Adding a Residue or Segment to a Universe
-To add a Residue or Segment to a topology, use the Universe.add_Residue or Universe.add_Segment methods.
To add a Residue or Segment to a topology, use the Universe.add_Residue or Universe.add_Segment methods.
>>> u = mda.Universe(PSF, DCD)
>>> u.segments
<SegmentGroup with 1 segment>
@@ -210,7 +210,7 @@
<AtomGroup with 0 atoms>
To assign the last 100 residues from the Universe to this new Segment:
To assign the last 100 residues from the Universe to this new Segment:
>>> u.residues[-100:].segments = newseg
>>> newseg.atoms
<AtomGroup with 1600 atoms>
diff --git a/2.7.0-dev0/atomgroup.html b/2.7.0-dev0/atomgroup.html
index c89ab29c1..250e13dcf 100644
--- a/2.7.0-dev0/atomgroup.html
+++ b/2.7.0-dev0/atomgroup.html
@@ -204,16 +204,16 @@
AtomGroup
-A Universe contains all particles in the molecular system. MDAnalysis calls a particle an Atom, regardless of whether it really is (e.g. it may be a united-atom particle or coarse-grained bead). Atoms are grouped with an AtomGroup; the ‘master’ AtomGroup of a Universe is accessible at Universe.atoms.
+A Universe contains all particles in the molecular system. MDAnalysis calls a particle an Atom, regardless of whether it really is (e.g. it may be a united-atom particle or coarse-grained bead). Atoms are grouped with an AtomGroup; the ‘master’ AtomGroup of a Universe is accessible at Universe.atoms.
Note
-The AtomGroup is probably the most important object in MDAnalysis. Virtually everything can be accessed through an AtomGroup.
+The AtomGroup is probably the most important object in MDAnalysis. Virtually everything can be accessed through an AtomGroup.
Creating an AtomGroup
Atom selection language
-AtomGroup instances are typically created with Universe.select_atoms or by manipulating another AtomGroup, e.g. by slicing.
+AtomGroup instances are typically created with Universe.select_atoms or by manipulating another AtomGroup, e.g. by slicing.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import PDB
@@ -228,12 +228,12 @@ Atom selection language
Indexing and slicing
-An AtomGroup can be indexed and sliced like a list:
+An AtomGroup can be indexed and sliced like a list:
In [5]: print(u.atoms[0])
<Atom 1: N of type N of resname MET, resid 1 and segid SYSTEM and altLoc >
-Slicing returns another AtomGroup. The below code returns an AtomGroup of every second element from the first to the 6th element, corresponding to indices 0, 2, and 4.
+Slicing returns another AtomGroup. The below code returns an AtomGroup of every second element from the first to the 6th element, corresponding to indices 0, 2, and 4.
In [6]: ag = u.atoms[0:6:2]
In [7]: ag.indices
@@ -247,7 +247,7 @@ Indexing and slicingOut[9]: array([ 0, 3, 47680, 10, 3])
-Boolean indexing allows you to pass in an array of True or False values to create a new AtomGroup from another. The array must be the same length as the original AtomGroup. This allows you to select atoms on conditions.
+Boolean indexing allows you to pass in an array of True or False values to create a new AtomGroup from another. The array must be the same length as the original AtomGroup. This allows you to select atoms on conditions.
In [10]: arr = u.atoms.resnames == 'ARG'
In [11]: len(arr) == len(u.atoms)
@@ -261,7 +261,7 @@ Indexing and slicing
Group operators and set methods
-MDAnalysis supports a number of ways to compare AtomGroups or construct a new one: group operators (e.g. concatenate(), subtract()) and set methods (e.g. union(), difference()). Group operators achieve a similar outcome to set methods. However, a key difference is that concatenate() and subtract() preserve the order of the atoms and any duplicates. union() and difference() return an AtomGroup where each atom is unique, and ordered by its topology index.
+MDAnalysis supports a number of ways to compare AtomGroups or construct a new one: group operators (e.g. concatenate(), subtract()) and set methods (e.g. union(), difference()). Group operators achieve a similar outcome to set methods. However, a key difference is that concatenate() and subtract() preserve the order of the atoms and any duplicates. union() and difference() return an AtomGroup where each atom is unique, and ordered by its topology index.
In [14]: ag1 = u.atoms[1:6]
In [15]: ag2 = u.atoms[8:3:-1]
@@ -312,7 +312,7 @@ Group operators and set methodsAtoms.
+
Each of these methods create groups that are sorted sets of unique Atoms.
Writing selections
Single AtomGroup
The typical situation is that one has an
-AtomGroup and wants to work with the
+AtomGroup and wants to work with the
same selection of atoms in a different package, for example, to
visualize the atoms in VMD.
In [1]: import MDAnalysis as mda
@@ -253,7 +253,7 @@ Single AtomGroupIn [4]: ag = u.select_atoms('resname ALA')
-As with a normal structure file, use AtomGroup.write method with the appropriate file extension.
+As with a normal structure file, use AtomGroup.write method with the appropriate file extension.
ag.write("ala_selection.vmd", name="alanine")
@@ -265,11 +265,11 @@ Single AtomGroupGraphics ‣
Representations window in the list Selections: Singlewords as
“alanine”.
-Names are not always required; if name is not passed to AtomGroup.write, MDAnalysis defaults to “mdanalysis001”, “mdanalysis002”, and so on.
+Names are not always required; if name is not passed to AtomGroup.write, MDAnalysis defaults to “mdanalysis001”, “mdanalysis002”, and so on.
Multiple selections
-AtomGroup.write can take additional keyword arguments, including mode. The default is mode='w', which will overwrite the provided filename. If mode='a', the selection is appended to the file.
+AtomGroup.write can take additional keyword arguments, including mode. The default is mode='w', which will overwrite the provided filename. If mode='a', the selection is appended to the file.
u.select_atoms('resname T*').write('residues.ndx',
name='TYR_THR',
mode='a')
@@ -302,7 +302,7 @@ Multiple selections'ri': residue index
-Alternatively, you can direcly use the selection writer itself as a context manager and write each AtomGroup inside the context. For example:
+Alternatively, you can direcly use the selection writer itself as a context manager and write each AtomGroup inside the context. For example:
with mda.selections.gromacs.SelectionWriter('residues.ndx', mode='w') as ndx:
ndx.write(u.select_atoms('resname T*'),
name='TYR_THR')
diff --git a/2.7.0-dev0/groups_of_atoms.html b/2.7.0-dev0/groups_of_atoms.html
index 4d4df5d38..82389f0ca 100644
--- a/2.7.0-dev0/groups_of_atoms.html
+++ b/2.7.0-dev0/groups_of_atoms.html
@@ -198,13 +198,13 @@
Groups of atoms
-MDAnalysis has a hierarchy of Atom containers that are used throughout the code.
+MDAnalysis has a hierarchy of Atom containers that are used throughout the code.
-First and foremost is the AtomGroup. An AtomGroup is the primary Atom container; virtually everything can be accessed through it, as detailed in AtomGroup. This includes chemically meaningful groups of Atoms such as a Residue or a Segment.
+First and foremost is the AtomGroup. An AtomGroup is the primary Atom container; virtually everything can be accessed through it, as detailed in AtomGroup. This includes chemically meaningful groups of Atoms such as a Residue or a Segment.
Residues and Segments
-A Residue is composed of Atoms, and a Segment is composed of Residues.
-The corresponding container groups are ResidueGroup and SegmentGroup. These have similar properties and available methods as AtomGroup.
+A Residue is composed of Atoms, and a Segment is composed of Residues.
+The corresponding container groups are ResidueGroup and SegmentGroup. These have similar properties and available methods as AtomGroup.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import TPR, XTC
@@ -232,7 +232,7 @@
Out[8]: <AtomGroup with 3341 atoms>
-Similarly, an Atom has direct knowledge of the Residue and Segment it belongs to. Note that an Atom belongs to one Residue and the residue belongs to one Segment, but a Segment has multiple residues.
+Similarly, an Atom has direct knowledge of the Residue and Segment it belongs to. Note that an Atom belongs to one Residue and the residue belongs to one Segment, but a Segment has multiple residues.
In [9]: a = u.atoms[0]
In [10]: a.residue
@@ -246,9 +246,9 @@
For information on adding custom Residues or Segments, have a look at Adding a Residue or Segment to a Universe.
-Access to other classes via the AtomGroup object can be pretty powerful, but also
+
Access to other classes via the AtomGroup object can be pretty powerful, but also
needs to be used with caution to avoid accessing data outside the intended selection. Therefore, we present two use
-cases showing commonly used applications, for which we define Universe
+cases showing commonly used applications, for which we define Universe
on a simple extract from the PDB file:
In [9]: import MDAnalysis as mda
@@ -306,7 +306,7 @@ Use case: Sequence of residues by segmentOut[15]: [array(['GLY'], dtype=object), array(['ALA', 'GLY'], dtype=object)]
-Note that accessing residues by first selecting the segments of an AtomGroup returns
+
Note that accessing residues by first selecting the segments of an AtomGroup returns
all the residues in that segment for both the ATOM and HETATM record types (no memory of the original selection).
The meaning of this is: “give me all residue names from segments in which there is at least one of the selected atoms”.
In [16]: selected_atoms = u.select_atoms("record_type ATOM")
@@ -349,10 +349,10 @@ Use case: Atoms list grouped by residues array(['N', 'CA', 'C', 'O'], dtype=object)]
-Note that accessing atoms by first selecting the residues of an AtomGroup also
+
Note that accessing atoms by first selecting the residues of an AtomGroup also
returns hydrogen atoms (no memory of the original selection). The meaning of this is “give me all atom names from
residues in which there is at least one of the selected atoms”. However, it doesn’t contain a nitrogen atom from XYZ
-residue as no atoms from this residue were in the AtomGroup.
+residue as no atoms from this residue were in the AtomGroup.
In [24]: all_atoms_in_residues = list()
In [25]: for seg in u.segments:
@@ -373,7 +373,7 @@ Use case: Atoms list grouped by residues
Fragments
Certain analysis methods in MDAnalysis also make use of additional ways to group atoms. A key concept is a fragment. A fragment is what is typically considered a molecule: an AtomGroup where any atom is reachable from any other atom in the AtomGroup by traversing bonds, and none of its atoms is bonded to any atoms outside the AtomGroup. (A ‘molecule’ in MDAnalysis methods refers to a GROMACS-specific concept). The fragments of a Universe are determined by MDAnalysis as a derived quantity. They can only be determined if bond information is available.
-The fragments of an AtomGroup are accessible via the fragments property. Below is a Universe from a GROMACS TPR file of lysozyme (PDB ID: 2LYZ) with 101 water molecules. While it has 230 residues, there are only 102 fragments: 1 protein and 101 water fragments.
+The fragments of an AtomGroup are accessible via the fragments property. Below is a Universe from a GROMACS TPR file of lysozyme (PDB ID: 2LYZ) with 101 water molecules. While it has 230 residues, there are only 102 fragments: 1 protein and 101 water fragments.
In [27]: from MDAnalysis.tests.datafiles import TPR2021
In [28]: u = mda.Universe(TPR2021)
@@ -386,19 +386,19 @@ FragmentsTopology objects for more on bonds and which file formats give MDAnalysis bond information.
-
You can also look at which fragment a particular Atom belongs to:
+You can also look at which fragment a particular Atom belongs to:
In [31]: u.atoms[0].fragment # first atom of lysozyme
Out[31]: <AtomGroup with 1960 atoms>
-and see which fragments are associated with atoms in a smaller AtomGroup:
+and see which fragments are associated with atoms in a smaller AtomGroup:
In [32]: u.atoms[1959:1961].fragments
Out[32]: (<AtomGroup with 1960 atoms>, <AtomGroup with 3 atoms>)
Note
-AtomGroup.fragments returns a tuple of fragments with at least one Atom in the AtomGroup, not a tuple of fragments where all Atoms are in the AtomGroup.
+AtomGroup.fragments returns a tuple of fragments with at least one Atom in the AtomGroup, not a tuple of fragments where all Atoms are in the AtomGroup.
diff --git a/2.7.0-dev0/preparing_releases_and_hotfixes.html b/2.7.0-dev0/preparing_releases_and_hotfixes.html
index 8e6d14e29..d180e2664 100644
--- a/2.7.0-dev0/preparing_releases_and_hotfixes.html
+++ b/2.7.0-dev0/preparing_releases_and_hotfixes.html
@@ -265,7 +265,7 @@ Summary of tasks
Getting the develop branch ready for a release
-Declare feature freeze on develop via discord and `GitHub Discussions (Anouncement)`_
Declare feature freeze on develop via discord and GitHub Discussions (Announcement)
Create a pre-release feature branch from develop
Finalise the CHANGELOG with the release number and date. Ensure that the CHANGELOG summarizes important changes and includes all authors that contributed to this release.
Make sure the version number matches the release version. The following files need to be updated: package/MDAnalysis/version.py, package/setup.py, testsuite/MDAnalysisTests/__init__.py, and testsuite/setup.py.
Input
Note
While you can set continuous=True for either XTC or TRR files, you cannot mix different formats.
-More information can be found at the API reference for ChainReader.
+More information can be found at the API reference for ChainReader.
Trajectory formats
-If no format keyword is provided, ChainReader will try to guess the format for each file from its extension. You can force ChainReader to use the same format for every file by using the format keyword. You can also specify which format to use by file, by passing in a sequence of (filename, format) tuples.
+If no format keyword is provided, ChainReader will try to guess the format for each file from its extension. You can force ChainReader to use the same format for every file by using the format keyword. You can also specify which format to use by file, by passing in a sequence of (filename, format) tuples.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import PDB, GRO
@@ -267,33 +267,33 @@ Reading trajectories into memoryAtomGroup.positions) without having
+AtomGroup.positions) without having
to write the entire state to file.
-
The most straightforward way to do this is to pass in_memory=True to Universe, which
+
The most straightforward way to do this is to pass in_memory=True to Universe, which
automatically transfers a trajectory to memory:
In [5]: from MDAnalysis.tests.datafiles import TPR, XTC
In [6]: universe = mda.Universe(TPR, XTC, in_memory=True)
-MDAnalysis uses the MemoryReader class to load this data in.
+MDAnalysis uses the MemoryReader class to load this data in.
Transferring trajectories into memory
The decision to transfer the trajectory to memory can be made at any
time with the
-transfer_to_memory() method
-of a Universe:
+transfer_to_memory() method
+of a Universe:
In [7]: universe = mda.Universe(TPR, XTC)
In [8]: universe.transfer_to_memory()
-This operation may take a while (passing verbose=True to transfer_to_memory() will display a progress bar). However, subsequent operations on the trajectory will be very fast.
+This operation may take a while (passing verbose=True to transfer_to_memory() will display a progress bar). However, subsequent operations on the trajectory will be very fast.
Building trajectories in memory
-MemoryReader can also be used to directly generate a trajectory as a numpy array.
+MemoryReader can also be used to directly generate a trajectory as a numpy array.
In [9]: from MDAnalysisTests.datafiles import PDB
In [10]: from MDAnalysis.coordinates.memory import MemoryReader
@@ -313,20 +313,20 @@ Building trajectories in memory [ 62.961, 47.239, 3.753]], dtype=float32)
-The load_new() method can be used to load coordinates into a Universe, replacing the old coordinates:
+The load_new() method can be used to load coordinates into a Universe, replacing the old coordinates:
In [14]: coordinates = np.random.rand(len(universe.atoms), 3)
In [15]: universe.load_new(coordinates, format=MemoryReader);
In [16]: universe.atoms.positions
Out[16]:
-array([[0.2858177 , 0.817896 , 0.67939776],
- [0.26678166, 0.6052552 , 0.8945049 ],
- [0.5940016 , 0.5817606 , 0.23828323],
+array([[0.22061782, 0.38768739, 0.83270067],
+ [0.98391145, 0.46591026, 0.23064709],
+ [0.1486696 , 0.68450224, 0.74135923],
...,
- [0.44501126, 0.8171845 , 0.72477216],
- [0.12251966, 0.71526116, 0.59587806],
- [0.48403212, 0.8573202 , 0.18094209]], dtype=float32)
+ [0.60320765, 0.67722976, 0.9369782 ],
+ [0.7628681 , 0.384521 , 0.4095801 ],
+ [0.95057976, 0.8024004 , 0.4677577 ]], 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([[0.2858177 , 0.817896 , 0.67939776],
- [0.26678166, 0.6052552 , 0.8945049 ],
- [0.5940016 , 0.5817606 , 0.23828323],
+array([[0.22061782, 0.38768739, 0.83270067],
+ [0.98391145, 0.46591026, 0.23064709],
+ [0.1486696 , 0.68450224, 0.74135923],
...,
- [0.44501126, 0.8171845 , 0.72477216],
- [0.12251966, 0.71526116, 0.59587806],
- [0.48403212, 0.8573202 , 0.18094209]], dtype=float32)
+ [0.60320765, 0.67722976, 0.9369782 ],
+ [0.7628681 , 0.384521 , 0.4095801 ],
+ [0.95057976, 0.8024004 , 0.4677577 ]], dtype=float32)
@@ -354,7 +354,7 @@ In-memory trajectories of an atom selection
Frames and trajectories
-MDAnalysis Universes can be written out to a number of formats with write(). For example, to write the current frame as a PDB:
+MDAnalysis Universes can be written out to a number of formats with write(). For example, to write the current frame as a PDB:
from MDAnalysis.tests.datafiles import PDB, TRR
u = mda.Universe(PDB, TRR)
ag = u.select_atoms("name CA")
@@ -392,11 +392,11 @@ PicklingOut[22]: <Universe with 3341 atoms>
-As for MDAnalysis.core.groups.AtomGroup, during serialization, it will be pickled with its bound
-MDAnalysis.core.universe.Universe. This means that after unpickling,
-a new MDAnalysis.core.universe.Universe will be created and
-be attached to the new MDAnalysis.core.groups.AtomGroup. If the Universe is serialized
-with its MDAnalysis.core.groups.AtomGroup, they will still be bound together afterwards:
+As for MDAnalysis.core.groups.AtomGroup, during serialization, it will be pickled with its bound
+MDAnalysis.core.universe.Universe. This means that after unpickling,
+a new MDAnalysis.core.universe.Universe will be created and
+be attached to the new MDAnalysis.core.groups.AtomGroup. If the Universe is serialized
+with its MDAnalysis.core.groups.AtomGroup, they will still be bound together afterwards:
In [23]: import pickle
In [24]: from MDAnalysis.tests.datafiles import PSF, DCD
@@ -418,8 +418,8 @@ Picklingg_pickled.universe is u_pickled: True
-If multiple MDAnalysis.core.groups.AtomGroups are bound to the same
-MDAnalysis.core.universe.Universe, they will also be bound to the same one
+
If multiple MDAnalysis.core.groups.AtomGroups are bound to the same
+MDAnalysis.core.universe.Universe, they will also be bound to the same one
after serialization:
In [1]: u = mda.Universe(PSF, DCD)
diff --git a/2.7.0-dev0/references.html b/2.7.0-dev0/references.html
index c1fc88894..775cead5b 100644
--- a/2.7.0-dev0/references.html
+++ b/2.7.0-dev0/references.html
@@ -195,7 +195,7 @@
MDAnalysis and the included algorithms are scientific software that
are described in academic publications. Please cite these papers when you use
MDAnalysis in published work.
