Index

Symbols

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__eq__() (MDAnalysis.coordinates.base.Timestep method) __getitem__() (MDAnalysis.coordinates.base.Timestep method) __init__() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.selections.base.SelectionWriterBase method) __iter__() (MDAnalysis.coordinates.base.Timestep method) __version__ (in module MDAnalysis.version) _apply() (MDAnalysis.coordinates.chain.ChainReader method) _chained_iterator() (MDAnalysis.coordinates.chain.ChainReader method) _check_pdb_coordinates() (MDAnalysis.coordinates.PDB.PDBWriter method) _fit_to() (in module MDAnalysis.analysis.align) _forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.Timestep attribute) _get() (MDAnalysis.coordinates.chain.ChainReader method) _get_bonded_hydrogens() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) _get_bonded_hydrogens_dist() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method)

_get_bonded_hydrogens_list() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) _get_local_frame() (MDAnalysis.coordinates.chain.ChainReader method) _get_same() (MDAnalysis.coordinates.chain.ChainReader method) _init_unitcell() (MDAnalysis.coordinates.base.Timestep method) _pos (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.Timestep attribute) _read_frame() (MDAnalysis.coordinates.chain.ChainReader method) _translate() (MDAnalysis.selections.base.SelectionWriterBase method) _update_frame() (MDAnalysis.coordinates.PDB.PDBWriter method) _velocities (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.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

active_reader (MDAnalysis.coordinates.chain.ChainReader attribute) add_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) add_Residue() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) add_Segment() (MDAnalysis.core.universe.Universe method) add_TopologyAttr() (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.universe.Universe method) addTimeseries() (MDAnalysis.core.Timeseries.TimeseriesCollection method) AffinityPropagation (class in MDAnalysis.analysis.encore.clustering.affinityprop) (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) AffinityPropagationNative (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) alignto() (in module MDAnalysis.analysis.align) AlignTraj (class in MDAnalysis.analysis.align) AltLocs (class in MDAnalysis.core.topologyattrs) AltlocSelection (class in MDAnalysis.core.selection) analysis_class() (in module MDAnalysis.analysis.base) AnalysisBase (class in MDAnalysis.analysis.base) AnalysisFromFunction (class in MDAnalysis.analysis.base) Angle (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.core.topologyobjects) angle (MDAnalysis.core.groups.AtomGroup attribute) angle() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.topologyobjects.Angle method) Angles (class in MDAnalysis.core.topologyattrs) angles (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] (class in MDAnalysis.analysis.hole) apply_PBC() (in module MDAnalysis.lib.distances), [1] Arcball (class in MDAnalysis.lib.transformations) arcball_nearest_axis() (in module MDAnalysis.lib.transformations) args (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) as_array() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) asiterable() (in module MDAnalysis.lib.util) atnr (MDAnalysis.topology.tpr.obj.Params attribute) Atom (class in MDAnalysis.core.groups) (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.topology.tpr.obj)

atom1 (MDAnalysis.core.topologyobjects.TopologyGroup attribute) atom2 (MDAnalysis.core.topologyobjects.TopologyGroup attribute) atom3 (MDAnalysis.core.topologyobjects.TopologyGroup attribute) atom4 (MDAnalysis.core.topologyobjects.TopologyGroup attribute) 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) AtomICodeSelection (class in MDAnalysis.core.selection) 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) AtomNameSelection (class in MDAnalysis.core.selection) AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch) atomnumber (MDAnalysis.topology.tpr.obj.Atom attribute) Atoms (class in MDAnalysis.topology.tpr.obj) atoms (MDAnalysis.analysis.diffusionmap.DistanceMatrix attribute) (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) (MDAnalysis.core.topologyobjects.TopologyObject attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) atoms2residues() (MDAnalysis.core.topology.TransTable method), [1] atoms2segments() (MDAnalysis.core.topology.TransTable method), [1] Atomtypes (class in MDAnalysis.core.topologyattrs) AtomTypeSelection (class in MDAnalysis.core.selection) attrname (MDAnalysis.core.topologyattrs.TopologyAttr attribute) aux_list (MDAnalysis.coordinates.base.ProtoReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) 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)

B

BackboneSelection (class in MDAnalysis.core.selection) BaseSelection (class in MDAnalysis.core.selection) 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) Bfactor2RMSF() (in module MDAnalysis.analysis.density) BfactorDensityCreator (class in MDAnalysis.analysis.density) Bfactors (class in MDAnalysis.core.topologyattrs) bIr (MDAnalysis.topology.tpr.obj.TpxHeader attribute) Bond (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.core.topologyobjects)

bond (MDAnalysis.core.groups.AtomGroup attribute) 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) bootstrapped_matrix() (in module MDAnalysis.analysis.encore.bootstrap) Box (class in MDAnalysis.topology.tpr.obj) box_volume() (in module MDAnalysis.lib.mdamath), [1] bsphere() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) bTop (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bV (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bX (MDAnalysis.topology.tpr.obj.TpxHeader attribute)

