From f2d3435ab4cdd7dad85c21804964e2ca46a3727f Mon Sep 17 00:00:00 2001 From: github-actions Date: Thu, 24 Oct 2024 19:39:39 +0000 Subject: [PATCH] rebuilt html docs for version 2.8.0-dev0 from branch develop with sphinx at d2729f7 --- .../_modules/MDAnalysis/topology/ITPParser.html | 10 +++++++++- .../analysis/wbridge_analysis.html | 4 ++-- 2.8.0-dev0/documentation_pages/coordinates/GSD.html | 12 ++++++------ 2.8.0-dev0/documentation_pages/coordinates/init.html | 2 +- 2.8.0-dev0/index.html | 2 +- 2.8.0-dev0/searchindex.js | 2 +- dev/_modules/MDAnalysis/topology/ITPParser.html | 10 +++++++++- .../analysis/wbridge_analysis.html | 4 ++-- dev/documentation_pages/coordinates/GSD.html | 12 ++++++------ dev/documentation_pages/coordinates/init.html | 2 +- dev/index.html | 2 +- dev/searchindex.js | 2 +- 12 files changed, 40 insertions(+), 24 deletions(-) diff --git a/2.8.0-dev0/_modules/MDAnalysis/topology/ITPParser.html b/2.8.0-dev0/_modules/MDAnalysis/topology/ITPParser.html index b9a2845e0e..539c4ecbe3 100644 --- a/2.8.0-dev0/_modules/MDAnalysis/topology/ITPParser.html +++ b/2.8.0-dev0/_modules/MDAnalysis/topology/ITPParser.html @@ -747,7 +747,15 @@

Source code for MDAnalysis.topology.ITPParser

if all(e.capitalize() in SYMB2Z for e in self.elements): attrs.append(Elements(np.array(self.elements, dtype=object), guessed=True)) - + warnings.warn( + "The elements attribute has been populated by guessing " + "elements from atom types. This behaviour has been " + "temporarily added to the ITPParser as we transition " + "to the new guessing API. " + "This behavior will be removed in release 3.0. " + "Please see issue #4698 for more information. ", + DeprecationWarning + ) else: warnings.warn("Element information is missing, elements attribute " "will not be populated. If needed these can be " diff --git a/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html b/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html index 6d54b28684..b5b66a8e99 100644 --- a/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html +++ b/2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html @@ -1048,7 +1048,7 @@

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

default atom names that are treated as hydrogen acceptors (see Default heavy atom names for CHARMM27 force field.); use the keyword acceptors to add a list of additional acceptor names.

@@ -1056,7 +1056,7 @@

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

default heavy atom names whose hydrogens are treated as donors (see Default heavy atom names for CHARMM27 force field.); use the keyword donors to add a list of additional donor names.

diff --git a/2.8.0-dev0/documentation_pages/coordinates/GSD.html b/2.8.0-dev0/documentation_pages/coordinates/GSD.html index c2238ba02c..630dab7945 100644 --- a/2.8.0-dev0/documentation_pages/coordinates/GSD.html +++ b/2.8.0-dev0/documentation_pages/coordinates/GSD.html @@ -214,7 +214,7 @@

7.7.1. ClassesAdded in version 0.17.0.

-

Changed in version 2.0.0: Now use a picklable gsd.hoomd.HOOMDTrajectory– +

Changed in version 2.0.0: Now use a picklable gsd.hoomd.HOOMDTrajectory– GSDPicklable

@@ -899,10 +899,10 @@

7.7.1. Classes class MDAnalysis.coordinates.GSD.GSDPicklable[source]

Hoomd GSD file object (read-only) that can be pickled.

-

This class provides a file-like object (as by gsd.hoomd.open(), +

This class provides a file-like object (as by gsd.hoomd.open(), namely gsd.hoodm.HOOMDTrajectory) that, unlike file objects, can be pickled. Only read mode is supported.

-

When the file is pickled, filename and mode of gsd.fl.GSDFile in +

When the file is pickled, filename and mode of gsd.fl.GSDFile in the file are saved. On unpickling, the file is opened by filename. This means that for a successful unpickle, the original file still has to be accessible with its filename.

@@ -914,7 +914,7 @@

7.7.1. Classes
Parameters:
-

file (gsd.fl.GSDFile) – File to access.

+

file (gsd.fl.GSDFile) – File to access.

Example

@@ -941,7 +941,7 @@

7.7.1. ClassesMDAnalysis.coordinates.GSD.gsd_pickle_open(name: str, mode: str = 'r')[source]

Open hoomd schema GSD file with pickle function implemented.

This function returns a GSDPicklable object. It can be used as a -context manager, and replace the built-in gsd.hoomd.open() function +context manager, and replace the built-in gsd.hoomd.open() function in read mode that only returns an unpicklable file object.

Schema version will depend on the version of gsd module.

@@ -979,7 +979,7 @@

7.7.1. Classes

See also

-

MDAnalysis.lib.util.anyopen(), MDAnalysis.lib.picklable_file_io.pickle_open(), MDAnalysis.lib.picklable_file_io.bz2_pickle_open(), MDAnalysis.lib.picklable_file_io.gzip_pickle_open(), gsd.hoomd.open()

+

MDAnalysis.lib.util.anyopen(), MDAnalysis.lib.picklable_file_io.pickle_open(), MDAnalysis.lib.picklable_file_io.bz2_pickle_open(), MDAnalysis.lib.picklable_file_io.gzip_pickle_open(), gsd.hoomd.open()

Added in version 2.0.0.

diff --git a/2.8.0-dev0/documentation_pages/coordinates/init.html b/2.8.0-dev0/documentation_pages/coordinates/init.html index 1b108b228e..f3654eff0b 100644 --- a/2.8.0-dev0/documentation_pages/coordinates/init.html +++ b/2.8.0-dev0/documentation_pages/coordinates/init.html @@ -375,7 +375,7 @@

7.1.4. Supported coordinate formats

HOOMD [1]

gsd

r

-

HOOMD GSD format (using gsd.hoomd). +

HOOMD GSD format (using gsd.hoomd). Module MDAnalysis.coordinates.GSD

GAMESS

diff --git a/2.8.0-dev0/index.html b/2.8.0-dev0/index.html index 9eaca0db60..07e88ab6cc 100644 --- a/2.8.0-dev0/index.html +++ b/2.8.0-dev0/index.html @@ -149,7 +149,7 @@

