Index

Symbols

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__eq__() (MDAnalysis.coordinates.timestep.Timestep method) __getitem__() (MDAnalysis.coordinates.timestep.Timestep method) __init__() (MDAnalysis.coordinates.timestep.Timestep method) (MDAnalysis.selections.base.SelectionWriterBase method) __iter__() (MDAnalysis.coordinates.timestep.Timestep method) __version__ (in module MDAnalysis.version) _apply() (MDAnalysis.coordinates.chain.ChainReader method) _auxdata (MDAnalysis.auxiliary.EDR.EDRReader attribute) _check_pdb_coordinates() (MDAnalysis.coordinates.PDB.PDBWriter method) _Deprecate (class in MDAnalysis.lib.util) _fit_to() (in module MDAnalysis.analysis.align) _forces (MDAnalysis.coordinates.timestep.Timestep attribute) _get() (MDAnalysis.coordinates.chain.ChainReader method) _get_local_frame() (MDAnalysis.coordinates.chain.ChainReader method) _get_same() (MDAnalysis.coordinates.chain.ChainReader method)

_infer_bo_and_charges() (in module MDAnalysis.converters.RDKit) _n_steps (MDAnalysis.auxiliary.EDR.EDRReader attribute) _pos (MDAnalysis.coordinates.timestep.Timestep attribute) _read_frame() (MDAnalysis.coordinates.chain.ChainReader method) _rebuild_conjugated_bonds() (in module MDAnalysis.converters.RDKit) _reopen() (MDAnalysis.coordinates.H5MD.H5MDReader method) _set_user_grid() (MDAnalysis.analysis.density.DensityAnalysis static method) _standardize_patterns() (in module MDAnalysis.converters.RDKit) _translate() (MDAnalysis.selections.base.SelectionWriterBase method) _update_frame() (MDAnalysis.coordinates.PDB.PDBWriter method) _velocities (MDAnalysis.coordinates.timestep.Timestep attribute) _write_head() (MDAnalysis.selections.base.SelectionWriterBase method) _write_pdb_bonds() (MDAnalysis.coordinates.PDB.PDBWriter method) _write_tail() (MDAnalysis.selections.base.SelectionWriterBase method) _write_timestep() (MDAnalysis.coordinates.PDB.PDBWriter method)

A

accepts_distance_matrix (MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans attribute) Accessor (class in MDAnalysis.core.accessors) accumulate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) active_reader (MDAnalysis.coordinates.chain.ChainReader property) add_angles() (MDAnalysis.core.universe.Universe method) add_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) add_bonds() (MDAnalysis.core.universe.Universe method) add_dihedrals() (MDAnalysis.core.universe.Universe method) add_impropers() (MDAnalysis.core.universe.Universe method) add_Residue() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) add_Segment() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) add_TopologyAttr() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) add_transformations() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) additional_blocks (MDAnalysis.coordinates.TNG.TNGReader property) AffinityPropagation (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) AffinityPropagation() (in module MDAnalysis.analysis.encore.clustering.affinityprop) AffinityPropagationNative (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) ag (MDAnalysis.analysis.msd.EinsteinMSD attribute) align_principal_axis() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) alignto() (in module MDAnalysis.analysis.align) AlignTraj (class in MDAnalysis.analysis.align) AltLocs (class in MDAnalysis.core.topologyattrs) analysis_class() (in module MDAnalysis.analysis.base) AnalysisBase (class in MDAnalysis.analysis.base) AnalysisFromFunction (class in MDAnalysis.analysis.base) Angle (class in MDAnalysis.core.topologyobjects) angle (MDAnalysis.core.groups.AtomGroup property) angle() (in module MDAnalysis.lib.mdamath) (MDAnalysis.core.topologyobjects.Angle method) Angles (class in MDAnalysis.core.topologyattrs) angles (MDAnalysis.analysis.dihedrals.Dihedral attribute) (MDAnalysis.analysis.dihedrals.Dihedral.results attribute) (MDAnalysis.analysis.dihedrals.Janin attribute) (MDAnalysis.analysis.dihedrals.Janin.results attribute) (MDAnalysis.analysis.dihedrals.Ramachandran attribute) (MDAnalysis.analysis.dihedrals.Ramachandran.results attribute) (MDAnalysis.core.universe.Universe attribute) angles() (MDAnalysis.core.topologyobjects.TopologyGroup method) AngularDistribution (class in MDAnalysis.analysis.waterdynamics) anyopen() (in module MDAnalysis.lib.util)

ApplicationError, [1] apply_PBC() (in module MDAnalysis.lib.distances) Arcball (class in MDAnalysis.lib.transformations) arcball_nearest_axis() (in module MDAnalysis.lib.transformations) args (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) Aromaticities (class in MDAnalysis.core.topologyattrs) AromaticSelection (class in MDAnalysis.core.selection) as_array() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) asiterable() (in module MDAnalysis.lib.util) asphericity() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) asunique() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) atnr (MDAnalysis.topology.tpr.obj.Params attribute) Atom (class in MDAnalysis.core.groups) (class in MDAnalysis.topology.tpr.obj) atom1 (MDAnalysis.core.topologyobjects.TopologyGroup property) atom2 (MDAnalysis.core.topologyobjects.TopologyGroup property) atom3 (MDAnalysis.core.topologyobjects.TopologyGroup property) atom4 (MDAnalysis.core.topologyobjects.TopologyGroup property) AtomAttr (class in MDAnalysis.core.topologyattrs) atomelements (in module MDAnalysis.topology.tables) AtomGroup (class in MDAnalysis.core.groups) atomgroup_intersection() (MDAnalysis.core.topologyobjects.TopologyGroup method) AtomicDistances (class in MDAnalysis.analysis.atomicdistances) Atomids (class in MDAnalysis.core.topologyattrs) Atomindices (class in MDAnalysis.core.topologyattrs) AtomKind (class in MDAnalysis.topology.tpr.obj) Atomnames (class in MDAnalysis.core.topologyattrs) atomnames (MDAnalysis.topology.tpr.obj.Atoms attribute) AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch) atomnumber (MDAnalysis.topology.tpr.obj.Atom attribute) Atoms (class in MDAnalysis.topology.tpr.obj) atoms (MDAnalysis.analysis.bat.BAT property) (MDAnalysis.analysis.diffusionmap.DistanceMatrix attribute) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.groups.UpdatingAtomGroup property) (MDAnalysis.core.topologyobjects.TopologyObject property) (MDAnalysis.core.universe.Universe attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) atoms2residues() (MDAnalysis.core.topology.TransTable method) atoms2segments() (MDAnalysis.core.topology.TransTable method) AtomStringAttr (class in MDAnalysis.core.topologyattrs) Atomtypes (class in MDAnalysis.core.topologyattrs) attach_auxiliary() (MDAnalysis.auxiliary.base.AuxReader method) attrname (MDAnalysis.core.topologyattrs.TopologyAttr attribute) augment_coordinates() (in module MDAnalysis.lib.distances) autocorrelation() (in module MDAnalysis.lib.correlations) aux_list (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) auxfile (MDAnalysis.auxiliary.base.AuxFileReader attribute) AuxFileReader (class in MDAnalysis.auxiliary.base) AuxReader (class in MDAnalysis.auxiliary.base) auxreader() (in module MDAnalysis.auxiliary.core) AuxStep (class in MDAnalysis.auxiliary.base) auxstep (MDAnalysis.auxiliary.base.AuxReader attribute) AverageStructure (class in MDAnalysis.analysis.align)

B

BackboneSelection (class in MDAnalysis.core.selection) BaseSelection (class in MDAnalysis.core.selection) BAT (class in MDAnalysis.analysis.bat) bat (MDAnalysis.analysis.bat.BAT.results attribute) bBox (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bbox() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) between() (in module MDAnalysis.analysis.distances) bF (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bfactor (MDAnalysis.core.groups.Atom property) bfactor() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactor_setter() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactors (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) bfactors() (MDAnalysis.core.topologyattrs.Tempfactors method) bfactors_setter() (MDAnalysis.core.topologyattrs.Tempfactors method) bin_radii() (MDAnalysis.analysis.hole2.HoleAnalysis method) bins (MDAnalysis.analysis.rdf.InterRDF attribute) (MDAnalysis.analysis.rdf.InterRDF.results attribute) (MDAnalysis.analysis.rdf.InterRDF_s attribute) (MDAnalysis.analysis.rdf.InterRDF_s.results attribute)

bIr (MDAnalysis.topology.tpr.obj.TpxHeader attribute) blocks (MDAnalysis.coordinates.TNG.TNGReader property) blocks_of() (in module MDAnalysis.lib.util) Bond (class in MDAnalysis.core.topologyobjects) bond (MDAnalysis.core.groups.AtomGroup property) bond_autocorrelation (MDAnalysis.analysis.polymer.PersistenceLength.results attribute) bonded_atoms (MDAnalysis.core.groups.Atom property) bonded_atoms() (MDAnalysis.core.topologyattrs.Bonds method) Bonds (class in MDAnalysis.core.topologyattrs) bonds (MDAnalysis.core.universe.Universe attribute) bonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) BoolSelection (class in MDAnalysis.core.selection) bootstrapped_matrix() (in module MDAnalysis.analysis.encore.bootstrap) Box (class in MDAnalysis.topology.tpr.obj) box_volume() (in module MDAnalysis.lib.mdamath) bsphere() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) bTop (MDAnalysis.topology.tpr.obj.TpxHeader attribute) BufferIOPicklable (class in MDAnalysis.lib.picklable_file_io) bV (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bX (MDAnalysis.topology.tpr.obj.TpxHeader attribute) ByNumSelection (class in MDAnalysis.core.selection) ByResSelection (class in MDAnalysis.core.selection) bz2_pickle_open() (in module MDAnalysis.lib.picklable_file_io) BZ2Picklable (class in MDAnalysis.lib.picklable_file_io)

C

cached() (in module MDAnalysis.lib.util) calc_angles() (in module MDAnalysis.lib.distances) calc_bonds() (in module MDAnalysis.lib.distances) calc_dihedrals() (in module MDAnalysis.lib.distances) calc_offsets() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) calc_representative() (MDAnalysis.auxiliary.base.AuxReader method) CalcRMSDRotationalMatrix() (in module MDAnalysis.lib.qcprot) capped_distance() (in module MDAnalysis.lib.distances) Cartesian() (MDAnalysis.analysis.bat.BAT method) cdf (MDAnalysis.analysis.rdf.InterRDF_s attribute) (MDAnalysis.analysis.rdf.InterRDF_s.results attribute) center() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) center_in_box (class in MDAnalysis.transformations.translate) center_of_charge() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method) center_of_geometry() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) center_of_mass() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) centers() (MDAnalysis.analysis.density.Density method) centroid (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) centroid() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) ces() (in module MDAnalysis.analysis.encore.similarity) ces_convergence() (in module MDAnalysis.analysis.encore.similarity) ChainIDs (class in MDAnalysis.core.topologyattrs) ChainReader (class in MDAnalysis.coordinates.chain) char (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) char_std (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) charge_density (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) charge_density_stddev (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) Charges (class in MDAnalysis.core.topologyattrs) chargeUnit_factor (in module MDAnalysis.units) charmm_bitfield (MDAnalysis.lib.formats.libdcd.DCDFile attribute) check_and_fix_long_filename() (in module MDAnalysis.analysis.hole2.utils) check_atomgroup_not_empty() (in module MDAnalysis.lib.util) check_box() (in module MDAnalysis.lib.util) check_chemfiles_version() (in module MDAnalysis.coordinates.chemfiles) check_compatible() (MDAnalysis.analysis.density.Density method) check_compressed_format() (in module MDAnalysis.lib.util) check_coords() (in module MDAnalysis.lib.util) check_slice_indices() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) ChemfilesPicklable (class in MDAnalysis.coordinates.chemfiles) ChemfilesReader (class in MDAnalysis.coordinates.chemfiles) ChemfilesWriter (class in MDAnalysis.coordinates.chemfiles) chi1_selection() (MDAnalysis.core.groups.Residue method) (MDAnalysis.core.topologyattrs.Atomnames method) chi1_selections() (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.topologyattrs.Atomnames method) clear_handlers() (in module MDAnalysis.lib.log) close() (MDAnalysis.auxiliary.base.AuxFileReader method) (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DLPoly.HistoryReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GMS.GMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.MOL2.MOL2Writer method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.PDB.PDBReader method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) (MDAnalysis.coordinates.TNG.TNGReader method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRJ.NCDFWriter method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TRZ.TRZReader method) (MDAnalysis.coordinates.TRZ.TRZWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) closeContactGNMAnalysis (class in MDAnalysis.analysis.gnm) closed (MDAnalysis.lib.util.NamedStream property) Cluster (class in MDAnalysis.analysis.encore.clustering.ClusterCollection) cluster() (in module MDAnalysis.analysis.encore.clustering.cluster) (MDAnalysis.analysis.psa.PSAnalysis method) ClusterCollection (class in MDAnalysis.analysis.encore.clustering.ClusterCollection) clustering_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) ClusteringMethod (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) clusters (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection attribute) CMap (class in MDAnalysis.core.topologyobjects) cmap (MDAnalysis.core.groups.AtomGroup property) CMaps (class in MDAnalysis.core.topologyattrs) collect() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) collect_hole() (in module MDAnalysis.analysis.hole2.utils) comment() (MDAnalysis.selections.base.SelectionWriterBase method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) commentfmt (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) compose_matrix() (in module MDAnalysis.lib.transformations) compressed (MDAnalysis.coordinates.chain.ChainReader property) concatenate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) concatenate_matrices() (in module MDAnalysis.lib.transformations) CONECT() (MDAnalysis.coordinates.PDB.PDBWriter method) ConfigReader (class in MDAnalysis.coordinates.DLPoly) conformational_distance_matrix() (in module MDAnalysis.analysis.encore.confdistmatrix) constant_dt (MDAnalysis.auxiliary.base.AuxReader property) constants (in module MDAnalysis.units) contact_matrix() (in module MDAnalysis.analysis.contacts) (in module MDAnalysis.analysis.distances) Contacts (class in MDAnalysis.analysis.contacts) continuation (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) conv_float() (in module MDAnalysis.lib.util) conversion_factor (in module MDAnalysis.units) ConversionWarning convert() (in module MDAnalysis.units) (MDAnalysis.converters.ParmEd.ParmEdConverter method) (MDAnalysis.converters.RDKit.RDKitConverter method) convert_aa_code() (in module MDAnalysis.lib.util) convert_density() (MDAnalysis.analysis.density.Density method) convert_dimensions_to_unitcell() (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCWriter method) convert_forces_from_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_forces_to_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_length() (MDAnalysis.analysis.density.Density method) convert_pos_from_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method)