-It is possible to automatically generate a list of references for any program that uses
+
It is possible to automatically generate a list of references for any program that uses
MDAnalysis. This list (in common reference manager formats) contains
the citations associated with the specific algorithms and libraries
that were used in the program.
diff --git a/2.7.0-dev0/searchindex.js b/2.7.0-dev0/searchindex.js
index 50c3f3129..a18c4c7c4 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", "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", "preparing_releases_and_hotfixes", "reading_and_writing", "references", "releases", "selections", "standard_selections", "testing", "topology_system", "trajectories/slicing_trajectories", "trajectories/trajectories", "trajectories/transformations", "units", "universe"], "filenames": ["advanced_topology.rst", "atomgroup.rst", "contributing.rst", "contributing_code.rst", "contributing_docs.rst", "datasets.rst", "examples/README.rst", "examples/analysis/README.rst", "examples/analysis/alignment_and_rms/README.rst", "examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb", "examples/analysis/alignment_and_rms/aligning_trajectory.ipynb", "examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb", "examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb", "examples/analysis/alignment_and_rms/rmsd.ipynb", "examples/analysis/alignment_and_rms/rmsf.ipynb", "examples/analysis/custom_parallel_analysis.ipynb", "examples/analysis/custom_trajectory_analysis.ipynb", "examples/analysis/distances_and_contacts/README.rst", "examples/analysis/distances_and_contacts/contacts_custom.ipynb", "examples/analysis/distances_and_contacts/contacts_native_fraction.ipynb", "examples/analysis/distances_and_contacts/contacts_q1q2.ipynb", "examples/analysis/distances_and_contacts/contacts_within_cutoff.ipynb", "examples/analysis/distances_and_contacts/distances_between_atomgroups.ipynb", "examples/analysis/distances_and_contacts/distances_between_selections.ipynb", "examples/analysis/distances_and_contacts/distances_within_selection.ipynb", "examples/analysis/hydrogen_bonds/README.rst", "examples/analysis/hydrogen_bonds/hbonds.ipynb", "examples/analysis/hydrogen_bonds/hbonds-lifetimes.ipynb", "examples/analysis/hydrogen_bonds/hbonds-selections.ipynb", "examples/analysis/polymers_and_membranes/README.rst", "examples/analysis/polymers_and_membranes/hole2.ipynb", "examples/analysis/polymers_and_membranes/polymer.ipynb", "examples/analysis/reduced_dimensions/README.rst", "examples/analysis/reduced_dimensions/diffusion_map.ipynb", "examples/analysis/reduced_dimensions/pca.ipynb", 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"formats/reference/tpr.rst", "formats/reference/trj.rst", "formats/reference/trr.rst", "formats/reference/trz.rst", "formats/reference/txyz.rst", "formats/reference/xml.rst", "formats/reference/xpdb.rst", "formats/reference/xtc.rst", "formats/reference/xyz.rst", "formats/selection_exporters.rst", "formats/topology.rst", "groups_of_atoms.rst", "index.rst", "installation.rst", "module_imports.rst", "preparing_releases_and_hotfixes.rst", "reading_and_writing.rst", "references.rst", "releases.md", "selections.rst", "standard_selections.rst", "testing.rst", "topology_system.rst", "trajectories/slicing_trajectories.rst", "trajectories/trajectories.rst", "trajectories/transformations.rst", "units.rst", "universe.rst"], "titles": ["Advanced topology concepts", "AtomGroup", "Contributing to MDAnalysis", "Contributing to the main codebase", "Contributing to the user guide", "Example data", "Examples", "Analysis", "Alignments and RMS fitting", "Aligning a structure to another", "Aligning a 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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, 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, 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, 99, 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, 33, 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, 100, 101, 102, 108], "_": [2, 13, 26, 31, 44, 48, 87, 99, 102], "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": [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], "export": [3, 4, 5, 48, 53, 104, 106], "workon_hom": 3, "mkdir": 3, "p": [3, 14, 16, 26, 27, 30, 33, 34, 38, 46, 48, 52, 53, 57, 61, 63, 67, 79, 81, 88, 95, 104, 105, 106, 107, 113, 114], "usr": 3, "sh": 3, 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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, 99, 100, 101, 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": 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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, 32, 34, 53, 104, 105, 112], "dataset": [5, 14, 15, 114], "primarili": 5, "workshop": 5, "interfac": [5, 26, 53], "cach": [5, 15, 100], "certain": [5, 7, 13, 17, 19, 21, 30, 40, 42, 53, 57, 61, 66, 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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], 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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], 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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, 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"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 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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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\ No newline at end of file
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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, 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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, 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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, 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], 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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, 99, 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, 33, 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, 100, 101, 102, 108], "_": [2, 13, 26, 31, 44, 48, 87, 99], "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": [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, 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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], "export": [3, 4, 5, 48, 53, 104, 106], "workon_hom": 3, "mkdir": 3, "p": [3, 14, 16, 26, 27, 30, 33, 34, 38, 46, 48, 52, 53, 57, 61, 63, 67, 79, 81, 88, 95, 104, 105, 106, 107, 113, 114], "usr": 3, "sh": 3, 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85], "quit": [3, 15, 34, 44, 96, 100, 114], "low": [3, 7, 12, 14, 32, 42], "256": 3, "increas": [3, 27, 33, 42, 43, 44, 85, 102, 105, 108], "ulimit": 3, "4096": 3, "appli": [3, 13, 16, 19, 30, 33, 36, 38, 42, 43, 44, 98, 104, 105, 106, 109, 111, 112], "high": [3, 4, 7, 14, 15, 32, 34, 42, 45, 52, 85, 106], "limit": [3, 15, 16, 30, 34, 36, 40, 55, 57, 88], "profil": 3, "mix": [3, 46, 103], "forg": [3, 100], "biopython": [3, 101, 105], "80": [3, 16, 19, 81, 82, 105, 106, 110], "networkx": [3, 105], "griddataformat": [3, 101], "mmtf": [3, 58, 59, 61, 97, 101, 106, 109], "joblib": [3, 15, 26], "scipi": [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, 52, 53, 55, 79, 101, 104, 105], "matplotlib": [3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 53, 57, 101], "tqdm": [3, 27, 105], "43": [3, 49, 57, 103], "threadpoolctl": 3, "fasten": 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"try": [3, 4, 43, 55, 78, 87, 92, 99, 100, 101, 103, 108], "conform": [3, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46, 53, 83, 104], "strategi": [3, 105], "thu": [3, 4, 53, 87], "79": [3, 52, 81, 82], "charact": [3, 30, 71, 81, 82, 83, 93, 106], "less": [3, 7, 18, 19, 26, 32, 34, 57, 68, 100], "break": [3, 27, 66, 101, 105, 108], "sensibli": 3, "indent": 3, "space": [3, 7, 32, 33, 41, 42, 43, 44, 48, 50, 83, 84, 100, 106, 108], "per": [3, 19, 26, 66, 83, 105, 108], "capitalclass": 3, "capit": 3, "noun": 3, "underscore_method": 3, "lower": [3, 7, 19, 24, 30, 32, 33, 34, 38, 40, 42, 43, 44, 57], "case": [3, 9, 10, 12, 13, 14, 15, 27, 28, 30, 36, 44, 48, 52, 53, 55, 57, 68, 82, 87, 89, 96, 99, 100, 104, 105, 106, 108, 111, 114], "underscor": 3, "id": [3, 13, 23, 24, 26, 42, 43, 44, 45, 50, 61, 65, 66, 69, 75, 83, 84, 87, 98, 104, 106, 109], "pycharm": 3, "extern": [3, 5, 7, 48, 100, 101, 105, 106], "tool": [3, 4, 7, 15, 19, 30, 33, 34, 48, 53, 67, 78, 80, 96, 99, 100, 103], "flake8": 3, "lint": 3, "emac": 3, "vim": 3, "check": [3, 4, 5, 11, 26, 27, 28, 50, 53, 57, 60, 66, 67, 72, 89, 102, 108], "elpi": 3, "autom": [3, 53, 102, 108], "formatt": 3, "autopep8": 3, "yapf": 3, "plugin": [3, 4, 95, 100, 101, 108], "strive": [3, 101, 108], "small": [3, 4, 5, 26, 27, 57, 78, 101, 108], "lightweight": [3, 15, 101], "visual": [3, 4, 14, 15, 48, 96, 100, 105], "reli": [3, 53, 60, 83, 100, 108], "treat": [3, 42, 45, 48, 53, 72, 82, 89, 114], "rule": [3, 4, 44, 99, 102, 106, 108], "setup": [3, 100, 101, 102, 105, 108], "script": [3, 7, 9, 10, 11, 12, 13, 14, 15, 33, 53, 83, 102, 104], "standard": [3, 7, 30, 37, 39, 42, 44, 53, 58, 59, 61, 65, 82, 84, 93, 97, 101, 105, 106], "pyx": 3, "convert": [3, 24, 37, 48, 52, 53, 57, 62, 63, 76, 78, 80, 81, 83, 86, 105, 113], "newer": [3, 86], "than": [3, 13, 14, 15, 18, 19, 26, 28, 30, 36, 40, 42, 50, 53, 57, 60, 65, 71, 75, 83, 88, 99, 105, 106, 108], "alreadi": [3, 7, 11, 14, 16, 33, 34, 46, 50, 53, 66, 99, 100, 106, 109], "forc": [3, 26, 50, 52, 53, 57, 58, 60, 61, 63, 89, 94, 103, 105, 106, 107, 109, 111, 114], "trigger": [3, 102, 108], "convers": [3, 13, 57, 99], "deliv": 3, "who": [3, 4, 7, 16, 101], "automat": [3, 7, 10, 16, 18, 30, 55, 57, 65, 66, 76, 79, 89, 94, 99, 101, 102, 103, 104, 106, 114], "outdat": 3, "place": [3, 10, 34, 94, 99, 102], "final": [3, 10, 13, 15, 19, 39, 40, 48, 87, 102, 106], "fortran": 3, "librari": [3, 9, 10, 14, 15, 19, 33, 34, 39, 46, 48, 50, 55, 58, 61, 62, 79, 80, 85, 99, 101, 102, 104, 105, 108], "dedic": 3, "src": [3, 84, 87], "tree": 3, "lib": [3, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 105, 108], "_distanc": 3, "distanc": [3, 6, 8, 13, 15, 16, 18, 19, 21, 26, 27, 30, 32, 33, 36, 38, 40, 42, 44, 50, 52, 53, 60, 105, 106, 109], "coordin": [3, 7, 8, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 28, 30, 32, 33, 34, 36, 38, 39, 42, 43, 44, 45, 49, 50, 52, 55, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 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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, 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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, 99, 100, 101, 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": 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100, "flag": 100, "optimis": 100, "addit": 100, "dataset": 100, "rule": 101, "suit": [101, 108], "core": 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
diff --git a/2.7.0-dev0/selections.html b/2.7.0-dev0/selections.html
index e6d6dc558..69719e826 100644
--- a/2.7.0-dev0/selections.html
+++ b/2.7.0-dev0/selections.html
@@ -216,14 +216,14 @@
Out[5]: <AtomGroup with 190 atoms>
-The select_atoms() method of a
-AtomGroup or a
-Universe returns an
-AtomGroup. These two methods have different behaviour: while Universe.select_atoms operates on all the atoms in the universe, AtomGroup.select_atoms only operates on the atoms within the original AtomGroup. A single selection phrase always returns an
-AtomGroup with atoms sorted according to their
+
The select_atoms() method of a
+AtomGroup or a
+Universe returns an
+AtomGroup. These two methods have different behaviour: while Universe.select_atoms operates on all the atoms in the universe, AtomGroup.select_atoms only operates on the atoms within the original AtomGroup. A single selection phrase always returns an
+AtomGroup with atoms sorted according to their
index in the topology. This is to ensure that there are not any duplicates,
which can happen with complicated selections. When order matters, you can pass in multiple phrases.
-This page documents selection keywords and their arguments. select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). For example, you can:
+This page documents selection keywords and their arguments. select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). For example, you can:
Pass in named AtomGroups as arguments:
@@ -445,15 +445,15 @@ Index
- group group-name
selects the atoms in the AtomGroup passed to the function as an
argument named group-name. Only the atoms common to group-name and the
-instance select_atoms() was called
+instance select_atoms() was called
from will be considered, unless group is preceded by the global
keyword. group-name will be included in the parsing just by comparison of
atom indices. This means that it is up to the user to make sure the
group-name group was defined in an appropriate Universe.
- global selection
by default, when issuing
-select_atoms() from an
-AtomGroup, selections and subselections
+select_atoms() from an
+AtomGroup, selections and subselections
are returned intersected with the atoms of that instance. Prefixing a
selection term with global causes its selection to be returned in its
entirety. As an example, the global keyword allows for
@@ -461,20 +461,20 @@
Index
a group that does not contain any proteins. Were global absent, the
result would be an empty selection since the protein subselection would
itself be empty. When calling
-select_atoms() from a
-Universe, global is ignored.
+select_atoms() from a
+Universe, global is ignored.
Dynamic selections
-By default select_atoms() returns an
-AtomGroup, in which the list of atoms is
+
By default select_atoms() returns an
+AtomGroup, in which the list of atoms is
constant across trajectory frame changes. If
-select_atoms() is invoked with named
+select_atoms() is invoked with named
argument updating set to True, an
-UpdatingAtomGroup instance will be returned
+UpdatingAtomGroup instance will be returned
instead.
# A dynamic selection of corner atoms:
In [12]: ag_updating = u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True)
@@ -483,10 +483,10 @@ Index
Out[13]: <AtomGroup with 917 atoms, with selection 'prop x < 5 and prop y < 5 and prop z < 5' on the entire Universe.>
-It behaves just like an AtomGroup
+
It behaves just like an AtomGroup
object, with the difference that the selection expressions are re-evaluated
every time the trajectory frame changes (this happens lazily, only when the
-UpdatingAtomGroup object is accessed so that
+UpdatingAtomGroup object is accessed so that
there is no redundant updating going on):
In [14]: u.trajectory.next()
Out[14]: < Timestep 1 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >
@@ -498,8 +498,8 @@ Index
Using the group selection keyword for
Preexisting selections and modifiers, one can
make updating selections depend on
-AtomGroup, or even other
-UpdatingAtomGroup, instances.
+AtomGroup, or even other
+UpdatingAtomGroup, instances.
