, 114], "compar": [1, 6, 7, 9, 10, 11, 12, 14, 15, 17, 19, 22, 32, 34, 40, 41, 42, 44, 45, 108], "one": [1, 2, 3, 4, 10, 11, 12, 13, 15, 19, 27, 28, 30, 31, 39, 46, 50, 53, 56, 57, 83, 87, 88, 91, 92, 96, 98, 99, 100, 103, 104, 105, 106, 108, 109, 114], "concaten": [1, 15, 53, 103, 106, 114], "subtract": [1, 13, 84], "union": [1, 106], "differ": [1, 3, 4, 7, 9, 10, 12, 13, 15, 16, 19, 26, 28, 34, 36, 38, 40, 41, 45, 46, 48, 50, 53, 55, 60, 66, 67, 70, 71, 75, 82, 87, 91, 93, 95, 96, 98, 99, 100, 102, 103, 104, 105, 106, 112, 114], "achiev": [1, 15], "similar": [1, 3, 4, 6, 12, 15, 19, 23, 24, 30, 32, 33, 34, 37, 38, 53, 73, 82, 83, 87, 92, 93, 98, 104], "outcom": [1, 105], "kei": [1, 2, 30, 38, 39, 49, 53, 57, 98, 99, 114], "preserv": [1, 4, 19, 66, 105], "ani": [1, 2, 3, 4, 11, 15, 16, 18, 27, 28, 30, 31, 37, 42, 43, 44, 46, 49, 50, 53, 56, 57, 61, 67, 89, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 112], "duplic": [1, 30, 53, 103, 106], "where": [1, 4, 5, 7, 9, 14, 15, 16, 19, 20, 21, 22, 27, 31, 32, 33, 36, 37, 38, 40, 43, 44, 46, 48, 50, 53, 57, 60, 61, 66, 71, 89, 98, 100, 102, 105, 106, 108, 109], "its": [1, 2, 3, 4, 7, 9, 13, 15, 18, 19, 20, 22, 30, 32, 33, 44, 46, 49, 52, 53, 98, 99, 100, 101, 103, 106, 108, 109, 111, 112], "topologi": [1, 5, 14, 15, 26, 28, 52, 53, 59, 63, 65, 66, 69, 70, 71, 72, 73, 76, 77, 78, 80, 81, 82, 83, 84, 91, 92, 93, 95, 98, 99, 103, 105, 106, 108, 111], "14": [1, 9, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 82, 98, 100, 103, 104, 105, 106, 109, 110, 112, 114], "ag1": [1, 40], "15": [1, 7, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 41, 42, 43, 44, 45, 48, 49, 50, 52, 53, 57, 81, 82, 98, 103, 104, 106, 109, 110, 112, 114], "ag2": [1, 40], "16": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 104, 105, 106, 109, 110, 111, 112], "concat": 1, "17": [1, 12, 15, 16, 19, 20, 21, 26, 27, 30, 33, 34, 36, 39, 42, 44, 48, 49, 50, 52, 53, 57, 69, 81, 82, 87, 98, 103, 104, 106, 109, 110, 111, 112], "18": [1, 9, 15, 16, 19, 26, 27, 30, 42, 44, 46, 48, 49, 50, 52, 53, 57, 78, 81, 82, 86, 98, 103, 105, 106, 109, 110, 112, 113], "19": [1, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 37, 40, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 104, 105, 106, 109, 112, 113], "avail": [1, 2, 3, 7, 15, 16, 19, 32, 33, 36, 40, 42, 43, 44, 53, 56, 57, 60, 66, 73, 77, 79, 82, 87, 96, 98, 99, 100, 102, 105, 106, 108, 109, 114], "keep": [1, 2, 3, 10, 14, 30, 34, 39, 43, 44, 48, 55, 72, 96, 99, 101, 102, 108], "well": [1, 2, 4, 7, 15, 32, 33, 44, 48, 61, 67, 99, 101, 105, 108], "equival": [1, 27, 48, 87], "result": [1, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 24, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 52, 53, 61, 89, 94, 105, 106, 108, 110], "t": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 48, 49, 50, 52, 53, 55, 56, 57, 66, 82, 92, 96, 98, 100, 103, 104, 105, 106, 107, 108, 110, 111, 112, 114], "sort": [1, 26, 27, 30, 34, 53, 105, 106], "isdisjoint": 1, "do": [1, 3, 4, 6, 10, 11, 12, 13, 15, 16, 19, 22, 26, 27, 28, 30, 34, 37, 42, 44, 45, 46, 48, 50, 52, 53, 95, 99, 101, 102, 103, 105, 108, 114], "share": [1, 3, 105], "issubset": 1, "part": [1, 2, 3, 4, 15, 30, 48, 57, 101, 103, 105, 106, 108, 111], "is_strict_subset": 1, "issuperset": 1, "is_strict_superset": 1, "both": [1, 3, 4, 13, 15, 16, 22, 30, 38, 48, 50, 52, 53, 60, 63, 72, 81, 85, 87, 91, 98, 100, 102, 103, 105, 108, 109, 114], "intersect": [1, 106], "common": [1, 3, 7, 12, 13, 14, 15, 22, 26, 31, 32, 34, 53, 55, 68, 70, 104, 106, 108], "symmetric_differ": 1, "separ": [1, 5, 7, 15, 16, 19, 30, 31, 36, 40, 42, 43, 81, 83, 84, 100, 102, 106, 108, 114], "properti": [1, 16, 30, 39, 53, 60, 98, 105, 106, 109, 111, 112], "level": [1, 3, 4, 15, 48, 85, 98, 101, 108, 114], "connect": [1, 3, 4, 33, 50, 52, 53, 60, 61, 82, 87, 91, 105, 114], "residu": [1, 3, 7, 13, 14, 17, 19, 21, 22, 26, 28, 30, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 55, 61, 65, 69, 70, 71, 72, 75, 81, 82, 83, 86, 87, 92, 93, 95, 96, 99, 105, 106, 109, 112, 114], "molecul": [1, 4, 10, 13, 26, 31, 38, 50, 55, 58, 61, 66, 78, 87, 92, 95, 98, 105, 106, 108, 109, 112], "segment": [1, 10, 49, 53, 61, 65, 70, 81, 87, 95, 99, 103, 105, 106, 109, 114], "20": [1, 15, 16, 19, 26, 30, 31, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 105, 106, 110, 111, 112, 113], "21": [1, 3, 9, 15, 16, 26, 27, 28, 30, 31, 33, 42, 44, 48, 49, 50, 52, 53, 57, 71, 81, 82, 98, 103, 104, 105, 106, 109, 112, 113, 114], "24": [1, 15, 16, 26, 27, 30, 34, 39, 44, 49, 50, 53, 57, 81, 82, 87, 98, 99, 103, 105, 112], "accord": [1, 13, 14, 87, 91, 106, 109], "produc": [1, 23, 27, 34, 53, 57, 67, 105, 108], "dictionari": [1, 18, 30, 57, 60, 89, 105, 108, 114], "22": [1, 15, 16, 26, 30, 44, 46, 48, 49, 50, 53, 57, 81, 82, 98, 103, 105, 106, 112], "mass": [1, 6, 7, 9, 10, 15, 16, 23, 24, 28, 30, 36, 40, 45, 46, 47, 48, 53, 55, 61, 63, 65, 66, 86, 87, 92, 97, 106, 109, 112, 113, 114], "32": [1, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 50, 52, 53, 55, 57, 98, 104, 105], "06": [1, 38, 104, 113], "008": [1, 53], "23853": 1, "11084": 1, "011": [1, 39, 53], "1040": [1, 98], "007": [1, 53, 82], "289": 1, "999": [1, 53, 65, 93], "11404": 1, "98977": 1, "multipl": [1, 3, 27, 39, 48, 53, 57, 62, 89, 94, 98, 100, 105, 106, 112, 114], "them": [1, 3, 4, 7, 9, 10, 13, 15, 18, 19, 22, 34, 38, 39, 42, 43, 44, 45, 46, 50, 52, 53, 55, 60, 61, 66, 68, 79, 81, 82, 89, 95, 101, 102, 103, 104, 105, 106, 108, 109, 112], "23": [1, 15, 16, 26, 30, 34, 44, 48, 49, 50, 53, 57, 81, 82, 87, 93, 98, 103, 106, 112], "sol": [1, 30, 36, 37, 40, 48, 50, 55, 87, 112], "22168": 1, "iter": [1, 12, 14, 15, 16, 30, 44, 49, 53, 103, 105, 108, 109, 110, 111], "atom1": [1, 95], "25": [1, 15, 26, 27, 30, 34, 46, 49, 50, 53, 57, 81, 82, 83, 98, 103, 105], "atom2": [1, 95], "26": [1, 15, 26, 30, 34, 49, 50, 53, 57, 81, 82, 83, 87, 93, 98, 103], "atom3": 1, "27": [1, 15, 26, 30, 49, 50, 53, 57, 81, 82, 93, 98, 103, 104, 107, 113], "28": [1, 3, 15, 30, 49, 50, 53, 57, 78, 98, 103], "ca": [1, 9, 10, 11, 12, 13, 14, 16, 18, 20, 21, 23, 24, 36, 37, 38, 39, 40, 42, 43, 44, 46, 53, 60, 98, 103, 106, 107], "c": [1, 3, 13, 27, 30, 31, 34, 36, 37, 38, 39, 46, 48, 50, 52, 53, 62, 67, 78, 81, 82, 85, 87, 88, 98, 100, 102, 103, 104, 105, 106, 107, 113], "cb": [1, 36, 53, 98], "h2": [1, 26, 28, 50, 78], "h": [1, 3, 27, 31, 36, 39, 45, 50, 52, 53, 78, 87, 96, 98, 103, 106], "neat": [1, 4], "shortcut": [1, 106], "simpli": [1, 3, 12, 13, 15, 21, 24, 26, 34, 40, 50, 52, 53, 60, 79, 84, 88, 101, 104, 105, 106, 109, 113], "29": [1, 13, 15, 30, 34, 46, 49, 50, 53, 57, 98, 103, 113], "30": [1, 13, 14, 15, 22, 23, 30, 33, 42, 49, 50, 53, 57, 78, 98, 103, 104, 110, 112, 113], "31": [1, 15, 16, 19, 30, 48, 49, 50, 53, 57, 81, 82, 98, 103], "altern": [1, 3, 13, 20, 30, 48, 57, 77, 81, 82, 96, 103, 106, 108, 109, 112], "provid": [1, 3, 4, 7, 12, 13, 15, 16, 17, 25, 26, 30, 31, 34, 37, 38, 43, 44, 46, 52, 53, 55, 57, 60, 61, 62, 65, 71, 81, 82, 83, 88, 94, 96, 99, 100, 103, 105, 106, 108, 109, 114], "belong": [1, 28, 50, 53, 61, 98, 106, 107], "33": [1, 15, 49, 50, 53, 57, 81, 82], "34": [1, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 37, 38, 39, 40, 42, 43, 44, 45, 49, 50, 52, 53, 55, 57, 81, 82, 98, 104], "These": [1, 3, 4, 5, 7, 8, 17, 24, 37, 43, 48, 53, 57, 72, 81, 82, 89, 94, 98, 106, 108, 109], "user": [1, 2, 3, 6, 7, 15, 19, 26, 28, 39, 42, 43, 44, 45, 49, 53, 60, 61, 66, 68, 69, 72, 78, 79, 87, 88, 100, 101, 102, 103, 105, 106, 108, 109, 114], "work": [1, 2, 4, 7, 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, 55, 56, 57, 62, 67, 79, 96, 99, 100, 102, 104, 105, 106, 108, 111], "35": [1, 19, 20, 30, 49, 50, 53, 57, 98, 103, 104], "null": 1, "36": [1, 49, 50, 53, 57, 83], "abov": [1, 3, 10, 13, 16, 23, 24, 26, 27, 28, 39, 48, 53, 55, 57, 83, 102, 103, 105, 106, 108, 109, 111], "37": [1, 38, 49, 50, 53, 57, 83, 98, 104], "For": [1, 2, 3, 4, 7, 9, 12, 13, 15, 16, 19, 26, 28, 30, 32, 33, 34, 37, 39, 40, 42, 43, 44, 46, 50, 52, 53, 55, 57, 60, 61, 66, 78, 83, 87, 89, 96, 98, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 114], "38": [1, 16, 23, 49, 52, 53, 57, 81, 82], "does_not_exist": 1, "39": [1, 13, 15, 16, 18, 20, 21, 23, 24, 26, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 50, 52, 53, 57, 81, 82], "40": [1, 19, 30, 49, 53, 57, 81, 82, 98, 103, 110], "have": [1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 18, 19, 22, 24, 26, 27, 30, 31, 33, 34, 36, 37, 40, 42, 44, 45, 46, 48, 50, 53, 55, 57, 60, 63, 66, 67, 69, 71, 75, 79, 81, 82, 84, 87, 89, 95, 98, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 114], "evalu": [1, 6, 7, 34, 41, 49, 106], "context": [1, 15, 30, 52, 53, 96, 108], "41": [1, 30, 49, 57, 81, 82, 98], "bool": [1, 3, 18, 50, 109, 110], "skip": [1, 3, 16, 46, 57, 100], "over": [1, 6, 7, 8, 12, 15, 16, 17, 18, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 53, 55, 72, 102, 103, 105, 108, 110, 111, 112], "instead": [1, 3, 4, 9, 10, 12, 14, 15, 16, 19, 23, 24, 30, 34, 37, 39, 43, 44, 48, 50, 55, 61, 81, 82, 88, 92, 93, 100, 105, 106, 108, 111, 114], "rais": [1, 3, 33, 49, 53, 65, 79, 81, 82, 83, 99, 100, 101, 105, 108], "error": [1, 3, 4, 9, 49, 53, 72, 79, 89, 94, 100, 101, 105, 108], "which": [1, 3, 4, 10, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 30, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 55, 57, 60, 61, 67, 68, 83, 87, 89, 91, 94, 96, 98, 99, 100, 102, 103, 105, 106, 108, 109, 112, 114], "help": [1, 2, 3, 4, 13, 16, 22, 96, 99, 100, 106, 108], "occasion": [1, 89, 94], "aris": [1, 4], "logic": 1, "too": [1, 16, 42, 44, 48, 53, 55, 56, 99, 108], "restrict": [1, 13, 14, 87], "geometr": [1, 6, 7, 26, 41, 52], "normal": [1, 3, 15, 30, 38, 39, 43, 44, 84, 91, 96, 102, 104, 105, 108], "static": [1, 10, 15, 53, 106, 109, 111, 114], "within": [1, 6, 7, 16, 17, 18, 19, 20, 22, 26, 28, 30, 36, 38, 40, 42, 43, 44, 45, 50, 53, 57, 60, 67, 77, 105, 106, 111, 112], "chang": [1, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 49, 53, 55, 57, 61, 71, 72, 81, 87, 89, 100, 102, 103, 106, 108, 111], "trajectori": [1, 5, 6, 8, 9, 17, 18, 20, 21, 26, 27, 32, 33, 36, 37, 38, 40, 42, 43, 44, 45, 48, 49, 50, 52, 54, 58, 59, 61, 66, 71, 72, 81, 82, 91, 93, 99, 104, 105, 106, 108, 112, 113, 114], "frame": [1, 7, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 26, 27, 30, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 46, 48, 49, 52, 55, 56, 61, 66, 71, 81, 82, 89, 94, 99, 105, 106, 108, 110, 111, 112, 114], "sever": [1, 3, 7, 16, 29, 30, 33, 34, 53, 82, 101, 105, 108, 114], "requir": [1, 3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 65, 66, 79, 81, 82, 83, 95, 96, 98, 100, 103, 105, 106, 108, 109], "function": [1, 2, 3, 4, 6, 7, 8, 13, 17, 19, 20, 21, 27, 30, 33, 34, 35, 37, 41, 42, 43, 44, 45, 46, 52, 53, 55, 56, 57, 85, 87, 98, 100, 101, 102, 104, 105, 106, 109, 111, 112, 114], "implement": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 39, 53, 57, 62, 66, 76, 82, 87, 95, 106, 112], "mani": [1, 2, 3, 4, 13, 15, 16, 21, 26, 30, 34, 39, 40, 42, 43, 44, 53, 99, 100, 108, 109, 111, 114], "interest": [1, 19, 30, 48, 53, 100], "bond": [1, 13, 31, 49, 52, 53, 55, 57, 61, 66, 78, 80, 81, 82, 84, 86, 91, 92, 97, 98, 99, 104, 105, 106, 109, 114], "angl": [1, 6, 7, 22, 26, 27, 28, 35, 39, 50, 53, 57, 61, 66, 67, 84, 86, 92, 97, 99, 104, 105, 106, 109, 113, 114], "dihedr": [1, 6, 7, 35, 53, 61, 66, 84, 86, 97, 105, 106, 109, 114], "improperdihedr": [1, 109], "present": [1, 3, 19, 21, 26, 27, 40, 52, 65, 68, 81, 92, 95, 98, 105], "residuegroup": [1, 53, 98, 105, 109], "free": [2, 3, 101], "open": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 87, 89, 94, 104, 108], "sourc": [2, 3, 4, 16, 30, 53, 57, 84, 96, 100, 102, 105, 108], "project": [2, 3, 4, 7, 32, 37, 39, 43, 44, 48, 99, 105], "It": [2, 3, 4, 7, 9, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 32, 33, 34, 36, 37, 40, 45, 48, 49, 50, 53, 57, 60, 61, 67, 76, 78, 82, 85, 87, 89, 99, 104, 106, 108, 110, 112, 114], "evolv": 2, "grow": [2, 5, 108], "demand": 2, "base": [2, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 19, 28, 33, 39, 42, 44, 46, 50, 52, 53, 60, 61, 65, 79, 87, 89, 94, 102, 103, 104, 105, 106, 107, 108, 109], "develop": [2, 15, 52, 72, 101, 108], "team": 2, "veri": [2, 3, 12, 13, 15, 19, 23, 24, 27, 44, 45, 48, 79, 93, 103, 108], "much": [2, 3, 10, 11, 12, 13, 14, 16, 19, 30, 34, 42, 43, 48, 50, 60, 105, 108], "welcom": 2, "take": [2, 3, 4, 7, 14, 15, 16, 17, 23, 26, 30, 33, 42, 44, 48, 93, 96, 99, 100, 103, 106, 108, 109, 112, 114], "form": [2, 13, 19, 26, 42, 53, 55, 60], "bug": [2, 3, 16, 88, 102], "report": [2, 52, 99, 108], "enhanc": [2, 3], "request": [2, 4, 101, 102, 108], "issu": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 50, 57, 61, 63, 67, 79, 84, 87, 89, 94, 99, 100, 101, 102, 106, 108], "tracker": [2, 87, 99, 108], "fix": [2, 3, 4, 48, 49, 68, 72, 102], "improv": [2, 27, 99, 108], "speed": [2, 105, 108], "clariti": [2, 26], "modernis": 2, "featur": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 83, 99, 100, 102, 114], "addit": [2, 3, 7, 44, 57, 61, 82, 96, 98, 101, 102, 103, 105, 106, 108, 109], "document": [2, 5, 7, 15, 19, 22, 26, 30, 43, 48, 53, 66, 76, 89, 94, 105, 106, 108, 113], "includ": [2, 3, 4, 7, 9, 10, 13, 14, 15, 16, 19, 34, 36, 37, 39, 43, 48, 50, 52, 53, 55, 57, 84, 85, 87, 95, 96, 98, 99, 100, 102, 104, 105, 106, 108, 109, 111, 112, 114], "typo": [2, 3], "build": [2, 15, 16, 50, 53, 65, 87, 99, 100, 105], "question": [2, 3, 99], "discuss": [2, 3, 15, 27, 60, 63, 79, 87, 99, 101, 108], "mdnalysi": 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19, 53, 87, 101, 105, 108, 110], "gnu": [2, 108], "gener": [2, 3, 4, 7, 8, 9, 10, 14, 15, 18, 19, 20, 28, 30, 34, 37, 38, 39, 48, 50, 53, 55, 58, 59, 61, 67, 77, 80, 89, 94, 99, 102, 103, 104, 105, 113, 114], "public": [2, 3, 16, 30, 99, 102, 104, 108], "licens": [2, 15, 105, 108], "later": [2, 4, 13, 15, 102, 105, 106], "copyleft": 2, "deriv": [2, 3, 84, 87, 98, 105, 109], "made": [2, 3, 4, 26, 48, 71, 103, 105, 106, 109], "Be": [2, 15, 100], "sure": [2, 3, 4, 18, 100, 102, 106, 108], "comfort": 2, "befor": [2, 3, 4, 13, 16, 30, 36, 45, 48, 60, 89, 100, 101, 102, 105, 106, 108, 111], "push": [2, 4, 15, 102, 108], "page": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 102, 104, 106, 108], "came": [2, 108], "panda": [2, 13, 15, 16, 18, 19, 20, 21, 26, 33, 34, 49, 53, 108], "guid": [2, 3, 6, 7, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 69, 100, 108], "idea": [2, 3, 53, 102], "If": [2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 16, 23, 26, 27, 30, 34, 36, 37, 38, 40, 42, 44, 46, 50, 52, 53, 55, 57, 61, 65, 66, 67, 68, 79, 81, 82, 83, 84, 88, 89, 92, 96, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "look": [2, 3, 4, 10, 12, 13, 15, 19, 23, 24, 26, 28, 36, 37, 39, 48, 55, 61, 83, 86, 92, 96, 98, 108, 111], "brand": 2, "we": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 68, 82, 88, 96, 98, 99, 100, 101, 102, 105, 108, 109], "recommend": [2, 3, 21, 26, 45, 61, 100, 101, 102, 108], "go": [2, 3, 4, 15, 16, 96, 102, 106], "main": [2, 4, 100], "codebas": [2, 16, 105], "your": [2, 4, 5, 6, 7, 10, 13, 15, 17, 19, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 61, 67, 75, 84, 87, 99, 100, 103, 104, 105, 108, 111, 112], "own": [2, 3, 4, 6, 7, 13, 15, 17, 19, 20, 21, 30, 42, 52, 53, 66, 99, 101, 108, 112], "encourag": [2, 108], "an": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 57, 60, 62, 66, 67, 69, 71, 72, 78, 80, 83, 84, 85, 87, 88, 89, 94, 96, 98, 99, 100, 101, 102, 104, 105, 106, 108, 110, 112, 114], "toolkit": [2, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 52, 53, 55, 99, 104], "mdakit": [2, 105], "standalon": [2, 16, 108], "solv": [2, 87], "specif": [2, 3, 4, 7, 14, 16, 26, 27, 29, 30, 36, 53, 56, 60, 66, 73, 98, 100, 101, 103, 104, 105, 108, 110, 114], "scientif": [2, 3, 15, 85, 104, 105], "technic": [2, 3, 4, 88], "problem": [2, 3, 4, 13, 61, 68, 87, 99], "option": [2, 9, 10, 14, 16, 19, 22, 23, 24, 30, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 57, 61, 66, 67, 82, 83, 95, 100, 103, 104, 105, 108, 109, 114], "regist": [2, 44], "registri": 2, "advertis": [2, 105], "broader": 2, "continu": [2, 3, 19, 27, 48, 89, 94, 102, 103, 105, 109, 114], "against": [2, 4, 102, 105], "latest": [2, 3, 15, 100, 108], "make": [2, 3, 4, 7, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 28, 33, 34, 38, 39, 40, 42, 43, 44, 45, 49, 53, 55, 56, 98, 100, 102, 103, 106, 108, 109, 111, 112, 114], "peopl": [2, 3, 102], "togeth": [2, 53, 99, 103, 112], "daunt": 2, "aspect": 2, "stick": [2, 50], "guidelin": [2, 105], "process": [2, 3, 7, 15, 17, 18, 19, 23, 24, 26, 27, 48, 67, 102, 105, 108, 114], "straightforward": [2, 53, 103, 106], "mostli": [2, 15], "troubl": [2, 40], "As": [2, 3, 4, 10, 12, 13, 14, 15, 16, 23, 24, 30, 33, 34, 39, 42, 43, 44, 48, 50, 53, 55, 57, 61, 84, 93, 95, 96, 98, 100, 102, 103, 105, 106, 108, 109, 113], "alwai": [2, 3, 4, 10, 15, 16, 20, 26, 33, 34, 53, 57, 60, 61, 67, 79, 81, 83, 84, 87, 88, 96, 99, 101, 103, 106, 108, 109, 111, 113], "difficulti": [2, 99], "feel": [2, 3], "ask": [2, 3, 16, 99, 100, 102, 108], "host": [2, 3, 5], "need": [2, 3, 7, 8, 9, 14, 15, 16, 19, 24, 30, 33, 34, 42, 43, 44, 46, 48, 50, 52, 53, 55, 67, 98, 99, 100, 101, 102, 103, 105, 108, 111, 112], "sign": [2, 34], "up": [2, 3, 4, 12, 15, 16, 27, 31, 42, 44, 46, 52, 53, 57, 66, 93, 96, 99, 100, 103, 105, 106, 108, 112], "account": [2, 3, 4, 7, 32, 34, 40, 49], "great": 2, "resourc": [2, 3, 15, 42, 44, 55, 99, 108], "learn": [2, 3, 7, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 42, 43, 44, 49, 99], "numpi": [2, 3, 10, 12, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 33, 34, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 100, 101, 102, 103, 105, 108, 109, 112], "matthew": [2, 52], "brett": 2, "pydagogu": 2, "instruct": [2, 53, 100], "instal": [2, 3, 4, 5, 7, 10, 30, 33, 34, 42, 43, 44, 46, 48, 53, 55, 79, 101, 104, 105, 108], "set": [2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 23, 26, 27, 30, 31, 34, 37, 46, 48, 50, 52, 53, 57, 61, 66, 67, 68, 81, 83, 87, 88, 89, 92, 96, 101, 102, 103, 104, 105, 106, 108, 109, 111, 114], "ssh": 2, "configur": [2, 7, 19, 23, 32, 41, 67, 108], "step": [2, 3, 10, 13, 14, 15, 16, 26, 34, 37, 39, 44, 48, 52, 53, 55, 57, 68, 72, 88, 105, 112, 114], "complet": [2, 3, 5, 30, 53, 57, 112], "seamlessli": [2, 67], "between": [2, 3, 4, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 21, 24, 26, 27, 30, 32, 33, 34, 36, 38, 39, 40, 41, 46, 50, 53, 60, 80, 82, 83, 91, 99, 105, 108, 114], "local": [2, 3, 4, 7, 15, 16, 19, 20, 32, 33, 39, 48, 101, 102, 104, 108], "repositori": [2, 3, 4, 5, 99, 102], "would": [3, 13, 15, 16, 19, 39, 43, 100, 101, 105, 106, 109], "start": [3, 4, 6, 12, 13, 15, 16, 26, 30, 50, 57, 61, 69, 83, 87, 91, 101, 105, 106, 108], "search": [3, 30, 106], "someon": 3, "els": [3, 37, 83, 101], "don": [3, 10, 11, 18, 24, 26, 30, 40, 42, 53, 55, 100, 105, 111], "follow": [3, 4, 13, 16, 18, 23, 26, 27, 30, 34, 38, 46, 48, 53, 57, 60, 61, 63, 65, 67, 79, 81, 83, 87, 88, 91, 95, 100, 101, 102, 103, 105, 106, 108, 109, 114], "minor": [3, 102, 105], "ahead": [3, 102, 108], "major": [3, 53, 102], "That": [3, 19], "other": [3, 4, 6, 7, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 37, 38, 39, 42, 43, 44, 45, 46, 49, 53, 60, 61, 66, 67, 68, 69, 71, 72, 76, 78, 79, 80, 81, 86, 87, 95, 96, 98, 99, 100, 105, 106, 108, 109, 112, 113], "weigh": 3, "should": [3, 4, 5, 12, 13, 14, 15, 22, 26, 27, 30, 31, 34, 36, 42, 44, 53, 57, 68, 72, 77, 78, 83, 87, 92, 100, 101, 102, 105, 108, 109, 114], "link": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 102, 104], "descript": [3, 5, 15, 30, 53, 57, 58, 61, 83, 87, 96, 97, 105, 108, 109], "here": [3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 60, 78, 100, 102, 105, 107, 109], "overview": [3, 4], "workflow": [3, 4, 48, 108], "inlin": [3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 53], "expand": [3, 4, 44, 84], "throughout": [3, 4, 9, 10, 14, 19, 26, 27, 30, 34, 39, 48, 50, 53, 55, 98, 105], "rest": [3, 4, 14, 19, 26], "isol": [3, 4], "version": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 67, 70, 71, 85, 99, 105, 109], "comput": [3, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 52, 53, 55, 56, 99, 100, 104, 108, 109, 113], "off": [3, 4, 12, 16, 46, 50, 89, 106, 108], "run": [3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 40, 42, 44, 46, 48, 49, 52, 53, 55, 59, 61, 97, 100, 101, 102, 105, 110], "hit": [3, 4, 108], "button": [3, 4], "want": [3, 4, 7, 9, 10, 15, 16, 18, 19, 21, 22, 23, 26, 30, 31, 36, 42, 43, 44, 48, 50, 52, 55, 96, 100, 108, 111], "clone": [3, 100], "machin": [3, 4, 15, 48, 100, 105, 108], "git": [3, 4, 100, 102], "http": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 100, 104, 105], "com": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 100, 104, 105, 108], "cd": [3, 4, 100, 102, 104, 108], "remot": [3, 4], "upstream": [3, 4], "directori": [3, 4, 5, 30, 89, 101, 102, 104], "ll": [3, 4, 27], "highli": [3, 26, 61, 85, 100], "experiment": [3, 30], "interfer": [3, 100], "stabl": [3, 13, 14, 22, 100], "sinc": [3, 4, 15, 45, 57, 67, 87, 102, 106], "split": [3, 5, 26, 36, 89, 94, 98, 103, 105], "actual": [3, 4, 5, 16, 40, 52, 56, 108, 111, 112], "suit": [3, 53, 100, 114], "mode": [3, 33, 34, 38, 96, 104], "either": [3, 12, 13, 15, 19, 27, 30, 43, 45, 57, 62, 83, 103, 106, 109], "time": [3, 4, 12, 13, 14, 15, 16, 18, 19, 20, 26, 30, 33, 34, 36, 37, 38, 40, 52, 53, 55, 56, 57, 61, 63, 67, 68, 72, 78, 79, 88, 89, 94, 99, 102, 103, 105, 106, 108, 111, 112, 114], "contributor": [3, 108], "lot": [3, 66, 108], "experi": 3, "manag": [3, 15, 30, 53, 96, 100, 104, 108], "strongli": [3, 100, 108], "suggest": [3, 12, 16, 19], "choos": [3, 10, 13, 16, 19, 20, 26, 30, 34, 36, 42, 43, 48, 49, 53, 103], "anaconda": 3, "miniconda": [3, 4], "date": [3, 4, 102], "updat": [3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 72, 99, 100, 105, 106, 108, 110, 114], "without": [3, 4, 13, 15, 28, 30, 34, 37, 50, 53, 61, 87, 99, 103, 104, 105, 106, 108, 109, 114], "touch": [3, 61], "exist": [3, 15, 19, 37, 53, 60, 103, 108, 109], "dev": [3, 102], "activ": [3, 4, 82, 100], "when": [3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 33, 34, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 57, 60, 61, 63, 66, 67, 79, 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trajectory to itself": [[12, "Pairwise-RMSD-of-a-trajectory-to-itself"]], "Pairwise RMSD between two trajectories": [[12, "Pairwise-RMSD-between-two-trajectories"]], "Calculating the root mean square deviation of atomic structures": [[13, "Calculating-the-root-mean-square-deviation-of-atomic-structures"]], "RMSD between two sets of coordinates": [[13, "RMSD-between-two-sets-of-coordinates"]], "RMSD of a Universe with multiple selections": [[13, "RMSD-of-a-Universe-with-multiple-selections"]], "Plotting the data": [[13, "Plotting-the-data"]], "RMSD of an AtomGroup with multiple selections": [[13, "RMSD-of-an-AtomGroup-with-multiple-selections"]], "Weighted RMSD of a trajectory": [[13, "Weighted-RMSD-of-a-trajectory"]], "Mass": [[13, "Mass"]], "Custom weights": [[13, "Custom-weights"]], "Calculating the root mean square fluctuation over a trajectory": [[14, "Calculating-the-root-mean-square-fluctuation-over-a-trajectory"]], "Creating an average structure": [[14, "Creating-an-average-structure"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Plotting RMSF": [[14, "Plotting-RMSF"]], "Visualising RMSF as B-factors": [[14, "Visualising-RMSF-as-B-factors"]], "Parallelizing analysis": [[15, "Parallelizing-analysis"]], "Radius of gyration": [[15, "Radius-of-gyration"], [16, "Radius-of-gyration"]], "Serial Analysis": [[15, "Serial-Analysis"]], "Parallelization in a simple per-frame fashion": [[15, "Parallelization-in-a-simple-per-frame-fashion"]], "Frame-wise form of the function": [[15, "Frame-wise-form-of-the-function"]], "Parallelization with multiprocessing": [[15, "Parallelization-with-multiprocessing"]], "Parallelization with dask": [[15, "Parallelization-with-dask"]], "Parallelization in a split-apply-combine fashion": [[15, "Parallelization-in-a-split-apply-combine-fashion"]], "Block analysis function": [[15, "Block-analysis-function"]], "Split the trajectory": [[15, "Split-the-trajectory"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Combine the results": [[15, "Combine-the-results"]], "Other possible parallelism approaches for multiple analyses": [[15, "Other-possible-parallelism-approaches-for-multiple-analyses"]], "See Also": [[15, "See-Also"]], "Writing your own trajectory analysis": [[16, "Writing-your-own-trajectory-analysis"]], "Creating an analysis from a function": [[16, "Creating-an-analysis-from-a-function"]], "Transforming a function into a class": [[16, "Transforming-a-function-into-a-class"]], "Creating your own class": [[16, "Creating-your-own-class"]], "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"]], "Write your own native contacts analysis method": [[18, "Write-your-own-native-contacts-analysis-method"]], "Defining salt bridges": [[18, "Defining-salt-bridges"]], "Define your own function": [[18, "Define-your-own-function"]], "Plotting": [[18, "Plotting"], [19, "Plotting"], [19, "id6"], [19, "id7"], [20, "Plotting"], [21, "Plotting"], [22, "Plotting"], [22, "id4"], [23, "Plotting"], [24, "Plotting"], [24, "id4"], [30, "Plotting"], [30, "id8"], [37, "Plotting"], [42, "Plotting"], [42, "id5"], [42, "id6"], [44, "Plotting"], [44, "id5"], [44, "id6"], [45, "Plotting"], [46, "Plotting"], [46, "id5"]], "Fraction of native contacts over a trajectory": [[19, "Fraction-of-native-contacts-over-a-trajectory"]], "Defining the groups for contact analysis": [[19, "Defining-the-groups-for-contact-analysis"], [21, "Defining-the-groups-for-contact-analysis"]], "Hard cutoff with a single reference": [[19, "Hard-cutoff-with-a-single-reference"]], "Radius cutoff": [[19, "Radius-cutoff"]], "Soft cutoff and multiple references": [[19, "Soft-cutoff-and-multiple-references"]], "Multiple references": [[19, "Multiple-references"]], "Soft cutoff": [[19, "Soft-cutoff"]], "Q1 vs Q2 contact analysis": [[20, "Q1-vs-Q2-contact-analysis"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Contact analysis: number of contacts within a cutoff": [[21, "Contact-analysis:-number-of-contacts-within-a-cutoff"]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Atom-wise distances between matching AtomGroups": [[22, "Atom-wise-distances-between-matching-AtomGroups"]], "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"]], "All distances between two selections": [[23, "All-distances-between-two-selections"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Plotting distance as a heatmap": [[23, "Plotting-distance-as-a-heatmap"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "All distances within a selection": [[24, "All-distances-within-a-selection"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating hydrogen bonds: the basics": [[26, "Calculating-hydrogen-bonds:-the-basics"]], "Hydrogen bonds": [[26, "Hydrogen-bonds"]], "Find water-water hydrogen bonds": [[26, "Find-water-water-hydrogen-bonds"]], "Accessing the results": [[26, "Accessing-the-results"]], "Helper functions": [[26, "Helper-functions"]], "Further analysis": [[26, "Further-analysis"]], "Store data": [[26, "Store-data"]], "Calculating hydrogen bond lifetimes": [[27, "Calculating-hydrogen-bond-lifetimes"]], "Find all hydrogen bonds": [[27, "Find-all-hydrogen-bonds"], [28, "Find-all-hydrogen-bonds"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Intermittent lifetime": [[27, "Intermittent-lifetime"]], "Hydrogen bond lifetime of individual hydrogen bonds": [[27, "Hydrogen-bond-lifetime-of-individual-hydrogen-bonds"]], "Calculating hydrogen bonds: advanced selections": [[28, "Calculating-hydrogen-bonds:-advanced-selections"]], "Use guess_acceptors and guess_hydrogens to create atom selections": [[28, "Use-guess_acceptors-and-guess_hydrogens-to-create-atom-selections"]], "More advanced selections": [[28, "More-advanced-selections"]], "Hydrogen bonds between specific groups": [[28, "Hydrogen-bonds-between-specific-groups"]], "Analysing pore dimensions with HOLE2": [[30, "Analysing-pore-dimensions-with-HOLE2"]], "Using HOLE with a PDB file": [[30, "Using-HOLE-with-a-PDB-file"]], "Using HOLE with a trajectory": [[30, "Using-HOLE-with-a-trajectory"]], "Working with the data": [[30, "Working-with-the-data"]], "Visualising the VMD surface": [[30, "Visualising-the-VMD-surface"]], "Ordering HOLE profiles with an order parameter": [[30, "Ordering-HOLE-profiles-with-an-order-parameter"]], "Deleting HOLE files": [[30, "Deleting-HOLE-files"]], "Determining the persistence length of a polymer": [[31, "Determining-the-persistence-length-of-a-polymer"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Non-linear dimension reduction to diffusion maps": [[33, "Non-linear-dimension-reduction-to-diffusion-maps"]], "Diffusion maps": [[33, "Diffusion-maps"]], "Principal component analysis of a trajectory": [[34, "Principal-component-analysis-of-a-trajectory"]], "Principal component analysis": [[34, "Principal-component-analysis"]], "Visualising projections into a reduced dimensional space": [[34, "Visualising-projections-into-a-reduced-dimensional-space"]], "Measuring convergence with cosine content": [[34, "Measuring-convergence-with-cosine-content"]], "Average radial distribution functions": [[36, "Average-radial-distribution-functions"]], "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 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"]], "Protein dihedral angle analysis": [[37, "Protein-dihedral-angle-analysis"]], "Selecting dihedral atom groups": [[37, "Selecting-dihedral-atom-groups"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Ramachandran analysis": [[37, "Ramachandran-analysis"]], "Janin analysis": [[37, "Janin-analysis"]], "Elastic network analysis": [[38, "Elastic-network-analysis"]], "Using a Gaussian network model": [[38, "Using-a-Gaussian-network-model"]], "Using a Gaussian network model with only close contacts": [[38, "Using-a-Gaussian-network-model-with-only-close-contacts"]], "Helix analysis": [[39, "Helix-analysis"], [39, "id6"]], "Running the analysis": [[39, "Running-the-analysis"]], "Calculating the RDF atom-to-atom": [[40, "Calculating-the-RDF-atom-to-atom"]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "The site-specific RDF without densities": [[40, "The-site-specific-RDF-without-densities"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, "Calculating-the-Clustering-Ensemble-Similarity-between-ensembles"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Trying out different clustering parameters": [[42, "Trying-out-different-clustering-parameters"]], "Estimating the error in a clustering ensemble similarity analysis": [[42, "Estimating-the-error-in-a-clustering-ensemble-similarity-analysis"]], "Evaluating convergence": [[43, "Evaluating-convergence"]], "Evaluating convergence with similarity measures": [[43, "Evaluating-convergence-with-similarity-measures"]], "Using default arguments with clustering ensemble similarity": [[43, "Using-default-arguments-with-clustering-ensemble-similarity"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Using default arguments with dimension reduction ensemble similarity": [[43, "Using-default-arguments-with-dimension-reduction-ensemble-similarity"]], "Comparing different dimensionality reduction methods": [[43, "Comparing-different-dimensionality-reduction-methods"]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, "Calculating-the-Dimension-Reduction-Ensemble-Similarity-between-ensembles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Trying out different dimension reduction parameters": [[44, "Trying-out-different-dimension-reduction-parameters"]], "Estimating the error in a dimension reduction ensemble similarity analysis": [[44, "Estimating-the-error-in-a-dimension-reduction-ensemble-similarity-analysis"]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, "Calculating-the-Harmonic-Ensemble-Similarity-between-ensembles"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Comparing the geometric similarity of trajectories": [[46, "Comparing-the-geometric-similarity-of-trajectories"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Generating paths": [[46, "Generating-paths"]], "Hausdorff method": [[46, "Hausdorff-method"]], "Discrete Fr\u00e9chet distances": [[46, "Discrete-Fr\u00e9chet-distances"]], "Calculating the solvent density around a protein": [[48, "Calculating-the-solvent-density-around-a-protein"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Visualisation": [[48, "Visualisation"]], "matplotlib (3D static plot)": [[48, "matplotlib-(3D-static-plot)"]], "nglview (interactive)": [[48, "nglview-(interactive)"]], "scikit-image (triangulated surface)": [[48, "scikit-image-(triangulated-surface)"]], "pyvista (3D surface)": [[48, "pyvista-(3D-surface)"]], "2D averaging": [[48, "2D-averaging"]], "Computing mass and charge density on each axis": [[49, "Computing-mass-and-charge-density-on-each-axis"]], "Constructing, modifying, and adding to a Universe": [[50, "Constructing,-modifying,-and-adding-to-a-Universe"]], "Creating and populating a Universe with water": [[50, "Creating-and-populating-a-Universe-with-water"]], "Creating a blank Universe": [[50, "Creating-a-blank-Universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding positions": [[50, "Adding-positions"]], "Adding bonds": [[50, "Adding-bonds"]], "Merging with a protein": [[50, "Merging-with-a-protein"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Tiling into a larger Universe": [[50, "Tiling-into-a-larger-Universe"]], "Acknowledgments": [[50, "Acknowledgments"]], "Other": [[51, "other"]], "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms": [[52, "Using-ParmEd-with-MDAnalysis-and-OpenMM-to-simulate-a-selection-of-atoms"]], "Loading files: the difference between ParmEd and MDAnalysis": [[52, "Loading-files:-the-difference-between-ParmEd-and-MDAnalysis"]], "Using MDAnalysis to select atoms": [[52, "Using-MDAnalysis-to-select-atoms"]], "Using ParmEd and OpenMM to create a simulation system": [[52, "Using-ParmEd-and-OpenMM-to-create-a-simulation-system"]], "Quick start guide": [[53, "Quick-start-guide"]], "Overview": [[53, "Overview"]], "Loading a structure or trajectory": [[53, "Loading-a-structure-or-trajectory"]], "Working with groups of atoms": [[53, "Working-with-groups-of-atoms"]], "Selecting atoms": [[53, "Selecting-atoms"]], "Getting atom information from AtomGroups": [[53, "Getting-atom-information-from-AtomGroups"]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Working with trajectories": [[53, "Working-with-trajectories"]], "Dynamic selection": [[53, "Dynamic-selection"]], "Writing out coordinates": [[53, "Writing-out-coordinates"]], "Single frame": [[53, "Single-frame"]], "Trajectories": [[53, "Trajectories"], [56, "trajectories"], [111, "trajectories"]], "RMSD": [[53, "RMSD"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Transformations": [[54, "transformations"]], "Centering a trajectory in the box": [[55, "Centering-a-trajectory-in-the-box"]], "Before transformation": [[55, "Before-transformation"]], "Unwrapping the protein": [[55, "Unwrapping-the-protein"]], "Centering in the box": [[55, "Centering-in-the-box"]], "Wrapping the solvent back into the box": [[55, "Wrapping-the-solvent-back-into-the-box"]], "Doing all this on-the-fly": [[55, "Doing-all-this-on-the-fly"]], "Frequently asked questions": [[56, "frequently-asked-questions"]], "Why do the atom positions change over trajectories?": [[56, "why-do-the-atom-positions-change-over-trajectories"]], "Auxiliary files": [[57, "auxiliary-files"]], "Supported formats": [[57, "supported-formats"]], "XVG Files": [[57, "xvg-files"]], "Reading data directly": [[57, "reading-data-directly"]], "Loading data into a Universe": [[57, "loading-data-into-a-universe"]], "Passing arguments to auxiliary data": [[57, "passing-arguments-to-auxiliary-data"]], "Iterating over auxiliary data": [[57, "iterating-over-auxiliary-data"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[57, "recreating-auxiliaries"]], "EDR Files": [[57, "edr-files"]], "Standalone Usage": [[57, "standalone-usage"]], "Unit Handling": [[57, "unit-handling"]], "Use with Trajectories": [[57, "use-with-trajectories"]], "Selecting Trajectory Frames Based on Auxiliary Data": [[57, "selecting-trajectory-frames-based-on-auxiliary-data"]], "Memory Usage": [[57, "memory-usage"]], "Coordinates": [[58, "coordinates"], [61, "coordinates"]], "Table of supported coordinate readers and the information read": [[58, "id2"], [61, "id12"]], "Format reference": [[59, "format-reference"]], "Guessing": [[60, "guessing"]], "Masses": [[60, "masses"]], "Types": [[60, "types"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Format overview": [[61, "format-overview"]], "Table of all supported formats in MDAnalysis": [[61, "id10"]], "Topology": [[61, "topology"], [97, "topology"]], "Table of supported topology parsers and the attributes read": [[61, "id11"], [97, "id1"]], "chemfiles (chemfiles Trajectory or file)": [[62, "chemfiles-chemfiles-trajectory-or-file"]], "CONFIG (DL_Poly Config)": [[63, "config-dl-poly-config"]], "HISTORY (DL_Poly Config)": [[63, "history-dl-poly-config"]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, "coor-nambdin-namd-binary-restart-files"]], "CRD (CHARMM CARD files)": [[65, "crd-charmm-card-files"]], "Reading in": [[65, "reading-in"], [66, "reading-in"], [67, "reading-in"], [70, "reading-in"], [71, "reading-in"], [72, "reading-in"], [76, "reading-in"], [79, "reading-in"], [81, "reading-in"], [82, "reading-in"], [83, "reading-in"], [84, "reading-in"], [85, "reading-in"], [88, "reading-in"], [89, "reading-in"], [94, "reading-in"], [95, "reading-in"]], "Writing out": [[65, "writing-out"], [66, "writing-out"], [67, "writing-out"], [71, "writing-out"], [79, "writing-out"], [81, "writing-out"], [82, "writing-out"], [83, "writing-out"], [89, "writing-out"]], "DATA (LAMMPS)": [[66, "data-lammps"]], "DCD (CHARMM, NAMD, or LAMMPS trajectory)": [[67, "dcd-charmm-namd-or-lammps-trajectory"]], "DCD (Flexible LAMMPS trajectory)": [[68, "dcd-flexible-lammps-trajectory"]], "DMS (Desmond Molecular Structure files)": [[69, "dms-desmond-molecular-structure-files"]], "GMS (Gamess trajectory)": [[70, "gms-gamess-trajectory"]], "GRO (GROMACS structure file)": [[71, "gro-gromacs-structure-file"]], "GSD (HOOMD GSD file)": [[72, "gsd-hoomd-gsd-file"]], "IN, FHIAIMS (FHI-aims input files)": [[73, "in-fhiaims-fhi-aims-input-files"]], "INPCRD, RESTRT (AMBER restart files)": [[74, "inpcrd-restrt-amber-restart-files"]], "ITP (GROMACS portable topology files)": [[75, "itp-gromacs-portable-topology-files"]], "LAMMPSDUMP (LAMMPS ascii dump file)": [[76, "lammpsdump-lammps-ascii-dump-file"]], "MMTF (Macromolecular Transmission Format)": [[77, "mmtf-macromolecular-transmission-format"]], "MOL2 (Tripos structure)": [[78, "mol2-tripos-structure"]], "MOL2 specification": [[78, "mol2-specification"]], "NCDF, NC (AMBER NetCDF trajectory)": [[79, "ncdf-nc-amber-netcdf-trajectory"]], "ParmEd (ParmEd Structure)": [[80, "parmed-parmed-structure"]], "PDB, ENT (Standard PDB file)": [[81, "pdb-ent-standard-pdb-file"]], "PDB specification": [[81, "pdb-specification"]], "CRYST1 fields": [[81, "id1"]], "ATOM/HETATM fields": [[81, "id2"]], "PDBQT (Autodock structure)": [[82, "pdbqt-autodock-structure"]], "PDBQT specification": [[82, "pdbqt-specification"]], "PDB format with AutoDOCK extensions for the PDBQT format.": [[82, "id1"]], "PQR file (PDB2PQR / APBS)": [[83, "pqr-file-pdb2pqr-apbs"]], "PQR specification": [[83, "pqr-specification"]], "PSF (CHARMM, NAMD, or XPLOR protein structure file)": [[84, "psf-charmm-namd-or-xplor-protein-structure-file"]], "PSF specification": [[84, "psf-specification"]], "TNG (Trajectory Next Generation)": [[85, "tng-trajectory-next-generation"]], "TOP, PRMTOP, PARM7 (AMBER topology)": [[86, "top-prmtop-parm7-amber-topology"]], "AMBER specification": [[86, "amber-specification"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Developer notes": [[86, "developer-notes"], [87, "developer-notes"], [89, "developer-notes"], [91, "developer-notes"]], "TPR (GROMACS run topology files)": [[87, "tpr-gromacs-run-topology-files"]], "Supported versions": [[87, "supported-versions"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[87, "id1"]], "TPR specification": [[87, "tpr-specification"]], "segid and chainID": [[87, "segid-and-chainid"]], "Bonds": [[87, "bonds"]], "GROMACS entries used to create bonds.": [[87, "id2"]], "GROMACS entries used to create angles.": [[87, "id3"]], "GROMACS entries used to create dihedrals.": [[87, "id4"]], "GROMACS entries used to create improper dihedrals.": [[87, "id5"]], "TRJ, MDCRD, CRDBOX (AMBER ASCII trajectory)": [[88, "trj-mdcrd-crdbox-amber-ascii-trajectory"]], "TRR (GROMACS lossless trajectory file)": [[89, "trr-gromacs-lossless-trajectory-file"]], "TRZ (IBIsCO and YASP trajectory)": [[90, "trz-ibisco-and-yasp-trajectory"]], "TXYZ, ARC (Tinker)": [[91, "txyz-arc-tinker"]], "XML (HOOMD)": [[92, "xml-hoomd"]], "XPDB (Extended PDB file)": [[93, "xpdb-extended-pdb-file"]], "XTC (GROMACS compressed trajectory file)": [[94, "xtc-gromacs-compressed-trajectory-file"]], "XYZ trajectory": [[95, "xyz-trajectory"]], "XYZ specification": [[95, "xyz-specification"]], "Note": [[95, "note"]], "Selection exporters": [[96, "selection-exporters"]], "Supported selection exporters": [[96, "id2"]], "Writing selections": [[96, "writing-selections"]], "Single AtomGroup": [[96, "single-atomgroup"]], "Multiple selections": [[96, "multiple-selections"]], "Reading in selections": [[96, "reading-in-selections"]], "Groups of atoms": [[98, "groups-of-atoms"]], "Residues and Segments": [[98, "residues-and-segments"]], "Use case: Sequence of residues by segment": [[98, "use-case-sequence-of-residues-by-segment"]], "Use case: Atoms list grouped by residues": [[98, "use-case-atoms-list-grouped-by-residues"]], "Fragments": [[98, "fragments"]], "Welcome to MDAnalysis User Guide\u2019s documentation!": [[99, "welcome-to-mdanalysis-user-guide-s-documentation"]], "Why MDAnalysis?": [[99, "why-mdanalysis"]], "Participating": [[99, "participating"]], "Communications": [[99, "communications"]], "Installation": [[100, "installation"]], "conda": [[100, "conda"]], "pip": [[100, "pip"]], "Development versions": [[100, "development-versions"]], "Testing": [[100, "testing"]], "Custom compiler flags and optimised installations": [[100, "custom-compiler-flags-and-optimised-installations"]], "Additional datasets": [[100, "additional-datasets"]], "Module imports in MDAnalysis": [[101, "module-imports-in-mdanalysis"]], "General rules for importing": [[101, "general-rules-for-importing"]], "Module imports in MDAnalysis.analysis": [[101, "module-imports-in-mdanalysis-analysis"]], "Module imports in the test suite": [[101, "module-imports-in-the-test-suite"]], "Module dependencies in the code": [[101, "module-dependencies-in-the-code"]], "List of core module dependencies": [[101, "list-of-core-module-dependencies"]], "Modules in the \u201ccore\u201d": [[101, "modules-in-the-core"]], "Optional modules in MDAnalysis.analysis and MDAnalysis.visualization": [[101, "optional-modules-in-mdanalysis-analysis-and-mdanalysis-visualization"]], "Preparing a release": [[102, "preparing-a-release"]], "Release policy and release numbering": [[102, "release-policy-and-release-numbering"]], "Typical workflow for preparing a release": [[102, "typical-workflow-for-preparing-a-release"]], "Summary of tasks": [[102, "summary-of-tasks"]], "Getting the develop branch ready for a release": [[102, "getting-the-develop-branch-ready-for-a-release"]], "Packaging the release": [[102, "packaging-the-release"]], "Completing the release": [[102, "completing-the-release"]], "Manually upload Cirrus CI wheels (temporary)": [[102, "manually-upload-cirrus-ci-wheels-temporary"]], "Update conda-forge packages": [[102, "update-conda-forge-packages"]], "Create a release of the UserGuide": [[102, "create-a-release-of-the-userguide"]], "Create a blog post outlining the release": [[102, "create-a-blog-post-outlining-the-release"]], "Increment develop branch files ready for the next version": [[102, "increment-develop-branch-files-ready-for-the-next-version"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Reading and writing files": [[103, "reading-and-writing-files"]], "Input": [[103, "input"]], "Reading multiple trajectories": [[103, "reading-multiple-trajectories"]], "Trajectory formats": [[103, "trajectory-formats"]], "In-memory trajectories": [[103, "in-memory-trajectories"]], "Reading trajectories into memory": [[103, "reading-trajectories-into-memory"]], "Transferring trajectories into memory": [[103, "transferring-trajectories-into-memory"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "In-memory trajectories of an atom selection": [[103, "in-memory-trajectories-of-an-atom-selection"]], "Output": [[103, "output"]], "Frames and trajectories": [[103, "frames-and-trajectories"]], "Pickling": [[103, "pickling"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "MDAnalysis Release Notes": [[105, "mdanalysis-release-notes"]], "Release 2.6.1 of MDAnalysis": [[105, "release-2-6-1-of-mdanalysis"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "New Contributors": [[105, "new-contributors"], [105, "id1"], [105, "id5"], [105, "id13"]], "Release 2.6.0 of MDAnalysis": [[105, "release-2-6-0-of-mdanalysis"]], "Major changes:": [[105, "major-changes"], [105, "id2"], [105, "id8"], [105, "id14"], [105, "id19"], [105, "id24"], [105, "id30"]], "Fixes:": [[105, "fixes"], [105, "id3"], [105, "id9"], [105, "id15"], [105, "id21"], [105, "id26"], [105, "id32"]], "Enhancements:": [[105, "enhancements"], [105, "id16"], [105, "id20"], [105, "id25"], [105, "id31"]], "Changes:": [[105, "changes"], [105, "id4"], [105, "id11"], [105, "id17"], [105, "id22"], [105, "id27"], [105, "id33"]], "Deprecations:": [[105, "deprecations"], [105, "id12"], [105, "id18"], [105, "id23"], [105, "id28"], [105, "id34"]], "Release 2.5.0 of MDAnalysis": [[105, "release-2-5-0-of-mdanalysis"]], "Enchancements:": [[105, "enchancements"], [105, "id10"]], "Release 2.4.3 of MDAnalysis": [[105, "release-2-4-3-of-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id6"], [105, "id7"]], "Release 2.4.2 of MDAnalysis": [[105, "release-2-4-2-of-mdanalysis"]], "Release 2.4.1 of MDAnalysis": [[105, "release-2-4-1-of-mdanalysis"]], "Release 2.4.0 of MDAnalysis": [[105, "release-2-4-0-of-mdanalysis"]], "Release 2.3.0 of MDAnalysis": [[105, "release-2-3-0-of-mdanalysis"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Release 2.2.0 of MDAnalysis": [[105, "release-2-2-0-of-mdanalysis"]], "Known test failures:": [[105, "known-test-failures"], [105, "id29"]], "Release 2.1.0 of MDAnalysis": [[105, "release-2-1-0-of-mdanalysis"]], "Release 2.0.0 of MDAnalysis": [[105, "release-2-0-0-of-mdanalysis"]], "Notes:": [[105, "notes"]], "Known issues:": [[105, "known-issues"]], "Selection Keywords": [[106, "selection-keywords"]], "Simple selections": [[106, "simple-selections"]], "Boolean": [[106, "boolean"]], "Geometric": [[106, "geometric"]], "Similarity and connectivity": [[106, "similarity-and-connectivity"]], "Index": [[106, "index"]], "Preexisting selections and modifiers": [[106, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[106, "dynamic-selections"]], "Ordered selections": [[106, "ordered-selections"]], "Standard residues in MDAnalysis selections": [[107, "standard-residues-in-mdanalysis-selections"]], "Proteins": [[107, "proteins"]], "Protein backbone": [[107, "protein-backbone"]], "Nucleic acids": [[107, "nucleic-acids"]], "Nucleic backbone": [[107, "nucleic-backbone"]], "Nucleobases": [[107, "nucleobases"]], "Nucleic sugars": [[107, "nucleic-sugars"]], "Tests in MDAnalysis": [[108, "tests-in-mdanalysis"]], "Running the test suite": [[108, "running-the-test-suite"]], "Testing in parallel": [[108, "testing-in-parallel"]], "Test coverage": [[108, "test-coverage"]], "Continuous Integration tools": [[108, "continuous-integration-tools"]], "GitHub Actions": [[108, "github-actions"]], "Azure": [[108, "azure"]], "Cirrus CI": [[108, "cirrus-ci"]], "Codecov": [[108, "codecov"]], "Writing new tests": [[108, "writing-new-tests"]], "General conventions": [[108, "general-conventions"]], "Assertions": [[108, "assertions"]], "Testing exceptions and warnings": [[108, "testing-exceptions-and-warnings"]], "Failing tests": [[108, "failing-tests"]], "Skipping tests": [[108, "skipping-tests"]], "Fixtures": [[108, "fixtures"]], "Testing the same function with different inputs": [[108, "testing-the-same-function-with-different-inputs"]], "Temporary files and directories": [[108, "temporary-files-and-directories"]], "Module imports": [[108, "module-imports"]], "Tests for analysis and visualization modules": [[108, "tests-for-analysis-and-visualization-modules"]], "Using test data files": [[108, "using-test-data-files"]], "The topology system": [[109, "the-topology-system"]], "Topology attributes": [[109, "topology-attributes"]], "Canonical attributes": [[109, "canonical-attributes"]], "Format-specific attributes": [[109, "format-specific-attributes"]], "Connectivity information": [[109, "connectivity-information"]], "Adding TopologyAttrs": [[109, "adding-topologyattrs"]], "Modifying TopologyAttrs": [[109, "modifying-topologyattrs"]], "Default values and attribute levels": [[109, "default-values-and-attribute-levels"]], "Topology objects": [[109, "topology-objects"]], "Adding to a Universe": [[109, "adding-to-a-universe"]], "Creating with an AtomGroup": [[109, "creating-with-an-atomgroup"]], "Deleting from a Universe": [[109, "deleting-from-a-universe"]], "Topology-specific methods": [[109, "topology-specific-methods"]], "Slicing trajectories": [[110, "slicing-trajectories"]], "On-the-fly transformations": [[112, "on-the-fly-transformations"]], "Example workflows": [[112, "example-workflows"]], "Custom transformations": [[112, "custom-transformations"]], "Units and constants": [[113, "units-and-constants"]], "Base units in MDAnalysis": [[113, "id1"]], "Unit conversion": [[113, "unit-conversion"]], "Constants": [[113, "constants"]], "Length": [[113, "length"]], "Density": [[113, "density"]], "Time": [[113, "time"]], "Charge": [[113, "charge"]], "Speed": [[113, "speed"]], "Force": [[113, "force"]], "Energy": [[113, "energy"]], "Universe": [[114, "universe"]], "Creating a Universe": [[114, "creating-a-universe"]], "Loading from files": [[114, "loading-from-files"]], "Constructing from AtomGroups": [[114, "constructing-from-atomgroups"]], "Constructing from scratch": [[114, "constructing-from-scratch"]], "Guessing topology attributes": [[114, "guessing-topology-attributes"]], "Universe properties and methods": [[114, "universe-properties-and-methods"]]}, "indexentries": {"x y z": [[83, "term-X-Y-Z"]], "atomname": [[83, "term-atomName"]], "chainid": [[83, "term-chainID"]], "charge": [[83, "term-charge"]], "radius": [[83, "term-radius"]], "recordname": [[83, "term-recordName"]], "residuename": [[83, "term-residueName"]], "residuenumber": [[83, "term-residueNumber"]], "serial": [[83, "term-serial"]], "duecredit_enable": [[104, "index-0"]], "environment variable": [[104, "index-0"]]}}) \ No newline at end of file diff --git a/2.7.0-dev0/standard_selections.html b/2.7.0-dev0/standard_selections.html index 9fbbd77ab..770c418d8 100644 --- a/2.7.0-dev0/standard_selections.html +++ b/2.7.0-dev0/standard_selections.html @@ -332,9 +332,9 @@