convert_pos_to_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_time_from_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_time_to_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_to (MDAnalysis.core.groups.AtomGroup attribute) convert_velocities_from_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_velocities_to_native() (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser method) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser method) (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.coordinates.base.ConverterBase method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) ConverterBase (class in MDAnalysis.coordinates.base) ConverterWrapper (class in MDAnalysis.core.accessors) coord (MDAnalysis.core.universe.Universe property) copy() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.timestep.Timestep method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.groups.UpdatingAtomGroup method) (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.topology.TransTable method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.universe.Universe method) copy_slice() (MDAnalysis.coordinates.timestep.Timestep method) correct_intermittency() (in module MDAnalysis.lib.correlations) cosine_content() (in module MDAnalysis.analysis.pca) count (MDAnalysis.analysis.rdf.InterRDF attribute) (MDAnalysis.analysis.rdf.InterRDF.results attribute) (MDAnalysis.analysis.rdf.InterRDF_s attribute) (MDAnalysis.analysis.rdf.InterRDF_s.results attribute) count_by_ids() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) count_by_time() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis method) count_by_type() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis method) covariance_matrix() (in module MDAnalysis.analysis.encore.covariance) CRDParser (class in MDAnalysis.topology.CRDParser) CRDReader (class in MDAnalysis.coordinates.CRD) CRDWriter (class in MDAnalysis.coordinates.CRD) create() (in module MDAnalysis.lib.log) create_vmd_surface() (in module MDAnalysis.analysis.hole2.utils) (MDAnalysis.analysis.hole2.HoleAnalysis method) CRYST1() (MDAnalysis.coordinates.PDB.PDBWriter method) cumulated_variance (MDAnalysis.analysis.pca.PCA attribute) (MDAnalysis.analysis.pca.PCA.results attribute) cumulative_clustering_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) cumulative_gen_kde_pdfs() (in module MDAnalysis.analysis.encore.similarity) cumulative_overlap() (in module MDAnalysis.analysis.pca) (MDAnalysis.analysis.pca.PCA method)

D

D (MDAnalysis.analysis.psa.PSAnalysis attribute) data (MDAnalysis.auxiliary.base.AuxStep property) (MDAnalysis.coordinates.timestep.Timestep attribute) data_blacklist (MDAnalysis.coordinates.H5MD.H5MDWriter attribute) data_dict (MDAnalysis.auxiliary.EDR.EDRReader attribute) data_selector (MDAnalysis.auxiliary.base.AuxReader property) DATAParser (class in MDAnalysis.topology.LAMMPSParser) DATAReader (class in MDAnalysis.coordinates.LAMMPS) DATAWriter (class in MDAnalysis.coordinates.LAMMPS) DBSCAN (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) DCDFile (class in MDAnalysis.lib.formats.libdcd) DCDReader (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) DCDWriter (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) decompose_matrix() (in module MDAnalysis.lib.transformations) dedent_docstring() (in module MDAnalysis.lib.util) DEFAULT_ACCEPTORS (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) DEFAULT_DONORS (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) default_format (MDAnalysis.analysis.density.Density attribute) default_numterms (MDAnalysis.selections.jmol.SelectionWriter attribute) define_unpack_real() (in module MDAnalysis.topology.tpr.utils) del_TopologyAttr() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) delete_angles() (MDAnalysis.core.universe.Universe method) delete_bonds() (MDAnalysis.core.universe.Universe method) delete_dihedrals() (MDAnalysis.core.universe.Universe method) delete_impropers() (MDAnalysis.core.universe.Universe method) delete_temporary_files() (MDAnalysis.analysis.hole2.HoleAnalysis method) delta (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.coordinates.TRZ.TRZReader property) Density (class in MDAnalysis.analysis.density) density (MDAnalysis.analysis.density.DensityAnalysis attribute) (MDAnalysis.analysis.density.DensityAnalysis.results attribute) DensityAnalysis (class in MDAnalysis.analysis.density) densityUnit_factor (in module MDAnalysis.units) deprecate() (in module MDAnalysis.lib.util) DielectricConstant (class in MDAnalysis.analysis.dielectric) difference() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) DiffusionMap (class in MDAnalysis.analysis.diffusionmap) Dihedral (class in MDAnalysis.analysis.dihedrals) (class in MDAnalysis.core.topologyobjects) dihedral (MDAnalysis.core.groups.AtomGroup property) dihedral() (in module MDAnalysis.lib.mdamath) (MDAnalysis.core.topologyobjects.Dihedral method) Dihedrals (class in MDAnalysis.core.topologyattrs) dihedrals (MDAnalysis.core.universe.Universe attribute) dihedrals() (MDAnalysis.core.topologyobjects.TopologyGroup method) dim (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) dim_fac (MDAnalysis.analysis.msd.EinsteinMSD attribute) DimensionalityReductionMethod (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) dimensions (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.universe.Universe attribute) dimred_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) dipole_moment() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method) dipole_vector() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method) discrete_frechet() (in module MDAnalysis.analysis.psa) discrete_jensen_shannon_divergence() (in module MDAnalysis.analysis.encore.similarity) discrete_kullback_leibler_divergence() (in module MDAnalysis.analysis.encore.similarity) dist() (in module MDAnalysis.analysis.distances) dist_mat_to_vec() (in module MDAnalysis.analysis.psa) dist_matrix (MDAnalysis.analysis.diffusionmap.DistanceMatrix attribute) (MDAnalysis.analysis.diffusionmap.DistanceMatrix.results attribute) distance() (MDAnalysis.core.topologyobjects.UreyBradley method) distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances) DistanceMatrix (class in MDAnalysis.analysis.diffusionmap)

DMSParser (class in MDAnalysis.topology.DMSParser) DMSReader (class in MDAnalysis.coordinates.DMS) do_atom() (in module MDAnalysis.topology.tpr.utils) do_atoms() (in module MDAnalysis.topology.tpr.utils) do_block() (in module MDAnalysis.topology.tpr.utils) do_blocka() (in module MDAnalysis.topology.tpr.utils) do_ffparams() (in module MDAnalysis.topology.tpr.utils) do_harm() (in module MDAnalysis.topology.tpr.utils) do_ilists() (in module MDAnalysis.topology.tpr.utils) do_iparams() (in module MDAnalysis.topology.tpr.utils) do_molblock() (in module MDAnalysis.topology.tpr.utils) do_moltype() (in module MDAnalysis.topology.tpr.utils) do_mtop() (in module MDAnalysis.topology.tpr.utils) do_resinfo() (in module MDAnalysis.topology.tpr.utils) do_rvec() (in module MDAnalysis.topology.tpr.utils) do_string() (MDAnalysis.topology.tpr.utils.TPXUnpacker method) (MDAnalysis.topology.tpr.utils.TPXUnpacker2020 method) do_symstr() (in module MDAnalysis.topology.tpr.utils) do_symtab() (in module MDAnalysis.topology.tpr.utils) down() (MDAnalysis.lib.transformations.Arcball method) drag() (MDAnalysis.lib.transformations.Arcball method) dres() (in module MDAnalysis.analysis.encore.similarity) dres_convergence() (in module MDAnalysis.analysis.encore.similarity) dt (MDAnalysis.auxiliary.base.AuxReader property) (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) dtype (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.core.selection.FloatRangeSelection attribute) (MDAnalysis.core.selection.RangeSelection attribute) (MDAnalysis.core.topologyattrs.AltLocs attribute) (MDAnalysis.core.topologyattrs.Aromaticities attribute) (MDAnalysis.core.topologyattrs.Atomids attribute) (MDAnalysis.core.topologyattrs.Atomindices attribute) (MDAnalysis.core.topologyattrs.Atomnames attribute) (MDAnalysis.core.topologyattrs.Atomtypes attribute) (MDAnalysis.core.topologyattrs.ChainIDs attribute) (MDAnalysis.core.topologyattrs.Charges attribute) (MDAnalysis.core.topologyattrs.Elements attribute) (MDAnalysis.core.topologyattrs.Epsilon14s attribute) (MDAnalysis.core.topologyattrs.Epsilons attribute) (MDAnalysis.core.topologyattrs.FormalCharges attribute) (MDAnalysis.core.topologyattrs.GBScreens attribute) (MDAnalysis.core.topologyattrs.ICodes attribute) (MDAnalysis.core.topologyattrs.Masses attribute) (MDAnalysis.core.topologyattrs.Molnums attribute) (MDAnalysis.core.topologyattrs.Moltypes attribute) (MDAnalysis.core.topologyattrs.NonbondedIndices attribute) (MDAnalysis.core.topologyattrs.Occupancies attribute) (MDAnalysis.core.topologyattrs.Radii attribute) (MDAnalysis.core.topologyattrs.RecordTypes attribute) (MDAnalysis.core.topologyattrs.Resids attribute) (MDAnalysis.core.topologyattrs.Resindices attribute) (MDAnalysis.core.topologyattrs.Resnames attribute) (MDAnalysis.core.topologyattrs.Resnums attribute) (MDAnalysis.core.topologyattrs.RMin14s attribute) (MDAnalysis.core.topologyattrs.RMins attribute) (MDAnalysis.core.topologyattrs.Segids attribute) (MDAnalysis.core.topologyattrs.Segindices attribute) (MDAnalysis.core.topologyattrs.SolventRadii attribute) (MDAnalysis.core.topologyattrs.Tempfactors attribute) (MDAnalysis.core.topologyattrs.TopologyAttr attribute) DUECREDIT_ENABLE dump_contents() (MDAnalysis.core.topologyobjects.TopologyGroup method) DumpReader (class in MDAnalysis.coordinates.LAMMPS) DuplicateWarning

E

edges (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.rdf.InterRDF attribute) (MDAnalysis.analysis.rdf.InterRDF.results attribute) (MDAnalysis.analysis.rdf.InterRDF_s attribute) (MDAnalysis.analysis.rdf.InterRDF_s.results attribute) EDRReader (class in MDAnalysis.auxiliary.EDR) EDRStep (class in MDAnalysis.auxiliary.EDR) eigenvalues (MDAnalysis.analysis.diffusionmap.DiffusionMap attribute) (MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results attribute) (MDAnalysis.analysis.gnm.GNMAnalysis.results attribute) eigenvectors (MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results attribute) (MDAnalysis.analysis.gnm.GNMAnalysis.results attribute) EinsteinMSD (class in MDAnalysis.analysis.msd) element_symbol (MDAnalysis.topology.tpr.obj.AtomKind property) Elements (class in MDAnalysis.core.topologyattrs) elements (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) emit() (MDAnalysis.lib.log.NullHandler method) empty() (MDAnalysis.core.universe.Universe class method) encode_block() (MDAnalysis.coordinates.MOL2.MOL2Writer method) encode_centroid_info() (in module MDAnalysis.analysis.encore.clustering.ClusteringMethod) END() (MDAnalysis.coordinates.PDB.PDBWriter method)

ENDMDL() (MDAnalysis.coordinates.PDB.PDBWriter method) environment variable $HOME DUECREDIT_ENABLE LD_LIBRARY_PATH, [1] OMP_NUM_THREADS PATH, [1], [2] eps (MDAnalysis.analysis.dielectric.DielectricConstant.results attribute) eps_mean (MDAnalysis.analysis.dielectric.DielectricConstant.results attribute) Epsilon14s (class in MDAnalysis.core.topologyattrs) Epsilons (class in MDAnalysis.core.topologyattrs) euler_from_quaternion() (in module MDAnalysis.lib.transformations) expect() (MDAnalysis.core.selection.SelectionParser method) export() (MDAnalysis.analysis.density.Density method) ext (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) ExtendedPDBParser (class in MDAnalysis.topology.ExtendedPDBParser) ExtendedPDBReader (class in MDAnalysis.coordinates.PDB) extract_box_info() (in module MDAnalysis.topology.tpr.utils)