Likewise, making an updating selection from an already updating group will
cause later updates to also reflect the updating of the base group:
Finally, a non-updating selection or a slicing/addition operation made on an
-UpdatingAtomGroup will return a static
-AtomGroup, which will no longer update
+UpdatingAtomGroup will return a static
+AtomGroup, which will no longer update
across frames:
In [20]: static_ag = ag_updating.select_atoms("resid 1:1000")
@@ -533,8 +533,8 @@ Index
Ordered selections
-select_atoms() sorts the atoms
-in the AtomGroup by atom index before
+
select_atoms() sorts the atoms
+in the AtomGroup by atom index before
returning them (this is to eliminate possible duplicates in the
selection). If the ordering of atoms is crucial (for instance when
describing angles or dihedrals) or if duplicate atoms are required
@@ -551,7 +551,7 @@
Index
A shortcut is to provide two or more selections to
-select_atoms(), which then
+select_atoms(), which then
does the concatenation automatically:
In [16]: list(u.select_atoms("resid 3 and name CA", "resid 2 and name CA"))
Out[16]:
diff --git a/2.7.0-dev0/standard_selections.html b/2.7.0-dev0/standard_selections.html
index 570c39671..fc3585e0a 100644
--- a/2.7.0-dev0/standard_selections.html
+++ b/2.7.0-dev0/standard_selections.html
@@ -332,10 +332,10 @@ Protein backbone
-CA
N
O
O
CA
C
N
Protein backbone
-DG3
DA
DC3
RG5
RU
DG5
DA3
DC
U
DT
RC
URA
THY
RA
DT3
RG
DG
CYT
A
DC5
DG3
RU3
U
DA5
RU5
DC
RU
DA
RG5
GUA
RA5
ADE
G
A
RU3
GUA
DC5
DT5
G
DC3
DT3
RC5
RG3
ADE
RG3
URA
CYT
T
DA3
RA3
C
RC5
RG
RA
DG5
DT
T
RC3
RC
DG
RU5
C
Nucleic backbone
-C3’
C5’
O5’
C5’
P
O3’
C3’
P
Nucleic backbone
-C5M
C4
N1
C5
O2
O6
C5M
C2
N3
C5
N7
N6
C4
N1
O6
N9
C8
O4
N3
C6
N2
O2
N4
N9
C8
N6
N2
Nucleic sugars
-C3’
C4’
C2’
O4’
O4’
C1’
C3’
C2’
C4’
The topology system
-MDAnalysis groups static data about a Universe into its topology. This is typically loaded from a topology file. Topology information falls into 3 categories:
+MDAnalysis groups static data about a Universe into its topology. This is typically loaded from a topology file. Topology information falls into 3 categories:
-Users will almost never interact directly with a Topology. Modifying atom containers or topology attributes is typically done through Universe. Methods for viewing containers or topology attributes, or for calculating topology object values, are accessed through AtomGroup.
+Users will almost never interact directly with a Topology. Modifying atom containers or topology attributes is typically done through Universe. Methods for viewing containers or topology attributes, or for calculating topology object values, are accessed through AtomGroup.
Topology attributes
-MDAnalysis supports a range of topology attributes for each Atom and AtomGroup. If an attribute is defined for an Atom, it will be for an AtomGroup, and vice versa – however, they are accessed with singular and plural versions of the attribute specifically.
+MDAnalysis supports a range of topology attributes for each Atom and AtomGroup. If an attribute is defined for an Atom, it will be for an AtomGroup, and vice versa – however, they are accessed with singular and plural versions of the attribute specifically.
Canonical attributes
-These attributes are derived for every Universe, including Universes created with empty(). They encode the MDAnalysis order of each object.
+These attributes are derived for every Universe, including Universes created with empty(). They encode the MDAnalysis order of each object.
Atom
Format-specific attributes
Adding TopologyAttrs
-Each of the attributes above can be added to a Universe if it was not available in the file with add_TopologyAttr().
-add_TopologyAttr() takes two arguments:
+Each of the attributes above can be added to a Universe if it was not available in the file with add_TopologyAttr().
+add_TopologyAttr() takes two arguments:
-topologyattr : the singular or plural name of a TopologyAttr, or a MDAnalysis TopologyAttr object. This must already have been defined as a TopologyAttr (see Adding custom TopologyAttrs for an example of adding a custom topology attribute).
topologyattr : the singular or plural name of a TopologyAttr, or a MDAnalysis TopologyAttr object. This must already have been defined as a TopologyAttr (see Adding custom TopologyAttrs for an example of adding a custom topology attribute).
values (optional) : if topologyattr is a string, the values for that attribute. This can be None if the attribute has default values defined, e.g. tempfactors.
@@ -519,7 +519,7 @@ Format-specific attributesOut[6]: array([0., 0., 0., ..., 0., 0., 0.])
-One way to modify topology attributes is to simply replace them with add_TopologyAttr():
+One way to modify topology attributes is to simply replace them with add_TopologyAttr():
In [7]: psf.add_TopologyAttr('tempfactors', range(len(psf.atoms)))
In [8]: psf.atoms.tempfactors
@@ -560,7 +560,7 @@ Modifying TopologyAttrsNote
This method cannot be used with connectivity attributes, i.e. bonds, angles, dihedrals, and impropers.
-Similarly to adding topology attributes with add_TopologyAttr(), the “level” of the attribute matters. Residue attributes can only be assigned to attributes at the Residue or ResidueGroup level. The same applies to attributes for Atoms and Segments. For example, we would get a NotImplementedError if we tried to assign resnames to an AtomGroup.
+Similarly to adding topology attributes with add_TopologyAttr(), the “level” of the attribute matters. Residue attributes can only be assigned to attributes at the Residue or ResidueGroup level. The same applies to attributes for Atoms and Segments. For example, we would get a NotImplementedError if we tried to assign resnames to an AtomGroup.
In [15]: pdb.residues[0].atoms.resnames = ['new_name']
NotImplementedErrorTraceback (most recent call last)
@@ -830,29 +830,29 @@ Modifying TopologyAttrs
Topology objects
-MDAnalysis defines four types of TopologyObject by connectivity:
+MDAnalysis defines four types of TopologyObject by connectivity:
-Bond
Angle
Dihedral
ImproperDihedral
The value of each topology object can be calculated with value().
-Each TopologyObject also contains the following attributes:
+Each TopologyObject also contains the following attributes:
-atoms : the ordered atoms in the object
indices : the ordered atom indices in the object
type : this is either the ‘type’ of the bond/angle/dihedral/improper, or a tuple of the atom types.
atoms : the ordered atoms in the object
indices : the ordered atom indices in the object
type : this is either the ‘type’ of the bond/angle/dihedral/improper, or a tuple of the atom types.
is_guessed : MDAnalysis can guess bonds. This property records if the object was read from a file or guessed.
-Groups of these are held in TopologyGroups. The master groups of TopologyObjects are accessible as properties of a Universe. TopologyObjects are typically read from a file with connectivity information (see the supported formats here). However, they can be created in two ways: by adding them to a Universe, or by creating them from an AtomGroup. Bonds can be guessed based on distance and Van der Waals’ radii with AtomGroup.guess_bonds.
+Groups of these are held in TopologyGroups. The master groups of TopologyObjects are accessible as properties of a Universe. TopologyObjects are typically read from a file with connectivity information (see the supported formats here). However, they can be created in two ways: by adding them to a Universe, or by creating them from an AtomGroup. Bonds can be guessed based on distance and Van der Waals’ radii with AtomGroup.guess_bonds.
Adding to a Universe
-As of version 0.21.0, there are specific methods for adding TopologyObjects to a Universe:
+As of version 0.21.0, there are specific methods for adding TopologyObjects to a Universe:
add_Bonds()
Adding to a UniverseThese accept the following values:
-a TopologyGroup
an iterable of atom indices
an iterable of TopologyObjects
an iterable of TopologyObjects
-Prior to version 0.21.0, objects could be added to a Universe with add_TopologyAttr().
+Prior to version 0.21.0, objects could be added to a Universe with add_TopologyAttr().
In [15]: hasattr(pdb, 'angles')
Out[15]: False
@@ -879,20 +879,20 @@ Adding to a UniverseOut[17]: <TopologyGroup containing 2 angles>
-Both of these methods add the new objects to the associated master TopologyGroup in the Universe.
+Both of these methods add the new objects to the associated master TopologyGroup in the Universe.
Creating with an AtomGroup
-An AtomGroup can be represented as a bond, angle, dihedral angle, or improper angle TopologyObject through the respective properties:
+An AtomGroup can be represented as a bond, angle, dihedral angle, or improper angle TopologyObject through the respective properties:
-The AtomGroup must contain the corresponding number of atoms, in the desired order. For example, a bond cannot be created from three atoms.
+The AtomGroup must contain the corresponding number of atoms, in the desired order. For example, a bond cannot be created from three atoms.
In [18]: pdb.atoms[[3, 4, 2]].bond
ValueErrorTraceback (most recent call last)
@@ -909,11 +909,11 @@ Creating with an AtomGroup47.770653826924175
-These AtomGroup TopologyObjects are not added to the associated master TopologyGroup in the Universe.
+These AtomGroup TopologyObjects are not added to the associated master TopologyGroup in the Universe.
Deleting from a Universe
-As of version 0.21.0, there are specific methods for deleting TopologyObjects from a Universe:
+As of version 0.21.0, there are specific methods for deleting TopologyObjects from a Universe:
delete_Bonds()
Deleting from a Universe
Topology-specific methods
-A number of analysis and transformation methods are defined for AtomGroup, ResidueGroup, and SegmentGroup that require specific properties to be available. The primary requirement is the positions attribute. With positions, you can easily compute a center of geometry:
+A number of analysis and transformation methods are defined for AtomGroup, ResidueGroup, and SegmentGroup that require specific properties to be available. The primary requirement is the positions attribute. With positions, you can easily compute a center of geometry:
>>> u.atoms.center_of_geometry()
array([-0.04223882, 0.01418196, -0.03504874])
@@ -957,63 +957,63 @@ Deleting from a UniverseCenter of (absolute) charge of (compounds of) the group .. math:: boldsymbol R = frac{sum_i vert q_i vert boldsymbol r_i} {sum_i vert q_i vert} where \(q_i\) is the charge and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
center_of_charge()
Center of (absolute) charge of (compounds of) the group .. math:: boldsymbol R = frac{sum_i vert q_i vert boldsymbol r_i} {sum_i vert q_i vert} where \(q_i\) is the charge and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
charges
dipole_moment()
Dipole moment of the group or compounds in a group
charges
dipole_vector()
Dipole vector of the group
charges
quadrupole_moment()
Quadrupole moment of the group according to [1]
charges
quadrupole_tensor()
Traceless quadrupole tensor of the group or compounds
charges
total_charge()
Total charge of (compounds of) the group
charges
align_principal_axis()
Align principal axis with index axis with vector
masses
asphericity()
Asphericity
masses
Center of mass of (compounds of) the group .. math:: boldsymbol R = frac{sum_i m_i boldsymbol r_i}{sum m_i} where \(m_i\) is the mass and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
center_of_mass()
Center of mass of (compounds of) the group .. math:: boldsymbol R = frac{sum_i m_i boldsymbol r_i}{sum m_i} where \(m_i\) is the mass and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
masses
gyration_moments()
Moments of the gyration tensor
masses
moment_of_inertia()
Moment of inertia tensor relative to center of mass
masses
principal_axes()
Calculate the principal axes from the moment of inertia
masses
radius_of_gyration()
Radius of gyration
masses
shape_parameter()
Shape parameter
masses
total_mass()
Total mass of (compounds of) the group
masses
-Indexing a trajectory shifts the Universe to point towards that particular frame, updating dynamic data such as Universe.atoms.positions.
+Indexing a trajectory shifts the Universe to point towards that particular frame, updating dynamic data such as Universe.atoms.positions.
Note
The trajectory frame is not read from the MD data. It is the internal index assigned by MDAnalysis.
@@ -210,7 +210,7 @@
Out[5]: 4
-Creating a FrameIterator by slicing a trajectory does not shift the Universe to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.
+Creating a FrameIterator by slicing a trajectory does not shift the Universe to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.
In [6]: fiter = u.trajectory[10::10]
In [7]: frames = [ts.frame for ts in fiter]
diff --git a/2.7.0-dev0/trajectories/transformations.html b/2.7.0-dev0/trajectories/transformations.html
index c3a78d562..88930fd80 100644
--- a/2.7.0-dev0/trajectories/transformations.html
+++ b/2.7.0-dev0/trajectories/transformations.html
@@ -195,7 +195,7 @@
On-the-fly transformations
An on-the-fly transformation is a function that silently modifies the dynamic data contained in a trajectory Timestep (typically coordinates) as it is loaded into memory. It is called for each current time step to transform data into your desired representation. A transformation function must also return the current Timestep, as transformations are often chained together.
-The MDAnalysis.transformations module contains a collection of transformations. For example, fit_rot_trans() can perform a mass-weighted alignment on an AtomGroup to a reference.
+The MDAnalysis.transformations module contains a collection of transformations. For example, fit_rot_trans() can perform a mass-weighted alignment on an AtomGroup to a reference.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import TPR, XTC
@@ -211,8 +211,8 @@
In [7]: u.trajectory.add_transformations(align_transform)
-Other implemented transformations include functions to translate, rotate, fit an AtomGroup to a reference, and wrap or unwrap groups in the unit cell. (Please see the MDAnalysis on-the-fly transformations blog post contains a more complete introduction to these fitting and wrapping functions.)
-Although you can only call add_transformations() once, you can pass in multiple transformations in a list, which will be executed in order.
+Other implemented transformations include functions to translate, rotate, fit an AtomGroup to a reference, and wrap or unwrap groups in the unit cell. (Please see the MDAnalysis on-the-fly transformations blog post contains a more complete introduction to these fitting and wrapping functions.)
+Although you can only call add_transformations() once, you can pass in multiple transformations in a list, which will be executed in order.
There is a transformations tutorial that shows in more detail how to use transformations. A few simple examples are given below.
Example workflows
@@ -238,7 +238,7 @@ Example workflowsPlease see the full tutorial for more information.
-
If your transformation does not depend on something within the Universe (e.g. a chosen AtomGroup), you can also create a Universe directly with transformations. The code below translates coordinates 1 angstrom up on the z-axis:
+If your transformation does not depend on something within the Universe (e.g. a chosen AtomGroup), you can also create a Universe directly with transformations. The code below translates coordinates 1 angstrom up on the z-axis:
In [13]: u = mda.Universe(TPR, XTC, transformations=[trans.translate([0, 0, 1])])
diff --git a/2.7.0-dev0/units.html b/2.7.0-dev0/units.html
index 6e775424f..b5ff9c2d1 100644
--- a/2.7.0-dev0/units.html
+++ b/2.7.0-dev0/units.html
@@ -258,11 +258,11 @@
Unit conversion
-Quantities can be converted from units with convert().
-convert() simply multiplies the initial quantity with a
+
Quantities can be converted from units with convert().
+convert() simply multiplies the initial quantity with a
precomputed conversion factor, as obtained from
-get_conversion_factor().
-The computed conversion factors for each quantity type are stored in MDAnalysis.units and shown below.
+get_conversion_factor().
+The computed conversion factors for each quantity type are stored in MDAnalysis.units and shown below.
Constants
diff --git a/2.7.0-dev0/universe.html b/2.7.0-dev0/universe.html
index edaf56c2b..002b8a4d6 100644
--- a/2.7.0-dev0/universe.html
+++ b/2.7.0-dev0/universe.html
@@ -204,13 +204,13 @@
If you wish to make an apple pie from scratch, you must first invent the universe.
—Carl Sagan, Cosmos
-MDAnalysis is structured around two fundamental classes: the Universe and the AtomGroup. Almost all code in MDAnalysis begins with Universe, which contains all the information describing a molecular dynamics system.
+MDAnalysis is structured around two fundamental classes: the Universe and the AtomGroup. Almost all code in MDAnalysis begins with Universe, which contains all the information describing a molecular dynamics system.
It has two key properties:
-atoms: an AtomGroup of the system’s atoms, providing access to important analysis methods (described below)
trajectory: the currently loaded trajectory reader
atoms: an AtomGroup of the system’s atoms, providing access to important analysis methods (described below)
trajectory: the currently loaded trajectory reader
-A Universe ties the static information from the “topology” (e.g. atom identities) to dynamically updating information from the “trajectory” (e.g. coordinates). A key feature of MDAnalysis is that an entire trajectory is not loaded into memory (unless the user explicitly does so with MemoryReader). Instead, the trajectory attribute provides a view on a specific frame of the trajectory. This allows the analysis of arbitrarily long trajectories without a significant impact on memory.
+A Universe ties the static information from the “topology” (e.g. atom identities) to dynamically updating information from the “trajectory” (e.g. coordinates). A key feature of MDAnalysis is that an entire trajectory is not loaded into memory (unless the user explicitly does so with MemoryReader). Instead, the trajectory attribute provides a view on a specific frame of the trajectory. This allows the analysis of arbitrarily long trajectories without a significant impact on memory.
Creating a Universe
@@ -224,7 +224,7 @@ Creating a UniverseUniverse constructor also takes optional arguments.
+
The default arguments should create a Universe suited for most analysis applications. However, the Universe constructor also takes optional arguments.
The following options specify how to treat the input:
format: the file format of the trajectory file/s. (default: None, formats are guessed)
Creating a Universetransformations: a function or list of functions for on-the-fly trajectory transformation.
in_memory: whether to load coordinates into memory (default: False)
in_memory_step: only read every nth frame into an in-memory representation. (default: 1)
is_anchor: whether to consider this Universe when unpickling AtomGroups (default: True)
anchor_name: the name of this Universe when unpickling AtomGroups (default: None, automatically generated)
is_anchor: whether to consider this Universe when unpickling AtomGroups (default: True)
anchor_name: the name of this Universe when unpickling AtomGroups (default: None, automatically generated)
You can also pass in keywords for parsing the topology or coordinates. For example, many file formats do not specify the timestep for their trajectory. In these cases, MDAnalysis assumes that the default timestep is 1 ps. If this is incorrect, you can pass in a dt argument to modify the timestep. This does not modify timesteps for formats that include time information.