    Protein backbone -

    C

    +

    O

    N

    -

    O

    +

    C

    CA

    @@ -347,43 +347,43 @@

    Protein backbone -

    RA5

    -

    RA3

    -

    DC

    +

    RA

    +

    DG3

    U

    -

    GUA

    -

    RU3

    -

    DA5

    -

    DA3

    - -

    RU5

    +

    DC

    +

    DT

    THY

    +

    ADE

    +

    RC3

    + +

    DA5

    A

    +

    GUA

    +

    DA3

    +

    RU5

    +

    RA3

    +

    DT5

    RU

    -

    ADE

    + +

    DG

    +

    RG3

    +

    DT3

    +

    RC5

    URA

    -

    RC3

    +

    RU3

    DC5

    +

    C

    -

    DT5

    -

    DT3

    -

    RA

    -

    DG5

    +

    DA

    T

    +

    CYT

    +

    RG5

    +

    RA5

    +

    DG5

    RG

    DC3

    -

    RG5

    -

    DA

    -

    DT

    -

    RC5

    -

    DG

    -

    C

    -

    RC

    -

    CYT

    -

    DG3

    - -

    RG3

    +

    RC

    G

    @@ -399,10 +399,10 @@

    Nucleic backbone -

    O3’

    +

    O5’

    P

    C3’

    -

    O5’

    +

    O3’

    C5’

    @@ -414,22 +414,22 @@

    Nucleic backbone

    O6

    -

    N1

    -

    C8

    -

    N6

    -

    N4

    +

    C6

    +

    C5

    O2

    +

    N3

    +

    N6

    N2

    -

    O4

    +

    C2

    -

    N9

    -

    C6

    +

    O4

    +

    N7

    +

    N4

    +

    N1

    +

    N9

    +

    C8

    C4

    C5M

    -

    C2

    -

    N3

    -

    C5

    -

    N7

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

    Nucleic sugars -

    C1’

    -

    O4’

    -

    C3’

    -

    C4’

    +

    C4’

    C2’

    +

    C1’

    +

    C3’

    +

    O4’

    diff --git a/2.7.0-dev0/testing.html b/2.7.0-dev0/testing.html index c156cdfde..de96bd59a 100644 --- a/2.7.0-dev0/testing.html +++ b/2.7.0-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 d1544b2f65facafeda6fd227240a076221c3e256..f09507d2fca4be01eb9bbdf876112f436ba09fb5 100644
GIT binary patch
delta 19
acmZ4CzrufmpbDFbfw6(9$!2ktiOc{$2?dM*

delta 19
acmZ4CzrufmpbDFzfw6&^!DexliOc{#*9C?E

diff --git a/dev/examples/analysis/hydrogen_bonds/hbonds.html b/dev/examples/analysis/hydrogen_bonds/hbonds.html
index 349e37d30..1cf94294d 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 0x7f23b3eedcd0>
+Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7fd022ba1b50>
 
    
 
    
 
    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 0x7f23b3a92910>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7fd022280670>]
 
 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 4f43b01e2..b00df45a3 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -190,7 +190,7 @@
   
    
 
    Welcome to MDAnalysis User Guide’s documentation!
    