C

cached() (in module MDAnalysis.lib.util) calc_angle() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis static method) calc_angles() (in module MDAnalysis.lib.distances), [1] calc_bonds() (in module MDAnalysis.lib.distances), [1] calc_dihedrals() (in module MDAnalysis.lib.distances), [1] calc_eucl_distance() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis static method) 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) center() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) center_of_geometry() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) CenterOfGeometry (class in MDAnalysis.core.Timeseries) CenterOfMass (class in MDAnalysis.core.Timeseries) 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), [1] ces_convergence() (in module MDAnalysis.analysis.encore.similarity) ChainIDs (class in MDAnalysis.core.topologyattrs) ChainReader (class in MDAnalysis.coordinates.chain) chargeUnit_factor (in module MDAnalysis.units) check_and_fix_long_filename() (MDAnalysis.analysis.hole.HOLE method) check_compatible() (MDAnalysis.analysis.density.Density method) check_slice_indices() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) chi1_selection() (MDAnalysis.core.topologyattrs.Atomnames method) clear() (MDAnalysis.core.Timeseries.TimeseriesCollection method) clear_handlers() (in module MDAnalysis.lib.log) close() (MDAnalysis.auxiliary.base.AuxFileReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GMS.GMSReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TRZ.TRZReader method), [1] (MDAnalysis.coordinates.TRZ.TRZWriter method), [1] (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.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader 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.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) closeContactGNMAnalysis (class in MDAnalysis.analysis.gnm) closed (MDAnalysis.lib.util.NamedStream attribute) 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) collect() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) 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) compose_matrix() (in module MDAnalysis.lib.transformations) compressed (MDAnalysis.coordinates.chain.ChainReader attribute) compute() (MDAnalysis.core.Timeseries.TimeseriesCollection method) 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 attribute) constants (in module MDAnalysis.units) contact_matrix() (in module MDAnalysis.analysis.contacts) (in module MDAnalysis.analysis.distances) ContactAnalysis (class in MDAnalysis.analysis.contacts) ContactAnalysis1 (class in MDAnalysis.analysis.contacts) Contacts (class in MDAnalysis.analysis.contacts) conv_float() (in module MDAnalysis.lib.util) conversion_factor (in module MDAnalysis.units) ConversionWarning convert() (in module MDAnalysis.units) 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.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.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_forces_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_length() (MDAnalysis.analysis.density.Density method) convert_pos_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method)

convert_pos_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_time_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_time_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_velocities_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) convert_velocities_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.base.TopologyReaderBase method) coord (MDAnalysis.core.universe.Universe attribute) copy() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.memory.Timestep method) copy_slice() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.memory.Timestep method) correl() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) cosine_content() (in module MDAnalysis.analysis.pca) count_by_time() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) count_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis 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() (MDAnalysis.analysis.hole.HOLE method) CRYST1() (MDAnalysis.coordinates.PDB.PDBWriter method) cumulated_variance (MDAnalysis.analysis.pca.PCA attribute) cumulative_clustering_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) cumulative_gen_kde_pdfs() (in module MDAnalysis.analysis.encore.similarity)

