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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) _Deprecate (class in MDAnalysis.lib.util) _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

accepts_distance_matrix (MDAnalysis.analysis.encore.clustering.ClusteringMethod.KMeans attribute) accumulate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) active_reader() (MDAnalysis.coordinates.chain.ChainReader property) add_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) add_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) add_transformations() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) AffinityPropagation (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) AffinityPropagation() (in module MDAnalysis.analysis.encore.clustering.affinityprop) AffinityPropagationNative (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) align_principal_axis() (MDAnalysis.core.topologyattrs.Masses method) 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.topologyobjects) angle() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.topologyobjects.Angle method) Angles (class in MDAnalysis.core.topologyattrs) angles (MDAnalysis.analysis.dihedrals.Dihedral attribute) (MDAnalysis.analysis.dihedrals.Janin attribute) (MDAnalysis.analysis.dihedrals.Ramachandran attribute) angles() (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.universe.Universe property) 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) Arcball (class in MDAnalysis.lib.transformations) arcball_nearest_axis() (in module MDAnalysis.lib.transformations) args (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) AroundSelection (class in MDAnalysis.core.selection) as_array() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) asiterable() (in module MDAnalysis.lib.util) asphericity() (MDAnalysis.core.topologyattrs.Masses method) atnr() (MDAnalysis.topology.tpr.obj.Params property) Atom (class in MDAnalysis.core.groups) (class in MDAnalysis.topology.tpr.obj) atom1() (MDAnalysis.core.topologyobjects.TopologyGroup property) atom2() (MDAnalysis.core.topologyobjects.TopologyGroup property) atom3() (MDAnalysis.core.topologyobjects.TopologyGroup property) atom4() (MDAnalysis.core.topologyobjects.TopologyGroup property) AtomAttr (class in MDAnalysis.core.topologyattrs) atomelements (in module MDAnalysis.topology.tables) AtomGroup (class in MDAnalysis.core.groups) atomgroup_intersection() (MDAnalysis.core.topologyobjects.TopologyGroup method) 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 property) AtomNameSelection (class in MDAnalysis.core.selection) AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch) atomnumber() (MDAnalysis.topology.tpr.obj.Atom property) Atoms (class in MDAnalysis.topology.tpr.obj) atoms (MDAnalysis.analysis.diffusionmap.DistanceMatrix attribute) atoms() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.groups.UpdatingAtomGroup property) (MDAnalysis.core.topologyobjects.TopologyObject property) (MDAnalysis.topology.tpr.obj.Atoms property) 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) augment_coordinates() (in module MDAnalysis.lib.distances) aux_list() (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) auxfile (MDAnalysis.auxiliary.base.AuxFileReader attribute) AuxFileReader (class in MDAnalysis.auxiliary.base) AuxReader (class in MDAnalysis.auxiliary.base) auxreader() (in module MDAnalysis.auxiliary.core) AuxStep (class in MDAnalysis.auxiliary.base) auxstep (MDAnalysis.auxiliary.base.AuxReader attribute)

B

BackboneSelection (class in MDAnalysis.core.selection) BaseSelection (class in MDAnalysis.core.selection) bbox() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) bBox() (MDAnalysis.topology.tpr.obj.TpxHeader property) between() (in module MDAnalysis.analysis.distances) bF() (MDAnalysis.topology.tpr.obj.TpxHeader property) Bfactor2RMSF() (in module MDAnalysis.analysis.density) BfactorDensityCreator (class in MDAnalysis.analysis.density) Bfactors (class in MDAnalysis.core.topologyattrs) bIr() (MDAnalysis.topology.tpr.obj.TpxHeader property) blocks_of() (in module MDAnalysis.lib.util) Bond (class in MDAnalysis.core.topologyobjects)

bond() (MDAnalysis.core.groups.AtomGroup property) bonded_atoms() (MDAnalysis.core.topologyattrs.Bonds method) Bonds (class in MDAnalysis.core.topologyattrs) bonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.universe.Universe property) 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 property) bV() (MDAnalysis.topology.tpr.obj.TpxHeader property) bX() (MDAnalysis.topology.tpr.obj.TpxHeader property)