F

F_ANGLES (in module MDAnalysis.topology.tpr.setting) F_ANGRES (in module MDAnalysis.topology.tpr.setting) F_ANGRESZ (in module MDAnalysis.topology.tpr.setting) F_ANHARM_POL (in module MDAnalysis.topology.tpr.setting) F_BHAM (in module MDAnalysis.topology.tpr.setting) F_BHAM_LR (in module MDAnalysis.topology.tpr.setting) F_BONDS (in module MDAnalysis.topology.tpr.setting) F_CBTDIHS (in module MDAnalysis.topology.tpr.setting) F_CMAP (in module MDAnalysis.topology.tpr.setting) F_COM_PULL (in module MDAnalysis.topology.tpr.setting) F_CONNBONDS (in module MDAnalysis.topology.tpr.setting) F_CONSTR (in module MDAnalysis.topology.tpr.setting) F_CONSTRNC (in module MDAnalysis.topology.tpr.setting) F_COUL14 (in module MDAnalysis.topology.tpr.setting) F_COUL_LR (in module MDAnalysis.topology.tpr.setting) F_COUL_RECIP (in module MDAnalysis.topology.tpr.setting) F_COUL_SR (in module MDAnalysis.topology.tpr.setting) F_CROSS_BOND_ANGLES (in module MDAnalysis.topology.tpr.setting) F_CROSS_BOND_BONDS (in module MDAnalysis.topology.tpr.setting) F_CUBICBONDS (in module MDAnalysis.topology.tpr.setting) F_DENSITYFITTING (in module MDAnalysis.topology.tpr.setting) F_DHDL_CON (in module MDAnalysis.topology.tpr.setting) F_DIHRES (in module MDAnalysis.topology.tpr.setting) F_DIHRESVIOL (in module MDAnalysis.topology.tpr.setting) F_DISPCORR (in module MDAnalysis.topology.tpr.setting) F_DISRES (in module MDAnalysis.topology.tpr.setting) F_DISRESVIOL (in module MDAnalysis.topology.tpr.setting) F_DKDL (in module MDAnalysis.topology.tpr.setting) F_DPD (in module MDAnalysis.topology.tpr.setting) F_DVDL (in module MDAnalysis.topology.tpr.setting) F_DVDL_BONDED (in module MDAnalysis.topology.tpr.setting) F_DVDL_COUL (in module MDAnalysis.topology.tpr.setting) F_DVDL_RESTRAINT (in module MDAnalysis.topology.tpr.setting) F_DVDL_TEMPERATURE (in module MDAnalysis.topology.tpr.setting) F_DVDL_VDW (in module MDAnalysis.topology.tpr.setting) F_ECONSERVED (in module MDAnalysis.topology.tpr.setting) F_EKIN (in module MDAnalysis.topology.tpr.setting) F_EPOT (in module MDAnalysis.topology.tpr.setting) F_EQM (in module MDAnalysis.topology.tpr.setting) F_ETOT (in module MDAnalysis.topology.tpr.setting) F_FBPOSRES (in module MDAnalysis.topology.tpr.setting) F_FENEBONDS (in module MDAnalysis.topology.tpr.setting) F_FOURDIHS (in module MDAnalysis.topology.tpr.setting) F_G96ANGLES (in module MDAnalysis.topology.tpr.setting) F_G96BONDS (in module MDAnalysis.topology.tpr.setting) F_GB12 (in module MDAnalysis.topology.tpr.setting) F_GB13 (in module MDAnalysis.topology.tpr.setting) F_GB14 (in module MDAnalysis.topology.tpr.setting) F_GBPOL (in module MDAnalysis.topology.tpr.setting) F_HARMONIC (in module MDAnalysis.topology.tpr.setting) F_IDIHS (in module MDAnalysis.topology.tpr.setting) F_LINEAR_ANGLES (in module MDAnalysis.topology.tpr.setting) F_LJ (in module MDAnalysis.topology.tpr.setting) F_LJ14 (in module MDAnalysis.topology.tpr.setting) F_LJ_LR (in module MDAnalysis.topology.tpr.setting) F_LJ_RECIP (in module MDAnalysis.topology.tpr.setting) F_LJC14_Q (in module MDAnalysis.topology.tpr.setting) F_LJC_PAIRS_NB (in module MDAnalysis.topology.tpr.setting) F_MORSE (in module MDAnalysis.topology.tpr.setting) F_NPSOLVATION (in module MDAnalysis.topology.tpr.setting) F_NRE (in module MDAnalysis.topology.tpr.setting) F_ORIRES (in module MDAnalysis.topology.tpr.setting) F_ORIRESDEV (in module MDAnalysis.topology.tpr.setting) F_PDIHS (in module MDAnalysis.topology.tpr.setting) F_PDISPCORR (in module MDAnalysis.topology.tpr.setting) F_PIDIHS (in module MDAnalysis.topology.tpr.setting) F_POLARIZATION (in module MDAnalysis.topology.tpr.setting) F_POSRES (in module MDAnalysis.topology.tpr.setting) F_PRES (in module MDAnalysis.topology.tpr.setting) F_QUARTIC_ANGLES (in module MDAnalysis.topology.tpr.setting) F_RBDIHS (in module MDAnalysis.topology.tpr.setting) F_RESTRANGLES (in module MDAnalysis.topology.tpr.setting) F_RESTRBONDS (in module MDAnalysis.topology.tpr.setting) F_RESTRDIHS (in module MDAnalysis.topology.tpr.setting) F_RF_EXCL (in module MDAnalysis.topology.tpr.setting) F_SETTLE (in module MDAnalysis.topology.tpr.setting) F_TABANGLES (in module MDAnalysis.topology.tpr.setting) F_TABBONDS (in module MDAnalysis.topology.tpr.setting) F_TABBONDSNC (in module MDAnalysis.topology.tpr.setting) F_TABDIHS (in module MDAnalysis.topology.tpr.setting) F_TEMP (in module MDAnalysis.topology.tpr.setting) F_THOLE_POL (in module MDAnalysis.topology.tpr.setting) F_UREY_BRADLEY (in module MDAnalysis.topology.tpr.setting) F_VSITE1 (in module MDAnalysis.topology.tpr.setting) F_VSITE2 (in module MDAnalysis.topology.tpr.setting) F_VSITE2FD (in module MDAnalysis.topology.tpr.setting) F_VSITE3 (in module MDAnalysis.topology.tpr.setting) F_VSITE3FAD (in module MDAnalysis.topology.tpr.setting) F_VSITE3FD (in module MDAnalysis.topology.tpr.setting) F_VSITE3OUT (in module MDAnalysis.topology.tpr.setting) F_VSITE4FD (in module MDAnalysis.topology.tpr.setting) F_VSITE4FDN (in module MDAnalysis.topology.tpr.setting) F_VSITEN (in module MDAnalysis.topology.tpr.setting)

F_VTEMP_NOLONGERUSED (in module MDAnalysis.topology.tpr.setting) F_WATER_POL (in module MDAnalysis.topology.tpr.setting) fasta2select() (in module MDAnalysis.analysis.align) FastCalcRMSDAndRotation() (in module MDAnalysis.lib.qcprot) FastNS (class in MDAnalysis.lib.nsgrid) fep_state (MDAnalysis.topology.tpr.obj.TpxHeader attribute) fetch_mmtf() (in module MDAnalysis.coordinates.MMTF) fgen (MDAnalysis.topology.tpr.obj.TpxHeader attribute) FHIAIMSParser (class in MDAnalysis.topology.FHIAIMSParser) FHIAIMSReader (class in MDAnalysis.coordinates.FHIAIMS) FHIAIMSWriter (class in MDAnalysis.coordinates.FHIAIMS) file_tag (MDAnalysis.topology.tpr.obj.TpxHeader attribute) FileFormatWarning FileIOPicklable (class in MDAnalysis.lib.picklable_file_io) filename (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.align.AverageStructure attribute) filename() (in module MDAnalysis.lib.util) fileno() (MDAnalysis.lib.util.NamedStream method) fileVersion_err() (in module MDAnalysis.topology.tpr.utils) find_fragments() (in module MDAnalysis.lib.mdamath) find_hydrogen_donors() (in module MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel) fit (MDAnalysis.analysis.polymer.PersistenceLength attribute) (MDAnalysis.analysis.polymer.PersistenceLength.results attribute) fit_exponential_decay() (in module MDAnalysis.analysis.polymer) fit_rot_trans (class in MDAnalysis.transformations.fit) fit_to_reference() (MDAnalysis.analysis.psa.Path method) fit_translation (class in MDAnalysis.transformations.fit) fixedwidth_bins() (in module MDAnalysis.lib.util) flatten_dict() (in module MDAnalysis.lib.util) FLOAT_PATTERN (in module MDAnalysis.core.selection) FloatRangeSelection (class in MDAnalysis.core.selection) fluct (MDAnalysis.analysis.dielectric.DielectricConstant.results attribute) flush() (MDAnalysis.lib.util.NamedStream method) fmt (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter attribute) (MDAnalysis.coordinates.GRO.GROWriter attribute) force (MDAnalysis.core.groups.Atom property) forces (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.core.groups.AtomGroup property) forceUnit_factor (in module MDAnalysis.units) FormalCharges (class in MDAnalysis.core.topologyattrs) format (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) format_from_filename_extension() (in module MDAnalysis.lib.util) FORTRAN_format_regex (in module MDAnalysis.lib.util) FORTRANReader (class in MDAnalysis.lib.util) fragindex (MDAnalysis.core.groups.Atom property) fragindex() (MDAnalysis.core.topologyattrs.Bonds method) fragindices (MDAnalysis.core.groups.AtomGroup property) fragindices() (MDAnalysis.core.topologyattrs.Bonds method) fragment (MDAnalysis.core.groups.Atom property) fragment() (MDAnalysis.core.topologyattrs.Bonds method) fragments (MDAnalysis.core.groups.AtomGroup property) fragments() (MDAnalysis.core.topologyattrs.Bonds method) frame (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.chain.ChainReader property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) frame_data (MDAnalysis.auxiliary.base.AuxReader attribute) frame_rep (MDAnalysis.auxiliary.base.AuxReader attribute) FrameIteratorAll (class in MDAnalysis.coordinates.base) FrameIteratorBase (class in MDAnalysis.coordinates.base) FrameIteratorIndices (class in MDAnalysis.coordinates.base) FrameIteratorSliced (class in MDAnalysis.coordinates.base) frames (MDAnalysis.analysis.base.AnalysisBase attribute) (MDAnalysis.analysis.base.AnalysisFromFunction.results attribute) (MDAnalysis.analysis.base.results attribute) from_blank() (MDAnalysis.core.topologyattrs.TopologyAttr class method) from_coordinates() (MDAnalysis.coordinates.timestep.Timestep method) from_smiles() (MDAnalysis.core.universe.Universe class method) from_timestep() (MDAnalysis.coordinates.timestep.Timestep method) from_unpacker() (MDAnalysis.topology.tpr.utils.TPXUnpacker2020 class method) ftupd (in module MDAnalysis.topology.tpr.setting) fudgeQQ (MDAnalysis.topology.tpr.obj.Params attribute) function (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) functype (MDAnalysis.topology.tpr.obj.Params attribute) fver (MDAnalysis.topology.tpr.obj.TpxHeader attribute)