In [7]: from MDAnalysis.tests.datafiles import PRM, TRJ
@@ -274,7 +274,7 @@ Creating a Universe
Constructing from AtomGroups
-A new Universe can be created from one or more AtomGroup instances with Merge(). The AtomGroup instances can come from different Universes, meaning that this is one way to concatenate selections from different datasets.
+A new Universe can be created from one or more AtomGroup instances with Merge(). The AtomGroup instances can come from different Universes, meaning that this is one way to concatenate selections from different datasets.
For example, to combine a protein, ligand, and solvent from separate PDB files:
u1 = mda.Universe("protein.pdb")
u2 = mda.Universe("ligand.pdb")
@@ -286,7 +286,7 @@ Constructing from AtomGroups
Constructing from scratch
-A Universe can be constructed from scratch with Universe.empty. There are three stages to this process:
+A Universe can be constructed from scratch with Universe.empty. There are three stages to this process:
Create the blank Universe with specified number of atoms. If coordinates, set trajectory=True.
Guessing topology attributesResidues and Segments are chemically meaningful groups of Atoms.
-
Modifying a topology is typically done through the Universe, which contains several methods for adding properties:
+Modifying a topology is typically done through the Universe, which contains several methods for adding properties:
-add_TopologyAttr()
add_Residue()
add_Segment()
See Topology attributes for more information on which topology attributes can be added, and examples/constructing_universe.ipynb for examples on adding attributes and Segments.
diff --git a/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf b/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf
index 452584a53..988b4e335 100644
Binary files a/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf and b/dev/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf differ
diff --git a/dev/_sources/preparing_releases_and_hotfixes.rst.txt b/dev/_sources/preparing_releases_and_hotfixes.rst.txt
index 333aac958..655a67972 100644
--- a/dev/_sources/preparing_releases_and_hotfixes.rst.txt
+++ b/dev/_sources/preparing_releases_and_hotfixes.rst.txt
@@ -67,7 +67,7 @@ Summary of tasks
Getting the develop branch ready for a release
----------------------------------------------
-#. Declare feature freeze on ``develop`` via `discord` and `GitHub Discussions (Anouncement)`_
+#. Declare feature freeze on ``develop`` via `discord` and `GitHub Discussions (Announcement)`_
#. Create a pre-release feature branch from ``develop``
diff --git a/dev/advanced_topology.html b/dev/advanced_topology.html
index bcf3fd81b..c6a89646d 100644
--- a/dev/advanced_topology.html
+++ b/dev/advanced_topology.html
@@ -197,7 +197,7 @@
Advanced topology concepts
Adding a Residue or Segment to a Universe
-To add a Residue or Segment to a topology, use the Universe.add_Residue or Universe.add_Segment methods.
+To add a Residue or Segment to a topology, use the Universe.add_Residue or Universe.add_Segment methods.
>>> u = mda.Universe(PSF, DCD)
>>> u.segments
<SegmentGroup with 1 segment>
@@ -210,7 +210,7 @@
<AtomGroup with 0 atoms>
-To assign the last 100 residues from the Universe to this new Segment:
+To assign the last 100 residues from the Universe to this new Segment:
>>> u.residues[-100:].segments = newseg
>>> newseg.atoms
<AtomGroup with 1600 atoms>
diff --git a/dev/atomgroup.html b/dev/atomgroup.html
index c89ab29c1..250e13dcf 100644
--- a/dev/atomgroup.html
+++ b/dev/atomgroup.html
@@ -204,16 +204,16 @@
AtomGroup
-A Universe contains all particles in the molecular system. MDAnalysis calls a particle an Atom, regardless of whether it really is (e.g. it may be a united-atom particle or coarse-grained bead). Atoms are grouped with an AtomGroup; the ‘master’ AtomGroup of a Universe is accessible at Universe.atoms.
+A Universe contains all particles in the molecular system. MDAnalysis calls a particle an Atom, regardless of whether it really is (e.g. it may be a united-atom particle or coarse-grained bead). Atoms are grouped with an AtomGroup; the ‘master’ AtomGroup of a Universe is accessible at Universe.atoms.
Note
-The AtomGroup is probably the most important object in MDAnalysis. Virtually everything can be accessed through an AtomGroup.
+The AtomGroup is probably the most important object in MDAnalysis. Virtually everything can be accessed through an AtomGroup.
Creating an AtomGroup
Atom selection language
-AtomGroup instances are typically created with Universe.select_atoms or by manipulating another AtomGroup, e.g. by slicing.
+AtomGroup instances are typically created with Universe.select_atoms or by manipulating another AtomGroup, e.g. by slicing.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import PDB
@@ -228,12 +228,12 @@ Atom selection language
Indexing and slicing
-An AtomGroup can be indexed and sliced like a list:
+An AtomGroup can be indexed and sliced like a list:
In [5]: print(u.atoms[0])
<Atom 1: N of type N of resname MET, resid 1 and segid SYSTEM and altLoc >
-Slicing returns another AtomGroup. The below code returns an AtomGroup of every second element from the first to the 6th element, corresponding to indices 0, 2, and 4.
+Slicing returns another AtomGroup. The below code returns an AtomGroup of every second element from the first to the 6th element, corresponding to indices 0, 2, and 4.
In [6]: ag = u.atoms[0:6:2]
In [7]: ag.indices
@@ -247,7 +247,7 @@ Indexing and slicingOut[9]: array([ 0, 3, 47680, 10, 3])
-Boolean indexing allows you to pass in an array of True or False values to create a new AtomGroup from another. The array must be the same length as the original AtomGroup. This allows you to select atoms on conditions.
+Boolean indexing allows you to pass in an array of True or False values to create a new AtomGroup from another. The array must be the same length as the original AtomGroup. This allows you to select atoms on conditions.
In [10]: arr = u.atoms.resnames == 'ARG'
In [11]: len(arr) == len(u.atoms)
@@ -261,7 +261,7 @@ Indexing and slicing
Group operators and set methods
-MDAnalysis supports a number of ways to compare AtomGroups or construct a new one: group operators (e.g. concatenate(), subtract()) and set methods (e.g. union(), difference()). Group operators achieve a similar outcome to set methods. However, a key difference is that concatenate() and subtract() preserve the order of the atoms and any duplicates. union() and difference() return an AtomGroup where each atom is unique, and ordered by its topology index.
+MDAnalysis supports a number of ways to compare AtomGroups or construct a new one: group operators (e.g. concatenate(), subtract()) and set methods (e.g. union(), difference()). Group operators achieve a similar outcome to set methods. However, a key difference is that concatenate() and subtract() preserve the order of the atoms and any duplicates. union() and difference() return an AtomGroup where each atom is unique, and ordered by its topology index.
In [14]: ag1 = u.atoms[1:6]
In [15]: ag2 = u.atoms[8:3:-1]
@@ -312,7 +312,7 @@ Group operators and set methodsAtoms.
+
Each of these methods create groups that are sorted sets of unique Atoms.
Operation
Group operators and set methods
Groupby and split
-An AtomGroup can be constructed from another by separating atoms by properties.
-AtomGroup.split can create a list of AtomGroups by splitting another AtomGroup by the ‘level’ of connectivity: one of atom, residue, molecule, or segment.
+An AtomGroup can be constructed from another by separating atoms by properties.
+AtomGroup.split can create a list of AtomGroups by splitting another AtomGroup by the ‘level’ of connectivity: one of atom, residue, molecule, or segment.
In [20]: ag1 = u.atoms[:100]
In [21]: ag1.split('residue')
@@ -388,7 +388,7 @@ Groupby and split <AtomGroup with 19 atoms>]
-An AtomGroup can also be separated according to values of topology attributes to produce a dictionary of {value:AtomGroup}.
+An AtomGroup can also be separated according to values of topology attributes to produce a dictionary of {value:AtomGroup}.
In [22]: u.atoms.groupby('masses')
Out[22]:
{32.06: <AtomGroup with 7 atoms>,
@@ -412,7 +412,7 @@ Groupby and split
Constructing from Atoms
-An AtomGroup can be created from an iterable of Atom instances:
+An AtomGroup can be created from an iterable of Atom instances:
In [24]: atom1 = u.atoms[4]
In [25]: atom2 = u.atoms[6]
@@ -425,7 +425,7 @@ Constructing from Atoms<AtomGroup [<Atom 5: CA of type C of resname MET, resid 1 and segid SYSTEM and altLoc >, <Atom 7: CB of type C of resname MET, resid 1 and segid SYSTEM and altLoc >, <Atom 3: H2 of type H of resname MET, resid 1 and segid SYSTEM and altLoc >]>
-A neat shortcut for this is to simply add an Atom to another Atom or AtomGroup:
+A neat shortcut for this is to simply add an Atom to another Atom or AtomGroup:
In [29]: ag = atom1 + atom2
In [30]: print(ag)
@@ -437,7 +437,7 @@ Constructing from Atoms<AtomGroup [<Atom 5: CA of type C of resname MET, resid 1 and segid SYSTEM and altLoc >, <Atom 7: CB of type C of resname MET, resid 1 and segid SYSTEM and altLoc >, <Atom 3: H2 of type H of resname MET, resid 1 and segid SYSTEM and altLoc >]>
-An alternative method is to provide a list of indices and the Universe that the Atoms belong to:
+An alternative method is to provide a list of indices and the Universe that the Atoms belong to:
In [33]: ag = mda.AtomGroup([4, 6, 2], u)
In [34]: print(ag)
@@ -447,22 +447,22 @@ Constructing from Atoms
Order and uniqueness
-These methods of creating an AtomGroup result in a sorted, unique list of atoms:
+These methods of creating an AtomGroup result in a sorted, unique list of atoms:
Atom selection language
Slicing
Boolean indexing
Set methods
AtomGroup.split and AtomGroup.groupby
-These methods return a user-ordered AtomGroup that can contain duplicates:
+These methods return a user-ordered AtomGroup that can contain duplicates:
Fancy indexing (with arrays or lists)
Group operations (AtomGroup.concatenate and AtomGroup.subtract)
Constructing directly from Atoms
Group operations (AtomGroup.concatenate and AtomGroup.subtract)
Constructing directly from Atoms
@@ -475,7 +475,7 @@ Empty AtomGroupsOut[36]: <AtomGroup with 0 atoms>
-The above is the same as creating an AtomGroup from an empty list and a Universe.
+The above is the same as creating an AtomGroup from an empty list and a Universe.
In [37]: mda.AtomGroup([], u)
Out[37]: <AtomGroup with 0 atoms>
@@ -509,7 +509,7 @@ Dynamically updating AtomGroups
Methods
-Most of the analysis functionality in MDAnalysis is implemented in the analysis module, but many interesting methods can be accessed from an AtomGroup directly. For example, Bonds, Angles, Dihedrals and ImproperDihedrals can be created from AtomGroups. Providing that required topology attributes are present, a number of analysis methods are also available to a AtomGroup, ResidueGroup, and SegmentGroup.
+Most of the analysis functionality in MDAnalysis is implemented in the analysis module, but many interesting methods can be accessed from an AtomGroup directly. For example, Bonds, Angles, Dihedrals and ImproperDihedrals can be created from AtomGroups. Providing that required topology attributes are present, a number of analysis methods are also available to a AtomGroup, ResidueGroup, and SegmentGroup.
diff --git a/dev/contributing_code.html b/dev/contributing_code.html
index a0c83db4a..16aa12a83 100644
--- a/dev/contributing_code.html
+++ b/dev/contributing_code.html
@@ -991,7 +991,7 @@ Documenting changes
Writing docs for abstract base classes
-MDAnalysis contains a number of abstract base classes, such as AnalysisBase. Developers who define new base classes, or modify existing ones, should follow these rules:
+MDAnalysis contains a number of abstract base classes, such as AnalysisBase. Developers who define new base classes, or modify existing ones, should follow these rules:
The class docstring needs to contain a list of methods that can be overwritten by inheritance from the base class. Distinguish and document methods as required or optional.
Writing docs for abstract base classesMDAnalysis.analysis.base.AnalysisBase for an example of this documentation.
+
See the documentation of MDAnalysis.analysis.base.AnalysisBase for an example of this documentation.
Adding your documentation to MDAnalysis
diff --git a/dev/examples/analysis/README.html b/dev/examples/analysis/README.html
index 8e4f34632..91af8d79b 100644
--- a/dev/examples/analysis/README.html
+++ b/dev/examples/analysis/README.html
@@ -272,7 +272,7 @@ Imports and dependencies
Alignments and RMS fitting
-The MDAnalysis.analysis.align and MDAnalysis.analysis.rms
+
The MDAnalysis.analysis.align and MDAnalysis.analysis.rms
modules contain the functions used for aligning structures,
aligning trajectories, and calculating root mean squared quantities.
Demonstrations of alignment are in align_structure,
@@ -300,7 +300,7 @@
Imports and dependencies
Distances and contacts
-The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays.
+The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays.
- Atom-wise distances between matching AtomGroups
@@ -309,7 +309,7 @@ Distances and contacts
Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.
-MDAnalysis.analysis.contacts contains functions and a class to analyse the fraction of native contacts over a trajectory.
+MDAnalysis.analysis.contacts contains functions and a class to analyse the fraction of native contacts over a trajectory.
- Fraction of native contacts over a trajectory
diff --git a/dev/examples/analysis/alignment_and_rms/README.html b/dev/examples/analysis/alignment_and_rms/README.html
index 687cfca88..a4cf83c0a 100644
--- a/dev/examples/analysis/alignment_and_rms/README.html
+++ b/dev/examples/analysis/alignment_and_rms/README.html
@@ -212,7 +212,7 @@
Alignments and RMS fitting
-The MDAnalysis.analysis.align and MDAnalysis.analysis.rms
+
The MDAnalysis.analysis.align and MDAnalysis.analysis.rms
modules contain the functions used for aligning structures,
aligning trajectories, and calculating root mean squared quantities.
Demonstrations of alignment are in align_structure,
diff --git a/dev/examples/analysis/distances_and_contacts/README.html b/dev/examples/analysis/distances_and_contacts/README.html
index ea85dab12..3aadbeaf3 100644
--- a/dev/examples/analysis/distances_and_contacts/README.html
+++ b/dev/examples/analysis/distances_and_contacts/README.html
@@ -213,7 +213,7 @@
Distances and contacts
-The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays.
+The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays.
- Atom-wise distances between matching AtomGroups
@@ -222,7 +222,7 @@ Distances and contacts
Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.
-MDAnalysis.analysis.contacts contains functions and a class to analyse the fraction of native contacts over a trajectory.
+MDAnalysis.analysis.contacts contains functions and a class to analyse the fraction of native contacts over a trajectory.
- Fraction of native contacts over a trajectory
diff --git a/dev/examples/analysis/hydrogen_bonds/hbonds.html b/dev/examples/analysis/hydrogen_bonds/hbonds.html
index af2d9cb5b..b15e23ff1 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°
+
Find water-water hydrogen bonds
diff --git a/dev/examples/constructing_universe.html b/dev/examples/constructing_universe.html
index db71f3178..c23f08e42 100644
--- a/dev/examples/constructing_universe.html
+++ b/dev/examples/constructing_universe.html
@@ -715,7 +715,7 @@ Adding a new segmentNMP: residues 30-59 (blue)
LID: residues 122-159 (yellow)
+
[26]:
diff --git a/dev/formats/auxiliary.html b/dev/formats/auxiliary.html
index e5c485c80..c97c1c16f 100644
--- a/dev/formats/auxiliary.html
+++ b/dev/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 0x7f570f9004c0>
+Out[4]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f4cbab38250>
In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.
@@ -283,7 +283,7 @@ Reading data directly50.0
-The auxreader() function uses the get_auxreader_for() to return an appropriate class. This can guess the format either from a filename, ‘
+The auxreader() function uses the get_auxreader_for() to return an appropriate class. This can guess the format either from a filename, ‘
In [7]: mda.auxiliary.core.get_auxreader_for(XVG_BZ2)
Out[7]: MDAnalysis.auxiliary.XVG.XVGReader
@@ -297,9 +297,9 @@ Reading data directly
Loading data into a Universe
Auxiliary data may be added to a trajectory Reader through the
-add_auxiliary() method. Auxiliary data
+add_auxiliary() method. Auxiliary data
may be passed in as a AuxReader instance, or directly as e.g. a filename, in
-which case get_auxreader_for() is used to
+which case get_auxreader_for() is used to
guess an appropriate reader.
In [9]: from MDAnalysis.tests.datafiles import PDB_xvf, TRR_xvf
@@ -355,9 +355,9 @@ Iterating over auxiliary data900.0000610351562 [nan nan nan nan]
-The trajectory ProtoReader methods
-next_as_aux() and
-iter_as_aux() allow for movement
+
The trajectory ProtoReader methods
+next_as_aux() and
+iter_as_aux() allow for movement
through only trajectory timesteps for which auxiliary data is available.