C

cached() (in module MDAnalysis.lib.util) calc_angles() (in module MDAnalysis.lib.distances) calc_bonds() (in module MDAnalysis.lib.distances) calc_dihedrals() (in module MDAnalysis.lib.distances) calc_offsets() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) calc_representative() (MDAnalysis.auxiliary.base.AuxReader method) CalcRMSDRotationalMatrix() (in module MDAnalysis.lib.qcprot) capped_distance() (in module MDAnalysis.lib.distances) center() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) center_in_box() (in module MDAnalysis.transformations.translate) center_of_geometry() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) center_of_mass() (MDAnalysis.core.topologyattrs.Masses method) centers() (MDAnalysis.analysis.density.Density method) centroid (MDAnalysis.analysis.encore.clustering.ClusterCollection.Cluster attribute) centroid() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) ces() (in module MDAnalysis.analysis.encore.similarity), [1] ces_convergence() (in module MDAnalysis.analysis.encore.similarity) ChainIDs (class in MDAnalysis.core.topologyattrs) ChainReader (class in MDAnalysis.coordinates.chain) Charges (class in MDAnalysis.core.topologyattrs) chargeUnit_factor (in module MDAnalysis.units) charmm_bitfield (MDAnalysis.lib.formats.libdcd.DCDFile attribute) check_and_fix_long_filename() (MDAnalysis.analysis.hole.HOLE method) check_box() (in module MDAnalysis.lib.util) check_compatible() (MDAnalysis.analysis.density.Density method) check_compressed_format() (in module MDAnalysis.lib.util) check_coords() (in module MDAnalysis.lib.util) check_slice_indices() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) chi1_selection() (MDAnalysis.core.topologyattrs.Atomnames method) clear_handlers() (in module MDAnalysis.lib.log) close() (MDAnalysis.auxiliary.base.AuxFileReader method) (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DLPoly.HistoryReader method) (MDAnalysis.coordinates.GMS.GMSReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.MOL2.MOL2Writer method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.PDB.PDBReader method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRJ.NCDFWriter method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TRZ.TRZReader method), [1] (MDAnalysis.coordinates.TRZ.TRZWriter method), [1] (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) (MDAnalysis.selections.charmm.SelectionWriter method), [1] (MDAnalysis.selections.gromacs.SelectionWriter method), [1] (MDAnalysis.selections.jmol.SelectionWriter method), [1] (MDAnalysis.selections.pymol.SelectionWriter method), [1] (MDAnalysis.selections.vmd.SelectionWriter method), [1] (MDAnalysis.topology.base.TopologyReaderBase 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.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) closeContactGNMAnalysis (class in MDAnalysis.analysis.gnm) closed() (MDAnalysis.lib.util.NamedStream property) Cluster (class in MDAnalysis.analysis.encore.clustering.ClusterCollection) cluster() (in module MDAnalysis.analysis.encore.clustering.cluster) (MDAnalysis.analysis.psa.PSAnalysis method) ClusterCollection (class in MDAnalysis.analysis.encore.clustering.ClusterCollection) clustering_ensemble_similarity() (in module MDAnalysis.analysis.encore.similarity) ClusteringMethod (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) clusters (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection attribute) collect() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.legacy.x3dna.X3DNA method) comment() (MDAnalysis.selections.base.SelectionWriterBase method) (MDAnalysis.selections.charmm.SelectionWriter method), [1] (MDAnalysis.selections.gromacs.SelectionWriter method), [1] (MDAnalysis.selections.jmol.SelectionWriter method), [1] (MDAnalysis.selections.pymol.SelectionWriter method), [1] (MDAnalysis.selections.vmd.SelectionWriter method), [1] compose_matrix() (in module MDAnalysis.lib.transformations) compressed() (MDAnalysis.coordinates.chain.ChainReader property) concatenate() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) concatenate_matrices() (in module MDAnalysis.lib.transformations) CONECT() (MDAnalysis.coordinates.PDB.PDBWriter method) ConfigReader (class in MDAnalysis.coordinates.DLPoly) conformational_distance_matrix() (in module MDAnalysis.analysis.encore.confdistmatrix) constant_dt() (MDAnalysis.auxiliary.base.AuxReader property) constants (in module MDAnalysis.units) contact_matrix() (in module MDAnalysis.analysis.contacts) (in module MDAnalysis.analysis.distances) Contacts (class in MDAnalysis.analysis.contacts) 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.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_forces_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_length() (MDAnalysis.analysis.density.Density method) convert_pos_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method)

convert_pos_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_time_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_time_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_velocities_from_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) convert_velocities_to_native() (MDAnalysis.coordinates.base.IOBase method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.WriterBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DATAWriter method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TRR.TRRWriter method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XDR.XDRBaseWriter method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XTC.XTCWriter method) (MDAnalysis.topology.base.TopologyReaderBase method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) coord() (MDAnalysis.core.universe.Universe property) copy() (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.memory.Timestep method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) (MDAnalysis.core.groups.UpdatingAtomGroup method) (MDAnalysis.core.topology.Topology method) (MDAnalysis.core.topology.TransTable method) (MDAnalysis.core.topologyattrs.TopologyAttr method) (MDAnalysis.core.universe.Universe method) copy_slice() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.memory.Timestep method) cosine_content() (in module MDAnalysis.analysis.pca) count_by_time() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis method) count_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis method) covariance_matrix() (in module MDAnalysis.analysis.encore.covariance) CRDParser (class in MDAnalysis.topology.CRDParser) CRDReader (class in MDAnalysis.coordinates.CRD) CRDWriter (class in MDAnalysis.coordinates.CRD) create() (in module MDAnalysis.lib.log) create_vmd_surface() (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 property) data_selector() (MDAnalysis.auxiliary.base.AuxReader property) DATAParser (class in MDAnalysis.topology.LAMMPSParser) DATAReader (class in MDAnalysis.coordinates.LAMMPS) DATAWriter (class in MDAnalysis.coordinates.LAMMPS) DBSCAN (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod) DCDFile (class in MDAnalysis.lib.formats.libdcd) DCDReader (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) DCDWriter (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) decompose_matrix() (in module MDAnalysis.lib.transformations) dedent_docstring() (in module MDAnalysis.lib.util) DEFAULT_ACCEPTORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis attribute) DEFAULT_DONORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis attribute) default_ignore_residues (MDAnalysis.analysis.hole.HOLE attribute) define_unpack_real() (in module MDAnalysis.topology.tpr.utils) delta (MDAnalysis.analysis.density.Density attribute) delta() (MDAnalysis.coordinates.TRZ.TRZReader property), [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) deprecate() (in module MDAnalysis.lib.util) difference() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) DiffusionMap (class in MDAnalysis.analysis.diffusionmap) Dihedral (class in MDAnalysis.analysis.dihedrals) (class in MDAnalysis.core.topologyobjects) dihedral() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.topologyobjects.Dihedral method) Dihedrals (class in MDAnalysis.core.topologyattrs) dihedrals() (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.universe.Universe property) DimensionalityReductionMethod (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.core.universe.Universe attribute) dimensions() (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.DLPoly.Timestep property) (MDAnalysis.coordinates.DMS.Timestep property) (MDAnalysis.coordinates.GRO.Timestep property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.coordinates.TRZ.Timestep property), [1] (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.universe.Universe property) 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_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances) 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.coordinates.base.Timestep attribute) dt() (MDAnalysis.auxiliary.base.AuxReader property) (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) dtype (MDAnalysis.core.topologyattrs.AltLocs attribute) (MDAnalysis.core.topologyattrs.Atomids attribute) (MDAnalysis.core.topologyattrs.Atomnames attribute) (MDAnalysis.core.topologyattrs.Atomtypes attribute) (MDAnalysis.core.topologyattrs.Bfactors attribute) (MDAnalysis.core.topologyattrs.ChainIDs attribute) (MDAnalysis.core.topologyattrs.Charges attribute) (MDAnalysis.core.topologyattrs.Elements attribute) (MDAnalysis.core.topologyattrs.ICodes attribute) (MDAnalysis.core.topologyattrs.Masses attribute) (MDAnalysis.core.topologyattrs.Molnums attribute) (MDAnalysis.core.topologyattrs.Moltypes attribute) (MDAnalysis.core.topologyattrs.Occupancies attribute) (MDAnalysis.core.topologyattrs.Radii attribute) (MDAnalysis.core.topologyattrs.RecordTypes attribute) (MDAnalysis.core.topologyattrs.Resids attribute) (MDAnalysis.core.topologyattrs.Resnames attribute) (MDAnalysis.core.topologyattrs.Resnums attribute) (MDAnalysis.core.topologyattrs.Segids attribute) (MDAnalysis.core.topologyattrs.Tempfactors attribute) (MDAnalysis.core.topologyattrs.TopologyAttr attribute) DUECREDIT_ENABLE dump_contents() (MDAnalysis.core.topologyobjects.TopologyGroup method) DuplicateWarning