 
    MDAnalysis version: 2.7.0-dev0
    
-
    Last updated: Nov 21, 2023
    
+
    Last updated: Nov 24, 2023
    
 
    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 23f89d779..ae930de7f 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([[0.95849204, 0.7487938 , 0.9704986 ],
-       [0.42354256, 0.2889326 , 0.06184179],
-       [0.5241738 , 0.642687  , 0.6946113 ],
+array([[0.01341493, 0.8954516 , 0.48900408],
+       [0.0416302 , 0.81844276, 0.6713378 ],
+       [0.32844332, 0.8965664 , 0.8370764 ],
        ...,
-       [0.7527609 , 0.1350824 , 0.80041414],
-       [0.1707926 , 0.5413459 , 0.8568687 ],
-       [0.0265642 , 0.16363254, 0.5556602 ]], dtype=float32)
+       [0.04501093, 0.29551986, 0.05062775],
+       [0.6661255 , 0.7034433 , 0.08090701],
+       [0.52956533, 0.7413073 , 0.81429756]], 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([[0.95849204, 0.7487938 , 0.9704986 ], - [0.42354256, 0.2889326 , 0.06184179], - [0.5241738 , 0.642687 , 0.6946113 ], +array([[0.01341493, 0.8954516 , 0.48900408], + [0.0416302 , 0.81844276, 0.6713378 ], + [0.32844332, 0.8965664 , 0.8370764 ], ..., - [0.7527609 , 0.1350824 , 0.80041414], - [0.1707926 , 0.5413459 , 0.8568687 ], - [0.0265642 , 0.16363254, 0.5556602 ]], dtype=float32) + [0.04501093, 0.29551986, 0.05062775], + [0.6661255 , 0.7034433 , 0.08090701], + [0.52956533, 0.7413073 , 0.81429756]], dtype=float32)