G

gather() (MDAnalysis.analysis.hole2.HoleAnalysis method) GBScreens (class in MDAnalysis.core.topologyattrs) gen_kde_pdfs() (in module MDAnalysis.analysis.encore.similarity) gen_selection_class() (in module MDAnalysis.core.selection) generate_grid() (in module MDAnalysis.analysis.gnm) generate_kirchoff() (MDAnalysis.analysis.gnm.closeContactGNMAnalysis method) (MDAnalysis.analysis.gnm.GNMAnalysis method) generate_paths() (MDAnalysis.analysis.psa.PSAnalysis method) generate_streamlines() (in module MDAnalysis.visualization.streamlines) generate_streamlines_3d() (in module MDAnalysis.visualization.streamlines_3D) generate_table() (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis method) get_array() (MDAnalysis.coordinates.memory.MemoryReader method) get_atom_mass() (in module MDAnalysis.topology.guessers) get_atoms() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) get_aux_descriptions() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) get_auxreader_for() (in module MDAnalysis.auxiliary.core) get_cdf() (MDAnalysis.analysis.rdf.InterRDF_s method) get_centroids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection method) get_connections() (MDAnalysis.core.groups.Atom method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.Residue method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.Segment method) (MDAnalysis.core.groups.SegmentGroup method) get_conversion_factor() (in module MDAnalysis.units) get_coord_axes() (in module MDAnalysis.analysis.psa) get_data() (MDAnalysis.auxiliary.EDR.EDRReader method) get_description() (MDAnalysis.auxiliary.base.AuxReader method) get_distance_matrix() (in module MDAnalysis.analysis.encore.confdistmatrix) get_distance_matrix_bootstrap_samples() (in module MDAnalysis.analysis.encore.bootstrap) get_ensemble_bootstrap_samples() (in module MDAnalysis.analysis.encore.bootstrap) get_ext() (in module MDAnalysis.lib.util) get_ids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection method) get_indices() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) get_matching_atoms() (in module MDAnalysis.analysis.align) get_msd_matrix() (in module MDAnalysis.analysis.psa) get_num_atoms() (MDAnalysis.analysis.psa.Path method) (MDAnalysis.analysis.psa.PSAnalysis method) get_num_paths() (MDAnalysis.analysis.psa.PSAnalysis method)

get_pair_distances() (MDAnalysis.lib.nsgrid.NSResults method) get_pairs() (MDAnalysis.lib.nsgrid.NSResults method) get_pairwise_distances() (MDAnalysis.analysis.psa.PSAnalysis method) get_path_metric_func() (in module MDAnalysis.analysis.psa) get_paths() (MDAnalysis.analysis.psa.PSAnalysis method) get_reader_for() (in module MDAnalysis.coordinates.core) get_residues() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_segments() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_weights() (in module MDAnalysis.lib.util) get_writer() (in module MDAnalysis.selections) get_writer_for() (in module MDAnalysis.coordinates.core) getconstrain() (MDAnalysis.lib.transformations.Arcball method) GMSParser (class in MDAnalysis.topology.GMSParser) GMSReader (class in MDAnalysis.coordinates.GMS) GNMAnalysis (class in MDAnalysis.analysis.gnm) grab_datafile() (MDAnalysis.topology.LAMMPSParser.DATAParser method) grab_not_keywords() (in module MDAnalysis.core.selection) greedy_splitext() (in module MDAnalysis.lib.util) grid (MDAnalysis.analysis.density.Density attribute) GROParser (class in MDAnalysis.topology.GROParser) GROReader (class in MDAnalysis.coordinates.GRO) group (MDAnalysis.core.topologyattrs.Tempfactors attribute) group() (MDAnalysis.analysis.leaflet.LeafletFinder method) group_same_or_consecutive_integers() (in module MDAnalysis.lib.util) groupby() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) groups() (MDAnalysis.analysis.leaflet.LeafletFinder method) groups_iter() (MDAnalysis.analysis.leaflet.LeafletFinder method) GROWriter (class in MDAnalysis.coordinates.GRO) gsd_pickle_open() (in module MDAnalysis.coordinates.GSD) GSDParser (class in MDAnalysis.topology.GSDParser) GSDPicklable (class in MDAnalysis.coordinates.GSD) GSDReader (class in MDAnalysis.coordinates.GSD) guess_acceptors() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) guess_angles() (in module MDAnalysis.topology.guessers) guess_aromaticities() (in module MDAnalysis.topology.guessers) guess_atom_charge() (in module MDAnalysis.topology.guessers) guess_atom_element() (in module MDAnalysis.topology.guessers) guess_atom_mass() (in module MDAnalysis.topology.guessers) guess_atom_type() (in module MDAnalysis.topology.guessers) guess_bonds() (in module MDAnalysis.topology.guessers) (MDAnalysis.core.groups.AtomGroup method) guess_cpoint() (MDAnalysis.analysis.hole2.HoleAnalysis method) guess_dihedrals() (in module MDAnalysis.topology.guessers) guess_donors() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) guess_flavour() (MDAnalysis.topology.PQRParser.PQRParser static method) guess_format() (in module MDAnalysis.lib.util) guess_gasteiger_charges() (in module MDAnalysis.topology.guessers) guess_hydrogens() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) guess_improper_dihedrals() (in module MDAnalysis.topology.guessers) guess_masses() (in module MDAnalysis.topology.guessers) guess_types() (in module MDAnalysis.topology.guessers) guessed_attributes (MDAnalysis.core.topology.Topology property) gyration_moments() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) gzip_pickle_open() (in module MDAnalysis.lib.picklable_file_io) GzipPicklable (class in MDAnalysis.lib.picklable_file_io)

H

H5MD_VERSION (MDAnalysis.coordinates.H5MD.H5MDWriter attribute) H5MDReader (class in MDAnalysis.coordinates.H5MD) H5MDWriter (class in MDAnalysis.coordinates.H5MD) H5PYPicklable (class in MDAnalysis.coordinates.H5MD) hard_cut_q() (in module MDAnalysis.analysis.contacts) harmonic_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) has_forces (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.H5MD.H5MDWriter property) (MDAnalysis.coordinates.timestep.Timestep attribute) has_positions (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.H5MD.H5MDWriter property) (MDAnalysis.coordinates.timestep.Timestep attribute) has_valid_coordinates() (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCWriter method) has_velocities (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.H5MD.H5MDWriter property) (MDAnalysis.coordinates.timestep.Timestep attribute)

hasmethod() (in module MDAnalysis.lib.util) hausdorff() (in module MDAnalysis.analysis.psa) hausdorff_avg() (in module MDAnalysis.analysis.psa) hausdorff_neighbors() (in module MDAnalysis.analysis.psa) hausdorff_pair (MDAnalysis.analysis.psa.PSAPair attribute) hausdorff_pairs (MDAnalysis.analysis.psa.PSAnalysis property) hausdorff_wavg() (in module MDAnalysis.analysis.psa) hbonds (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis attribute) (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.results attribute) header (MDAnalysis.lib.formats.libdcd.DCDFile attribute) HEADER() (MDAnalysis.coordinates.PDB.PDBWriter method) hes() (in module MDAnalysis.analysis.encore.similarity) hist_bin_edges (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) histogram_radii() (MDAnalysis.analysis.hole2.HoleAnalysis method) HistoryReader (class in MDAnalysis.coordinates.DLPoly) hole() (in module MDAnalysis.analysis.hole2) HoleAnalysis (class in MDAnalysis.analysis.hole2) HoomdXMLParser (class in MDAnalysis.topology.HoomdXMLParser) HydrogenBondAnalysis (class in MDAnalysis.analysis.hydrogenbonds.hbond_analysis) HydrogenBondAutoCorrel (class in MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel) hydroxyl() (in module MDAnalysis.analysis.nuclinfo)

I

iatoms (MDAnalysis.topology.tpr.obj.Ilist attribute) ICodes (class in MDAnalysis.core.topologyattrs) id (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) ik (MDAnalysis.topology.tpr.obj.Ilist attribute) Ilist (class in MDAnalysis.topology.tpr.obj) improper (MDAnalysis.core.groups.AtomGroup property) improper() (MDAnalysis.core.topologyobjects.ImproperDihedral method) ImproperDihedral (class in MDAnalysis.core.topologyobjects) Impropers (class in MDAnalysis.core.topologyattrs) impropers (MDAnalysis.core.universe.Universe attribute) indices (MDAnalysis.core.topologyobjects.TopologyGroup property) (MDAnalysis.core.topologyobjects.TopologyObject property) initial_time (MDAnalysis.auxiliary.base.AuxReader property) InnerProduct() (in module MDAnalysis.lib.qcprot) INPReader (class in MDAnalysis.coordinates.INPCRD) INT_PATTERN (in module MDAnalysis.core.selection) interaction_types (in module MDAnalysis.topology.tpr.setting) InteractionKind (class in MDAnalysis.topology.tpr.obj) interpolated (MDAnalysis.analysis.density.Density property) interpolation_spline_order (MDAnalysis.analysis.density.Density property) InterRDF (class in MDAnalysis.analysis.rdf) InterRDF_s (class in MDAnalysis.analysis.rdf) intersection() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) IOBase (class in MDAnalysis.coordinates.base) is_guessed (MDAnalysis.core.topologyattrs.TopologyAttr property) is_keyword() (in module MDAnalysis.core.selection) is_periodic() (MDAnalysis.coordinates.TRJ.NCDFWriter method) is_strict_subset() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) is_strict_superset() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) is_uptodate (MDAnalysis.core.groups.UpdatingAtomGroup property) isdisjoint() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) isstream() (in module MDAnalysis.lib.util) issubset() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) issuperset() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) isunique (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property)

iter_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) iter_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) iterable() (in module MDAnalysis.lib.util) ITPParser (class in MDAnalysis.topology.ITPParser) ix (MDAnalysis.core.groups.Atom property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) ix_array (MDAnalysis.core.groups.Atom property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property)

J

Janin (class in MDAnalysis.analysis.dihedrals) Janin_ref (in module MDAnalysis.analysis.data.filenames)

join() (in module MDAnalysis.selections.base) join_separated_values() (in module MDAnalysis.core.selection)

K

keys() (MDAnalysis.core.topologyobjects.TopologyDict method) KMeans (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod)

kv2dict() (in module MDAnalysis.topology.tables) kwargs (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) (MDAnalysis.core.universe.Universe property)

L

lamb (MDAnalysis.topology.tpr.obj.TpxHeader attribute) LammpsDumpParser (class in MDAnalysis.topology.LAMMPSParser) lb (MDAnalysis.analysis.polymer.PersistenceLength attribute) (MDAnalysis.analysis.polymer.PersistenceLength.results attribute) LD_LIBRARY_PATH, [1] LeafletFinder (class in MDAnalysis.analysis.leaflet) length() (MDAnalysis.core.topologyobjects.Bond method) lengthUnit_factor (in module MDAnalysis.units) lg2() (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation static method)

lifetime() (MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis method) LinearDensity (class in MDAnalysis.analysis.lineardensity) load() (MDAnalysis.analysis.bat.BAT method) (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.psa.PSAnalysis method) load_new() (MDAnalysis.core.universe.Universe method) loadz() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) lp (MDAnalysis.analysis.polymer.PersistenceLength attribute) (MDAnalysis.analysis.polymer.PersistenceLength.results attribute) ltruncate_int() (in module MDAnalysis.lib.util)

M

M (MDAnalysis.analysis.dielectric.DielectricConstant.results attribute) m (MDAnalysis.topology.tpr.obj.Atom attribute) M2 (MDAnalysis.analysis.dielectric.DielectricConstant.results attribute) major_pair() (in module MDAnalysis.analysis.nuclinfo) make_density() (MDAnalysis.analysis.density.Density method) make_downshift_arrays() (in module MDAnalysis.core.topology) make_whole() (in module MDAnalysis.lib.mdamath) mass_density (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) mass_density_stddev (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) Masses (class in MDAnalysis.core.topologyattrs) masses (in module MDAnalysis.topology.tables) matrix() (MDAnalysis.lib.transformations.Arcball method) matrix_id (MDAnalysis.analysis.psa.PSAPair attribute) MAX_CHEMFILES_VERSION (in module MDAnalysis.coordinates.chemfiles) mB (MDAnalysis.topology.tpr.obj.Atom attribute) MDAnalysis.analysis.align module MDAnalysis.analysis.atomicdistances module MDAnalysis.analysis.base module MDAnalysis.analysis.bat module MDAnalysis.analysis.contacts module MDAnalysis.analysis.data.filenames module MDAnalysis.analysis.density module MDAnalysis.analysis.dielectric module MDAnalysis.analysis.diffusionmap module MDAnalysis.analysis.dihedrals module MDAnalysis.analysis.distances module MDAnalysis.analysis.encore.bootstrap module MDAnalysis.analysis.encore.clustering.affinityprop module MDAnalysis.analysis.encore.clustering.cluster module MDAnalysis.analysis.encore.clustering.ClusterCollection module MDAnalysis.analysis.encore.clustering.ClusteringMethod module MDAnalysis.analysis.encore.confdistmatrix module MDAnalysis.analysis.encore.covariance module MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod module MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality module MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed module MDAnalysis.analysis.encore.similarity module MDAnalysis.analysis.encore.utils module MDAnalysis.analysis.gnm module MDAnalysis.analysis.hbonds.hbond_autocorrel module MDAnalysis.analysis.helix_analysis module MDAnalysis.analysis.hole2 module MDAnalysis.analysis.hole2.templates module MDAnalysis.analysis.hole2.utils module MDAnalysis.analysis.hydrogenbonds.hbond_analysis module MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel module MDAnalysis.analysis.hydrogenbonds.wbridge_analysis module MDAnalysis.analysis.leaflet module MDAnalysis.analysis.legacy.x3dna module MDAnalysis.analysis.lineardensity module MDAnalysis.analysis.msd module MDAnalysis.analysis.nucleicacids module MDAnalysis.analysis.nuclinfo module MDAnalysis.analysis.pca module MDAnalysis.analysis.polymer module MDAnalysis.analysis.psa module MDAnalysis.analysis.rdf module MDAnalysis.analysis.rms module MDAnalysis.analysis.waterdynamics module MDAnalysis.auxiliary.__init__ module MDAnalysis.auxiliary.base module MDAnalysis.auxiliary.core module MDAnalysis.auxiliary.EDR module MDAnalysis.auxiliary.XVG module MDAnalysis.converters module MDAnalysis.converters.OpenMM module MDAnalysis.converters.OpenMMParser module MDAnalysis.converters.ParmEd module MDAnalysis.converters.ParmEdParser module MDAnalysis.converters.RDKit module MDAnalysis.converters.RDKitParser module MDAnalysis.coordinates.__init__ module MDAnalysis.coordinates.base module MDAnalysis.coordinates.chain module MDAnalysis.coordinates.chemfiles module MDAnalysis.coordinates.core module MDAnalysis.coordinates.CRD module MDAnalysis.coordinates.DCD module MDAnalysis.coordinates.DLPoly module MDAnalysis.coordinates.DMS module MDAnalysis.coordinates.FHIAIMS module MDAnalysis.coordinates.GMS module MDAnalysis.coordinates.GRO module MDAnalysis.coordinates.GSD module MDAnalysis.coordinates.H5MD module MDAnalysis.coordinates.INPCRD module MDAnalysis.coordinates.LAMMPS module MDAnalysis.coordinates.memory module MDAnalysis.coordinates.MMTF module MDAnalysis.coordinates.MOL2 module MDAnalysis.coordinates.NAMDBIN module MDAnalysis.coordinates.null module MDAnalysis.coordinates.PDB module MDAnalysis.coordinates.PDBQT module MDAnalysis.coordinates.PQR module MDAnalysis.coordinates.timestep module MDAnalysis.coordinates.TNG module MDAnalysis.coordinates.TRJ module MDAnalysis.coordinates.TRR module MDAnalysis.coordinates.TRZ module MDAnalysis.coordinates.TXYZ module MDAnalysis.coordinates.XDR module MDAnalysis.coordinates.XTC module MDAnalysis.coordinates.XYZ module MDAnalysis.core.__init__ module MDAnalysis.core.accessors module MDAnalysis.core.groups module MDAnalysis.core.selection module MDAnalysis.core.topology module MDAnalysis.core.topologyattrs module MDAnalysis.core.topologyobjects module MDAnalysis.core.universe module MDAnalysis.exceptions module MDAnalysis.lib module MDAnalysis.lib.c_distances module MDAnalysis.lib.c_distances_openmp module MDAnalysis.lib.correlations module MDAnalysis.lib.distances module MDAnalysis.lib.formats.libdcd module MDAnalysis.lib.formats.libmdaxdr module MDAnalysis.lib.log module MDAnalysis.lib.mdamath module MDAnalysis.lib.NeighborSearch module MDAnalysis.lib.nsgrid module MDAnalysis.lib.picklable_file_io module MDAnalysis.lib.pkdtree module MDAnalysis.lib.qcprot module MDAnalysis.lib.transformations module MDAnalysis.lib.util module MDAnalysis.selections.base module MDAnalysis.selections.charmm module MDAnalysis.selections.gromacs module MDAnalysis.selections.jmol module MDAnalysis.selections.pymol module MDAnalysis.selections.vmd module MDAnalysis.topology.__init__ module MDAnalysis.topology.base module MDAnalysis.topology.core module MDAnalysis.topology.CRDParser module MDAnalysis.topology.DLPolyParser module MDAnalysis.topology.DMSParser module MDAnalysis.topology.ExtendedPDBParser module MDAnalysis.topology.FHIAIMSParser module MDAnalysis.topology.GMSParser module MDAnalysis.topology.GROParser module MDAnalysis.topology.GSDParser module