MDAnalysis documentation

2.8.0-dev0

Date:
-

Oct 20, 2024

+

Oct 24, 2024

MDAnalysis (www.mdanalysis.org) is an object-oriented python diff --git a/2.8.0-dev0/searchindex.js b/2.8.0-dev0/searchindex.js index ff31004e62..6183aff641 100644 --- a/2.8.0-dev0/searchindex.js +++ b/2.8.0-dev0/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"AMBER PRMTOP topology parser": [[151, null]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[74, null]], "ASCII TRAJ trajectories": [[74, "ascii-traj-trajectories"]], "About the algorithm": [[115, "about-the-algorithm"]], "About the code": [[115, "about-the-code"]], "Accessing auxiliary attributes": [[48, "accessing-auxiliary-attributes"]], "Adding EDR data to trajectories": [[44, "adding-edr-data-to-trajectories"]], "Adding an auxiliary to a trajectory": [[48, "adding-an-auxiliary-to-a-trajectory"]], "Adding parallelization to your own analysis class": [[34, "adding-parallelization-to-your-own-analysis-class"]], "Additional dependencies": [[43, "additional-dependencies"]], "Algorithm": [[27, "algorithm"]], 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"MDAnalysis.topology.tpr.obj.Atoms.atomnames", false]], "atomneighborsearch (class in mdanalysis.lib.neighborsearch)": [[106, "MDAnalysis.lib.NeighborSearch.AtomNeighborSearch", false]], "atomnumber (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.atomnumber", false]], "atoms (class in mdanalysis.topology.tpr.obj)": [[158, "MDAnalysis.topology.tpr.obj.Atoms", false]], "atoms (mdanalysis.analysis.bat.bat property)": [[4, "MDAnalysis.analysis.bat.BAT.atoms", false]], "atoms (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.atoms", false]], "atoms (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.atoms", false]], "atoms (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.atoms", false]], "atoms (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.atoms", false]], "atoms 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"MDAnalysis.coordinates.TRR.TRRReader.copy", false]], "copy() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.copy", false]], "copy() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.copy", false]], "copy() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.copy", false]], "copy() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.copy", false]], "copy() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.copy", false]], "copy() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.copy", false]], "copy() (mdanalysis.core.groups.updatingatomgroup method)": [[92, "MDAnalysis.core.groups.UpdatingAtomGroup.copy", false]], "copy() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.copy", false]], "copy() (mdanalysis.core.topology.transtable method)": [[95, "MDAnalysis.core.topology.TransTable.copy", false]], "copy() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.copy", false]], "copy() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.copy", false]], "copy() (mdanalysis.guesser.base.guesserbase method)": [[102, "MDAnalysis.guesser.base.GuesserBase.copy", false]], "copy() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.copy", false]], "copy_slice() (mdanalysis.coordinates.timestep.timestep method)": [[89, "MDAnalysis.coordinates.timestep.Timestep.copy_slice", false]], "correct_intermittency() (in module mdanalysis.lib.correlations)": [[109, "MDAnalysis.lib.correlations.correct_intermittency", false]], "cosine_content() (in module mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.cosine_content", false]], "count 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"MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time", false]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type", false]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_type", false]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.covariance_matrix", false]], "crdparser (class in mdanalysis.topology.crdparser)": [[133, "MDAnalysis.topology.CRDParser.CRDParser", false]], "crdreader (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDReader", false]], "crdwriter (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDWriter", false]], "create() (in module 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"MDAnalysis.analysis.pca.PCA.cumulative_overlap", false]], "data (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.data", false]], "data (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.data", false]], "data_blacklist (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.data_blacklist", false]], "data_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.data_dict", false]], "data_selector (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.data_selector", false]], "dataparser (class in mdanalysis.topology.lammpsparser)": [[143, "MDAnalysis.topology.LAMMPSParser.DATAParser", false]], "datareader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader", false]], "datawriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter", false]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN", false]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[111, "MDAnalysis.lib.formats.libdcd.DCDFile", false]], "dcdreader (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDReader", false]], "dcdreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader", false]], "dcdwriter (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter", false]], "dcdwriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter", false]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.decompose_matrix", false]], "dedent_docstring() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.dedent_docstring", false]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS", false]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS", false]], "default_format (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.default_format", false]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms", false]], "defaultguesser (class in mdanalysis.guesser.default_guesser)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser", false]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.define_unpack_real", false]], "del_topologyattr() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.del_TopologyAttr", false]], "del_topologyattr() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.del_TopologyAttr", false]], "delete_angles() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_angles", false]], "delete_bonds() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_bonds", false]], "delete_dihedrals() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_dihedrals", false]], "delete_impropers() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_impropers", false]], "delta (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.delta", false]], "delta (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.delta", false]], "density (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.Density", false]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.density", false]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.results.density", false]], "densityanalysis (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.DensityAnalysis", false]], "densityunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.densityUnit_factor", false]], "deprecate() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.deprecate", false]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant", false]], "difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.difference", false]], "difference() 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false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], 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attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Molnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.moltypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Moltypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.nonbondedindices attribute)": [[96, "MDAnalysis.core.topologyattrs.NonbondedIndices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[123, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[158, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[113, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [120, "index-0", false], [120, "index-1", false], [123, "index-0", false], [161, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[136, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[118, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[115, "MDAnalysis.lib.nsgrid.FastNS", 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false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, 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"MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter 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"MDAnalysis.exceptions.SelectionError", false]], "selectionparser (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SelectionParser", false]], "selectionwarning": [[100, "MDAnalysis.exceptions.SelectionWarning", false]], "selectionwriter (class in mdanalysis.selections.charmm)": [[126, "MDAnalysis.selections.charmm.SelectionWriter", false]], "selectionwriter (class in mdanalysis.selections.gromacs)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter", false]], "selectionwriter (class in mdanalysis.selections.jmol)": [[128, "MDAnalysis.selections.jmol.SelectionWriter", false]], "selectionwriter (class in mdanalysis.selections.pymol)": [[129, "MDAnalysis.selections.pymol.SelectionWriter", false]], "selectionwriter (class in mdanalysis.selections.vmd)": [[130, "MDAnalysis.selections.vmd.SelectionWriter", false]], "selectionwriterbase (class in mdanalysis.selections.base)": [[125, "MDAnalysis.selections.base.SelectionWriterBase", false]], "self_capped_distance() 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"set_atoms() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.atomindices method)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.atomstringattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomStringAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.set_atoms", false]], "set_atoms() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.set_atoms", false]], "set_aux_attribute() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.set_aux_attribute", false]], "set_aux_attribute() 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"MDAnalysis.coordinates.LAMMPS.DATAReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.set_aux_attribute", false]], "set_aux_attribute() 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"MDAnalysis.core.topologyattrs.AtomAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentstringattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentStringAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.set_segments", false]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.setaxes", false]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[119, 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"MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[158, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], "skip_timestep (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep", false]], "skipper() (mdanalysis.topology.topparser.topparser method)": [[151, "MDAnalysis.topology.TOPParser.TOPParser.skipper", false]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume", false]], "smartsselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SmartsSelection", false]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.soft_cut_q", false]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve", false]], "solventradii (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii", false]], "sort() 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mdanalysis.lib.log)": [[113, "MDAnalysis.lib.log.start_logging", false]], "static_variables() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.static_variables", false]], "std() (mdanalysis.analysis.legacy.x3dna.x3dna method)": [[28, "MDAnalysis.analysis.legacy.x3dna.X3DNA.std", false]], "std() (mdanalysis.analysis.legacy.x3dna.x3dnatraj method)": [[28, "MDAnalysis.analysis.legacy.x3dna.X3DNAtraj.std", false]], "step (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.step", false]], "step (mdanalysis.auxiliary.base.auxstep attribute)": [[46, "MDAnalysis.auxiliary.base.AuxStep.step", false]], "step_to_frame() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.step_to_frame", false]], "step_to_time() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.step_to_time", false]], "stochasticproximityembedding() (in module 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"MDAnalysis.core.groups.AtomGroup.subtract", false]], "subtract() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.subtract", false]], "subtract() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.subtract", false]], "summary (mdanalysis.analysis.helix_analysis.helanal.results attribute)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL.results.summary", false]], "supported_versions (in module mdanalysis.topology.tpr)": [[158, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS", false]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS", false]], "symmetric_difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.symmetric_difference", false]], "symmetric_difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.symmetric_difference", false]], 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"MDAnalysis.lib.formats.libmdaxdr.XTCFile.tell", false]], "tell() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.tell", false]], "tempfactors (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors", false]], "terms (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.terms", false]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.TextIOPicklable", false]], "time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.time", false]], "time (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.time", false]], "time (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.time", false]], "time (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.time", false]], "time 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false]], "timeseries() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.timeseries", false]], "timestep (class in mdanalysis.coordinates.timestep)": [[89, "MDAnalysis.coordinates.timestep.Timestep", false]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps", false]], 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"MDAnalysis.core.groups.SegmentGroup.total_charge", false]], "total_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.total_charge", false]], "total_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.total_mass", false]], "total_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.total_mass", false]], "totaltime (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.totaltime", false]], "totaltime (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.totaltime", false]], "totaltime 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[[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.totaltime", false]], "totaltime (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.totaltime", false]], "totaltime (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.totaltime", false]], "totaltime (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.totaltime", false]], "totaltime (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.totaltime", false]], "tp (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.tp", false]], "tprparser (class in 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false]], "transformations (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.transformations", false]], "transformations (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.transformations", false]], "transformations (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.transformations", false]], "transformations (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dcdreader property)": [[65, 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164, 166, 167, 168], "unit_dict": 44, "unit_divisor": 113, "unit_scal": 113, "unit_typ": 169, "unitari": 69, "unitcel": [11, 56, 59, 63, 65, 69, 70, 75, 78, 79, 80, 81, 85, 86, 89, 92, 110, 111, 114, 117, 120], "uniti": 7, "unitless": [5, 141], "univers": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 26, 27, 28, 31, 33, 34, 35, 36, 38, 40, 42, 43, 44, 48, 50, 51, 52, 53, 56, 59, 61, 62, 63, 65, 67, 69, 71, 73, 74, 75, 77, 78, 79, 80, 81, 83, 85, 86, 90, 91, 92, 93, 96, 97, 99, 100, 101, 102, 103, 104, 114, 116, 118, 119, 120, 122, 124, 132, 133, 134, 135, 136, 137, 138, 139, 140, 142, 143, 144, 145, 147, 148, 149, 153, 154, 155, 157, 158, 159, 160, 163], "universe2": 86, "universe_valid": 120, "unives": 92, "unk": 61, "unknown": [7, 103, 145, 147, 151], "unless": [0, 44, 51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 82, 84, 85, 86, 92, 96, 98, 113, 119, 120, 124, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 155], "unlik": [10, 19, 62, 63, 65, 72, 74, 83, 85, 92, 116], "unload": 74, "unmaintain": 28, "unmodifi": [51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 82, 86, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 155], "unoffici": 69, "unord": 12, "unpack": [120, 158], "unpack_fstr": 158, "unpack_int64": 158, "unpack_r": 158, "unpack_str": 158, "unpack_uchar": 158, "unpack_uint64": 158, "unpack_ushort": 158, "unpair": 53, "unpickl": [62, 63, 74, 81, 82, 83, 88, 92, 98, 116], "unrecognis": 151, "unscal": 65, "unsign": 158, "unspecifi": 113, "unsupported_backend": [2, 3, 4, 7, 10, 12, 21, 26, 31, 32, 34, 35, 40], "unsymmetr": [92, 96], "until": [0, 3, 9, 35, 42, 48, 53, 69, 85, 92, 94, 103, 133, 151], "unus": [5, 21, 40, 69, 74, 151], "unusu": 12, "unwrap": [31, 40, 65, 92, 96, 114, 160, 166], "unwrap_imag": 65, "unzip": [5, 122], "up": [3, 5, 11, 15, 21, 26, 28, 31, 35, 42, 46, 56, 59, 61, 63, 65, 69, 71, 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159, 160, 163, 166, 167], "userblock_s": 63, "userwarn": [7, 147, 157], "usr": 142, "usual": [2, 3, 8, 10, 43, 44, 52, 53, 70, 74, 79, 83, 85, 96, 98, 114, 120, 151], "util": [13, 14, 15, 16, 18, 19, 31, 39, 40, 43, 62, 88, 94, 116, 121, 136, 159], "v": [8, 10, 12, 38, 51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 75, 77, 78, 79, 81, 86, 92, 94, 96, 105, 114, 119, 123, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 155, 158, 164], "v0": 119, "v1": [10, 119, 171], "v108": 63, "v110": 63, "v112": 63, "v1i1e6324": 31, "v2": [4, 9, 10, 12, 21, 25, 28, 31, 40, 86, 109, 115], "v3": [0, 1, 7, 8, 13, 22, 23, 24, 25, 26, 33, 35, 36, 37, 41, 42, 53, 171, 172], "v4": 53, "v6": 53, "val": [10, 94, 96, 151], "valenc": 53, "valid": [0, 2, 9, 10, 32, 34, 35, 38, 40, 46, 48, 56, 59, 62, 63, 65, 69, 74, 75, 77, 78, 79, 81, 83, 86, 105, 115, 120, 142, 147, 152, 153], "valu": [0, 3, 4, 5, 7, 9, 10, 12, 15, 16, 18, 19, 21, 22, 26, 28, 31, 32, 34, 35, 38, 39, 40, 42, 44, 45, 46, 48, 51, 52, 53, 54, 56, 59, 62, 63, 65, 69, 71, 74, 75, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 92, 94, 95, 96, 97, 98, 101, 102, 103, 105, 109, 110, 111, 112, 113, 114, 115, 116, 118, 119, 120, 122, 124, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 155, 158, 161, 169, 171, 172], "value_kei": 39, "valueerror": [2, 3, 4, 7, 10, 12, 31, 32, 35, 39, 40, 46, 47, 48, 53, 55, 56, 59, 62, 63, 65, 69, 71, 74, 75, 76, 77, 78, 79, 81, 82, 84, 86, 91, 92, 94, 96, 98, 100, 103, 114, 116, 119, 120, 145, 155, 169], "van": [9, 72, 105], "var": 113, "varepsilon": 8, "varepsilon_": 8, "vari": [31, 46, 63, 69, 83, 140, 162], "variabl": [0, 1, 6, 9, 15, 18, 31, 35, 44, 63, 72, 74, 80, 85, 109, 120, 123, 161], "varianc": [15, 35], "variant": [149, 150], "variat": [103, 140], "varibal": 160, "variou": [15, 18, 27, 31, 36, 40, 51, 63, 72, 85, 93, 98, 121, 156, 157], "vcl2": 110, "vdw": [92, 103, 105], "vdwradii": [92, 98, 103, 105], "ve": [3, 63, 122], "vec": 110, "vec1": 114, "vec2": 114, "vec3": 114, "vector": [0, 4, 24, 33, 35, 36, 39, 56, 59, 61, 85, 89, 92, 96, 97, 110, 111, 112, 114, 119, 120, 122, 162, 166, 167], "vector_of_best_fit": 24, "vectoris": 110, "vel": [59, 61], "velavan": [24, 123], "veloc": [46, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 85, 86, 87, 89, 92, 98, 100, 109, 112, 133, 135, 136, 137, 138, 139, 140, 141, 142, 143, 145, 146, 147, 148, 149, 150, 151, 152, 153, 155], "velocityunit": 63, "ver_str": 158, "verbos": [0, 3, 4, 5, 7, 8, 9, 10, 12, 15, 16, 24, 30, 31, 32, 34, 35, 36, 38, 40, 42, 86, 98, 113], "veri": [0, 19, 29, 42, 63, 69, 71, 74, 86, 92, 103, 112, 113, 120, 122, 124], "verifi": [82, 92], "vermaa": 164, "versa": [9, 42, 95], "versatil": 28, "version": [0, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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"visual": [7, 19, 28, 31, 36, 113, 123, 125, 131, 160], "visualis": 36, "vmd": [7, 26, 27, 56, 69, 80, 92, 94, 103, 111, 125, 131, 174], "vol": 73, "vol4": 73, "volum": [7, 30, 85, 89, 105, 114, 169], "volumetr": 7, "von": 31, "voxel": 7, "vsite1": 158, "vsite2": 158, "vsite2fd": 158, "vsite3": 158, "vsite3fad": 158, "vsite3fd": 158, "vsite3out": 158, "vsite4fd": 158, "vsite4fdn": 158, "vsiten": 158, "vstack": 39, "vtemp": 158, "vx": 59, "vy": 59, "vz": 59, "w": [10, 21, 35, 40, 42, 61, 63, 65, 69, 83, 85, 105, 111, 112, 116, 119, 120, 123, 125, 126, 127, 128, 129, 130, 131], "w477": 5, "w482": 5, "w_": 35, "w_i": 40, "wa": [0, 3, 4, 10, 12, 22, 23, 26, 28, 30, 31, 32, 34, 35, 36, 38, 40, 42, 46, 52, 53, 56, 59, 60, 62, 63, 65, 69, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 83, 84, 85, 89, 91, 92, 94, 95, 96, 97, 98, 109, 110, 111, 115, 120, 124, 125, 157, 163, 165, 166, 167, 168], "waal": 105, "wai": [0, 3, 5, 7, 9, 10, 12, 15, 16, 21, 26, 27, 31, 34, 39, 44, 46, 53, 74, 81, 82, 85, 88, 91, 98, 119, 121, 122, 124, 125, 126, 127, 128, 129, 130, 146, 160, 163], "walk": 31, "wall": 110, "walt": 9, "wang": [24, 25], "want": [0, 3, 4, 5, 7, 10, 12, 19, 21, 26, 29, 31, 32, 34, 35, 39, 40, 42, 44, 52, 61, 63, 74, 91, 92, 98, 101, 103, 131, 151, 174], "warn": [2, 7, 10, 30, 32, 34, 44, 46, 56, 59, 61, 62, 63, 65, 69, 73, 75, 77, 78, 79, 81, 86, 92, 94, 96, 98, 120, 124, 151, 164, 165], "warn_if_not_uniqu": 120, "warning_messag": 2, "wasn": [34, 95], "wassenaar": 114, "watch": 56, "water": [0, 7, 8, 9, 11, 22, 26, 43, 92, 93, 98, 109, 122, 123, 124, 142, 158, 169], "water1_acceptor": 42, "water1_donor": 42, "water1_donor_heavi": 42, "water2": 42, "water2_acceptor": 42, "water_acceptors_sel": 26, "water_hydrogens_sel": 26, "water_select": 42, "water_shel": [92, 93], "water_shell_prev": 92, "waterbridgeanalysi": 43, "waterbridgeanalysis_otherff": 42, "waterdcd": 22, "waterdynam": [43, 109, 123], "waterpol": 158, "waterpsf": 22, "watson": [32, 33], "watsoncrickdist": 32, 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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "11.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "11.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "11.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "11.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "11.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "11. Auxiliary modules", "8. Converter modules", "8.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "8.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "8.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "8.8. Base classes \u2014 MDAnalysis.converters.base", "7.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "7.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "7.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "7.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "7.26. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "7.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "7.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "7.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "7.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "7.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "7.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "7.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "7.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "7.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "7.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "7.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "7.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "7.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "7.19. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "7.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "7.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "7.22. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "7.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "7.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "7.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "7.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "7.31. Base classes \u2014 MDAnalysis.coordinates.base", "7.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "7.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "7.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "7.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "7.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "7.29. Null output \u2014 MDAnalysis.coordinates.null", "7.33. Serialization of Coordinate Readers", "7.30. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "7. Coordinates modules", "8.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "12.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "12.1. Core functions of MDAnalysis", "12.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "12.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "12.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "12.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "12.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "12. Core modules", "17. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "6. Guesser modules", "6.1.2.3. Base guesser classes \u2014 MDAnalysis.guesser.base", "6.1.2.2. Default Guesser", "6.1.2.1. Context-specific guessers \u2014 MDAnalysis.guesser", "6.1.2.4. MDAnalysis topology tables", "14.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "14.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "14.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "14.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "14.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "14.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "14.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "14.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "14.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "14.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "14.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "14.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "14.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "14.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "14.2.10. Helper functions \u2014 MDAnalysis.lib.util", "14. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "18. References", "3. Selection commands", "10.2.6. Base classes for the selection writers", "10.2.4. CHARMM selections", "10.2.3. Gromacs selections", "10.2.5. Jmol selections", "10.2.2. PyMOL selections", "10.2.1. VMD selections", "10. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.26. Utility functions for the TPR topology parser", "5. Topology modules", "9. 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"close() (mdanalysis.topology.lammpsparser.dataparser method)": [[143, "MDAnalysis.topology.LAMMPSParser.DATAParser.close", false]], "close() (mdanalysis.topology.minimalparser.minimalparser method)": [[146, "MDAnalysis.topology.MinimalParser.MinimalParser.close", false]], "close() (mdanalysis.topology.mol2parser.mol2parser method)": [[145, "MDAnalysis.topology.MOL2Parser.MOL2Parser.close", false]], "close() (mdanalysis.topology.pdbparser.pdbparser method)": [[147, "MDAnalysis.topology.PDBParser.PDBParser.close", false]], "close() (mdanalysis.topology.pdbqtparser.pdbqtparser method)": [[148, "MDAnalysis.topology.PDBQTParser.PDBQTParser.close", false]], "close() (mdanalysis.topology.pqrparser.pqrparser method)": [[149, "MDAnalysis.topology.PQRParser.PQRParser.close", false]], "close() (mdanalysis.topology.psfparser.psfparser method)": [[150, "MDAnalysis.topology.PSFParser.PSFParser.close", false]], "close() (mdanalysis.topology.topparser.topparser method)": [[151, 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mdanalysis.topology.dmsparser)": [[135, "MDAnalysis.topology.DMSParser.DMSParser", false]], "dmsreader (class in mdanalysis.coordinates.dms)": [[58, "MDAnalysis.coordinates.DMS.DMSReader", false]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_atom", false]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_atoms", false]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_block", false]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_blocka", false]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_ffparams", false]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_harm", false]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_ilists", false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp_ndarray", false]], "dt (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.dt", false]], "dt (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.dt", false]], "dt (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.dt", false]], "dt (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.dt", false]], "dt (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dt", false]], "dt (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.dt", false]], "dt (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.dt", false]], "dt (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.dt", false]], "dt (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.dt", false]], "dt (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.dt", false]], "dt (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dt", false]], "dt (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.dt", false]], "dt (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.dt", false]], "dt (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.dt", false]], "dt (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.dt", false]], "dtype (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dtype", false]], "dtype (mdanalysis.core.selection.floatrangeselection attribute)": [[94, "MDAnalysis.core.selection.FloatRangeSelection.dtype", false]], "dtype (mdanalysis.core.selection.rangeselection attribute)": [[94, "MDAnalysis.core.selection.RangeSelection.dtype", false]], "dtype (mdanalysis.core.topologyattrs.altlocs attribute)": [[96, "MDAnalysis.core.topologyattrs.AltLocs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.aromaticities attribute)": [[96, "MDAnalysis.core.topologyattrs.Aromaticities.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomids attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilons.dtype", false]], "dtype (mdanalysis.core.topologyattrs.formalcharges attribute)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.gbscreens attribute)": [[96, "MDAnalysis.core.topologyattrs.GBScreens.dtype", false]], "dtype (mdanalysis.core.topologyattrs.icodes attribute)": [[96, "MDAnalysis.core.topologyattrs.ICodes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.masses attribute)": [[96, "MDAnalysis.core.topologyattrs.Masses.dtype", false]], "dtype (mdanalysis.core.topologyattrs.molnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Molnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.moltypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Moltypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.nonbondedindices attribute)": [[96, "MDAnalysis.core.topologyattrs.NonbondedIndices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[123, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[158, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[113, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [120, "index-0", false], [120, "index-1", false], [123, "index-0", false], [161, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[136, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[118, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[115, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[137, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.frame", false]], "frame (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.frame", false]], "frame (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.frame", false]], "frame (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.frame", false]], "frame (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.frame", false]], "frame (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.frame", false]], "frame (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.frame", false]], "frame (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.frame", false]], "frame (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.frame", false]], "frame (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.frame", false]], "frame (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.frame", false]], "frame (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.frame", false]], "frame (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.frame", false]], "frame (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.frame", false]], "frame_data (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_data", false]], "frame_rep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.frame_rep", false]], "frameiteratorall (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorAll", false]], "frameiteratorbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorBase", false]], "frameiteratorindices (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorIndices", false]], "frameiteratorsliced (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.FrameIteratorSliced", false]], "frames (mdanalysis.analysis.base.analysisbase attribute)": [[3, "MDAnalysis.analysis.base.AnalysisBase.frames", false]], "frames (mdanalysis.analysis.base.analysisfromfunction.results attribute)": [[3, "MDAnalysis.analysis.base.AnalysisFromFunction.results.frames", false]], "frames (mdanalysis.analysis.base.results attribute)": [[3, "MDAnalysis.analysis.base.results.frames", false]], "from_blank() (mdanalysis.core.topologyattrs.topologyattr class method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.from_blank", false]], "from_coordinates() 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(mdanalysis.topology.tpr.obj.params attribute)": [[158, "MDAnalysis.topology.tpr.obj.Params.functype", false]], "fver (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.fver", false]], "gbscreens (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.GBScreens", false]], "gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.gen_kde_pdfs", false]], "gen_selection_class() (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.gen_selection_class", false]], "generate_grid() (in module mdanalysis.analysis.gnm)": [[21, "MDAnalysis.analysis.gnm.generate_grid", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.closecontactgnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.generate_kirchoff", false]], "generate_kirchoff() (mdanalysis.analysis.gnm.gnmanalysis method)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.generate_kirchoff", false]], "generate_streamlines() (in module mdanalysis.visualization.streamlines)": [[171, "MDAnalysis.visualization.streamlines.generate_streamlines", false]], "generate_streamlines_3d() (in module mdanalysis.visualization.streamlines_3d)": [[172, "MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d", false]], "generate_table() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.generate_table", false]], "get_array() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_array", false]], "get_atom_mass() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.get_atom_mass", false]], "get_atoms() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.atomindices method)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.resindices method)": [[96, "MDAnalysis.core.topologyattrs.Resindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.get_atoms", false]], "get_atoms() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.get_atoms", false]], "get_aux_attribute() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.get_aux_attribute", false]], "get_aux_attribute() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.get_aux_attribute", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.get_aux_descriptions", false]], "get_aux_descriptions() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.get_aux_descriptions", false]], 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"mdanalysis.coordinates.inpcrd": [[64, "module-MDAnalysis.coordinates.INPCRD", false]], "mdanalysis.coordinates.lammps": [[65, "module-MDAnalysis.coordinates.LAMMPS", false]], "mdanalysis.coordinates.memory": [[86, "module-MDAnalysis.coordinates.memory", false]], "mdanalysis.coordinates.mmtf": [[66, "module-MDAnalysis.coordinates.MMTF", false]], "mdanalysis.coordinates.mol2": [[67, "module-MDAnalysis.coordinates.MOL2", false]], "mdanalysis.coordinates.namdbin": [[68, "module-MDAnalysis.coordinates.NAMDBIN", false]], "mdanalysis.coordinates.null": [[87, "module-MDAnalysis.coordinates.null", false]], "mdanalysis.coordinates.pdb": [[69, "module-MDAnalysis.coordinates.PDB", false]], "mdanalysis.coordinates.pdbqt": [[70, "module-MDAnalysis.coordinates.PDBQT", false]], "mdanalysis.coordinates.pqr": [[71, "module-MDAnalysis.coordinates.PQR", false]], "mdanalysis.coordinates.timestep": [[89, "module-MDAnalysis.coordinates.timestep", false]], "mdanalysis.coordinates.tng": [[72, "module-MDAnalysis.coordinates.TNG", false]], "mdanalysis.coordinates.trc": [[73, "module-MDAnalysis.coordinates.TRC", false]], "mdanalysis.coordinates.trj": [[74, "module-MDAnalysis.coordinates.TRJ", false]], "mdanalysis.coordinates.trr": [[75, "module-MDAnalysis.coordinates.TRR", false]], "mdanalysis.coordinates.trz": [[76, "module-MDAnalysis.coordinates.TRZ", false]], "mdanalysis.coordinates.txyz": [[77, "module-MDAnalysis.coordinates.TXYZ", false]], "mdanalysis.coordinates.xdr": [[78, "module-MDAnalysis.coordinates.XDR", false]], "mdanalysis.coordinates.xtc": [[79, "module-MDAnalysis.coordinates.XTC", false]], "mdanalysis.coordinates.xyz": [[80, "module-MDAnalysis.coordinates.XYZ", false]], "mdanalysis.core.__init__": [[93, "module-MDAnalysis.core.__init__", false]], "mdanalysis.core.accessors": [[91, "module-MDAnalysis.core.accessors", false]], "mdanalysis.core.groups": [[92, "module-MDAnalysis.core.groups", false]], "mdanalysis.core.selection": [[94, 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"mdanalysis.topology.tprparser": [[152, "module-MDAnalysis.topology.TPRParser", false]], "mdanalysis.topology.txyzparser": [[153, "module-MDAnalysis.topology.TXYZParser", false]], "mdanalysis.topology.xyzparser": [[154, "module-MDAnalysis.topology.XYZParser", false]], "mdanalysis.transformations": [[160, "module-MDAnalysis.transformations", false]], "mdanalysis.transformations.base": [[161, "module-MDAnalysis.transformations.base", false]], "mdanalysis.transformations.boxdimensions": [[162, "module-MDAnalysis.transformations.boxdimensions", false]], "mdanalysis.transformations.fit": [[163, "module-MDAnalysis.transformations.fit", false]], "mdanalysis.transformations.nojump": [[164, "module-MDAnalysis.transformations.nojump", false]], "mdanalysis.transformations.positionaveraging": [[165, "module-MDAnalysis.transformations.positionaveraging", false]], "mdanalysis.transformations.rotate": [[166, "module-MDAnalysis.transformations.rotate", false]], "mdanalysis.transformations.translate": 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"psi_selections() (mdanalysis.core.topologyattrs.atomnames method)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.psi_selections", false]], "ptype (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.ptype", false]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[20, "MDAnalysis.analysis.encore.cutils.PureRMSD", false]], "q (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.q", false]], "q1q2() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.q1q2", false]], "qb (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.qB", false]], "quadrupole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.quadrupole_moment", false]], "quadrupole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.quadrupole_moment", false]], "quadrupole_moment() 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false]], "rewind() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.rewind", false]], "rewind() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.rewind", false]], "rewind() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.rewind", false]], "rmin14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.RMin14s", false]], "rmins (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.RMins", false]], "rmsd (class in mdanalysis.analysis.rms)": [[40, "MDAnalysis.analysis.rms.RMSD", false]], "rmsd (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.rmsd", false]], "rmsd (mdanalysis.analysis.align.aligntraj.results attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.results.rmsd", false]], "rmsd (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.rmsd", false]], "rmsd (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.rmsd", false]], "rmsd (mdanalysis.analysis.rms.rmsd attribute)": [[40, "MDAnalysis.analysis.rms.RMSD.rmsd", false]], "rmsd (mdanalysis.analysis.rms.rmsd.results attribute)": [[40, "MDAnalysis.analysis.rms.RMSD.results.rmsd", false]], "rmsd() (in module mdanalysis.analysis.rms)": [[40, "MDAnalysis.analysis.rms.rmsd", false]], "rmsf (class in mdanalysis.analysis.rms)": [[40, "MDAnalysis.analysis.rms.RMSF", false]], "rmsf (mdanalysis.analysis.rms.rmsf attribute)": [[40, "MDAnalysis.analysis.rms.RMSF.rmsf", false]], "rmsf (mdanalysis.analysis.rms.rmsf.results attribute)": [[40, "MDAnalysis.analysis.rms.RMSF.results.rmsf", false]], "rmsip() (in module mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.rmsip", false]], "rmsip() (mdanalysis.analysis.pca.pca method)": [[35, 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(mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.time", false]], "time (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.time", false]], "time (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.time", false]], "time (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.time", false]], "time (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.time", false]], "time (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.time", false]], "time (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.time", false]], "time (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.time", false]], "time_selector 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"MDAnalysis.coordinates.DCD.DCDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.timeseries", false]], "timestep (class in mdanalysis.coordinates.timestep)": [[89, "MDAnalysis.coordinates.timestep.Timestep", false]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps", false]], 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"MDAnalysis.core.topology.Topology", false]], "topologyattr (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr", false]], "topologydict (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyDict", false]], "topologygroup (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup", false]], "topologyobject (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject", false]], "topologyreaderbase (class in mdanalysis.topology.base)": [[155, "MDAnalysis.topology.base.TopologyReaderBase", false]], "topparser (class in mdanalysis.topology.topparser)": [[151, "MDAnalysis.topology.TOPParser.TOPParser", false]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors", false]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_alpha", false]], "tors_beta() 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"MDAnalysis.core.groups.SegmentGroup.total_charge", false]], "total_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.total_charge", false]], "total_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.total_mass", false]], "total_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.total_mass", false]], "totaltime (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.totaltime", false]], "totaltime (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.totaltime", false]], "totaltime 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[[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.totaltime", false]], "totaltime (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.totaltime", false]], "totaltime (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.totaltime", false]], "totaltime (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.totaltime", false]], "totaltime (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.totaltime", false]], "tp (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.tp", false]], "tprparser (class in 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false]], "transformations (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.transformations", false]], "transformations (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.transformations", false]], "transformations (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.transformations", false]], "transformations (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dcdreader property)": [[65, 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111, 113, 116, 117, 118, 122, 123, 124, 136, 142, 147, 161, 164, 170, 174], "your": [0, 3, 4, 7, 10, 12, 19, 21, 24, 26, 28, 31, 32, 35, 40, 42, 43, 52, 56, 63, 65, 74, 80, 93, 97, 110, 113, 123, 160], "yourmodul": 123, "yourscript": 123, "yourself": [10, 120, 124], "ysu": 65, "ython": 34, "yu": 65, "yy": 7, "yz": [31, 163], "z": [6, 7, 9, 15, 31, 56, 59, 63, 65, 69, 70, 71, 75, 78, 79, 80, 81, 85, 92, 94, 96, 110, 114, 119, 120, 124, 143, 158, 160, 172], "z1": [7, 172], "z2": 7, "z_lower": 172, "z_plus_view": 172, "z_upper": 172, "z_valu": 172, "zaxi": 119, "zcen": 92, "zdim": 7, "zerbino": 123, "zero": [9, 19, 20, 56, 61, 63, 69, 80, 92, 96, 98, 100, 110, 111, 112, 113, 114, 120, 141, 151], "zeta": 33, "zheng": 9, "zhiyi": 42, "zhou": [109, 123], "zink": 105, "ziolek": 123, "zip": [21, 110, 122], "zmax": [92, 115, 124, 172], "zmin": [92, 115, 124, 172], "zn": 105, "znd": 38, "zone": [92, 124], "zr": 105, "zsu": 65, "zu": 65, "zvalu": 69, "zz": 7, "\u00e1": 109, "\u00e5": [3, 5, 7, 22, 26, 42, 56, 59, 65, 69, 71, 74, 86, 89, 92, 96, 109, 162, 169], "\u00e5ngstrom": 63, "\u00e5ngstr\u00f6m": [7, 59, 65, 74, 169], "\u00ed": 109, "\u03b1": 12, "\u03bc": 169, "\u03c0": [12, 114], "\u03c6": 10, "\u03c8": 10}, "titles": ["4.3.1. Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "11.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "11.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "11.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "11.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "11.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "11. Auxiliary modules", "8. Converter modules", "8.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "8.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "8.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "8.8. Base classes \u2014 MDAnalysis.converters.base", "7.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "7.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "7.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "7.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "7.26. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "7.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "7.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "7.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "7.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "7.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "7.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "7.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "7.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "7.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "7.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "7.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "7.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "7.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "7.19. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "7.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "7.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "7.22. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "7.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "7.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "7.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "7.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "7.31. Base classes \u2014 MDAnalysis.coordinates.base", "7.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "7.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "7.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "7.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "7.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "7.29. Null output \u2014 MDAnalysis.coordinates.null", "7.33. Serialization of Coordinate Readers", "7.30. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "7. Coordinates modules", "8.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "12.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "12.1. Core functions of MDAnalysis", "12.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "12.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "12.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "12.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "12.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "12. Core modules", "17. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "6. Guesser modules", "6.1.2.3. Base guesser classes \u2014 MDAnalysis.guesser.base", "6.1.2.2. Default Guesser", "6.1.2.1. Context-specific guessers \u2014 MDAnalysis.guesser", "6.1.2.4. MDAnalysis topology tables", "14.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "14.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "14.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "14.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "14.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "14.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "14.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "14.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "14.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "14.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "14.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "14.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "14.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "14.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "14.2.10. Helper functions \u2014 MDAnalysis.lib.util", "14. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "18. References", "3. Selection commands", "10.2.6. Base classes for the selection writers", "10.2.4. CHARMM selections", "10.2.3. Gromacs selections", "10.2.5. Jmol selections", "10.2.2. PyMOL selections", "10.2.1. VMD selections", "10. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.26. Utility functions for the TPR topology parser", "5. Topology modules", "9. Trajectory transformations (\u201con-the-fly\u201d transformations)", "9.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "9.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "9.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "9.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "9.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "9.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "9.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "9.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "16. Constants and unit conversion \u2014 MDAnalysis.units", "15. Version information for MDAnalysis - MDAnalysis.version", "13.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "13.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "13. Visualization modules", "MDAnalysis documentation"], "titleterms": {"2d": 171, "3d": 172, "For": 34, "In": 86, "No": 164, "One": 5, "The": [26, 132], "To": 88, "_single_fram": 34, "_singleframeread": 88, "about": 115, "acceler": 110, "access": [48, 88], "accessor": 91, "acid": [32, 33, 43], "ad": [34, 44, 48], "addit": 43, "aggreg": 39, "aim": [59, 137], "algebra": 114, "algorithm": [15, 18, 27, 115, 123], "align": [0, 118], "also": 25, "amber": [74, 151], "an": [31, 48, 63, 86], "analysi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43], "analysisbas": 34, "angl": [4, 10, 33, 103, 157], "api": [48, 85, 101], "appli": 34, "applic": [4, 10, 12, 28, 40], "arbitrari": 86, "aromat": 103, "arrai": [86, 110, 120], "ascii": 74, "assign": 12, "atom": [1, 42, 94, 143, 157], "atomgroup": [91, 131], "atomicdist": 1, "attribut": [48, 85, 96], "autocorrel": [22, 23, 109], "auxiliari": [44, 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"updat": 32, "us": [3, 24, 26, 34, 42, 43, 83, 86, 101, 110, 122, 123], "usag": [0, 1, 44], "user": [99, 174], "util": [20, 21, 25, 28, 109, 120, 158], "variabl": 142, "version": [152, 170], "visual": [171, 172, 173], "vmd": 130, "volumetr": 43, "warn": 100, "water": [41, 42], "waterbridgeanalysi": 42, "waterdynam": 41, "when": 34, "whole": 123, "work": [22, 34, 67, 69], "workflow": 160, "wrap": 168, "wrapper": 106, "write": [3, 5, 34, 61, 63, 131], "writer": [81, 85, 125, 131], "x3dna": 28, "xdr": [78, 112], "xml": 141, "xtc": 79, "xvg": 45, "xyz": [80, 154], "your": [5, 34]}}) \ No newline at end of file diff --git a/dev/_modules/MDAnalysis/topology/ITPParser.html b/dev/_modules/MDAnalysis/topology/ITPParser.html index b9a2845e0e..539c4ecbe3 100644 --- a/dev/_modules/MDAnalysis/topology/ITPParser.html +++ b/dev/_modules/MDAnalysis/topology/ITPParser.html @@ -747,7 +747,15 @@