In [17]: for ts in u_long.trajectory.iter_as_aux('protein_force'):
....: print(ts.time, ts.aux.protein_force[:4])
@@ -383,7 +383,7 @@ Iterating over auxiliary dataiter_auxiliary() allows iteration
+iter_auxiliary() allows iteration
over the auxiliary independent of the trajectory.
In [21]: for step in u_short.trajectory.iter_auxiliary('protein_force'):
....: print(step.data)
@@ -409,18 +409,18 @@ Iterating over auxiliary data
Accessing auxiliary attributes
To check the values of attributes of an added auxiliary, use
-get_aux_attribute().
+get_aux_attribute().
In [23]: u.trajectory.get_aux_attribute('protein_force', 'dt')
Out[23]: 50.0
If attributes are settable, they can be changed using
-set_aux_attribute().
+set_aux_attribute().
In [24]: u.trajectory.set_aux_attribute('protein_force', 'data_selector', [1])
The auxiliary may be renamed using set_aux_attribute with ‘auxname’, or more
-directly by using rename_aux().
+directly by using rename_aux().
In [25]: u.trajectory.ts.aux.protein_force
Out[25]:
array([ 0. , 200.71288, -1552.2849 , ..., 128.4072 ,
@@ -438,9 +438,9 @@ Accessing auxiliary attributes
Recreating auxiliaries
To recreate an auxiliary, the set of attributes necessary to replicate it can
-first be obtained with get_description().
+first be obtained with get_description().
The returned dictionary can then be passed to
-auxreader() to load a new copy of the
+auxreader() to load a new copy of the
original auxiliary reader.
In [28]: description = aux.get_description()
@@ -460,15 +460,15 @@ Recreating auxiliariesIn [30]: del aux
In [31]: mda.auxiliary.core.auxreader(**description)
-Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f571d14d0d0>
+Out[31]: <MDAnalysis.auxiliary.XVG.XVGReader at 0x7f4cbb093cd0>
The ‘description’ of any or all the auxiliaries added to a trajectory can be
-obtained using get_aux_descriptions().
+obtained using get_aux_descriptions().
In [32]: descriptions = u.trajectory.get_aux_descriptions(['f'])
-To reload, pass the dictionary into add_auxiliary().
+To reload, pass the dictionary into add_auxiliary().
In [33]: u2 = mda.Universe(PDB, TRR)
In [34]: for desc in descriptions:
@@ -575,7 +575,7 @@ Standalone UsageIn [45]: import matplotlib.pyplot as plt
In [46]: plt.plot(temp["Time"], temp["Temperature"])
-Out[46]: [<matplotlib.lines.Line2D at 0x7f571c362970>]
+Out[46]: [<matplotlib.lines.Line2D at 0x7f4cba732160>]
In [47]: plt.ylabel("Temperature [K]")
Out[47]: Text(0, 0.5, 'Temperature [K]')
diff --git a/dev/formats/guessing.html b/dev/formats/guessing.html
index 38063ba07..cd68f2bdf 100644
--- a/dev/formats/guessing.html
+++ b/dev/formats/guessing.html
@@ -238,7 +238,7 @@ Bonds, Angles, Dihedrals, Impropers4
-The method available to users is AtomGroup.guess_bonds, which allows users to pass in a dictionary of van der Waals’ radii for atom types. This guesses bonds, angles, and dihedrals (but not impropers) for the specified AtomGroup and adds it to the underlying Universe.
+The method available to users is AtomGroup.guess_bonds, which allows users to pass in a dictionary of van der Waals’ radii for atom types. This guesses bonds, angles, and dihedrals (but not impropers) for the specified AtomGroup and adds it to the underlying Universe.
diff --git a/dev/formats/reference/chemfiles.html b/dev/formats/reference/chemfiles.html
index c7be23b17..cd82d3f65 100644
--- a/dev/formats/reference/chemfiles.html
+++ b/dev/formats/reference/chemfiles.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.chemfiles.ChemfilesReader
Coordinate writer
MDAnalysis.coordinates.chemfiles.ChemfilesWriter
diff --git a/dev/formats/reference/config.html b/dev/formats/reference/config.html
index 9d449f9cd..79232ae50 100644
--- a/dev/formats/reference/config.html
+++ b/dev/formats/reference/config.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.DLPoly.ConfigReader
Topology parser
MDAnalysis.topology.DLPolyParser.ConfigParser
@@ -244,10 +244,10 @@
Coordinate reader
MDAnalysis.coordinates.DLPoly.HistoryReader
Topology parser
MDAnalysis.topology.DLPolyParser.HistoryParser
diff --git a/dev/formats/reference/coor.html b/dev/formats/reference/coor.html
index 67f46a6f6..8e8a48e8d 100644
--- a/dev/formats/reference/coor.html
+++ b/dev/formats/reference/coor.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.NAMDBIN.NAMDBINReader
Coordinate writer
MDAnalysis.coordinates.NAMDBIN.NAMDBINWriter
diff --git a/dev/formats/reference/crd.html b/dev/formats/reference/crd.html
index 44d26e866..a5dae2fd7 100644
--- a/dev/formats/reference/crd.html
+++ b/dev/formats/reference/crd.html
@@ -235,13 +235,13 @@
Coordinate reader
MDAnalysis.coordinates.CRD.CRDReader
Coordinate writer
MDAnalysis.coordinates.CRD.CRDWriter
Topology parser
MDAnalysis.topology.CRDParser.CRDParser
diff --git a/dev/formats/reference/data.html b/dev/formats/reference/data.html
index 8bcd4a623..dfad31367 100644
--- a/dev/formats/reference/data.html
+++ b/dev/formats/reference/data.html
@@ -235,13 +235,13 @@
Coordinate reader
MDAnalysis.coordinates.LAMMPS.DATAReader
Coordinate writer
MDAnalysis.coordinates.LAMMPS.DATAWriter
Topology parser
MDAnalysis.topology.LAMMPSParser.DATAParser
diff --git a/dev/formats/reference/dcd.html b/dev/formats/reference/dcd.html
index e27970a3b..aa8ed3557 100644
--- a/dev/formats/reference/dcd.html
+++ b/dev/formats/reference/dcd.html
@@ -235,10 +235,10 @@
Coordinate reader
MDAnalysis.coordinates.DCD.DCDReader
Coordinate writer
MDAnalysis.coordinates.DCD.DCDWriter
@@ -246,7 +246,7 @@
Reading in
Unitcell dimensions
-Generally, DCD trajectories produced by any code can be read (with the DCDReader) although there can be issues with the unitcell dimensions (simulation box).
+
Generally, DCD trajectories produced by any code can be read (with the DCDReader) although there can be issues with the unitcell dimensions (simulation box).
Currently, MDAnalysis tries to guess the correct format for the unitcell representation but it can be wrong.
Check the unitcell dimensions, especially for triclinic unitcells (see Issue 187).
MDAnalysis always uses (*A*, *B*, *C*, *alpha*, *beta*, *gamma*) to
diff --git a/dev/formats/reference/dcd_lammps.html b/dev/formats/reference/dcd_lammps.html
index d921ff99e..dc4bd4c76 100644
--- a/dev/formats/reference/dcd_lammps.html
+++ b/dev/formats/reference/dcd_lammps.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.LAMMPS.DCDReader
Coordinate writer
MDAnalysis.coordinates.LAMMPS.DCDWriter
@@ -249,9 +249,9 @@
the unit from the file. By default, we assume that the unit for
length is the ångström and the unit for time is the femtosecond. If this is
not true, then the user should supply the appropriate units in the
-keywords timeunit and/or lengthunit to DCDWriter and
-Universe (which then calls
-DCDReader).
+keywords timeunit and/or lengthunit to DCDWriter and
+Universe (which then calls
+DCDReader).
diff --git a/dev/formats/reference/dms.html b/dev/formats/reference/dms.html
index f46214b89..0edfc57ae 100644
--- a/dev/formats/reference/dms.html
+++ b/dev/formats/reference/dms.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.DMS.DMSReader
Topology parser
MDAnalysis.topology.DMSParser.DMSParser
diff --git a/dev/formats/reference/gms.html b/dev/formats/reference/gms.html
index 2ceaa305d..aca8b819e 100644
--- a/dev/formats/reference/gms.html
+++ b/dev/formats/reference/gms.html
@@ -234,10 +234,10 @@
Coordinate reader
MDAnalysis.coordinates.GMS.GMSReader
Topology parser
MDAnalysis.topology.GMSParser.GMSParser
diff --git a/dev/formats/reference/gro.html b/dev/formats/reference/gro.html
index 90ab78529..413ac29b6 100644
--- a/dev/formats/reference/gro.html
+++ b/dev/formats/reference/gro.html
@@ -235,13 +235,13 @@
Coordinate reader
MDAnalysis.coordinates.GRO.GROReader
Coordinate writer
MDAnalysis.coordinates.GRO.GROWriter
Topology parser
MDAnalysis.topology.GROParser.GROParser
diff --git a/dev/formats/reference/gsd.html b/dev/formats/reference/gsd.html
index fc01b8e13..db11fe82e 100644
--- a/dev/formats/reference/gsd.html
+++ b/dev/formats/reference/gsd.html
@@ -234,10 +234,10 @@
Coordinate reader
MDAnalysis.coordinates.GSD.GSDReader
Topology parser
MDAnalysis.topology.GSDParser.GSDParser
diff --git a/dev/formats/reference/in.html b/dev/formats/reference/in.html
index 83cb7d399..6d0026216 100644
--- a/dev/formats/reference/in.html
+++ b/dev/formats/reference/in.html
@@ -231,13 +231,13 @@
Coordinate reader
MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader
Coordinate writer
MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter
Topology parser
MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser
diff --git a/dev/formats/reference/inpcrd.html b/dev/formats/reference/inpcrd.html
index 1f7f7090b..6b9429622 100644
--- a/dev/formats/reference/inpcrd.html
+++ b/dev/formats/reference/inpcrd.html
@@ -231,7 +231,7 @@
Coordinate reader
MDAnalysis.coordinates.INPCRD.INPReader
diff --git a/dev/formats/reference/itp.html b/dev/formats/reference/itp.html
index 9c7250ba8..8b6e3d702 100644
--- a/dev/formats/reference/itp.html
+++ b/dev/formats/reference/itp.html
@@ -231,7 +231,7 @@
Topology parser
MDAnalysis.topology.ITPParser.ITPParser
diff --git a/dev/formats/reference/lammpsdump.html b/dev/formats/reference/lammpsdump.html
index 2448dc65a..e5da651c6 100644
--- a/dev/formats/reference/lammpsdump.html
+++ b/dev/formats/reference/lammpsdump.html
@@ -234,10 +234,10 @@
Coordinate reader
MDAnalysis.coordinates.LAMMPS.DumpReader
Topology parser
MDAnalysis.topology.LAMMPSParser.LammpsDumpParser
diff --git a/dev/formats/reference/mmtf.html b/dev/formats/reference/mmtf.html
index 8f7dba107..dc39cd1fc 100644
--- a/dev/formats/reference/mmtf.html
+++ b/dev/formats/reference/mmtf.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.MMTF.MMTFReader
Topology parser
MDAnalysis.topology.MMTFParser.MMTFParser
diff --git a/dev/formats/reference/mol2.html b/dev/formats/reference/mol2.html
index 17672707b..68e2ff311 100644
--- a/dev/formats/reference/mol2.html
+++ b/dev/formats/reference/mol2.html
@@ -234,20 +234,20 @@
Coordinate reader
MDAnalysis.coordinates.MOL2.MOL2Reader
Coordinate writer
MDAnalysis.coordinates.MOL2.MOL2Writer
Topology parser
MDAnalysis.topology.MOL2Parser.MOL2Parser
The Tripos molecule structure format (MOL2) is a commonly used format. It is used, for instance, by the DOCK docking code.
Warning
-MOL2Writer can only be used to write out previously loaded MOL2 files.
+
MOL2Writer can only be used to write out previously loaded MOL2 files.
For example, if you’re trying to convert a PDB file to MOL2, you should
use other tools such as rdkit.
Here is an example how to use rdkit to convert a PDB to MOL:
diff --git a/dev/formats/reference/ncdf.html b/dev/formats/reference/ncdf.html
index fa23aa3c8..9b0e24784 100644
--- a/dev/formats/reference/ncdf.html
+++ b/dev/formats/reference/ncdf.html
@@ -235,10 +235,10 @@
Coordinate reader
MDAnalysis.coordinates.TRJ.NCDFReader
Coordinate writer
MDAnalysis.coordinates.TRJ.NCDFWriter
diff --git a/dev/formats/reference/parmed.html b/dev/formats/reference/parmed.html
index 743aeda30..190a30b1e 100644
--- a/dev/formats/reference/parmed.html
+++ b/dev/formats/reference/parmed.html
@@ -231,13 +231,13 @@
Converter
MDAnalysis.converters.ParmEd.ParmEdConverter
Coordinate reader
MDAnalysis.converters.ParmEd.ParmEdReader
Topology parser
MDAnalysis.converters.ParmEdParser.ParmEdParser
diff --git a/dev/formats/reference/pdb.html b/dev/formats/reference/pdb.html
index f13426e05..fc2e44dae 100644
--- a/dev/formats/reference/pdb.html
+++ b/dev/formats/reference/pdb.html
@@ -236,13 +236,13 @@
Coordinate reader
MDAnalysis.coordinates.PDB.PDBReader
Coordinate writer
MDAnalysis.coordinates.PDB.PDBWriter
Topology parser
MDAnalysis.topology.PDBParser.PDBParser
diff --git a/dev/formats/reference/pdbqt.html b/dev/formats/reference/pdbqt.html
index e8ea38394..a6398eaa6 100644
--- a/dev/formats/reference/pdbqt.html
+++ b/dev/formats/reference/pdbqt.html
@@ -236,13 +236,13 @@
Coordinate reader
MDAnalysis.coordinates.PDBQT.PDBQTReader
Coordinate writer
MDAnalysis.coordinates.PDBQT.PDBQTWriter
Topology parser
MDAnalysis.topology.PDBQTParser.PDBQTParser
diff --git a/dev/formats/reference/pqr.html b/dev/formats/reference/pqr.html
index 017951b75..3e231181a 100644
--- a/dev/formats/reference/pqr.html
+++ b/dev/formats/reference/pqr.html
@@ -236,13 +236,13 @@
Coordinate reader
MDAnalysis.coordinates.PQR.PQRReader
Coordinate writer
MDAnalysis.coordinates.PQR.PQRWriter
Topology parser
MDAnalysis.topology.PQRParser.PQRParser
diff --git a/dev/formats/reference/psf.html b/dev/formats/reference/psf.html
index a8e45ca97..4e9dae65a 100644
--- a/dev/formats/reference/psf.html
+++ b/dev/formats/reference/psf.html
@@ -235,7 +235,7 @@
Topology parser
MDAnalysis.topology.PSFParser.PSFParser
diff --git a/dev/formats/reference/tng.html b/dev/formats/reference/tng.html
index a286c1bed..f8c6712da 100644
--- a/dev/formats/reference/tng.html
+++ b/dev/formats/reference/tng.html
@@ -234,7 +234,7 @@
Coordinate reader
MDAnalysis.coordinates.TNG.TNGReader
diff --git a/dev/formats/reference/top.html b/dev/formats/reference/top.html
index a29ecee48..bb942c983 100644
--- a/dev/formats/reference/top.html
+++ b/dev/formats/reference/top.html
@@ -235,7 +235,7 @@
Topology parser
MDAnalysis.topology.TOPParser.TOPParser
diff --git a/dev/formats/reference/tpr.html b/dev/formats/reference/tpr.html
index a2d803a04..8ad300b24 100644
--- a/dev/formats/reference/tpr.html
+++ b/dev/formats/reference/tpr.html
@@ -240,7 +240,7 @@
Topology parser
MDAnalysis.topology.TPRParser.TPRParser
diff --git a/dev/formats/reference/trj.html b/dev/formats/reference/trj.html
index 111aaab82..471dee966 100644
--- a/dev/formats/reference/trj.html
+++ b/dev/formats/reference/trj.html
@@ -234,7 +234,7 @@
Coordinate reader
MDAnalysis.coordinates.TRJ.TRJReader
@@ -245,7 +245,7 @@
suffix ‘.crd’. This extension conflicts with the CHARMM CRD
format and MDAnalysis will not correctly autodetect AMBER “.crd”
trajectories. Instead, explicitly provide the format="TRJ"
-argument to Universe:
+argument to Universe:
u = MDAnalysis.Universe("top.prmtop", "traj.crd", format="TRJ")
diff --git a/dev/formats/reference/trr.html b/dev/formats/reference/trr.html
index a777e7281..1412ad617 100644
--- a/dev/formats/reference/trr.html
+++ b/dev/formats/reference/trr.html
@@ -236,10 +236,10 @@
Coordinate reader
MDAnalysis.coordinates.TRR.TRRReader
Coordinate writer
MDAnalysis.coordinates.TRR.TRRWriter
diff --git a/dev/formats/reference/trz.html b/dev/formats/reference/trz.html
index 462442982..9f948596e 100644
--- a/dev/formats/reference/trz.html
+++ b/dev/formats/reference/trz.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.TRZ.TRZReader
Coordinate writer
MDAnalysis.coordinates.TRZ.TRZWriter
diff --git a/dev/formats/reference/txyz.html b/dev/formats/reference/txyz.html
index a732d8a37..a1aea7944 100644
--- a/dev/formats/reference/txyz.html
+++ b/dev/formats/reference/txyz.html
@@ -234,10 +234,10 @@
Coordinate reader
MDAnalysis.coordinates.TXYZ.TXYZReader
Topology parser
MDAnalysis.topology.TXYZParser.TXYZParser
diff --git a/dev/formats/reference/xml.html b/dev/formats/reference/xml.html
index 7704c6a3e..f5dc50b96 100644
--- a/dev/formats/reference/xml.html
+++ b/dev/formats/reference/xml.html
@@ -232,7 +232,7 @@
Topology parser
MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser
diff --git a/dev/formats/reference/xpdb.html b/dev/formats/reference/xpdb.html
index 1ffd33c14..ac17d57fe 100644
--- a/dev/formats/reference/xpdb.html
+++ b/dev/formats/reference/xpdb.html
@@ -231,10 +231,10 @@
Coordinate reader
MDAnalysis.coordinates.PDB.ExtendedPDBReader
Topology parser
MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser
diff --git a/dev/formats/reference/xtc.html b/dev/formats/reference/xtc.html
index 8e6c4438f..3650e5869 100644
--- a/dev/formats/reference/xtc.html
+++ b/dev/formats/reference/xtc.html
@@ -234,10 +234,10 @@
Coordinate reader
MDAnalysis.coordinates.XTC.XTCReader
Coordinate writer
MDAnalysis.coordinates.XTC.XTCWriter
diff --git a/dev/formats/reference/xyz.html b/dev/formats/reference/xyz.html
index 8b3a241d1..20b546e8f 100644
--- a/dev/formats/reference/xyz.html
+++ b/dev/formats/reference/xyz.html
@@ -238,13 +238,13 @@
Coordinate reader
MDAnalysis.coordinates.XYZ.XYZReader
Coordinate writer
MDAnalysis.coordinates.XYZ.XYZWriter
Topology parser
MDAnalysis.topology.XYZParser.XYZParser
diff --git a/dev/formats/selection_exporters.html b/dev/formats/selection_exporters.html
index 9524e9b70..635a39351 100644
--- a/dev/formats/selection_exporters.html
+++ b/dev/formats/selection_exporters.html
@@ -212,27 +212,27 @@
str
CHARMM selection of individual atoms
MDAnalysis.selections.charmm.SelectionWriter
ndx
GROMACS index file
MDAnalysis.selections.gromacs.SelectionWriter
spt
Jmol selection commands
MDAnalysis.selections.jmol.SelectionWriter
pml
PyMOL selection string
MDAnalysis.selections.pymol.SelectionWriter
vmd
VMD macros, available in Representations
MDAnalysis.selections.vmd.SelectionWriter
@@ -241,7 +241,7 @@ Writing selections
Single AtomGroup
The typical situation is that one has an
-AtomGroup and wants to work with the
+AtomGroup and wants to work with the
same selection of atoms in a different package, for example, to
visualize the atoms in VMD.