MDAnalysis.topology.guessers module MDAnalysis.topology.HoomdXMLParser module MDAnalysis.topology.ITPParser module MDAnalysis.topology.LAMMPSParser module MDAnalysis.topology.MinimalParser module MDAnalysis.topology.MMTFParser module MDAnalysis.topology.MOL2Parser module MDAnalysis.topology.PDBParser module MDAnalysis.topology.PDBQTParser module MDAnalysis.topology.PQRParser module MDAnalysis.topology.PSFParser module MDAnalysis.topology.tables module MDAnalysis.topology.TOPParser module MDAnalysis.topology.tpr module MDAnalysis.topology.tpr.obj module MDAnalysis.topology.tpr.setting module MDAnalysis.topology.tpr.utils module MDAnalysis.topology.TPRParser module MDAnalysis.topology.TXYZParser module MDAnalysis.topology.XYZParser module MDAnalysis.transformations module MDAnalysis.transformations.base module MDAnalysis.transformations.boxdimensions module MDAnalysis.transformations.fit module MDAnalysis.transformations.nojump module MDAnalysis.transformations.positionaveraging module MDAnalysis.transformations.rotate module MDAnalysis.transformations.translate module MDAnalysis.transformations.wrap module MDAnalysis.units module MDAnalysis.version module MDAnalysis.visualization.streamlines module MDAnalysis.visualization.streamlines_3D module MDANALYSIS_BASE_UNITS (in module MDAnalysis.units) mean() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) mean_std() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) MeanSquareDisplacement (class in MDAnalysis.analysis.waterdynamics) MemoryReader (class in MDAnalysis.coordinates.memory) Merge() (in module MDAnalysis.core.universe) merge_universes() (in module MDAnalysis.analysis.encore.utils) metadata (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) MIN_CHEMFILES_VERSION (in module MDAnalysis.coordinates.chemfiles) min_radius() (MDAnalysis.analysis.hole2.HoleAnalysis method) MinimalParser (class in MDAnalysis.topology.MinimalParser) minimize_vectors() (in module MDAnalysis.lib.distances) minor_pair() (in module MDAnalysis.analysis.nuclinfo) MissingDataWarning ml_covariance_estimator() (in module MDAnalysis.analysis.encore.covariance) MMTFParser (class in MDAnalysis.topology.MMTFParser) MMTFReader (class in MDAnalysis.coordinates.MMTF) mobile_atoms (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.align.AverageStructure attribute) MODEL() (MDAnalysis.coordinates.PDB.PDBWriter method) models (MDAnalysis.core.universe.Universe property) module MDAnalysis.analysis.align MDAnalysis.analysis.atomicdistances MDAnalysis.analysis.base MDAnalysis.analysis.bat MDAnalysis.analysis.contacts MDAnalysis.analysis.data.filenames MDAnalysis.analysis.density MDAnalysis.analysis.dielectric MDAnalysis.analysis.diffusionmap MDAnalysis.analysis.dihedrals MDAnalysis.analysis.distances MDAnalysis.analysis.encore.bootstrap MDAnalysis.analysis.encore.clustering.affinityprop MDAnalysis.analysis.encore.clustering.cluster MDAnalysis.analysis.encore.clustering.ClusterCollection MDAnalysis.analysis.encore.clustering.ClusteringMethod MDAnalysis.analysis.encore.confdistmatrix MDAnalysis.analysis.encore.covariance MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed MDAnalysis.analysis.encore.similarity MDAnalysis.analysis.encore.utils MDAnalysis.analysis.gnm MDAnalysis.analysis.hbonds.hbond_autocorrel MDAnalysis.analysis.helix_analysis MDAnalysis.analysis.hole2 MDAnalysis.analysis.hole2.templates MDAnalysis.analysis.hole2.utils MDAnalysis.analysis.hydrogenbonds.hbond_analysis MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel MDAnalysis.analysis.hydrogenbonds.wbridge_analysis MDAnalysis.analysis.leaflet MDAnalysis.analysis.legacy.x3dna MDAnalysis.analysis.lineardensity MDAnalysis.analysis.msd MDAnalysis.analysis.nucleicacids MDAnalysis.analysis.nuclinfo MDAnalysis.analysis.pca MDAnalysis.analysis.polymer MDAnalysis.analysis.psa MDAnalysis.analysis.rdf MDAnalysis.analysis.rms MDAnalysis.analysis.waterdynamics MDAnalysis.auxiliary.__init__ MDAnalysis.auxiliary.base MDAnalysis.auxiliary.core MDAnalysis.auxiliary.EDR MDAnalysis.auxiliary.XVG MDAnalysis.converters MDAnalysis.converters.OpenMM MDAnalysis.converters.OpenMMParser MDAnalysis.converters.ParmEd MDAnalysis.converters.ParmEdParser MDAnalysis.converters.RDKit MDAnalysis.converters.RDKitParser MDAnalysis.coordinates.__init__ MDAnalysis.coordinates.base MDAnalysis.coordinates.chain MDAnalysis.coordinates.chemfiles MDAnalysis.coordinates.core MDAnalysis.coordinates.CRD MDAnalysis.coordinates.DCD MDAnalysis.coordinates.DLPoly MDAnalysis.coordinates.DMS MDAnalysis.coordinates.FHIAIMS MDAnalysis.coordinates.GMS MDAnalysis.coordinates.GRO MDAnalysis.coordinates.GSD MDAnalysis.coordinates.H5MD MDAnalysis.coordinates.INPCRD MDAnalysis.coordinates.LAMMPS MDAnalysis.coordinates.memory MDAnalysis.coordinates.MMTF MDAnalysis.coordinates.MOL2 MDAnalysis.coordinates.NAMDBIN MDAnalysis.coordinates.null MDAnalysis.coordinates.PDB MDAnalysis.coordinates.PDBQT MDAnalysis.coordinates.PQR MDAnalysis.coordinates.timestep MDAnalysis.coordinates.TNG MDAnalysis.coordinates.TRJ MDAnalysis.coordinates.TRR MDAnalysis.coordinates.TRZ MDAnalysis.coordinates.TXYZ MDAnalysis.coordinates.XDR MDAnalysis.coordinates.XTC MDAnalysis.coordinates.XYZ MDAnalysis.core.__init__ MDAnalysis.core.accessors MDAnalysis.core.groups MDAnalysis.core.selection MDAnalysis.core.topology MDAnalysis.core.topologyattrs MDAnalysis.core.topologyobjects MDAnalysis.core.universe MDAnalysis.exceptions MDAnalysis.lib MDAnalysis.lib.c_distances MDAnalysis.lib.c_distances_openmp MDAnalysis.lib.correlations MDAnalysis.lib.distances MDAnalysis.lib.formats.libdcd MDAnalysis.lib.formats.libmdaxdr MDAnalysis.lib.log MDAnalysis.lib.mdamath MDAnalysis.lib.NeighborSearch MDAnalysis.lib.nsgrid MDAnalysis.lib.picklable_file_io MDAnalysis.lib.pkdtree MDAnalysis.lib.qcprot MDAnalysis.lib.transformations MDAnalysis.lib.util MDAnalysis.selections.base MDAnalysis.selections.charmm MDAnalysis.selections.gromacs MDAnalysis.selections.jmol MDAnalysis.selections.pymol MDAnalysis.selections.vmd MDAnalysis.topology.__init__ MDAnalysis.topology.base MDAnalysis.topology.core MDAnalysis.topology.CRDParser MDAnalysis.topology.DLPolyParser MDAnalysis.topology.DMSParser MDAnalysis.topology.ExtendedPDBParser MDAnalysis.topology.FHIAIMSParser MDAnalysis.topology.GMSParser MDAnalysis.topology.GROParser MDAnalysis.topology.GSDParser MDAnalysis.topology.guessers MDAnalysis.topology.HoomdXMLParser MDAnalysis.topology.ITPParser MDAnalysis.topology.LAMMPSParser MDAnalysis.topology.MinimalParser MDAnalysis.topology.MMTFParser MDAnalysis.topology.MOL2Parser MDAnalysis.topology.PDBParser MDAnalysis.topology.PDBQTParser MDAnalysis.topology.PQRParser MDAnalysis.topology.PSFParser MDAnalysis.topology.tables MDAnalysis.topology.TOPParser MDAnalysis.topology.tpr MDAnalysis.topology.tpr.obj MDAnalysis.topology.tpr.setting MDAnalysis.topology.tpr.utils MDAnalysis.topology.TPRParser MDAnalysis.topology.TXYZParser MDAnalysis.topology.XYZParser MDAnalysis.transformations MDAnalysis.transformations.base MDAnalysis.transformations.boxdimensions MDAnalysis.transformations.fit MDAnalysis.transformations.nojump MDAnalysis.transformations.positionaveraging MDAnalysis.transformations.rotate MDAnalysis.transformations.translate MDAnalysis.transformations.wrap MDAnalysis.units MDAnalysis.version MDAnalysis.visualization.streamlines MDAnalysis.visualization.streamlines_3D MOL2Parser (class in MDAnalysis.topology.MOL2Parser) MOL2Reader (class in MDAnalysis.coordinates.MOL2) MOL2Writer (class in MDAnalysis.coordinates.MOL2) molb_natoms_mol (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nmol (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nposres_xA (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nposres_xB (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_type (MDAnalysis.topology.tpr.obj.Molblock attribute) Molblock (class in MDAnalysis.topology.tpr.obj) MoleculeKind (class in MDAnalysis.topology.tpr.obj) Molnums (class in MDAnalysis.core.topologyattrs) Moltypes (class in MDAnalysis.core.topologyattrs) moltypes (MDAnalysis.topology.tpr.obj.Mtop attribute) moment_of_inertia() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) move_atom() (MDAnalysis.core.topology.TransTable method) move_residue() (MDAnalysis.core.topology.TransTable method) move_to_ts() (MDAnalysis.auxiliary.base.AuxReader method) msds_by_particle (MDAnalysis.analysis.msd.EinsteinMSD.results attribute) Mtop (class in MDAnalysis.topology.tpr.obj) MultiPDBWriter (class in MDAnalysis.coordinates.PDB)