Source code for MDAnalysis.topology.ITPParser

if all(e.capitalize() in SYMB2Z for e in self.elements): attrs.append(Elements(np.array(self.elements, dtype=object), guessed=True)) - + warnings.warn( + "The elements attribute has been populated by guessing " + "elements from atom types. This behaviour has been " + "temporarily added to the ITPParser as we transition " + "to the new guessing API. " + "This behavior will be removed in release 3.0. " + "Please see issue #4698 for more information. ", + DeprecationWarning + ) else: warnings.warn("Element information is missing, elements attribute " "will not be populated. If needed these can be " diff --git a/dev/documentation_pages/analysis/wbridge_analysis.html b/dev/documentation_pages/analysis/wbridge_analysis.html index 6d54b28684..b5b66a8e99 100644 --- a/dev/documentation_pages/analysis/wbridge_analysis.html +++ b/dev/documentation_pages/analysis/wbridge_analysis.html @@ -1048,7 +1048,7 @@

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

default atom names that are treated as hydrogen acceptors (see Default heavy atom names for CHARMM27 force field.); use the keyword acceptors to add a list of additional acceptor names.

@@ -1056,7 +1056,7 @@

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

default heavy atom names whose hydrogens are treated as donors (see Default heavy atom names for CHARMM27 force field.); use the keyword donors to add a list of additional donor names.

diff --git a/dev/documentation_pages/coordinates/GSD.html b/dev/documentation_pages/coordinates/GSD.html index c2238ba02c..630dab7945 100644 --- a/dev/documentation_pages/coordinates/GSD.html +++ b/dev/documentation_pages/coordinates/GSD.html @@ -214,7 +214,7 @@

7.7.1. ClassesAdded in version 0.17.0.

-

Changed in version 2.0.0: Now use a picklable gsd.hoomd.HOOMDTrajectory– +

Changed in version 2.0.0: Now use a picklable gsd.hoomd.HOOMDTrajectory– GSDPicklable

@@ -899,10 +899,10 @@

7.7.1. Classes class MDAnalysis.coordinates.GSD.GSDPicklable[source]

Hoomd GSD file object (read-only) that can be pickled.

-

This class provides a file-like object (as by gsd.hoomd.open(), +

This class provides a file-like object (as by gsd.hoomd.open(), namely gsd.hoodm.HOOMDTrajectory) that, unlike file objects, can be pickled. Only read mode is supported.

-

When the file is pickled, filename and mode of gsd.fl.GSDFile in +

When the file is pickled, filename and mode of gsd.fl.GSDFile in the file are saved. On unpickling, the file is opened by filename. This means that for a successful unpickle, the original file still has to be accessible with its filename.

@@ -914,7 +914,7 @@

7.7.1. Classes
Parameters:
-

file (gsd.fl.GSDFile) – File to access.

+

file (gsd.fl.GSDFile) – File to access.

Example

@@ -941,7 +941,7 @@

7.7.1. ClassesMDAnalysis.coordinates.GSD.gsd_pickle_open(name: str, mode: str = 'r')[source]

Open hoomd schema GSD file with pickle function implemented.

This function returns a GSDPicklable object. It can be used as a -context manager, and replace the built-in gsd.hoomd.open() function +context manager, and replace the built-in gsd.hoomd.open() function in read mode that only returns an unpicklable file object.

Schema version will depend on the version of gsd module.

@@ -979,7 +979,7 @@

7.7.1. Classes

See also

-

MDAnalysis.lib.util.anyopen(), MDAnalysis.lib.picklable_file_io.pickle_open(), MDAnalysis.lib.picklable_file_io.bz2_pickle_open(), MDAnalysis.lib.picklable_file_io.gzip_pickle_open(), gsd.hoomd.open()

+

MDAnalysis.lib.util.anyopen(), MDAnalysis.lib.picklable_file_io.pickle_open(), MDAnalysis.lib.picklable_file_io.bz2_pickle_open(), MDAnalysis.lib.picklable_file_io.gzip_pickle_open(), gsd.hoomd.open()

Added in version 2.0.0.

diff --git a/dev/documentation_pages/coordinates/init.html b/dev/documentation_pages/coordinates/init.html index 1b108b228e..f3654eff0b 100644 --- a/dev/documentation_pages/coordinates/init.html +++ b/dev/documentation_pages/coordinates/init.html @@ -375,7 +375,7 @@

7.1.4. Supported coordinate formats

HOOMD [1]

gsd

r

-

HOOMD GSD format (using gsd.hoomd). +

HOOMD GSD format (using gsd.hoomd). Module MDAnalysis.coordinates.GSD

GAMESS

diff --git a/dev/index.html b/dev/index.html index 9eaca0db60..07e88ab6cc 100644 --- a/dev/index.html +++ b/dev/index.html @@ -149,7 +149,7 @@