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) emit() (MDAnalysis.lib.log.NullHandler method) empty() (MDAnalysis.core.universe.Universe class method) encode_block() (MDAnalysis.coordinates.MOL2.MOL2Writer method) encode_centroid_info() (in module MDAnalysis.analysis.encore.clustering.ClusteringMethod) END() (MDAnalysis.coordinates.PDB.PDBWriter method)

ENDMDL() (MDAnalysis.coordinates.PDB.PDBWriter method) environment variable $HOME DUECREDIT_ENABLE LD_LIBRARY_PATH, [1] 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

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

F_VSITE2 (in module MDAnalysis.topology.tpr.setting) F_VSITE3 (in module MDAnalysis.topology.tpr.setting) F_VSITE3FAD (in module MDAnalysis.topology.tpr.setting) F_VSITE3FD (in module MDAnalysis.topology.tpr.setting) F_VSITE3OUT (in module MDAnalysis.topology.tpr.setting) F_VSITE4FD (in module MDAnalysis.topology.tpr.setting) F_VSITE4FDN (in module MDAnalysis.topology.tpr.setting) F_VSITEN (in module MDAnalysis.topology.tpr.setting) F_VTEMP_NOLONGERUSED (in module MDAnalysis.topology.tpr.setting) F_WATER_POL (in module MDAnalysis.topology.tpr.setting) fasta2select() (in module MDAnalysis.analysis.align) FastCalcRMSDAndRotation() (in module MDAnalysis.lib.qcprot) FastNS (class in MDAnalysis.lib.nsgrid) fep_state() (MDAnalysis.topology.tpr.obj.TpxHeader property) fetch_mmtf() (in module MDAnalysis.coordinates.MMTF) fgen() (MDAnalysis.topology.tpr.obj.TpxHeader property) file_tag() (MDAnalysis.topology.tpr.obj.TpxHeader property) FileFormatWarning filename (MDAnalysis.analysis.align.AlignTraj attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) filename() (in module MDAnalysis.lib.util) (MDAnalysis.coordinates.chain.ChainReader property) fileno() (MDAnalysis.lib.util.NamedStream method) fileVersion_err() (in module MDAnalysis.topology.tpr.utils) find_fragments() (in module MDAnalysis.lib.mdamath) find_hydrogen_donors() (in module MDAnalysis.analysis.hbonds.hbond_autocorrel) fit (MDAnalysis.analysis.polymer.PersistenceLength attribute) fit_exponential_decay() (in module MDAnalysis.analysis.polymer) fit_rot_trans() (in module MDAnalysis.transformations.fit) fit_to_reference() (MDAnalysis.analysis.psa.Path method) fit_translation() (in module MDAnalysis.transformations.fit) 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__) flatten_dict() (in module MDAnalysis.lib.util) flush() (MDAnalysis.lib.util.NamedStream method) fmt (MDAnalysis.coordinates.GRO.GROWriter attribute) force() (MDAnalysis.core.groups.Atom property) forces (MDAnalysis.coordinates.base.Timestep attribute) forces() (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.core.groups.AtomGroup property) forceUnit_factor (in module MDAnalysis.units) format_from_filename_extension() (in module MDAnalysis.lib.util) FORTRAN_format_regex (in module MDAnalysis.lib.util) FORTRANReader (class in MDAnalysis.lib.util) fragindex() (MDAnalysis.core.topologyattrs.Bonds method) fragindices() (MDAnalysis.core.topologyattrs.Bonds method) fragment() (MDAnalysis.core.topologyattrs.Bonds method) fragments() (MDAnalysis.core.topologyattrs.Bonds method) frame (MDAnalysis.coordinates.TRZ.Timestep attribute) frame() (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.chain.ChainReader property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) frame_data (MDAnalysis.auxiliary.base.AuxReader attribute) frame_rep (MDAnalysis.auxiliary.base.AuxReader attribute) FrameIteratorAll (class in MDAnalysis.coordinates.base) FrameIteratorBase (class in MDAnalysis.coordinates.base) FrameIteratorIndices (class in MDAnalysis.coordinates.base) FrameIteratorSliced (class in MDAnalysis.coordinates.base) from_blank() (MDAnalysis.core.topologyattrs.TopologyAttr class method) from_coordinates() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.memory.Timestep class method) from_timestep() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.memory.Timestep class method) ftupd (in module MDAnalysis.topology.tpr.setting) fudgeQQ() (MDAnalysis.topology.tpr.obj.Params property) function (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) functype() (MDAnalysis.topology.tpr.obj.Params property) fver() (MDAnalysis.topology.tpr.obj.TpxHeader property)

G

gen_kde_pdfs() (in module MDAnalysis.analysis.encore.similarity) generate_grid() (in module MDAnalysis.analysis.gnm) generate_kirchoff() (MDAnalysis.analysis.gnm.closeContactGNMAnalysis method) (MDAnalysis.analysis.gnm.GNMAnalysis method) generate_paths() (MDAnalysis.analysis.psa.PSAnalysis method) generate_streamlines() (in module MDAnalysis.visualization.streamlines) generate_streamlines_3d() (in module MDAnalysis.visualization.streamlines_3D) generate_table() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis method) get_array() (MDAnalysis.coordinates.memory.MemoryReader method) get_atom_mass() (in module MDAnalysis.topology.guessers) get_atoms() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) get_aux_descriptions() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) get_auxreader_for() (in module MDAnalysis.auxiliary.core) get_cdf() (MDAnalysis.analysis.rdf.InterRDF_s method) get_centroids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection method) get_conversion_factor() (in module MDAnalysis.units) get_coord_axes() (in module MDAnalysis.analysis.psa) get_description() (MDAnalysis.auxiliary.base.AuxReader method) get_distance_matrix() (in module MDAnalysis.analysis.encore.confdistmatrix) get_distance_matrix_bootstrap_samples() (in module MDAnalysis.analysis.encore.bootstrap) get_distances() (MDAnalysis.lib.nsgrid.NSResults method) get_ensemble_bootstrap_samples() (in module MDAnalysis.analysis.encore.bootstrap) get_ext() (in module MDAnalysis.lib.util) get_ids() (MDAnalysis.analysis.encore.clustering.ClusterCollection.ClusterCollection method) get_indices() (MDAnalysis.lib.nsgrid.NSResults method) (MDAnalysis.lib.pkdtree.PeriodicKDTree method) get_matching_atoms() (in module MDAnalysis.analysis.align) get_msd_matrix() (in module MDAnalysis.analysis.psa) get_num_atoms() (MDAnalysis.analysis.psa.Path method) (MDAnalysis.analysis.psa.PSAnalysis method)