N

n_atoms (MDAnalysis.analysis.atomicdistances.AtomicDistances attribute) (MDAnalysis.coordinates.GMS.GMSReader property) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.coordinates.TRZ.TRZReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XYZ.XYZReader property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.topology.TransTable attribute) n_fragments (MDAnalysis.core.groups.AtomGroup property) n_fragments() (MDAnalysis.core.topologyattrs.Bonds method) n_frames (MDAnalysis.analysis.atomicdistances.AtomicDistances attribute) (MDAnalysis.analysis.msd.EinsteinMSD attribute) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.TNG.TNGReader property) (MDAnalysis.coordinates.TRJ.TRJReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TRZ.TRZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) n_jobs (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) n_particles (MDAnalysis.analysis.msd.EinsteinMSD attribute) n_residues (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.topology.TransTable attribute) n_segments (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.topology.TransTable attribute) n_steps (MDAnalysis.auxiliary.base.AuxReader property) NAMDBINReader (class in MDAnalysis.coordinates.NAMDBIN) NAMDBINWriter (class in MDAnalysis.coordinates.NAMDBIN) NamedStream (class in MDAnalysis.lib.util) Namespace (class in MDAnalysis.lib.util) natoms (MDAnalysis.topology.tpr.obj.TpxHeader attribute) NCDFPicklable (class in MDAnalysis.coordinates.TRJ) NCDFReader (class in MDAnalysis.coordinates.TRJ) NCDFWriter (class in MDAnalysis.coordinates.TRJ) ndo_int() (in module MDAnalysis.topology.tpr.utils) ndo_ivec() (in module MDAnalysis.topology.tpr.utils) ndo_real() (in module MDAnalysis.topology.tpr.utils) ndo_rvec() (in module MDAnalysis.topology.tpr.utils) nearest_neighbors (MDAnalysis.analysis.psa.PSAnalysis property) (MDAnalysis.analysis.psa.PSAPair attribute) network (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results attribute) next() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.lib.transformations.Arcball method)

next_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) next_nonempty_frame() (MDAnalysis.auxiliary.base.AuxReader method) ngtc (MDAnalysis.topology.tpr.obj.TpxHeader attribute) nmolblock (MDAnalysis.topology.tpr.obj.Mtop attribute) nmoltype (MDAnalysis.topology.tpr.obj.Mtop attribute) NoDataError NoJump (class in MDAnalysis.transformations.nojump) NonbondedIndices (class in MDAnalysis.core.topologyattrs) norm() (in module MDAnalysis.lib.mdamath) normal() (in module MDAnalysis.lib.mdamath) Note (MDAnalysis.analysis.lineardensity.LinearDensity attribute) npaths (MDAnalysis.analysis.psa.PSAPair attribute) nr (MDAnalysis.topology.tpr.obj.Atoms attribute) (MDAnalysis.topology.tpr.obj.Ilist attribute) nres (MDAnalysis.topology.tpr.obj.Atoms attribute) nruns (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) NSResults (class in MDAnalysis.lib.nsgrid) ntypes (MDAnalysis.topology.tpr.obj.Params attribute) NucleicBackboneSelection (class in MDAnalysis.core.selection) NucleicSelection (class in MDAnalysis.core.selection) NucleicSugarSelection (class in MDAnalysis.core.selection) NucPairDist (class in MDAnalysis.analysis.nucleicacids) NullHandler (class in MDAnalysis.lib.log) NullWriter (class in MDAnalysis.coordinates.null) number_of_atoms() (MDAnalysis.topology.tpr.obj.MoleculeKind method) number_of_matches() (MDAnalysis.lib.util.FORTRANReader method) number_of_residues() (MDAnalysis.topology.tpr.obj.MoleculeKind method)

O

Occupancies (class in MDAnalysis.core.topologyattrs) offsets (MDAnalysis.lib.formats.libmdaxdr.TRRFile attribute) (MDAnalysis.lib.formats.libmdaxdr.XTCFile attribute) offsets_filename() (in module MDAnalysis.coordinates.XDR) omega_selection() (MDAnalysis.core.groups.Residue method) (MDAnalysis.core.topologyattrs.Atomnames method) omega_selections() (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.topologyattrs.Atomnames method) OMP_NUM_THREADS open() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) open_trajectory() (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRZ.TRZReader method) openany() (in module MDAnalysis.lib.util) OpenMMAppReader (class in MDAnalysis.converters.OpenMM) OpenMMAppTopologyParser (class in MDAnalysis.converters.OpenMMParser) OpenMMSimulationReader (class in MDAnalysis.converters.OpenMM) OpenMMTopologyParser (class in MDAnalysis.converters.OpenMMParser)

optimize_cutoff() (in module MDAnalysis.analysis.leaflet) order_list() (in module MDAnalysis.analysis.gnm) origin (MDAnalysis.analysis.density.Density attribute) OtherWriter() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) outfiles (MDAnalysis.analysis.hole2.HoleAnalysis attribute) (MDAnalysis.analysis.hole2.HoleAnalysis.results attribute) over_order_parameters() (MDAnalysis.analysis.hole2.HoleAnalysis method)

P

p_components (MDAnalysis.analysis.pca.PCA attribute) (MDAnalysis.analysis.pca.PCA.results attribute) pack_into_box() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) pair_distances (MDAnalysis.analysis.nucleicacids.NucPairDist.results attribute) (MDAnalysis.analysis.nucleicacids.WatsonCrickDist.results attribute) pair_id (MDAnalysis.analysis.psa.PSAPair attribute) ParallelCalculation (class in MDAnalysis.analysis.encore.utils) Params (class in MDAnalysis.topology.tpr.obj) ParmEdConverter (class in MDAnalysis.converters.ParmEd) ParmEdParser (class in MDAnalysis.converters.ParmEdParser) ParmEdReader (class in MDAnalysis.converters.ParmEd) parse() (MDAnalysis.converters.ParmEdParser.ParmEdParser method) (MDAnalysis.converters.RDKitParser.RDKitParser method) (MDAnalysis.core.selection.SelectionParser method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.GSDParser.GSDParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.ITPParser.ITPParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) (MDAnalysis.topology.XYZParser.XYZParser method) parse_bonded() (MDAnalysis.topology.TOPParser.TOPParser method) parse_charges() (MDAnalysis.topology.TOPParser.TOPParser method) parse_chunks() (MDAnalysis.topology.TOPParser.TOPParser method) parse_dihedrals() (MDAnalysis.topology.TOPParser.TOPParser method) parse_elements() (MDAnalysis.topology.TOPParser.TOPParser method) parse_FORTRAN_format() (MDAnalysis.lib.util.FORTRANReader method) parse_masses() (MDAnalysis.topology.TOPParser.TOPParser method) parse_n_atoms() (MDAnalysis.coordinates.base.ProtoReader class method) (MDAnalysis.coordinates.base.ReaderBase class method) (MDAnalysis.coordinates.base.SingleFrameReaderBase class method) (MDAnalysis.coordinates.DCD.DCDReader static method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader class method) (MDAnalysis.coordinates.GSD.GSDReader class method) (MDAnalysis.coordinates.H5MD.H5MDReader static method) (MDAnalysis.coordinates.INPCRD.INPReader static method) (MDAnalysis.coordinates.LAMMPS.DATAReader class method) (MDAnalysis.coordinates.LAMMPS.DCDReader static method) (MDAnalysis.coordinates.LAMMPS.DumpReader class method) (MDAnalysis.coordinates.memory.MemoryReader static method) (MDAnalysis.coordinates.NAMDBIN.NAMDBINReader static method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader class method) (MDAnalysis.coordinates.TNG.TNGReader static method) (MDAnalysis.coordinates.TRJ.NCDFReader static method) (MDAnalysis.coordinates.TRR.TRRReader class method) (MDAnalysis.coordinates.TXYZ.TXYZReader class method) (MDAnalysis.coordinates.XDR.XDRBaseReader class method) (MDAnalysis.coordinates.XTC.XTCReader class method) parse_names() (MDAnalysis.topology.TOPParser.TOPParser method) parse_residue() (in module MDAnalysis.lib.util) parse_residx() (MDAnalysis.topology.TOPParser.TOPParser method) parse_resnames() (MDAnalysis.topology.TOPParser.TOPParser method) parse_type_indices() (MDAnalysis.topology.TOPParser.TOPParser method) parse_types() (MDAnalysis.topology.TOPParser.TOPParser method) parsesection_mapper() (MDAnalysis.topology.TOPParser.TOPParser method) partner() (MDAnalysis.core.topologyobjects.Bond method) (MDAnalysis.core.topologyobjects.UreyBradley method) PATH, [1], [2] Path (class in MDAnalysis.analysis.psa) path (MDAnalysis.analysis.psa.Path attribute) path_select (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute)

paths (MDAnalysis.analysis.psa.PSAnalysis attribute) pbc (MDAnalysis.lib.pkdtree.PeriodicKDTree property) PCA (class in MDAnalysis.analysis.pca) PDBParser (class in MDAnalysis.topology.PDBParser) PDBQTParser (class in MDAnalysis.topology.PDBQTParser) PDBQTReader (class in MDAnalysis.coordinates.PDBQT) PDBQTWriter (class in MDAnalysis.coordinates.PDBQT) PDBReader (class in MDAnalysis.coordinates.PDB) PDBWriter (class in MDAnalysis.coordinates.PDB) pdot() (in module MDAnalysis.lib.mdamath) per_object (MDAnalysis.core.topologyattrs.TopologyAttr attribute) periodic (MDAnalysis.coordinates.chain.ChainReader property) PeriodicKDTree (class in MDAnalysis.lib.pkdtree) PersistenceLength (class in MDAnalysis.analysis.polymer) phase_as() (in module MDAnalysis.analysis.nuclinfo) phase_cp() (in module MDAnalysis.analysis.nuclinfo) phi_selection() (MDAnalysis.core.groups.Residue method) (MDAnalysis.core.topologyattrs.Atomnames method) phi_selections() (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.topologyattrs.Atomnames method) pickle_open() (in module MDAnalysis.lib.picklable_file_io) place() (MDAnalysis.lib.transformations.Arcball method) plot() (MDAnalysis.analysis.dihedrals.Janin method) (MDAnalysis.analysis.dihedrals.Ramachandran method) (MDAnalysis.analysis.hole2.HoleAnalysis method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) (MDAnalysis.analysis.polymer.PersistenceLength method) (MDAnalysis.analysis.psa.PSAnalysis method) plot3D() (MDAnalysis.analysis.hole2.HoleAnalysis method) plot3D_order_parameters() (MDAnalysis.analysis.hole2.HoleAnalysis method) plot_annotated_heatmap() (MDAnalysis.analysis.psa.PSAnalysis method) plot_mean_profile() (MDAnalysis.analysis.hole2.HoleAnalysis method) plot_nearest_neighbors() (MDAnalysis.analysis.psa.PSAnalysis method) plot_order_parameters() (MDAnalysis.analysis.hole2.HoleAnalysis method) pnorm() (in module MDAnalysis.lib.mdamath) pos (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) pos_std (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) position (MDAnalysis.core.groups.Atom property) PositionAverager (class in MDAnalysis.transformations.positionaveraging) positions (MDAnalysis.analysis.align.AverageStructure attribute) (MDAnalysis.analysis.align.AverageStructure.results attribute) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.core.groups.AtomGroup property) PQRParser (class in MDAnalysis.topology.PQRParser) PQRReader (class in MDAnalysis.coordinates.PQR) PQRWriter (class in MDAnalysis.coordinates.PQR) precision (MDAnalysis.topology.tpr.obj.TpxHeader attribute) prepare_ensembles_for_convergence_increasing_window() (in module MDAnalysis.analysis.encore.similarity) principal_axes() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) PrincipalComponentAnalysis (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) process() (MDAnalysis.topology.tpr.obj.InteractionKind method) profiles (MDAnalysis.analysis.hole2.HoleAnalysis attribute) (MDAnalysis.analysis.hole2.HoleAnalysis.results attribute) (MDAnalysis.analysis.legacy.x3dna.X3DNA attribute) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj attribute) ProgressBar (class in MDAnalysis.lib.log) project_single_frame() (MDAnalysis.analysis.pca.PCA method) projection_from_matrix() (in module MDAnalysis.lib.transformations) PropertySelection (class in MDAnalysis.core.selection) ProteinSelection (class in MDAnalysis.core.selection) ProtoReader (class in MDAnalysis.coordinates.base) psa_pairs (MDAnalysis.analysis.psa.PSAnalysis property) PSAnalysis (class in MDAnalysis.analysis.psa) PSAPair (class in MDAnalysis.analysis.psa) pseudo_dihe_baseflip() (in module MDAnalysis.analysis.nuclinfo) PSFParser (class in MDAnalysis.topology.PSFParser) psi_selection() (MDAnalysis.core.groups.Residue method) (MDAnalysis.core.topologyattrs.Atomnames method) psi_selections() (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.topologyattrs.Atomnames method) ptype (MDAnalysis.topology.tpr.obj.Atom attribute) PureRMSD() (in module MDAnalysis.analysis.encore.cutils)

Q

q (MDAnalysis.topology.tpr.obj.Atom attribute) q1q2() (in module MDAnalysis.analysis.contacts) qB (MDAnalysis.topology.tpr.obj.Atom attribute) quadrupole_moment() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method)

quadrupole_tensor() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method) quaternion_imag() (in module MDAnalysis.lib.transformations) quaternion_real() (in module MDAnalysis.lib.transformations)