In [1]: import MDAnalysis as mda
@@ -253,7 +253,7 @@ Single AtomGroupIn [4]: ag = u.select_atoms('resname ALA')
-As with a normal structure file, use AtomGroup.write method with the appropriate file extension.
+As with a normal structure file, use AtomGroup.write method with the appropriate file extension.
ag.write("ala_selection.vmd", name="alanine")
@@ -265,11 +265,11 @@ Single AtomGroupGraphics ‣
Representations window in the list Selections: Singlewords as
“alanine”.
-Names are not always required; if name is not passed to AtomGroup.write, MDAnalysis defaults to “mdanalysis001”, “mdanalysis002”, and so on.
+Names are not always required; if name is not passed to AtomGroup.write, MDAnalysis defaults to “mdanalysis001”, “mdanalysis002”, and so on.
Multiple selections
-AtomGroup.write can take additional keyword arguments, including mode. The default is mode='w', which will overwrite the provided filename. If mode='a', the selection is appended to the file.
+AtomGroup.write can take additional keyword arguments, including mode. The default is mode='w', which will overwrite the provided filename. If mode='a', the selection is appended to the file.
u.select_atoms('resname T*').write('residues.ndx',
name='TYR_THR',
mode='a')
@@ -302,7 +302,7 @@ Multiple selections'ri': residue index
-Alternatively, you can direcly use the selection writer itself as a context manager and write each AtomGroup inside the context. For example:
+Alternatively, you can direcly use the selection writer itself as a context manager and write each AtomGroup inside the context. For example:
with mda.selections.gromacs.SelectionWriter('residues.ndx', mode='w') as ndx:
ndx.write(u.select_atoms('resname T*'),
name='TYR_THR')
diff --git a/dev/groups_of_atoms.html b/dev/groups_of_atoms.html
index 4d4df5d38..82389f0ca 100644
--- a/dev/groups_of_atoms.html
+++ b/dev/groups_of_atoms.html
@@ -198,13 +198,13 @@
Groups of atoms
-MDAnalysis has a hierarchy of Atom containers that are used throughout the code.
+MDAnalysis has a hierarchy of Atom containers that are used throughout the code.
-First and foremost is the AtomGroup. An AtomGroup is the primary Atom container; virtually everything can be accessed through it, as detailed in AtomGroup. This includes chemically meaningful groups of Atoms such as a Residue or a Segment.
+First and foremost is the AtomGroup. An AtomGroup is the primary Atom container; virtually everything can be accessed through it, as detailed in AtomGroup. This includes chemically meaningful groups of Atoms such as a Residue or a Segment.
Residues and Segments
-A Residue is composed of Atoms, and a Segment is composed of Residues.
-The corresponding container groups are ResidueGroup and SegmentGroup. These have similar properties and available methods as AtomGroup.
+A Residue is composed of Atoms, and a Segment is composed of Residues.
+The corresponding container groups are ResidueGroup and SegmentGroup. These have similar properties and available methods as AtomGroup.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import TPR, XTC
@@ -232,7 +232,7 @@
Out[8]: <AtomGroup with 3341 atoms>
-Similarly, an Atom has direct knowledge of the Residue and Segment it belongs to. Note that an Atom belongs to one Residue and the residue belongs to one Segment, but a Segment has multiple residues.
+Similarly, an Atom has direct knowledge of the Residue and Segment it belongs to. Note that an Atom belongs to one Residue and the residue belongs to one Segment, but a Segment has multiple residues.
In [9]: a = u.atoms[0]
In [10]: a.residue
@@ -246,9 +246,9 @@
For information on adding custom Residues or Segments, have a look at Adding a Residue or Segment to a Universe.
-Access to other classes via the AtomGroup object can be pretty powerful, but also
+
Access to other classes via the AtomGroup object can be pretty powerful, but also
needs to be used with caution to avoid accessing data outside the intended selection. Therefore, we present two use
-cases showing commonly used applications, for which we define Universe
+cases showing commonly used applications, for which we define Universe
on a simple extract from the PDB file:
In [9]: import MDAnalysis as mda
@@ -306,7 +306,7 @@ Use case: Sequence of residues by segmentOut[15]: [array(['GLY'], dtype=object), array(['ALA', 'GLY'], dtype=object)]
-Note that accessing residues by first selecting the segments of an AtomGroup returns
+
Note that accessing residues by first selecting the segments of an AtomGroup returns
all the residues in that segment for both the ATOM and HETATM record types (no memory of the original selection).
The meaning of this is: “give me all residue names from segments in which there is at least one of the selected atoms”.
In [16]: selected_atoms = u.select_atoms("record_type ATOM")
@@ -349,10 +349,10 @@ Use case: Atoms list grouped by residues array(['N', 'CA', 'C', 'O'], dtype=object)]
-Note that accessing atoms by first selecting the residues of an AtomGroup also
+
Note that accessing atoms by first selecting the residues of an AtomGroup also
returns hydrogen atoms (no memory of the original selection). The meaning of this is “give me all atom names from
residues in which there is at least one of the selected atoms”. However, it doesn’t contain a nitrogen atom from XYZ
-residue as no atoms from this residue were in the AtomGroup.
+residue as no atoms from this residue were in the AtomGroup.
In [24]: all_atoms_in_residues = list()
In [25]: for seg in u.segments:
@@ -373,7 +373,7 @@ Use case: Atoms list grouped by residues
Fragments
Certain analysis methods in MDAnalysis also make use of additional ways to group atoms. A key concept is a fragment. A fragment is what is typically considered a molecule: an AtomGroup where any atom is reachable from any other atom in the AtomGroup by traversing bonds, and none of its atoms is bonded to any atoms outside the AtomGroup. (A ‘molecule’ in MDAnalysis methods refers to a GROMACS-specific concept). The fragments of a Universe are determined by MDAnalysis as a derived quantity. They can only be determined if bond information is available.
-The fragments of an AtomGroup are accessible via the fragments property. Below is a Universe from a GROMACS TPR file of lysozyme (PDB ID: 2LYZ) with 101 water molecules. While it has 230 residues, there are only 102 fragments: 1 protein and 101 water fragments.
+The fragments of an AtomGroup are accessible via the fragments property. Below is a Universe from a GROMACS TPR file of lysozyme (PDB ID: 2LYZ) with 101 water molecules. While it has 230 residues, there are only 102 fragments: 1 protein and 101 water fragments.
In [27]: from MDAnalysis.tests.datafiles import TPR2021
In [28]: u = mda.Universe(TPR2021)
@@ -386,19 +386,19 @@ FragmentsTopology objects for more on bonds and which file formats give MDAnalysis bond information.
-
You can also look at which fragment a particular Atom belongs to:
+You can also look at which fragment a particular Atom belongs to:
In [31]: u.atoms[0].fragment # first atom of lysozyme
Out[31]: <AtomGroup with 1960 atoms>
-and see which fragments are associated with atoms in a smaller AtomGroup:
+and see which fragments are associated with atoms in a smaller AtomGroup:
In [32]: u.atoms[1959:1961].fragments
Out[32]: (<AtomGroup with 1960 atoms>, <AtomGroup with 3 atoms>)
Note
-AtomGroup.fragments returns a tuple of fragments with at least one Atom in the AtomGroup, not a tuple of fragments where all Atoms are in the AtomGroup.
+AtomGroup.fragments returns a tuple of fragments with at least one Atom in the AtomGroup, not a tuple of fragments where all Atoms are in the AtomGroup.
diff --git a/dev/preparing_releases_and_hotfixes.html b/dev/preparing_releases_and_hotfixes.html
index 8e6d14e29..d180e2664 100644
--- a/dev/preparing_releases_and_hotfixes.html
+++ b/dev/preparing_releases_and_hotfixes.html
@@ -265,7 +265,7 @@ Summary of tasks
Getting the develop branch ready for a release
-Declare feature freeze on develop via discord and `GitHub Discussions (Anouncement)`_
Declare feature freeze on develop via discord and GitHub Discussions (Announcement)
Create a pre-release feature branch from develop
Finalise the CHANGELOG with the release number and date. Ensure that the CHANGELOG summarizes important changes and includes all authors that contributed to this release.
Make sure the version number matches the release version. The following files need to be updated: package/MDAnalysis/version.py, package/setup.py, testsuite/MDAnalysisTests/__init__.py, and testsuite/setup.py.
Input
Note
While you can set continuous=True for either XTC or TRR files, you cannot mix different formats.
-More information can be found at the API reference for ChainReader.
+More information can be found at the API reference for ChainReader.
Trajectory formats
-If no format keyword is provided, ChainReader will try to guess the format for each file from its extension. You can force ChainReader to use the same format for every file by using the format keyword. You can also specify which format to use by file, by passing in a sequence of (filename, format) tuples.
+If no format keyword is provided, ChainReader will try to guess the format for each file from its extension. You can force ChainReader to use the same format for every file by using the format keyword. You can also specify which format to use by file, by passing in a sequence of (filename, format) tuples.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import PDB, GRO
@@ -267,33 +267,33 @@ Reading trajectories into memoryAtomGroup.positions) without having
+AtomGroup.positions) without having
to write the entire state to file.
-
The most straightforward way to do this is to pass in_memory=True to Universe, which
+
The most straightforward way to do this is to pass in_memory=True to Universe, which
automatically transfers a trajectory to memory:
In [5]: from MDAnalysis.tests.datafiles import TPR, XTC
In [6]: universe = mda.Universe(TPR, XTC, in_memory=True)
-MDAnalysis uses the MemoryReader class to load this data in.
+MDAnalysis uses the MemoryReader class to load this data in.
Transferring trajectories into memory
The decision to transfer the trajectory to memory can be made at any
time with the
-transfer_to_memory() method
-of a Universe:
+transfer_to_memory() method
+of a Universe:
In [7]: universe = mda.Universe(TPR, XTC)
In [8]: universe.transfer_to_memory()
-This operation may take a while (passing verbose=True to transfer_to_memory() will display a progress bar). However, subsequent operations on the trajectory will be very fast.
+This operation may take a while (passing verbose=True to transfer_to_memory() will display a progress bar). However, subsequent operations on the trajectory will be very fast.
Building trajectories in memory
-MemoryReader can also be used to directly generate a trajectory as a numpy array.
+MemoryReader can also be used to directly generate a trajectory as a numpy array.
In [9]: from MDAnalysisTests.datafiles import PDB
In [10]: from MDAnalysis.coordinates.memory import MemoryReader
@@ -313,20 +313,20 @@ Building trajectories in memory [ 62.961, 47.239, 3.753]], dtype=float32)
-The load_new() method can be used to load coordinates into a Universe, replacing the old coordinates:
+The load_new() method can be used to load coordinates into a Universe, replacing the old coordinates:
In [14]: coordinates = np.random.rand(len(universe.atoms), 3)
In [15]: universe.load_new(coordinates, format=MemoryReader);
In [16]: universe.atoms.positions
Out[16]:
-array([[0.2858177 , 0.817896 , 0.67939776],
- [0.26678166, 0.6052552 , 0.8945049 ],
- [0.5940016 , 0.5817606 , 0.23828323],
+array([[0.22061782, 0.38768739, 0.83270067],
+ [0.98391145, 0.46591026, 0.23064709],
+ [0.1486696 , 0.68450224, 0.74135923],
...,
- [0.44501126, 0.8171845 , 0.72477216],
- [0.12251966, 0.71526116, 0.59587806],
- [0.48403212, 0.8573202 , 0.18094209]], dtype=float32)
+ [0.60320765, 0.67722976, 0.9369782 ],
+ [0.7628681 , 0.384521 , 0.4095801 ],
+ [0.95057976, 0.8024004 , 0.4677577 ]], 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([[0.2858177 , 0.817896 , 0.67939776],
- [0.26678166, 0.6052552 , 0.8945049 ],
- [0.5940016 , 0.5817606 , 0.23828323],
+array([[0.22061782, 0.38768739, 0.83270067],
+ [0.98391145, 0.46591026, 0.23064709],
+ [0.1486696 , 0.68450224, 0.74135923],
...,
- [0.44501126, 0.8171845 , 0.72477216],
- [0.12251966, 0.71526116, 0.59587806],
- [0.48403212, 0.8573202 , 0.18094209]], dtype=float32)
+ [0.60320765, 0.67722976, 0.9369782 ],
+ [0.7628681 , 0.384521 , 0.4095801 ],
+ [0.95057976, 0.8024004 , 0.4677577 ]], dtype=float32)
@@ -354,7 +354,7 @@ In-memory trajectories of an atom selection
Frames and trajectories
-MDAnalysis Universes can be written out to a number of formats with write(). For example, to write the current frame as a PDB:
+MDAnalysis Universes can be written out to a number of formats with write(). For example, to write the current frame as a PDB:
from MDAnalysis.tests.datafiles import PDB, TRR
u = mda.Universe(PDB, TRR)
ag = u.select_atoms("name CA")
@@ -392,11 +392,11 @@ PicklingOut[22]: <Universe with 3341 atoms>
-As for MDAnalysis.core.groups.AtomGroup, during serialization, it will be pickled with its bound
-MDAnalysis.core.universe.Universe. This means that after unpickling,
-a new MDAnalysis.core.universe.Universe will be created and
-be attached to the new MDAnalysis.core.groups.AtomGroup. If the Universe is serialized
-with its MDAnalysis.core.groups.AtomGroup, they will still be bound together afterwards:
+As for MDAnalysis.core.groups.AtomGroup, during serialization, it will be pickled with its bound
+MDAnalysis.core.universe.Universe. This means that after unpickling,
+a new MDAnalysis.core.universe.Universe will be created and
+be attached to the new MDAnalysis.core.groups.AtomGroup. If the Universe is serialized
+with its MDAnalysis.core.groups.AtomGroup, they will still be bound together afterwards:
In [23]: import pickle
In [24]: from MDAnalysis.tests.datafiles import PSF, DCD
@@ -418,8 +418,8 @@ Picklingg_pickled.universe is u_pickled: True
-If multiple MDAnalysis.core.groups.AtomGroups are bound to the same
-MDAnalysis.core.universe.Universe, they will also be bound to the same one
+
If multiple MDAnalysis.core.groups.AtomGroups are bound to the same
+MDAnalysis.core.universe.Universe, they will also be bound to the same one
after serialization:
In [1]: u = mda.Universe(PSF, DCD)
diff --git a/dev/references.html b/dev/references.html
index c1fc88894..775cead5b 100644
--- a/dev/references.html
+++ b/dev/references.html
@@ -195,7 +195,7 @@
MDAnalysis and the included algorithms are scientific software that
are described in academic publications. Please cite these papers when you use
MDAnalysis in published work.