D

D (MDAnalysis.analysis.psa.PSAnalysis attribute) data (MDAnalysis.auxiliary.base.AuxStep attribute) data_selector (MDAnalysis.auxiliary.base.AuxReader attribute) 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) 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) DEFAULT_ACCEPTORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) DEFAULT_DONORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) default_ignore_residues (MDAnalysis.analysis.hole.HOLE attribute) define_unpack_real() (in module MDAnalysis.topology.tpr.utils) delta (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] Density (class in MDAnalysis.analysis.density) Density() (MDAnalysis.analysis.density.BfactorDensityCreator method) density_from_PDB() (in module MDAnalysis.analysis.density) density_from_Universe() (in module MDAnalysis.analysis.density) densityUnit_factor (in module MDAnalysis.units) 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.core.Timeseries) (class in MDAnalysis.core.topologyobjects) dihedral (MDAnalysis.core.groups.AtomGroup attribute) dihedral() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.topologyobjects.Dihedral method) Dihedrals (class in MDAnalysis.core.topologyattrs) dihedrals (MDAnalysis.core.universe.Universe attribute) dihedrals() (MDAnalysis.core.topologyobjects.TopologyGroup method) DimensionalityReductionMethod (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.GRO.Timestep attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute), [1] (MDAnalysis.coordinates.memory.Timestep attribute) (MDAnalysis.core.universe.Universe attribute), [1] dimred_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) 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) Distance (class in MDAnalysis.core.Timeseries) distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances), [1] DistanceMatrix (class in MDAnalysis.analysis.diffusionmap) DistanceSelection (class in MDAnalysis.core.selection) 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_atomtypes() (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_groups() (in module MDAnalysis.topology.tpr.utils) do_grps() (in module MDAnalysis.topology.tpr.utils) do_harm() (in module MDAnalysis.topology.tpr.utils) do_ilists() (in module MDAnalysis.topology.tpr.utils) do_inputrec() (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() (in module MDAnalysis.topology.tpr.utils) do_symstr() (in module MDAnalysis.topology.tpr.utils) do_symtab() (in module MDAnalysis.topology.tpr.utils) doc() (MDAnalysis.core.__init__.Flags method) down() (MDAnalysis.lib.transformations.Arcball method) drag() (MDAnalysis.lib.transformations.Arcball method) dres() (in module MDAnalysis.analysis.encore.similarity), [1] dres_convergence() (in module MDAnalysis.analysis.encore.similarity) dt (MDAnalysis.auxiliary.base.AuxReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.base.ProtoReader attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) (MDAnalysis.coordinates.memory.Timestep attribute) dump_contents() (MDAnalysis.core.topologyobjects.TopologyGroup method)

E

echo() (in module MDAnalysis.lib.log) (MDAnalysis.lib.log.ProgressMeter method) edges (MDAnalysis.analysis.density.Density attribute) eigenvalues (MDAnalysis.analysis.diffusionmap.DiffusionMap attribute) Elements (class in MDAnalysis.core.topologyattrs) elements (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) 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 PATH, [1] euler_from_quaternion() (in module MDAnalysis.lib.transformations) expect() (MDAnalysis.core.selection.SelectionParser method) export() (MDAnalysis.analysis.density.Density method) ExtendedPDBParser (class in MDAnalysis.topology.ExtendedPDBParser) ExtendedPDBReader (class in MDAnalysis.coordinates.PDB) extract_box_info() (in module MDAnalysis.topology.tpr.utils)

F

fasta2select() (in module MDAnalysis.analysis.align) FastCalcRMSDAndRotation() (in module MDAnalysis.lib.qcprot) fep_state (MDAnalysis.topology.tpr.obj.TpxHeader attribute) fetch_mmtf() (in module MDAnalysis.coordinates.MMTF) fgen (MDAnalysis.topology.tpr.obj.TpxHeader attribute) file_tag (MDAnalysis.topology.tpr.obj.TpxHeader attribute) FileFormatWarning filename (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) (MDAnalysis.coordinates.chain.ChainReader attribute) filename() (in module MDAnalysis.lib.util) fileno() (MDAnalysis.lib.util.NamedStream method) fileVersion_err() (in module MDAnalysis.topology.tpr.utils) FinishTimeException fit_exponential_decay() (in module MDAnalysis.analysis.polymer) fit_to_reference() (MDAnalysis.analysis.psa.Path method) fixedwidth_bins() (in module MDAnalysis.lib.util) Flag (class in MDAnalysis.core.__init__) Flags (class in MDAnalysis.core.__init__) flags (in module MDAnalysis.core.__init__) flagsDocs (class in MDAnalysis.core.__init__) flush() (MDAnalysis.lib.util.NamedStream method) fmt (MDAnalysis.coordinates.GRO.GROWriter attribute) force (MDAnalysis.core.groups.Atom attribute) forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute) (MDAnalysis.core.groups.AtomGroup attribute) forceUnit_factor (in module MDAnalysis.units)

FORTRAN_format_regex (in module MDAnalysis.lib.util) FORTRANReader (class in MDAnalysis.lib.util) fragment() (MDAnalysis.core.topologyattrs.Bonds method) fragments() (MDAnalysis.core.topologyattrs.Bonds method) frame (MDAnalysis.coordinates.base.ProtoReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.chain.ChainReader attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) frame_data (MDAnalysis.auxiliary.base.AuxReader attribute) frame_rep (MDAnalysis.auxiliary.base.AuxReader attribute) from_coordinates() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.memory.Timestep method) from_timestep() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.memory.Timestep 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