    diff --git a/dev/searchindex.js b/dev/searchindex.js index 3fc79fdd6..0c212c24c 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["advanced_topology", "atomgroup", "contributing", "contributing_code", "contributing_docs", "datasets", "examples/README", "examples/analysis/README", "examples/analysis/alignment_and_rms/README", "examples/analysis/alignment_and_rms/aligning_structure_to_another", "examples/analysis/alignment_and_rms/aligning_trajectory", "examples/analysis/alignment_and_rms/aligning_trajectory_to_frame", "examples/analysis/alignment_and_rms/pairwise_rmsd", "examples/analysis/alignment_and_rms/rmsd", "examples/analysis/alignment_and_rms/rmsf", "examples/analysis/custom_parallel_analysis", "examples/analysis/custom_trajectory_analysis", "examples/analysis/distances_and_contacts/README", "examples/analysis/distances_and_contacts/contacts_custom", "examples/analysis/distances_and_contacts/contacts_native_fraction", "examples/analysis/distances_and_contacts/contacts_q1q2", "examples/analysis/distances_and_contacts/contacts_within_cutoff", "examples/analysis/distances_and_contacts/distances_between_atomgroups", "examples/analysis/distances_and_contacts/distances_between_selections", "examples/analysis/distances_and_contacts/distances_within_selection", "examples/analysis/hydrogen_bonds/README", "examples/analysis/hydrogen_bonds/hbonds", "examples/analysis/hydrogen_bonds/hbonds-lifetimes", "examples/analysis/hydrogen_bonds/hbonds-selections", "examples/analysis/polymers_and_membranes/README", "examples/analysis/polymers_and_membranes/hole2", "examples/analysis/polymers_and_membranes/polymer", "examples/analysis/reduced_dimensions/README", "examples/analysis/reduced_dimensions/diffusion_map", "examples/analysis/reduced_dimensions/pca", "examples/analysis/structure/README", "examples/analysis/structure/average_rdf", "examples/analysis/structure/dihedrals", "examples/analysis/structure/elastic_network", "examples/analysis/structure/helanal", "examples/analysis/structure/site_specific_rdf", "examples/analysis/trajectory_similarity/README", "examples/analysis/trajectory_similarity/clustering_ensemble_similarity", "examples/analysis/trajectory_similarity/convergence", "examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity", "examples/analysis/trajectory_similarity/harmonic_ensemble_similarity", "examples/analysis/trajectory_similarity/psa", "examples/analysis/volumetric/README", "examples/analysis/volumetric/density_analysis", "examples/analysis/volumetric/linear_density", "examples/constructing_universe", "examples/other/README", "examples/other/parmed_sim", "examples/quickstart", "examples/transformations/README", "examples/transformations/center_protein_in_box", "faq", "formats/auxiliary", "formats/coordinates", "formats/format_reference", "formats/guessing", "formats/index", "formats/reference/chemfiles", "formats/reference/config", "formats/reference/coor", "formats/reference/crd", "formats/reference/data", "formats/reference/dcd", "formats/reference/dcd_lammps", "formats/reference/dms", "formats/reference/gms", "formats/reference/gro", "formats/reference/gsd", "formats/reference/in", "formats/reference/inpcrd", "formats/reference/itp", "formats/reference/lammpsdump", "formats/reference/mmtf", "formats/reference/mol2", "formats/reference/ncdf", "formats/reference/parmed", "formats/reference/pdb", "formats/reference/pdbqt", "formats/reference/pqr", "formats/reference/psf", "formats/reference/tng", "formats/reference/top", "formats/reference/tpr", "formats/reference/trj", "formats/reference/trr", "formats/reference/trz", "formats/reference/txyz", "formats/reference/xml", "formats/reference/xpdb", "formats/reference/xtc", "formats/reference/xyz", "formats/selection_exporters", "formats/topology", "groups_of_atoms", "index", "installation", "module_imports", 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selections", "Polymers and membranes", "Analysing pore dimensions with HOLE2", "Determining the persistence length of a polymer", "Dimension reduction", "Non-linear dimension reduction to diffusion maps", "Principal component analysis of a trajectory", "Structure", "Average radial distribution functions", "Protein dihedral angle analysis", "Elastic network analysis", "Helix analysis", "Calculating the RDF atom-to-atom", "Trajectory similarity", "Calculating the Clustering Ensemble Similarity between ensembles", "Evaluating convergence", "Calculating the Dimension Reduction Ensemble Similarity between ensembles", "Calculating the Harmonic Ensemble Similarity between ensembles", "Comparing the geometric similarity of trajectories", "Volumetric analyses", "Calculating the solvent density around a protein", "Computing mass and charge density on each axis", "Constructing, modifying, and adding to a Universe", "Other", "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of 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4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114], "7": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114], "dev0": [0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114], "univers": [1, 3, 5, 6, 7, 9, 11, 12, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 56, 60, 61, 62, 66, 68, 71, 77, 80, 81, 82, 88, 89, 93, 94, 95, 96, 98, 99, 103, 105, 106, 108, 110, 111, 112], "contain": [1, 3, 4, 7, 8, 12, 14, 15, 17, 26, 30, 34, 37, 39, 40, 41, 42, 44, 46, 48, 50, 53, 55, 57, 66, 72, 81, 84, 87, 88, 89, 91, 92, 93, 96, 98, 101, 102, 103, 104, 105, 106, 108, 109, 111, 112, 114], "all": [1, 2, 3, 4, 6, 7, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 26, 30, 33, 34, 37, 38, 44, 46, 48, 50, 53, 57, 66, 81, 83, 92, 95, 98, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "particl": [1, 9, 13, 14, 34, 36, 40, 50, 52, 53, 72, 105], "molecular": [1, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 58, 59, 61, 66, 80, 85, 97, 99, 104, 114], "system": [1, 2, 3, 4, 14, 15, 22, 26, 30, 36, 40, 50, 53, 57, 61, 80, 81, 83, 105, 108, 114], "regardless": [1, 3, 53, 113], "whether": [1, 3, 9, 10, 14, 16, 34, 50, 114], "realli": [1, 13, 15, 108], "g": [1, 3, 4, 5, 7, 14, 15, 19, 20, 26, 30, 32, 33, 34, 37, 53, 57, 67, 80, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 112, 113, 114], "mai": [1, 3, 4, 7, 9, 12, 14, 15, 16, 18, 19, 26, 27, 28, 30, 32, 33, 34, 36, 38, 42, 43, 44, 48, 50, 53, 57, 93, 100, 101, 102, 103, 105, 111], "unit": [1, 5, 26, 48, 49, 50, 52, 53, 63, 66, 67, 68, 76, 79, 81, 82, 88, 101, 103, 105, 106, 108, 112], "coars": [1, 9, 19, 20, 53, 104], "grain": [1, 9, 19, 20, 53, 104], "bead": [1, 9, 53], "": [1, 2, 3, 4, 9, 10, 13, 16, 19, 26, 27, 30, 33, 34, 37, 39, 40, 42, 44, 45, 48, 50, 52, 53, 55, 56, 57, 60, 67, 81, 87, 96, 98, 101, 102, 103, 104, 105, 109, 111, 113, 114], "master": [1, 3, 109, 114], "The": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 56, 57, 60, 61, 62, 66, 67, 68, 69, 70, 72, 73, 77, 78, 79, 80, 83, 84, 85, 86, 87, 88, 89, 92, 93, 94, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 110, 111, 112, 113, 114], "probabl": [1, 7, 15, 38, 41, 42, 44, 53, 88], "import": [1, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 56, 57, 60, 78, 83, 87, 93, 96, 98, 102, 103, 105, 106, 109, 110, 111, 112, 114], "virtual": [1, 3, 4, 93, 98], "everyth": [1, 3, 48, 53, 98, 101, 102], "can": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 61, 62, 63, 64, 66, 67, 68, 69, 70, 71, 72, 74, 78, 79, 80, 81, 83, 84, 89, 91, 92, 94, 95, 96, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "through": [1, 2, 3, 7, 12, 14, 15, 32, 41, 49, 53, 57, 98, 103, 105, 106, 109, 111, 114], "instanc": [1, 36, 50, 53, 57, 78, 106, 114], "typic": [1, 3, 7, 8, 13, 14, 26, 50, 52, 53, 96, 98, 99, 108, 109, 111, 112, 114], "select_atom": [1, 9, 11, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 26, 31, 34, 36, 37, 40, 48, 50, 52, 53, 55, 96, 98, 103, 105, 106, 110, 111, 112, 114], "manipul": [1, 53, 80, 99], "test": [1, 2, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 70, 93, 96, 98, 102, 103, 106, 109, 110, 111, 112, 114], "datafil": [1, 5, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 93, 96, 98, 101, 103, 106, 108, 109, 110, 111, 112, 114], "pdb": [1, 9, 10, 13, 14, 22, 23, 24, 34, 37, 46, 50, 52, 53, 57, 58, 59, 61, 77, 78, 83, 96, 97, 98, 103, 105, 108, 109, 114], "3": [1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 81, 82, 83, 84, 87, 93, 94, 95, 96, 98, 103, 104, 106, 108, 109, 110, 111, 112, 113, 114], "4": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 78, 82, 83, 87, 88, 93, 96, 98, 100, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "resnam": [1, 18, 19, 21, 26, 27, 28, 36, 37, 40, 48, 50, 53, 55, 61, 65, 72, 81, 82, 86, 87, 96, 97, 98, 105, 106, 109, 112], "arg": [1, 15, 18, 19, 21, 27, 28, 53, 83, 98, 106, 107, 109], "out": [1, 3, 4, 9, 10, 11, 12, 14, 19, 30, 34, 39, 48, 50, 52, 55, 57, 61, 70, 78, 93, 98, 102, 103, 105, 106, 109, 110, 111, 113, 114], "312": [1, 98, 104, 108], "see": [1, 2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 26, 27, 28, 30, 32, 33, 34, 37, 38, 40, 42, 43, 44, 46, 48, 50, 52, 53, 55, 56, 57, 60, 61, 63, 66, 67, 69, 76, 81, 84, 87, 94, 96, 98, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "more": [1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 33, 34, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 53, 56, 57, 60, 61, 65, 69, 87, 98, 101, 103, 105, 106, 108, 109, 112, 114], "inform": [1, 3, 4, 7, 10, 12, 14, 15, 16, 19, 22, 26, 28, 30, 32, 33, 34, 37, 40, 42, 43, 44, 46, 50, 52, 56, 57, 60, 62, 63, 66, 69, 70, 71, 72, 80, 81, 82, 84, 87, 88, 94, 95, 98, 101, 103, 105, 106, 108, 111, 112, 114], "like": [1, 3, 4, 5, 13, 16, 19, 26, 30, 34, 39, 40, 43, 48, 53, 55, 57, 60, 83, 100, 106, 108], "list": [1, 2, 3, 5, 13, 15, 16, 19, 26, 30, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 57, 61, 65, 67, 82, 87, 96, 99, 100, 102, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114], "5": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 67, 71, 78, 82, 87, 93, 98, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "print": [1, 5, 9, 10, 11, 13, 14, 15, 19, 23, 26, 27, 28, 30, 31, 34, 36, 37, 39, 40, 42, 43, 44, 45, 46, 49, 50, 53, 57, 101, 103, 108, 109, 110, 111, 114], "n": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 83, 95, 96, 98, 104, 105, 106, 107, 113], "type": [1, 3, 26, 42, 50, 52, 53, 58, 61, 65, 66, 72, 80, 81, 82, 83, 84, 85, 86, 87, 91, 92, 96, 97, 98, 104, 105, 106, 109, 113], "met": [1, 53, 83, 107, 109], "resid": [1, 13, 14, 23, 24, 26, 27, 36, 40, 46, 50, 53, 61, 65, 66, 69, 72, 75, 81, 82, 87, 89, 98, 105, 106, 109], "altloc": [1, 14, 61, 81, 82, 97, 106, 109], "return": [1, 3, 4, 9, 10, 13, 15, 16, 18, 19, 20, 21, 22, 24, 27, 30, 33, 34, 37, 40, 42, 44, 50, 53, 57, 98, 102, 105, 106, 108, 110, 111, 112], "below": [1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 61, 98, 103, 106, 107, 108, 109, 112, 113, 114], "code": [1, 2, 4, 5, 6, 7, 11, 13, 14, 15, 16, 30, 36, 48, 50, 57, 67, 78, 81, 82, 84, 93, 98, 99, 102, 103, 104, 105, 106, 108, 109, 112, 114], "everi": [1, 3, 4, 10, 14, 15, 16, 24, 27, 30, 31, 34, 37, 39, 42, 44, 48, 50, 52, 53, 57, 60, 61, 98, 103, 105, 106, 108, 109, 111, 114], "second": [1, 10, 12, 18, 19, 21, 40, 44, 53, 113], "element": [1, 42, 50, 53, 60, 61, 65, 66, 70, 81, 82, 86, 97, 105, 109, 114], "first": [1, 3, 4, 7, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 49, 50, 53, 55, 57, 61, 69, 72, 81, 83, 89, 94, 98, 100, 101, 105, 106, 108, 110, 111, 114], "6th": [1, 106], "correspond": [1, 3, 12, 13, 14, 16, 24, 26, 27, 40, 55, 71, 98, 108, 109], "indic": [1, 3, 12, 13, 14, 19, 24, 26, 27, 30, 33, 34, 38, 40, 43, 50, 53, 81, 82, 84, 87, 91, 96, 101, 105, 106, 108, 109, 110], "6": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 66, 69, 78, 81, 82, 83, 84, 87, 91, 93, 98, 102, 103, 104, 106, 109, 110, 111, 112, 114], "ag": [1, 10, 13, 40, 96, 98, 103], "also": [1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 32, 34, 37, 39, 40, 41, 42, 44, 48, 53, 55, 57, 61, 62, 81, 82, 87, 89, 98, 100, 101, 102, 103, 105, 106, 108, 109, 110, 111, 112, 113, 114], "support": [1, 3, 13, 19, 30, 46, 53, 66, 71, 72, 82, 84, 85, 88, 100, 103, 105, 106, 109, 111, 114], "fanci": [1, 53, 110], "pass": [1, 3, 4, 13, 16, 18, 19, 22, 23, 24, 26, 28, 30, 31, 34, 36, 37, 39, 42, 43, 44, 45, 49, 50, 53, 55, 60, 61, 62, 66, 80, 81, 93, 95, 96, 100, 102, 103, 105, 106, 108, 110, 112, 114], "ndarrai": [1, 53, 110], "8": [1, 4, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 87, 98, 103, 105, 106, 109, 110, 111, 112, 114], "10": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 71, 78, 82, 83, 87, 98, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "9": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 84, 87, 98, 102, 103, 105, 106, 108, 109, 110, 111, 112, 114], "47680": 1, "boolean": [1, 53, 108, 110], "allow": [1, 2, 3, 10, 13, 14, 19, 27, 28, 30, 36, 37, 40, 42, 43, 44, 52, 53, 56, 57, 60, 96, 99, 100, 103, 105, 106, 108, 110, 114], "you": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 60, 61, 62, 64, 67, 78, 79, 80, 89, 96, 98, 99, 100, 101, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "true": [1, 3, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 30, 34, 37, 38, 40, 42, 44, 45, 46, 48, 50, 52, 53, 55, 66, 68, 89, 94, 103, 105, 106, 108, 110, 114], "fals": [1, 4, 9, 11, 14, 19, 20, 26, 27, 30, 40, 44, 46, 48, 50, 53, 57, 78, 103, 105, 106, 108, 109, 110, 114], "valu": [1, 3, 7, 8, 11, 12, 13, 14, 15, 19, 24, 26, 27, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 57, 60, 65, 66, 67, 76, 81, 82, 83, 89, 92, 105, 106, 108, 110, 114], "must": [1, 2, 3, 4, 11, 12, 13, 16, 18, 22, 23, 26, 27, 30, 31, 34, 42, 43, 46, 48, 50, 53, 60, 66, 79, 83, 84, 100, 101, 108, 109, 112, 114], "same": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 24, 26, 28, 30, 31, 33, 34, 36, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 67, 93, 95, 96, 98, 102, 103, 105, 106, 109, 110, 114], "length": [1, 3, 6, 7, 12, 13, 22, 24, 27, 29, 39, 40, 42, 44, 45, 46, 48, 50, 52, 53, 63, 66, 67, 68, 71, 79, 88, 99, 104, 105, 110, 111], "origin": [1, 3, 4, 7, 9, 13, 14, 23, 27, 32, 33, 34, 39, 50, 53, 55, 57, 67, 98, 102, 106, 108, 110, 113], "condit": [1, 15, 105, 106, 108, 110, 112], "arr": 1, "11": [1, 3, 9, 10, 13, 14, 15, 16, 19, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 83, 87, 98, 103, 104, 105, 106, 109, 110, 112, 113, 114], "len": [1, 12, 23, 24, 30, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 50, 53, 57, 98, 103, 108, 109, 111], "12": [1, 3, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 33, 34, 36, 37, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 82, 86, 98, 103, 104, 106, 109, 110, 111, 112, 113, 114], "13": [1, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 34, 36, 37, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 106, 109, 110, 112, 114], "number": [1, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 50, 52, 53, 57, 60, 65, 69, 71, 72, 75, 81, 82, 83, 84, 85, 87, 89, 91, 92, 93, 96, 103, 105, 106, 108, 109, 114], "wai": [1, 3, 4, 7, 10, 12, 13, 14, 15, 16, 18, 19, 26, 27, 30, 33, 34, 48, 52, 53, 79, 98, 99, 103, 105, 106, 108, 109, 111, 114], "compar": [1, 6, 7, 9, 10, 11, 12, 14, 15, 17, 19, 22, 32, 34, 40, 41, 42, 44, 45, 108], "one": [1, 2, 3, 4, 10, 11, 12, 13, 15, 19, 27, 28, 30, 31, 39, 46, 50, 53, 56, 57, 83, 87, 88, 91, 92, 96, 98, 99, 100, 103, 104, 105, 106, 108, 109, 114], "concaten": [1, 15, 53, 103, 106, 114], "subtract": [1, 13, 84], "union": [1, 106], "differ": [1, 3, 4, 7, 9, 10, 12, 13, 15, 16, 19, 26, 28, 34, 36, 38, 40, 41, 45, 46, 48, 50, 53, 55, 60, 66, 67, 70, 71, 75, 82, 87, 91, 93, 95, 96, 98, 99, 100, 102, 103, 104, 105, 106, 112, 114], "achiev": [1, 15], "similar": [1, 3, 4, 6, 12, 15, 19, 23, 24, 30, 32, 33, 34, 37, 38, 53, 73, 82, 83, 87, 92, 93, 98, 104], "outcom": [1, 105], "kei": [1, 2, 30, 38, 39, 49, 53, 57, 98, 99, 114], "preserv": [1, 4, 19, 66, 105], "ani": [1, 2, 3, 4, 11, 15, 16, 18, 27, 28, 30, 31, 37, 42, 43, 44, 46, 49, 50, 53, 56, 57, 61, 67, 89, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 112], "duplic": [1, 30, 53, 103, 106], "where": [1, 4, 5, 7, 9, 14, 15, 16, 19, 20, 21, 22, 27, 31, 32, 33, 36, 37, 38, 40, 43, 44, 46, 48, 50, 53, 57, 60, 61, 66, 71, 89, 98, 100, 102, 105, 106, 108, 109], "its": [1, 2, 3, 4, 7, 9, 13, 15, 18, 19, 20, 22, 30, 32, 33, 44, 46, 49, 52, 53, 98, 99, 100, 101, 103, 106, 108, 109, 111, 112], "topologi": [1, 5, 14, 15, 26, 28, 52, 53, 59, 63, 65, 66, 69, 70, 71, 72, 73, 76, 77, 78, 80, 81, 82, 83, 84, 91, 92, 93, 95, 98, 99, 103, 105, 106, 108, 111], "14": [1, 9, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 82, 98, 100, 103, 104, 105, 106, 109, 110, 112, 114], "ag1": [1, 40], "15": [1, 7, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 41, 42, 43, 44, 45, 48, 49, 50, 52, 53, 57, 81, 82, 98, 103, 104, 106, 109, 110, 112, 114], "ag2": [1, 40], "16": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 104, 105, 106, 109, 110, 111, 112], "concat": 1, "17": [1, 12, 15, 16, 19, 20, 21, 26, 27, 30, 33, 34, 36, 39, 42, 44, 48, 49, 50, 52, 53, 57, 69, 81, 82, 87, 98, 103, 104, 106, 109, 110, 111, 112], "18": [1, 9, 15, 16, 19, 26, 27, 30, 42, 44, 46, 48, 49, 50, 52, 53, 57, 78, 81, 82, 86, 98, 103, 105, 106, 109, 110, 112, 113], "19": [1, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 37, 40, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 104, 105, 106, 109, 112, 113], "avail": [1, 2, 3, 7, 15, 16, 19, 32, 33, 36, 40, 42, 43, 44, 53, 56, 57, 60, 66, 73, 77, 79, 82, 87, 96, 98, 99, 100, 102, 105, 106, 108, 109, 114], "keep": [1, 2, 3, 10, 14, 30, 34, 39, 43, 44, 48, 55, 72, 96, 99, 101, 102, 108], "well": [1, 2, 4, 7, 15, 32, 33, 44, 48, 61, 67, 99, 101, 105, 108], "equival": [1, 27, 48, 87], "result": [1, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 24, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 52, 53, 61, 89, 94, 105, 106, 108, 110], "t": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 48, 49, 50, 52, 53, 55, 56, 57, 66, 82, 92, 96, 98, 100, 103, 104, 105, 106, 107, 108, 110, 111, 112, 114], "sort": [1, 26, 27, 30, 34, 53, 105, 106], "isdisjoint": 1, "do": [1, 3, 4, 6, 10, 11, 12, 13, 15, 16, 19, 22, 26, 27, 28, 30, 34, 37, 42, 44, 45, 46, 48, 50, 52, 53, 95, 99, 101, 102, 103, 105, 108, 114], "share": [1, 3, 105], "issubset": 1, "part": [1, 2, 3, 4, 15, 30, 48, 57, 101, 103, 105, 106, 108, 111], "is_strict_subset": 1, "issuperset": 1, "is_strict_superset": 1, "both": [1, 3, 4, 13, 15, 16, 22, 30, 38, 48, 50, 52, 53, 60, 63, 72, 81, 85, 87, 91, 98, 100, 102, 103, 105, 108, 109, 114], "intersect": [1, 106], "common": [1, 3, 7, 12, 13, 14, 15, 22, 26, 31, 32, 34, 53, 55, 68, 70, 104, 106, 108], "symmetric_differ": 1, "separ": [1, 5, 7, 15, 16, 19, 30, 31, 36, 40, 42, 43, 81, 83, 84, 100, 102, 106, 108, 114], "properti": [1, 16, 30, 39, 53, 60, 98, 105, 106, 109, 111, 112], "level": [1, 3, 4, 15, 48, 85, 98, 101, 108, 114], "connect": [1, 3, 4, 33, 50, 52, 53, 60, 61, 82, 87, 91, 105, 114], "residu": [1, 3, 7, 13, 14, 17, 19, 21, 22, 26, 28, 30, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 55, 61, 65, 69, 70, 71, 72, 75, 81, 82, 83, 86, 87, 92, 93, 95, 96, 99, 105, 106, 109, 112, 114], "molecul": [1, 4, 10, 13, 26, 31, 38, 50, 55, 58, 61, 66, 78, 87, 92, 95, 98, 105, 106, 108, 109, 112], "segment": [1, 10, 49, 53, 61, 65, 70, 81, 87, 95, 99, 103, 105, 106, 109, 114], "20": [1, 15, 16, 19, 26, 30, 31, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 105, 106, 110, 111, 112, 113], "21": [1, 3, 9, 15, 16, 26, 27, 28, 30, 31, 33, 42, 44, 48, 49, 50, 52, 53, 57, 71, 81, 82, 98, 99, 103, 104, 105, 106, 109, 112, 113, 114], "24": [1, 15, 16, 26, 27, 30, 34, 39, 44, 49, 50, 53, 57, 81, 82, 87, 98, 103, 105, 112], "accord": [1, 13, 14, 87, 91, 106, 109], "produc": [1, 23, 27, 34, 53, 57, 67, 105, 108], "dictionari": [1, 18, 30, 57, 60, 89, 105, 108, 114], "22": [1, 15, 16, 26, 30, 44, 46, 48, 49, 50, 53, 57, 81, 82, 98, 103, 105, 106, 112], "mass": [1, 6, 7, 9, 10, 15, 16, 23, 24, 28, 30, 36, 40, 45, 46, 47, 48, 53, 55, 61, 63, 65, 66, 86, 87, 92, 97, 106, 109, 112, 113, 114], "32": [1, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 50, 52, 53, 55, 57, 98, 104, 105], "06": [1, 38, 104, 113], "008": [1, 53], "23853": 1, "11084": 1, "011": [1, 39, 53], "1040": [1, 98], "007": [1, 53, 82], "289": 1, "999": [1, 53, 65, 93], "11404": 1, "98977": 1, "multipl": [1, 3, 27, 39, 48, 53, 57, 62, 89, 94, 98, 100, 105, 106, 112, 114], "them": [1, 3, 4, 7, 9, 10, 13, 15, 18, 19, 22, 34, 38, 39, 42, 43, 44, 45, 46, 50, 52, 53, 55, 60, 61, 66, 68, 79, 81, 82, 89, 95, 101, 102, 103, 104, 105, 106, 108, 109, 112], "23": [1, 15, 16, 26, 30, 34, 44, 48, 49, 50, 53, 57, 81, 82, 87, 93, 98, 103, 106, 112], "sol": [1, 30, 36, 37, 40, 48, 50, 55, 87, 112], "22168": 1, "iter": [1, 12, 14, 15, 16, 30, 44, 49, 53, 103, 105, 108, 109, 110, 111], "atom1": [1, 95], "25": [1, 15, 26, 27, 30, 34, 46, 49, 50, 53, 57, 81, 82, 83, 98, 103, 105], "atom2": [1, 95], "26": [1, 15, 26, 30, 34, 49, 50, 53, 57, 81, 82, 83, 87, 93, 98, 103], "atom3": 1, "27": [1, 15, 26, 30, 49, 50, 53, 57, 81, 82, 93, 98, 103, 104, 107, 113], "28": [1, 3, 15, 30, 49, 50, 53, 57, 78, 98, 103], "ca": [1, 9, 10, 11, 12, 13, 14, 16, 18, 20, 21, 23, 24, 36, 37, 38, 39, 40, 42, 43, 44, 46, 53, 60, 98, 103, 106, 107], "c": [1, 3, 13, 27, 30, 31, 34, 36, 37, 38, 39, 46, 48, 50, 52, 53, 62, 67, 78, 81, 82, 85, 87, 88, 98, 100, 102, 103, 104, 105, 106, 107, 113], "cb": [1, 36, 53, 98], "h2": [1, 26, 28, 50, 78], "h": [1, 3, 27, 31, 36, 39, 45, 50, 52, 53, 78, 87, 96, 98, 103, 106], "neat": [1, 4], "shortcut": [1, 106], "simpli": [1, 3, 12, 13, 15, 21, 24, 26, 34, 40, 50, 52, 53, 60, 79, 84, 88, 101, 104, 105, 106, 109, 113], "29": [1, 13, 15, 30, 34, 46, 49, 50, 53, 57, 98, 103, 113], "30": [1, 13, 14, 15, 22, 23, 30, 33, 42, 49, 50, 53, 57, 78, 98, 103, 104, 110, 112, 113], "31": [1, 15, 16, 19, 30, 48, 49, 50, 53, 57, 81, 82, 98, 103], "altern": [1, 3, 13, 20, 30, 48, 57, 77, 81, 82, 96, 103, 106, 108, 109, 112], "provid": [1, 3, 4, 7, 12, 13, 15, 16, 17, 25, 26, 30, 31, 34, 37, 38, 43, 44, 46, 52, 53, 55, 57, 60, 61, 62, 65, 71, 81, 82, 83, 88, 94, 96, 99, 100, 103, 105, 106, 108, 109, 114], "belong": [1, 28, 50, 53, 61, 98, 106, 107], "33": [1, 15, 49, 50, 53, 57, 81, 82], "34": [1, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 37, 38, 39, 40, 42, 43, 44, 45, 49, 50, 52, 53, 55, 57, 81, 82, 98, 104], "These": [1, 3, 4, 5, 7, 8, 17, 24, 37, 43, 48, 53, 57, 72, 81, 82, 89, 94, 98, 106, 108, 109], "user": [1, 2, 3, 6, 7, 15, 19, 26, 28, 39, 42, 43, 44, 45, 49, 53, 60, 61, 66, 68, 69, 72, 78, 79, 87, 88, 100, 101, 102, 103, 105, 106, 108, 109, 114], "work": [1, 2, 4, 7, 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, 55, 56, 57, 62, 67, 79, 96, 99, 100, 102, 104, 105, 106, 108, 111], "35": [1, 19, 20, 30, 49, 50, 53, 57, 98, 103, 104], "null": 1, "36": [1, 49, 50, 53, 57, 83], "abov": [1, 3, 10, 13, 16, 23, 24, 26, 27, 28, 39, 48, 53, 55, 57, 83, 102, 103, 105, 106, 108, 109, 111], "37": [1, 38, 49, 50, 53, 57, 83, 98, 104], "For": [1, 2, 3, 4, 7, 9, 12, 13, 15, 16, 19, 26, 28, 30, 32, 33, 34, 37, 39, 40, 42, 43, 44, 46, 50, 52, 53, 55, 57, 60, 61, 66, 78, 83, 87, 89, 96, 98, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 114], "38": [1, 16, 23, 49, 52, 53, 57, 81, 82], "does_not_exist": 1, "39": [1, 13, 15, 16, 18, 20, 21, 23, 24, 26, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 50, 52, 53, 57, 81, 82], "40": [1, 19, 30, 49, 53, 57, 81, 82, 98, 103, 110], "have": [1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 18, 19, 22, 24, 26, 27, 30, 31, 33, 34, 36, 37, 40, 42, 44, 45, 46, 48, 50, 53, 55, 57, 60, 63, 66, 67, 69, 71, 75, 79, 81, 82, 84, 87, 89, 95, 98, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 114], "evalu": [1, 6, 7, 34, 41, 49, 106], "context": [1, 15, 30, 52, 53, 96, 108], "41": [1, 30, 49, 57, 81, 82, 98], "bool": [1, 3, 18, 50, 109, 110], "skip": [1, 3, 16, 46, 57, 100], "over": [1, 6, 7, 8, 12, 15, 16, 17, 18, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 53, 55, 72, 102, 103, 105, 108, 110, 111, 112], "instead": [1, 3, 4, 9, 10, 12, 14, 15, 16, 19, 23, 24, 30, 34, 37, 39, 43, 44, 48, 50, 55, 61, 81, 82, 88, 92, 93, 100, 105, 106, 108, 111, 114], "rais": [1, 3, 33, 49, 53, 65, 79, 81, 82, 83, 99, 100, 101, 105, 108], "error": [1, 3, 4, 9, 49, 53, 72, 79, 89, 94, 100, 101, 105, 108], "which": [1, 3, 4, 10, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 30, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 55, 57, 60, 61, 67, 68, 83, 87, 89, 91, 94, 96, 98, 99, 100, 102, 103, 105, 106, 108, 109, 112, 114], "help": [1, 2, 3, 4, 13, 16, 22, 96, 99, 100, 106, 108], "occasion": [1, 89, 94], "aris": [1, 4], "logic": 1, "too": [1, 16, 42, 44, 48, 53, 55, 56, 99, 108], "restrict": [1, 13, 14, 87], "geometr": [1, 6, 7, 26, 41, 52], "normal": [1, 3, 15, 30, 38, 39, 43, 44, 84, 91, 96, 102, 104, 105, 108], "static": [1, 10, 15, 53, 106, 109, 111, 114], "within": [1, 6, 7, 16, 17, 18, 19, 20, 22, 26, 28, 30, 36, 38, 40, 42, 43, 44, 45, 50, 53, 57, 60, 67, 77, 105, 106, 111, 112], "chang": [1, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 49, 53, 55, 57, 61, 71, 72, 81, 87, 89, 100, 102, 103, 106, 108, 111], "trajectori": [1, 5, 6, 8, 9, 17, 18, 20, 21, 26, 27, 32, 33, 36, 37, 38, 40, 42, 43, 44, 45, 48, 49, 50, 52, 54, 58, 59, 61, 66, 71, 72, 81, 82, 91, 93, 99, 104, 105, 106, 108, 112, 113, 114], "frame": [1, 7, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 26, 27, 30, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 46, 48, 49, 52, 55, 56, 61, 66, 71, 81, 82, 89, 94, 99, 105, 106, 108, 110, 111, 112, 114], "sever": [1, 3, 7, 16, 29, 30, 33, 34, 53, 82, 101, 105, 108, 114], "requir": [1, 3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 65, 66, 79, 81, 82, 83, 95, 96, 98, 100, 103, 105, 106, 108, 109], "function": [1, 2, 3, 4, 6, 7, 8, 13, 17, 19, 20, 21, 27, 30, 33, 34, 35, 37, 41, 42, 43, 44, 45, 46, 52, 53, 55, 56, 57, 85, 87, 98, 100, 101, 102, 104, 105, 106, 109, 111, 112, 114], "implement": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 39, 53, 57, 62, 66, 76, 82, 87, 95, 106, 112], "mani": [1, 2, 3, 4, 13, 15, 16, 21, 26, 30, 34, 39, 40, 42, 43, 44, 53, 99, 100, 108, 109, 111, 114], "interest": [1, 19, 30, 48, 53, 100], "bond": [1, 13, 31, 49, 52, 53, 55, 57, 61, 66, 78, 80, 81, 82, 84, 86, 91, 92, 97, 98, 99, 104, 105, 106, 109, 114], "angl": [1, 6, 7, 22, 26, 27, 28, 35, 39, 50, 53, 57, 61, 66, 67, 84, 86, 92, 97, 99, 104, 105, 106, 109, 113, 114], "dihedr": [1, 6, 7, 35, 53, 61, 66, 84, 86, 97, 105, 106, 109, 114], "improperdihedr": [1, 109], "present": [1, 3, 19, 21, 26, 27, 40, 52, 65, 68, 81, 92, 95, 98, 105], "residuegroup": [1, 53, 98, 105, 109], "free": [2, 3, 101], "open": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 87, 89, 94, 104, 108], "sourc": [2, 3, 4, 16, 30, 53, 57, 84, 96, 100, 102, 105, 108], "project": [2, 3, 4, 7, 32, 37, 39, 43, 44, 48, 99, 105], "It": [2, 3, 4, 7, 9, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 32, 33, 34, 36, 37, 40, 45, 48, 49, 50, 53, 57, 60, 61, 67, 76, 78, 82, 85, 87, 89, 99, 104, 106, 108, 110, 112, 114], "evolv": 2, "grow": [2, 5, 108], "demand": 2, "base": [2, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 19, 28, 33, 39, 42, 44, 46, 50, 52, 53, 60, 61, 65, 79, 87, 89, 94, 102, 103, 104, 105, 106, 107, 108, 109], "develop": [2, 15, 52, 72, 101, 108], "team": 2, "veri": [2, 3, 12, 13, 15, 19, 23, 24, 27, 44, 45, 48, 79, 93, 103, 108], "much": [2, 3, 10, 11, 12, 13, 14, 16, 19, 30, 34, 42, 43, 48, 50, 60, 105, 108], "welcom": 2, "take": [2, 3, 4, 7, 14, 15, 16, 17, 23, 26, 30, 33, 42, 44, 48, 93, 96, 99, 100, 103, 106, 108, 109, 112, 114], "form": [2, 13, 19, 26, 42, 53, 55, 60], "bug": [2, 3, 16, 88, 102], "report": [2, 52, 99, 108], "enhanc": [2, 3], "request": [2, 4, 101, 102, 108], "issu": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 50, 57, 61, 63, 67, 79, 84, 87, 89, 94, 99, 100, 101, 102, 106, 108], "tracker": [2, 87, 99, 108], "fix": [2, 3, 4, 48, 49, 68, 72, 102], "improv": [2, 27, 99, 108], "speed": [2, 105, 108], "clariti": [2, 26], "modernis": 2, "featur": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 83, 99, 100, 102, 114], "addit": [2, 3, 7, 44, 57, 61, 82, 96, 98, 101, 102, 103, 105, 106, 108, 109], "document": [2, 5, 7, 15, 19, 22, 26, 30, 43, 48, 53, 66, 76, 89, 94, 105, 106, 108, 113], "includ": [2, 3, 4, 7, 9, 10, 13, 14, 15, 16, 19, 34, 36, 37, 39, 43, 48, 50, 52, 53, 55, 57, 84, 85, 87, 95, 96, 98, 99, 100, 102, 104, 105, 106, 108, 109, 111, 112, 114], "typo": [2, 3], "build": [2, 15, 16, 50, 53, 65, 87, 99, 100, 105], "question": [2, 3, 99], "discuss": [2, 3, 15, 27, 60, 63, 79, 87, 99, 101, 108], "mdnalysi": [2, 99, 108], "mail": [2, 99, 100, 101, 102, 108], "commun": [2, 3, 88], "subscrib": [2, 99], "conduct": [2, 99], "member": 2, "agre": [2, 99], "adher": [2, 102], "pleas": [2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 61, 87, 99, 100, 102, 104, 105, 112], "read": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 30, 33, 38, 39, 43, 44, 49, 50, 52, 60, 62, 63, 64, 74, 80, 90, 91, 92, 99, 105, 106, 109, 110, 111, 113, 114], "mdanalysistest": [2, 3, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 55, 57, 100, 101, 102, 103, 105, 108], "packag": [2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 79, 86, 96, 100, 101, 104, 105, 106, 108], "distribut": [2, 3, 6, 7, 15, 30, 35, 38, 41, 42, 44, 45, 70, 100, 102], "under": [2, 3, 15, 19, 53, 87, 101, 105, 108, 110], "gnu": [2, 108], "gener": [2, 3, 4, 7, 8, 9, 10, 14, 15, 18, 19, 20, 28, 30, 34, 37, 38, 39, 48, 50, 53, 55, 58, 59, 61, 67, 77, 80, 89, 94, 99, 102, 103, 104, 105, 113, 114], "public": [2, 3, 16, 30, 99, 102, 104, 108], "licens": [2, 15, 105, 108], "later": [2, 4, 13, 15, 102, 105, 106], "copyleft": 2, "deriv": [2, 3, 84, 87, 98, 105, 109], "made": [2, 3, 4, 26, 48, 71, 103, 105, 106, 109], "Be": [2, 15, 100], "sure": [2, 3, 4, 18, 100, 102, 106, 108], "comfort": 2, "befor": [2, 3, 4, 13, 16, 30, 36, 45, 48, 60, 89, 100, 101, 102, 105, 106, 108, 111], "push": [2, 4, 15, 102, 108], "page": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 102, 104, 106, 108], "came": [2, 108], "panda": [2, 13, 15, 16, 18, 19, 20, 21, 26, 33, 34, 49, 53, 108], "guid": [2, 3, 6, 7, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 69, 100, 108], "idea": [2, 3, 53, 102], "If": [2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 16, 23, 26, 27, 30, 34, 36, 37, 38, 40, 42, 44, 46, 50, 52, 53, 55, 57, 61, 65, 66, 67, 68, 79, 81, 82, 83, 84, 88, 89, 92, 96, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "look": [2, 3, 4, 10, 12, 13, 15, 19, 23, 24, 26, 28, 36, 37, 39, 48, 55, 61, 83, 86, 92, 96, 98, 108, 111], "brand": 2, "we": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 68, 82, 88, 96, 98, 99, 100, 101, 102, 105, 108, 109], "recommend": [2, 3, 21, 26, 45, 61, 100, 101, 102, 108], "go": [2, 3, 4, 15, 16, 96, 102, 106], "main": [2, 4, 100], "codebas": [2, 16, 105], "your": [2, 4, 5, 6, 7, 10, 13, 15, 17, 19, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 61, 67, 75, 84, 87, 99, 100, 103, 104, 105, 108, 111, 112], "own": [2, 3, 4, 6, 7, 13, 15, 17, 19, 20, 21, 30, 42, 52, 53, 66, 99, 101, 108, 112], "encourag": [2, 108], "an": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 57, 60, 62, 66, 67, 69, 71, 72, 78, 80, 83, 84, 85, 87, 88, 89, 94, 96, 98, 99, 100, 101, 102, 104, 105, 106, 108, 110, 112, 114], "toolkit": 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"peopl": [2, 3, 102], "togeth": [2, 53, 99, 103, 112], "daunt": 2, "aspect": 2, "stick": [2, 50], "guidelin": [2, 105], "process": [2, 3, 7, 15, 17, 18, 19, 23, 24, 26, 27, 48, 67, 102, 105, 108, 114], "straightforward": [2, 53, 103, 106], "mostli": [2, 15], "troubl": [2, 40], "As": [2, 3, 4, 10, 12, 13, 14, 15, 16, 23, 24, 30, 33, 34, 39, 42, 43, 44, 48, 50, 53, 55, 57, 61, 84, 93, 95, 96, 98, 100, 102, 103, 105, 106, 108, 109, 113], "alwai": [2, 3, 4, 10, 15, 16, 20, 26, 33, 34, 53, 57, 60, 61, 67, 79, 81, 83, 84, 87, 88, 96, 99, 101, 103, 106, 108, 109, 111, 113], "difficulti": [2, 99], "feel": [2, 3], "ask": [2, 3, 16, 99, 100, 102, 108], "host": [2, 3, 5], "need": [2, 3, 7, 8, 9, 14, 15, 16, 19, 24, 30, 33, 34, 42, 43, 44, 46, 48, 50, 52, 53, 55, 67, 98, 99, 100, 101, 102, 103, 105, 108, 111, 112], "sign": [2, 34], "up": [2, 3, 4, 12, 15, 16, 27, 31, 42, 44, 46, 52, 53, 57, 66, 93, 96, 99, 100, 103, 105, 106, 108, 112], "account": [2, 3, 4, 7, 32, 34, 40, 49], "great": 2, "resourc": [2, 3, 15, 42, 44, 55, 99, 108], "learn": [2, 3, 7, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 42, 43, 44, 49, 99], "numpi": [2, 3, 10, 12, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 33, 34, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 100, 101, 102, 103, 105, 108, 109, 112], "matthew": [2, 52], "brett": 2, "pydagogu": 2, "instruct": [2, 53, 100], "instal": [2, 3, 4, 5, 7, 10, 30, 33, 34, 42, 43, 44, 46, 48, 53, 55, 79, 101, 104, 105, 108], "set": [2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 23, 26, 27, 30, 31, 34, 37, 46, 48, 50, 52, 53, 57, 61, 66, 67, 68, 81, 83, 87, 88, 89, 92, 96, 101, 102, 103, 104, 105, 106, 108, 109, 111, 114], "ssh": 2, "configur": [2, 7, 19, 23, 32, 41, 67, 108], "step": [2, 3, 10, 13, 14, 15, 16, 26, 34, 37, 39, 44, 48, 52, 53, 55, 57, 68, 72, 88, 105, 112, 114], "complet": [2, 3, 5, 30, 53, 57, 112], "seamlessli": [2, 67], "between": [2, 3, 4, 6, 7, 8, 9, 11, 14, 16, 17, 18, 19, 21, 24, 26, 27, 30, 32, 33, 34, 36, 38, 39, 40, 41, 46, 50, 53, 60, 80, 82, 83, 91, 99, 105, 108, 114], "local": [2, 3, 4, 7, 15, 16, 19, 20, 32, 33, 39, 48, 101, 102, 104, 108], "repositori": [2, 3, 4, 5, 99, 102], "would": [3, 13, 15, 16, 19, 39, 43, 100, 101, 105, 106, 109], "start": [3, 4, 6, 12, 13, 15, 16, 26, 30, 50, 57, 61, 69, 83, 87, 91, 101, 105, 106, 108], "search": [3, 30, 106], "someon": 3, "els": [3, 37, 83, 101], "don": [3, 10, 11, 18, 24, 26, 30, 40, 42, 53, 55, 100, 105, 111], "follow": [3, 4, 13, 16, 18, 23, 26, 27, 30, 34, 38, 46, 48, 53, 57, 60, 61, 63, 65, 67, 79, 81, 83, 87, 88, 91, 95, 100, 101, 102, 103, 105, 106, 108, 109, 114], "minor": [3, 102, 105], "ahead": [3, 102, 108], "major": [3, 53, 102], "That": [3, 19], "other": [3, 4, 6, 7, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 37, 38, 39, 42, 43, 44, 45, 46, 49, 53, 60, 61, 66, 67, 68, 69, 71, 72, 76, 78, 79, 80, 81, 86, 87, 95, 96, 98, 99, 100, 105, 106, 108, 109, 112, 113], "weigh": 3, "should": [3, 4, 5, 12, 13, 14, 15, 22, 26, 27, 30, 31, 34, 36, 42, 44, 53, 57, 68, 72, 77, 78, 83, 87, 92, 100, 101, 102, 105, 108, 109, 114], "link": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 102, 104], "descript": [3, 5, 15, 30, 53, 57, 58, 61, 83, 87, 96, 97, 105, 108, 109], "here": [3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 60, 78, 100, 102, 105, 107, 109], "overview": [3, 4], "workflow": [3, 4, 48, 108], "inlin": [3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 53], "expand": [3, 4, 44, 84], "throughout": [3, 4, 9, 10, 14, 19, 26, 27, 30, 34, 39, 48, 50, 53, 55, 98, 105], "rest": [3, 4, 14, 19, 26], "isol": [3, 4], "version": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 67, 70, 71, 85, 99, 105, 109], "comput": [3, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 52, 53, 55, 56, 99, 100, 104, 108, 109, 113], "off": [3, 4, 12, 16, 46, 50, 89, 106, 108], "run": [3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 40, 42, 44, 46, 48, 49, 52, 53, 55, 59, 61, 97, 100, 101, 102, 105, 110], "hit": [3, 4, 108], "button": [3, 4], "want": [3, 4, 7, 9, 10, 15, 16, 18, 19, 21, 22, 23, 26, 30, 31, 36, 42, 43, 44, 48, 50, 52, 55, 96, 100, 108, 111], "clone": [3, 100], "machin": [3, 4, 15, 48, 100, 105, 108], "git": [3, 4, 100, 102], "http": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 100, 104, 105], "com": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 100, 104, 105, 108], "cd": [3, 4, 100, 102, 104, 108], "remot": [3, 4], "upstream": [3, 4], "directori": [3, 4, 5, 30, 89, 101, 102, 104], "ll": [3, 4, 27], "highli": [3, 26, 61, 85, 100], "experiment": [3, 30], "interfer": [3, 100], "stabl": [3, 13, 14, 22, 100], "sinc": [3, 4, 15, 45, 57, 67, 87, 102, 106], "split": [3, 5, 26, 36, 89, 94, 98, 103, 105], "actual": [3, 4, 5, 16, 40, 52, 56, 108, 111, 112], "suit": [3, 53, 100, 114], "mode": [3, 33, 34, 38, 96, 104], "either": [3, 12, 13, 15, 19, 27, 30, 43, 45, 57, 62, 83, 103, 106, 109], "time": [3, 4, 12, 13, 14, 15, 16, 18, 19, 20, 26, 30, 33, 34, 36, 37, 38, 40, 52, 53, 55, 56, 57, 61, 63, 67, 68, 72, 78, 79, 88, 89, 94, 99, 102, 103, 105, 106, 108, 111, 112, 114], "contributor": [3, 108], "lot": [3, 66, 108], "experi": 3, "manag": [3, 15, 30, 53, 96, 100, 104, 108], "strongli": [3, 100, 108], "suggest": [3, 12, 16, 19], "choos": [3, 10, 13, 16, 19, 20, 26, 30, 34, 36, 42, 43, 48, 49, 53, 103], "anaconda": 3, "miniconda": [3, 4], "date": [3, 4, 102], "updat": [3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 72, 99, 100, 105, 106, 108, 110, 114], "without": [3, 4, 13, 15, 28, 30, 34, 37, 50, 53, 61, 87, 99, 103, 104, 105, 106, 108, 109, 114], "touch": [3, 61], "exist": [3, 15, 19, 37, 53, 60, 103, 108, 109], "dev": [3, 102], "activ": [3, 4, 82, 100], "when": [3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 33, 34, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 57, 60, 61, 63, 66, 67, 79, 83, 87, 89, 99, 100, 101, 102, 103, 104, 105, 106, 108, 109, 111, 113, 114], "info": [3, 27], "current": [3, 4, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 38, 39, 42, 43, 44, 45, 48, 49, 50, 53, 55, 57, 63, 67, 70, 72, 79, 81, 84, 87, 88, 89, 96, 100, 102, 103, 104, 106, 111, 112, 114], "finish": [3, 16], "deactiv": 3, "root": [3, 6, 7, 8, 9, 11, 15, 16, 38, 78, 82], "full": [3, 4, 26, 30, 44, 57, 66, 85, 89, 100, 102, 112], "detail": [3, 15, 30, 45, 53, 61, 80, 81, 98, 105, 108, 112], "purpos": [3, 19, 28], "leverag": [3, 15], "what": [3, 6, 30, 50, 53, 98, 101, 108, 109], "let": [3, 4, 16, 26, 27, 40, 102], "done": [3, 14, 16, 30, 109, 114], "m": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 102, 104, 113], "my": [3, 4, 5, 18, 48], "env": [3, 4, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 108], "folder": [3, 30, 108], "termin": [3, 5], "myproject": 3, "bin": [3, 9, 10, 11, 12, 13, 14, 26, 30, 33, 36, 40, 48, 49, 104, 105], "now": [3, 4, 11, 14, 16, 19, 27, 40, 43, 46, 48, 50, 52, 55, 81, 102, 105], "via": [3, 4, 26, 27, 28, 33, 43, 77, 98, 100, 102, 104, 105, 107], "affect": [3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 27, 33, 38, 39, 43, 44, 49, 105], "global": [3, 7, 32, 33, 34, 101, 106], "session": [3, 5], "virtualenvwrapp": 3, "easier": [3, 4, 13, 26, 33, 34, 44, 55, 105], "organis": [3, 108], "singl": [3, 13, 15, 26, 27, 38, 46, 57, 61, 81, 105, 106, 108, 114], "so": [3, 5, 10, 11, 13, 14, 15, 16, 19, 22, 23, 24, 30, 34, 36, 37, 40, 42, 45, 48, 50, 55, 57, 60, 83, 87, 88, 92, 96, 102, 103, 105, 106, 108, 109, 114], "scatter": [3, 33, 34, 37, 44, 48], "command": [3, 4, 5, 48, 53, 66, 68, 76, 96, 100, 104, 108], "easi": [3, 12, 18, 104, 112], "creation": [3, 57, 78, 102, 105], "delet": [3, 102], "copi": [3, 4, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 33, 38, 39, 42, 43, 44, 45, 49, 50, 57, 102, 105, 108], "tab": [3, 83], "outsid": [3, 31, 49, 55, 57, 98, 101, 105], "Then": [3, 4, 12, 13, 15, 18, 24, 53], "load": [3, 4, 30, 50, 61, 78, 89, 99, 103, 105, 109, 111, 112], "bashrc": [3, 5], "execut": [3, 4, 15, 30, 48, 