get_num_paths() (MDAnalysis.analysis.psa.PSAnalysis method) get_pair_distances() (MDAnalysis.lib.nsgrid.NSResults method) get_pairs() (MDAnalysis.lib.nsgrid.NSResults method) get_pairwise_distances() (MDAnalysis.analysis.psa.PSAnalysis method) get_path_metric_func() (in module MDAnalysis.analysis.psa) get_paths() (MDAnalysis.analysis.psa.PSAnalysis method) get_reader_for() (in module MDAnalysis.coordinates.core) get_residues() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_segments() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.Charges method) (MDAnalysis.core.topologyattrs.Masses method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) get_weights() (in module MDAnalysis.lib.util) get_writer() (in module MDAnalysis.selections) get_writer_for() (in module MDAnalysis.coordinates.core) getconstrain() (MDAnalysis.lib.transformations.Arcball method) GMSParser (class in MDAnalysis.topology.GMSParser) GMSReader (class in MDAnalysis.coordinates.GMS) GNMAnalysis (class in MDAnalysis.analysis.gnm) grab_datafile() (MDAnalysis.topology.LAMMPSParser.DATAParser method) grab_not_keywords() (in module MDAnalysis.core.selection) greedy_splitext() (in module MDAnalysis.lib.util) grid (MDAnalysis.analysis.density.Density attribute) GROParser (class in MDAnalysis.topology.GROParser) GROReader (class in MDAnalysis.coordinates.GRO) group() (MDAnalysis.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) GSDReader (class in MDAnalysis.coordinates.GSD) 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_flavour() (MDAnalysis.topology.PQRParser.PQRParser static method) 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 property)

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) has_forces() (MDAnalysis.coordinates.memory.Timestep property) has_positions (MDAnalysis.coordinates.base.Timestep attribute) has_positions() (MDAnalysis.coordinates.memory.Timestep property) 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) has_velocities() (MDAnalysis.coordinates.memory.Timestep property) hasmethod() (in module MDAnalysis.lib.util) hausdorff() (in module MDAnalysis.analysis.psa) hausdorff_avg() (in module MDAnalysis.analysis.psa)

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

isunique() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) items() (MDAnalysis.core.__init__.Flags method) iter_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) iter_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) iterable() (in module MDAnalysis.lib.util) ix() (MDAnalysis.core.groups.Atom property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) ix_array() (MDAnalysis.core.groups.Atom property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.Residue property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property)

J

Janin (class in MDAnalysis.analysis.dihedrals)

Janin_ref (in module MDAnalysis.analysis.data.filenames) join() (in module MDAnalysis.selections.base)

K

keys() (MDAnalysis.core.topologyobjects.TopologyDict method) kinetic_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) KMeans (class in MDAnalysis.analysis.encore.clustering.ClusteringMethod)

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

L

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

lg2() (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation static method) LinearDensity (class in MDAnalysis.analysis.lineardensity) load() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.psa.PSAnalysis method) load_new() (MDAnalysis.core.universe.Universe method) loadz() (MDAnalysis.analysis.encore.utils.TriangularMatrix method) lp (MDAnalysis.analysis.polymer.PersistenceLength attribute) ltruncate_int() (in module MDAnalysis.lib.util)

M

m() (MDAnalysis.topology.tpr.obj.Atom property) 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) Masses (class in MDAnalysis.core.topologyattrs) masses (in module MDAnalysis.topology.tables) matrix() (MDAnalysis.lib.transformations.Arcball method) matrix_id (MDAnalysis.analysis.psa.PSAPair attribute) mB() (MDAnalysis.topology.tpr.obj.Atom property) MDAnalysis.analysis.align (module) MDAnalysis.analysis.base (module) MDAnalysis.analysis.contacts (module) MDAnalysis.analysis.data.filenames (module) MDAnalysis.analysis.density (module) MDAnalysis.analysis.diffusionmap (module) MDAnalysis.analysis.dihedrals (module) MDAnalysis.analysis.distances (module) MDAnalysis.analysis.encore.bootstrap (module) MDAnalysis.analysis.encore.clustering.affinityprop (module) MDAnalysis.analysis.encore.clustering.cluster (module) MDAnalysis.analysis.encore.clustering.ClusterCollection (module) MDAnalysis.analysis.encore.clustering.ClusteringMethod (module) MDAnalysis.analysis.encore.confdistmatrix (module) MDAnalysis.analysis.encore.covariance (module) MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod (module) MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality (module) MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed (module) MDAnalysis.analysis.encore.similarity (module) MDAnalysis.analysis.encore.utils (module) MDAnalysis.analysis.gnm (module) MDAnalysis.analysis.hbonds.hbond_analysis (module) MDAnalysis.analysis.hbonds.hbond_autocorrel (module) MDAnalysis.analysis.hbonds.wbridge_analysis (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.GSD (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.TXYZ (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.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.libdcd (module) MDAnalysis.lib.formats.libmdaxdr (module)