-It is possible to automatically generate a list of references for any program that uses
+
It is possible to automatically generate a list of references for any program that uses
MDAnalysis. This list (in common reference manager formats) contains
the citations associated with the specific algorithms and libraries
that were used in the program.
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 50c3f3129..a18c4c7c4 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", "preparing_releases_and_hotfixes", "reading_and_writing", "references", "releases", "selections", "standard_selections", "testing", "topology_system", "trajectories/slicing_trajectories", "trajectories/trajectories", "trajectories/transformations", "units", "universe"], "filenames": ["advanced_topology.rst", "atomgroup.rst", "contributing.rst", "contributing_code.rst", "contributing_docs.rst", "datasets.rst", "examples/README.rst", "examples/analysis/README.rst", "examples/analysis/alignment_and_rms/README.rst", "examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb", "examples/analysis/alignment_and_rms/aligning_trajectory.ipynb", "examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb", "examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb", "examples/analysis/alignment_and_rms/rmsd.ipynb", "examples/analysis/alignment_and_rms/rmsf.ipynb", "examples/analysis/custom_parallel_analysis.ipynb", "examples/analysis/custom_trajectory_analysis.ipynb", "examples/analysis/distances_and_contacts/README.rst", "examples/analysis/distances_and_contacts/contacts_custom.ipynb", "examples/analysis/distances_and_contacts/contacts_native_fraction.ipynb", "examples/analysis/distances_and_contacts/contacts_q1q2.ipynb", "examples/analysis/distances_and_contacts/contacts_within_cutoff.ipynb", "examples/analysis/distances_and_contacts/distances_between_atomgroups.ipynb", "examples/analysis/distances_and_contacts/distances_between_selections.ipynb", "examples/analysis/distances_and_contacts/distances_within_selection.ipynb", "examples/analysis/hydrogen_bonds/README.rst", "examples/analysis/hydrogen_bonds/hbonds.ipynb", "examples/analysis/hydrogen_bonds/hbonds-lifetimes.ipynb", "examples/analysis/hydrogen_bonds/hbonds-selections.ipynb", "examples/analysis/polymers_and_membranes/README.rst", "examples/analysis/polymers_and_membranes/hole2.ipynb", "examples/analysis/polymers_and_membranes/polymer.ipynb", "examples/analysis/reduced_dimensions/README.rst", "examples/analysis/reduced_dimensions/diffusion_map.ipynb", "examples/analysis/reduced_dimensions/pca.ipynb", 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"formats/reference/tpr.rst", "formats/reference/trj.rst", "formats/reference/trr.rst", "formats/reference/trz.rst", "formats/reference/txyz.rst", "formats/reference/xml.rst", "formats/reference/xpdb.rst", "formats/reference/xtc.rst", "formats/reference/xyz.rst", "formats/selection_exporters.rst", "formats/topology.rst", "groups_of_atoms.rst", "index.rst", "installation.rst", "module_imports.rst", "preparing_releases_and_hotfixes.rst", "reading_and_writing.rst", "references.rst", "releases.md", "selections.rst", "standard_selections.rst", "testing.rst", "topology_system.rst", "trajectories/slicing_trajectories.rst", "trajectories/trajectories.rst", "trajectories/transformations.rst", "units.rst", "universe.rst"], "titles": ["Advanced topology concepts", "AtomGroup", "Contributing to MDAnalysis", "Contributing to the main codebase", "Contributing to the user guide", "Example data", "Examples", "Analysis", "Alignments and RMS fitting", "Aligning a structure to another", "Aligning a 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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, 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, 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, 99, 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, 33, 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, 100, 101, 102, 108], "_": [2, 13, 26, 31, 44, 48, 87, 99, 102], "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": [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], "export": [3, 4, 5, 48, 53, 104, 106], "workon_hom": 3, "mkdir": 3, "p": [3, 14, 16, 26, 27, 30, 33, 34, 38, 46, 48, 52, 53, 57, 61, 63, 67, 79, 81, 88, 95, 104, 105, 106, 107, 113, 114], "usr": 3, "sh": 3, 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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, 99, 100, 101, 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": 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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, 32, 34, 53, 104, 105, 112], "dataset": [5, 14, 15, 114], "primarili": 5, "workshop": 5, "interfac": [5, 26, 53], "cach": [5, 15, 100], "certain": [5, 7, 13, 17, 19, 21, 30, 40, 42, 53, 57, 61, 66, 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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], 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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], 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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, 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"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 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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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\ No newline at end of file
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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, 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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, 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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, 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], 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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, 99, 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, 33, 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, 100, 101, 102, 108], "_": [2, 13, 26, 31, 44, 48, 87, 99], "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": [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, 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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], "export": [3, 4, 5, 48, 53, 104, 106], "workon_hom": 3, "mkdir": 3, "p": [3, 14, 16, 26, 27, 30, 33, 34, 38, 46, 48, 52, 53, 57, 61, 63, 67, 79, 81, 88, 95, 104, 105, 106, 107, 113, 114], "usr": 3, "sh": 3, 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85], "quit": [3, 15, 34, 44, 96, 100, 114], "low": [3, 7, 12, 14, 32, 42], "256": 3, "increas": [3, 27, 33, 42, 43, 44, 85, 102, 105, 108], "ulimit": 3, "4096": 3, "appli": [3, 13, 16, 19, 30, 33, 36, 38, 42, 43, 44, 98, 104, 105, 106, 109, 111, 112], "high": [3, 4, 7, 14, 15, 32, 34, 42, 45, 52, 85, 106], "limit": [3, 15, 16, 30, 34, 36, 40, 55, 57, 88], "profil": 3, "mix": [3, 46, 103], "forg": [3, 100], "biopython": [3, 101, 105], "80": [3, 16, 19, 81, 82, 105, 106, 110], "networkx": [3, 105], "griddataformat": [3, 101], "mmtf": [3, 58, 59, 61, 97, 101, 106, 109], "joblib": [3, 15, 26], "scipi": [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, 52, 53, 55, 79, 101, 104, 105], "matplotlib": [3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 30, 31, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 49, 53, 57, 101], "tqdm": [3, 27, 105], "43": [3, 49, 57, 103], "threadpoolctl": 3, "fasten": 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"try": [3, 4, 43, 55, 78, 87, 92, 99, 100, 101, 103, 108], "conform": [3, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 32, 33, 34, 37, 38, 41, 42, 43, 44, 45, 46, 53, 83, 104], "strategi": [3, 105], "thu": [3, 4, 53, 87], "79": [3, 52, 81, 82], "charact": [3, 30, 71, 81, 82, 83, 93, 106], "less": [3, 7, 18, 19, 26, 32, 34, 57, 68, 100], "break": [3, 27, 66, 101, 105, 108], "sensibli": 3, "indent": 3, "space": [3, 7, 32, 33, 41, 42, 43, 44, 48, 50, 83, 84, 100, 106, 108], "per": [3, 19, 26, 66, 83, 105, 108], "capitalclass": 3, "capit": 3, "noun": 3, "underscore_method": 3, "lower": [3, 7, 19, 24, 30, 32, 33, 34, 38, 40, 42, 43, 44, 57], "case": [3, 9, 10, 12, 13, 14, 15, 27, 28, 30, 36, 44, 48, 52, 53, 55, 57, 68, 82, 87, 89, 96, 99, 100, 104, 105, 106, 108, 111, 114], "underscor": 3, "id": [3, 13, 23, 24, 26, 42, 43, 44, 45, 50, 61, 65, 66, 69, 75, 83, 84, 87, 98, 104, 106, 109], "pycharm": 3, "extern": [3, 5, 7, 48, 100, 101, 105, 106], "tool": [3, 4, 7, 15, 19, 30, 33, 34, 48, 53, 67, 78, 80, 96, 99, 100, 103], "flake8": 3, "lint": 3, "emac": 3, "vim": 3, "check": [3, 4, 5, 11, 26, 27, 28, 50, 53, 57, 60, 66, 67, 72, 89, 102, 108], "elpi": 3, "autom": [3, 53, 102, 108], "formatt": 3, "autopep8": 3, "yapf": 3, "plugin": [3, 4, 95, 100, 101, 108], "strive": [3, 101, 108], "small": [3, 4, 5, 26, 27, 57, 78, 101, 108], "lightweight": [3, 15, 101], "visual": [3, 4, 14, 15, 48, 96, 100, 105], "reli": [3, 53, 60, 83, 100, 108], "treat": [3, 42, 45, 48, 53, 72, 82, 89, 114], "rule": [3, 4, 44, 99, 102, 106, 108], "setup": [3, 100, 101, 102, 105, 108], "script": [3, 7, 9, 10, 11, 12, 13, 14, 15, 33, 53, 83, 102, 104], "standard": [3, 7, 30, 37, 39, 42, 44, 53, 58, 59, 61, 65, 82, 84, 93, 97, 101, 105, 106], "pyx": 3, "convert": [3, 24, 37, 48, 52, 53, 57, 62, 63, 76, 78, 80, 81, 83, 86, 105, 113], "newer": [3, 86], "than": [3, 13, 14, 15, 18, 19, 26, 28, 30, 36, 40, 42, 50, 53, 57, 60, 65, 71, 75, 83, 88, 99, 105, 106, 108], "alreadi": [3, 7, 11, 14, 16, 33, 34, 46, 50, 53, 66, 99, 100, 106, 109], "forc": [3, 26, 50, 52, 53, 57, 58, 60, 61, 63, 89, 94, 103, 105, 106, 107, 109, 111, 114], "trigger": [3, 102, 108], "convers": [3, 13, 57, 99], "deliv": 3, "who": [3, 4, 7, 16, 101], "automat": [3, 7, 10, 16, 18, 30, 55, 57, 65, 66, 76, 79, 89, 94, 99, 101, 102, 103, 104, 106, 114], "outdat": 3, "place": [3, 10, 34, 94, 99, 102], "final": [3, 10, 13, 15, 19, 39, 40, 48, 87, 102, 106], "fortran": 3, "librari": [3, 9, 10, 14, 15, 19, 33, 34, 39, 46, 48, 50, 55, 58, 61, 62, 79, 80, 85, 99, 101, 102, 104, 105, 108], "dedic": 3, "src": [3, 84, 87], "tree": 3, "lib": [3, 11, 12, 13, 15, 16, 18, 20, 21, 28, 33, 37, 38, 40, 42, 43, 44, 45, 49, 105, 108], "_distanc": 3, "distanc": [3, 6, 8, 13, 15, 16, 18, 19, 21, 26, 27, 30, 32, 33, 36, 38, 40, 42, 44, 50, 52, 53, 60, 105, 106, 109], "coordin": [3, 7, 8, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 28, 30, 32, 33, 34, 36, 38, 39, 42, 43, 44, 45, 49, 50, 52, 55, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 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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, 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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, 99, 100, 101, 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": 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100, "flag": 100, "optimis": 100, "addit": 100, "dataset": 100, "rule": 101, "suit": [101, 108], "core": 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
diff --git a/dev/selections.html b/dev/selections.html
index e6d6dc558..69719e826 100644
--- a/dev/selections.html
+++ b/dev/selections.html
@@ -216,14 +216,14 @@
Out[5]: <AtomGroup with 190 atoms>
-The select_atoms() method of a
-AtomGroup or a
-Universe returns an
-AtomGroup. These two methods have different behaviour: while Universe.select_atoms operates on all the atoms in the universe, AtomGroup.select_atoms only operates on the atoms within the original AtomGroup. A single selection phrase always returns an
-AtomGroup with atoms sorted according to their
+
The select_atoms() method of a
+AtomGroup or a
+Universe returns an
+AtomGroup. These two methods have different behaviour: while Universe.select_atoms operates on all the atoms in the universe, AtomGroup.select_atoms only operates on the atoms within the original AtomGroup. A single selection phrase always returns an
+AtomGroup with atoms sorted according to their
index in the topology. This is to ensure that there are not any duplicates,
which can happen with complicated selections. When order matters, you can pass in multiple phrases.
-This page documents selection keywords and their arguments. select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). For example, you can:
+This page documents selection keywords and their arguments. select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). For example, you can:
Pass in named AtomGroups as arguments:
@@ -445,15 +445,15 @@ Index
- group group-name
selects the atoms in the AtomGroup passed to the function as an
argument named group-name. Only the atoms common to group-name and the
-instance select_atoms() was called
+instance select_atoms() was called
from will be considered, unless group is preceded by the global
keyword. group-name will be included in the parsing just by comparison of
atom indices. This means that it is up to the user to make sure the
group-name group was defined in an appropriate Universe.
- global selection
by default, when issuing
-select_atoms() from an
-AtomGroup, selections and subselections
+select_atoms() from an
+AtomGroup, selections and subselections
are returned intersected with the atoms of that instance. Prefixing a
selection term with global causes its selection to be returned in its
entirety. As an example, the global keyword allows for
@@ -461,20 +461,20 @@
Index
a group that does not contain any proteins. Were global absent, the
result would be an empty selection since the protein subselection would
itself be empty. When calling
-select_atoms() from a
-Universe, global is ignored.
+select_atoms() from a
+Universe, global is ignored.
Dynamic selections
-By default select_atoms() returns an
-AtomGroup, in which the list of atoms is
+
By default select_atoms() returns an
+AtomGroup, in which the list of atoms is
constant across trajectory frame changes. If
-select_atoms() is invoked with named
+select_atoms() is invoked with named
argument updating set to True, an
-UpdatingAtomGroup instance will be returned
+UpdatingAtomGroup instance will be returned
instead.
# A dynamic selection of corner atoms:
In [12]: ag_updating = u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True)
@@ -483,10 +483,10 @@ Index
Out[13]: <AtomGroup with 917 atoms, with selection 'prop x < 5 and prop y < 5 and prop z < 5' on the entire Universe.>
-It behaves just like an AtomGroup
+
It behaves just like an AtomGroup
object, with the difference that the selection expressions are re-evaluated
every time the trajectory frame changes (this happens lazily, only when the
-UpdatingAtomGroup object is accessed so that
+UpdatingAtomGroup object is accessed so that
there is no redundant updating going on):
In [14]: u.trajectory.next()
Out[14]: < Timestep 1 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] >
@@ -498,8 +498,8 @@ Index
Using the group selection keyword for
Preexisting selections and modifiers, one can
make updating selections depend on
-AtomGroup, or even other
-UpdatingAtomGroup, instances.
+AtomGroup, or even other
+UpdatingAtomGroup, instances.
Likewise, making an updating selection from an already updating group will
cause later updates to also reflect the updating of the base group:
Finally, a non-updating selection or a slicing/addition operation made on an
-UpdatingAtomGroup will return a static
-AtomGroup, which will no longer update
+UpdatingAtomGroup will return a static
+AtomGroup, which will no longer update
across frames:
In [20]: static_ag = ag_updating.select_atoms("resid 1:1000")
@@ -533,8 +533,8 @@ Index
Ordered selections
-select_atoms() sorts the atoms
-in the AtomGroup by atom index before
+
select_atoms() sorts the atoms
+in the AtomGroup by atom index before
returning them (this is to eliminate possible duplicates in the
selection). If the ordering of atoms is crucial (for instance when
describing angles or dihedrals) or if duplicate atoms are required
@@ -551,7 +551,7 @@
Index
A shortcut is to provide two or more selections to
-select_atoms(), which then
+select_atoms(), which then
does the concatenation automatically:
In [16]: list(u.select_atoms("resid 3 and name CA", "resid 2 and name CA"))
Out[16]:
diff --git a/dev/standard_selections.html b/dev/standard_selections.html
index 570c39671..fc3585e0a 100644
--- a/dev/standard_selections.html
+++ b/dev/standard_selections.html
@@ -332,10 +332,10 @@ Protein backbone
-CA
N
O
O
CA
C
N
Protein backbone
-DG3
DA
DC3
RG5
RU
DG5
DA3
DC
U
DT
RC
URA
THY
RA
DT3
RG
DG
CYT
A
DC5
DG3
RU3
U
DA5
RU5
DC
RU
DA
RG5
GUA
RA5
ADE
G
A
RU3
GUA
DC5
DT5
G
DC3
DT3
RC5
RG3
ADE
RG3
URA
CYT
T
DA3
RA3
C
RC5
RG
RA
DG5
DT
T
RC3
RC
DG
RU5
C
Nucleic backbone
-C3’
C5’
O5’
C5’
P
O3’
C3’
P
Nucleic backbone
-C5M
C4
N1
C5
O2
O6
C5M
C2
N3
C5
N7
N6
C4
N1
O6
N9
C8
O4
N3
C6
N2
O2
N4
N9
C8
N6
N2
Nucleic sugars
-C3’
C4’
C2’
O4’
O4’
C1’
C3’
C2’
C4’
The topology system
-MDAnalysis groups static data about a Universe into its topology. This is typically loaded from a topology file. Topology information falls into 3 categories:
+MDAnalysis groups static data about a Universe into its topology. This is typically loaded from a topology file. Topology information falls into 3 categories:
-Users will almost never interact directly with a Topology. Modifying atom containers or topology attributes is typically done through Universe. Methods for viewing containers or topology attributes, or for calculating topology object values, are accessed through AtomGroup.