gen_kde_pdfs() (in module MDAnalysis.analysis.encore.similarity) generate_grid() (in module MDAnalysis.analysis.gnm) generate_kirchoff() (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.hbonds.hbond_analysis.HydrogenBondAnalysis method) get_array() (MDAnalysis.coordinates.memory.MemoryReader method) get_atom_mass() (in module MDAnalysis.topology.guessers) get_atoms() (MDAnalysis.core.topologyattrs.TopologyAttr method) get_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) get_aux_descriptions() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) get_auxreader_for() (in module MDAnalysis.auxiliary.core) get_centroids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection method) get_conversion_factor() (in module MDAnalysis.units) get_coord_axes() (in module MDAnalysis.analysis.psa) get_description() (MDAnalysis.auxiliary.base.AuxReader method) get_distance_array() (MDAnalysis.analysis.contacts.ContactAnalysis 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_ids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection 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_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.TopologyAttr method) get_segments() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) 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.analysis.leaflet.LeafletFinder method) 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) guess_angles() (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.hole.HOLEtraj method) guess_dihedrals() (in module MDAnalysis.topology.guessers) guess_format() (in module MDAnalysis.lib.util) 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 attribute)

H

hard_cut_q() (in module MDAnalysis.analysis.contacts) harmonic_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) has_forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute) has_positions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute) has_valid_coordinates() (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDWriter 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.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.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 attribute) hausdorff_wavg() (in module MDAnalysis.analysis.psa) HEADER() (MDAnalysis.coordinates.PDB.PDBWriter method) helanal_main() (in module MDAnalysis.analysis.helanal) helanal_trajectory() (in module MDAnalysis.analysis.helanal) hes() (in module MDAnalysis.analysis.encore.similarity), [1] HistoryReader (class in MDAnalysis.coordinates.DLPoly) HOLE (class in MDAnalysis.analysis.hole) HOLE_MAX_LENGTH (MDAnalysis.analysis.hole.HOLE attribute) HOLEtraj (class in MDAnalysis.analysis.hole) HoomdXMLParser (class in MDAnalysis.topology.HoomdXMLParser) HydrogenBondAnalysis (class in MDAnalysis.analysis.hbonds.hbond_analysis) HydrogenBondAutoCorrel (class in MDAnalysis.analysis.hbonds.hbond_autocorrel) HydrogenBondLifetimes (class in MDAnalysis.analysis.waterdynamics) 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 attribute) 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 attribute) (MDAnalysis.core.topologyobjects.TopologyObject attribute) initial_time (MDAnalysis.auxiliary.base.AuxReader attribute) InnerProduct() (in module MDAnalysis.lib.qcprot) INPReader (class in MDAnalysis.coordinates.INPCRD) interaction_types (in module MDAnalysis.topology.tpr.setting) InteractionKind (class in MDAnalysis.topology.tpr.obj) interpolated (MDAnalysis.analysis.density.Density attribute) InterRDF (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) iparams (MDAnalysis.topology.tpr.obj.Params attribute) is_anchor (MDAnalysis.core.universe.Universe attribute) is_guessed (MDAnalysis.core.topologyattrs.TopologyAttr attribute) 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 attribute) 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) iter_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) iter_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) iterable() (in module MDAnalysis.lib.util) ix (MDAnalysis.core.groups.Atom attribute) (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.Residue attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.Segment attribute) (MDAnalysis.core.groups.SegmentGroup attribute) ix_array (MDAnalysis.core.groups.Atom attribute) (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.Residue attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.Segment attribute) (MDAnalysis.core.groups.SegmentGroup attribute)

J

join() (in module MDAnalysis.selections.base)

K

keys() (MDAnalysis.core.topologyobjects.TopologyDict method) kinetic_energy (MDAnalysis.coordinates.TRZ.Timestep attribute)

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

L

lamb (MDAnalysis.topology.tpr.obj.TpxHeader attribute) LAMMPSDataConverter (class in MDAnalysis.topology.LAMMPSParser) 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)

LinearDensity (class in MDAnalysis.analysis.lineardensity) load() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 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)