108, 112], "decid": 3, "store": [3, 5, 12, 30, 34, 39, 48, 53, 57, 69, 85, 88, 89, 94, 105, 113], 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112], "mention": 3, "entiti": 3, "versionchang": 3, "although": [3, 7, 16, 30, 48, 63, 67, 79, 82, 83, 84, 105, 111, 112], "accept": [3, 13, 30, 43, 44, 53, 105, 106, 109, 112], "assum": [3, 50, 53, 57, 60, 61, 66, 67, 68, 79, 83, 88, 100, 114], "longer": [3, 12, 27, 57, 71, 105, 106, 108], "remov": [3, 4, 28, 30, 37, 40, 53, 102, 105, 108], "futur": [3, 15, 101, 105, 108], "enclos": 3, "scope": [3, 108], "whole": [3, 42, 53, 55, 105, 108, 112], "toc": 3, "analysisbas": [3, 15, 16, 105], "ones": [3, 33, 87, 106], "overwritten": 3, "inherit": [3, 108], "distinguish": [3, 34], "minim": [3, 7, 8, 108], "demonstr": [3, 7, 8, 13, 18, 19, 26, 30], "best": [3, 12, 19, 20, 104, 108], "practic": [3, 12, 48, 105], "intent": 3, "behind": 3, "choic": [3, 4, 38, 108], "api": [3, 9, 10, 11, 13, 14, 15, 19, 22, 23, 24, 30, 31, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 49, 85, 102, 103, 105], "promot": 3, "unifi": 3, "concis": 3, "come": [3, 53, 84, 99, 102, 108, 114], "overwrit": [3, 30, 96], "restructur": 3, "put": [3, 4, 16, 50], "amend": [3, 105], "friend": 3, "pile": 3, "onto": [3, 7, 30, 32, 33, 34, 37, 43, 44, 48, 111], "preview": 3, "ipython": [3, 4, 50, 109], "mark": [3, 30, 103, 104, 108], "oper": [3, 9, 15, 16, 30, 39, 53, 103, 105, 106], "docstr": 4, "class": [4, 7, 12, 13, 14, 15, 17, 18, 19, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 49, 53, 57, 83, 96, 98, 100, 101, 103, 105, 108, 109, 113, 114], "ensur": [4, 36, 100, 102, 103, 106, 108], "nbsphinx": 4, "dure": [4, 10, 13, 15, 19, 57, 89, 103], "doc": [4, 9, 10, 11, 13, 14, 22, 23, 24, 30, 31, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 49, 102], "python": [4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 87, 98, 99, 100, 101, 102, 104, 105], "mean": [4, 6, 7, 8, 9, 11, 16, 19, 24, 26, 27, 30, 32, 33, 34, 39, 42, 43, 45, 48, 69, 75, 80, 84, 87, 98, 99, 100, 103, 105, 106, 108, 114], "bit": [4, 12, 105], "complex": [4, 15, 16, 28, 53, 99], "branch": [4, 82, 105, 108], "view": [4, 6, 14, 19, 30, 34, 39, 48, 50, 55, 108, 109, 114], "cell": [4, 9, 10, 11, 14, 19, 26, 34, 39, 48, 49, 50, 53, 55, 67, 81, 82, 105, 106, 108, 112], "applic": [4, 37, 58, 61, 66, 98, 114], "pull": [4, 10, 45, 70, 82, 101, 102, 105, 108, 111], "github": [4, 6, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 100, 102, 105], "depend": [4, 10, 16, 26, 53, 60, 61, 68, 100, 102, 104, 105, 106, 108, 112], "nglview": [4, 9, 10, 14, 19, 34, 39, 50, 52, 55, 104], "conda": [4, 7, 53, 79], "mamba": [4, 100], "micromamba": [4, 108], "yml": [4, 108], "quiet": 4, "nbextens": 4, "enabl": [4, 15, 85, 89, 94, 104, 105, 108], "sy": [4, 52], "output": [4, 10, 14, 16, 30, 34, 38, 39, 40, 42, 43, 44, 48, 53, 55, 63, 70, 72, 83, 105, 108, 112], "browser": [4, 108], "homepag": 4, "abil": [4, 105], "interact": [4, 6, 9, 10, 12, 14, 19, 26, 27, 28, 34, 36, 39, 50, 52, 55, 87, 104, 109], "viewer": 4, "jupyer": 4, "widget": [4, 9, 10, 14, 19, 34, 39, 48, 50, 55, 100], "whenev": [4, 102, 108], "advantag": 4, "determin": [4, 6, 7, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 29, 33, 34, 37, 46, 53, 57, 98, 104], "still": [4, 10, 15, 27, 60, 101, 102, 103, 105, 108], "gave": 4, "were": [4, 19, 28, 34, 67, 98, 102, 104, 105, 106, 108], "ini": 4, "sanitize_output": 4, "cfg": [4, 100], "polymers_and_membran": 4, "ipynb": [4, 43, 114], "replac": [4, 53, 100, 103, 105, 109], "regex": 4, "download": [4, 5, 6, 14, 15, 100, 102, 108], "scan": 4, "match": [4, 6, 7, 9, 10, 13, 17, 37, 44, 100, 102, 105, 106, 108], "word": [4, 37, 104], "exactli": [4, 16, 88, 109], "bar": [4, 15, 31, 100, 103, 105], "tend": 4, "correct": [4, 14, 26, 50, 53, 67, 102, 104, 105, 108], "memori": [4, 10, 11, 12, 14, 15, 26, 45, 53, 55, 56, 98, 99, 105, 108, 111, 112, 114], "locat": [4, 5, 9, 81, 82, 102, 106, 109], "allevi": 4, "regular": [4, 57, 87], "know": [4, 15, 16, 50, 53, 102, 108], "vari": [4, 37, 38, 44], "dynam": [4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 52, 55, 99, 104, 105, 110, 111, 112, 114], "constant": [4, 26, 33, 49, 52, 66, 76, 105, 106], "won": 4, "prevent": [4, 105], "spuriou": 4, "possibl": [4, 28, 30, 46, 57, 60, 82, 99, 103, 104, 106, 108], "extra": [4, 15, 16, 30, 83, 100], "softwar": [4, 15, 42, 43, 44, 45, 100, 104, 106, 108], "program": [4, 7, 14, 30, 34, 39, 50, 53, 93, 96, 99, 100, 104], "therefor": [4, 13, 14, 15, 19, 33, 37, 42, 43, 50, 52, 53, 72, 79, 92, 95, 98, 108], "ignor": [4, 9, 10, 14, 22, 23, 24, 27, 30, 33, 34, 37, 46, 50, 52, 53, 81, 82, 84, 95, 105, 106, 114], "unless": [4, 42, 61, 87, 100, 106, 114], "Of": 4, "cours": [4, 37, 55], "occur": [4, 19], "unix": [4, 30, 106], "impli": 4, "environment": 4, "path_to_hole2": 4, "ex": [4, 30], "usual": [4, 13, 34, 53, 56, 82], "difficult": [4, 7, 19, 32, 40, 55], "emb": [4, 7, 32, 33, 55], "imag": [4, 9, 10, 12, 14, 15, 19, 22, 23, 34, 39, 50, 55, 105, 108], "edit": [4, 34, 102, 104], "conf": 4, "url": [4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104], "site": [4, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 36, 37, 38, 42, 43, 44, 45, 49, 108], "site_url": 4, "person": 4, "my_user_nam": 4, "io": [4, 15, 79, 98], "macro": [4, 53, 96], "right": [4, 13, 14, 31, 40, 81, 106], "dropdown": 4, "websit": [4, 15], "publish": [4, 9, 10, 11, 12, 13, 14, 16, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 61, 102, 104], "my_branch": 4, "constantli": [4, 33], "pip": [4, 7, 53, 101, 104, 105, 108], "sphinx_autobuild": 4, "webserv": 4, "localhost": 4, "8000": [4, 83], "refresh": 4, "inconsist": [4, 105], "whitespac": [4, 83], "miss": [4, 27, 50, 57, 81, 82, 84, 101, 103, 105, 108], "carriag": 4, "perform": [4, 13, 15, 26, 43, 44, 48, 52, 85, 100, 108, 111, 112], "uninstal": 4, "offer": [5, 48, 105], "collect": [5, 6, 7, 30, 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44, 45, 53, 57, 83, 105, 109, 112], "rm": [6, 11, 12, 13, 14, 26, 27, 30, 53, 110], "fit": [6, 14, 27, 31, 39, 42, 46, 48, 53, 56, 112], "structur": [6, 8, 10, 11, 12, 16, 17, 19, 20, 21, 30, 34, 37, 38, 39, 41, 46, 52, 56, 58, 59, 61, 96, 97, 103, 104, 106, 108, 111, 114], "calcul": [6, 7, 8, 9, 10, 11, 16, 18, 19, 25, 33, 34, 35, 39, 41, 46, 47, 53, 55, 57, 61, 100, 104, 105, 109], "squar": [6, 7, 8, 9, 11, 12, 15, 16, 24, 38, 104, 105], "deviat": [6, 7, 8, 9, 11, 30, 37, 39, 42, 44, 83, 104], "pairwis": [6, 7, 8, 13, 14, 19, 39, 40], "rmsd": [6, 7, 8, 9, 10, 11, 14, 30, 33, 41, 46, 57, 104, 110], "fluctuat": [6, 7, 8, 13, 19, 27, 34], "contact": [6, 99, 104], "wise": [6, 7, 17, 23, 53], "fraction": [6, 7, 17, 18, 20, 21, 76], "nativ": [6, 7, 15, 17, 20, 21, 63, 100, 104], "q1": [6, 7, 17, 18, 19, 21], "q2": [6, 7, 17, 18, 19, 21], "cutoff": [6, 7, 17, 18, 20, 26, 38, 57, 106], "write": [6, 7, 9, 11, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 30, 34, 46, 48, 50, 52, 61, 62, 64, 68, 78, 90, 99, 105, 111, 113, 114], "harmon": [6, 7, 19, 20, 33, 41, 87, 104], "ensembl": [6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 41, 46, 48, 49, 50, 55, 104], "cluster": [6, 7, 15, 41, 44, 46], "dimens": [6, 22, 23, 26, 29, 37, 41, 49, 50, 55, 67, 81, 82, 104, 105, 106, 111, 112, 114], "reduct": [6, 34, 41, 104], "converg": [6, 7, 12, 13, 38, 41, 42, 104], "elast": [6, 7, 35], "network": [6, 7, 35], "averag": [6, 7, 8, 16, 26, 27, 31, 34, 35, 39, 40, 42, 44, 45, 49, 55], "radial": [6, 7, 35], "rdf": [6, 7, 35, 36, 105], "helix": [6, 7, 35, 104, 105], "princip": [6, 7, 32, 33, 43, 44, 104, 109], "compon": [6, 7, 32, 33, 43, 44, 104, 108], "non": [6, 7, 13, 19, 32, 36, 57, 60, 88, 105, 106], "linear": [6, 7, 31, 32, 34], "diffus": [6, 7, 32, 34, 104], "polym": [6, 104], "membran": [6, 26, 27, 28, 30], "persist": [6, 7, 10, 15, 26, 29, 53, 55, 111], "pore": [6, 7, 29, 104], "hole2": [6, 7, 29, 105], "volumetr": 6, "charg": [6, 7, 13, 28, 47, 48, 61, 66, 81, 82, 83, 86, 87, 92, 97, 105, 106, 109, 114], "densiti": [6, 7, 36, 42, 44, 47, 52, 57, 105], "axi": [6, 7, 10, 12, 15, 16, 22, 30, 34, 39, 44, 47, 48, 50, 55, 71, 109, 112], "solvent": [6, 7, 40, 47, 50, 114], "around": [6, 7, 13, 14, 16, 19, 22, 26, 28, 30, 34, 36, 40, 42, 47, 50, 52, 53, 99, 100, 106, 114], "data": [7, 15, 19, 20, 27, 32, 33, 34, 37, 39, 42, 43, 44, 46, 53, 55, 56, 58, 59, 61, 81, 82, 83, 84, 85, 89, 94, 95, 97, 98, 99, 103, 105, 109, 110, 111, 112, 113], "rang": [7, 15, 16, 30, 33, 34, 36, 40, 44, 50, 53, 57, 101, 106, 109], "algorithm": [7, 8, 9, 10, 11, 12, 13, 14, 16, 19, 33, 34, 39, 41, 42, 43, 44, 48, 52, 53, 60, 100, 104], "quantiti": [7, 8, 19, 53, 98, 105, 113], "uniqu": [7, 26, 34, 40, 57, 105, 108], "bundl": 7, "contribut": [7, 13, 36, 99, 102, 105, 108], "variou": [7, 26, 85, 105], "research": [7, 15, 19, 20, 104], "citat": 7, "parallel": [7, 100, 105], "paralleliz": 7, "encor": [7, 41, 42, 43, 44, 45, 104, 105], "hole": [7, 100, 104, 105], "yourself": [7, 30, 37, 45, 48], "align_structur": [7, 8], "align_trajectory_first": [7, 8], "align_trajectori": [7, 8], "rmsf": [7, 8, 12, 13], "sens": [7, 8, 84, 108, 109], "fast": [7, 8, 9, 10, 11, 12, 13, 14, 15, 33, 53, 79, 99, 103, 104], "qcp": [7, 8, 9, 10, 11, 12, 13, 14, 33], "the05": [7, 8, 9, 10, 11, 12, 13, 14, 33, 104], "lat09": [7, 8, 9, 10, 11, 14, 104], "cite": [7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 104], "rapidli": [7, 17, 37], "retain": [7, 17, 19, 21, 85], "insight": [7, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 55, 104], "fold": [7, 17, 19, 20, 104], "movement": [7, 13, 17, 19, 34, 57], "3n": [7, 32, 34, 41], "dimension": [7, 12, 32, 33, 41, 44, 45, 104], "tpb": [7, 41, 42, 43, 44, 45, 104], "estim": [7, 12, 41, 45], "measur": [7, 12, 13, 16, 30, 31, 41, 48, 66, 108], "pair": [7, 26, 28, 30, 36, 40, 41, 44, 46, 105], "transit": [7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 50, 53, 55, 104], "reduc": [7, 11, 30, 33, 41, 42, 43, 44, 85, 94, 100], "remain": [7, 13, 16, 19, 24, 27, 32, 49, 53, 57, 104, 105, 108, 111], "extract": [7, 26, 32, 53, 57, 98, 104], "motion": [7, 32, 34, 38], "physic": [7, 32, 33, 34, 104], "state": [7, 12, 13, 14, 15, 19, 32, 33, 34, 38, 53, 102, 103, 104, 111], "represent": [7, 32, 48, 67, 76, 96, 105, 112, 114], "explor": [7, 15, 32], "techniqu": [7, 32, 33, 34], "varianc": [7, 32, 34, 42, 43], "largest": [7, 32, 34, 46, 108], "uncorrel": [7, 27, 32, 34], "success": [7, 32, 34, 46], "essenti": [7, 32, 33, 34, 104, 108], "subspac": [7, 32, 34, 43], "visualis": [7, 9, 10, 19, 22, 23, 24, 32, 33, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 50, 55, 99], "repres": [7, 12, 13, 15, 20, 27, 32, 33, 34, 38, 39, 40, 42, 43, 44, 48, 50, 53, 57, 60, 67, 103, 109], "neighour": [7, 32, 33], "geometri": [7, 13, 23, 30, 32, 33, 37, 39, 48, 50, 53, 104, 106, 109, 112], "intrins": [7, 32, 33], "manifold": [7, 32, 33], "suitabl": [7, 16, 32, 33, 49], "sampl": [7, 9, 10, 11, 12, 13, 18, 19, 20, 21, 30, 32, 33, 34, 39, 42, 43, 44, 53, 104], "replica": [7, 32, 33], "exchang": [7, 32, 33], "simul": [7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 51, 53, 55, 57, 58, 61, 67, 68, 85, 104], "region": [7, 14, 32, 33, 37, 43], "disconnect": [7, 32, 33], "meaning": [7, 32, 33, 53, 98, 114], "cannot": [7, 15, 32, 33, 37, 60, 68, 81, 82, 83, 103, 108, 109], "approxim": [7, 32, 33], "pca": [7, 32, 34, 43, 44, 105], "explicit": [7, 32, 33, 109], "eigenvector": [7, 32, 33, 34, 38], "immedi": [7, 15, 19, 32, 33, 102, 108], "hydrogen_bond": [7, 25], "basic": [7, 18, 19, 21, 25, 27, 28, 53, 65, 87], "advanc": [7, 15, 25, 26, 27, 46, 100], "lifetim": [7, 25, 26, 28, 89], "decemb": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 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"References"], [15, "References"], [16, "References"], [18, "References"], [19, "References"], [20, "References"], [21, "References"], [22, "References"], [23, "References"], [24, "References"], [26, "References"], [27, "References"], [28, "References"], [30, "References"], [31, "References"], [33, "References"], [34, "References"], [36, "References"], [37, "References"], [38, "References"], [39, "References"], [40, "References"], [42, "References"], [43, "References"], [44, "References"], [45, "References"], [45, "id5"], [46, "References"], [48, "References"], [49, "References"], [50, "References"], [52, "References"], [53, "References"], [55, "References"], [104, "references"]], "Aligning a trajectory to a reference": [[10, "Aligning-a-trajectory-to-a-reference"]], "Aligning a trajectory with AlignTraj": [[10, "Aligning-a-trajectory-with-AlignTraj"]], "Copying coordinates into a new Universe": [[10, "Copying-coordinates-into-a-new-Universe"]], "Writing trajectories to a file": [[10, 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"RMSD-between-two-sets-of-coordinates"]], "RMSD of a Universe with multiple selections": [[13, "RMSD-of-a-Universe-with-multiple-selections"]], "Plotting the data": [[13, "Plotting-the-data"]], "RMSD of an AtomGroup with multiple selections": [[13, "RMSD-of-an-AtomGroup-with-multiple-selections"]], "Weighted RMSD of a trajectory": [[13, "Weighted-RMSD-of-a-trajectory"]], "Mass": [[13, "Mass"]], "Custom weights": [[13, "Custom-weights"]], "Calculating the root mean square fluctuation over a trajectory": [[14, "Calculating-the-root-mean-square-fluctuation-over-a-trajectory"]], "Creating an average structure": [[14, "Creating-an-average-structure"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Plotting RMSF": [[14, "Plotting-RMSF"]], "Visualising RMSF as B-factors": [[14, "Visualising-RMSF-as-B-factors"]], "Parallelizing analysis": [[15, "Parallelizing-analysis"]], "Radius of gyration": [[15, "Radius-of-gyration"], [16, "Radius-of-gyration"]], "Serial Analysis": [[15, "Serial-Analysis"]], "Parallelization in a simple per-frame fashion": [[15, "Parallelization-in-a-simple-per-frame-fashion"]], "Frame-wise form of the function": [[15, "Frame-wise-form-of-the-function"]], "Parallelization with multiprocessing": [[15, "Parallelization-with-multiprocessing"]], "Parallelization with dask": [[15, "Parallelization-with-dask"]], "Parallelization in a split-apply-combine fashion": [[15, "Parallelization-in-a-split-apply-combine-fashion"]], "Block analysis function": [[15, "Block-analysis-function"]], "Split the trajectory": [[15, "Split-the-trajectory"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Combine the results": [[15, "Combine-the-results"]], "Other possible parallelism approaches for multiple analyses": [[15, "Other-possible-parallelism-approaches-for-multiple-analyses"]], "See Also": [[15, "See-Also"]], "Writing your own trajectory analysis": 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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"]], "Write your own native contacts analysis method": [[18, "Write-your-own-native-contacts-analysis-method"]], "Defining salt bridges": [[18, "Defining-salt-bridges"]], "Define your own function": [[18, "Define-your-own-function"]], "Plotting": [[18, "Plotting"], [19, "Plotting"], [19, "id6"], [19, "id7"], [20, "Plotting"], [21, "Plotting"], [22, "Plotting"], [22, "id4"], [23, "Plotting"], [24, "Plotting"], [24, "id4"], [30, "Plotting"], [30, "id8"], [37, "Plotting"], [42, "Plotting"], [42, "id5"], [42, "id6"], [44, "Plotting"], [44, "id5"], [44, "id6"], [45, "Plotting"], [46, "Plotting"], [46, "id5"]], "Fraction of native contacts over a trajectory": [[19, "Fraction-of-native-contacts-over-a-trajectory"]], "Defining the groups for contact analysis": [[19, "Defining-the-groups-for-contact-analysis"], [21, "Defining-the-groups-for-contact-analysis"]], "Hard cutoff with a single reference": [[19, "Hard-cutoff-with-a-single-reference"]], "Radius cutoff": [[19, "Radius-cutoff"]], "Soft cutoff and multiple references": [[19, "Soft-cutoff-and-multiple-references"]], "Multiple references": [[19, "Multiple-references"]], "Soft cutoff": [[19, "Soft-cutoff"]], "Q1 vs Q2 contact analysis": [[20, "Q1-vs-Q2-contact-analysis"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Contact analysis: number of contacts within a cutoff": [[21, "Contact-analysis:-number-of-contacts-within-a-cutoff"]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Atom-wise distances between matching AtomGroups": [[22, "Atom-wise-distances-between-matching-AtomGroups"]], "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"]], "All distances between two selections": [[23, "All-distances-between-two-selections"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Plotting distance as a heatmap": [[23, "Plotting-distance-as-a-heatmap"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "All distances within a selection": [[24, "All-distances-within-a-selection"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating hydrogen bonds: the basics": [[26, "Calculating-hydrogen-bonds:-the-basics"]], "Hydrogen bonds": [[26, "Hydrogen-bonds"]], "Find water-water hydrogen bonds": [[26, "Find-water-water-hydrogen-bonds"]], "Accessing the results": [[26, "Accessing-the-results"]], "Helper functions": [[26, "Helper-functions"]], "Further analysis": [[26, "Further-analysis"]], "Store data": [[26, "Store-data"]], "Calculating hydrogen bond lifetimes": [[27, "Calculating-hydrogen-bond-lifetimes"]], "Find all hydrogen bonds": [[27, "Find-all-hydrogen-bonds"], [28, "Find-all-hydrogen-bonds"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Intermittent lifetime": [[27, "Intermittent-lifetime"]], "Hydrogen bond lifetime of individual hydrogen bonds": [[27, "Hydrogen-bond-lifetime-of-individual-hydrogen-bonds"]], "Calculating hydrogen bonds: advanced selections": [[28, "Calculating-hydrogen-bonds:-advanced-selections"]], "Use guess_acceptors and guess_hydrogens to create atom selections": [[28, "Use-guess_acceptors-and-guess_hydrogens-to-create-atom-selections"]], "More advanced selections": [[28, "More-advanced-selections"]], "Hydrogen bonds between specific groups": [[28, "Hydrogen-bonds-between-specific-groups"]], "Analysing pore dimensions with HOLE2": [[30, "Analysing-pore-dimensions-with-HOLE2"]], "Using HOLE with a PDB file": [[30, "Using-HOLE-with-a-PDB-file"]], "Using HOLE with a trajectory": [[30, "Using-HOLE-with-a-trajectory"]], "Working with the data": [[30, "Working-with-the-data"]], "Visualising the VMD surface": [[30, "Visualising-the-VMD-surface"]], "Ordering HOLE profiles with an order parameter": [[30, "Ordering-HOLE-profiles-with-an-order-parameter"]], "Deleting HOLE files": [[30, "Deleting-HOLE-files"]], "Determining the persistence length of a polymer": [[31, "Determining-the-persistence-length-of-a-polymer"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Non-linear dimension reduction to diffusion maps": [[33, "Non-linear-dimension-reduction-to-diffusion-maps"]], "Diffusion maps": [[33, "Diffusion-maps"]], "Principal component analysis of a trajectory": [[34, "Principal-component-analysis-of-a-trajectory"]], "Principal component analysis": [[34, "Principal-component-analysis"]], "Visualising projections into a reduced dimensional space": [[34, "Visualising-projections-into-a-reduced-dimensional-space"]], "Measuring convergence with cosine content": [[34, "Measuring-convergence-with-cosine-content"]], "Average radial distribution functions": [[36, "Average-radial-distribution-functions"]], "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 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"]], "Protein dihedral angle analysis": [[37, "Protein-dihedral-angle-analysis"]], "Selecting dihedral atom groups": [[37, "Selecting-dihedral-atom-groups"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Ramachandran analysis": [[37, "Ramachandran-analysis"]], "Janin analysis": [[37, "Janin-analysis"]], "Elastic network analysis": [[38, "Elastic-network-analysis"]], "Using a Gaussian network model": [[38, "Using-a-Gaussian-network-model"]], "Using a Gaussian network model with only close contacts": [[38, "Using-a-Gaussian-network-model-with-only-close-contacts"]], "Helix analysis": [[39, "Helix-analysis"], [39, "id6"]], "Running the analysis": [[39, "Running-the-analysis"]], "Calculating the RDF atom-to-atom": [[40, "Calculating-the-RDF-atom-to-atom"]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "The site-specific RDF without densities": [[40, "The-site-specific-RDF-without-densities"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, "Calculating-the-Clustering-Ensemble-Similarity-between-ensembles"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Trying out different clustering parameters": [[42, "Trying-out-different-clustering-parameters"]], "Estimating the error in a clustering ensemble similarity analysis": [[42, "Estimating-the-error-in-a-clustering-ensemble-similarity-analysis"]], "Evaluating convergence": [[43, "Evaluating-convergence"]], "Evaluating convergence with similarity measures": [[43, "Evaluating-convergence-with-similarity-measures"]], "Using default arguments with clustering ensemble similarity": [[43, "Using-default-arguments-with-clustering-ensemble-similarity"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Using default arguments with dimension reduction ensemble similarity": [[43, "Using-default-arguments-with-dimension-reduction-ensemble-similarity"]], "Comparing different dimensionality reduction methods": [[43, "Comparing-different-dimensionality-reduction-methods"]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, "Calculating-the-Dimension-Reduction-Ensemble-Similarity-between-ensembles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Trying out different dimension reduction parameters": [[44, "Trying-out-different-dimension-reduction-parameters"]], "Estimating the error in a dimension reduction ensemble similarity analysis": [[44, "Estimating-the-error-in-a-dimension-reduction-ensemble-similarity-analysis"]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, "Calculating-the-Harmonic-Ensemble-Similarity-between-ensembles"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Comparing the geometric similarity of trajectories": [[46, "Comparing-the-geometric-similarity-of-trajectories"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Generating paths": [[46, "Generating-paths"]], "Hausdorff method": [[46, "Hausdorff-method"]], "Discrete Fr\u00e9chet distances": [[46, "Discrete-Fr\u00e9chet-distances"]], "Calculating the solvent density around a protein": [[48, "Calculating-the-solvent-density-around-a-protein"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Visualisation": [[48, "Visualisation"]], "matplotlib (3D static plot)": [[48, "matplotlib-(3D-static-plot)"]], "nglview (interactive)": [[48, "nglview-(interactive)"]], "scikit-image (triangulated surface)": [[48, "scikit-image-(triangulated-surface)"]], "pyvista (3D surface)": [[48, "pyvista-(3D-surface)"]], "2D averaging": [[48, "2D-averaging"]], "Computing mass and charge density on each axis": [[49, "Computing-mass-and-charge-density-on-each-axis"]], "Constructing, modifying, and adding to a Universe": [[50, "Constructing,-modifying,-and-adding-to-a-Universe"]], "Creating and populating a Universe with water": [[50, "Creating-and-populating-a-Universe-with-water"]], "Creating a blank Universe": [[50, "Creating-a-blank-Universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding positions": [[50, "Adding-positions"]], "Adding bonds": [[50, "Adding-bonds"]], "Merging with a protein": [[50, "Merging-with-a-protein"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Tiling into a larger Universe": [[50, "Tiling-into-a-larger-Universe"]], "Acknowledgments": [[50, "Acknowledgments"]], "Other": [[51, "other"]], "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms": [[52, "Using-ParmEd-with-MDAnalysis-and-OpenMM-to-simulate-a-selection-of-atoms"]], "Loading files: the difference between ParmEd and MDAnalysis": [[52, "Loading-files:-the-difference-between-ParmEd-and-MDAnalysis"]], "Using MDAnalysis to select atoms": [[52, "Using-MDAnalysis-to-select-atoms"]], "Using ParmEd and OpenMM to create a simulation system": [[52, "Using-ParmEd-and-OpenMM-to-create-a-simulation-system"]], "Quick start guide": [[53, "Quick-start-guide"]], "Overview": [[53, "Overview"]], "Loading a structure or trajectory": [[53, "Loading-a-structure-or-trajectory"]], "Working with groups of atoms": [[53, "Working-with-groups-of-atoms"]], "Selecting atoms": [[53, "Selecting-atoms"]], "Getting atom information from AtomGroups": [[53, "Getting-atom-information-from-AtomGroups"]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Working with trajectories": [[53, "Working-with-trajectories"]], "Dynamic selection": [[53, "Dynamic-selection"]], "Writing out coordinates": [[53, "Writing-out-coordinates"]], "Single frame": [[53, "Single-frame"]], "Trajectories": [[53, "Trajectories"], [56, "trajectories"], [111, "trajectories"]], "RMSD": [[53, "RMSD"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Transformations": [[54, "transformations"]], "Centering a trajectory in the box": [[55, "Centering-a-trajectory-in-the-box"]], "Before transformation": [[55, "Before-transformation"]], "Unwrapping the protein": [[55, "Unwrapping-the-protein"]], "Centering in the box": [[55, "Centering-in-the-box"]], "Wrapping the solvent back into the box": [[55, "Wrapping-the-solvent-back-into-the-box"]], "Doing all this on-the-fly": [[55, "Doing-all-this-on-the-fly"]], "Frequently asked questions": [[56, "frequently-asked-questions"]], "Why do the atom positions change over trajectories?": [[56, "why-do-the-atom-positions-change-over-trajectories"]], "Auxiliary files": [[57, "auxiliary-files"]], "Supported formats": [[57, "supported-formats"]], "XVG Files": [[57, "xvg-files"]], "Reading data directly": [[57, "reading-data-directly"]], "Loading data into a Universe": [[57, "loading-data-into-a-universe"]], "Passing arguments to auxiliary data": [[57, "passing-arguments-to-auxiliary-data"]], "Iterating over auxiliary data": [[57, "iterating-over-auxiliary-data"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[57, "recreating-auxiliaries"]], "EDR Files": [[57, "edr-files"]], "Standalone Usage": [[57, "standalone-usage"]], "Unit Handling": [[57, "unit-handling"]], "Use with Trajectories": [[57, "use-with-trajectories"]], "Selecting Trajectory Frames Based on Auxiliary Data": [[57, "selecting-trajectory-frames-based-on-auxiliary-data"]], "Memory Usage": [[57, "memory-usage"]], "Coordinates": [[58, "coordinates"], [61, "coordinates"]], "Table of supported coordinate readers and the information read": [[58, "id2"], [61, "id12"]], "Format reference": [[59, "format-reference"]], "Guessing": [[60, "guessing"]], "Masses": [[60, "masses"]], "Types": [[60, "types"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Format overview": [[61, "format-overview"]], "Table of all supported formats in MDAnalysis": [[61, "id10"]], "Topology": [[61, "topology"], [97, "topology"]], "Table of supported topology parsers and the attributes read": [[61, "id11"], [97, "id1"]], "chemfiles (chemfiles Trajectory or file)": [[62, "chemfiles-chemfiles-trajectory-or-file"]], "CONFIG (DL_Poly Config)": [[63, "config-dl-poly-config"]], "HISTORY (DL_Poly Config)": [[63, "history-dl-poly-config"]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, "coor-nambdin-namd-binary-restart-files"]], "CRD (CHARMM CARD files)": [[65, "crd-charmm-card-files"]], "Reading in": [[65, "reading-in"], [66, "reading-in"], [67, "reading-in"], [70, "reading-in"], [71, "reading-in"], [72, "reading-in"], [76, "reading-in"], [79, "reading-in"], [81, "reading-in"], [82, "reading-in"], [83, "reading-in"], [84, "reading-in"], [85, "reading-in"], [88, "reading-in"], [89, "reading-in"], [94, "reading-in"], [95, "reading-in"]], "Writing out": [[65, "writing-out"], [66, "writing-out"], [67, "writing-out"], [71, "writing-out"], [79, "writing-out"], [81, "writing-out"], [82, "writing-out"], [83, "writing-out"], [89, "writing-out"]], "DATA (LAMMPS)": [[66, "data-lammps"]], "DCD (CHARMM, NAMD, or LAMMPS trajectory)": [[67, "dcd-charmm-namd-or-lammps-trajectory"]], "DCD (Flexible LAMMPS trajectory)": [[68, "dcd-flexible-lammps-trajectory"]], "DMS (Desmond Molecular Structure files)": [[69, "dms-desmond-molecular-structure-files"]], "GMS (Gamess trajectory)": [[70, "gms-gamess-trajectory"]], "GRO (GROMACS structure file)": [[71, "gro-gromacs-structure-file"]], "GSD (HOOMD GSD file)": [[72, "gsd-hoomd-gsd-file"]], "IN, FHIAIMS (FHI-aims input files)": [[73, "in-fhiaims-fhi-aims-input-files"]], "INPCRD, RESTRT (AMBER restart files)": [[74, "inpcrd-restrt-amber-restart-files"]], "ITP (GROMACS portable topology files)": [[75, "itp-gromacs-portable-topology-files"]], "LAMMPSDUMP (LAMMPS ascii dump file)": [[76, "lammpsdump-lammps-ascii-dump-file"]], "MMTF (Macromolecular Transmission Format)": [[77, "mmtf-macromolecular-transmission-format"]], "MOL2 (Tripos structure)": [[78, "mol2-tripos-structure"]], "MOL2 specification": [[78, "mol2-specification"]], "NCDF, NC (AMBER NetCDF trajectory)": [[79, "ncdf-nc-amber-netcdf-trajectory"]], "ParmEd (ParmEd Structure)": [[80, "parmed-parmed-structure"]], "PDB, ENT (Standard PDB file)": [[81, "pdb-ent-standard-pdb-file"]], "PDB specification": [[81, "pdb-specification"]], "CRYST1 fields": [[81, "id1"]], "ATOM/HETATM fields": [[81, "id2"]], "PDBQT (Autodock structure)": [[82, "pdbqt-autodock-structure"]], "PDBQT specification": [[82, "pdbqt-specification"]], "PDB format with AutoDOCK extensions for the PDBQT format.": [[82, "id1"]], "PQR file (PDB2PQR / APBS)": [[83, "pqr-file-pdb2pqr-apbs"]], "PQR specification": [[83, "pqr-specification"]], "PSF (CHARMM, NAMD, or XPLOR protein structure file)": [[84, "psf-charmm-namd-or-xplor-protein-structure-file"]], "PSF specification": [[84, "psf-specification"]], "TNG (Trajectory Next Generation)": [[85, "tng-trajectory-next-generation"]], "TOP, PRMTOP, PARM7 (AMBER topology)": [[86, "top-prmtop-parm7-amber-topology"]], "AMBER specification": [[86, "amber-specification"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Developer notes": [[86, "developer-notes"], [87, "developer-notes"], [89, "developer-notes"], [91, "developer-notes"]], "TPR (GROMACS run topology files)": [[87, "tpr-gromacs-run-topology-files"]], "Supported versions": [[87, "supported-versions"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[87, "id1"]], "TPR specification": [[87, "tpr-specification"]], "segid and chainID": [[87, "segid-and-chainid"]], "Bonds": [[87, "bonds"]], "GROMACS entries used to create bonds.": [[87, "id2"]], "GROMACS entries used to create angles.": [[87, "id3"]], "GROMACS entries used to create dihedrals.": [[87, "id4"]], "GROMACS entries used to create improper dihedrals.": [[87, "id5"]], "TRJ, MDCRD, CRDBOX (AMBER ASCII trajectory)": [[88, "trj-mdcrd-crdbox-amber-ascii-trajectory"]], "TRR (GROMACS lossless trajectory file)": [[89, "trr-gromacs-lossless-trajectory-file"]], "TRZ (IBIsCO and YASP trajectory)": [[90, "trz-ibisco-and-yasp-trajectory"]], "TXYZ, ARC (Tinker)": [[91, "txyz-arc-tinker"]], "XML (HOOMD)": [[92, "xml-hoomd"]], "XPDB (Extended PDB file)": [[93, "xpdb-extended-pdb-file"]], "XTC (GROMACS compressed trajectory file)": [[94, "xtc-gromacs-compressed-trajectory-file"]], "XYZ trajectory": [[95, "xyz-trajectory"]], "XYZ specification": [[95, "xyz-specification"]], "Note": [[95, "note"]], "Selection exporters": [[96, "selection-exporters"]], "Supported selection exporters": [[96, "id2"]], "Writing selections": [[96, "writing-selections"]], "Single AtomGroup": [[96, "single-atomgroup"]], "Multiple selections": [[96, "multiple-selections"]], "Reading in selections": [[96, "reading-in-selections"]], "Groups of atoms": [[98, "groups-of-atoms"]], "Residues and Segments": [[98, "residues-and-segments"]], "Use case: Sequence of residues by segment": [[98, "use-case-sequence-of-residues-by-segment"]], "Use case: Atoms list grouped by residues": [[98, "use-case-atoms-list-grouped-by-residues"]], "Fragments": [[98, "fragments"]], "Welcome to MDAnalysis User Guide\u2019s documentation!": [[99, "welcome-to-mdanalysis-user-guide-s-documentation"]], "Why MDAnalysis?": [[99, "why-mdanalysis"]], "Participating": [[99, "participating"]], "Communications": [[99, "communications"]], "Installation": [[100, "installation"]], "conda": [[100, "conda"]], "pip": [[100, "pip"]], "Development versions": [[100, "development-versions"]], "Testing": [[100, "testing"]], "Custom compiler flags and optimised installations": [[100, "custom-compiler-flags-and-optimised-installations"]], "Additional datasets": [[100, "additional-datasets"]], "Module imports in MDAnalysis": [[101, "module-imports-in-mdanalysis"]], "General rules for importing": [[101, "general-rules-for-importing"]], "Module imports in MDAnalysis.analysis": [[101, "module-imports-in-mdanalysis-analysis"]], "Module imports in the test suite": [[101, "module-imports-in-the-test-suite"]], "Module dependencies in the code": [[101, "module-dependencies-in-the-code"]], "List of core module dependencies": [[101, "list-of-core-module-dependencies"]], "Modules in the \u201ccore\u201d": [[101, "modules-in-the-core"]], "Optional modules in MDAnalysis.analysis and MDAnalysis.visualization": [[101, "optional-modules-in-mdanalysis-analysis-and-mdanalysis-visualization"]], "Preparing a release": [[102, "preparing-a-release"]], "Release policy and release numbering": [[102, "release-policy-and-release-numbering"]], "Typical workflow for preparing a release": [[102, "typical-workflow-for-preparing-a-release"]], "Summary of tasks": [[102, "summary-of-tasks"]], "Getting the develop branch ready for a release": [[102, "getting-the-develop-branch-ready-for-a-release"]], "Packaging the release": [[102, "packaging-the-release"]], "Completing the release": [[102, "completing-the-release"]], "Manually upload Cirrus CI wheels (temporary)": [[102, "manually-upload-cirrus-ci-wheels-temporary"]], "Update conda-forge packages": [[102, "update-conda-forge-packages"]], "Create a release of the UserGuide": [[102, "create-a-release-of-the-userguide"]], "Create a blog post outlining the release": [[102, "create-a-blog-post-outlining-the-release"]], "Increment develop branch files ready for the next version": [[102, "increment-develop-branch-files-ready-for-the-next-version"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Reading and writing files": [[103, "reading-and-writing-files"]], "Input": [[103, "input"]], "Reading multiple trajectories": [[103, "reading-multiple-trajectories"]], "Trajectory formats": [[103, "trajectory-formats"]], "In-memory trajectories": [[103, "in-memory-trajectories"]], "Reading trajectories into memory": [[103, "reading-trajectories-into-memory"]], "Transferring trajectories into memory": [[103, "transferring-trajectories-into-memory"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "In-memory trajectories of an atom selection": [[103, "in-memory-trajectories-of-an-atom-selection"]], "Output": [[103, "output"]], "Frames and trajectories": [[103, "frames-and-trajectories"]], "Pickling": [[103, "pickling"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "MDAnalysis Release Notes": [[105, "mdanalysis-release-notes"]], "Release 2.6.1 of MDAnalysis": [[105, "release-2-6-1-of-mdanalysis"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "New Contributors": [[105, "new-contributors"], [105, "id1"], [105, "id5"], [105, "id13"]], "Release 2.6.0 of MDAnalysis": [[105, "release-2-6-0-of-mdanalysis"]], "Major changes:": [[105, "major-changes"], [105, "id2"], [105, "id8"], [105, "id14"], [105, "id19"], [105, "id24"], [105, "id30"]], "Fixes:": [[105, "fixes"], [105, "id3"], [105, "id9"], [105, "id15"], [105, "id21"], [105, "id26"], [105, "id32"]], "Enhancements:": [[105, "enhancements"], [105, "id16"], [105, "id20"], [105, "id25"], [105, "id31"]], "Changes:": [[105, "changes"], [105, "id4"], [105, "id11"], [105, "id17"], [105, "id22"], [105, "id27"], [105, "id33"]], "Deprecations:": [[105, "deprecations"], [105, "id12"], [105, "id18"], [105, "id23"], [105, "id28"], [105, "id34"]], "Release 2.5.0 of MDAnalysis": [[105, "release-2-5-0-of-mdanalysis"]], "Enchancements:": [[105, "enchancements"], [105, "id10"]], "Release 2.4.3 of MDAnalysis": [[105, "release-2-4-3-of-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id6"], [105, "id7"]], "Release 2.4.2 of MDAnalysis": [[105, "release-2-4-2-of-mdanalysis"]], "Release 2.4.1 of MDAnalysis": [[105, "release-2-4-1-of-mdanalysis"]], "Release 2.4.0 of MDAnalysis": [[105, "release-2-4-0-of-mdanalysis"]], "Release 2.3.0 of MDAnalysis": [[105, "release-2-3-0-of-mdanalysis"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Release 2.2.0 of MDAnalysis": [[105, "release-2-2-0-of-mdanalysis"]], "Known test failures:": [[105, "known-test-failures"], [105, "id29"]], "Release 2.1.0 of MDAnalysis": [[105, 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112, 114], "inform": [1, 3, 4, 7, 10, 12, 14, 15, 16, 19, 22, 26, 28, 30, 32, 33, 34, 37, 40, 42, 43, 44, 46, 50, 52, 56, 57, 60, 62, 63, 66, 69, 70, 71, 72, 80, 81, 82, 84, 87, 88, 94, 95, 98, 101, 103, 105, 106, 108, 111, 112, 114], "like": [1, 3, 4, 5, 13, 16, 19, 26, 30, 34, 39, 40, 43, 48, 53, 55, 57, 60, 83, 100, 106, 108], "list": [1, 2, 3, 5, 13, 15, 16, 19, 26, 30, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 57, 61, 65, 67, 82, 87, 96, 99, 100, 102, 104, 105, 106, 107, 108, 109, 111, 112, 113, 114], "5": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 67, 71, 78, 82, 87, 93, 98, 102, 103, 104, 106, 108, 109, 110, 111, 112, 114], "print": [1, 5, 9, 10, 11, 13, 14, 15, 19, 23, 26, 27, 28, 30, 31, 34, 36, 37, 39, 40, 42, 43, 44, 45, 46, 49, 50, 53, 57, 101, 103, 108, 109, 110, 111, 114], "n": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 83, 95, 96, 98, 104, 105, 106, 107, 113], "type": [1, 3, 26, 42, 50, 52, 53, 58, 61, 65, 66, 72, 80, 81, 82, 83, 84, 85, 86, 87, 91, 92, 96, 97, 98, 104, 105, 106, 109, 113], "met": [1, 53, 83, 107, 109], "resid": [1, 13, 14, 23, 24, 26, 27, 36, 40, 46, 50, 53, 61, 65, 66, 69, 72, 75, 81, 82, 87, 89, 98, 105, 106, 109], "altloc": [1, 14, 61, 81, 82, 97, 106, 109], "return": [1, 3, 4, 9, 10, 13, 15, 16, 18, 19, 20, 21, 22, 24, 27, 30, 33, 34, 37, 40, 42, 44, 50, 53, 57, 98, 102, 105, 106, 108, 110, 111, 112], "below": [1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 61, 98, 103, 106, 107, 108, 109, 112, 113, 114], "code": [1, 2, 4, 5, 6, 7, 11, 13, 14, 15, 16, 30, 36, 48, 50, 57, 67, 78, 81, 82, 84, 93, 98, 99, 102, 103, 104, 105, 106, 108, 109, 112, 114], "everi": [1, 3, 4, 10, 14, 15, 16, 24, 27, 30, 31, 34, 37, 39, 42, 44, 48, 50, 52, 53, 57, 60, 61, 98, 103, 105, 106, 108, 109, 111, 114], "second": [1, 10, 12, 18, 19, 21, 40, 44, 53, 113], "element": [1, 42, 50, 53, 60, 61, 65, 66, 70, 81, 82, 86, 97, 105, 109, 114], "first": [1, 3, 4, 7, 9, 10, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 24, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 49, 50, 53, 55, 57, 61, 69, 72, 81, 83, 89, 94, 98, 100, 101, 105, 106, 108, 110, 111, 114], "6th": [1, 106], "correspond": [1, 3, 12, 13, 14, 16, 24, 26, 27, 40, 55, 71, 98, 108, 109], "indic": [1, 3, 12, 13, 14, 19, 24, 26, 27, 30, 33, 34, 38, 40, 43, 50, 53, 81, 82, 84, 87, 91, 96, 101, 105, 106, 108, 109, 110], "6": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 66, 69, 78, 81, 82, 83, 84, 87, 91, 93, 98, 102, 103, 104, 106, 109, 110, 111, 112, 114], "ag": [1, 10, 13, 40, 96, 98, 103], "also": [1, 2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 32, 34, 37, 39, 40, 41, 42, 44, 48, 53, 55, 57, 61, 62, 81, 82, 87, 89, 98, 100, 101, 102, 103, 105, 106, 