MDAnalysis.lib.log (module) MDAnalysis.lib.mdamath (module) MDAnalysis.lib.NeighborSearch (module) MDAnalysis.lib.nsgrid (module) MDAnalysis.lib.pkdtree (module) MDAnalysis.lib.qcprot (module) MDAnalysis.lib.transformations (module) MDAnalysis.lib.util (module) MDAnalysis.selections.base (module) MDAnalysis.selections.charmm (module) MDAnalysis.selections.gromacs (module) MDAnalysis.selections.jmol (module) MDAnalysis.selections.pymol (module) MDAnalysis.selections.vmd (module) MDAnalysis.topology.__init__ (module) MDAnalysis.topology.base (module) MDAnalysis.topology.core (module) MDAnalysis.topology.CRDParser (module) MDAnalysis.topology.DLPolyParser (module) MDAnalysis.topology.DMSParser (module) MDAnalysis.topology.ExtendedPDBParser (module) MDAnalysis.topology.GMSParser (module) MDAnalysis.topology.GROParser (module) MDAnalysis.topology.guessers (module) MDAnalysis.topology.HoomdXMLParser (module) MDAnalysis.topology.LAMMPSParser (module) MDAnalysis.topology.MinimalParser (module) MDAnalysis.topology.MMTFParser (module) MDAnalysis.topology.MOL2Parser (module) MDAnalysis.topology.PDBParser (module) MDAnalysis.topology.PDBQTParser (module) MDAnalysis.topology.PQRParser (module) MDAnalysis.topology.PSFParser (module) MDAnalysis.topology.tables (module) MDAnalysis.topology.TOPParser (module) MDAnalysis.topology.tpr (module) MDAnalysis.topology.tpr.obj (module) MDAnalysis.topology.tpr.setting (module) MDAnalysis.topology.tpr.utils (module) MDAnalysis.topology.TPRParser (module) MDAnalysis.topology.TXYZParser (module) MDAnalysis.topology.XYZParser (module) MDAnalysis.transformations (module) MDAnalysis.transformations.fit (module) MDAnalysis.transformations.positionaveraging (module) MDAnalysis.transformations.rotate (module) MDAnalysis.transformations.translate (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) MinimalParser (class in MDAnalysis.topology.MinimalParser) 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 property) molb_nmol() (MDAnalysis.topology.tpr.obj.Molblock property) molb_nposres_xA() (MDAnalysis.topology.tpr.obj.Molblock property) molb_nposres_xB() (MDAnalysis.topology.tpr.obj.Molblock property) molb_type() (MDAnalysis.topology.tpr.obj.Molblock property) Molblock (class in MDAnalysis.topology.tpr.obj) MoleculeKind (class in MDAnalysis.topology.tpr.obj) MoleculeTypeSelection (class in MDAnalysis.core.selection) Molnums (class in MDAnalysis.core.topologyattrs) Moltypes (class in MDAnalysis.core.topologyattrs) moltypes() (MDAnalysis.topology.tpr.obj.Mtop property) moment_of_inertia() (MDAnalysis.core.topologyattrs.Masses method) move_atom() (MDAnalysis.core.topology.TransTable method) move_residue() (MDAnalysis.core.topology.TransTable method) move_to_ts() (MDAnalysis.auxiliary.base.AuxReader method) Mtop (class in MDAnalysis.topology.tpr.obj) MultiPDBWriter (class in MDAnalysis.coordinates.PDB)

N

n_atoms (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.core.topology.TransTable attribute) n_atoms() (MDAnalysis.coordinates.GMS.GMSReader property) (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.coordinates.TRZ.TRZReader property), [1] (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XYZ.XYZReader property) (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) N_Avogadro (in module MDAnalysis.units) n_fragments() (MDAnalysis.core.topologyattrs.Bonds method) n_frames() (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.TRJ.TRJReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TRZ.TRZReader property), [1] (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) n_jobs (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) n_residues (MDAnalysis.core.topology.TransTable attribute) n_residues() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) n_segments (MDAnalysis.core.topology.TransTable attribute) n_segments() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) n_steps() (MDAnalysis.auxiliary.base.AuxReader property) NamedStream (class in MDAnalysis.lib.util) Namespace (class in MDAnalysis.lib.util) natoms() (MDAnalysis.topology.tpr.obj.TpxHeader property) 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.PSAPair attribute) nearest_neighbors() (MDAnalysis.analysis.psa.PSAnalysis property) network() (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis property) next() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.lib.transformations.Arcball method)

next_as_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) next_nonempty_frame() (MDAnalysis.auxiliary.base.AuxReader method) ngtc() (MDAnalysis.topology.tpr.obj.TpxHeader property) nmolblock() (MDAnalysis.topology.tpr.obj.Mtop property) nmoltype() (MDAnalysis.topology.tpr.obj.Mtop property) 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 property) (MDAnalysis.topology.tpr.obj.Ilist property) nres() (MDAnalysis.topology.tpr.obj.Atoms property) nruns (MDAnalysis.analysis.encore.utils.ParallelCalculation attribute) NSResults (class in MDAnalysis.lib.nsgrid) ntypes() (MDAnalysis.topology.tpr.obj.Params property) 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

Occupancies (class in MDAnalysis.core.topologyattrs) offsets (MDAnalysis.lib.formats.libmdaxdr.TRRFile attribute) (MDAnalysis.lib.formats.libmdaxdr.XTCFile attribute) offsets_filename() (in module MDAnalysis.coordinates.XDR) omega_selection() (MDAnalysis.core.topologyattrs.Atomnames method) open() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) open_trajectory() (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.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.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method)