R

r_cov (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) Radii (class in MDAnalysis.core.topologyattrs) radius_cut_q() (in module MDAnalysis.analysis.contacts) radius_of_gyration() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) Rama_ref (in module MDAnalysis.analysis.data.filenames) Ramachandran (class in MDAnalysis.analysis.dihedrals) RANGE_PATTERN (in module MDAnalysis.core.selection) RangeSelection (class in MDAnalysis.core.selection) rdf (MDAnalysis.analysis.rdf.InterRDF attribute) (MDAnalysis.analysis.rdf.InterRDF.results attribute) (MDAnalysis.analysis.rdf.InterRDF_s attribute) (MDAnalysis.analysis.rdf.InterRDF_s.results attribute) RDKitConverter (class in MDAnalysis.converters.RDKit) RDKitParser (class in MDAnalysis.converters.RDKitParser) RDKitReader (class in MDAnalysis.converters.RDKit) read() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.FORTRANReader method) read_all_times() (MDAnalysis.auxiliary.EDR.EDRReader method) (MDAnalysis.auxiliary.XVG.XVGFileReader method) (MDAnalysis.auxiliary.XVG.XVGReader method) read_attributes (MDAnalysis.core.topology.Topology property) read_DATA_timestep() (MDAnalysis.topology.LAMMPSParser.DATAParser method) read_direct_x() (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) read_direct_xvf() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) read_numpy_offsets() (in module MDAnalysis.coordinates.XDR) read_tpxheader() (in module MDAnalysis.topology.tpr.utils) read_ts() (MDAnalysis.auxiliary.base.AuxReader method) readable() (MDAnalysis.lib.util.NamedStream method) reader() (in module MDAnalysis.coordinates.core) ReaderBase (class in MDAnalysis.coordinates.base) readframes() (MDAnalysis.lib.formats.libdcd.DCDFile method) readline() (MDAnalysis.lib.util.NamedStream method) realpath() (in module MDAnalysis.lib.util) RecordTypes (class in MDAnalysis.core.topologyattrs) reduce_dimensionality() (in module MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality) ref_frame (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) reference_atoms (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.align.AverageStructure attribute) reflection_from_matrix() (in module MDAnalysis.lib.transformations) rel (MDAnalysis.topology.tpr.obj.Box attribute) remap_angles() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_bonds() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_dihe() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_impr() (MDAnalysis.topology.tpr.obj.MoleculeKind method) REMARK() (MDAnalysis.coordinates.PDB.PDBWriter method) remove_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) rename_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) reppow (MDAnalysis.topology.tpr.obj.Params attribute) represent_ts_as (MDAnalysis.auxiliary.base.AuxReader property) resample() (MDAnalysis.analysis.density.Density method) resample_factor() (MDAnalysis.analysis.density.Density method) reset() (MDAnalysis.lib.util.NamedStream method) Resids (class in MDAnalysis.core.topologyattrs) ResidSelection (class in MDAnalysis.core.selection) Residue (class in MDAnalysis.core.groups)

ResidueAttr (class in MDAnalysis.core.topologyattrs) ResidueGroup (class in MDAnalysis.core.groups) residues (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.universe.Universe attribute) residues2atoms_1d() (MDAnalysis.core.topology.TransTable method) residues2atoms_2d() (MDAnalysis.core.topology.TransTable method) residues2segments() (MDAnalysis.core.topology.TransTable method) ResidueStringAttr (class in MDAnalysis.core.topologyattrs) resind (MDAnalysis.topology.tpr.obj.Atom attribute) Resindices (class in MDAnalysis.core.topologyattrs) Resnames (class in MDAnalysis.core.topologyattrs) resnames (MDAnalysis.topology.tpr.obj.Atoms attribute) Resnums (class in MDAnalysis.core.topologyattrs) Results (class in MDAnalysis.analysis.base) (class in MDAnalysis.analysis.lineardensity) results (MDAnalysis.analysis.atomicdistances.AtomicDistances attribute) (MDAnalysis.analysis.base.AnalysisBase attribute) return_empty_on_apply() (in module MDAnalysis.core.selection) rewind() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) RMin14s (class in MDAnalysis.core.topologyattrs) RMins (class in MDAnalysis.core.topologyattrs) RMSD (class in MDAnalysis.analysis.rms) rmsd (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.align.AlignTraj.results attribute) (MDAnalysis.analysis.align.AverageStructure attribute) (MDAnalysis.analysis.align.AverageStructure.results attribute) (MDAnalysis.analysis.rms.RMSD attribute) (MDAnalysis.analysis.rms.RMSD.results attribute) rmsd() (in module MDAnalysis.analysis.rms) RMSF (class in MDAnalysis.analysis.rms) rmsf (MDAnalysis.analysis.rms.RMSF attribute) (MDAnalysis.analysis.rms.RMSF.results attribute) rmsip() (in module MDAnalysis.analysis.pca) (MDAnalysis.analysis.pca.PCA method) rotate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) rotateby (class in MDAnalysis.transformations.rotate) rotateby() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) rotation_from_matrix() (in module MDAnalysis.lib.transformations) rotation_matrix() (in module MDAnalysis.analysis.align) rotaxis() (in module MDAnalysis.lib.transformations) RSChirality (class in MDAnalysis.core.topologyattrs) run() (MDAnalysis.analysis.base.AnalysisBase method) (MDAnalysis.analysis.bat.BAT method) (MDAnalysis.analysis.density.DensityAnalysis method) (MDAnalysis.analysis.diffusionmap.DiffusionMap method) (MDAnalysis.analysis.dihedrals.Dihedral method) (MDAnalysis.analysis.dihedrals.Janin method) (MDAnalysis.analysis.dihedrals.Ramachandran method) (MDAnalysis.analysis.encore.utils.ParallelCalculation method) (MDAnalysis.analysis.hole2.HoleAnalysis method) (MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) (MDAnalysis.analysis.msd.EinsteinMSD method) (MDAnalysis.analysis.nucleicacids.NucPairDist method) (MDAnalysis.analysis.nucleicacids.WatsonCrickDist method) (MDAnalysis.analysis.pca.PCA method) (MDAnalysis.analysis.psa.Path method) (MDAnalysis.analysis.psa.PSAnalysis method) (MDAnalysis.analysis.rms.RMSD method) (MDAnalysis.analysis.rms.RMSF method) (MDAnalysis.analysis.waterdynamics.AngularDistribution method) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement method) (MDAnalysis.analysis.waterdynamics.SurvivalProbability method) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation method) run_hole() (in module MDAnalysis.analysis.hole2.utils) run_pairs_analysis() (MDAnalysis.analysis.psa.PSAnalysis method) run_x3dna() (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) runtyp (MDAnalysis.coordinates.GMS.GMSReader property)

S

SameSelection (class in MDAnalysis.core.selection) sarrus_det() (in module MDAnalysis.lib.mdamath) save() (MDAnalysis.analysis.bat.BAT method) (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) save_paths() (MDAnalysis.analysis.psa.PSAnalysis method) savez() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) scale_from_matrix() (in module MDAnalysis.lib.transformations) search() (MDAnalysis.lib.NeighborSearch.AtomNeighborSearch method) (MDAnalysis.lib.nsgrid.FastNS method) (MDAnalysis.lib.pkdtree.PeriodicKDTree method) search_pairs() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) search_tree() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) seek() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) seekable() (MDAnalysis.lib.util.NamedStream method) Segids (class in MDAnalysis.core.topologyattrs) Segindices (class in MDAnalysis.core.topologyattrs) Segment (class in MDAnalysis.core.groups) segment (MDAnalysis.core.groups.Residue property) SegmentAttr (class in MDAnalysis.core.topologyattrs) SegmentGroup (class in MDAnalysis.core.groups) segments (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.universe.Universe attribute) segments2atoms_1d() (MDAnalysis.core.topology.TransTable method) segments2atoms_2d() (MDAnalysis.core.topology.TransTable method) segments2residues_1d() (MDAnalysis.core.topology.TransTable method) segments2residues_2d() (MDAnalysis.core.topology.TransTable method) SegmentStringAttr (class in MDAnalysis.core.topologyattrs) select (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) select_atoms() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.universe.Universe method) select_bonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) selectBonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) SelectionError SelectionParser (class in MDAnalysis.core.selection) SelectionWarning SelectionWriter (class in MDAnalysis.selections.charmm) (class in MDAnalysis.selections.gromacs) (class in MDAnalysis.selections.jmol) (class in MDAnalysis.selections.pymol) (class in MDAnalysis.selections.vmd) SelectionWriterBase (class in MDAnalysis.selections.base) self_capped_distance() (in module MDAnalysis.lib.distances) self_distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances) self_search() (MDAnalysis.lib.nsgrid.FastNS method) sequence() (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.topologyattrs.Resnames method) sequence_alignment() (in module MDAnalysis.analysis.align) set_array() (MDAnalysis.coordinates.memory.MemoryReader method) set_atoms() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.AtomStringAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) set_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method)

set_coords() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) set_dimensions (class in MDAnalysis.transformations.boxdimensions) set_offsets() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) set_residues() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.ResidueStringAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) set_rmsd_matrix_elements() (in module MDAnalysis.analysis.encore.confdistmatrix) set_segments() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.SegmentStringAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) setaxes() (MDAnalysis.lib.transformations.Arcball method) setconstrain() (MDAnalysis.lib.transformations.Arcball method) shape_parameter() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) shear_from_matrix() (in module MDAnalysis.lib.transformations) shrinkage_covariance_estimator() (in module MDAnalysis.analysis.encore.covariance) SIMPLE2_RAD (in module MDAnalysis.analysis.hole2.templates) SingleCharSelection (class in MDAnalysis.core.selection) SingleFrameReaderBase (class in MDAnalysis.coordinates.base) singular (MDAnalysis.core.topologyattrs.TopologyAttr attribute) size (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) (MDAnalysis.core.topology.TransTable attribute) (MDAnalysis.topology.tpr.obj.Box attribute) sizeOfTprBody (MDAnalysis.topology.tpr.obj.TpxHeader attribute) sizes() (MDAnalysis.analysis.leaflet.LeafletFinder method) skip_timestep (MDAnalysis.coordinates.TRZ.TRZReader property) skipper() (MDAnalysis.topology.TOPParser.TOPParser method) slice_volume (MDAnalysis.analysis.lineardensity.LinearDensity.results.x attribute) SmartsSelection (class in MDAnalysis.core.selection) soft_cut_q() (in module MDAnalysis.analysis.contacts) solve() (MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) SolventRadii (class in MDAnalysis.core.topologyattrs) sort() (MDAnalysis.core.groups.AtomGroup method) sort_backbone() (in module MDAnalysis.analysis.polymer) sorted_profiles_iter() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) special_blocks (MDAnalysis.coordinates.TNG.TNGReader property) speedUnit_factor (in module MDAnalysis.units) sphpdbs (MDAnalysis.analysis.hole2.HoleAnalysis attribute) (MDAnalysis.analysis.hole2.HoleAnalysis.results attribute) split() (MDAnalysis.core.groups.AtomGroup method) sqnorm() (in module MDAnalysis.analysis.psa) start_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) static_variables() (in module MDAnalysis.lib.util) std() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) step (MDAnalysis.auxiliary.base.AuxReader property) (MDAnalysis.auxiliary.base.AuxStep attribute) step_to_frame() (MDAnalysis.auxiliary.base.AuxReader method) step_to_time() (MDAnalysis.auxiliary.base.AuxReader method) StochasticProximityEmbedding() (in module MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed) StochasticProximityEmbeddingNative (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) stop_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) store_init_arguments() (in module MDAnalysis.lib.util) stp() (in module MDAnalysis.lib.mdamath) StreamWarning subtract() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) SUPPORTED_VERSIONS (in module MDAnalysis.topology.tpr) (in module MDAnalysis.topology.tpr.setting) SurvivalProbability (class in MDAnalysis.analysis.waterdynamics) symmetric_difference() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method)