M

m (MDAnalysis.topology.tpr.obj.Atom 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), [1] masses (in module MDAnalysis.topology.tables) matrix() (MDAnalysis.lib.transformations.Arcball method) matrix_id (MDAnalysis.analysis.psa.PSAPair attribute) mB (MDAnalysis.topology.tpr.obj.Atom attribute) MDAnalysis.analysis.align (module) MDAnalysis.analysis.base (module) MDAnalysis.analysis.contacts (module) MDAnalysis.analysis.density (module) MDAnalysis.analysis.diffusionmap (module) MDAnalysis.analysis.distances (module) MDAnalysis.analysis.encore.bootstrap (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.similarity (module) MDAnalysis.analysis.encore.utils (module) MDAnalysis.analysis.gnm (module) MDAnalysis.analysis.hbonds.hbond_analysis (module) MDAnalysis.analysis.hbonds.hbond_autocorrel (module) MDAnalysis.analysis.helanal (module) MDAnalysis.analysis.hole (module) MDAnalysis.analysis.leaflet (module) MDAnalysis.analysis.legacy.x3dna (module) MDAnalysis.analysis.lineardensity (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.XVG (module) MDAnalysis.coordinates.__init__ (module) MDAnalysis.coordinates.base (module) MDAnalysis.coordinates.chain (module) MDAnalysis.coordinates.core (module) MDAnalysis.coordinates.CRD (module) MDAnalysis.coordinates.DCD (module) MDAnalysis.coordinates.DLPoly (module) MDAnalysis.coordinates.DMS (module) MDAnalysis.coordinates.GMS (module) MDAnalysis.coordinates.GRO (module) MDAnalysis.coordinates.INPCRD (module) MDAnalysis.coordinates.LAMMPS (module) MDAnalysis.coordinates.memory (module) MDAnalysis.coordinates.MMTF (module) MDAnalysis.coordinates.MOL2 (module) MDAnalysis.coordinates.null (module) MDAnalysis.coordinates.PDB (module) MDAnalysis.coordinates.PDBQT (module) MDAnalysis.coordinates.PQR (module) MDAnalysis.coordinates.TRJ (module) MDAnalysis.coordinates.TRR (module) MDAnalysis.coordinates.TRZ (module) MDAnalysis.coordinates.XDR (module) MDAnalysis.coordinates.XTC (module) MDAnalysis.coordinates.XYZ (module) MDAnalysis.core.__init__ (module) MDAnalysis.core.groups (module) MDAnalysis.core.selection (module) MDAnalysis.core.Timeseries (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.distances (module) MDAnalysis.lib.formats.libmdaxdr (module) MDAnalysis.lib.log (module) MDAnalysis.lib.mdamath (module) MDAnalysis.lib.NeighborSearch (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.GMSParser (module) MDAnalysis.topology.GROParser (module) MDAnalysis.topology.guessers (module) MDAnalysis.topology.HoomdXMLParser (module) MDAnalysis.topology.LAMMPSParser (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.XYZParser (module) MDAnalysis.units (module) MDAnalysis.version (module) MDAnalysis.visualization.streamlines (module) MDAnalysis.visualization.streamlines_3D (module) mean() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) mean_atoms (MDAnalysis.analysis.pca.PCA attribute) 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_radius() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) 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) MODEL() (MDAnalysis.coordinates.PDB.PDBWriter method) 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) moltypes (MDAnalysis.topology.tpr.obj.Mtop attribute) move_atom() (MDAnalysis.core.topology.TransTable method) move_residue() (MDAnalysis.core.topology.TransTable method) move_to_ts() (MDAnalysis.auxiliary.base.AuxReader method) Mtop (class in MDAnalysis.topology.tpr.obj) MultiPDBWriter (class in MDAnalysis.coordinates.PDB)

N

n_atoms (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.GMS.GMSReader attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.XYZ.XYZReader attribute) (MDAnalysis.coordinates.memory.Timestep attribute) (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) (MDAnalysis.core.topology.TransTable attribute) N_Avogadro (in module MDAnalysis.units) n_frames (MDAnalysis.coordinates.TRJ.TRJReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) n_jobs (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) n_residues (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) (MDAnalysis.core.topology.TransTable attribute) n_segments (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) (MDAnalysis.core.topology.TransTable attribute) n_steps (MDAnalysis.auxiliary.base.AuxReader attribute) NamedStream (class in MDAnalysis.lib.util) Namespace (class in MDAnalysis.lib.util) natoms (MDAnalysis.topology.tpr.obj.TpxHeader attribute) 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 attribute) (MDAnalysis.analysis.psa.PSAPair attribute) next (MDAnalysis.lib.formats.libmdaxdr.TRRFile attribute) (MDAnalysis.lib.formats.libmdaxdr.XTCFile attribute) next() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.lib.transformations.Arcball method)

next_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader 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 norm() (in module MDAnalysis.lib.mdamath), [1] normal() (in module MDAnalysis.lib.mdamath), [1] notwithin_coordinates_factory() (in module MDAnalysis.analysis.density) 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) 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) 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

offsets (MDAnalysis.lib.formats.libmdaxdr.TRRFile attribute) (MDAnalysis.lib.formats.libmdaxdr.XTCFile attribute) offsets_filename() (in module MDAnalysis.coordinates.XDR) omega_selection() (MDAnalysis.core.topologyattrs.Atomnames method) one_to_many_pointers() (in module MDAnalysis.lib.mdamath) open() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) open_trajectory() (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRZ.TRZReader method), [1] openany() (in module MDAnalysis.lib.util) 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.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) output_exists() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method)