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.MinimalParser.MinimalParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.TXYZParser.TXYZParser method) (MDAnalysis.topology.XYZParser.XYZParser method) parse_bonded() (MDAnalysis.topology.TOPParser.TOPParser method) parse_charges() (MDAnalysis.topology.TOPParser.TOPParser method) parse_chunks() (MDAnalysis.topology.TOPParser.TOPParser method) parse_dihedrals() (MDAnalysis.topology.TOPParser.TOPParser method) parse_elements() (MDAnalysis.topology.TOPParser.TOPParser method) parse_FORTRAN_format() (MDAnalysis.lib.util.FORTRANReader method) parse_masses() (MDAnalysis.topology.TOPParser.TOPParser method) parse_n_atoms() (MDAnalysis.coordinates.base.ProtoReader class method) (MDAnalysis.coordinates.base.ReaderBase class method) (MDAnalysis.coordinates.base.SingleFrameReaderBase class method) (MDAnalysis.coordinates.DCD.DCDReader static method) (MDAnalysis.coordinates.GSD.GSDReader class method) (MDAnalysis.coordinates.INPCRD.INPReader static method) (MDAnalysis.coordinates.LAMMPS.DATAReader class method) (MDAnalysis.coordinates.LAMMPS.DCDReader static method) (MDAnalysis.coordinates.memory.MemoryReader static method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader class method) (MDAnalysis.coordinates.TRJ.NCDFReader static method) (MDAnalysis.coordinates.TRR.TRRReader class method) (MDAnalysis.coordinates.TXYZ.TXYZReader class method) (MDAnalysis.coordinates.XDR.XDRBaseReader class method) (MDAnalysis.coordinates.XTC.XTCReader class method) parse_names() (MDAnalysis.topology.TOPParser.TOPParser method) parse_residue() (in module MDAnalysis.lib.util) parse_residx() (MDAnalysis.topology.TOPParser.TOPParser method) parse_resnames() (MDAnalysis.topology.TOPParser.TOPParser method) parse_type_indices() (MDAnalysis.topology.TOPParser.TOPParser method) parse_types() (MDAnalysis.topology.TOPParser.TOPParser method) parsesection_mapper() (MDAnalysis.topology.TOPParser.TOPParser method) partner() (MDAnalysis.core.topologyobjects.Bond method) 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) pbc() (MDAnalysis.lib.pkdtree.PeriodicKDTree property)

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) periodic() (MDAnalysis.coordinates.chain.ChainReader property) PeriodicKDTree (class in MDAnalysis.lib.pkdtree) PersistenceLength (class in MDAnalysis.analysis.polymer) phase_as() (in module MDAnalysis.analysis.nuclinfo) phase_cp() (in module MDAnalysis.analysis.nuclinfo) phi_selection() (MDAnalysis.core.topologyattrs.Atomnames method) place() (MDAnalysis.lib.transformations.Arcball method) plot() (MDAnalysis.analysis.dihedrals.Janin method) (MDAnalysis.analysis.dihedrals.Ramachandran 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) PointSelection (class in MDAnalysis.core.selection) position() (MDAnalysis.core.groups.Atom property) PositionAverager (class in MDAnalysis.transformations.positionaveraging) positions (MDAnalysis.coordinates.base.Timestep attribute) positions() (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.core.groups.AtomGroup property) 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 property) 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) principal_axes() (MDAnalysis.core.topologyattrs.Masses method) 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 property) PSAnalysis (class in MDAnalysis.analysis.psa) PSAPair (class in MDAnalysis.analysis.psa) pseudo_dihe_baseflip() (in module MDAnalysis.analysis.nuclinfo) PSFParser (class in MDAnalysis.topology.PSFParser) psi_selection() (MDAnalysis.core.topologyattrs.Atomnames method) ptype() (MDAnalysis.topology.tpr.obj.Atom property) PureRMSD() (in module MDAnalysis.analysis.encore.cutils)

Q

q() (MDAnalysis.topology.tpr.obj.Atom property) q1q2() (in module MDAnalysis.analysis.contacts)

qB() (MDAnalysis.topology.tpr.obj.Atom property) quaternion_imag() (in module MDAnalysis.lib.transformations) quaternion_real() (in module MDAnalysis.lib.transformations)

R

r_cov (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis attribute) Radii (class in MDAnalysis.core.topologyattrs) radius_cut_q() (in module MDAnalysis.analysis.contacts) radius_of_gyration() (MDAnalysis.core.topologyattrs.Masses method) Rama_ref (in module MDAnalysis.analysis.data.filenames) Ramachandran (class in MDAnalysis.analysis.dihedrals) read() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.FORTRANReader method) read_all_times() (MDAnalysis.auxiliary.XVG.XVGFileReader method) (MDAnalysis.auxiliary.XVG.XVGReader method) read_attributes() (MDAnalysis.core.topology.Topology property) 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) readframes() (MDAnalysis.lib.formats.libdcd.DCDFile method) readline() (MDAnalysis.lib.util.NamedStream method) realpath() (in module MDAnalysis.lib.util) RecordTypes (class in MDAnalysis.core.topologyattrs) RecordTypeSelection (class in MDAnalysis.core.selection) 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 property) remap_angles() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_bonds() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_dihe() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_impr() (MDAnalysis.topology.tpr.obj.MoleculeKind method) REMARK() (MDAnalysis.coordinates.PDB.PDBWriter method) remove_anchor() (MDAnalysis.core.universe.Universe method) remove_auxiliary() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) rename_aux() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) reppow() (MDAnalysis.topology.tpr.obj.Params property) represent_ts_as() (MDAnalysis.auxiliary.base.AuxReader property) resample() (MDAnalysis.analysis.density.Density method) resample_factor() (MDAnalysis.analysis.density.Density method) reset() (MDAnalysis.lib.util.NamedStream method) Resids (class in MDAnalysis.core.topologyattrs) ResidSelection (class in MDAnalysis.core.selection) Residue (class in MDAnalysis.core.groups) ResidueAttr (class in MDAnalysis.core.topologyattrs)

ResidueGroup (class in MDAnalysis.core.groups) ResidueNameSelection (class in MDAnalysis.core.selection) residues() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.Segment property) (MDAnalysis.core.groups.SegmentGroup property) 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 property) Resindices (class in MDAnalysis.core.topologyattrs) Resnames (class in MDAnalysis.core.topologyattrs) resnames() (MDAnalysis.topology.tpr.obj.Atoms property) Resnums (class in MDAnalysis.core.topologyattrs) results (MDAnalysis.analysis.base.AnalysisFromFunction attribute) (MDAnalysis.analysis.lineardensity.LinearDensity attribute) (MDAnalysis.analysis.polymer.PersistenceLength attribute) rewind() (MDAnalysis.auxiliary.base.AuxReader method) (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.chain.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) 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() (in module MDAnalysis.transformations.rotate) (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.diffusionmap.DiffusionMap method) (MDAnalysis.analysis.dihedrals.Dihedral method) (MDAnalysis.analysis.dihedrals.Janin method) (MDAnalysis.analysis.dihedrals.Ramachandran method) (MDAnalysis.analysis.encore.utils.ParallelCalculation method) (MDAnalysis.analysis.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.Path method) (MDAnalysis.analysis.psa.PSAnalysis method) (MDAnalysis.analysis.rdf.InterRDF method) (MDAnalysis.analysis.rdf.InterRDF_s method) (MDAnalysis.analysis.rms.RMSD method) (MDAnalysis.analysis.rms.RMSF 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 property)