T

table (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) TABLE_ATOMELEMENTS (in module MDAnalysis.topology.tables) TABLE_MASSES (in module MDAnalysis.topology.tables) TABLE_VDWRADII (in module MDAnalysis.topology.tables) tell() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) Tempfactors (class in MDAnalysis.core.topologyattrs) terms (MDAnalysis.auxiliary.EDR.EDRReader attribute) TextIOPicklable (class in MDAnalysis.lib.picklable_file_io) time (MDAnalysis.auxiliary.base.AuxReader property) (MDAnalysis.auxiliary.base.AuxStep property) (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.chain.ChainReader property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) time_selector (MDAnalysis.auxiliary.base.AuxReader property) times (MDAnalysis.analysis.base.AnalysisBase attribute) (MDAnalysis.analysis.base.AnalysisFromFunction.results attribute) (MDAnalysis.analysis.base.results attribute) (MDAnalysis.analysis.gnm.closeContactGNMAnalysis.results attribute) (MDAnalysis.analysis.gnm.GNMAnalysis.results attribute) (MDAnalysis.analysis.nucleicacids.NucPairDist attribute) (MDAnalysis.analysis.nucleicacids.WatsonCrickDist attribute) timeseries (MDAnalysis.analysis.base.AnalysisFromFunction.results attribute) (MDAnalysis.analysis.base.results attribute) (MDAnalysis.analysis.contacts.Contacts attribute) (MDAnalysis.analysis.contacts.Contacts.results attribute) (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results attribute) (MDAnalysis.analysis.msd.EinsteinMSD.results attribute) timeseries() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) Timestep (class in MDAnalysis.coordinates.timestep) timesteps (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis attribute) timesteps_by_type() (MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis method) timeUnit_factor (in module MDAnalysis.units) TITLE() (MDAnalysis.coordinates.PDB.PDBWriter method) TNGReader (class in MDAnalysis.coordinates.TNG) to_indices() (MDAnalysis.core.topologyobjects.TopologyGroup method) to_path() (MDAnalysis.analysis.psa.Path method) top (MDAnalysis.core.topologyattrs.TopologyAttr attribute) topDict (MDAnalysis.core.topologyobjects.TopologyGroup property) Topology (class in MDAnalysis.core.topology) TopologyAttr (class in MDAnalysis.core.topologyattrs) TopologyDict (class in MDAnalysis.core.topologyobjects) TopologyGroup (class in MDAnalysis.core.topologyobjects) TopologyObject (class in MDAnalysis.core.topologyobjects) TopologyReaderBase (class in MDAnalysis.topology.base) TOPParser (class in MDAnalysis.topology.TOPParser) tors() (in module MDAnalysis.analysis.nuclinfo) tors_alpha() (in module MDAnalysis.analysis.nuclinfo) tors_beta() (in module MDAnalysis.analysis.nuclinfo) tors_chi() (in module MDAnalysis.analysis.nuclinfo) tors_delta() (in module MDAnalysis.analysis.nuclinfo) tors_eps() (in module MDAnalysis.analysis.nuclinfo)

tors_gamma() (in module MDAnalysis.analysis.nuclinfo) tors_zeta() (in module MDAnalysis.analysis.nuclinfo) total_charge() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Charges method) total_mass() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.topologyattrs.Masses method) totaltime (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) tp (MDAnalysis.topology.tpr.obj.Atom attribute) TPRParser (class in MDAnalysis.topology.TPRParser) TpxHeader (class in MDAnalysis.topology.tpr.obj) TPXUnpacker (class in MDAnalysis.topology.tpr.utils) TPXUnpacker2020 (class in MDAnalysis.topology.tpr.utils) trajectory (MDAnalysis.core.universe.Universe attribute) transfer_to_memory() (MDAnalysis.core.universe.Universe method) transform() (MDAnalysis.analysis.diffusionmap.DiffusionMap method) (MDAnalysis.analysis.pca.PCA method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) transform_RtoS() (in module MDAnalysis.lib.distances) transform_StoR() (in module MDAnalysis.lib.distances) TransformationBase (class in MDAnalysis.transformations.base) transformations (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.H5MD.H5MDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.LAMMPS.DumpReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) translate (class in MDAnalysis.transformations.translate) translate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) translation_from_matrix() (in module MDAnalysis.lib.transformations) TransTable (class in MDAnalysis.core.topology) TriangularMatrix (class in MDAnalysis.analysis.encore.utils) triclinic_box() (in module MDAnalysis.lib.mdamath) triclinic_dimensions (MDAnalysis.coordinates.timestep.Timestep attribute) triclinic_vectors() (in module MDAnalysis.lib.mdamath) TRJReader (class in MDAnalysis.coordinates.TRJ) trm_indices() (in module MDAnalysis.analysis.encore.utils) trm_indices_diag() (in module MDAnalysis.analysis.encore.utils) trm_indices_nodiag() (in module MDAnalysis.analysis.encore.utils) TRRFile (class in MDAnalysis.lib.formats.libmdaxdr) TRRReader (class in MDAnalysis.coordinates.TRR) TRRWriter (class in MDAnalysis.coordinates.TRR) truncate() (MDAnalysis.lib.util.NamedStream method) TRZReader (class in MDAnalysis.coordinates.TRZ) TRZWriter (class in MDAnalysis.coordinates.TRZ) ts (MDAnalysis.coordinates.TRZ.TRZReader attribute) (MDAnalysis.core.groups.AtomGroup property) TXYZParser (class in MDAnalysis.topology.TXYZParser) TXYZReader (class in MDAnalysis.coordinates.TXYZ) type (MDAnalysis.core.topologyobjects.TopologyObject property) (MDAnalysis.topology.tpr.obj.Atoms attribute) typeB (MDAnalysis.topology.tpr.obj.Atom attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) types() (MDAnalysis.core.topologyobjects.TopologyGroup method)

U

u_fitted (MDAnalysis.analysis.psa.Path attribute) u_original (MDAnalysis.analysis.psa.Path attribute) u_reference (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) uncomment() (in module MDAnalysis.auxiliary.XVG) undo_augment() (in module MDAnalysis.lib.distances) union() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) unique (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) unique_int_1d() (in module MDAnalysis.lib.util) unique_rows() (in module MDAnalysis.lib.util) unit_dict (MDAnalysis.auxiliary.EDR.EDRReader attribute) unit_types (in module MDAnalysis.units) units (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.converters.OpenMM.OpenMMAppReader attribute) (MDAnalysis.converters.OpenMM.OpenMMSimulationReader attribute) (MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser attribute) (MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser attribute) (MDAnalysis.converters.ParmEd.ParmEdConverter attribute) (MDAnalysis.converters.ParmEd.ParmEdReader attribute) (MDAnalysis.converters.ParmEdParser.ParmEdParser attribute) (MDAnalysis.converters.RDKit.RDKitConverter attribute) (MDAnalysis.converters.RDKit.RDKitReader attribute) (MDAnalysis.converters.RDKitParser.RDKitParser attribute) (MDAnalysis.coordinates.base.ConverterBase attribute) (MDAnalysis.coordinates.base.IOBase attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.base.WriterBase attribute) (MDAnalysis.coordinates.chain.ChainReader property) (MDAnalysis.coordinates.CRD.CRDReader attribute) (MDAnalysis.coordinates.CRD.CRDWriter attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DLPoly.ConfigReader attribute) (MDAnalysis.coordinates.DLPoly.HistoryReader attribute) (MDAnalysis.coordinates.DMS.DMSReader attribute) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader attribute) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter attribute) (MDAnalysis.coordinates.GMS.GMSReader attribute) (MDAnalysis.coordinates.GRO.GROReader attribute) (MDAnalysis.coordinates.GRO.GROWriter attribute) (MDAnalysis.coordinates.GSD.GSDReader attribute) (MDAnalysis.coordinates.H5MD.H5MDReader attribute) (MDAnalysis.coordinates.H5MD.H5MDWriter attribute) (MDAnalysis.coordinates.INPCRD.INPReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAWriter attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.LAMMPS.DumpReader attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) (MDAnalysis.coordinates.MOL2.MOL2Reader attribute) (MDAnalysis.coordinates.MOL2.MOL2Writer attribute) (MDAnalysis.coordinates.NAMDBIN.NAMDBINReader attribute) (MDAnalysis.coordinates.NAMDBIN.NAMDBINWriter attribute) (MDAnalysis.coordinates.null.NullWriter attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.PDB.PDBReader attribute) (MDAnalysis.coordinates.PDB.PDBWriter attribute) (MDAnalysis.coordinates.PDBQT.PDBQTReader attribute) (MDAnalysis.coordinates.PDBQT.PDBQTWriter attribute) (MDAnalysis.coordinates.PQR.PQRReader attribute) (MDAnalysis.coordinates.PQR.PQRWriter attribute) (MDAnalysis.coordinates.TNG.TNGReader attribute) (MDAnalysis.coordinates.TRJ.NCDFReader attribute) (MDAnalysis.coordinates.TRJ.NCDFWriter attribute) (MDAnalysis.coordinates.TRJ.TRJReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.TRR.TRRWriter attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute) (MDAnalysis.coordinates.TRZ.TRZWriter attribute) (MDAnalysis.coordinates.TXYZ.TXYZReader attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XDR.XDRBaseWriter attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.XTC.XTCWriter attribute) (MDAnalysis.coordinates.XYZ.XYZReader attribute) (MDAnalysis.coordinates.XYZ.XYZWriter attribute) (MDAnalysis.topology.base.TopologyReaderBase attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.FHIAIMSParser.FHIAIMSParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.GSDParser.GSDParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.ITPParser.ITPParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MinimalParser.MinimalParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.TXYZParser.TXYZParser attribute)

Universe (class in MDAnalysis.core.universe) universe (MDAnalysis.analysis.align.AverageStructure attribute) (MDAnalysis.analysis.align.AverageStructure.results attribute) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.topologyobjects.TopologyGroup property) universes (MDAnalysis.analysis.psa.PSAnalysis attribute) unpack_fstring() (MDAnalysis.topology.tpr.utils.TPXUnpacker2020 method) unpack_int64() (MDAnalysis.topology.tpr.utils.TPXUnpacker method) unpack_uchar() (MDAnalysis.topology.tpr.utils.TPXUnpacker method) (MDAnalysis.topology.tpr.utils.TPXUnpacker2020 method) unpack_uint64() (MDAnalysis.topology.tpr.utils.TPXUnpacker method) unpack_ushort() (MDAnalysis.topology.tpr.utils.TPXUnpacker method) (MDAnalysis.topology.tpr.utils.TPXUnpacker2020 method) unwrap (class in MDAnalysis.transformations.wrap) unwrap() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) update() (MDAnalysis.analysis.leaflet.LeafletFinder method) update_selection() (MDAnalysis.core.groups.UpdatingAtomGroup method) update_ts() (MDAnalysis.auxiliary.base.AuxReader method) UpdatingAtomGroup (class in MDAnalysis.core.groups) UreyBradley (class in MDAnalysis.core.topologyobjects) ureybradley (MDAnalysis.core.groups.AtomGroup property) UreyBradleys (class in MDAnalysis.core.topologyattrs)

V

v (MDAnalysis.topology.tpr.obj.Box attribute) validate_atom_types() (in module MDAnalysis.topology.guessers) value() (MDAnalysis.core.topologyobjects.Angle method) (MDAnalysis.core.topologyobjects.Bond method) (MDAnalysis.core.topologyobjects.Dihedral method) (MDAnalysis.core.topologyobjects.UreyBradley method) values() (MDAnalysis.core.topologyobjects.TopologyGroup method)

variance (MDAnalysis.analysis.pca.PCA attribute) (MDAnalysis.analysis.pca.PCA.results attribute) vdwradii (in module MDAnalysis.topology.tables) velocities (MDAnalysis.coordinates.timestep.Timestep attribute) (MDAnalysis.core.groups.AtomGroup property) velocity (MDAnalysis.core.groups.Atom property) ver_str (MDAnalysis.topology.tpr.obj.TpxHeader attribute) volume (MDAnalysis.coordinates.timestep.Timestep attribute)

W

warn_if_not_unique() (in module MDAnalysis.lib.util) water (in module MDAnalysis.units) WaterBridgeAnalysis (class in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis) WaterOrientationalRelaxation (class in MDAnalysis.analysis.waterdynamics) WatsonCrickDist (class in MDAnalysis.analysis.nucleicacids) wc_pair() (in module MDAnalysis.analysis.nuclinfo) which() (in module MDAnalysis.lib.util) worker() (MDAnalysis.analysis.encore.utils.ParallelCalculation method) wrap (class in MDAnalysis.transformations.wrap) wrap() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) writable() (MDAnalysis.lib.util.NamedStream method) write() (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.CRD.CRDWriter method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSWriter method) (MDAnalysis.coordinates.GRO.GROWriter method) (MDAnalysis.coordinates.H5MD.H5MDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) (MDAnalysis.coordinates.PQR.PQRWriter method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.selections.base.SelectionWriterBase method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method)

write_all_timesteps() (MDAnalysis.coordinates.PDB.PDBWriter method) write_header() (MDAnalysis.lib.formats.libdcd.DCDFile method) write_output() (in module MDAnalysis.analysis.encore.similarity) write_preamble() (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) write_selection() (MDAnalysis.analysis.leaflet.LeafletFinder method) write_simplerad2() (in module MDAnalysis.analysis.hole2.utils) writer() (in module MDAnalysis.coordinates.core) Writer() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.CRD.CRDReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.FHIAIMS.FHIAIMSReader method) (MDAnalysis.coordinates.GRO.GROReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.H5MD.H5MDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DumpReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.NAMDBIN.NAMDBINReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.PDB.PDBReader method) (MDAnalysis.coordinates.PDBQT.PDBQTReader method) (MDAnalysis.coordinates.PQR.PQRReader method) (MDAnalysis.coordinates.TNG.TNGReader method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRZ.TRZReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XYZ.XYZReader method) WriterBase (class in MDAnalysis.coordinates.base)

X

x (MDAnalysis.analysis.polymer.PersistenceLength.results attribute) X3DNA (class in MDAnalysis.analysis.legacy.x3dna) X3DNAtraj (class in MDAnalysis.analysis.legacy.x3dna) XDRBaseReader (class in MDAnalysis.coordinates.XDR) XDRBaseWriter (class in MDAnalysis.coordinates.XDR) XTCFile (class in MDAnalysis.lib.formats.libmdaxdr) XTCReader (class in MDAnalysis.coordinates.XTC)

XTCWriter (class in MDAnalysis.coordinates.XTC) XVGFileReader (class in MDAnalysis.auxiliary.XVG) XVGReader (class in MDAnalysis.auxiliary.XVG) XVGStep (class in MDAnalysis.auxiliary.XVG) XYZParser (class in MDAnalysis.topology.XYZParser) XYZReader (class in MDAnalysis.coordinates.XYZ) XYZWriter (class in MDAnalysis.coordinates.XYZ)