108, 109, 110, 111, 112, 113, 114], "support": [1, 3, 13, 19, 30, 46, 53, 66, 71, 72, 82, 84, 85, 88, 100, 103, 105, 106, 109, 111, 114], "fanci": [1, 53, 110], "pass": [1, 3, 4, 13, 16, 18, 19, 22, 23, 24, 26, 28, 30, 31, 34, 36, 37, 39, 42, 43, 44, 45, 49, 50, 53, 55, 60, 61, 62, 66, 80, 81, 93, 95, 96, 100, 102, 103, 105, 106, 108, 110, 112, 114], "ndarrai": [1, 53, 110], "8": [1, 4, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 87, 98, 103, 105, 106, 109, 110, 111, 112, 114], "10": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 71, 78, 82, 83, 87, 98, 103, 104, 105, 106, 108, 109, 110, 111, 112, 113, 114], "9": 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24, 26, 27, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 57, 60, 65, 66, 67, 76, 81, 82, 83, 89, 92, 105, 106, 108, 110, 114], "must": [1, 2, 3, 4, 11, 12, 13, 16, 18, 22, 23, 26, 27, 30, 31, 34, 42, 43, 46, 48, 50, 53, 60, 66, 79, 83, 84, 100, 101, 108, 109, 112, 114], "same": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 24, 26, 28, 30, 31, 33, 34, 36, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 67, 93, 95, 96, 98, 102, 103, 105, 106, 109, 110, 114], "length": [1, 3, 6, 7, 12, 13, 22, 24, 27, 29, 39, 40, 42, 44, 45, 46, 48, 50, 52, 53, 63, 66, 67, 68, 71, 79, 88, 99, 104, 105, 110, 111], "origin": [1, 3, 4, 7, 9, 13, 14, 23, 27, 32, 33, 34, 39, 50, 53, 55, 57, 67, 98, 102, 106, 108, 110, 113], "condit": [1, 15, 105, 106, 108, 110, 112], "arr": 1, "11": [1, 3, 9, 10, 13, 14, 15, 16, 19, 24, 26, 27, 28, 30, 33, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 78, 81, 82, 83, 87, 98, 103, 104, 105, 106, 109, 110, 112, 113, 114], "len": [1, 12, 23, 24, 30, 33, 34, 36, 37, 38, 40, 42, 44, 45, 46, 48, 50, 53, 57, 98, 103, 108, 109, 111], "12": [1, 3, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 33, 34, 36, 37, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 55, 57, 78, 82, 86, 98, 103, 104, 106, 109, 110, 111, 112, 113, 114], "13": [1, 9, 10, 13, 14, 15, 16, 19, 26, 27, 30, 34, 36, 37, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 106, 109, 110, 112, 114], "number": [1, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 27, 30, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 50, 52, 53, 57, 60, 65, 69, 71, 72, 75, 81, 82, 83, 84, 85, 87, 89, 91, 92, 93, 96, 103, 105, 106, 108, 109, 114], "wai": [1, 3, 4, 7, 10, 12, 13, 14, 15, 16, 18, 19, 26, 27, 30, 33, 34, 48, 52, 53, 79, 98, 99, 103, 105, 106, 108, 109, 111, 114], "compar": [1, 6, 7, 9, 10, 11, 12, 14, 15, 17, 19, 22, 32, 34, 40, 41, 42, 44, 45, 108], "one": [1, 2, 3, 4, 10, 11, 12, 13, 15, 19, 27, 28, 30, 31, 39, 46, 50, 53, 56, 57, 83, 87, 88, 91, 92, 96, 98, 99, 100, 103, 104, 105, 106, 108, 109, 114], "concaten": [1, 15, 53, 103, 106, 114], "subtract": [1, 13, 84], "union": [1, 106], "differ": [1, 3, 4, 7, 9, 10, 12, 13, 15, 16, 19, 26, 28, 34, 36, 38, 40, 41, 45, 46, 48, 50, 53, 55, 60, 66, 67, 70, 71, 75, 82, 87, 91, 93, 95, 96, 98, 99, 100, 102, 103, 104, 105, 106, 112, 114], "achiev": [1, 15], "similar": [1, 3, 4, 6, 12, 15, 19, 23, 24, 30, 32, 33, 34, 37, 38, 53, 73, 82, 83, 87, 92, 93, 98, 104], "outcom": [1, 105], "kei": [1, 2, 30, 38, 39, 49, 53, 57, 98, 99, 114], "preserv": [1, 4, 19, 66, 105], "ani": [1, 2, 3, 4, 11, 15, 16, 18, 27, 28, 30, 31, 37, 42, 43, 44, 46, 49, 50, 53, 56, 57, 61, 67, 89, 98, 99, 100, 101, 102, 103, 104, 105, 106, 108, 112], "duplic": [1, 30, 53, 103, 106], "where": [1, 4, 5, 7, 9, 14, 15, 16, 19, 20, 21, 22, 27, 31, 32, 33, 36, 37, 38, 40, 43, 44, 46, 48, 50, 53, 57, 60, 61, 66, 71, 89, 98, 100, 102, 105, 106, 108, 109], "its": [1, 2, 3, 4, 7, 9, 13, 15, 18, 19, 20, 22, 30, 32, 33, 44, 46, 49, 52, 53, 98, 99, 100, 101, 103, 106, 108, 109, 111, 112], "topologi": [1, 5, 14, 15, 26, 28, 52, 53, 59, 63, 65, 66, 69, 70, 71, 72, 73, 76, 77, 78, 80, 81, 82, 83, 84, 91, 92, 93, 95, 98, 99, 103, 105, 106, 108, 111], "14": [1, 9, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 42, 43, 44, 48, 49, 50, 52, 53, 55, 57, 82, 98, 100, 103, 104, 105, 106, 109, 110, 112, 114], "ag1": [1, 40], "15": [1, 7, 10, 13, 15, 16, 19, 26, 27, 30, 34, 36, 40, 41, 42, 43, 44, 45, 48, 49, 50, 52, 53, 57, 81, 82, 98, 103, 104, 106, 109, 110, 112, 114], "ag2": [1, 40], "16": [1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 57, 81, 82, 98, 103, 104, 105, 106, 109, 110, 111, 112], "concat": 1, "17": [1, 12, 15, 16, 19, 20, 21, 26, 27, 30, 33, 34, 36, 39, 42, 44, 48, 49, 50, 52, 53, 57, 69, 81, 82, 87, 98, 103, 104, 106, 109, 110, 111, 112], "18": [1, 9, 15, 16, 19, 26, 27, 30, 42, 44, 46, 48, 49, 50, 52, 53, 57, 78, 81, 82, 86, 98, 103, 105, 106, 109, 110, 112, 113], "19": [1, 15, 16, 19, 22, 23, 24, 26, 27, 28, 30, 37, 40, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 104, 105, 106, 109, 112, 113], "avail": [1, 2, 3, 7, 15, 16, 19, 32, 33, 36, 40, 42, 43, 44, 53, 56, 57, 60, 66, 73, 77, 79, 82, 87, 96, 98, 99, 100, 102, 105, 106, 108, 109, 114], "keep": [1, 2, 3, 10, 14, 30, 34, 39, 43, 44, 48, 55, 72, 96, 99, 101, 102, 108], "well": [1, 2, 4, 7, 15, 32, 33, 44, 48, 61, 67, 99, 101, 105, 108], "equival": [1, 27, 48, 87], "result": [1, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 24, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 52, 53, 61, 89, 94, 105, 106, 108, 110], "t": [1, 3, 4, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 48, 49, 50, 52, 53, 55, 56, 57, 66, 82, 92, 96, 98, 100, 103, 104, 105, 106, 107, 108, 110, 111, 112, 114], "sort": [1, 26, 27, 30, 34, 53, 105, 106], "isdisjoint": 1, "do": [1, 3, 4, 6, 10, 11, 12, 13, 15, 16, 19, 22, 26, 27, 28, 30, 34, 37, 42, 44, 45, 46, 48, 50, 52, 53, 95, 99, 101, 102, 103, 105, 108, 114], "share": [1, 3, 105], "issubset": 1, "part": [1, 2, 3, 4, 15, 30, 48, 57, 101, 103, 105, 106, 108, 111], "is_strict_subset": 1, "issuperset": 1, "is_strict_superset": 1, "both": [1, 3, 4, 13, 15, 16, 22, 30, 38, 48, 50, 52, 53, 60, 63, 72, 81, 85, 87, 91, 98, 100, 102, 103, 105, 108, 109, 114], "intersect": [1, 106], "common": [1, 3, 7, 12, 13, 14, 15, 22, 26, 31, 32, 34, 53, 55, 68, 70, 104, 106, 108], "symmetric_differ": 1, "separ": [1, 5, 7, 15, 16, 19, 30, 31, 36, 40, 42, 43, 81, 83, 84, 100, 102, 106, 108, 114], "properti": [1, 16, 30, 39, 53, 60, 98, 105, 106, 109, 111, 112], "level": [1, 3, 4, 15, 48, 85, 98, 101, 108, 114], "connect": [1, 3, 4, 33, 50, 52, 53, 60, 61, 82, 87, 91, 105, 114], "residu": [1, 3, 7, 13, 14, 17, 19, 21, 22, 26, 28, 30, 36, 37, 38, 39, 40, 48, 49, 50, 52, 53, 55, 61, 65, 69, 70, 71, 72, 75, 81, 82, 83, 86, 87, 92, 93, 95, 96, 99, 105, 106, 109, 112, 114], "molecul": [1, 4, 10, 13, 26, 31, 38, 50, 55, 58, 61, 66, 78, 87, 92, 95, 98, 105, 106, 108, 109, 112], "segment": [1, 10, 49, 53, 61, 65, 70, 81, 87, 95, 99, 103, 105, 106, 109, 114], "20": [1, 15, 16, 19, 26, 30, 31, 42, 44, 48, 49, 50, 52, 53, 57, 82, 98, 103, 105, 106, 110, 111, 112, 113], "21": [1, 3, 9, 15, 16, 26, 27, 28, 30, 31, 33, 42, 44, 48, 49, 50, 52, 53, 57, 71, 81, 82, 98, 103, 104, 105, 106, 109, 112, 113, 114], "24": [1, 15, 16, 26, 27, 30, 34, 39, 44, 49, 50, 53, 57, 81, 82, 87, 98, 99, 103, 105, 112], "accord": [1, 13, 14, 87, 91, 106, 109], "produc": [1, 23, 27, 34, 53, 57, 67, 105, 108], "dictionari": [1, 18, 30, 57, 60, 89, 105, 108, 114], "22": [1, 15, 16, 26, 30, 44, 46, 48, 49, 50, 53, 57, 81, 82, 98, 103, 105, 106, 112], "mass": [1, 6, 7, 9, 10, 15, 16, 23, 24, 28, 30, 36, 40, 45, 46, 47, 48, 53, 55, 61, 63, 65, 66, 86, 87, 92, 97, 106, 109, 112, 113, 114], "32": [1, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 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104, 107, 113], "28": [1, 3, 15, 30, 49, 50, 53, 57, 78, 98, 103], "ca": [1, 9, 10, 11, 12, 13, 14, 16, 18, 20, 21, 23, 24, 36, 37, 38, 39, 40, 42, 43, 44, 46, 53, 60, 98, 103, 106, 107], "c": [1, 3, 13, 27, 30, 31, 34, 36, 37, 38, 39, 46, 48, 50, 52, 53, 62, 67, 78, 81, 82, 85, 87, 88, 98, 100, 102, 103, 104, 105, 106, 107, 113], "cb": [1, 36, 53, 98], "h2": [1, 26, 28, 50, 78], "h": [1, 3, 27, 31, 36, 39, 45, 50, 52, 53, 78, 87, 96, 98, 103, 106], "neat": [1, 4], "shortcut": [1, 106], "simpli": [1, 3, 12, 13, 15, 21, 24, 26, 34, 40, 50, 52, 53, 60, 79, 84, 88, 101, 104, 105, 106, 109, 113], "29": [1, 13, 15, 30, 34, 46, 49, 50, 53, 57, 98, 103, 113], "30": [1, 13, 14, 15, 22, 23, 30, 33, 42, 49, 50, 53, 57, 78, 98, 103, 104, 110, 112, 113], "31": [1, 15, 16, 19, 30, 48, 49, 50, 53, 57, 81, 82, 98, 103], "altern": [1, 3, 13, 20, 30, 48, 57, 77, 81, 82, 96, 103, 106, 108, 109, 112], "provid": [1, 3, 4, 7, 12, 13, 15, 16, 17, 25, 26, 30, 31, 34, 37, 38, 43, 44, 46, 52, 53, 55, 57, 60, 61, 62, 65, 71, 81, 82, 83, 88, 94, 96, 99, 100, 103, 105, 106, 108, 109, 114], "belong": [1, 28, 50, 53, 61, 98, 106, 107], "33": [1, 15, 49, 50, 53, 57, 81, 82], "34": [1, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 37, 38, 39, 40, 42, 43, 44, 45, 49, 50, 52, 53, 55, 57, 81, 82, 98, 104], "These": [1, 3, 4, 5, 7, 8, 17, 24, 37, 43, 48, 53, 57, 72, 81, 82, 89, 94, 98, 106, 108, 109], "user": [1, 2, 3, 6, 7, 15, 19, 26, 28, 39, 42, 43, 44, 45, 49, 53, 60, 61, 66, 68, 69, 72, 78, 79, 87, 88, 100, 101, 102, 103, 105, 106, 108, 109, 114], "work": [1, 2, 4, 7, 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, 55, 56, 57, 62, 67, 79, 96, 99, 100, 102, 104, 105, 106, 108, 111], "35": [1, 19, 20, 30, 49, 50, 53, 57, 98, 103, 104], "null": 1, "36": [1, 49, 50, 53, 57, 83], "abov": [1, 3, 10, 13, 16, 23, 24, 26, 27, 28, 39, 48, 53, 55, 57, 83, 102, 103, 105, 106, 108, 109, 111], "37": [1, 38, 49, 50, 53, 57, 83, 98, 104], "For": [1, 2, 3, 4, 7, 9, 12, 13, 15, 16, 19, 26, 28, 30, 32, 33, 34, 37, 39, 40, 42, 43, 44, 46, 50, 52, 53, 55, 57, 60, 61, 66, 78, 83, 87, 89, 96, 98, 100, 101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112, 114], "38": [1, 16, 23, 49, 52, 53, 57, 81, 82], "does_not_exist": 1, "39": [1, 13, 15, 16, 18, 20, 21, 23, 24, 26, 30, 31, 36, 37, 38, 39, 40, 42, 43, 44, 48, 49, 50, 52, 53, 57, 81, 82], "40": [1, 19, 30, 49, 53, 57, 81, 82, 98, 103, 110], "have": [1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 18, 19, 22, 24, 26, 27, 30, 31, 33, 34, 36, 37, 40, 42, 44, 45, 46, 48, 50, 53, 55, 57, 60, 63, 66, 67, 69, 71, 75, 79, 81, 82, 84, 87, 89, 95, 98, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 114], "evalu": [1, 6, 7, 34, 41, 49, 106], "context": [1, 15, 30, 52, 53, 96, 108], "41": [1, 30, 49, 57, 81, 82, 98], "bool": [1, 3, 18, 50, 109, 110], "skip": [1, 3, 16, 46, 57, 100], "over": [1, 6, 7, 8, 12, 15, 16, 17, 18, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 53, 55, 72, 102, 103, 105, 108, 110, 111, 112], "instead": [1, 3, 4, 9, 10, 12, 14, 15, 16, 19, 23, 24, 30, 34, 37, 39, 43, 44, 48, 50, 55, 61, 81, 82, 88, 92, 93, 100, 105, 106, 108, 111, 114], "rais": [1, 3, 33, 49, 53, 65, 79, 81, 82, 83, 99, 100, 101, 105, 108], "error": [1, 3, 4, 9, 49, 53, 72, 79, 89, 94, 100, 101, 105, 108], "which": [1, 3, 4, 10, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 30, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 50, 53, 55, 57, 60, 61, 67, 68, 83, 87, 89, 91, 94, 96, 98, 99, 100, 102, 103, 105, 106, 108, 109, 112, 114], "help": [1, 2, 3, 4, 13, 16, 22, 96, 99, 100, 106, 108], "occasion": [1, 89, 94], "aris": [1, 4], "logic": 1, "too": [1, 16, 42, 44, 48, 53, 55, 56, 99, 108], "restrict": [1, 13, 14, 87], "geometr": [1, 6, 7, 26, 41, 52], "normal": [1, 3, 15, 30, 38, 39, 43, 44, 84, 91, 96, 102, 104, 105, 108], "static": [1, 10, 15, 53, 106, 109, 111, 114], "within": [1, 6, 7, 16, 17, 18, 19, 20, 22, 26, 28, 30, 36, 38, 40, 42, 43, 44, 45, 50, 53, 57, 60, 67, 77, 105, 106, 111, 112], "chang": [1, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 49, 53, 55, 57, 61, 71, 72, 81, 87, 89, 100, 102, 103, 106, 108, 111], "trajectori": [1, 5, 6, 8, 9, 17, 18, 20, 21, 26, 27, 32, 33, 36, 37, 38, 40, 42, 43, 44, 45, 48, 49, 50, 52, 54, 58, 59, 61, 66, 71, 72, 81, 82, 91, 93, 99, 104, 105, 106, 108, 112, 113, 114], "frame": [1, 7, 9, 10, 12, 13, 14, 16, 17, 18, 19, 20, 21, 26, 27, 30, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 46, 48, 49, 52, 55, 56, 61, 66, 71, 81, 82, 89, 94, 99, 105, 106, 108, 110, 111, 112, 114], "sever": [1, 3, 7, 16, 29, 30, 33, 34, 53, 82, 101, 105, 108, 114], "requir": [1, 3, 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 65, 66, 79, 81, 82, 83, 95, 96, 98, 100, 103, 105, 106, 108, 109], "function": [1, 2, 3, 4, 6, 7, 8, 13, 17, 19, 20, 21, 27, 30, 33, 34, 35, 37, 41, 42, 43, 44, 45, 46, 52, 53, 55, 56, 57, 85, 87, 98, 100, 101, 102, 104, 105, 106, 109, 111, 112, 114], "implement": [1, 3, 7, 9, 10, 11, 12, 13, 14, 15, 16, 32, 33, 34, 39, 53, 57, 62, 66, 76, 82, 87, 95, 106, 112], "mani": [1, 2, 3, 4, 13, 15, 16, 21, 26, 30, 34, 39, 40, 42, 43, 44, 53, 99, 100, 108, 109, 111, 114], "interest": [1, 19, 30, 48, 53, 100], "bond": [1, 13, 31, 49, 52, 53, 55, 57, 61, 66, 78, 80, 81, 82, 84, 86, 91, 92, 97, 98, 99, 104, 105, 106, 109, 114], "angl": [1, 6, 7, 22, 26, 27, 28, 35, 39, 50, 53, 57, 61, 66, 67, 84, 86, 92, 97, 99, 104, 105, 106, 109, 113, 114], "dihedr": [1, 6, 7, 35, 53, 61, 66, 84, 86, 97, 105, 106, 109, 114], "improperdihedr": [1, 109], "present": [1, 3, 19, 21, 26, 27, 40, 52, 65, 68, 81, 92, 95, 98, 105], "residuegroup": [1, 53, 98, 105, 109], "free": [2, 3, 101], "open": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 87, 89, 94, 104, 108], "sourc": [2, 3, 4, 16, 30, 53, 57, 84, 96, 100, 102, 105, 108], "project": [2, 3, 4, 7, 32, 37, 39, 43, 44, 48, 99, 105], "It": [2, 3, 4, 7, 9, 12, 13, 14, 15, 16, 21, 22, 26, 27, 28, 30, 32, 33, 34, 36, 37, 40, 45, 48, 49, 50, 53, 57, 60, 61, 67, 76, 78, 82, 85, 87, 89, 99, 104, 106, 108, 110, 112, 114], "evolv": 2, "grow": [2, 5, 108], "demand": 2, "base": [2, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 19, 28, 33, 39, 42, 44, 46, 50, 52, 53, 60, 61, 65, 79, 87, 89, 94, 102, 103, 104, 105, 106, 107, 108, 109], "develop": [2, 15, 52, 72, 101, 108], "team": 2, "veri": [2, 3, 12, 13, 15, 19, 23, 24, 27, 44, 45, 48, 79, 93, 103, 108], "much": [2, 3, 10, 11, 12, 13, 14, 16, 19, 30, 34, 42, 43, 48, 50, 60, 105, 108], "welcom": 2, "take": [2, 3, 4, 7, 14, 15, 16, 17, 23, 26, 30, 33, 42, 44, 48, 93, 96, 99, 100, 103, 106, 108, 109, 112, 114], "form": [2, 13, 19, 26, 42, 53, 55, 60], "bug": [2, 3, 16, 88, 102], "report": [2, 52, 99, 108], "enhanc": [2, 3], "request": [2, 4, 101, 102, 108], "issu": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 50, 57, 61, 63, 67, 79, 84, 87, 89, 94, 99, 100, 101, 102, 106, 108], "tracker": [2, 87, 99, 108], "fix": [2, 3, 4, 48, 49, 68, 72, 102], "improv": [2, 27, 99, 108], "speed": [2, 105, 108], "clariti": [2, 26], "modernis": 2, "featur": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 83, 99, 100, 102, 114], "addit": [2, 3, 7, 44, 57, 61, 82, 96, 98, 101, 102, 103, 105, 106, 108, 109], "document": [2, 5, 7, 15, 19, 22, 26, 30, 43, 48, 53, 66, 76, 89, 94, 105, 106, 108, 113], "includ": [2, 3, 4, 7, 9, 10, 13, 14, 15, 16, 19, 34, 36, 37, 39, 43, 48, 50, 52, 53, 55, 57, 84, 85, 87, 95, 96, 98, 99, 100, 102, 104, 105, 106, 108, 109, 111, 112, 114], "typo": [2, 3], "build": [2, 15, 16, 50, 53, 65, 87, 99, 100, 105], "question": [2, 3, 99], "discuss": [2, 3, 15, 27, 60, 63, 79, 87, 99, 101, 108], "mdnalysi": [2, 99, 108], "mail": [2, 99, 100, 101, 102, 108], "commun": [2, 3, 88], "subscrib": [2, 99], "conduct": [2, 99], "member": 2, "agre": [2, 99], "adher": [2, 102], "pleas": [2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 61, 87, 99, 100, 102, 104, 105, 112], "read": [2, 3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 30, 33, 38, 39, 43, 44, 49, 50, 52, 60, 62, 63, 64, 74, 80, 90, 91, 92, 99, 105, 106, 109, 110, 111, 113, 114], "mdanalysistest": [2, 3, 9, 10, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 55, 57, 100, 101, 102, 103, 105, 108], "packag": [2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 79, 86, 96, 100, 101, 104, 105, 106, 108], "distribut": [2, 3, 6, 7, 15, 30, 35, 38, 41, 42, 44, 45, 70, 100, 102], "under": [2, 3, 15, 19, 53, 87, 101, 105, 108, 110], "gnu": [2, 108], "gener": [2, 3, 4, 7, 8, 9, 10, 14, 15, 18, 19, 20, 28, 30, 34, 37, 38, 39, 48, 50, 53, 55, 58, 59, 61, 67, 77, 80, 89, 94, 99, 102, 103, 104, 105, 113, 114], "public": [2, 3, 16, 30, 99, 102, 104, 108], "licens": [2, 15, 105, 108], "later": [2, 4, 13, 15, 102, 105, 106], "copyleft": 2, "deriv": [2, 3, 84, 87, 98, 105, 109], "made": [2, 3, 4, 26, 48, 71, 103, 105, 106, 109], "Be": [2, 15, 100], "sure": [2, 3, 4, 18, 100, 102, 106, 108], "comfort": 2, "befor": [2, 3, 4, 13, 16, 30, 36, 45, 48, 60, 89, 100, 101, 102, 105, 106, 108, 111], "push": [2, 4, 15, 102, 108], "page": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 61, 102, 104, 106, 108], "came": [2, 108], "panda": [2, 13, 15, 16, 18, 19, 20, 21, 26, 33, 34, 49, 53, 108], "guid": [2, 3, 6, 7, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 69, 100, 108], "idea": [2, 3, 53, 102], "If": [2, 3, 4, 7, 9, 10, 11, 12, 13, 15, 16, 23, 26, 27, 30, 34, 36, 37, 38, 40, 42, 44, 46, 50, 52, 53, 55, 57, 61, 65, 66, 67, 68, 79, 81, 82, 83, 84, 88, 89, 92, 96, 99, 100, 101, 102, 103, 105, 106, 108, 109, 112, 114], "look": [2, 3, 4, 10, 12, 13, 15, 19, 23, 24, 26, 28, 36, 37, 39, 48, 55, 61, 83, 86, 92, 96, 98, 108, 111], "brand": 2, "we": [2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 68, 82, 88, 96, 98, 99, 100, 101, 102, 105, 108, 109], "recommend": [2, 3, 21, 26, 45, 61, 100, 101, 102, 108], "go": [2, 3, 4, 15, 16, 96, 102, 106], "main": [2, 4, 100], "codebas": [2, 16, 105], "your": [2, 4, 5, 6, 7, 10, 13, 15, 17, 19, 20, 21, 22, 26, 27, 30, 32, 34, 36, 37, 40, 42, 43, 44, 45, 46, 48, 49, 50, 53, 55, 60, 61, 67, 75, 84, 87, 99, 100, 103, 104, 105, 108, 111, 112], "own": [2, 3, 4, 6, 7, 13, 15, 17, 19, 20, 21, 30, 42, 52, 53, 66, 99, 101, 108, 112], "encourag": [2, 108], "an": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 31, 33, 34, 37, 38, 39, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53, 57, 60, 62, 66, 67, 69, 71, 72, 78, 80, 83, 84, 85, 87, 88, 89, 94, 96, 98, 99, 100, 101, 102, 104, 105, 106, 108, 110, 112, 114], "toolkit": [2, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 52, 53, 55, 99, 104], "mdakit": [2, 105], "standalon": [2, 16, 108], "solv": [2, 87], "specif": [2, 3, 4, 7, 14, 16, 26, 27, 29, 30, 36, 53, 56, 60, 66, 73, 98, 100, 101, 103, 104, 105, 108, 110, 114], "scientif": [2, 3, 15, 85, 104, 105], "technic": [2, 3, 4, 88], "problem": [2, 3, 4, 13, 61, 68, 87, 99], "option": [2, 9, 10, 14, 16, 19, 22, 23, 24, 30, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 57, 61, 66, 67, 82, 83, 95, 100, 103, 104, 105, 108, 109, 114], "regist": [2, 44], "registri": 2, "advertis": [2, 105], "broader": 2, "continu": [2, 3, 19, 27, 48, 89, 94, 102, 103, 105, 109, 114], "against": [2, 4, 102, 105], "latest": [2, 3, 15, 100, 108], "make": [2, 3, 4, 7, 8, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 24, 26, 28, 33, 34, 38, 39, 40, 42, 43, 44, 45, 49, 53, 55, 56, 98, 100, 102, 103, 106, 108, 109, 111, 112, 114], "peopl": [2, 3, 102], "togeth": [2, 53, 99, 103, 112], "daunt": 2, "aspect": 2, "stick": [2, 50], "guidelin": [2, 105], "process": [2, 3, 7, 15, 17, 18, 19, 23, 24, 26, 27, 48, 67, 102, 105, 108, 114], "straightforward": [2, 53, 103, 106], "mostli": [2, 15], "troubl": [2, 40], "As": [2, 3, 4, 10, 12, 13, 14, 15, 16, 23, 24, 30, 33, 34, 39, 42, 43, 44, 48, 50, 53, 55, 57, 61, 84, 93, 95, 96, 98, 100, 102, 103, 105, 106, 108, 109, 113], "alwai": [2, 3, 4, 10, 15, 16, 20, 26, 33, 34, 53, 57, 60, 61, 67, 79, 81, 83, 84, 87, 88, 96, 99, 101, 103, 106, 108, 109, 111, 113], "difficulti": [2, 99], "feel": [2, 3], "ask": [2, 3, 16, 99, 100, 102, 108], "host": [2, 3, 5], "need": 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30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 96, 104], "compli": 3, "show": [3, 9, 10, 13, 14, 15, 19, 23, 24, 26, 27, 34, 37, 39, 44, 48, 50, 52, 53, 55, 57, 98, 106, 108, 112], "warn": [3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 50, 52, 53, 57, 61, 65, 81, 82, 89, 100, 101], "manual": [3, 4, 12, 50, 53, 87, 108], "fault": 3, "Or": [3, 30, 57], "ok": [3, 100, 101, 102, 108], "just": [3, 4, 23, 30, 48, 55, 57, 82, 98, 102, 106, 108, 112], "happi": [3, 22], "revis": 3, "two": [3, 4, 5, 6, 7, 8, 10, 15, 17, 19, 26, 27, 31, 32, 38, 42, 44, 46, 50, 53, 60, 98, 99, 103, 105, 106, 109, 114], "rather": [3, 16, 19, 26, 36, 40, 53, 83, 99, 105, 108], "thing": [3, 4], "sai": 3, "messag": [3, 42, 53, 89, 100, 101, 102], "onc": [3, 16, 39, 53, 55, 102, 104, 105, 108, 111, 112], "ve": [3, 108], "statu": [3, 15, 82], "tell": [3, 4, 19, 53, 84, 93, 108], "track": [3, 30, 34, 105], 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53, 57, 60, 102, 103, 105, 106, 109, 112, 113, 114], "v": [3, 6, 7, 17, 18, 19, 21, 34, 104, 105], "describ": [3, 7, 15, 32, 34, 36, 39, 40, 87, 103, 104, 106, 108, 114], "usernam": 3, "yet": [3, 108], "happen": [3, 89, 101, 106], "submit": [3, 108], "while": [3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 28, 30, 33, 34, 37, 38, 39, 42, 43, 44, 45, 46, 49, 52, 53, 80, 83, 84, 87, 98, 100, 102, 103, 106, 108, 111], "avoid": [3, 14, 15, 16, 36, 42, 44, 48, 57, 98, 100, 101, 102, 105], "merg": [3, 4, 9, 10, 19, 34, 102, 103, 105, 108, 114], "conflict": [3, 4, 88, 108], "retriev": [3, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 55, 104], "replai": 3, "top": [3, 4, 44, 59, 61, 87, 88, 96, 97, 101, 108, 109], "lead": [3, 4, 105, 114], "resolv": [3, 48, 99], "uncommit": 3, "stash": 3, "prior": [3, 28, 71, 87, 105, 109], "effect": [3, 7, 10, 32, 43, 100], "reappli": 3, "f": [3, 4, 11, 15, 26, 27, 28, 30, 34, 37, 39, 40, 46, 53, 57, 60, 98, 104, 105, 113], "approach": [3, 4, 27, 33, 38, 104], "failur": [3, 4, 102, 108], "review": [3, 4, 104], "eventu": 3, "navig": [3, 4], "click": [3, 108], "okai": 3, "checklist": 3, "refer": [3, 6, 7, 8, 17, 82, 89, 98, 103, 105, 112], "send": 3, "sent": 3, "maintain": [3, 4, 6, 99, 108], "travi": [3, 108], "appveyor": [3, 108], "codecov": 3, "fail": [3, 71, 83, 88, 89, 94, 100, 102, 105], "did": [3, 14, 81, 105], "restart": [3, 53, 58, 59, 61, 102], "kind": [3, 4, 13, 99, 114], "map": [3, 4, 6, 7, 12, 15, 30, 32, 34, 44, 46, 48, 57, 104, 108], "how": [3, 4, 10, 12, 13, 14, 15, 16, 18, 21, 23, 24, 27, 28, 30, 34, 38, 39, 40, 42, 43, 44, 53, 55, 71, 78, 84, 100, 102, 106, 108, 112, 113, 114], "combin": [3, 4, 7, 26, 32, 34, 42, 50, 53, 87, 106, 114], "topic": [3, 4], "analys": [3, 4, 6, 13, 16, 17, 25, 26, 28, 29, 52, 53, 99, 105], "itself": [3, 4, 5, 6, 7, 8, 9, 10, 16, 19, 30, 34, 39, 68, 79, 96, 106], "larg": [3, 4, 7, 10, 13, 15, 17, 19, 20, 33, 36, 40, 50, 53, 55, 56, 83, 101, 102, 104, 105, 107, 108], "meant": [3, 4], "usag": [3, 4, 26, 34, 53, 99], "individu": [3, 4, 7, 13, 30, 38, 49, 53, 57, 77, 96], "deprec": [3, 4, 108], "notic": [3, 4, 16], "string": [3, 4, 19, 28, 39, 81, 83, 96, 105, 106, 108, 109], "wide": [3, 61], "nice": 3, "text": [3, 13, 15, 16, 20, 21, 23, 24, 30, 36, 38, 40, 43, 44, 57], "napoleon": 3, "specifi": [3, 16, 19, 26, 27, 30, 42, 43, 44, 49, 53, 57, 60, 61, 66, 83, 93, 103, 106, 108, 114], "extend": [3, 23, 24, 50, 58, 59, 61, 65, 84, 97, 106], "manner": [3, 102], "onlin": [3, 6, 10], "find": [3, 4, 7, 16, 19, 25, 37, 40, 55, 67, 92], "particular": [3, 4, 22, 30, 40, 46, 48, 67, 91, 98, 100, 108, 110, 111], "been": [3, 15, 16, 18, 37, 48, 53, 60, 67, 70, 87, 102, 104, 105, 108, 109], "written": [3, 10, 53, 66, 71, 76, 79, 81, 83, 84, 87, 89, 93, 96, 103, 105], "documentation_pag": 3, "www": [3, 4, 19, 20, 30, 34, 37, 99, 104], "org": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 99, 104], "html": [3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104, 108], "importerror": [3, 101, 108], "build_ext": 3, "inplac": [3, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 28, 33, 38, 39, 42, 43, 44, 45, 49], "retri": 3, "home": [3, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49], "index": [3, 4, 11, 13, 15, 16, 19, 26, 27, 30, 31, 33, 34, 40, 48, 53, 56, 75, 83, 84, 87, 96, 103, 105, 108, 109, 110, 111], "tinker": [3, 58, 59, 61, 97], "cycl": [3, 30, 44, 104, 108], "rebuild": [3, 4], "becom": [3, 4, 7, 9, 10, 31, 32, 33, 36, 40, 109], "tediou": [3, 4], "autobuild": [3, 4], "sentenc": 3, "doe": [3, 4, 10, 13, 14, 15, 16, 19, 27, 30, 34, 40, 48, 52, 53, 55, 57, 63, 66, 71, 72, 80, 81, 82, 84, 87, 88, 92, 100, 101, 102, 105, 106, 108, 109, 110, 111, 112, 114], "def": [3, 10, 15, 16, 18, 21, 27, 44, 50, 105, 108, 112], "func": [3, 15], "arg1": 3, "arg2": 3, "summari": [3, 39, 53, 104, 108], "paramet": [3, 16, 43, 52, 53, 86, 104, 105, 108, 109], "int": [3, 26, 30, 50, 109, 114], "str": [3, 96, 108], "further": [3, 13, 15, 27, 50, 52, 53, 60, 62, 87, 98, 100, 105, 106], "breakdown": [3, 114], "variabl": [3, 4, 5, 30, 34, 49, 100, 104, 105], "markup": 3, "least": [3, 16, 31, 39, 42, 46, 67, 83, 98, 108], "head": [3, 18, 19, 20, 21, 33, 34, 53], "otherwis": [3, 4, 11, 34, 44, 55, 83, 89, 108], "parser": [3, 63, 65, 66, 69, 70, 71, 72, 73, 75, 76, 77, 78, 80, 81, 82, 83, 84, 86, 87, 91, 92, 93, 95, 99, 105, 106, 114], "render": [3, 4, 10, 48, 55, 102], "correctli": [3, 4, 60, 67, 88, 104, 105, 108], "bla": 3, "THE": 3, "versionad": 3, "properli": [3, 102, 105], "mess": [3, 15], "sometim": [3, 15, 50, 57, 60, 61, 71, 89, 105, 111, 114], "tri": [3, 61, 67, 79, 86, 109, 114], "across": [3, 12, 48, 50, 89, 94, 102, 106], "n_atom": [3, 10, 15, 26, 50, 53, 103, 105, 108, 109, 111, 114], "n_residu": [3, 37, 39, 50, 53, 109], "mathjax": 3, "latex": 3, "math": [3, 105, 109], "tag": [3, 100, 102, 105], "block": [3, 12, 16, 30, 36, 53, 85, 99], "equat": [3, 13, 14, 108], "pi": [3, 36, 113], "direct": [3, 4, 30, 46, 57, 87, 98, 105], "ident": [3, 4, 12, 16, 42, 44, 72, 87, 114], "raw": [3, 103], "prefix": [3, 4, 106], "letter": [3, 33, 83, 104], "backslash": 3, "unexpect": [3, 16], "rotat": [3, 7, 8, 9, 10, 11, 13, 14, 38, 48, 53, 104, 109, 112], "matrix": [3, 7, 8, 9, 10, 11, 12, 13, 14, 24, 34, 38, 39, 42, 44, 45, 46, 53, 104], "select": [3, 4, 6, 7, 9, 10, 11, 12, 14, 16, 17, 18, 19, 22, 25, 26, 27, 30, 31, 33, 34, 36, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 51, 66, 98, 99, 105, 110, 114], "mathsf": [3, 13], "3x3": 3, "orthogon": [3, 7, 32, 34, 52, 81, 82], "transform": [3, 6, 7, 13, 15, 32, 33, 34, 105, 109, 111, 114], "vector": [3, 7, 13, 24, 31, 32, 33, 34, 39, 48, 50, 67, 105, 109], "mathbf": [3, 13, 14, 16, 31, 34, 36], "rightarrow": 3, "stackoverflow": [3, 48], "express": [3, 4, 13, 106], "construct": [3, 6, 7, 15, 32, 34, 99], "annot": [3, 46, 105], "quickli": [3, 26, 83, 99], "newli": [3, 102, 105], "primari": [3, 53, 98, 109], "y": [3, 12, 13, 15, 16, 19, 20, 34, 48, 49, 50, 57, 66, 81, 82, 83, 95, 106], "z": [3, 15, 16, 26, 33, 39, 48, 50, 57, 66, 81, 82, 83, 95, 104, 106, 112], "mention": 3, "entiti": 3, "versionchang": 3, "although": [3, 7, 16, 30, 48, 63, 67, 79, 82, 83, 84, 105, 111, 112], "accept": [3, 13, 30, 43, 44, 53, 105, 106, 109, 112], "assum": [3, 50, 53, 57, 60, 61, 66, 67, 68, 79, 83, 88, 100, 114], "longer": [3, 12, 27, 57, 71, 105, 106, 108], "remov": [3, 4, 28, 30, 37, 40, 53, 102, 105, 108], "futur": [3, 15, 101, 105, 108], "enclos": 3, "scope": [3, 108], "whole": [3, 42, 53, 55, 105, 108, 112], "toc": 3, "analysisbas": [3, 15, 16, 105], "ones": [3, 33, 87, 106], "overwritten": 3, "inherit": [3, 108], "distinguish": [3, 34], "minim": [3, 7, 8, 108], "demonstr": [3, 7, 8, 13, 18, 19, 26, 30], "best": [3, 12, 19, 20, 104, 108], "practic": [3, 12, 48, 105], "intent": 3, "behind": 3, "choic": [3, 4, 38, 108], "api": [3, 9, 10, 11, 13, 14, 15, 19, 22, 23, 24, 30, 31, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 49, 85, 102, 103, 105], "promot": 3, "unifi": 3, "concis": 3, "come": [3, 53, 84, 99, 102, 108, 114], "overwrit": [3, 30, 96], "restructur": 3, "put": [3, 4, 16, 50], "amend": [3, 105], "friend": 3, "pile": 3, "onto": [3, 7, 30, 32, 33, 34, 37, 43, 44, 48, 111], "preview": 3, "ipython": [3, 4, 50, 109], "mark": [3, 30, 103, 104, 108], "oper": [3, 9, 15, 16, 30, 39, 53, 103, 105, 106], "docstr": 4, "class": [4, 7, 12, 13, 14, 15, 17, 18, 19, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 49, 53, 57, 83, 96, 98, 100, 101, 103, 105, 108, 109, 113, 114], "ensur": [4, 36, 100, 102, 103, 106, 108], "nbsphinx": 4, "dure": [4, 10, 13, 15, 19, 57, 89, 103], "doc": [4, 9, 10, 11, 13, 14, 22, 23, 24, 30, 31, 34, 36, 37, 38, 40, 42, 43, 44, 45, 46, 49, 102], "python": [4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 53, 55, 87, 98, 99, 100, 101, 102, 104, 105], "mean": [4, 6, 7, 8, 9, 11, 16, 19, 24, 26, 27, 30, 32, 33, 34, 39, 42, 43, 45, 48, 69, 75, 80, 84, 87, 98, 99, 100, 103, 105, 106, 108, 114], "bit": [4, 12, 105], "complex": [4, 15, 16, 28, 53, 99], "branch": [4, 82, 105, 108], "view": [4, 6, 14, 19, 30, 34, 39, 48, 50, 55, 108, 109, 114], "cell": [4, 9, 10, 11, 14, 19, 26, 34, 39, 48, 49, 50, 53, 55, 67, 81, 82, 105, 106, 108, 112], "applic": [4, 37, 58, 61, 66, 98, 114], "pull": [4, 10, 45, 70, 82, 101, 102, 105, 108, 111], "github": [4, 6, 11, 12, 13, 15, 16, 18, 19, 20, 21, 26, 33, 38, 39, 43, 44, 49, 100, 102, 105], "depend": [4, 10, 16, 26, 53, 60, 61, 68, 100, 102, 104, 105, 106, 108, 112], "nglview": [4, 9, 10, 14, 19, 34, 39, 50, 52, 55, 104], "conda": [4, 7, 53, 79], "mamba": [4, 100], "micromamba": [4, 108], "yml": [4, 108], "quiet": 4, "nbextens": 4, "enabl": [4, 15, 85, 89, 94, 104, 105, 108], "sy": [4, 52], "output": [4, 10, 14, 16, 30, 34, 38, 39, 40, 42, 43, 44, 48, 53, 55, 63, 70, 72, 83, 105, 108, 112], "browser": [4, 108], "homepag": 4, "abil": [4, 105], "interact": [4, 6, 9, 10, 12, 14, 19, 26, 27, 28, 34, 36, 39, 50, 52, 55, 87, 104, 109], "viewer": 4, "jupyer": 4, "widget": [4, 9, 10, 14, 19, 34, 39, 48, 50, 55, 100], "whenev": [4, 102, 108], "advantag": 4, "determin": [4, 6, 7, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 29, 33, 34, 37, 46, 53, 57, 98, 104], "still": [4, 10, 15, 27, 60, 101, 102, 103, 105, 108], "gave": 4, "were": [4, 19, 28, 34, 67, 98, 102, 104, 105, 106, 108], "ini": 4, "sanitize_output": 4, "cfg": [4, 100], "polymers_and_membran": 4, "ipynb": [4, 43, 114], "replac": [4, 53, 100, 103, 105, 109], "regex": 4, "download": [4, 5, 6, 14, 15, 100, 102, 108], "scan": 4, "match": [4, 6, 7, 9, 10, 13, 17, 37, 44, 100, 102, 105, 106, 108], "word": [4, 37, 104], "exactli": [4, 16, 88, 109], "bar": [4, 15, 31, 100, 103, 105], "tend": 4, "correct": [4, 14, 26, 50, 53, 67, 102, 104, 105, 108], "memori": [4, 10, 11, 12, 14, 15, 26, 45, 53, 55, 56, 98, 99, 105, 108, 111, 112, 114], "locat": [4, 5, 9, 81, 82, 102, 106, 109], "allevi": 4, "regular": [4, 57, 87], "know": [4, 15, 16, 50, 53, 102, 108], "vari": [4, 37, 38, 44], "dynam": [4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 52, 55, 99, 104, 105, 110, 111, 112, 114], "constant": [4, 26, 33, 49, 52, 66, 76, 105, 106], "won": 4, "prevent": [4, 105], "spuriou": 4, "possibl": [4, 28, 30, 46, 57, 60, 82, 99, 103, 104, 106, 108], "extra": [4, 15, 16, 30, 83, 100], "softwar": [4, 15, 42, 43, 44, 45, 100, 104, 106, 108], "program": [4, 7, 14, 30, 34, 39, 50, 53, 93, 96, 99, 100, 104], "therefor": [4, 13, 14, 15, 19, 33, 37, 42, 43, 50, 52, 53, 72, 79, 92, 95, 98, 108], "ignor": [4, 9, 10, 14, 22, 23, 24, 27, 30, 33, 34, 37, 46, 50, 52, 53, 81, 82, 84, 95, 105, 106, 114], 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"wise": [6, 7, 17, 23, 53], "fraction": [6, 7, 17, 18, 20, 21, 76], "nativ": [6, 7, 15, 17, 20, 21, 63, 100, 104], "q1": [6, 7, 17, 18, 19, 21], "q2": [6, 7, 17, 18, 19, 21], "cutoff": [6, 7, 17, 18, 20, 26, 38, 57, 106], "write": [6, 7, 9, 11, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 30, 34, 46, 48, 50, 52, 61, 62, 64, 68, 78, 90, 99, 105, 111, 113, 114], "harmon": [6, 7, 19, 20, 33, 41, 87, 104], "ensembl": [6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 41, 46, 48, 49, 50, 55, 104], "cluster": [6, 7, 15, 41, 44, 46], "dimens": [6, 22, 23, 26, 29, 37, 41, 49, 50, 55, 67, 81, 82, 104, 105, 106, 111, 112, 114], "reduct": [6, 34, 41, 104], "converg": [6, 7, 12, 13, 38, 41, 42, 104], "elast": [6, 7, 35], "network": [6, 7, 35], "averag": [6, 7, 8, 16, 26, 27, 31, 34, 35, 39, 40, 42, 44, 45, 49, 55], "radial": [6, 7, 35], "rdf": [6, 7, 35, 36, 105], "helix": [6, 7, 35, 104, 105], "princip": [6, 7, 32, 33, 43, 44, 104, 109], "compon": [6, 7, 32, 33, 43, 44, 104, 108], "non": [6, 7, 13, 19, 32, 36, 57, 60, 88, 105, 106], "linear": [6, 7, 31, 32, 34], "diffus": [6, 7, 32, 34, 104], "polym": [6, 104], "membran": [6, 26, 27, 28, 30], "persist": [6, 7, 10, 15, 26, 29, 53, 55, 111], "pore": [6, 7, 29, 104], "hole2": [6, 7, 29, 105], "volumetr": 6, "charg": [6, 7, 13, 28, 47, 48, 61, 66, 81, 82, 83, 86, 87, 92, 97, 105, 106, 109, 114], "densiti": [6, 7, 36, 42, 44, 47, 52, 57, 105], "axi": [6, 7, 10, 12, 15, 16, 22, 30, 34, 39, 44, 47, 48, 50, 55, 71, 109, 112], "solvent": [6, 7, 40, 47, 50, 114], "around": [6, 7, 13, 14, 16, 19, 22, 26, 28, 30, 34, 36, 40, 42, 47, 50, 52, 53, 99, 100, 106, 114], "data": [7, 15, 19, 20, 27, 32, 33, 34, 37, 39, 42, 43, 44, 46, 53, 55, 56, 58, 59, 61, 81, 82, 83, 84, 85, 89, 94, 95, 97, 98, 99, 103, 105, 109, 110, 111, 112, 113], "rang": [7, 15, 16, 30, 33, 34, 36, 40, 44, 50, 53, 57, 101, 106, 109], "algorithm": [7, 8, 9, 10, 11, 12, 13, 14, 16, 19, 33, 34, 39, 41, 42, 43, 44, 48, 52, 53, 60, 100, 104], "quantiti": [7, 8, 19, 53, 98, 105, 113], "uniqu": [7, 26, 34, 40, 57, 105, 108], "bundl": 7, "contribut": [7, 13, 36, 99, 102, 105, 108], "variou": [7, 26, 85, 105], "research": [7, 15, 19, 20, 104], "citat": 7, "parallel": [7, 100, 105], "paralleliz": 7, "encor": [7, 41, 42, 43, 44, 45, 104, 105], "hole": [7, 100, 104, 105], "yourself": [7, 30, 37, 45, 48], "align_structur": [7, 8], "align_trajectory_first": [7, 8], "align_trajectori": [7, 8], "rmsf": [7, 8, 12, 13], "sens": [7, 8, 84, 108, 109], "fast": [7, 8, 9, 10, 11, 12, 13, 14, 15, 33, 53, 79, 99, 103, 104], "qcp": [7, 8, 9, 10, 11, 12, 13, 14, 33], "the05": [7, 8, 9, 10, 11, 12, 13, 14, 33, 104], "lat09": [7, 8, 9, 10, 11, 14, 104], "cite": [7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 30, 33, 34, 38, 39, 42, 43, 44, 45, 46, 53, 104], "rapidli": [7, 17, 37], "retain": [7, 17, 19, 21, 85], "insight": [7, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 55, 104], "fold": [7, 17, 19, 20, 104], "movement": [7, 13, 17, 19, 34, 57], "3n": [7, 32, 34, 41], "dimension": [7, 12, 32, 33, 41, 44, 45, 104], "tpb": [7, 41, 42, 43, 44, 45, 104], "estim": [7, 12, 41, 45], "measur": [7, 12, 13, 16, 30, 31, 41, 48, 66, 108], "pair": [7, 26, 28, 30, 36, 40, 41, 44, 46, 105], "transit": [7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 50, 53, 55, 104], "reduc": [7, 11, 30, 33, 41, 42, 43, 44, 85, 94, 100], "remain": [7, 13, 16, 19, 24, 27, 32, 49, 53, 57, 104, 105, 108, 111], "extract": [7, 26, 32, 53, 57, 98, 104], "motion": [7, 32, 34, 38], "physic": [7, 32, 33, 34, 104], "state": [7, 12, 13, 14, 15, 19, 32, 33, 34, 38, 53, 102, 103, 104, 111], "represent": [7, 32, 48, 67, 76, 96, 105, 112, 114], "explor": [7, 15, 32], "techniqu": [7, 32, 33, 34], "varianc": [7, 32, 34, 42, 43], "largest": [7, 32, 34, 46, 108], "uncorrel": [7, 27, 32, 34], "success": [7, 32, 34, 46], "essenti": [7, 32, 33, 34, 104, 108], "subspac": [7, 32, 34, 43], "visualis": [7, 9, 10, 19, 22, 23, 24, 32, 33, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 50, 55, 99], "repres": [7, 12, 13, 15, 20, 27, 32, 33, 34, 38, 39, 40, 42, 43, 44, 48, 50, 53, 57, 60, 67, 103, 109], "neighour": [7, 32, 33], "geometri": [7, 13, 23, 30, 32, 33, 37, 39, 48, 50, 53, 104, 106, 109, 112], "intrins": [7, 32, 33], "manifold": [7, 32, 33], "suitabl": [7, 16, 32, 33, 49], "sampl": [7, 9, 10, 11, 12, 13, 18, 19, 20, 21, 30, 32, 33, 34, 39, 42, 43, 44, 53, 104], "replica": [7, 32, 33], "exchang": [7, 32, 33], "simul": [7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 51, 53, 55, 57, 58, 61, 67, 68, 85, 104], "region": [7, 14, 32, 33, 37, 43], "disconnect": [7, 32, 33], "meaning": [7, 32, 33, 53, 98, 114], "cannot": [7, 15, 32, 33, 37, 60, 68, 81, 82, 83, 103, 108, 109], "approxim": [7, 32, 33], "pca": [7, 32, 34, 43, 44, 105], "explicit": [7, 32, 33, 109], "eigenvector": [7, 32, 33, 34, 38], "immedi": [7, 15, 19, 32, 33, 102, 108], "hydrogen_bond": [7, 25], "basic": [7, 18, 19, 21, 25, 27, 28, 53, 65, 87], "advanc": [7, 15, 25, 26, 27, 46, 100], "lifetim": [7, 25, 26, 28, 89], "decemb": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 104], "2022": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 105], "minimum": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 52, 55, 61, 102, 105, 108], "madwb11": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104], "glb": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104], "ncr18": [9, 10, 55, 104], "minimis": [9, 10, 11, 12, 13, 14, 42, 43, 52], "crd": [9, 10, 12, 13, 45, 46, 52, 53, 58, 59, 61, 88, 97, 105, 109], "dcd2": [9, 10, 12, 16, 38, 42, 44, 45, 46], "nv": [9, 10, 14, 19, 34, 39, 48, 50, 55], "suppress": [9, 10, 14, 22, 23, 24, 27, 30, 34, 46, 50, 52, 53], "filterwarn": [9, 10, 14, 22, 23, 24, 27, 30, 34, 46, 50, 52, 53], "adenyl": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 104], "kinas": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 104], "phosophotransferas": [9, 10, 11, 12, 13, 14, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 55], "enzym": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55], "bdpw09": [9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 33, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 55, 104], "close": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 33, 34, 37, 39, 40, 42, 43, 44, 45, 46, 48, 50, 53, 55, 104], "adk_open": [9, 10, 12, 19], "adk_clos": [9, 10, 12, 19], "adk_open_view": [9, 19], "show_mdanalysi": [9, 10, 14, 19, 34, 39, 48, 50, 55], "adk_closed_view": [9, 19], "even": [9, 15, 18, 22, 48, 53, 60, 61, 66, 68, 102, 104, 105, 106, 108, 109, 110, 111], "obviou": [9, 10], "posit": [9, 10, 11, 13, 14, 15, 16, 19, 20, 21, 23, 24, 26, 34, 38, 45, 48, 52, 66, 67, 76, 103, 105, 106, 108, 109, 110, 111, 112], "merged_view": [9, 10], "mobil": [9, 11, 13, 14], "target": [9, 13, 23, 100, 105], "old_rmsd": 9, "new_rmsd": 9, "By": [9, 19, 26, 30, 42, 44, 49, 61, 66, 68, 99, 106], "match_atom": [9, 10], "attempt": [9, 81, 105], "712154435976014": 9, "817293751703919": 9, "aligned_view": 9, 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26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 40, 42, 43, 44, 46, 48, 49, 50, 52, 53], "reset_view": 9, "save": [9, 10, 13, 14, 15, 16, 19, 26, 34, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 88, 96, 105, 108], "from_file_view": 9, "oliv": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104], "beckstein": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 104], "elizabeth": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 55, 104], "j": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 48, 49, 50, 52, 53, 55, 104, 113], "den": [9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 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"blog": 102, "post": 102, "outlin": 102, "increment": 102, "clean": 102, "up": 102, "old": 102, "In": 103, "transfer": 103, "output": 103, "pickl": 103, "6": 105, "bug": 105, "fix": 105, "contributor": 105, "0": 105, "major": 105, "enhanc": 105, "deprec": 105, "5": 105, "enchanc": 105, "4": 105, "3": 105, "czi": 105, "eoss": 105, "perform": 105, "improv": 105, "known": 105, "failur": 105, "issu": 105, "boolean": 106, "connect": [106, 109], "preexist": 106, "nucleic": 107, "acid": 107, "nucleobas": 107, "sugar": 107, "coverag": 108, "continu": 