+Users will almost never interact directly with a Topology. Modifying atom containers or topology attributes is typically done through Universe. Methods for viewing containers or topology attributes, or for calculating topology object values, are accessed through AtomGroup.
Topology attributes
-MDAnalysis supports a range of topology attributes for each Atom and AtomGroup. If an attribute is defined for an Atom, it will be for an AtomGroup, and vice versa – however, they are accessed with singular and plural versions of the attribute specifically.
+MDAnalysis supports a range of topology attributes for each Atom and AtomGroup. If an attribute is defined for an Atom, it will be for an AtomGroup, and vice versa – however, they are accessed with singular and plural versions of the attribute specifically.
Canonical attributes
-These attributes are derived for every Universe, including Universes created with empty(). They encode the MDAnalysis order of each object.
+These attributes are derived for every Universe, including Universes created with empty(). They encode the MDAnalysis order of each object.
Atom
Format-specific attributes
Adding TopologyAttrs
-Each of the attributes above can be added to a Universe if it was not available in the file with add_TopologyAttr().
-add_TopologyAttr() takes two arguments:
+Each of the attributes above can be added to a Universe if it was not available in the file with add_TopologyAttr().
+add_TopologyAttr() takes two arguments:
-topologyattr : the singular or plural name of a TopologyAttr, or a MDAnalysis TopologyAttr object. This must already have been defined as a TopologyAttr (see Adding custom TopologyAttrs for an example of adding a custom topology attribute).
topologyattr : the singular or plural name of a TopologyAttr, or a MDAnalysis TopologyAttr object. This must already have been defined as a TopologyAttr (see Adding custom TopologyAttrs for an example of adding a custom topology attribute).
values (optional) : if topologyattr is a string, the values for that attribute. This can be None if the attribute has default values defined, e.g. tempfactors.
@@ -519,7 +519,7 @@ Format-specific attributesOut[6]: array([0., 0., 0., ..., 0., 0., 0.])
-One way to modify topology attributes is to simply replace them with add_TopologyAttr():
+One way to modify topology attributes is to simply replace them with add_TopologyAttr():
In [7]: psf.add_TopologyAttr('tempfactors', range(len(psf.atoms)))
In [8]: psf.atoms.tempfactors
@@ -560,7 +560,7 @@ Modifying TopologyAttrsNote
This method cannot be used with connectivity attributes, i.e. bonds, angles, dihedrals, and impropers.
-Similarly to adding topology attributes with add_TopologyAttr(), the “level” of the attribute matters. Residue attributes can only be assigned to attributes at the Residue or ResidueGroup level. The same applies to attributes for Atoms and Segments. For example, we would get a NotImplementedError if we tried to assign resnames to an AtomGroup.
+Similarly to adding topology attributes with add_TopologyAttr(), the “level” of the attribute matters. Residue attributes can only be assigned to attributes at the Residue or ResidueGroup level. The same applies to attributes for Atoms and Segments. For example, we would get a NotImplementedError if we tried to assign resnames to an AtomGroup.
In [15]: pdb.residues[0].atoms.resnames = ['new_name']
NotImplementedErrorTraceback (most recent call last)
@@ -830,29 +830,29 @@ Modifying TopologyAttrs
Topology objects
-MDAnalysis defines four types of TopologyObject by connectivity:
+MDAnalysis defines four types of TopologyObject by connectivity:
-Bond
Angle
Dihedral
ImproperDihedral
The value of each topology object can be calculated with value().
-Each TopologyObject also contains the following attributes:
+Each TopologyObject also contains the following attributes:
-atoms : the ordered atoms in the object
indices : the ordered atom indices in the object
type : this is either the ‘type’ of the bond/angle/dihedral/improper, or a tuple of the atom types.
atoms : the ordered atoms in the object
indices : the ordered atom indices in the object
type : this is either the ‘type’ of the bond/angle/dihedral/improper, or a tuple of the atom types.
is_guessed : MDAnalysis can guess bonds. This property records if the object was read from a file or guessed.
-Groups of these are held in TopologyGroups. The master groups of TopologyObjects are accessible as properties of a Universe. TopologyObjects are typically read from a file with connectivity information (see the supported formats here). However, they can be created in two ways: by adding them to a Universe, or by creating them from an AtomGroup. Bonds can be guessed based on distance and Van der Waals’ radii with AtomGroup.guess_bonds.
+Groups of these are held in TopologyGroups. The master groups of TopologyObjects are accessible as properties of a Universe. TopologyObjects are typically read from a file with connectivity information (see the supported formats here). However, they can be created in two ways: by adding them to a Universe, or by creating them from an AtomGroup. Bonds can be guessed based on distance and Van der Waals’ radii with AtomGroup.guess_bonds.
Adding to a Universe
-As of version 0.21.0, there are specific methods for adding TopologyObjects to a Universe:
+As of version 0.21.0, there are specific methods for adding TopologyObjects to a Universe:
add_Bonds()
Adding to a UniverseThese accept the following values:
-a TopologyGroup
an iterable of atom indices
an iterable of TopologyObjects
an iterable of TopologyObjects
-Prior to version 0.21.0, objects could be added to a Universe with add_TopologyAttr().
+Prior to version 0.21.0, objects could be added to a Universe with add_TopologyAttr().
In [15]: hasattr(pdb, 'angles')
Out[15]: False
@@ -879,20 +879,20 @@ Adding to a UniverseOut[17]: <TopologyGroup containing 2 angles>
-Both of these methods add the new objects to the associated master TopologyGroup in the Universe.
+Both of these methods add the new objects to the associated master TopologyGroup in the Universe.
Creating with an AtomGroup
-An AtomGroup can be represented as a bond, angle, dihedral angle, or improper angle TopologyObject through the respective properties:
+An AtomGroup can be represented as a bond, angle, dihedral angle, or improper angle TopologyObject through the respective properties:
-The AtomGroup must contain the corresponding number of atoms, in the desired order. For example, a bond cannot be created from three atoms.
+The AtomGroup must contain the corresponding number of atoms, in the desired order. For example, a bond cannot be created from three atoms.
In [18]: pdb.atoms[[3, 4, 2]].bond
ValueErrorTraceback (most recent call last)
@@ -909,11 +909,11 @@ Creating with an AtomGroup47.770653826924175
-These AtomGroup TopologyObjects are not added to the associated master TopologyGroup in the Universe.
+These AtomGroup TopologyObjects are not added to the associated master TopologyGroup in the Universe.
Deleting from a Universe
-As of version 0.21.0, there are specific methods for deleting TopologyObjects from a Universe:
+As of version 0.21.0, there are specific methods for deleting TopologyObjects from a Universe:
delete_Bonds()
Deleting from a Universe
Topology-specific methods
-A number of analysis and transformation methods are defined for AtomGroup, ResidueGroup, and SegmentGroup that require specific properties to be available. The primary requirement is the positions attribute. With positions, you can easily compute a center of geometry:
+A number of analysis and transformation methods are defined for AtomGroup, ResidueGroup, and SegmentGroup that require specific properties to be available. The primary requirement is the positions attribute. With positions, you can easily compute a center of geometry:
>>> u.atoms.center_of_geometry()
array([-0.04223882, 0.01418196, -0.03504874])
@@ -957,63 +957,63 @@ Deleting from a UniverseCenter of (absolute) charge of (compounds of) the group .. math:: boldsymbol R = frac{sum_i vert q_i vert boldsymbol r_i} {sum_i vert q_i vert} where \(q_i\) is the charge and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
center_of_charge()
Center of (absolute) charge of (compounds of) the group .. math:: boldsymbol R = frac{sum_i vert q_i vert boldsymbol r_i} {sum_i vert q_i vert} where \(q_i\) is the charge and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
charges
dipole_moment()
Dipole moment of the group or compounds in a group
charges
dipole_vector()
Dipole vector of the group
charges
quadrupole_moment()
Quadrupole moment of the group according to [1]
charges
quadrupole_tensor()
Traceless quadrupole tensor of the group or compounds
charges
total_charge()
Total charge of (compounds of) the group
charges
align_principal_axis()
Align principal axis with index axis with vector
masses
asphericity()
Asphericity
masses
Center of mass of (compounds of) the group .. math:: boldsymbol R = frac{sum_i m_i boldsymbol r_i}{sum m_i} where \(m_i\) is the mass and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
center_of_mass()
Center of mass of (compounds of) the group .. math:: boldsymbol R = frac{sum_i m_i boldsymbol r_i}{sum m_i} where \(m_i\) is the mass and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup
masses
gyration_moments()
Moments of the gyration tensor
masses
moment_of_inertia()
Moment of inertia tensor relative to center of mass
masses
principal_axes()
Calculate the principal axes from the moment of inertia
masses
radius_of_gyration()
Radius of gyration
masses
shape_parameter()
Shape parameter
masses
total_mass()
Total mass of (compounds of) the group
masses
-Indexing a trajectory shifts the Universe to point towards that particular frame, updating dynamic data such as Universe.atoms.positions.
+Indexing a trajectory shifts the Universe to point towards that particular frame, updating dynamic data such as Universe.atoms.positions.
Note
The trajectory frame is not read from the MD data. It is the internal index assigned by MDAnalysis.
@@ -210,7 +210,7 @@
Out[5]: 4
-Creating a FrameIterator by slicing a trajectory does not shift the Universe to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.
+Creating a FrameIterator by slicing a trajectory does not shift the Universe to a new frame, but iterating over the sliced trajectory will rewind the trajectory back to the first frame.
In [6]: fiter = u.trajectory[10::10]
In [7]: frames = [ts.frame for ts in fiter]
diff --git a/dev/trajectories/transformations.html b/dev/trajectories/transformations.html
index c3a78d562..88930fd80 100644
--- a/dev/trajectories/transformations.html
+++ b/dev/trajectories/transformations.html
@@ -195,7 +195,7 @@
On-the-fly transformations
An on-the-fly transformation is a function that silently modifies the dynamic data contained in a trajectory Timestep (typically coordinates) as it is loaded into memory. It is called for each current time step to transform data into your desired representation. A transformation function must also return the current Timestep, as transformations are often chained together.
-The MDAnalysis.transformations module contains a collection of transformations. For example, fit_rot_trans() can perform a mass-weighted alignment on an AtomGroup to a reference.
+The MDAnalysis.transformations module contains a collection of transformations. For example, fit_rot_trans() can perform a mass-weighted alignment on an AtomGroup to a reference.
In [1]: import MDAnalysis as mda
In [2]: from MDAnalysis.tests.datafiles import TPR, XTC
@@ -211,8 +211,8 @@
In [7]: u.trajectory.add_transformations(align_transform)
-Other implemented transformations include functions to translate, rotate, fit an AtomGroup to a reference, and wrap or unwrap groups in the unit cell. (Please see the MDAnalysis on-the-fly transformations blog post contains a more complete introduction to these fitting and wrapping functions.)
-Although you can only call add_transformations() once, you can pass in multiple transformations in a list, which will be executed in order.
+Other implemented transformations include functions to translate, rotate, fit an AtomGroup to a reference, and wrap or unwrap groups in the unit cell. (Please see the MDAnalysis on-the-fly transformations blog post contains a more complete introduction to these fitting and wrapping functions.)
+Although you can only call add_transformations() once, you can pass in multiple transformations in a list, which will be executed in order.
There is a transformations tutorial that shows in more detail how to use transformations. A few simple examples are given below.
Example workflows
@@ -238,7 +238,7 @@ Example workflowsPlease see the full tutorial for more information.
-
If your transformation does not depend on something within the Universe (e.g. a chosen AtomGroup), you can also create a Universe directly with transformations. The code below translates coordinates 1 angstrom up on the z-axis:
+If your transformation does not depend on something within the Universe (e.g. a chosen AtomGroup), you can also create a Universe directly with transformations. The code below translates coordinates 1 angstrom up on the z-axis:
In [13]: u = mda.Universe(TPR, XTC, transformations=[trans.translate([0, 0, 1])])
diff --git a/dev/units.html b/dev/units.html
index 6e775424f..b5ff9c2d1 100644
--- a/dev/units.html
+++ b/dev/units.html
@@ -258,11 +258,11 @@
Unit conversion
-Quantities can be converted from units with convert().
-convert() simply multiplies the initial quantity with a
+
Quantities can be converted from units with convert().
+convert() simply multiplies the initial quantity with a
precomputed conversion factor, as obtained from
-get_conversion_factor().
-The computed conversion factors for each quantity type are stored in MDAnalysis.units and shown below.
+get_conversion_factor().
+The computed conversion factors for each quantity type are stored in MDAnalysis.units and shown below.
Constants
diff --git a/dev/universe.html b/dev/universe.html
index edaf56c2b..002b8a4d6 100644
--- a/dev/universe.html
+++ b/dev/universe.html
@@ -204,13 +204,13 @@
If you wish to make an apple pie from scratch, you must first invent the universe.
—Carl Sagan, Cosmos
-MDAnalysis is structured around two fundamental classes: the Universe and the AtomGroup. Almost all code in MDAnalysis begins with Universe, which contains all the information describing a molecular dynamics system.
+MDAnalysis is structured around two fundamental classes: the Universe and the AtomGroup. Almost all code in MDAnalysis begins with Universe, which contains all the information describing a molecular dynamics system.
It has two key properties:
-atoms: an AtomGroup of the system’s atoms, providing access to important analysis methods (described below)
trajectory: the currently loaded trajectory reader
atoms: an AtomGroup of the system’s atoms, providing access to important analysis methods (described below)
trajectory: the currently loaded trajectory reader
-A Universe ties the static information from the “topology” (e.g. atom identities) to dynamically updating information from the “trajectory” (e.g. coordinates). A key feature of MDAnalysis is that an entire trajectory is not loaded into memory (unless the user explicitly does so with MemoryReader). Instead, the trajectory attribute provides a view on a specific frame of the trajectory. This allows the analysis of arbitrarily long trajectories without a significant impact on memory.
+A Universe ties the static information from the “topology” (e.g. atom identities) to dynamically updating information from the “trajectory” (e.g. coordinates). A key feature of MDAnalysis is that an entire trajectory is not loaded into memory (unless the user explicitly does so with MemoryReader). Instead, the trajectory attribute provides a view on a specific frame of the trajectory. This allows the analysis of arbitrarily long trajectories without a significant impact on memory.
Creating a Universe
@@ -224,7 +224,7 @@ Creating a UniverseUniverse constructor also takes optional arguments.
+
The default arguments should create a Universe suited for most analysis applications. However, the Universe constructor also takes optional arguments.
The following options specify how to treat the input:
format: the file format of the trajectory file/s. (default: None, formats are guessed)
Creating a Universetransformations: a function or list of functions for on-the-fly trajectory transformation.
in_memory: whether to load coordinates into memory (default: False)
in_memory_step: only read every nth frame into an in-memory representation. (default: 1)
is_anchor: whether to consider this Universe when unpickling AtomGroups (default: True)
anchor_name: the name of this Universe when unpickling AtomGroups (default: None, automatically generated)
is_anchor: whether to consider this Universe when unpickling AtomGroups (default: True)
anchor_name: the name of this Universe when unpickling AtomGroups (default: None, automatically generated)
You can also pass in keywords for parsing the topology or coordinates. For example, many file formats do not specify the timestep for their trajectory. In these cases, MDAnalysis assumes that the default timestep is 1 ps. If this is incorrect, you can pass in a dt argument to modify the timestep. This does not modify timesteps for formats that include time information.
In [7]: from MDAnalysis.tests.datafiles import PRM, TRJ
@@ -274,7 +274,7 @@ Creating a Universe
Constructing from AtomGroups
-A new Universe can be created from one or more AtomGroup instances with Merge(). The AtomGroup instances can come from different Universes, meaning that this is one way to concatenate selections from different datasets.
+A new Universe can be created from one or more AtomGroup instances with Merge(). The AtomGroup instances can come from different Universes, meaning that this is one way to concatenate selections from different datasets.
For example, to combine a protein, ligand, and solvent from separate PDB files:
u1 = mda.Universe("protein.pdb")
u2 = mda.Universe("ligand.pdb")
@@ -286,7 +286,7 @@ Constructing from AtomGroups
Constructing from scratch
-A Universe can be constructed from scratch with Universe.empty. There are three stages to this process:
+A Universe can be constructed from scratch with Universe.empty. There are three stages to this process:
Create the blank Universe with specified number of atoms. If coordinates, set trajectory=True.
Guessing topology attributesResidues and Segments are chemically meaningful groups of Atoms.
-
Modifying a topology is typically done through the Universe, which contains several methods for adding properties:
+Modifying a topology is typically done through the Universe, which contains several methods for adding properties:
-add_TopologyAttr()
add_Residue()
add_Segment()
See Topology attributes for more information on which topology attributes can be added, and examples/constructing_universe.ipynb for examples on adding attributes and Segments.