P

p_components (MDAnalysis.analysis.pca.PCA attribute) pack_into_box() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) pair_id (MDAnalysis.analysis.psa.PSAPair attribute) ParallelCalculation (class in MDAnalysis.analysis.encore.utils) Params (class in MDAnalysis.topology.tpr.obj) parse() (MDAnalysis.core.selection.SelectionParser method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser 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.XYZParser.XYZParser method) parse_FORTRAN_format() (MDAnalysis.lib.util.FORTRANReader method) parse_residue() (in module MDAnalysis.lib.util) partner() (MDAnalysis.core.topologyobjects.Bond method) PATH, [1] 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) PCA (class in MDAnalysis.analysis.pca) pca_space (MDAnalysis.analysis.pca.PCA attribute) 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) per_object (MDAnalysis.core.topologyattrs.TopologyAttr attribute) perform_fit() (MDAnalysis.analysis.polymer.PersistenceLength method) periodic (MDAnalysis.coordinates.chain.ChainReader attribute) PersistenceLength (class in MDAnalysis.analysis.polymer) phase_as() (in module MDAnalysis.analysis.nuclinfo) phase_cp() (in module MDAnalysis.analysis.nuclinfo)

phi_selection() (MDAnalysis.core.topologyattrs.Atomnames method) place() (MDAnalysis.lib.transformations.Arcball method) plot() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj 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.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) plot_annotated_heatmap() (MDAnalysis.analysis.psa.PSAnalysis method) plot_nearest_neighbors() (MDAnalysis.analysis.psa.PSAnalysis method) plot_qavg() (MDAnalysis.analysis.contacts.ContactAnalysis1 method) position (MDAnalysis.core.groups.Atom attribute) positions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.core.groups.AtomGroup attribute) potential_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) 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) pressure (MDAnalysis.coordinates.TRZ.Timestep attribute) pressure_tensor (MDAnalysis.coordinates.TRZ.Timestep attribute) PrincipalComponentAnalysis (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) process() (MDAnalysis.topology.tpr.obj.InteractionKind method) profiles (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.legacy.x3dna.X3DNA attribute) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj attribute) ProgressMeter (class in MDAnalysis.lib.log) projection_from_matrix() (in module MDAnalysis.lib.transformations) prop() (MDAnalysis.core.__init__.Flag method) PropertySelection (class in MDAnalysis.core.selection) ProteinSelection (class in MDAnalysis.core.selection) ProtoReader (class in MDAnalysis.coordinates.base) psa_pairs (MDAnalysis.analysis.psa.PSAnalysis attribute) 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.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) qarray() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method)

qB (MDAnalysis.topology.tpr.obj.Atom attribute) qN() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) quaternion_imag() (in module MDAnalysis.lib.transformations) quaternion_real() (in module MDAnalysis.lib.transformations)

R

r_cov (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) Radii (class in MDAnalysis.core.topologyattrs) radius_cut_q() (in module MDAnalysis.analysis.contacts) read() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.FORTRANReader method) read_all_times() (MDAnalysis.auxiliary.XVG.XVGFileReader method) (MDAnalysis.auxiliary.XVG.XVGReader method) read_attributes (MDAnalysis.core.topology.Topology attribute) read_DATA_timestep() (MDAnalysis.topology.LAMMPSParser.DATAParser 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) realpath() (in module MDAnalysis.lib.util) reduce_dimensionality() (in module MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality) ref_frame (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) ref_select (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) reference_atoms (MDAnalysis.analysis.align.AlignTraj attribute) reflection_from_matrix() (in module MDAnalysis.lib.transformations) register() (MDAnalysis.core.__init__.Flags method) 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) remark_max_length (MDAnalysis.coordinates.PDB.PDBWriter attribute) remove_anchor() (MDAnalysis.core.universe.Universe method) remove_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) rename_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) reppow (MDAnalysis.topology.tpr.obj.Params attribute) represent_ts_as (MDAnalysis.auxiliary.base.AuxReader attribute) 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) ResidueNameSelection (class in MDAnalysis.core.selection) residues (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) residues2atoms_1d() (MDAnalysis.core.topology.TransTable method), [1] residues2atoms_2d() (MDAnalysis.core.topology.TransTable method), [1] residues2segments() (MDAnalysis.core.topology.TransTable method), [1] resind (MDAnalysis.topology.tpr.obj.Atom attribute) Resindices (class in MDAnalysis.core.topologyattrs) resnames (MDAnalysis.topology.tpr.obj.Atoms attribute) results (MDAnalysis.analysis.base.AnalysisFromFunction attribute) rewind() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.memory.MemoryReader method) RMSD (class in MDAnalysis.analysis.rms) rmsd (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.rms.RMSD attribute) rmsd() (in module MDAnalysis.analysis.rms) RMSF (class in MDAnalysis.analysis.rms) rmsf (MDAnalysis.analysis.rms.RMSF attribute) rotate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) 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) run() (MDAnalysis.analysis.base.AnalysisBase method) (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) (MDAnalysis.analysis.diffusionmap.DiffusionMap method) (MDAnalysis.analysis.encore.clustering.affinityprop.AffinityPropagation method) (MDAnalysis.analysis.encore.utils.ParallelCalculation method) (MDAnalysis.analysis.gnm.GNMAnalysis method) (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) (MDAnalysis.analysis.psa.PSAnalysis method) (MDAnalysis.analysis.psa.Path method) (MDAnalysis.analysis.rms.RMSD method) (MDAnalysis.analysis.waterdynamics.AngularDistribution method) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes method) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement method) (MDAnalysis.analysis.waterdynamics.SurvivalProbability method) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation method) run_hole() (MDAnalysis.analysis.hole.HOLEtraj method) run_pairs_analysis() (MDAnalysis.analysis.psa.PSAnalysis method) run_x3dna() (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) runtyp (MDAnalysis.coordinates.GMS.GMSReader attribute)