108, "integr": 108, "tool": 108, "action": 108, "azur": 108, "codecov": 108, "convent": 108, "assert": 108, "except": 108, "warn": 108, "fail": 108, "skip": 108, "fixtur": 108, "same": 108, "directori": 108, "canon": 109, "valu": 109, "level": 109, "object": 109, "convers": 113, "speed": 113, "forc": 113, "energi": 113, "scratch": 114, "properti": 114}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "nbsphinx": 4, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Advanced topology concepts": [[0, "advanced-topology-concepts"]], "Adding a Residue or Segment to a Universe": [[0, "adding-a-residue-or-segment-to-a-universe"]], "Molecules": [[0, "molecules"]], "Adding custom TopologyAttrs": [[0, "adding-custom-topologyattrs"]], "AtomGroup": [[1, "atomgroup"]], "Creating an AtomGroup": [[1, "creating-an-atomgroup"]], "Atom selection language": [[1, "atom-selection-language"], [106, "atom-selection-language"]], "Indexing and slicing": [[1, "indexing-and-slicing"]], "Group operators and set methods": [[1, "group-operators-and-set-methods"]], "Groupby and split": [[1, "groupby-and-split"]], "Constructing from Atoms": [[1, "constructing-from-atoms"]], "Order and uniqueness": [[1, "order-and-uniqueness"]], "Empty AtomGroups": [[1, "empty-atomgroups"]], "Dynamically updating AtomGroups": [[1, "dynamically-updating-atomgroups"]], "Methods": [[1, "methods"]], "Contributing to MDAnalysis": [[2, "contributing-to-mdanalysis"], [16, "Contributing-to-MDAnalysis"]], "Where to start?": [[2, "where-to-start"]], "Version control, Git, and GitHub": [[2, "version-control-git-and-github"]], "Getting started with Git": [[2, "getting-started-with-git"]], "Contributing to the main codebase": [[3, "contributing-to-the-main-codebase"]], "Working with the code": [[3, "working-with-the-code"]], "Forking": [[3, "forking"]], "Creating a development environment": [[3, "creating-a-development-environment"], [4, "creating-a-development-environment"]], "With conda": [[3, "with-conda"], [3, "id1"]], "With pip and virtualenv": [[3, "with-pip-and-virtualenv"], [3, "id2"]], "On a Mac": [[3, "on-a-mac"]], "Building MDAnalysis": [[3, "building-mdanalysis"]], "Branches in MDAnalysis": [[3, "branches-in-mdanalysis"]], "Creating a branch": [[3, "creating-a-branch"]], "Writing new code": [[3, "writing-new-code"]], "Code formatting in Python": [[3, "code-formatting-in-python"]], "Modules and dependencies": [[3, "modules-and-dependencies"]], "Developing in Cython": [[3, "developing-in-cython"]], "Testing your code": [[3, "testing-your-code"]], "Documenting your code": [[3, "documenting-your-code"]], "Ensure PEP8 compliance (mandatory) and format your code with Darker (optional)": [[3, "ensure-pep8-compliance-mandatory-and-format-your-code-with-darker-optional"]], "Adding your code to MDAnalysis": [[3, "adding-your-code-to-mdanalysis"]], "Committing your code": [[3, "committing-your-code"]], "Pushing your code to GitHub": [[3, "pushing-your-code-to-github"]], "Rebasing your code": [[3, "rebasing-your-code"]], "Creating a pull request": [[3, "creating-a-pull-request"]], "Working with the code documentation": [[3, "working-with-the-code-documentation"]], "Building the documentation": [[3, "building-the-documentation"]], "Where to write docstrings": [[3, "where-to-write-docstrings"]], "Guidelines for writing docstrings": [[3, "guidelines-for-writing-docstrings"]], "Documenting changes": [[3, "documenting-changes"]], "Writing docs for abstract base classes": [[3, "writing-docs-for-abstract-base-classes"]], "Adding your documentation to MDAnalysis": [[3, "adding-your-documentation-to-mdanalysis"]], "Viewing the documentation interactively": [[3, "viewing-the-documentation-interactively"]], "Contributing to the user guide": [[4, "contributing-to-the-user-guide"]], "Forking and cloning the User Guide": [[4, "forking-and-cloning-the-user-guide"]], "Building the user guide": [[4, "building-the-user-guide"]], "Saving state in Jupyter notebooks": [[4, "saving-state-in-jupyter-notebooks"]], "Test with pytest and nbval": [[4, "test-with-pytest-and-nbval"]], "Sanitization": [[4, "sanitization"]], "On the hole2 notebook": [[4, "on-the-hole2-notebook"]], "Adding changes to the UserGuide": [[4, "adding-changes-to-the-userguide"]], "Automatically building documentation": [[4, "automatically-building-documentation"]], "Using pre-commit hooks": [[4, "using-pre-commit-hooks"]], "Example data": [[5, "example-data"]], "MDAnalysisTests": [[5, "mdanalysistests"]], "MDAnalysisData": [[5, "mdanalysisdata"]], "Examples": [[6, "examples"]], "General": [[6, null]], "Analysis": [[6, null], [7, "analysis"], [53, "Analysis"]], "Imports and dependencies": [[7, "imports-and-dependencies"]], "Alignments and RMS fitting": [[7, "alignments-and-rms-fitting"], [8, "alignments-and-rms-fitting"]], "Distances and contacts": [[7, "distances-and-contacts"], [17, "distances-and-contacts"]], "Trajectory similarity": [[7, "trajectory-similarity"], [41, "trajectory-similarity"]], "Structure": [[7, "structure"], [35, "structure"]], "Volumetric analyses": [[7, "volumetric-analyses"], [47, "volumetric-analyses"]], "Dimension reduction": [[7, "dimension-reduction"], [32, "dimension-reduction"]], "Polymers and membranes": [[7, "polymers-and-membranes"], [29, "polymers-and-membranes"]], "Hydrogen Bond Analysis": [[7, "hydrogen-bond-analysis"], [25, "hydrogen-bond-analysis"]], "Aligning a structure to another": [[9, "Aligning-a-structure-to-another"]], "Loading files": [[9, "Loading-files"], [10, "Loading-files"], [11, "Loading-files"], [12, "Loading-files"], [13, "Loading-files"], [14, "Loading-files"], [15, "Loading-files"], [16, "Loading-files"], [18, "Loading-files"], [19, "Loading-files"], [20, "Loading-files"], [21, "Loading-files"], [22, "Loading-files"], [23, "Loading-files"], [24, "Loading-files"], [26, "Loading-files"], [27, "Loading-files"], [28, "Loading-files"], [31, "Loading-files"], [33, "Loading-files"], [34, "Loading-files"], [36, "Loading-files"], [37, "Loading-files"], [38, "Loading-files"], [39, "Loading-files"], [40, "Loading-files"], [42, "Loading-files"], [43, "Loading-files"], [44, "Loading-files"], [45, "Loading-files"], [46, "Loading-files"], [48, "Loading-files"], [49, "Loading-files"], [55, "Loading-files"]], "Aligning a structure with align.alignto": [[9, "Aligning-a-structure-with-align.alignto"]], "References": [[9, "References"], [10, "References"], [11, "References"], [12, "References"], [13, "References"], [14, "References"], [15, "References"], [16, "References"], [18, "References"], [19, "References"], [20, "References"], [21, "References"], [22, "References"], [23, "References"], [24, "References"], [26, "References"], [27, "References"], [28, "References"], [30, "References"], [31, "References"], [33, "References"], [34, "References"], [36, "References"], [37, "References"], [38, "References"], [39, "References"], [40, "References"], [42, "References"], [43, "References"], [44, "References"], [45, "References"], [45, "id5"], [46, "References"], [48, "References"], [49, "References"], [50, "References"], [52, "References"], [53, "References"], [55, "References"], [104, "references"]], "Aligning a trajectory to a reference": [[10, "Aligning-a-trajectory-to-a-reference"]], "Aligning a trajectory with AlignTraj": [[10, "Aligning-a-trajectory-with-AlignTraj"]], "Copying coordinates into a new Universe": [[10, "Copying-coordinates-into-a-new-Universe"]], "Writing trajectories to a file": [[10, "Writing-trajectories-to-a-file"]], "Aligning a trajectory to itself": [[11, "Aligning-a-trajectory-to-itself"]], "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"]], "Calculating the pairwise RMSD of a trajectory": [[12, "Calculating-the-pairwise-RMSD-of-a-trajectory"]], "Background": [[12, "Background"], [13, "Background"], [14, "Background"], [15, "Background"], [18, "Background"], [19, "Background"], [20, "Background"], [21, "Background"], [30, "Background"]], "Pairwise RMSD of a trajectory to itself": [[12, "Pairwise-RMSD-of-a-trajectory-to-itself"]], "Pairwise RMSD between two trajectories": [[12, "Pairwise-RMSD-between-two-trajectories"]], "Calculating the root mean square deviation of atomic structures": [[13, "Calculating-the-root-mean-square-deviation-of-atomic-structures"]], "RMSD between two sets of coordinates": [[13, "RMSD-between-two-sets-of-coordinates"]], "RMSD of a Universe with multiple selections": [[13, "RMSD-of-a-Universe-with-multiple-selections"]], "Plotting the data": [[13, "Plotting-the-data"]], "RMSD of an AtomGroup with multiple selections": [[13, "RMSD-of-an-AtomGroup-with-multiple-selections"]], "Weighted RMSD of a trajectory": [[13, "Weighted-RMSD-of-a-trajectory"]], "Mass": [[13, "Mass"]], "Custom weights": [[13, "Custom-weights"]], "Calculating the root mean square fluctuation over a trajectory": [[14, "Calculating-the-root-mean-square-fluctuation-over-a-trajectory"]], "Creating an average structure": [[14, "Creating-an-average-structure"]], "Aligning the trajectory to a reference": [[14, "Aligning-the-trajectory-to-a-reference"]], "Calculating RMSF": [[14, "Calculating-RMSF"]], "Plotting RMSF": [[14, "Plotting-RMSF"]], "Visualising RMSF as B-factors": [[14, "Visualising-RMSF-as-B-factors"]], "Parallelizing analysis": [[15, "Parallelizing-analysis"]], "Radius of gyration": [[15, "Radius-of-gyration"], [16, "Radius-of-gyration"]], "Serial Analysis": [[15, "Serial-Analysis"]], "Parallelization in a simple per-frame fashion": [[15, "Parallelization-in-a-simple-per-frame-fashion"]], "Frame-wise form of the function": [[15, "Frame-wise-form-of-the-function"]], "Parallelization with multiprocessing": [[15, "Parallelization-with-multiprocessing"]], "Parallelization with dask": [[15, "Parallelization-with-dask"]], "Parallelization in a split-apply-combine fashion": [[15, "Parallelization-in-a-split-apply-combine-fashion"]], "Block analysis function": [[15, "Block-analysis-function"]], "Split the trajectory": [[15, "Split-the-trajectory"]], "Apply the analysis per block": [[15, "Apply-the-analysis-per-block"]], "Combine the results": [[15, "Combine-the-results"]], "Other possible parallelism approaches for multiple analyses": [[15, "Other-possible-parallelism-approaches-for-multiple-analyses"]], "See Also": [[15, "See-Also"]], "Writing your own trajectory analysis": [[16, "Writing-your-own-trajectory-analysis"]], "Creating an analysis from a function": [[16, "Creating-an-analysis-from-a-function"]], "Transforming a function into a class": [[16, "Transforming-a-function-into-a-class"]], "Creating your own class": [[16, "Creating-your-own-class"]], "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"]], "Write your own native contacts analysis method": [[18, "Write-your-own-native-contacts-analysis-method"]], "Defining salt bridges": [[18, "Defining-salt-bridges"]], "Define your own function": [[18, "Define-your-own-function"]], "Plotting": [[18, "Plotting"], [19, "Plotting"], [19, "id6"], [19, "id7"], [20, "Plotting"], [21, "Plotting"], [22, "Plotting"], [22, "id4"], [23, "Plotting"], [24, "Plotting"], [24, "id4"], [30, "Plotting"], [30, "id8"], [37, "Plotting"], [42, "Plotting"], [42, "id5"], [42, "id6"], [44, "Plotting"], [44, "id5"], [44, "id6"], [45, "Plotting"], [46, "Plotting"], [46, "id5"]], "Fraction of native contacts over a trajectory": [[19, "Fraction-of-native-contacts-over-a-trajectory"]], "Defining the groups for contact analysis": [[19, "Defining-the-groups-for-contact-analysis"], [21, "Defining-the-groups-for-contact-analysis"]], "Hard cutoff with a single reference": [[19, "Hard-cutoff-with-a-single-reference"]], "Radius cutoff": [[19, "Radius-cutoff"]], "Soft cutoff and multiple references": [[19, "Soft-cutoff-and-multiple-references"]], "Multiple references": [[19, "Multiple-references"]], "Soft cutoff": [[19, "Soft-cutoff"]], "Q1 vs Q2 contact analysis": [[20, "Q1-vs-Q2-contact-analysis"]], "Calculating Q1 vs Q2": [[20, "Calculating-Q1-vs-Q2"]], "Contact analysis: number of contacts within a cutoff": [[21, "Contact-analysis:-number-of-contacts-within-a-cutoff"]], "Calculating number of contacts within a cutoff": [[21, "Calculating-number-of-contacts-within-a-cutoff"]], "Atom-wise distances between matching AtomGroups": [[22, "Atom-wise-distances-between-matching-AtomGroups"]], "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"]], "All distances between two selections": [[23, "All-distances-between-two-selections"]], "Calculating atom-to-atom distances between non-matching coordinate arrays": [[23, "Calculating-atom-to-atom-distances-between-non-matching-coordinate-arrays"]], "Plotting distance as a heatmap": [[23, "Plotting-distance-as-a-heatmap"]], "Calculating residue-to-residue distances": [[23, "Calculating-residue-to-residue-distances"]], "All distances within a selection": [[24, "All-distances-within-a-selection"]], "Calculating atom-wise distances": [[24, "Calculating-atom-wise-distances"]], "Calculating distances for each residue": [[24, "Calculating-distances-for-each-residue"]], "Calculating hydrogen bonds: the basics": [[26, "Calculating-hydrogen-bonds:-the-basics"]], "Hydrogen bonds": [[26, "Hydrogen-bonds"]], "Find water-water hydrogen bonds": [[26, "Find-water-water-hydrogen-bonds"]], "Accessing the results": [[26, "Accessing-the-results"]], "Helper functions": [[26, "Helper-functions"]], "Further analysis": [[26, "Further-analysis"]], "Store data": [[26, "Store-data"]], "Calculating hydrogen bond lifetimes": [[27, "Calculating-hydrogen-bond-lifetimes"]], "Find all hydrogen bonds": [[27, "Find-all-hydrogen-bonds"], [28, "Find-all-hydrogen-bonds"]], "Calculate hydrogen bond lifetimes": [[27, "Calculate-hydrogen-bond-lifetimes"]], "Calculating the time constant": [[27, "Calculating-the-time-constant"]], "Intermittent lifetime": [[27, "Intermittent-lifetime"]], "Hydrogen bond lifetime of individual hydrogen bonds": [[27, "Hydrogen-bond-lifetime-of-individual-hydrogen-bonds"]], "Calculating hydrogen bonds: advanced selections": [[28, "Calculating-hydrogen-bonds:-advanced-selections"]], "Use guess_acceptors and guess_hydrogens to create atom selections": [[28, "Use-guess_acceptors-and-guess_hydrogens-to-create-atom-selections"]], "More advanced selections": [[28, "More-advanced-selections"]], "Hydrogen bonds between specific groups": [[28, "Hydrogen-bonds-between-specific-groups"]], "Analysing pore dimensions with HOLE2": [[30, "Analysing-pore-dimensions-with-HOLE2"]], "Using HOLE with a PDB file": [[30, "Using-HOLE-with-a-PDB-file"]], "Using HOLE with a trajectory": [[30, "Using-HOLE-with-a-trajectory"]], "Working with the data": [[30, "Working-with-the-data"]], "Visualising the VMD surface": [[30, "Visualising-the-VMD-surface"]], "Ordering HOLE profiles with an order parameter": [[30, "Ordering-HOLE-profiles-with-an-order-parameter"]], "Deleting HOLE files": [[30, "Deleting-HOLE-files"]], "Determining the persistence length of a polymer": [[31, "Determining-the-persistence-length-of-a-polymer"]], "Choosing the chains and backbone atoms": [[31, "Choosing-the-chains-and-backbone-atoms"]], "Calculating the persistence length": [[31, "Calculating-the-persistence-length"]], "Non-linear dimension reduction to diffusion maps": [[33, "Non-linear-dimension-reduction-to-diffusion-maps"]], "Diffusion maps": [[33, "Diffusion-maps"]], "Principal component analysis of a trajectory": [[34, "Principal-component-analysis-of-a-trajectory"]], "Principal component analysis": [[34, "Principal-component-analysis"]], "Visualising projections into a reduced dimensional space": [[34, "Visualising-projections-into-a-reduced-dimensional-space"]], "Measuring convergence with cosine content": [[34, "Measuring-convergence-with-cosine-content"]], "Average radial distribution functions": [[36, "Average-radial-distribution-functions"]], "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 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"]], "Protein dihedral angle analysis": [[37, "Protein-dihedral-angle-analysis"]], "Selecting dihedral atom groups": [[37, "Selecting-dihedral-atom-groups"]], "Calculating dihedral angles": [[37, "Calculating-dihedral-angles"]], "Ramachandran analysis": [[37, "Ramachandran-analysis"]], "Janin analysis": [[37, "Janin-analysis"]], "Elastic network analysis": [[38, "Elastic-network-analysis"]], "Using a Gaussian network model": [[38, "Using-a-Gaussian-network-model"]], "Using a Gaussian network model with only close contacts": [[38, "Using-a-Gaussian-network-model-with-only-close-contacts"]], "Helix analysis": [[39, "Helix-analysis"], [39, "id6"]], "Running the analysis": [[39, "Running-the-analysis"]], "Calculating the RDF atom-to-atom": [[40, "Calculating-the-RDF-atom-to-atom"]], "Calculating the site-specific radial distribution function": [[40, "Calculating-the-site-specific-radial-distribution-function"]], "The site-specific RDF without densities": [[40, "The-site-specific-RDF-without-densities"]], "Calculating the Clustering Ensemble Similarity between ensembles": [[42, "Calculating-the-Clustering-Ensemble-Similarity-between-ensembles"]], "Calculating clustering similarity with default settings": [[42, "Calculating-clustering-similarity-with-default-settings"]], "Calculating clustering similarity with one method": [[42, "Calculating-clustering-similarity-with-one-method"]], "Calculating clustering similarity with multiple methods": [[42, "Calculating-clustering-similarity-with-multiple-methods"]], "Trying out different clustering parameters": [[42, "Trying-out-different-clustering-parameters"]], "Estimating the error in a clustering ensemble similarity analysis": [[42, "Estimating-the-error-in-a-clustering-ensemble-similarity-analysis"]], "Evaluating convergence": [[43, "Evaluating-convergence"]], "Evaluating convergence with similarity measures": [[43, "Evaluating-convergence-with-similarity-measures"]], "Using default arguments with clustering ensemble similarity": [[43, "Using-default-arguments-with-clustering-ensemble-similarity"]], "Comparing different clustering methods": [[43, "Comparing-different-clustering-methods"]], "Using default arguments with dimension reduction ensemble similarity": [[43, "Using-default-arguments-with-dimension-reduction-ensemble-similarity"]], "Comparing different dimensionality reduction methods": [[43, "Comparing-different-dimensionality-reduction-methods"]], "Calculating the Dimension Reduction Ensemble Similarity between ensembles": [[44, "Calculating-the-Dimension-Reduction-Ensemble-Similarity-between-ensembles"]], "Calculating dimension reduction similarity with default settings": [[44, "Calculating-dimension-reduction-similarity-with-default-settings"]], "Calculating dimension reduction similarity with one method": [[44, "Calculating-dimension-reduction-similarity-with-one-method"]], "Calculating dimension reduction similarity with multiple methods": [[44, "Calculating-dimension-reduction-similarity-with-multiple-methods"]], "Trying out different dimension reduction parameters": [[44, "Trying-out-different-dimension-reduction-parameters"]], "Estimating the error in a dimension reduction ensemble similarity analysis": [[44, "Estimating-the-error-in-a-dimension-reduction-ensemble-similarity-analysis"]], "Calculating the Harmonic Ensemble Similarity between ensembles": [[45, "Calculating-the-Harmonic-Ensemble-Similarity-between-ensembles"]], "Calculating harmonic similarity": [[45, "Calculating-harmonic-similarity"]], "Comparing the geometric similarity of trajectories": [[46, "Comparing-the-geometric-similarity-of-trajectories"]], "Aligning trajectories": [[46, "Aligning-trajectories"]], "Generating paths": [[46, "Generating-paths"]], "Hausdorff method": [[46, "Hausdorff-method"]], "Discrete Fr\u00e9chet distances": [[46, "Discrete-Fr\u00e9chet-distances"]], "Calculating the solvent density around a protein": [[48, "Calculating-the-solvent-density-around-a-protein"]], "Centering, aligning, and making molecules whole with on-the-fly transformations": [[48, "Centering,-aligning,-and-making-molecules-whole-with-on-the-fly-transformations"]], "Analysing the density of water around the protein": [[48, "Analysing-the-density-of-water-around-the-protein"]], "Visualisation": [[48, "Visualisation"]], "matplotlib (3D static plot)": [[48, "matplotlib-(3D-static-plot)"]], "nglview (interactive)": [[48, "nglview-(interactive)"]], "scikit-image (triangulated surface)": [[48, "scikit-image-(triangulated-surface)"]], "pyvista (3D surface)": [[48, "pyvista-(3D-surface)"]], "2D averaging": [[48, "2D-averaging"]], "Computing mass and charge density on each axis": [[49, "Computing-mass-and-charge-density-on-each-axis"]], "Constructing, modifying, and adding to a Universe": [[50, "Constructing,-modifying,-and-adding-to-a-Universe"]], "Creating and populating a Universe with water": [[50, "Creating-and-populating-a-Universe-with-water"]], "Creating a blank Universe": [[50, "Creating-a-blank-Universe"]], "Adding topology attributes": [[50, "Adding-topology-attributes"]], "Adding positions": [[50, "Adding-positions"]], "Adding bonds": [[50, "Adding-bonds"]], "Merging with a protein": [[50, "Merging-with-a-protein"]], "Adding a new segment": [[50, "Adding-a-new-segment"]], "Tiling into a larger Universe": [[50, "Tiling-into-a-larger-Universe"]], "Acknowledgments": [[50, "Acknowledgments"]], "Other": [[51, "other"]], "Using ParmEd with MDAnalysis and OpenMM to simulate a selection of atoms": [[52, "Using-ParmEd-with-MDAnalysis-and-OpenMM-to-simulate-a-selection-of-atoms"]], "Loading files: the difference between ParmEd and MDAnalysis": [[52, "Loading-files:-the-difference-between-ParmEd-and-MDAnalysis"]], "Using MDAnalysis to select atoms": [[52, "Using-MDAnalysis-to-select-atoms"]], "Using ParmEd and OpenMM to create a simulation system": [[52, "Using-ParmEd-and-OpenMM-to-create-a-simulation-system"]], "Quick start guide": [[53, "Quick-start-guide"]], "Overview": [[53, "Overview"]], "Loading a structure or trajectory": [[53, "Loading-a-structure-or-trajectory"]], "Working with groups of atoms": [[53, "Working-with-groups-of-atoms"]], "Selecting atoms": [[53, "Selecting-atoms"]], "Getting atom information from AtomGroups": [[53, "Getting-atom-information-from-AtomGroups"]], "AtomGroup positions and methods": [[53, "AtomGroup-positions-and-methods"]], "Working with trajectories": [[53, "Working-with-trajectories"]], "Dynamic selection": [[53, "Dynamic-selection"]], "Writing out coordinates": [[53, "Writing-out-coordinates"]], "Single frame": [[53, "Single-frame"]], "Trajectories": [[53, "Trajectories"], [56, "trajectories"], [111, "trajectories"]], "RMSD": [[53, "RMSD"]], "Automatic citations with duecredit": [[53, "Automatic-citations-with-duecredit"]], "Transformations": [[54, "transformations"]], "Centering a trajectory in the box": [[55, "Centering-a-trajectory-in-the-box"]], "Before transformation": [[55, "Before-transformation"]], "Unwrapping the protein": [[55, "Unwrapping-the-protein"]], "Centering in the box": [[55, "Centering-in-the-box"]], "Wrapping the solvent back into the box": [[55, "Wrapping-the-solvent-back-into-the-box"]], "Doing all this on-the-fly": [[55, "Doing-all-this-on-the-fly"]], "Frequently asked questions": [[56, "frequently-asked-questions"]], "Why do the atom positions change over trajectories?": [[56, "why-do-the-atom-positions-change-over-trajectories"]], "Auxiliary files": [[57, "auxiliary-files"]], "Supported formats": [[57, "supported-formats"]], "XVG Files": [[57, "xvg-files"]], "Reading data directly": [[57, "reading-data-directly"]], "Loading data into a Universe": [[57, "loading-data-into-a-universe"]], "Passing arguments to auxiliary data": [[57, "passing-arguments-to-auxiliary-data"]], "Iterating over auxiliary data": [[57, "iterating-over-auxiliary-data"]], "Accessing auxiliary attributes": [[57, "accessing-auxiliary-attributes"]], "Recreating auxiliaries": [[57, "recreating-auxiliaries"]], "EDR Files": [[57, "edr-files"]], "Standalone Usage": [[57, "standalone-usage"]], "Unit Handling": [[57, "unit-handling"]], "Use with Trajectories": [[57, "use-with-trajectories"]], "Selecting Trajectory Frames Based on Auxiliary Data": [[57, "selecting-trajectory-frames-based-on-auxiliary-data"]], "Memory Usage": [[57, "memory-usage"]], "Coordinates": [[58, "coordinates"], [61, "coordinates"]], "Table of supported coordinate readers and the information read": [[58, "id2"], [61, "id12"]], "Format reference": [[59, "format-reference"]], "Guessing": [[60, "guessing"]], "Masses": [[60, "masses"]], "Types": [[60, "types"]], "Bonds, Angles, Dihedrals, Impropers": [[60, "bonds-angles-dihedrals-impropers"]], "Format overview": [[61, "format-overview"]], "Table of all supported formats in MDAnalysis": [[61, "id10"]], "Topology": [[61, "topology"], [97, "topology"]], "Table of supported topology parsers and the attributes read": [[61, "id11"], [97, "id1"]], "chemfiles (chemfiles Trajectory or file)": [[62, "chemfiles-chemfiles-trajectory-or-file"]], "CONFIG (DL_Poly Config)": [[63, "config-dl-poly-config"]], "HISTORY (DL_Poly Config)": [[63, "history-dl-poly-config"]], "COOR, NAMBDIN (NAMD binary restart files)": [[64, "coor-nambdin-namd-binary-restart-files"]], "CRD (CHARMM CARD files)": [[65, "crd-charmm-card-files"]], "Reading in": [[65, "reading-in"], [66, "reading-in"], [67, "reading-in"], [70, "reading-in"], [71, "reading-in"], [72, "reading-in"], [76, "reading-in"], [79, "reading-in"], [81, "reading-in"], [82, "reading-in"], [83, "reading-in"], [84, "reading-in"], [85, "reading-in"], [88, "reading-in"], [89, "reading-in"], [94, "reading-in"], [95, "reading-in"]], "Writing out": [[65, "writing-out"], [66, "writing-out"], [67, "writing-out"], [71, "writing-out"], [79, "writing-out"], [81, "writing-out"], [82, "writing-out"], [83, "writing-out"], [89, "writing-out"]], "DATA (LAMMPS)": [[66, "data-lammps"]], "DCD (CHARMM, NAMD, or LAMMPS trajectory)": [[67, "dcd-charmm-namd-or-lammps-trajectory"]], "DCD (Flexible LAMMPS trajectory)": [[68, "dcd-flexible-lammps-trajectory"]], "DMS (Desmond Molecular Structure files)": [[69, "dms-desmond-molecular-structure-files"]], "GMS (Gamess trajectory)": [[70, "gms-gamess-trajectory"]], "GRO (GROMACS structure file)": [[71, "gro-gromacs-structure-file"]], "GSD (HOOMD GSD file)": [[72, "gsd-hoomd-gsd-file"]], "IN, FHIAIMS (FHI-aims input files)": [[73, "in-fhiaims-fhi-aims-input-files"]], "INPCRD, RESTRT (AMBER restart files)": [[74, "inpcrd-restrt-amber-restart-files"]], "ITP (GROMACS portable topology files)": [[75, "itp-gromacs-portable-topology-files"]], "LAMMPSDUMP (LAMMPS ascii dump file)": [[76, "lammpsdump-lammps-ascii-dump-file"]], "MMTF (Macromolecular Transmission Format)": [[77, "mmtf-macromolecular-transmission-format"]], "MOL2 (Tripos structure)": [[78, "mol2-tripos-structure"]], "MOL2 specification": [[78, "mol2-specification"]], "NCDF, NC (AMBER NetCDF trajectory)": [[79, "ncdf-nc-amber-netcdf-trajectory"]], "ParmEd (ParmEd Structure)": [[80, "parmed-parmed-structure"]], "PDB, ENT (Standard PDB file)": [[81, "pdb-ent-standard-pdb-file"]], "PDB specification": [[81, "pdb-specification"]], "CRYST1 fields": [[81, "id1"]], "ATOM/HETATM fields": [[81, "id2"]], "PDBQT (Autodock structure)": [[82, "pdbqt-autodock-structure"]], "PDBQT specification": [[82, "pdbqt-specification"]], "PDB format with AutoDOCK extensions for the PDBQT format.": [[82, "id1"]], "PQR file (PDB2PQR / APBS)": [[83, "pqr-file-pdb2pqr-apbs"]], "PQR specification": [[83, "pqr-specification"]], "PSF (CHARMM, NAMD, or XPLOR protein structure file)": [[84, "psf-charmm-namd-or-xplor-protein-structure-file"]], "PSF specification": [[84, "psf-specification"]], "TNG (Trajectory Next Generation)": [[85, "tng-trajectory-next-generation"]], "TOP, PRMTOP, PARM7 (AMBER topology)": [[86, "top-prmtop-parm7-amber-topology"]], "AMBER specification": [[86, "amber-specification"]], "Attributes parsed from AMBER keywords": [[86, "id1"]], "Developer notes": [[86, "developer-notes"], [87, "developer-notes"], [89, "developer-notes"], [91, "developer-notes"]], "TPR (GROMACS run topology files)": [[87, "tpr-gromacs-run-topology-files"]], "Supported versions": [[87, "supported-versions"]], "TPR format versions and generations read by MDAnalysis.topology.TPRParser.parse().": [[87, "id1"]], "TPR specification": [[87, "tpr-specification"]], "segid and chainID": [[87, "segid-and-chainid"]], "Bonds": [[87, "bonds"]], "GROMACS entries used to create bonds.": [[87, "id2"]], "GROMACS entries used to create angles.": [[87, "id3"]], "GROMACS entries used to create dihedrals.": [[87, "id4"]], "GROMACS entries used to create improper dihedrals.": [[87, "id5"]], "TRJ, MDCRD, CRDBOX (AMBER ASCII trajectory)": [[88, "trj-mdcrd-crdbox-amber-ascii-trajectory"]], "TRR (GROMACS lossless trajectory file)": [[89, "trr-gromacs-lossless-trajectory-file"]], "TRZ (IBIsCO and YASP trajectory)": [[90, "trz-ibisco-and-yasp-trajectory"]], "TXYZ, ARC (Tinker)": [[91, "txyz-arc-tinker"]], "XML (HOOMD)": [[92, "xml-hoomd"]], "XPDB (Extended PDB file)": [[93, "xpdb-extended-pdb-file"]], "XTC (GROMACS compressed trajectory file)": [[94, "xtc-gromacs-compressed-trajectory-file"]], "XYZ trajectory": [[95, "xyz-trajectory"]], "XYZ specification": [[95, "xyz-specification"]], "Note": [[95, "note"]], "Selection exporters": [[96, "selection-exporters"]], "Supported selection exporters": [[96, "id2"]], "Writing selections": [[96, "writing-selections"]], "Single AtomGroup": [[96, "single-atomgroup"]], "Multiple selections": [[96, "multiple-selections"]], "Reading in selections": [[96, "reading-in-selections"]], "Groups of atoms": [[98, "groups-of-atoms"]], "Residues and Segments": [[98, "residues-and-segments"]], "Use case: Sequence of residues by segment": [[98, "use-case-sequence-of-residues-by-segment"]], "Use case: Atoms list grouped by residues": [[98, "use-case-atoms-list-grouped-by-residues"]], "Fragments": [[98, "fragments"]], "Welcome to MDAnalysis User Guide\u2019s documentation!": [[99, "welcome-to-mdanalysis-user-guide-s-documentation"]], "Why MDAnalysis?": [[99, "why-mdanalysis"]], "Participating": [[99, "participating"]], "Communications": [[99, "communications"]], "Installation": [[100, "installation"]], "conda": [[100, "conda"]], "pip": [[100, "pip"]], "Development versions": [[100, "development-versions"]], "Testing": [[100, "testing"]], "Custom compiler flags and optimised installations": [[100, "custom-compiler-flags-and-optimised-installations"]], "Additional datasets": [[100, "additional-datasets"]], "Module imports in MDAnalysis": [[101, "module-imports-in-mdanalysis"]], "General rules for importing": [[101, "general-rules-for-importing"]], "Module imports in MDAnalysis.analysis": [[101, "module-imports-in-mdanalysis-analysis"]], "Module imports in the test suite": [[101, "module-imports-in-the-test-suite"]], "Module dependencies in the code": [[101, "module-dependencies-in-the-code"]], "List of core module dependencies": [[101, "list-of-core-module-dependencies"]], "Modules in the \u201ccore\u201d": [[101, "modules-in-the-core"]], "Optional modules in MDAnalysis.analysis and MDAnalysis.visualization": [[101, "optional-modules-in-mdanalysis-analysis-and-mdanalysis-visualization"]], "Preparing a release": [[102, "preparing-a-release"]], "Release policy and release numbering": [[102, "release-policy-and-release-numbering"]], "Typical workflow for preparing a release": [[102, "typical-workflow-for-preparing-a-release"]], "Summary of tasks": [[102, "summary-of-tasks"]], "Getting the develop branch ready for a release": [[102, "getting-the-develop-branch-ready-for-a-release"]], "Packaging the release": [[102, "packaging-the-release"]], "Completing the release": [[102, "completing-the-release"]], "Manually upload Cirrus CI wheels (temporary)": [[102, "manually-upload-cirrus-ci-wheels-temporary"]], "Update conda-forge packages": [[102, "update-conda-forge-packages"]], "Create a release of the UserGuide": [[102, "create-a-release-of-the-userguide"]], "Create a blog post outlining the release": [[102, "create-a-blog-post-outlining-the-release"]], "Increment develop branch files ready for the next version": [[102, "increment-develop-branch-files-ready-for-the-next-version"]], "Clean up old developer builds of the documentation": [[102, "clean-up-old-developer-builds-of-the-documentation"]], "Reading and writing files": [[103, "reading-and-writing-files"]], "Input": [[103, "input"]], "Reading multiple trajectories": [[103, "reading-multiple-trajectories"]], "Trajectory formats": [[103, "trajectory-formats"]], "In-memory trajectories": [[103, "in-memory-trajectories"]], "Reading trajectories into memory": [[103, "reading-trajectories-into-memory"]], "Transferring trajectories into memory": [[103, "transferring-trajectories-into-memory"]], "Building trajectories in memory": [[103, "building-trajectories-in-memory"]], "In-memory trajectories of an atom selection": [[103, "in-memory-trajectories-of-an-atom-selection"]], "Output": [[103, "output"]], "Frames and trajectories": [[103, "frames-and-trajectories"]], "Pickling": [[103, "pickling"]], "Citations using Duecredit": [[104, "citations-using-duecredit"]], "MDAnalysis Release Notes": [[105, "mdanalysis-release-notes"]], "Release 2.6.1 of MDAnalysis": [[105, "release-2-6-1-of-mdanalysis"]], "Bug fixes and changes": [[105, "bug-fixes-and-changes"]], "New Contributors": [[105, "new-contributors"], [105, "id1"], [105, "id5"], [105, "id13"]], "Release 2.6.0 of MDAnalysis": [[105, "release-2-6-0-of-mdanalysis"]], "Major changes:": [[105, "major-changes"], [105, "id2"], [105, "id8"], [105, "id14"], [105, "id19"], [105, "id24"], [105, "id30"]], "Fixes:": [[105, "fixes"], [105, "id3"], [105, "id9"], [105, "id15"], [105, "id21"], [105, "id26"], [105, "id32"]], "Enhancements:": [[105, "enhancements"], [105, "id16"], [105, "id20"], [105, "id25"], [105, "id31"]], "Changes:": [[105, "changes"], [105, "id4"], [105, "id11"], [105, "id17"], [105, "id22"], [105, "id27"], [105, "id33"]], "Deprecations:": [[105, "deprecations"], [105, "id12"], [105, "id18"], [105, "id23"], [105, "id28"], [105, "id34"]], "Release 2.5.0 of MDAnalysis": [[105, "release-2-5-0-of-mdanalysis"]], "Enchancements:": [[105, "enchancements"], [105, "id10"]], "Release 2.4.3 of MDAnalysis": [[105, "release-2-4-3-of-mdanalysis"]], "Bug fixes": [[105, "bug-fixes"], [105, "id6"], [105, "id7"]], "Release 2.4.2 of MDAnalysis": [[105, "release-2-4-2-of-mdanalysis"]], "Release 2.4.1 of MDAnalysis": [[105, "release-2-4-1-of-mdanalysis"]], "Release 2.4.0 of MDAnalysis": [[105, "release-2-4-0-of-mdanalysis"]], "Release 2.3.0 of MDAnalysis": [[105, "release-2-3-0-of-mdanalysis"]], "CZI EOSS Performance Improvements:": [[105, "czi-eoss-performance-improvements"]], "Release 2.2.0 of MDAnalysis": [[105, "release-2-2-0-of-mdanalysis"]], "Known test failures:": [[105, "known-test-failures"], [105, "id29"]], "Release 2.1.0 of MDAnalysis": [[105, "release-2-1-0-of-mdanalysis"]], "Release 2.0.0 of MDAnalysis": [[105, "release-2-0-0-of-mdanalysis"]], "Notes:": [[105, "notes"]], "Known issues:": [[105, "known-issues"]], "Selection Keywords": [[106, "selection-keywords"]], "Simple selections": [[106, "simple-selections"]], "Boolean": [[106, "boolean"]], "Geometric": [[106, "geometric"]], "Similarity and connectivity": [[106, "similarity-and-connectivity"]], "Index": [[106, "index"]], "Preexisting selections and modifiers": [[106, "preexisting-selections-and-modifiers"]], "Dynamic selections": [[106, "dynamic-selections"]], "Ordered selections": [[106, "ordered-selections"]], "Standard residues in MDAnalysis selections": [[107, "standard-residues-in-mdanalysis-selections"]], "Proteins": [[107, "proteins"]], "Protein backbone": [[107, "protein-backbone"]], "Nucleic acids": [[107, "nucleic-acids"]], "Nucleic backbone": [[107, "nucleic-backbone"]], "Nucleobases": [[107, "nucleobases"]], "Nucleic sugars": [[107, "nucleic-sugars"]], "Tests in MDAnalysis": [[108, "tests-in-mdanalysis"]], "Running the test suite": [[108, "running-the-test-suite"]], "Testing in parallel": [[108, "testing-in-parallel"]], "Test coverage": [[108, "test-coverage"]], "Continuous Integration tools": [[108, "continuous-integration-tools"]], "GitHub Actions": [[108, "github-actions"]], "Azure": [[108, "azure"]], "Cirrus CI": [[108, "cirrus-ci"]], "Codecov": [[108, "codecov"]], "Writing new tests": [[108, "writing-new-tests"]], "General conventions": [[108, "general-conventions"]], "Assertions": [[108, "assertions"]], "Testing exceptions and warnings": [[108, "testing-exceptions-and-warnings"]], "Failing tests": [[108, "failing-tests"]], "Skipping tests": [[108, "skipping-tests"]], "Fixtures": [[108, "fixtures"]], "Testing the same function with different inputs": [[108, "testing-the-same-function-with-different-inputs"]], "Temporary files and directories": [[108, "temporary-files-and-directories"]], "Module imports": [[108, "module-imports"]], "Tests for analysis and visualization modules": [[108, "tests-for-analysis-and-visualization-modules"]], "Using test data files": [[108, "using-test-data-files"]], "The topology system": [[109, "the-topology-system"]], "Topology attributes": [[109, "topology-attributes"]], "Canonical attributes": [[109, "canonical-attributes"]], "Format-specific attributes": [[109, "format-specific-attributes"]], "Connectivity information": [[109, "connectivity-information"]], "Adding TopologyAttrs": [[109, "adding-topologyattrs"]], "Modifying TopologyAttrs": [[109, "modifying-topologyattrs"]], "Default values and attribute levels": [[109, "default-values-and-attribute-levels"]], "Topology objects": [[109, "topology-objects"]], "Adding to a Universe": [[109, "adding-to-a-universe"]], "Creating with an AtomGroup": [[109, "creating-with-an-atomgroup"]], "Deleting from a Universe": [[109, "deleting-from-a-universe"]], "Topology-specific methods": [[109, "topology-specific-methods"]], "Slicing trajectories": [[110, "slicing-trajectories"]], "On-the-fly transformations": [[112, "on-the-fly-transformations"]], "Example workflows": [[112, "example-workflows"]], "Custom transformations": [[112, "custom-transformations"]], "Units and constants": [[113, "units-and-constants"]], "Base units in MDAnalysis": [[113, "id1"]], "Unit conversion": [[113, "unit-conversion"]], "Constants": [[113, "constants"]], "Length": [[113, "length"]], "Density": [[113, "density"]], "Time": [[113, "time"]], "Charge": [[113, "charge"]], "Speed": [[113, "speed"]], "Force": [[113, "force"]], "Energy": [[113, "energy"]], "Universe": [[114, "universe"]], "Creating a Universe": [[114, "creating-a-universe"]], "Loading from files": [[114, "loading-from-files"]], "Constructing from AtomGroups": [[114, "constructing-from-atomgroups"]], "Constructing from scratch": [[114, "constructing-from-scratch"]], "Guessing topology attributes": [[114, "guessing-topology-attributes"]], "Universe properties and methods": [[114, "universe-properties-and-methods"]]}, "indexentries": {"x y z": [[83, "term-X-Y-Z"]], "atomname": [[83, "term-atomName"]], "chainid": [[83, "term-chainID"]], "charge": [[83, "term-charge"]], "radius": [[83, "term-radius"]], "recordname": [[83, "term-recordName"]], "residuename": [[83, "term-residueName"]], "residuenumber": [[83, "term-residueNumber"]], "serial": [[83, "term-serial"]], "duecredit_enable": [[104, "index-0"]], "environment variable": [[104, "index-0"]]}}) \ No newline at end of file diff --git a/dev/standard_selections.html b/dev/standard_selections.html index 9fbbd77ab..770c418d8 100644 --- a/dev/standard_selections.html +++ b/dev/standard_selections.html @@ -332,9 +332,9 @@