MDAnalysis documentation

2.8.0-dev0

Date:
-

Oct 20, 2024

+

Oct 24, 2024

MDAnalysis (www.mdanalysis.org) is an object-oriented python diff --git a/dev/searchindex.js b/dev/searchindex.js index ff31004e62..6183aff641 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"AMBER PRMTOP topology parser": [[151, null]], "AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ": [[74, null]], "ASCII TRAJ trajectories": [[74, "ascii-traj-trajectories"]], "About the algorithm": [[115, "about-the-algorithm"]], "About the code": [[115, "about-the-code"]], "Accessing auxiliary attributes": [[48, "accessing-auxiliary-attributes"]], "Adding EDR data to trajectories": [[44, "adding-edr-data-to-trajectories"]], "Adding an auxiliary to a trajectory": [[48, "adding-an-auxiliary-to-a-trajectory"]], "Adding parallelization to your own analysis class": [[34, "adding-parallelization-to-your-own-analysis-class"]], "Additional dependencies": [[43, "additional-dependencies"]], "Algorithm": [[27, "algorithm"]], "Analysis Classes": [[10, "analysis-classes"]], "Analysis backends \u2014 MDAnalysis.analysis.backends": [[2, null]], "Analysis building blocks \u2014 MDAnalysis.analysis.base": [[3, null]], "Analysis classes": [[4, "analysis-classes"], [12, "analysis-classes"], [28, "analysis-classes"], [40, "analysis-classes"]], "Analysis data files": [[6, null]], "Analysis modules": [[43, null]], "Analysis results and their aggregation \u2014 MDAnalysis.analysis.results": [[39, null]], "Analysis tasks": [[21, "analysis-tasks"]], "Angles": [[103, "angles"]], "Aromaticities": [[103, "aromaticities"]], "Arrays": [[120, "arrays"]], "Assigning secondary structure of a PDB file": [[12, "assigning-secondary-structure-of-a-pdb-file"]], "Atom selection Hierarchy \u2014 MDAnalysis.core.selection": [[94, null]], "Atom styles": [[143, "atom-styles"]], "AtomGroup accessors \u2014 MDAnalysis.core.accessors": [[91, null]], "Attributes": [[48, "attributes"], [48, "id2"], [85, "attributes"], [85, "id19"], [85, "id21"]], "Autocorrelation 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"id5"]], "BaseReaderTest and MultiframeReaderTest": [[88, "basereadertest-and-multiframereadertest"]], "Basic usage": [[1, "basic-usage"]], "Binary NetCDF trajectories": [[74, "binary-netcdf-trajectories"]], "Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat": [[4, null]], "Bonds": [[103, "bonds"]], "Boolean": [[124, "boolean"]], "Building blocks for Analysis": [[43, "building-blocks-for-analysis"]], "Building blocks for Transformation Classes": [[160, "building-blocks-for-transformation-classes"]], "Building parallel h5py and HDF5 on Linux": [[63, "building-parallel-h5py-and-hdf5-on-linux"]], "CHARMM selections": [[126, null]], "CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD": [[55, null]], "CRD topology parser": [[133, null]], "Calculating RMSD for multiple domains": [[40, "calculating-rmsd-for-multiple-domains"]], "Calculating average secondary structure of a trajectory": [[12, "calculating-average-secondary-structure-of-a-trajectory"]], "Calculating path similarity \u2014 MDAnalysis.analysis.psa": [[37, null]], "Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms": [[40, null]], "Capabilities": [[69, "capabilities"]], "ChainReader \u2014 MDAnalysis.coordinates.chain": [[82, null]], "Chemical units": [[92, "chemical-units"]], "Citation": [[174, "citation"]], "Citations for included algorithms and modules": [[123, "citations-for-included-algorithms-and-modules"]], "Citations for the whole MDAnalysis library": [[123, "citations-for-the-whole-mdanalysis-library"]], "Citations using Duecredit": [[123, "citations-using-duecredit"]], "Class decorators": [[120, "class-decorators"]], "Class definitions for the TPRParser": [[158, "class-definitions-for-the-tprparser"]], "Classes": [[2, "classes"], [3, "classes"], [5, "classes"], [9, "classes"], [24, "classes"], [31, "classes"], [39, "classes"], [42, "classes"], [44, "classes"], [51, "classes"], [51, "id5"], [52, "classes"], [52, "id2"], [53, "classes"], [53, 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MDAnalysis.analysis.encore.clustering.ClusterCollection": [[15, "cluster-representation-mdanalysis-analysis-encore-clustering-clustercollection"]], "Clustering": [[15, null]], "Clustering algorithms": [[15, "clustering-algorithms"]], "Code management": [[120, "code-management"]], "Code snippets": [[122, "code-snippets"]], "Collections": [[92, "collections"]], "Combining Multiple Replicates": [[31, "combining-multiple-replicates"]], "Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core": [[47, null]], "Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core": [[84, null]], "Common functions for topology building \u2014 MDAnalysis.topology.core": [[156, null]], "Common usage": [[0, "common-usage"]], "Computing Self-Diffusivity": [[31, "computing-self-diffusivity"]], "Computing an MSD": [[31, "computing-an-msd"]], "Connectivity": [[114, "connectivity"]], "Constants and unit conversion \u2014 MDAnalysis.units": [[169, null]], "Constructing a Reader from a numpy array": [[86, "constructing-a-reader-from-a-numpy-array"]], "Containers and lists": [[120, "containers-and-lists"]], "Context-specific guessers \u2014 MDAnalysis.guesser": [[104, null]], "Convenience functions": [[113, "convenience-functions"]], "Conversions": [[169, "conversions"]], "Converter modules": [[50, null]], "Converters": [[81, "converters"]], "Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align": [[0, null]], "Coordinates modules": [[90, null]], "Core Topology Objects \u2014 MDAnalysis.core.topologyobjects": [[97, null]], "Core Topology object \u2014 MDAnalysis.core.topology": [[95, null]], "Core functions of MDAnalysis": [[93, null]], "Core modules": [[99, null]], "Core object: Universe \u2014 MDAnalysis.core.universe": [[98, null]], "Core objects: Containers \u2014 MDAnalysis.core.groups": [[92, null]], "Correlations utilities \u2014 MDAnalysis.lib.correlations": [[109, null]], "Covariance calculation \u2014 encore.covariance": [[17, null]], "Creating an in-memory trajectory of a sub-system": [[86, "creating-an-in-memory-trajectory-of-a-sub-system"]], "Creating complex transformation classes": [[160, "creating-complex-transformation-classes"]], "Creating complex transformation closure functions": [[160, "creating-complex-transformation-closure-functions"]], "Creating densities": [[7, "creating-densities"]], "Creating transformations": [[160, "creating-transformations"]], "Current Limitations": [[72, "current-limitations"]], "Currently implemented picklable IO Formats": [[88, "currently-implemented-picklable-io-formats"]], "Currently implemented transformations": [[160, "currently-implemented-transformations"]], "Custom exceptions and warnings \u2014 MDAnalysis.exceptions": [[100, null]], "DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD": [[56, null]], "DESRES Molecular Structure file format topology parser": [[135, null]], "DESRES file format \u2014 MDAnalysis.coordinates.DMS": [[58, null]], "DL Poly format Topology 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"development-notes"]], "Dielectric \u2014 MDAnalysis.analysis.dielectric": [[8, null]], "Diffusion Map tutorial": [[9, "diffusion-map-tutorial"]], "Diffusion map \u2014 MDAnalysis.analysis.diffusionmap": [[9, null]], "Dihedral angles": [[33, "dihedral-angles"]], "Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals": [[10, null]], "Dihedrals": [[103, "dihedrals"]], "Dimensionality Reduction": [[43, "dimensionality-reduction"]], "Dimensionality reduction": [[18, null]], "Dimensionality reduction algorithms": [[18, "dimensionality-reduction-algorithms"]], "Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix": [[16, null]], "Distance analysis \u2014 MDAnalysis.analysis.distances": [[11, null]], "Distance calculation library \u2014 MDAnalysis.lib.c_distances": [[107, null]], "Distances": [[32, "distances"], [33, "distances"]], "Distances and contacts": [[43, "distances-and-contacts"]], "Dump files": [[65, "dump-files"]], "Dynamic selections": [[124, "dynamic-selections"]], "EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR": [[44, null]], "ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore": [[13, null]], "Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm": [[21, null]], "Elements": [[103, "elements"]], "Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity": [[19, null]], "Example applications": [[4, "example-applications"], [10, "example-applications"], [12, "example-applications"], [28, "example-applications"], [40, "example-applications"]], "Example for working with mol2 files": [[67, "example-for-working-with-mol2-files"]], "Example of using a standard analysis tool": [[3, "example-of-using-a-standard-analysis-tool"]], "Example use": [[24, "example-use"]], "Example use of HydrogenBondAnalysis": [[26, "example-use-of-hydrogenbondanalysis"]], "Example uses of guessers": [[101, "example-uses-of-guessers"]], "Example: Loading a LAMMPS simulation": [[65, "example-loading-a-lammps-simulation"]], "Example: Loading an H5MD simulation": [[63, "example-loading-an-h5md-simulation"]], "Example: Opening an H5MD file in parallel": [[63, "example-opening-an-h5md-file-in-parallel"]], "Example: Writing an H5MD file": [[63, "example-writing-an-h5md-file"]], "Examples": [[122, "examples"]], "Examples for contact analysis": [[5, "examples-for-contact-analysis"]], "Examples for working with PDB files": [[69, "examples-for-working-with-pdb-files"]], "Extended PDB topology parser": [[136, null]], "FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser": [[137, null]], "FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS": [[59, null]], "Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot": [[118, null]], "Fast _single_frame compared to reading from disk": [[34, "fast-single-frame-compared-to-reading-from-disk"]], "Fast distance array computation \u2014 MDAnalysis.lib.distances": [[110, null]], "File Access": [[88, 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"Getting involved": [[174, "getting-involved"]], "Getting started with analysis": [[43, "getting-started-with-analysis"]], "Gromacs portable run input TPR format parser": [[152, null]], "Gromacs selections": [[127, null]], "Guesser modules": [[101, null]], "Guessing behavior": [[103, "guessing-behavior"]], "Guessing using guess_TopologyAttrs() API": [[101, "guessing-using-guess-topologyattrs-api"]], "H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD": [[63, null]], "HELANAL \u2014 analysis of protein helices": [[24, null]], "HOLE Analysis \u2014 MDAnalysis.analysis.hole2": [[25, "id4"]], "HOLE Analysis \u2014 mdahole2.analysis.templates": [[25, "hole-analysis-mdahole2-analysis-templates"]], "HOLE Analysis \u2014 mdahole2.analysis.utils": [[25, "hole-analysis-mdahole2-analysis-utils"]], "HOLE analysis \u2014 MDAnalysis.analysis.hole2": [[25, null]], "HOOMD XML topology parser": [[141, null]], "Heavy atom types for GLYCAM06 force field.": [[42, "id4"]], "Helper classes": [[81, "helper-classes"]], "Helper classes for parallelization": [[34, "helper-classes-for-parallelization"]], "Helper functions": [[0, "helper-functions"], [83, "helper-functions"], [95, "helper-functions"]], "Helper functions \u2014 MDAnalysis.lib.util": [[120, null]], "Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations": [[119, null]], "How does parallelization work": [[34, "how-does-parallelization-work"]], "How to perform WaterBridgeAnalysis": [[42, "how-to-perform-waterbridgeanalysis"]], "How to serialize a new reader": [[88, "how-to-serialize-a-new-reader"]], "How to transformations": [[160, "how-to-transformations"]], "How to use parallelization": [[34, "how-to-use-parallelization"]], "How to use the MemoryReader": [[86, "how-to-use-the-memoryreader"]], "How to write selections": [[131, "how-to-write-selections"]], "Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis": [[26, null]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)": [[23, null]], "Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel": [[22, null]], "Hydrogen bonding": [[43, "hydrogen-bonding"]], "INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD": [[64, null]], "ITP topology parser": [[142, null]], "Implementation notes": [[169, "implementation-notes"]], "Important objects for users": [[99, "important-objects-for-users"]], "Improper Dihedrals": [[103, "improper-dihedrals"]], "In-memory representation of arbitrary trajectories": [[86, "in-memory-representation-of-arbitrary-trajectories"]], "Included trajectories": [[122, "included-trajectories"]], "Index": [[124, "index"]], "Indices and tables": [[174, "indices-and-tables"]], "Input": [[22, "input"], [26, "input"]], "Installing MDAnalysis": [[174, "installing-mdanalysis"]], "Intermittency Function": [[109, "intermittency-function"]], "Iterating by an auxiliary": [[48, "iterating-by-an-auxiliary"]], "Janin analysis": [[10, "janin-analysis"]], "Jmol selections": [[128, null]], "LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS": [[65, null]], "LAMMPSParser": [[143, null]], "Leaflet identification \u2014 MDAnalysis.analysis.leaflet": [[27, null]], "Legacy analysis modules": [[43, "legacy-analysis-modules"]], "Legacy modules": [[29, "legacy-modules"]], "Levels": [[92, "levels"]], "Libmdanalysis": [[121, "libmdanalysis"]], "Library functions \u2014 MDAnalysis.lib": [[121, null]], "Linear Density \u2014 MDAnalysis.analysis.lineardensity": [[30, null]], "Linear algebra": [[114, "linear-algebra"]], "Liquids": [[43, "liquids"]], "List of modules": [[121, "list-of-modules"]], "Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd": [[111, null]], "Low level file formats": [[121, "low-level-file-formats"]], "Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr": [[112, null]], "Low-level modules for MDAnalysis.lib.distances": [[110, "low-level-modules-for-mdanalysis-lib-distances"]], "MDAnalysis documentation": [[174, null]], "MDAnalysis topology tables": [[105, null]], "MDAnalysis.analysis.legacy \u2014 Legacy analysis code": [[29, null]], "MMTF Topology Parser": [[144, null]], "MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF": [[66, null]], "MOL2 file format \u2014 MDAnalysis.coordinates.MOL2": [[67, null], [145, null]], "MOL2 format notes": [[67, "mol2-format-notes"]], "Macromolecules": [[43, "macromolecules"]], "Masses": [[103, "masses"]], "Mathematical helper functions \u2014 MDAnalysis.lib.mdamath": [[114, null]], "Mean Squared Displacement \u2014 MDAnalysis.analysis.msd": [[31, null]], "Membranes and membrane proteins": [[43, "membranes-and-membrane-proteins"]], "Methods": [[48, "methods"], [48, "id3"], [85, "methods"], [85, "id18"], [85, "id20"], [85, "id22"]], "Methods in AnalysisBase for parallelization": [[34, "methods-in-analysisbase-for-parallelization"]], "Minimal topology parser": [[146, null]], "Miscellaneous": [[88, "miscellaneous"]], "Module": [[25, "module-MDAnalysis.analysis.hole2"]], "Modules": [[13, "modules"]], "Modules and packages": [[120, "modules-and-packages"]], "Multiple selections": [[131, "multiple-selections"]], "NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN": [[68, null]], "Native contacts analysis \u2014 MDAnalysis.analysis.contacts": [[5, null]], "Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch": [[106, null]], "Neighbor search library \u2014 MDAnalysis.lib.nsgrid": [[115, null]], "No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump": [[164, null]], "Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo": [[33, null]], "Nucleic acids": [[43, "nucleic-acids"]], "Null output \u2014 MDAnalysis.coordinates.null": [[87, null]], "One-dimensional contact analysis": [[5, "one-dimensional-contact-analysis"]], "OpenMM structure I/O \u2014 MDAnalysis.converters.OpenMM": [[51, "openmm-structure-i-o-mdanalysis-converters-openmm"]], "OpenMM topology parser MDAnalysis.converters.OpenMMParser": [[51, null]], "Ordered selections": [[124, "ordered-selections"]], "Other functions and classes for logging purposes": [[113, "other-functions-and-classes-for-logging-purposes"]], "Out of memory issues": [[34, "out-of-memory-issues"]], "Output": [[22, "output"], [26, "output"]], "Output as Network": [[42, "output-as-network"]], "Output as Timeseries": [[42, "output-as-timeseries"]], "Overview": [[121, "overview"]], "Overview over MDAnalysis": [[122, null]], "PCA Tutorial": [[35, "pca-tutorial"]], "PDB Topology Parser": [[147, null]], "PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB": [[69, null]], "PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT": [[70, null]], "PDBQT topology parser": [[148, null]], "PQR file format \u2014 MDAnalysis.coordinates.PQR": [[71, null]], "PQR topology parser": [[149, null]], "PSF topology parser": [[150, null]], "Parallel analysis": [[34, null]], "Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp": [[108, null]], "ParmEd structure I/O \u2014 MDAnalysis.converters.ParmEd": [[52, "parmed-structure-i-o-mdanalysis-converters-parmed"]], "ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser": [[52, null]], "Pattern matching": [[124, "pattern-matching"]], "PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree": [[117, null]], "Phases": [[33, "phases"]], "Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io": [[116, null]], "Polymer analysis \u2014 MDAnalysis.analysis.polymer": [[36, null]], "Polymers": [[43, "polymers"]], "Preexisting selections and modifiers": [[124, "preexisting-selections-and-modifiers"]], "Preprocessor variables": [[142, "preprocessor-variables"]], "Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca": [[35, null]], "Private attributes": [[85, "private-attributes"]], "Progress bar is missing": [[34, "progress-bar-is-missing"]], "PyMOL selections": [[129, null]], "RDKit molecule I/O \u2014 MDAnalysis.converters.RDKit": [[53, "rdkit-molecule-i-o-mdanalysis-converters-rdkit"]], "RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser": [[53, null]], "RMS-fitting tutorial": [[0, "rms-fitting-tutorial"]], "Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf": [[38, null]], "Ramachandran analysis": [[10, "ramachandran-analysis"]], "Readers": [[81, "readers"], [85, "readers"]], "Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory": [[86, null]], "Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles": [[83, null]], "Recreating auxiliaries": [[48, "recreating-auxiliaries"]], "Reference plots": [[10, "reference-plots"]], "References": [[13, "references"], [123, null]], "References and footnotes": [[169, "references-and-footnotes"]], "Registry": [[48, "registry"], [85, 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mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader", false]], "auxreader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxReader", false]], "auxreader() (in module mdanalysis.auxiliary.core)": [[47, "MDAnalysis.auxiliary.core.auxreader", false]], "auxstep (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxStep", false]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.auxstep", false]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure", false]], "backboneselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BackboneSelection", false]], "backendbase (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendBase", false]], "backenddask (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendDask", false]], "backendmultiprocessing (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendMultiprocessing", false]], "backendserial (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendSerial", false]], "baseselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BaseSelection", false]], "bat (class in mdanalysis.analysis.bat)": [[4, "MDAnalysis.analysis.bat.BAT", false]], "bat (mdanalysis.analysis.bat.bat.results attribute)": [[4, "MDAnalysis.analysis.bat.BAT.results.bat", false]], "bbox (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bBox", false]], "bbox() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bbox", false]], "bbox() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bbox", false]], "bbox() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bbox", false]], "between() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.between", false]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bF", false]], "bfactor (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bfactor", false]], "bfactor() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor", false]], "bfactor_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor_setter", false]], "bfactors (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.bfactors", false]], "bfactors (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.segment property)": [[92, "MDAnalysis.core.groups.Segment.bfactors", false]], "bfactors (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.bfactors", false]], "bfactors() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors", false]], "bfactors_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors_setter", false]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins", false]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr", false]], "blocks (mdanalysis.coordinates.tng.tngreader property)": [[72, "MDAnalysis.coordinates.TNG.TNGReader.blocks", false]], "blocks_of() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.blocks_of", false]], "bond (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Bond", false]], "bond (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bond", false]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation", false]], "bonded_atoms (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bonded_atoms", false]], "bonded_atoms() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.bonded_atoms", false]], "bonds (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Bonds", false]], "bonds (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.bonds", false]], "bonds() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.bonds", false]], "boolselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BoolSelection", false]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[14, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix", false]], "box (class in mdanalysis.topology.tpr.obj)": [[158, "MDAnalysis.topology.tpr.obj.Box", false]], "box_volume() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.box_volume", false]], "bsphere() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.bsphere", false]], "bsphere() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.bsphere", false]], "btop (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bTop", false]], "bufferiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.BufferIOPicklable", false]], "bv (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bV", false]], "bx (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bX", false]], "bynumselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByNumSelection", false]], "byresselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.ByResSelection", false]], "bz2_pickle_open() (in module 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method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.calc_representative", false]], "calcrmsdrotationalmatrix() (in module mdanalysis.lib.qcprot)": [[118, "MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix", false]], "capped_distance() (in module mdanalysis.lib.distances)": [[110, "MDAnalysis.lib.distances.capped_distance", false]], "cartesian() (mdanalysis.analysis.bat.bat method)": [[4, "MDAnalysis.analysis.bat.BAT.Cartesian", false]], "cdf (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.cdf", false]], "cdf (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.cdf", false]], "center() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center", false]], "center() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center", false]], "center() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center", false]], "center_in_box (class in mdanalysis.transformations.translate)": [[167, "MDAnalysis.transformations.translate.center_in_box", false]], "center_of_charge() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_charge", false]], "center_of_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.center_of_charge", false]], "center_of_geometry() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_geometry", false]], "center_of_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.center_of_mass", false]], "centers() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.centers", false]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, 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attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char", false]], "char_std (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.char_std", false]], "charge_density (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density", false]], "charge_density_stddev (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.charge_density_stddev", false]], "charges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Charges", false]], "chargeunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.chargeUnit_factor", false]], "charmm_bitfield (mdanalysis.lib.formats.libdcd.dcdfile attribute)": [[111, "MDAnalysis.lib.formats.libdcd.DCDFile.charmm_bitfield", false]], "check_atomgroup_not_empty() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.check_atomgroup_not_empty", false]], "check_box() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.check_box", false]], "check_chemfiles_version() (in module mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.check_chemfiles_version", false]], "check_compatible() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.check_compatible", false]], "check_compressed_format() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.check_compressed_format", false]], "check_coords() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.check_coords", false]], "check_slice_indices() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.check_slice_indices", false]], "check_slice_indices() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.check_slice_indices", false]], "chemfilespicklable (class in mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.ChemfilesPicklable", false]], "chemfilesreader (class in mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.ChemfilesReader", false]], "chemfileswriter (class in mdanalysis.coordinates.chemfiles)": [[83, "MDAnalysis.coordinates.chemfiles.ChemfilesWriter", false]], "chi1_selection() (mdanalysis.core.groups.residue method)": [[92, "MDAnalysis.core.groups.Residue.chi1_selection", false]], "chi1_selection() (mdanalysis.core.topologyattrs.atomnames method)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.chi1_selection", false]], "chi1_selections() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.chi1_selections", false]], "chi1_selections() (mdanalysis.core.topologyattrs.atomnames method)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.chi1_selections", false]], "clear_handlers() (in module mdanalysis.lib.log)": [[113, "MDAnalysis.lib.log.clear_handlers", false]], "close() (mdanalysis.auxiliary.base.auxfilereader method)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader.close", false]], "close() (mdanalysis.converters.base.converterbase method)": [[54, "MDAnalysis.converters.base.ConverterBase.close", false]], "close() (mdanalysis.converters.openmmparser.openmmapptopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser.close", false]], "close() (mdanalysis.converters.openmmparser.openmmtopologyparser method)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser.close", false]], "close() (mdanalysis.converters.parmedparser.parmedparser method)": [[52, "MDAnalysis.converters.ParmEdParser.ParmEdParser.close", false]], "close() (mdanalysis.converters.rdkitparser.rdkitparser method)": [[53, "MDAnalysis.converters.RDKitParser.RDKitParser.close", false]], "close() (mdanalysis.coordinates.base.converterbase method)": [[81, "MDAnalysis.coordinates.base.ConverterBase.close", false]], "close() (mdanalysis.coordinates.base.iobase method)": [[81, "MDAnalysis.coordinates.base.IOBase.close", false]], "close() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.close", false]], "close() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.close", false]], "close() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.close", false]], "close() (mdanalysis.coordinates.chain.chainreader method)": [[82, "MDAnalysis.coordinates.chain.ChainReader.close", false]], "close() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.close", false]], "close() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.close", false]], "close() (mdanalysis.coordinates.dlpoly.historyreader method)": [[57, "MDAnalysis.coordinates.DLPoly.HistoryReader.close", false]], "close() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.close", false]], "close() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.close", false]], "close() (mdanalysis.coordinates.gms.gmsreader method)": [[60, "MDAnalysis.coordinates.GMS.GMSReader.close", false]], "close() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.close", false]], "close() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.close", false]], "close() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.close", false]], "close() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.close", false]], "close() (mdanalysis.coordinates.lammps.datawriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter.close", false]], "close() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.close", false]], "close() (mdanalysis.coordinates.lammps.dcdwriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter.close", false]], "close() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.close", false]], "close() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.close", false]], "close() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.close", false]], "close() 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"MDAnalysis.coordinates.LAMMPS.DATAWriter", false]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN", false]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[111, "MDAnalysis.lib.formats.libdcd.DCDFile", false]], "dcdreader (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDReader", false]], "dcdreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader", false]], "dcdwriter (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter", false]], "dcdwriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter", false]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.decompose_matrix", false]], "dedent_docstring() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.dedent_docstring", false]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS", false]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS", false]], "default_format (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.default_format", false]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms", false]], "defaultguesser (class in mdanalysis.guesser.default_guesser)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser", false]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.define_unpack_real", false]], "del_topologyattr() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.del_TopologyAttr", false]], "del_topologyattr() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.del_TopologyAttr", false]], "delete_angles() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_angles", false]], "delete_bonds() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_bonds", false]], "delete_dihedrals() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_dihedrals", false]], "delete_impropers() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_impropers", false]], "delta (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.delta", false]], "delta (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.delta", false]], "density (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.Density", false]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.density", false]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.results.density", false]], "densityanalysis (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.DensityAnalysis", false]], "densityunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.densityUnit_factor", false]], "deprecate() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.deprecate", false]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant", false]], "difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.difference", false]], "difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.difference", false]], "difference() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.difference", false]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap", false]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[10, "MDAnalysis.analysis.dihedrals.Dihedral", false]], "dihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Dihedral", false]], "dihedral (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dihedral", false]], "dihedral() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.dihedral", false]], "dihedral() (mdanalysis.core.topologyobjects.dihedral method)": [[97, "MDAnalysis.core.topologyobjects.Dihedral.dihedral", false]], "dihedrals (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Dihedrals", false]], "dihedrals (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dihedrals", false]], "dihedrals() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dihedrals", false]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim", false]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac", false]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[18, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod", false]], "dimensions (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dimensions", false]], "dimensions (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.dimensions", false]], "dimensions (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dimensions", false]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity", false]], "dipole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_moment", false]], "dipole_vector() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_vector", false]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence", false]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence", false]], "dist() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.dist", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix", false]], "distance() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.distance", false]], "distance_array() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.distance_array", false]], "distance_array() (in module mdanalysis.lib.distances)": [[110, "MDAnalysis.lib.distances.distance_array", false]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix", false]], "distances (mdanalysis.analysis.nucleicacids.majorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.minorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.distances", false]], "dmsparser (class in 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false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray 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(mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[123, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": 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attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[158, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[113, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [120, "index-0", false], [120, "index-1", false], [123, "index-0", false], [161, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[136, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[118, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[115, "MDAnalysis.lib.nsgrid.FastNS", false]], "fep_state (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.fep_state", false]], "fgen (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.fgen", false]], "fhiaimsparser (class in mdanalysis.topology.fhiaimsparser)": [[137, "MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser", false]], "fhiaimsreader (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader", false]], "fhiaimswriter (class in mdanalysis.coordinates.fhiaims)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter", false]], "file_tag (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.file_tag", false]], "fileformatwarning": [[100, "MDAnalysis.exceptions.FileFormatWarning", false]], "fileiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.FileIOPicklable", false]], "filename (mdanalysis.analysis.align.aligntraj attribute)": [[0, "MDAnalysis.analysis.align.AlignTraj.filename", false]], "filename (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.filename", false]], "filename() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.filename", false]], "fileno() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.fileno", false]], "fileversion_err() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.fileVersion_err", false]], "find_fragments() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.find_fragments", false]], "find_hydrogen_donors() (in module mdanalysis.analysis.hydrogenbonds.hbond_autocorrel)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.find_hydrogen_donors", false]], "fit (mdanalysis.analysis.polymer.persistencelength attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.fit", false]], "fit (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.fit", false]], "fit_exponential_decay() (in module mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.fit_exponential_decay", false]], "fit_rot_trans (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_rot_trans", false]], "fit_translation (class in mdanalysis.transformations.fit)": [[163, "MDAnalysis.transformations.fit.fit_translation", false]], "fixedwidth_bins() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.fixedwidth_bins", false]], "flatten_dict() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.flatten_dict", false]], "flatten_sequence() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.flatten_sequence", false]], "float_mean() (mdanalysis.analysis.results.resultsgroup static method)": [[39, "MDAnalysis.analysis.results.ResultsGroup.float_mean", false]], "float_pattern (in module mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FLOAT_PATTERN", false]], "floatrangeselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.FloatRangeSelection", false]], "fluct (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.fluct", false]], "flush() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.flush", false]], "fmt (mdanalysis.coordinates.fhiaims.fhiaimswriter attribute)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.fmt", false]], "fmt (mdanalysis.coordinates.gro.growriter attribute)": [[61, "MDAnalysis.coordinates.GRO.GROWriter.fmt", false]], "force (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.force", false]], "forces (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.forces", false]], "forces (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.forces", false]], "forceunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.forceUnit_factor", false]], "formalcharges (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.FormalCharges", false]], "format (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.format", false]], "format (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.format", false]], "format (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.format", false]], "format (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.format", false]], "format (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.format", false]], "format_from_filename_extension() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.format_from_filename_extension", false]], "fortran_format_regex (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.FORTRAN_format_regex", false]], "fortranreader (class in mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.FORTRANReader", false]], "fragindex (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragindex", false]], "fragindex() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindex", false]], "fragindices (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragindices", false]], "fragindices() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragindices", false]], "fragment (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.fragment", false]], "fragment() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragment", false]], "fragments (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.fragments", false]], "fragments() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.fragments", false]], "frame (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.frame", false]], "frame (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.frame", false]], "frame (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.frame", false]], "frame (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.frame", false]], "frame (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.frame", false]], "frame (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.frame", false]], "frame (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.frame", false]], "frame (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.frame", false]], "frame (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.frame", false]], "frame (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.frame", false]], "frame (mdanalysis.coordinates.pdb.extendedpdbreader property)": 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"MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[149, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.guess_format", false]], "guess_gasteiger_charges() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_gasteiger_charges", false]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens", false]], "guess_improper_dihedrals() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_improper_dihedrals", false]], "guess_masses() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_masses", false]], "guess_topologyattrs() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.guess_TopologyAttrs", false]], "guess_types() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_types", false]], "guessed_attributes (mdanalysis.core.topology.topology property)": [[95, "MDAnalysis.core.topology.Topology.guessed_attributes", false]], "guesserbase (class in mdanalysis.guesser.base)": [[102, "MDAnalysis.guesser.base.GuesserBase", false]], "gyration_moments() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.gyration_moments", false]], "gyration_moments() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.gyration_moments", false]], "gzip_pickle_open() (in module mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.gzip_pickle_open", false]], "gzippicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.GzipPicklable", false]], "h5md_version (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.H5MD_VERSION", false]], "h5mdreader (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader", false]], "h5mdwriter (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter", false]], "h5pypicklable (class in mdanalysis.coordinates.h5md)": [[63, "MDAnalysis.coordinates.H5MD.H5PYPicklable", false]], "hard_cut_q() (in module mdanalysis.analysis.contacts)": 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"MDAnalysis.coordinates.timestep.Timestep.has_positions", false]], "has_valid_coordinates() (mdanalysis.coordinates.base.writerbase method)": [[81, "MDAnalysis.coordinates.base.WriterBase.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.dcd.dcdwriter method)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.fhiaims.fhiaimswriter method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.h5md.h5mdwriter method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.datawriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.lammps.dcdwriter method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.trr.trrwriter method)": [[75, "MDAnalysis.coordinates.TRR.TRRWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xdr.xdrbasewriter method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseWriter.has_valid_coordinates", false]], "has_valid_coordinates() (mdanalysis.coordinates.xtc.xtcwriter method)": [[79, "MDAnalysis.coordinates.XTC.XTCWriter.has_valid_coordinates", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.has_velocities", false]], "has_velocities (mdanalysis.coordinates.h5md.h5mdwriter property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.has_velocities", false]], "has_velocities (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.has_velocities", false]], "hasmethod() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.hasmethod", false]], "hbonds 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"MDAnalysis.analysis.nuclinfo.hydroxyl", false]], "iatoms (mdanalysis.topology.tpr.obj.ilist attribute)": [[158, "MDAnalysis.topology.tpr.obj.Ilist.iatoms", false]], "icodes (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.ICodes", false]], "id (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.id", false]], "ik (mdanalysis.topology.tpr.obj.ilist attribute)": [[158, "MDAnalysis.topology.tpr.obj.Ilist.ik", false]], "ilist (class in mdanalysis.topology.tpr.obj)": [[158, "MDAnalysis.topology.tpr.obj.Ilist", false]], "improper (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.improper", false]], "improper() (mdanalysis.core.topologyobjects.improperdihedral method)": [[97, "MDAnalysis.core.topologyobjects.ImproperDihedral.improper", false]], "improperdihedral (class in mdanalysis.core.topologyobjects)": [[97, 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"MDAnalysis.topology.TOPParser.TOPParser.parsesection_mapper", false]], "partner() (mdanalysis.core.topologyobjects.bond method)": [[97, "MDAnalysis.core.topologyobjects.Bond.partner", false]], "partner() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.partner", false]], "path": [[120, "index-0", false]], "pbc (mdanalysis.lib.pkdtree.periodickdtree property)": [[117, "MDAnalysis.lib.pkdtree.PeriodicKDTree.pbc", false]], "pca (class in mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.PCA", false]], "pdbparser (class in mdanalysis.topology.pdbparser)": [[147, "MDAnalysis.topology.PDBParser.PDBParser", false]], "pdbqtparser (class in mdanalysis.topology.pdbqtparser)": [[148, "MDAnalysis.topology.PDBQTParser.PDBQTParser", false]], "pdbqtreader (class in mdanalysis.coordinates.pdbqt)": [[70, "MDAnalysis.coordinates.PDBQT.PDBQTReader", false]], "pdbqtwriter (class in mdanalysis.coordinates.pdbqt)": [[70, "MDAnalysis.coordinates.PDBQT.PDBQTWriter", false]], "pdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.PDBReader", false]], "pdbwriter (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter", false]], "pdot() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.pdot", false]], "per_object (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.per_object", false]], "periodic (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.periodic", false]], "periodickdtree (class in mdanalysis.lib.pkdtree)": [[117, "MDAnalysis.lib.pkdtree.PeriodicKDTree", false]], "persistencelength (class in mdanalysis.analysis.polymer)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength", false]], "phase_as() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.phase_as", false]], "phase_cp() (in module 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"MDAnalysis.core.groups.Atom.position", false]], "positionaverager (class in mdanalysis.transformations.positionaveraging)": [[165, "MDAnalysis.transformations.positionaveraging.PositionAverager", false]], "positions (mdanalysis.analysis.align.averagestructure attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.positions", false]], "positions (mdanalysis.analysis.align.averagestructure.results attribute)": [[0, "MDAnalysis.analysis.align.AverageStructure.results.positions", false]], "positions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.positions", false]], "positions (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.positions", false]], "pqrparser (class in mdanalysis.topology.pqrparser)": [[149, "MDAnalysis.topology.PQRParser.PQRParser", false]], "pqrreader (class in mdanalysis.coordinates.pqr)": [[71, "MDAnalysis.coordinates.PQR.PQRReader", false]], "pqrwriter (class in 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"psi_selections() (mdanalysis.core.topologyattrs.atomnames method)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.psi_selections", false]], "ptype (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.ptype", false]], "purermsd() (in module mdanalysis.analysis.encore.cutils)": [[20, "MDAnalysis.analysis.encore.cutils.PureRMSD", false]], "q (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.q", false]], "q1q2() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.q1q2", false]], "qb (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.qB", false]], "quadrupole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.quadrupole_moment", false]], "quadrupole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.quadrupole_moment", false]], "quadrupole_moment() 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"MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[158, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], 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"MDAnalysis.core.groups.AtomGroup.subtract", false]], "subtract() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.subtract", false]], "subtract() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.subtract", false]], "summary (mdanalysis.analysis.helix_analysis.helanal.results attribute)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL.results.summary", false]], "supported_versions (in module mdanalysis.topology.tpr)": [[158, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS", false]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS", false]], "symmetric_difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.symmetric_difference", false]], "symmetric_difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.symmetric_difference", false]], 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"MDAnalysis.lib.formats.libmdaxdr.XTCFile.tell", false]], "tell() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.tell", false]], "tempfactors (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors", false]], "terms (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.terms", false]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.TextIOPicklable", false]], "time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.time", false]], "time (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.time", false]], "time (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.time", false]], "time (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.time", false]], "time 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false]], "timeseries() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.timeseries", false]], "timestep (class in mdanalysis.coordinates.timestep)": [[89, "MDAnalysis.coordinates.timestep.Timestep", false]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps", false]], 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Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "11.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "11.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "11.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "11.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "11.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "11. Auxiliary modules", "8. Converter modules", "8.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "8.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "8.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "8.8. Base classes \u2014 MDAnalysis.converters.base", "7.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "7.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "7.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "7.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "7.26. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "7.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "7.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "7.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "7.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "7.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "7.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "7.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "7.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "7.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "7.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "7.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "7.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "7.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "7.19. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "7.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "7.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "7.22. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "7.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "7.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "7.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "7.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "7.31. Base classes \u2014 MDAnalysis.coordinates.base", "7.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "7.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "7.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "7.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "7.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "7.29. Null output \u2014 MDAnalysis.coordinates.null", "7.33. Serialization of Coordinate Readers", "7.30. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "7. Coordinates modules", "8.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "12.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "12.1. Core functions of MDAnalysis", "12.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "12.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "12.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "12.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "12.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "12. Core modules", "17. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "6. Guesser modules", "6.1.2.3. Base guesser classes \u2014 MDAnalysis.guesser.base", "6.1.2.2. Default Guesser", "6.1.2.1. Context-specific guessers \u2014 MDAnalysis.guesser", "6.1.2.4. MDAnalysis topology tables", "14.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "14.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "14.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "14.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "14.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "14.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "14.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "14.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "14.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "14.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "14.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "14.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "14.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "14.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "14.2.10. Helper functions \u2014 MDAnalysis.lib.util", "14. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "18. References", "3. Selection commands", "10.2.6. Base classes for the selection writers", "10.2.4. CHARMM selections", "10.2.3. Gromacs selections", "10.2.5. Jmol selections", "10.2.2. PyMOL selections", "10.2.1. VMD selections", "10. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.26. Utility functions for the TPR topology parser", "5. Topology modules", "9. Trajectory transformations (\u201con-the-fly\u201d transformations)", "9.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "9.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "9.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "9.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "9.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "9.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "9.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "9.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "16. Constants and unit conversion \u2014 MDAnalysis.units", "15. Version information for MDAnalysis - MDAnalysis.version", "13.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "13.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "13. 