S

save() (MDAnalysis.analysis.contacts.Contacts method) (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.diffusionmap.DistanceMatrix method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) (MDAnalysis.analysis.lineardensity.LinearDensity method) (MDAnalysis.analysis.rms.RMSD method) save_paths() (MDAnalysis.analysis.psa.PSAnalysis method) save_result() (MDAnalysis.analysis.psa.PSAnalysis method) save_results() (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) save_table() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) savez() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) scale_from_matrix() (in module MDAnalysis.lib.transformations) search() (MDAnalysis.lib.NeighborSearch.AtomNeighborSearch method) seek() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) seekable() (MDAnalysis.lib.util.NamedStream method) Segindices (class in MDAnalysis.core.topologyattrs) Segment (class in MDAnalysis.core.groups) SegmentAttr (class in MDAnalysis.core.topologyattrs) SegmentGroup (class in MDAnalysis.core.groups) SegmentNameSelection (class in MDAnalysis.core.selection) segments (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) segments2atoms_1d() (MDAnalysis.core.topology.TransTable method), [1] segments2atoms_2d() (MDAnalysis.core.topology.TransTable method), [1] segments2residues_1d() (MDAnalysis.core.topology.TransTable method), [1] segments2residues_2d() (MDAnalysis.core.topology.TransTable method), [1] 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_distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances), [1] seq2str() (in module MDAnalysis.analysis.hole) sequence_alignment() (in module MDAnalysis.analysis.align) set_array() (MDAnalysis.coordinates.memory.MemoryReader method) set_atoms() (MDAnalysis.core.topologyattrs.TopologyAttr method) set_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method)