S

sarrus_det() (in module MDAnalysis.lib.mdamath), [1] save() (MDAnalysis.analysis.contacts.Contacts method) (MDAnalysis.analysis.density.Density 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) (MDAnalysis.lib.nsgrid.FastNS method) (MDAnalysis.lib.pkdtree.PeriodicKDTree method) search_pairs() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) search_tree() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) seek() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) seekable() (MDAnalysis.lib.util.NamedStream method) Segids (class in MDAnalysis.core.topologyattrs) Segindices (class in MDAnalysis.core.topologyattrs) Segment (class in MDAnalysis.core.groups) segment() (MDAnalysis.core.groups.Residue property) SegmentAttr (class in MDAnalysis.core.topologyattrs) SegmentGroup (class in MDAnalysis.core.groups) SegmentNameSelection (class in MDAnalysis.core.selection) segments() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) 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), [1] (class in MDAnalysis.selections.gromacs), [1] (class in MDAnalysis.selections.jmol), [1] (class in MDAnalysis.selections.pymol), [1] (class in MDAnalysis.selections.vmd), [1] SelectionWriterBase (class in MDAnalysis.selections.base) self_capped_distance() (in module MDAnalysis.lib.distances) self_distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances) self_search() (MDAnalysis.lib.nsgrid.FastNS method) seq2str() (in module MDAnalysis.analysis.hole) sequence() (MDAnalysis.core.topologyattrs.Resnames method) sequence_alignment() (in module MDAnalysis.analysis.align) set_array() (MDAnalysis.coordinates.memory.MemoryReader method) set_atoms() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.Atomindices method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) set_aux_attribute() (MDAnalysis.coordinates.base.ProtoReader method) (MDAnalysis.coordinates.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) (MDAnalysis.coordinates.PDB.ExtendedPDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method)

set_coords() (MDAnalysis.lib.pkdtree.PeriodicKDTree method) set_offsets() (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) set_residues() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Resindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) set_rmsd_matrix_elements() (in module MDAnalysis.analysis.encore.confdistmatrix) set_segments() (MDAnalysis.core.topologyattrs.AtomAttr method) (MDAnalysis.core.topologyattrs.ResidueAttr method) (MDAnalysis.core.topologyattrs.Segindices method) (MDAnalysis.core.topologyattrs.SegmentAttr method) (MDAnalysis.core.topologyattrs.TopologyAttr method) setaxes() (MDAnalysis.lib.transformations.Arcball method) setconstrain() (MDAnalysis.lib.transformations.Arcball method) setdefault() (MDAnalysis.core.__init__.Flags method) shape_parameter() (MDAnalysis.core.topologyattrs.Masses method) shear_from_matrix() (in module MDAnalysis.lib.transformations) shrinkage_covariance_estimator() (in module MDAnalysis.analysis.encore.covariance) SIMPLE2_RAD (in module MDAnalysis.analysis.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) size() (MDAnalysis.core.topology.TransTable property) (MDAnalysis.topology.tpr.obj.Box property) sizes() (MDAnalysis.analysis.leaflet.LeafletFinder method) skip_timestep() (MDAnalysis.coordinates.TRZ.TRZReader property), [1] skipper() (MDAnalysis.topology.TOPParser.TOPParser method) soft_cut_q() (in module MDAnalysis.analysis.contacts) solve() (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) sort_backbone() (in module MDAnalysis.analysis.polymer) 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) SphericalLayerSelection (class in MDAnalysis.core.selection) SphericalZoneSelection (class in MDAnalysis.core.selection) split() (MDAnalysis.core.groups.AtomGroup method) sqnorm() (in module MDAnalysis.analysis.psa) start_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) static_variables() (in module MDAnalysis.lib.util) std() (MDAnalysis.analysis.legacy.x3dna.X3DNA method) (MDAnalysis.analysis.legacy.x3dna.X3DNAtraj method) step (MDAnalysis.auxiliary.base.AuxStep attribute) step() (MDAnalysis.auxiliary.base.AuxReader property) step_to_frame() (MDAnalysis.auxiliary.base.AuxReader method) step_to_time() (MDAnalysis.auxiliary.base.AuxReader method) StochasticProximityEmbedding() (in module MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed) StochasticProximityEmbeddingNative (class in MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod) stop_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) 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) TABLE_VDWRADII (in module MDAnalysis.topology.tables) tell() (MDAnalysis.lib.formats.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.lib.util.NamedStream method) temperature (MDAnalysis.coordinates.TRZ.Timestep attribute) Tempfactors (class in MDAnalysis.core.topologyattrs) time (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) time() (MDAnalysis.auxiliary.base.AuxReader property) (MDAnalysis.auxiliary.base.AuxStep property) (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.chain.ChainReader property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.memory.Timestep property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) time_selector() (MDAnalysis.auxiliary.base.AuxReader property) timeseries (MDAnalysis.analysis.contacts.Contacts attribute) timeseries() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis property) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis property) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader method) Timestep (class in MDAnalysis.coordinates.base) (class in MDAnalysis.coordinates.DLPoly) (class in MDAnalysis.coordinates.DMS) (class in MDAnalysis.coordinates.GRO) (class in MDAnalysis.coordinates.memory) (class in MDAnalysis.coordinates.TRJ) (class in MDAnalysis.coordinates.TRZ), [1] timesteps (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis attribute) timesteps_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) (MDAnalysis.analysis.hbonds.wbridge_analysis.WaterBridgeAnalysis 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 property) Topology (class in MDAnalysis.core.topology) TopologyAttr (class in MDAnalysis.core.topologyattrs) TopologyDict (class in MDAnalysis.core.topologyobjects) TopologyGroup (class in MDAnalysis.core.topologyobjects) TopologyObject (class in MDAnalysis.core.topologyobjects) TopologyReaderBase (class in MDAnalysis.topology.base) TOPParser (class in MDAnalysis.topology.TOPParser) tors() (in module MDAnalysis.analysis.nuclinfo) tors_alpha() (in module MDAnalysis.analysis.nuclinfo) tors_beta() (in module MDAnalysis.analysis.nuclinfo) tors_chi() (in module MDAnalysis.analysis.nuclinfo) tors_delta() (in module MDAnalysis.analysis.nuclinfo) tors_eps() (in module MDAnalysis.analysis.nuclinfo) tors_gamma() (in module MDAnalysis.analysis.nuclinfo) tors_zeta() (in module MDAnalysis.analysis.nuclinfo) total_charge() (MDAnalysis.core.topologyattrs.Charges method) total_energy (MDAnalysis.coordinates.TRZ.Timestep attribute)