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mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.AtomStringAttr", false]], "atomtypes (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes", false]], "attach_auxiliary() (mdanalysis.auxiliary.base.auxreader method)": [[46, "MDAnalysis.auxiliary.base.AuxReader.attach_auxiliary", false]], "attrname (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.attrname", false]], "augment_coordinates() (in module mdanalysis.lib.distances)": [[110, "MDAnalysis.lib.distances.augment_coordinates", false]], "autocorrelation() (in module mdanalysis.lib.correlations)": [[109, "MDAnalysis.lib.correlations.autocorrelation", false]], "aux_list (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.aux_list", false]], "aux_list (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.aux_list", false]], "aux_list 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"MDAnalysis.coordinates.LAMMPS.DumpReader.aux_list", false]], "aux_list (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.aux_list", false]], "aux_list (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.aux_list", false]], "aux_list (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.aux_list", false]], "aux_list (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.aux_list", false]], "aux_list (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.aux_list", false]], "auxfile (mdanalysis.auxiliary.base.auxfilereader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader.auxfile", false]], "auxfilereader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxFileReader", false]], "auxreader (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxReader", false]], "auxreader() (in module mdanalysis.auxiliary.core)": [[47, "MDAnalysis.auxiliary.core.auxreader", false]], "auxstep (class in mdanalysis.auxiliary.base)": [[46, "MDAnalysis.auxiliary.base.AuxStep", false]], "auxstep (mdanalysis.auxiliary.base.auxreader attribute)": [[46, "MDAnalysis.auxiliary.base.AuxReader.auxstep", false]], "averagestructure (class in mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.AverageStructure", false]], "backboneselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BackboneSelection", false]], "backendbase (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendBase", false]], "backenddask (class in mdanalysis.analysis.backends)": [[2, "MDAnalysis.analysis.backends.BackendDask", false]], 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"MDAnalysis.core.groups.SegmentGroup.bbox", false]], "between() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.between", false]], "bf (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bF", false]], "bfactor (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bfactor", false]], "bfactor() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor", false]], "bfactor_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactor_setter", false]], "bfactors (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.residue property)": [[92, "MDAnalysis.core.groups.Residue.bfactors", false]], "bfactors (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.bfactors", false]], "bfactors (mdanalysis.core.groups.segment property)": [[92, "MDAnalysis.core.groups.Segment.bfactors", false]], "bfactors (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.bfactors", false]], "bfactors() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors", false]], "bfactors_setter() (mdanalysis.core.topologyattrs.tempfactors method)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.bfactors_setter", false]], "bins (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.bins", false]], "bins (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.bins", false]], "bir (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.bIr", false]], "blocks (mdanalysis.coordinates.tng.tngreader property)": [[72, "MDAnalysis.coordinates.TNG.TNGReader.blocks", false]], "blocks_of() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.blocks_of", false]], "bond (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Bond", false]], "bond (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.bond", false]], "bond_autocorrelation (mdanalysis.analysis.polymer.persistencelength.results attribute)": [[36, "MDAnalysis.analysis.polymer.PersistenceLength.results.bond_autocorrelation", false]], "bonded_atoms (mdanalysis.core.groups.atom property)": [[92, "MDAnalysis.core.groups.Atom.bonded_atoms", false]], "bonded_atoms() (mdanalysis.core.topologyattrs.bonds method)": [[96, "MDAnalysis.core.topologyattrs.Bonds.bonded_atoms", false]], "bonds (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Bonds", false]], "bonds (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.bonds", false]], "bonds() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.bonds", false]], "boolselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.BoolSelection", false]], "bootstrapped_matrix() (in module mdanalysis.analysis.encore.bootstrap)": [[14, "MDAnalysis.analysis.encore.bootstrap.bootstrapped_matrix", false]], "box (class in mdanalysis.topology.tpr.obj)": [[158, "MDAnalysis.topology.tpr.obj.Box", false]], "box_volume() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.box_volume", false]], "bsphere() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.bsphere", false]], "bsphere() 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"MDAnalysis.core.groups.ResidueGroup.center_of_geometry", false]], "center_of_geometry() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_geometry", false]], "center_of_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.center_of_mass", false]], "center_of_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.center_of_mass", false]], "centers() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.centers", false]], "centroid (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, 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(mdanalysis.core.topology.transtable method)": [[95, "MDAnalysis.core.topology.TransTable.copy", false]], "copy() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.copy", false]], "copy() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.copy", false]], "copy() (mdanalysis.guesser.base.guesserbase method)": [[102, "MDAnalysis.guesser.base.GuesserBase.copy", false]], "copy() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.copy", false]], "copy_slice() (mdanalysis.coordinates.timestep.timestep method)": [[89, "MDAnalysis.coordinates.timestep.Timestep.copy_slice", false]], "correct_intermittency() (in module mdanalysis.lib.correlations)": [[109, "MDAnalysis.lib.correlations.correct_intermittency", false]], "cosine_content() (in module mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.cosine_content", false]], "count 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"MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time", false]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.count_by_type", false]], "count_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_type", false]], "covariance_matrix() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.covariance_matrix", false]], "crdparser (class in mdanalysis.topology.crdparser)": [[133, "MDAnalysis.topology.CRDParser.CRDParser", false]], "crdreader (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDReader", false]], "crdwriter (class in mdanalysis.coordinates.crd)": [[55, "MDAnalysis.coordinates.CRD.CRDWriter", false]], "create() (in module mdanalysis.lib.log)": [[113, "MDAnalysis.lib.log.create", false]], "cryst1() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.CRYST1", false]], "cumulated_variance (mdanalysis.analysis.pca.pca attribute)": [[35, "MDAnalysis.analysis.pca.PCA.cumulated_variance", false]], "cumulated_variance (mdanalysis.analysis.pca.pca.results attribute)": [[35, "MDAnalysis.analysis.pca.PCA.results.cumulated_variance", false]], "cumulative_clustering_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.cumulative_clustering_ensemble_similarity", false]], "cumulative_gen_kde_pdfs() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.cumulative_gen_kde_pdfs", false]], "cumulative_overlap() (in module mdanalysis.analysis.pca)": [[35, "MDAnalysis.analysis.pca.cumulative_overlap", false]], "cumulative_overlap() (mdanalysis.analysis.pca.pca method)": [[35, "MDAnalysis.analysis.pca.PCA.cumulative_overlap", false]], "data (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.data", false]], "data (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.data", false]], "data_blacklist (mdanalysis.coordinates.h5md.h5mdwriter attribute)": [[63, "MDAnalysis.coordinates.H5MD.H5MDWriter.data_blacklist", false]], "data_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.data_dict", false]], "data_selector (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.data_selector", false]], "dataparser (class in mdanalysis.topology.lammpsparser)": [[143, "MDAnalysis.topology.LAMMPSParser.DATAParser", false]], "datareader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader", false]], "datawriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAWriter", false]], "dbscan (class in mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.DBSCAN", false]], "dcdfile (class in mdanalysis.lib.formats.libdcd)": [[111, "MDAnalysis.lib.formats.libdcd.DCDFile", false]], "dcdreader (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDReader", false]], "dcdreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader", false]], "dcdwriter (class in mdanalysis.coordinates.dcd)": [[56, "MDAnalysis.coordinates.DCD.DCDWriter", false]], "dcdwriter (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDWriter", false]], "decompose_matrix() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.decompose_matrix", false]], "dedent_docstring() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.dedent_docstring", false]], "default_acceptors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS", false]], "default_donors (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS", false]], "default_format (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.default_format", false]], "default_numterms (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.default_numterms", false]], "defaultguesser (class in mdanalysis.guesser.default_guesser)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser", false]], "define_unpack_real() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.define_unpack_real", false]], "del_topologyattr() (mdanalysis.core.topology.topology method)": [[95, "MDAnalysis.core.topology.Topology.del_TopologyAttr", false]], "del_topologyattr() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.del_TopologyAttr", false]], "delete_angles() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_angles", false]], "delete_bonds() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_bonds", false]], "delete_dihedrals() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_dihedrals", false]], "delete_impropers() (mdanalysis.core.universe.universe method)": [[98, "MDAnalysis.core.universe.Universe.delete_impropers", false]], "delta (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.delta", false]], "delta (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.delta", false]], "density (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.Density", false]], "density (mdanalysis.analysis.density.densityanalysis attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.density", false]], "density (mdanalysis.analysis.density.densityanalysis.results attribute)": [[7, "MDAnalysis.analysis.density.DensityAnalysis.results.density", false]], "densityanalysis (class in mdanalysis.analysis.density)": [[7, "MDAnalysis.analysis.density.DensityAnalysis", false]], "densityunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.densityUnit_factor", false]], "deprecate() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.deprecate", false]], "dielectricconstant (class in mdanalysis.analysis.dielectric)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant", false]], "difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.difference", false]], "difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.difference", false]], "difference() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.difference", false]], "diffusionmap (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap", false]], "dihedral (class in mdanalysis.analysis.dihedrals)": [[10, "MDAnalysis.analysis.dihedrals.Dihedral", false]], "dihedral (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.Dihedral", false]], "dihedral (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dihedral", false]], "dihedral() (in module mdanalysis.lib.mdamath)": [[114, "MDAnalysis.lib.mdamath.dihedral", false]], "dihedral() (mdanalysis.core.topologyobjects.dihedral method)": [[97, "MDAnalysis.core.topologyobjects.Dihedral.dihedral", false]], "dihedrals (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Dihedrals", false]], "dihedrals (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dihedrals", false]], "dihedrals() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dihedrals", false]], "dim (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.dim", false]], "dim_fac (mdanalysis.analysis.msd.einsteinmsd attribute)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.dim_fac", false]], "dimensionalityreductionmethod (class in mdanalysis.analysis.encore.dimensionality_reduction.dimensionalityreductionmethod)": [[18, "MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod.DimensionalityReductionMethod", false]], "dimensions (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dimensions", false]], "dimensions (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dimensions", false]], "dimensions (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.dimensions", false]], "dimensions (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.dimensions", false]], "dimensions (mdanalysis.core.universe.universe attribute)": [[98, "MDAnalysis.core.universe.Universe.dimensions", false]], "dimred_ensemble_similarity() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dimred_ensemble_similarity", false]], "dipole_moment() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_moment", false]], "dipole_moment() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_moment", false]], "dipole_vector() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.dipole_vector", false]], "dipole_vector() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.dipole_vector", false]], "discrete_jensen_shannon_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_jensen_shannon_divergence", false]], "discrete_kullback_leibler_divergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.discrete_kullback_leibler_divergence", false]], "dist() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.dist", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.dist_matrix", false]], "dist_matrix (mdanalysis.analysis.diffusionmap.distancematrix.results attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix.results.dist_matrix", false]], "distance() (mdanalysis.core.topologyobjects.ureybradley method)": [[97, "MDAnalysis.core.topologyobjects.UreyBradley.distance", false]], "distance_array() (in module mdanalysis.analysis.distances)": [[11, "MDAnalysis.analysis.distances.distance_array", false]], "distance_array() (in module mdanalysis.lib.distances)": [[110, "MDAnalysis.lib.distances.distance_array", false]], "distancematrix (class in mdanalysis.analysis.diffusionmap)": [[9, "MDAnalysis.analysis.diffusionmap.DistanceMatrix", false]], "distances (mdanalysis.analysis.nucleicacids.majorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MajorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.minorpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.MinorPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.nucpairdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.NucPairDist.results.distances", false]], "distances (mdanalysis.analysis.nucleicacids.watsoncrickdist.results attribute)": [[32, "MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results.distances", false]], "dmsparser (class in mdanalysis.topology.dmsparser)": [[135, "MDAnalysis.topology.DMSParser.DMSParser", false]], "dmsreader (class in mdanalysis.coordinates.dms)": [[58, "MDAnalysis.coordinates.DMS.DMSReader", false]], "do_atom() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_atom", false]], "do_atoms() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_atoms", false]], "do_block() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_block", false]], "do_blocka() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_blocka", false]], "do_ffparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_ffparams", false]], "do_harm() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_harm", false]], "do_ilists() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_ilists", false]], "do_iparams() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_iparams", false]], "do_molblock() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_molblock", false]], "do_moltype() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_moltype", false]], "do_mtop() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_mtop", false]], "do_resinfo() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_resinfo", false]], "do_rvec() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_rvec", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker.do_string", false]], "do_string() (mdanalysis.topology.tpr.utils.tpxunpacker2020 method)": [[158, "MDAnalysis.topology.tpr.utils.TPXUnpacker2020.do_string", false]], "do_symstr() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symstr", false]], "do_symtab() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.do_symtab", false]], "down() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.down", false]], "drag() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.drag", false]], "dres() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres", false]], "dres_convergence() (in module mdanalysis.analysis.encore.similarity)": [[19, "MDAnalysis.analysis.encore.similarity.dres_convergence", false]], "dssp (class in mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP", false]], "dssp (mdanalysis.analysis.dssp.dssp.dssp.results attribute)": [[12, "MDAnalysis.analysis.dssp.dssp.DSSP.results.dssp", false]], "dssp_ndarray 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(mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.dt", false]], "dt (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.dt", false]], "dt (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.dt", false]], "dt (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.dt", false]], "dt (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.dt", false]], "dt (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.dt", false]], "dt (mdanalysis.coordinates.txyz.txyzreader 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attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.atomtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.Atomtypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.chainids attribute)": [[96, "MDAnalysis.core.topologyattrs.ChainIDs.dtype", false]], "dtype (mdanalysis.core.topologyattrs.charges attribute)": [[96, "MDAnalysis.core.topologyattrs.Charges.dtype", false]], "dtype (mdanalysis.core.topologyattrs.elements attribute)": [[96, "MDAnalysis.core.topologyattrs.Elements.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilon14s attribute)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.epsilons 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(mdanalysis.core.topologyattrs.occupancies attribute)": [[96, "MDAnalysis.core.topologyattrs.Occupancies.dtype", false]], "dtype (mdanalysis.core.topologyattrs.radii attribute)": [[96, "MDAnalysis.core.topologyattrs.Radii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.recordtypes attribute)": [[96, "MDAnalysis.core.topologyattrs.RecordTypes.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resids attribute)": [[96, "MDAnalysis.core.topologyattrs.Resids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Resindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnames attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnames.dtype", false]], "dtype (mdanalysis.core.topologyattrs.resnums attribute)": [[96, "MDAnalysis.core.topologyattrs.Resnums.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmin14s attribute)": [[96, "MDAnalysis.core.topologyattrs.RMin14s.dtype", false]], "dtype (mdanalysis.core.topologyattrs.rmins attribute)": [[96, "MDAnalysis.core.topologyattrs.RMins.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segids attribute)": [[96, "MDAnalysis.core.topologyattrs.Segids.dtype", false]], "dtype (mdanalysis.core.topologyattrs.segindices attribute)": [[96, "MDAnalysis.core.topologyattrs.Segindices.dtype", false]], "dtype (mdanalysis.core.topologyattrs.solventradii attribute)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii.dtype", false]], "dtype (mdanalysis.core.topologyattrs.tempfactors attribute)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors.dtype", false]], "dtype (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.dtype", false]], "duecredit_enable": [[123, "index-0", false]], "dump_contents() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.dump_contents", false]], "dumpreader (class in mdanalysis.coordinates.lammps)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader", false]], "duplicatewarning": [[100, "MDAnalysis.exceptions.DuplicateWarning", false]], "edges (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF.results.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.edges", false]], "edges (mdanalysis.analysis.rdf.interrdf_s.results attribute)": [[38, "MDAnalysis.analysis.rdf.InterRDF_s.results.edges", false]], "edrreader (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader", false]], "edrstep (class in mdanalysis.auxiliary.edr)": [[44, "MDAnalysis.auxiliary.EDR.EDRStep", false]], "eigenvalues (mdanalysis.analysis.diffusionmap.diffusionmap attribute)": [[9, "MDAnalysis.analysis.diffusionmap.DiffusionMap.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvalues", false]], "eigenvalues (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvalues", false]], "eigenvectors (mdanalysis.analysis.gnm.closecontactgnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results.eigenvectors", false]], "eigenvectors (mdanalysis.analysis.gnm.gnmanalysis.results attribute)": [[21, "MDAnalysis.analysis.gnm.GNMAnalysis.results.eigenvectors", false]], "einsteinmsd (class in mdanalysis.analysis.msd)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD", false]], "element_symbol (mdanalysis.topology.tpr.obj.atomkind property)": [[158, "MDAnalysis.topology.tpr.obj.AtomKind.element_symbol", false]], "elements (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Elements", false]], "elements (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.elements", false]], "emit() (mdanalysis.lib.log.nullhandler method)": [[113, "MDAnalysis.lib.log.NullHandler.emit", false]], "empty() (mdanalysis.core.universe.universe class method)": [[98, "MDAnalysis.core.universe.Universe.empty", false]], "encode_block() (mdanalysis.coordinates.mol2.mol2writer method)": [[67, "MDAnalysis.coordinates.MOL2.MOL2Writer.encode_block", false]], "encode_centroid_info() (in module mdanalysis.analysis.encore.clustering.clusteringmethod)": [[15, "MDAnalysis.analysis.encore.clustering.ClusteringMethod.encode_centroid_info", false]], "end() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.END", false]], "endmdl() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.ENDMDL", false]], "environment variable": [[74, "index-0", false], [74, "index-1", false], [120, "index-0", false], [120, "index-1", false], [123, "index-0", false], [161, "index-0", false]], "eps (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps", false]], "eps_mean (mdanalysis.analysis.dielectric.dielectricconstant.results attribute)": [[8, "MDAnalysis.analysis.dielectric.DielectricConstant.results.eps_mean", false]], "epsilon14s (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilon14s", false]], "epsilons (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Epsilons", false]], "euler_from_quaternion() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.euler_from_quaternion", false]], "expect() (mdanalysis.core.selection.selectionparser method)": [[94, "MDAnalysis.core.selection.SelectionParser.expect", false]], "export() (mdanalysis.analysis.density.density method)": [[7, "MDAnalysis.analysis.density.Density.export", false]], "ext (mdanalysis.selections.charmm.selectionwriter attribute)": [[126, "MDAnalysis.selections.charmm.SelectionWriter.ext", false]], "ext (mdanalysis.selections.gromacs.selectionwriter attribute)": [[127, "MDAnalysis.selections.gromacs.SelectionWriter.ext", false]], "ext (mdanalysis.selections.jmol.selectionwriter attribute)": [[128, "MDAnalysis.selections.jmol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.pymol.selectionwriter attribute)": [[129, "MDAnalysis.selections.pymol.SelectionWriter.ext", false]], "ext (mdanalysis.selections.vmd.selectionwriter attribute)": [[130, "MDAnalysis.selections.vmd.SelectionWriter.ext", false]], "extendedpdbparser (class in mdanalysis.topology.extendedpdbparser)": [[136, "MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser", false]], "extendedpdbreader (class in mdanalysis.coordinates.pdb)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader", false]], "extract_box_info() (in module mdanalysis.topology.tpr.utils)": [[158, "MDAnalysis.topology.tpr.utils.extract_box_info", false]], "f_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGLES", false]], "f_angres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRES", false]], "f_angresz (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANGRESZ", false]], "f_anharm_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ANHARM_POL", false]], "f_bham (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM", false]], "f_bham_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BHAM_LR", false]], "f_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_BONDS", false]], "f_cbtdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CBTDIHS", false]], "f_cmap (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CMAP", false]], "f_com_pull (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COM_PULL", false]], "f_connbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONNBONDS", false]], "f_constr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTR", false]], "f_constrnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CONSTRNC", false]], "f_coul14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL14", false]], "f_coul_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_LR", false]], "f_coul_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_RECIP", false]], "f_coul_sr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_COUL_SR", false]], "f_cross_bond_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_ANGLES", false]], "f_cross_bond_bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CROSS_BOND_BONDS", false]], "f_cubicbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_CUBICBONDS", false]], "f_densityfitting (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DENSITYFITTING", false]], "f_dhdl_con (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DHDL_CON", false]], "f_dihres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRES", false]], "f_dihresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DIHRESVIOL", false]], "f_dispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISPCORR", false]], "f_disres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRES", false]], "f_disresviol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DISRESVIOL", false]], "f_dkdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DKDL", false]], "f_dpd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DPD", false]], "f_dvdl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL", false]], "f_dvdl_bonded (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_BONDED", false]], "f_dvdl_coul (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_COUL", false]], "f_dvdl_restraint (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_RESTRAINT", false]], "f_dvdl_temperature (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_TEMPERATURE", false]], "f_dvdl_vdw (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_DVDL_VDW", false]], "f_econserved (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ECONSERVED", false]], "f_ekin (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EKIN", false]], "f_epot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EPOT", false]], "f_eqm (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_EQM", false]], "f_etot (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ETOT", false]], "f_fbposres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FBPOSRES", false]], "f_fenebonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FENEBONDS", false]], "f_fourdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_FOURDIHS", false]], "f_g96angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96ANGLES", false]], "f_g96bonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_G96BONDS", false]], "f_gb12 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB12", false]], "f_gb13 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB13", false]], "f_gb14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GB14", false]], "f_gbpol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_GBPOL", false]], "f_harmonic (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_HARMONIC", false]], "f_idihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_IDIHS", false]], "f_linear_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LINEAR_ANGLES", false]], "f_lj (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ", false]], "f_lj14 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ14", false]], "f_lj_lr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_LR", false]], "f_lj_recip (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJ_RECIP", false]], "f_ljc14_q (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC14_Q", false]], "f_ljc_pairs_nb (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_LJC_PAIRS_NB", false]], "f_morse (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_MORSE", false]], "f_npsolvation (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NPSOLVATION", false]], "f_nre (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_NRE", false]], "f_orires (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRES", false]], "f_oriresdev (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_ORIRESDEV", false]], "f_pdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDIHS", false]], "f_pdispcorr (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PDISPCORR", false]], "f_pidihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PIDIHS", false]], "f_polarization (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POLARIZATION", false]], "f_posres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_POSRES", false]], "f_pres (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_PRES", false]], "f_quartic_angles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_QUARTIC_ANGLES", false]], "f_rbdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RBDIHS", false]], "f_restrangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRANGLES", false]], "f_restrbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRBONDS", false]], "f_restrdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RESTRDIHS", false]], "f_rf_excl (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_RF_EXCL", false]], "f_settle (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_SETTLE", false]], "f_tabangles (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABANGLES", false]], "f_tabbonds (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDS", false]], "f_tabbondsnc (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABBONDSNC", false]], "f_tabdihs (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TABDIHS", false]], "f_temp (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_TEMP", false]], "f_thole_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_THOLE_POL", false]], "f_urey_bradley (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_UREY_BRADLEY", false]], "f_vsite1 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE1", false]], "f_vsite2 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2", false]], "f_vsite2fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE2FD", false]], "f_vsite3 (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3", false]], "f_vsite3fad (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FAD", false]], "f_vsite3fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3FD", false]], "f_vsite3out (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE3OUT", false]], "f_vsite4fd (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FD", false]], "f_vsite4fdn (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITE4FDN", false]], "f_vsiten (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VSITEN", false]], "f_vtemp_nolongerused (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_VTEMP_NOLONGERUSED", false]], "f_water_pol (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.F_WATER_POL", false]], "fasta2select() (in module mdanalysis.analysis.align)": [[0, "MDAnalysis.analysis.align.fasta2select", false]], "fastcalcrmsdandrotation() (in module mdanalysis.lib.qcprot)": [[118, "MDAnalysis.lib.qcprot.FastCalcRMSDAndRotation", false]], "fastns (class in mdanalysis.lib.nsgrid)": [[115, "MDAnalysis.lib.nsgrid.FastNS", 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"MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_donors", false]], "guess_flavour() (mdanalysis.topology.pqrparser.pqrparser static method)": [[149, "MDAnalysis.topology.PQRParser.PQRParser.guess_flavour", false]], "guess_format() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.guess_format", false]], "guess_gasteiger_charges() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_gasteiger_charges", false]], "guess_hydrogens() (mdanalysis.analysis.hydrogenbonds.hbond_analysis.hydrogenbondanalysis method)": [[26, "MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.guess_hydrogens", false]], "guess_improper_dihedrals() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, "MDAnalysis.guesser.default_guesser.DefaultGuesser.guess_improper_dihedrals", false]], "guess_masses() (mdanalysis.guesser.default_guesser.defaultguesser method)": [[103, 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"MDAnalysis.coordinates.LAMMPS.DATAReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.set_aux_attribute", false]], "set_aux_attribute() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.set_aux_attribute", false]], "set_coords() (mdanalysis.lib.pkdtree.periodickdtree method)": [[117, "MDAnalysis.lib.pkdtree.PeriodicKDTree.set_coords", false]], "set_dimensions (class in mdanalysis.transformations.boxdimensions)": [[162, "MDAnalysis.transformations.boxdimensions.set_dimensions", false]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.trrfile method)": [[112, "MDAnalysis.lib.formats.libmdaxdr.TRRFile.set_offsets", false]], "set_offsets() (mdanalysis.lib.formats.libmdaxdr.xtcfile method)": [[112, "MDAnalysis.lib.formats.libmdaxdr.XTCFile.set_offsets", false]], "set_residues() (mdanalysis.core.topologyattrs.atomattr method)": [[96, "MDAnalysis.core.topologyattrs.AtomAttr.set_residues", false]], "set_residues() 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"MDAnalysis.core.topologyattrs.AtomAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.residueattr method)": [[96, "MDAnalysis.core.topologyattrs.ResidueAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segindices method)": [[96, "MDAnalysis.core.topologyattrs.Segindices.