    Protein backbone -

    C

    +

    O

    N

    -

    O

    +

    C

    CA

    @@ -347,43 +347,43 @@

    Protein backbone -

    RA5

    -

    RA3

    -

    DC

    +

    RA

    +

    DG3

    U

    -

    GUA

    -

    RU3

    -

    DA5

    -

    DA3

    - -

    RU5

    +

    DC

    +

    DT

    THY

    +

    ADE

    +

    RC3

    + +

    DA5

    A

    +

    GUA

    +

    DA3

    +

    RU5

    +

    RA3

    +

    DT5

    RU

    -

    ADE

    + +

    DG

    +

    RG3

    +

    DT3

    +

    RC5

    URA

    -

    RC3

    +

    RU3

    DC5

    +

    C

    -

    DT5

    -

    DT3

    -

    RA

    -

    DG5

    +

    DA

    T

    +

    CYT

    +

    RG5

    +

    RA5

    +

    DG5

    RG

    DC3

    -

    RG5

    -

    DA

    -

    DT

    -

    RC5

    -

    DG

    -

    C

    -

    RC

    -

    CYT

    -

    DG3

    - -

    RG3

    +

    RC

    G

    @@ -399,10 +399,10 @@

    Nucleic backbone -

    O3’

    +

    O5’

    P

    C3’

    -

    O5’

    +

    O3’

    C5’

    @@ -414,22 +414,22 @@

    Nucleic backbone

    O6

    -

    N1

    -

    C8

    -

    N6

    -

    N4

    +

    C6

    +

    C5

    O2

    +

    N3

    +

    N6

    N2

    -

    O4

    +

    C2

    -

    N9

    -

    C6

    +

    O4

    +

    N7

    +

    N4

    +

    N1

    +

    N9

    +

    C8

    C4

    C5M

    -

    C2

    -

    N3

    -

    C5

    -

    N7

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

    Nucleic sugars -

    C1’

    -

    O4’

    -

    C3’

    -

    C4’

    +

    C4’

    C2’

    +

    C1’

    +

    C3’

    +

    O4’

    diff --git a/dev/testing.html b/dev/testing.html index c156cdfde..de96bd59a 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)