set_offsets() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) set_residues() (MDAnalysis.core.topologyattrs.TopologyAttr method) set_rmsd_matrix_elements() (in module MDAnalysis.analysis.encore.confdistmatrix) set_segments() (MDAnalysis.core.topologyattrs.TopologyAttr method) setaxes() (MDAnalysis.lib.transformations.Arcball method) setconstrain() (MDAnalysis.lib.transformations.Arcball method) shape (MDAnalysis.core.Timeseries.Timeseries attribute) shear_from_matrix() (in module MDAnalysis.lib.transformations) shrinkage_covariance_estimator() (in module MDAnalysis.analysis.encore.covariance) SIMPLE2_RAD (in module MDAnalysis.analysis.hole) 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), [1] (MDAnalysis.topology.tpr.obj.Box attribute) sizes() (MDAnalysis.analysis.leaflet.LeafletFinder method) skip_timestep (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] skipper() (MDAnalysis.topology.TOPParser.TOPParser method) soft_cut_q() (in module MDAnalysis.analysis.contacts) solve() (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) sorted_profiles_iter() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) speedUnit_factor (in module MDAnalysis.units) split() (MDAnalysis.core.groups.AtomGroup method) sqnorm() (in module MDAnalysis.analysis.psa) start_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) std() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) step (MDAnalysis.auxiliary.base.AuxReader attribute) (MDAnalysis.auxiliary.base.AuxStep attribute) step_to_frame() (MDAnalysis.auxiliary.base.AuxReader method) step_to_time() (MDAnalysis.auxiliary.base.AuxReader method) stochasticproxembed (in module MDAnalysis.analysis.encore.dimensionality_reduction) StochasticProximityEmbeddingNative (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) stop_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) stp() (in module MDAnalysis.lib.mdamath), [1] StreamWarning StringSelection (class in MDAnalysis.core.selection) 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.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) TABLE_ATOMELEMENTS (in module MDAnalysis.topology.tables) TABLE_MASSES (in module MDAnalysis.topology.tables) tell() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) temperature (MDAnalysis.coordinates.TRZ.Timestep attribute) Tempfactors (class in MDAnalysis.core.topologyattrs) time (MDAnalysis.auxiliary.base.AuxReader attribute) (MDAnalysis.auxiliary.base.AuxStep attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.base.ProtoReader attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.chain.ChainReader attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) (MDAnalysis.coordinates.memory.Timestep attribute) time_selector (MDAnalysis.auxiliary.base.AuxReader attribute) Timeseries (class in MDAnalysis.core.Timeseries) timeseries (MDAnalysis.analysis.contacts.Contacts attribute) (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) timeseries() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) TimeseriesCollection (class in MDAnalysis.core.Timeseries) Timestep (class in MDAnalysis.coordinates.base) (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.GRO) (class in MDAnalysis.coordinates.TRJ) (class in MDAnalysis.coordinates.TRZ), [1] (class in MDAnalysis.coordinates.memory) timesteps (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) timesteps_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) timeUnit_factor (in module MDAnalysis.units) TITLE() (MDAnalysis.coordinates.PDB.PDBWriter method) 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 attribute) 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_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) totaltime (MDAnalysis.coordinates.base.ProtoReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.PDB.ExtendedPDBReader attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.XDR.XDRBaseReader attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.base.ReaderBase attribute) (MDAnalysis.coordinates.base.SingleFrameReaderBase attribute) (MDAnalysis.coordinates.memory.MemoryReader attribute) tp (MDAnalysis.topology.tpr.obj.Atom attribute) TPRParser (class in MDAnalysis.topology.TPRParser) TpxHeader (class in MDAnalysis.topology.tpr.obj) trajectory (MDAnalysis.core.universe.Universe attribute), [1] 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), [1] transform_StoR() (in module MDAnalysis.lib.distances), [1] 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), [1] triclinic_dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute) triclinic_vectors() (in module MDAnalysis.lib.mdamath), [1] 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), [1] TRZWriter (class in MDAnalysis.coordinates.TRZ), [1] ts (MDAnalysis.core.groups.AtomGroup attribute) type (MDAnalysis.core.topologyobjects.TopologyObject attribute) (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) union() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) unique (MDAnalysis.core.groups.AtomGroup attribute) (MDAnalysis.core.groups.ResidueGroup attribute) (MDAnalysis.core.groups.SegmentGroup attribute) unit_types (in module MDAnalysis.units)

units (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.coordinates.base.IOBase attribute) (MDAnalysis.coordinates.chain.ChainReader attribute) Universe (class in MDAnalysis.core.universe) universe (MDAnalysis.core.topologyobjects.TopologyGroup attribute) universes (MDAnalysis.analysis.psa.PSAnalysis attribute) update() (MDAnalysis.analysis.leaflet.LeafletFinder method) (MDAnalysis.core.__init__.Flags method) (MDAnalysis.lib.log.ProgressMeter method) update_selection() (MDAnalysis.core.groups.UpdatingAtomGroup method) update_ts() (MDAnalysis.auxiliary.base.AuxReader method) UpdatingAtomGroup (class in MDAnalysis.core.groups)

V

v (MDAnalysis.topology.tpr.obj.Box attribute) value() (MDAnalysis.core.topologyobjects.Angle method) (MDAnalysis.core.topologyobjects.Bond method) (MDAnalysis.core.topologyobjects.Dihedral method) values() (MDAnalysis.core.topologyobjects.TopologyGroup method) variance (MDAnalysis.analysis.pca.PCA attribute) velocities (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute) (MDAnalysis.core.groups.AtomGroup attribute)

velocity (MDAnalysis.core.groups.Atom attribute) ver_str (MDAnalysis.topology.tpr.obj.TpxHeader attribute) volume (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.memory.Timestep attribute)

W

water (in module MDAnalysis.units) WaterDipole (class in MDAnalysis.core.Timeseries) WaterOrientationalRelaxation (class in MDAnalysis.analysis.waterdynamics) wc_pair() (in module MDAnalysis.analysis.nuclinfo) which() (in module MDAnalysis.lib.util) worker() (MDAnalysis.analysis.encore.utils.ParallelCalculation method) 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.GRO.GROWriter method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.MOL2.MOL2Writer 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.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_next_timestep() (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.MOL2.MOL2Writer method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.TRJ.NCDFWriter method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.XYZ.XYZWriter 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.hole) writePDB() (MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter method) writePSF() (MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter method) writer() (in module MDAnalysis.coordinates.core) Writer() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.CRD.CRDReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GRO.GROReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.PDB.PDBReader method) (MDAnalysis.coordinates.PDBQT.PDBQTReader method) (MDAnalysis.coordinates.PQR.PQRReader method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.memory.MemoryReader method) WriterBase (class in MDAnalysis.coordinates.base)

X

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)