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.segmentstringattr method)": [[96, "MDAnalysis.core.topologyattrs.SegmentStringAttr.set_segments", false]], "set_segments() (mdanalysis.core.topologyattrs.topologyattr method)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.set_segments", false]], "setaxes() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.setaxes", false]], "setconstrain() (mdanalysis.lib.transformations.arcball method)": [[119, "MDAnalysis.lib.transformations.Arcball.setconstrain", false]], "shape_parameter() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.shape_parameter", false]], "shape_parameter() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.shape_parameter", false]], "shear_from_matrix() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.shear_from_matrix", false]], "shrinkage_covariance_estimator() (in module mdanalysis.analysis.encore.covariance)": [[17, "MDAnalysis.analysis.encore.covariance.shrinkage_covariance_estimator", false]], "singlecharselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SingleCharSelection", false]], "singleframereaderbase (class in mdanalysis.coordinates.base)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase", false]], "singular (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.singular", false]], "size (mdanalysis.analysis.encore.clustering.clustercollection.cluster attribute)": [[15, "MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster.size", false]], "size (mdanalysis.core.topology.transtable attribute)": [[95, "MDAnalysis.core.topology.TransTable.size", false]], "size (mdanalysis.topology.tpr.obj.box attribute)": [[158, "MDAnalysis.topology.tpr.obj.Box.size", false]], "sizeoftprbody (mdanalysis.topology.tpr.obj.tpxheader attribute)": [[158, "MDAnalysis.topology.tpr.obj.TpxHeader.sizeOfTprBody", false]], "sizes() (mdanalysis.analysis.leaflet.leafletfinder method)": [[27, "MDAnalysis.analysis.leaflet.LeafletFinder.sizes", false]], "skip_timestep (mdanalysis.coordinates.trz.trzreader property)": [[76, "MDAnalysis.coordinates.TRZ.TRZReader.skip_timestep", false]], "skipper() (mdanalysis.topology.topparser.topparser method)": [[151, "MDAnalysis.topology.TOPParser.TOPParser.skipper", false]], "slice_volume (mdanalysis.analysis.lineardensity.lineardensity.results.x attribute)": [[30, "MDAnalysis.analysis.lineardensity.LinearDensity.results.x.slice_volume", false]], "smartsselection (class in mdanalysis.core.selection)": [[94, "MDAnalysis.core.selection.SmartsSelection", false]], "soft_cut_q() (in module mdanalysis.analysis.contacts)": [[5, "MDAnalysis.analysis.contacts.soft_cut_q", false]], "solve() (mdanalysis.analysis.hydrogenbonds.hbond_autocorrel.hydrogenbondautocorrel method)": [[22, "MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel.solve", false]], "solventradii (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.SolventRadii", false]], "sort() 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"MDAnalysis.core.groups.AtomGroup.subtract", false]], "subtract() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.subtract", false]], "subtract() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.subtract", false]], "summary (mdanalysis.analysis.helix_analysis.helanal.results attribute)": [[24, "MDAnalysis.analysis.helix_analysis.HELANAL.results.summary", false]], "supported_versions (in module mdanalysis.topology.tpr)": [[158, "MDAnalysis.topology.tpr.SUPPORTED_VERSIONS", false]], "supported_versions (in module mdanalysis.topology.tpr.setting)": [[158, "MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS", false]], "symmetric_difference() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.symmetric_difference", false]], "symmetric_difference() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.symmetric_difference", false]], 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"MDAnalysis.lib.formats.libmdaxdr.XTCFile.tell", false]], "tell() (mdanalysis.lib.util.namedstream method)": [[120, "MDAnalysis.lib.util.NamedStream.tell", false]], "tempfactors (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.Tempfactors", false]], "terms (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.terms", false]], "textiopicklable (class in mdanalysis.lib.picklable_file_io)": [[116, "MDAnalysis.lib.picklable_file_io.TextIOPicklable", false]], "time (mdanalysis.auxiliary.base.auxreader property)": [[46, "MDAnalysis.auxiliary.base.AuxReader.time", false]], "time (mdanalysis.auxiliary.base.auxstep property)": [[46, "MDAnalysis.auxiliary.base.AuxStep.time", false]], "time (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.time", false]], "time (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.time", false]], "time (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.time", false]], "time (mdanalysis.coordinates.chain.chainreader property)": [[82, "MDAnalysis.coordinates.chain.ChainReader.time", false]], "time (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.time", false]], "time (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.time", false]], "time (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.time", false]], "time (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.time", false]], "time (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.time", false]], "time (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.time", false]], "time (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.time", false]], "time (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.time", false]], "time (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.time", false]], "time (mdanalysis.coordinates.timestep.timestep attribute)": [[89, "MDAnalysis.coordinates.timestep.Timestep.time", false]], "time (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.time", false]], "time (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.time", false]], "time (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.time", false]], "time (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.time", false]], "time_selector 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attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timeseries", false]], "timeseries (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis.results attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries", false]], "timeseries (mdanalysis.analysis.msd.einsteinmsd.results attribute)": [[31, "MDAnalysis.analysis.msd.EinsteinMSD.results.timeseries", false]], "timeseries() (mdanalysis.coordinates.base.protoreader method)": [[81, "MDAnalysis.coordinates.base.ProtoReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.base.readerbase method)": [[81, "MDAnalysis.coordinates.base.ReaderBase.timeseries", false]], "timeseries() (mdanalysis.coordinates.base.singleframereaderbase method)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.timeseries", false]], "timeseries() (mdanalysis.coordinates.dcd.dcdreader method)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.fhiaims.fhiaimsreader method)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.gsd.gsdreader method)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.h5md.h5mdreader method)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.datareader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.dcdreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.lammps.dumpreader method)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.memory.memoryreader method)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.pdb.extendedpdbreader method)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.trr.trrreader method)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.txyz.txyzreader method)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xdr.xdrbasereader method)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.timeseries", false]], "timeseries() (mdanalysis.coordinates.xtc.xtcreader method)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.timeseries", false]], "timestep (class in mdanalysis.coordinates.timestep)": [[89, "MDAnalysis.coordinates.timestep.Timestep", false]], "timesteps (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis attribute)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps", false]], "timesteps_by_type() (mdanalysis.analysis.hydrogenbonds.wbridge_analysis.waterbridgeanalysis method)": [[42, "MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.timesteps_by_type", false]], "timeunit_factor (in module mdanalysis.units)": [[169, "MDAnalysis.units.timeUnit_factor", false]], "title() (mdanalysis.coordinates.pdb.pdbwriter method)": [[69, "MDAnalysis.coordinates.PDB.PDBWriter.TITLE", false]], "tngreader (class in mdanalysis.coordinates.tng)": [[72, "MDAnalysis.coordinates.TNG.TNGReader", false]], "to_indices() (mdanalysis.core.topologyobjects.topologygroup method)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.to_indices", false]], "top (mdanalysis.core.topologyattrs.topologyattr attribute)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr.top", false]], "topdict (mdanalysis.core.topologyobjects.topologygroup property)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup.topDict", false]], "topology (class in mdanalysis.core.topology)": [[95, "MDAnalysis.core.topology.Topology", false]], "topologyattr (class in mdanalysis.core.topologyattrs)": [[96, "MDAnalysis.core.topologyattrs.TopologyAttr", false]], "topologydict (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyDict", false]], "topologygroup (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyGroup", false]], "topologyobject (class in mdanalysis.core.topologyobjects)": [[97, "MDAnalysis.core.topologyobjects.TopologyObject", false]], "topologyreaderbase (class in mdanalysis.topology.base)": [[155, "MDAnalysis.topology.base.TopologyReaderBase", false]], "topparser (class in mdanalysis.topology.topparser)": [[151, "MDAnalysis.topology.TOPParser.TOPParser", false]], "tors() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors", false]], "tors_alpha() (in module mdanalysis.analysis.nuclinfo)": [[33, "MDAnalysis.analysis.nuclinfo.tors_alpha", false]], "tors_beta() 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"MDAnalysis.core.groups.SegmentGroup.total_charge", false]], "total_charge() (mdanalysis.core.topologyattrs.charges method)": [[96, "MDAnalysis.core.topologyattrs.Charges.total_charge", false]], "total_mass() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.total_mass", false]], "total_mass() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.total_mass", false]], "total_mass() (mdanalysis.core.topologyattrs.masses method)": [[96, "MDAnalysis.core.topologyattrs.Masses.total_mass", false]], "totaltime (mdanalysis.coordinates.base.protoreader property)": [[81, "MDAnalysis.coordinates.base.ProtoReader.totaltime", false]], "totaltime (mdanalysis.coordinates.base.readerbase property)": [[81, "MDAnalysis.coordinates.base.ReaderBase.totaltime", false]], "totaltime (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.totaltime", false]], "totaltime (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.totaltime", false]], "totaltime (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.totaltime", false]], "totaltime (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.totaltime", false]], "totaltime (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.totaltime", false]], "totaltime (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.totaltime", false]], "totaltime (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.totaltime", false]], "totaltime (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.totaltime", false]], "totaltime (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.totaltime", false]], "tp (mdanalysis.topology.tpr.obj.atom attribute)": [[158, "MDAnalysis.topology.tpr.obj.Atom.tp", false]], "tprparser (class in 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false]], "transformations (mdanalysis.coordinates.base.singleframereaderbase property)": [[81, "MDAnalysis.coordinates.base.SingleFrameReaderBase.transformations", false]], "transformations (mdanalysis.coordinates.dcd.dcdreader property)": [[56, "MDAnalysis.coordinates.DCD.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.fhiaims.fhiaimsreader property)": [[59, "MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader.transformations", false]], "transformations (mdanalysis.coordinates.gsd.gsdreader property)": [[62, "MDAnalysis.coordinates.GSD.GSDReader.transformations", false]], "transformations (mdanalysis.coordinates.h5md.h5mdreader property)": [[63, "MDAnalysis.coordinates.H5MD.H5MDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.datareader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DATAReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dcdreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DCDReader.transformations", false]], "transformations (mdanalysis.coordinates.lammps.dumpreader property)": [[65, "MDAnalysis.coordinates.LAMMPS.DumpReader.transformations", false]], "transformations (mdanalysis.coordinates.memory.memoryreader property)": [[86, "MDAnalysis.coordinates.memory.MemoryReader.transformations", false]], "transformations (mdanalysis.coordinates.pdb.extendedpdbreader property)": [[69, "MDAnalysis.coordinates.PDB.ExtendedPDBReader.transformations", false]], "transformations (mdanalysis.coordinates.trr.trrreader property)": [[75, "MDAnalysis.coordinates.TRR.TRRReader.transformations", false]], "transformations (mdanalysis.coordinates.txyz.txyzreader property)": [[77, "MDAnalysis.coordinates.TXYZ.TXYZReader.transformations", false]], "transformations (mdanalysis.coordinates.xdr.xdrbasereader property)": [[78, "MDAnalysis.coordinates.XDR.XDRBaseReader.transformations", false]], "transformations (mdanalysis.coordinates.xtc.xtcreader property)": [[79, "MDAnalysis.coordinates.XTC.XTCReader.transformations", false]], "translate (class in mdanalysis.transformations.translate)": [[167, "MDAnalysis.transformations.translate.translate", false]], "translate() (in module mdanalysis.analysis.dssp.dssp)": [[12, "MDAnalysis.analysis.dssp.dssp.translate", false]], "translate() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.translate", false]], "translate() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.translate", false]], "translate() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.translate", false]], "translation_from_matrix() (in module mdanalysis.lib.transformations)": [[119, "MDAnalysis.lib.transformations.translation_from_matrix", false]], "transtable (class in mdanalysis.core.topology)": [[95, "MDAnalysis.core.topology.TransTable", false]], "trcreader (class in mdanalysis.coordinates.trc)": [[73, 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"union() (mdanalysis.core.groups.atomgroup method)": [[92, "MDAnalysis.core.groups.AtomGroup.union", false]], "union() (mdanalysis.core.groups.residuegroup method)": [[92, "MDAnalysis.core.groups.ResidueGroup.union", false]], "union() (mdanalysis.core.groups.segmentgroup method)": [[92, "MDAnalysis.core.groups.SegmentGroup.union", false]], "unique (mdanalysis.core.groups.atomgroup property)": [[92, "MDAnalysis.core.groups.AtomGroup.unique", false]], "unique (mdanalysis.core.groups.residuegroup property)": [[92, "MDAnalysis.core.groups.ResidueGroup.unique", false]], "unique (mdanalysis.core.groups.segmentgroup property)": [[92, "MDAnalysis.core.groups.SegmentGroup.unique", false]], "unique_int_1d() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.unique_int_1d", false]], "unique_rows() (in module mdanalysis.lib.util)": [[120, "MDAnalysis.lib.util.unique_rows", false]], "unit_dict (mdanalysis.auxiliary.edr.edrreader attribute)": [[44, "MDAnalysis.auxiliary.EDR.EDRReader.unit_dict", false]], "unit_types (in module mdanalysis.units)": [[169, "MDAnalysis.units.unit_types", false]], "units (mdanalysis.analysis.density.density attribute)": [[7, "MDAnalysis.analysis.density.Density.units", false]], "units (mdanalysis.converters.base.converterbase attribute)": [[54, "MDAnalysis.converters.base.ConverterBase.units", false]], "units (mdanalysis.converters.openmm.openmmappreader attribute)": [[51, "MDAnalysis.converters.OpenMM.OpenMMAppReader.units", false]], "units (mdanalysis.converters.openmm.openmmsimulationreader attribute)": [[51, "MDAnalysis.converters.OpenMM.OpenMMSimulationReader.units", false]], "units (mdanalysis.converters.openmmparser.openmmapptopologyparser attribute)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser.units", false]], "units (mdanalysis.converters.openmmparser.openmmtopologyparser attribute)": [[51, "MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser.units", false]], "units 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111, 113, 116, 117, 118, 122, 123, 124, 136, 142, 147, 161, 164, 170, 174], "your": [0, 3, 4, 7, 10, 12, 19, 21, 24, 26, 28, 31, 32, 35, 40, 42, 43, 52, 56, 63, 65, 74, 80, 93, 97, 110, 113, 123, 160], "yourmodul": 123, "yourscript": 123, "yourself": [10, 120, 124], "ysu": 65, "ython": 34, "yu": 65, "yy": 7, "yz": [31, 163], "z": [6, 7, 9, 15, 31, 56, 59, 63, 65, 69, 70, 71, 75, 78, 79, 80, 81, 85, 92, 94, 96, 110, 114, 119, 120, 124, 143, 158, 160, 172], "z1": [7, 172], "z2": 7, "z_lower": 172, "z_plus_view": 172, "z_upper": 172, "z_valu": 172, "zaxi": 119, "zcen": 92, "zdim": 7, "zerbino": 123, "zero": [9, 19, 20, 56, 61, 63, 69, 80, 92, 96, 98, 100, 110, 111, 112, 113, 114, 120, 141, 151], "zeta": 33, "zheng": 9, "zhiyi": 42, "zhou": [109, 123], "zink": 105, "ziolek": 123, "zip": [21, 110, 122], "zmax": [92, 115, 124, 172], "zmin": [92, 115, 124, 172], "zn": 105, "znd": 38, "zone": [92, 124], "zr": 105, "zsu": 65, "zu": 65, "zvalu": 69, "zz": 7, "\u00e1": 109, "\u00e5": [3, 5, 7, 22, 26, 42, 56, 59, 65, 69, 71, 74, 86, 89, 92, 96, 109, 162, 169], "\u00e5ngstrom": 63, "\u00e5ngstr\u00f6m": [7, 59, 65, 74, 169], "\u00ed": 109, "\u03b1": 12, "\u03bc": 169, "\u03c0": [12, 114], "\u03c6": 10, "\u03c8": 10}, "titles": ["4.3.1. Coordinate fitting and alignment \u2014 MDAnalysis.analysis.align", "4.3.4. Simple atomic distance analysis \u2014 MDAnalysis.analysis.atomicdistances", "4.2.2. Analysis backends \u2014 MDAnalysis.analysis.backends", "4.2.1. Analysis building blocks \u2014 MDAnalysis.analysis.base", "4.3.8. Bond-Angle-Torsion coordinates analysis \u2014 MDAnalysis.analysis.bat", "4.3.2. Native contacts analysis \u2014 MDAnalysis.analysis.contacts", "4.12.1. Analysis data files", "4.9.1. Generating densities from trajectories \u2014 MDAnalysis.analysis.density", "4.9.4. Dielectric \u2014 MDAnalysis.analysis.dielectric", "4.10.1. Diffusion map \u2014 MDAnalysis.analysis.diffusionmap", "4.8.1.3. Dihedral angles analysis \u2014 MDAnalysis.analysis.dihedrals", "4.3.3. Distance analysis \u2014 MDAnalysis.analysis.distances", "4.8.1.4. Secondary structure assignment (helix, sheet and loop) \u2014 MDAnalysis.analysis.dssp", "4.3.7. ENCORE Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore", "4.3.7.1.6. bootstrap procedures \u2014 MDAnalysis.analysis.ensemble.bootstrap", "4.3.7.1.2. Clustering", "4.3.7.1.4. Distance Matrix calculation \u2014 MDAnalysis.analysis.ensemble.confdistmatrix", "4.3.7.1.5. Covariance calculation \u2014 encore.covariance", "4.3.7.1.3. Dimensionality reduction", "4.3.7.1.1. Ensemble Similarity Calculations \u2014 MDAnalysis.analysis.encore.similarity", "4.3.7.1.7. Utility functions for ENCORE", "4.8.1.1. Elastic network analysis of MD trajectories \u2014 MDAnalysis.analysis.gnm", "4.4.2. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel", "4.4.4. Hydrogen bond autocorrelation \u2014 MDAnalysis.analysis.hbonds.hbond_autocorrel (deprecated)", "4.8.1.2. HELANAL \u2014 analysis of protein helices", "4.5.1. HOLE analysis \u2014 MDAnalysis.analysis.hole2", "4.4.1. Hydrogen Bond Analysis \u2014 MDAnalysis.analysis.hydrogenbonds.hbond_analysis", "4.5.2. Leaflet identification \u2014 MDAnalysis.analysis.leaflet", "4.11.1.1.1. Generation and Analysis of X3DNA helicoidal parameter profiles \u2014 MDAnalysis.analysis.legacy.x3dna", "4.11.1. MDAnalysis.analysis.legacy \u2014 Legacy analysis code", "4.9.2. Linear Density \u2014 MDAnalysis.analysis.lineardensity", "4.8.2.2. Mean Squared Displacement \u2014 MDAnalysis.analysis.msd", "4.6.2. Updated nucleic acid analysis \u2014 MDAnalysis.analysis.nucleicacids", "4.6.1. Nucleic acid analysis \u2014 MDAnalysis.analysis.nuclinfo", "4.2.4. Parallel analysis", "4.10.2. Principal Component Analysis (PCA) \u2014 MDAnalysis.analysis.pca", "4.7.1. Polymer analysis \u2014 MDAnalysis.analysis.polymer", "4.3.6. Calculating path similarity \u2014 MDAnalysis.analysis.psa", "4.8.2.1. Radial Distribution Functions \u2014 MDAnalysis.analysis.rdf", "4.2.3. Analysis results and their aggregation \u2014 MDAnalysis.analysis.results", "4.3.5. Calculating root mean square quantities \u2014 MDAnalysis.analysis.rms", "4.9.3. Water dynamics analysis \u2014 MDAnalysis.analysis.waterdynamics", "4.4.3. Water Bridge analysis \u2014 MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis", "4. Analysis modules", "11.5. EDR auxiliary reader \u2014 MDAnalysis.auxiliary.EDR", "11.4. XVG auxiliary reader \u2014 MDAnalysis.auxiliary.XVG", "11.2. Auxiliary Readers \u2014 MDAnalysis.auxiliary.base", "11.3. Common functions for auxiliary reading \u2014 MDAnalysis.auxiliary.core", "11.1. Auxiliary Readers \u2014 MDAnalysis.auxiliary", "11. Auxiliary modules", "8. Converter modules", "8.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser", "8.1. ParmEd topology parser \u2014 MDAnalysis.converters.ParmEdParser", "8.3. RDKit topology parser \u2014 MDAnalysis.converters.RDKitParser", "8.8. Base classes \u2014 MDAnalysis.converters.base", "7.2. CRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.CRD", "7.3. DCD trajectory I/O \u2014 MDAnalysis.coordinates.DCD", "7.4. DL_Poly format reader MDAnalysis.coordinates.DLPoly", "7.5. DESRES file format \u2014 MDAnalysis.coordinates.DMS", "7.26. FHI-AIMS file format \u2014 MDAnalysis.coordinates.FHIAIMS", "7.6. GAMESS trajectory reader \u2014 MDAnalysis.coordinates.GMS", "7.8. GRO file format \u2014 MDAnalysis.coordinates.GRO", "7.7. GSD trajectory reader \u2014 MDAnalysis.coordinates.GSD", "7.9. H5MD trajectories \u2014 MDAnalysis.coordinates.H5MD", "7.10. INPCRD structure files in MDAnalysis \u2014 MDAnalysis.coordinates.INPCRD", "7.11. LAMMPS DCD trajectory and DATA I/O \u2014 MDAnalysis.coordinates.LAMMPS", "7.12. MMTF trajectory reader \u2014 MDAnalysis.coordinates.MMTF", "7.13. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "7.14. NAMDBIN files format \u2014 MDAnalysis.coordinates.NAMDBIN", "7.15. PDB structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDB", "7.16. PDBQT structure files in MDAnalysis \u2014 MDAnalysis.coordinates.PDBQT", "7.17. PQR file format \u2014 MDAnalysis.coordinates.PQR", "7.18. TNG trajectory files \u2014 MDAnalysis.coordinates.TNG", "7.19. GROMOS11 trajectory reader \u2014 MDAnalysis.coordinates.TRC", "7.20. AMBER trajectories \u2014 MDAnalysis.coordinates.TRJ", "7.21. TRR trajectory files \u2014 MDAnalysis.coordinates.TRR", "7.22. TRZ trajectory I/O \u2014 MDAnalysis.coordinates.TRZ", "7.23. TXYZ file format \u2014 MDAnalysis.coordinates.TXYZ", "7.35. XDR based trajectory files \u2014 MDAnalysis.coordinates.XDR", "7.24. XTC trajectory files \u2014 MDAnalysis.coordinates.XTC", "7.25. XYZ trajectory reader \u2014 MDAnalysis.coordinates.XYZ", "7.31. Base classes \u2014 MDAnalysis.coordinates.base", "7.34. ChainReader \u2014 MDAnalysis.coordinates.chain", "7.28. Reading trajectories with chemfiles \u2014 MDAnalysis.coordinates.chemfiles", "7.32. Common functions for coordinate reading \u2014 MDAnalysis.coordinates.core", "7.1. Trajectory Readers and Writers \u2014 MDAnalysis.coordinates", "7.27. Reading trajectories from memory \u2014 MDAnalysis.coordinates.memory", "7.29. Null output \u2014 MDAnalysis.coordinates.null", "7.33. Serialization of Coordinate Readers", "7.30. Timestep Class \u2014 MDAnalysis.coordinates.timestep", "7. Coordinates modules", "8.7. AtomGroup accessors \u2014 MDAnalysis.core.accessors", "12.2.2. Core objects: Containers \u2014 MDAnalysis.core.groups", "12.1. Core functions of MDAnalysis", "12.4.1. Atom selection Hierarchy \u2014 MDAnalysis.core.selection", "12.3.1. Core Topology object \u2014 MDAnalysis.core.topology", "12.3.3. Topology attribute objects \u2014 MDAnalysis.core.topologyattrs", "12.3.2. Core Topology Objects \u2014 MDAnalysis.core.topologyobjects", "12.2.1. Core object: Universe \u2014 MDAnalysis.core.universe", "12. Core modules", "17. Custom exceptions and warnings \u2014 MDAnalysis.exceptions", "6. Guesser modules", "6.1.2.3. Base guesser classes \u2014 MDAnalysis.guesser.base", "6.1.2.2. Default Guesser", "6.1.2.1. Context-specific guessers \u2014 MDAnalysis.guesser", "6.1.2.4. MDAnalysis topology tables", "14.2.3. Neighbor Search wrapper for MDAnalysis \u2014 MDAnalysis.lib.NeighborSearch", "14.2.2.1. Distance calculation library \u2014 MDAnalysis.lib.c_distances", "14.2.2.2. Parallel distance calculation library \u2014 MDAnalysis.lib.c_distances_openmp", "14.2.11. Correlations utilities \u2014 MDAnalysis.lib.correlations", "14.2.1. Fast distance array computation \u2014 MDAnalysis.lib.distances", "14.3.2. Low level DCD trajectory reading - MDAnalysis.lib.formats.libdcd", "14.3.1. Low-level Gromacs XDR trajectory reading \u2014 MDAnalysis.lib.formats.libmdaxdr", "14.2.6. Setting up logging \u2014 MDAnalysis.lib.log", "14.2.7. Mathematical helper functions \u2014 MDAnalysis.lib.mdamath", "14.2.4. Neighbor search library \u2014 MDAnalysis.lib.nsgrid", "14.2.14. Picklable read-only I/O classes \u2014 MDAnalysis.lib.picklable_file_io", "14.2.5. PeriodicKDTree \u2014 MDAnalysis.lib.pkdtree", "14.2.9. Fast QCP RMSD structure alignment \u2014 MDAnalysis.lib.qcprot", "14.2.8. Homogeneous Transformation Matrices and Quaternions \u2014 MDAnalysis.lib.transformations", "14.2.10. Helper functions \u2014 MDAnalysis.lib.util", "14. Library functions \u2014 MDAnalysis.lib", "1. Overview over MDAnalysis", "18. References", "3. Selection commands", "10.2.6. Base classes for the selection writers", "10.2.4. CHARMM selections", "10.2.3. Gromacs selections", "10.2.5. Jmol selections", "10.2.2. PyMOL selections", "10.2.1. VMD selections", "10. Selection exporters", "2. The topology system", "5.2. CRD topology parser", "5.3. DL Poly format Topology Readers \u2014 MDAnalysis.topology.DLPolyParser", "5.4. DESRES Molecular Structure file format topology parser", "5.16. Extended PDB topology parser", "5.5. FHI-AIMS Topology Parser \u2014 MDAnalysis.topolgy.FHIAIMSParser", "5.6. GAMESS Topology Parser", "5.7. GRO topology parser", "5.8. GSD topology parser", "5.9. HOOMD XML topology parser", "5.10. ITP topology parser", "5.11. LAMMPSParser", "5.13. MMTF Topology Parser", "5.14. MOL2 file format \u2014 MDAnalysis.coordinates.MOL2", "5.12. Minimal topology parser", "5.15. PDB Topology Parser", "5.17. PDBQT topology parser", "5.18. PQR topology parser", "5.19. PSF topology parser", "5.20. AMBER PRMTOP topology parser", "5.21. Gromacs portable run input TPR format parser", "5.22. TXYZ topology parser", "5.23. XYZ Topology Parser", "5.24. Base topology reader classes \u2014 MDAnalysis.topology.base", "5.25. Common functions for topology building \u2014 MDAnalysis.topology.core", "5.1. Topology readers \u2014 MDAnalysis.topology", "5.26. Utility functions for the TPR topology parser", "5. Topology modules", "9. Trajectory transformations (\u201con-the-fly\u201d transformations)", "9.5.1. Transformations Base Class \u2014 MDAnalysis.transformations.base", "9.6.7. Set box dimensions \u2014 MDAnalysis.transformations.boxdimensions", "9.6.4. Fitting transformations \u2014 MDAnalysis.transformations.fit", "9.6.6. No Jump Trajectory Unwrapping \u2014 MDAnalysis.transformations.nojump", "9.6.3. Trajectory Coordinate Averaging \u2014 MDAnalysis.transformations.positionaveraging", "9.6.2. Trajectory rotation \u2014 MDAnalysis.transformations.rotate", "9.6.1. Trajectory translation \u2014 MDAnalysis.transformations.translate", "9.6.5. Wrap/unwrap transformations \u2014 MDAnalysis.transformations.wrap", "16. Constants and unit conversion \u2014 MDAnalysis.units", "15. Version information for MDAnalysis - MDAnalysis.version", "13.1.1. Streamplots (2D) \u2014 MDAnalysis.visualization.streamlines", "13.1.2. Streamplots (3D) \u2014 MDAnalysis.visualization.streamlines_3D", "13. 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