total_mass() (MDAnalysis.core.topologyattrs.Masses method) totaltime() (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) tp() (MDAnalysis.topology.tpr.obj.Atom property) TPRParser (class in MDAnalysis.topology.TPRParser) TpxHeader (class in MDAnalysis.topology.tpr.obj) trajectory (MDAnalysis.core.universe.Universe attribute) trajectory() (MDAnalysis.core.universe.Universe property) transfer_to_memory() (MDAnalysis.core.universe.Universe method) transform() (MDAnalysis.analysis.diffusionmap.DiffusionMap method) (MDAnalysis.analysis.pca.PCA method) (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) transform_RtoS() (in module MDAnalysis.lib.distances) transform_StoR() (in module MDAnalysis.lib.distances) transformations() (MDAnalysis.coordinates.base.ProtoReader property) (MDAnalysis.coordinates.base.ReaderBase property) (MDAnalysis.coordinates.base.SingleFrameReaderBase property) (MDAnalysis.coordinates.DCD.DCDReader property) (MDAnalysis.coordinates.GSD.GSDReader property) (MDAnalysis.coordinates.LAMMPS.DATAReader property) (MDAnalysis.coordinates.LAMMPS.DCDReader property) (MDAnalysis.coordinates.memory.MemoryReader property) (MDAnalysis.coordinates.PDB.ExtendedPDBReader property) (MDAnalysis.coordinates.TRR.TRRReader property) (MDAnalysis.coordinates.TXYZ.TXYZReader property) (MDAnalysis.coordinates.XDR.XDRBaseReader property) (MDAnalysis.coordinates.XTC.XTCReader property) translate() (in module MDAnalysis.transformations.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) triclinic_dimensions() (MDAnalysis.coordinates.memory.Timestep property) 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.coordinates.TRZ.TRZReader attribute), [1] ts() (MDAnalysis.core.groups.AtomGroup property) TXYZParser (class in MDAnalysis.topology.TXYZParser) TXYZReader (class in MDAnalysis.coordinates.TXYZ) type() (MDAnalysis.core.topologyobjects.TopologyObject property) (MDAnalysis.topology.tpr.obj.Atoms property) typeB() (MDAnalysis.topology.tpr.obj.Atom property) (MDAnalysis.topology.tpr.obj.Atoms property) types() (MDAnalysis.core.topologyobjects.TopologyGroup method)

U

u_fitted (MDAnalysis.analysis.psa.Path attribute) u_original (MDAnalysis.analysis.psa.Path attribute) u_reference (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) uncomment() (in module MDAnalysis.auxiliary.XVG) undo_augment() (in module MDAnalysis.lib.distances) union() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) unique() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) unique_int_1d() (in module MDAnalysis.lib.util) unique_rows() (in module MDAnalysis.lib.util) unit_types (in module MDAnalysis.units) units (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.coordinates.base.IOBase attribute)

units() (MDAnalysis.coordinates.chain.ChainReader property) Universe (class in MDAnalysis.core.universe) universe() (MDAnalysis.core.groups.AtomGroup property) (MDAnalysis.core.groups.ResidueGroup property) (MDAnalysis.core.groups.SegmentGroup property) (MDAnalysis.core.topologyobjects.TopologyGroup property) universes (MDAnalysis.analysis.psa.PSAnalysis attribute) unwrap() (MDAnalysis.core.groups.AtomGroup method) (MDAnalysis.core.groups.ResidueGroup method) (MDAnalysis.core.groups.SegmentGroup method) 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 property) validate_atom_types() (in module MDAnalysis.topology.guessers) validate_dimensions() (MDAnalysis.core.selection.DistanceSelection method) value() (MDAnalysis.core.topologyobjects.Angle method) (MDAnalysis.core.topologyobjects.Bond method) (MDAnalysis.core.topologyobjects.Dihedral method) values() (MDAnalysis.core.__init__.Flags method) (MDAnalysis.core.topologyobjects.TopologyGroup method)

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

W

warn_if_not_unique() (in module MDAnalysis.lib.util) water (in module MDAnalysis.units) WaterBridgeAnalysis (class in MDAnalysis.analysis.hbonds.wbridge_analysis) 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.libdcd.DCDFile method) (MDAnalysis.lib.formats.libmdaxdr.TRRFile method) (MDAnalysis.lib.formats.libmdaxdr.XTCFile method) (MDAnalysis.selections.base.SelectionWriterBase method) (MDAnalysis.selections.charmm.SelectionWriter method), [1] (MDAnalysis.selections.gromacs.SelectionWriter method), [1] (MDAnalysis.selections.jmol.SelectionWriter method), [1] (MDAnalysis.selections.pymol.SelectionWriter method), [1] (MDAnalysis.selections.vmd.SelectionWriter method), [1] write_all_timesteps() (MDAnalysis.coordinates.PDB.PDBWriter method) write_header() (MDAnalysis.lib.formats.libdcd.DCDFile 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), [1] (MDAnalysis.selections.gromacs.SelectionWriter method), [1] (MDAnalysis.selections.jmol.SelectionWriter method), [1] (MDAnalysis.selections.pymol.SelectionWriter method), [1] (MDAnalysis.selections.vmd.SelectionWriter method), [1] 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.base.ReaderBase method) (MDAnalysis.coordinates.base.SingleFrameReaderBase method) (MDAnalysis.coordinates.CRD.CRDReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GRO.GROReader method) (MDAnalysis.coordinates.GSD.GSDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.memory.MemoryReader 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.TRZ.TRZReader method), [1] (MDAnalysis.coordinates.TXYZ.TXYZReader method) (MDAnalysis.coordinates.XDR.XDRBaseReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.XYZ.XYZReader method) WriterBase (class in MDAnalysis.coordinates.base)

X

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)