Index

_

__add__() (MDAnalysis.core.topologyobjects.TopologyGroup method) __contains__() (MDAnalysis.core.topologyobjects.TopologyDict method) (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.topologyobjects.TopologyObject method) __del__() (MDAnalysis.lib.util.NamedStream method) __delattr__ (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __eq__() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.topologyobjects.TopologyObject method) __format__() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj 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) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) __ge__() (MDAnalysis.core.AtomGroup.Atom method) (MDAnalysis.lib.util.NamedStream method) __getattribute__ (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __getitem__() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.topologyobjects.TopologyDict method) (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.core.topologyobjects.TopologyObject method) __getnewargs__() (MDAnalysis.topology.tpr.obj.Atom method) (MDAnalysis.topology.tpr.obj.Atoms method) (MDAnalysis.topology.tpr.obj.Box method) (MDAnalysis.topology.tpr.obj.Ilist method) (MDAnalysis.topology.tpr.obj.Molblock method) (MDAnalysis.topology.tpr.obj.Mtop method) (MDAnalysis.topology.tpr.obj.Params method) (MDAnalysis.topology.tpr.obj.TPRTopology method) (MDAnalysis.topology.tpr.obj.TpxHeader method) __getstate__() (MDAnalysis.topology.tpr.obj.Atom method) (MDAnalysis.topology.tpr.obj.Atoms method) (MDAnalysis.topology.tpr.obj.Box method) (MDAnalysis.topology.tpr.obj.Ilist method) (MDAnalysis.topology.tpr.obj.Molblock method) (MDAnalysis.topology.tpr.obj.Mtop method) (MDAnalysis.topology.tpr.obj.Params method) (MDAnalysis.topology.tpr.obj.TPRTopology method) (MDAnalysis.topology.tpr.obj.TpxHeader method) __gt__() (MDAnalysis.core.AtomGroup.Atom method) (MDAnalysis.lib.util.NamedStream method) __hash__ (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __hash__() (MDAnalysis.core.topologyobjects.TopologyObject method) __init__() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.selections.base.SelectionWriter method) __iter__() (MDAnalysis.coordinates.base.ChainReader method) (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.core.topologyobjects.TopologyDict method) (MDAnalysis.core.topologyobjects.TopologyGroup method) __le__() (MDAnalysis.core.AtomGroup.Atom method) (MDAnalysis.lib.util.NamedStream method) __len__() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.topologyobjects.TopologyDict method) (MDAnalysis.core.topologyobjects.TopologyGroup method) (MDAnalysis.lib.util.FORTRANReader method) __reduce__() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj 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) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) __reduce_ex__() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj 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) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) __repr__ (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __repr__() (MDAnalysis.topology.tpr.obj.Atom method) (MDAnalysis.topology.tpr.obj.Atoms method) (MDAnalysis.topology.tpr.obj.Box method) (MDAnalysis.topology.tpr.obj.Ilist method) (MDAnalysis.topology.tpr.obj.Molblock method) (MDAnalysis.topology.tpr.obj.Mtop method) (MDAnalysis.topology.tpr.obj.Params method) (MDAnalysis.topology.tpr.obj.TPRTopology method) (MDAnalysis.topology.tpr.obj.TpxHeader method)

__setattr__ (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __sizeof__() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj 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) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) __str__ (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.waterdynamics.AngularDistribution attribute) (MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes attribute) (MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement attribute) (MDAnalysis.analysis.waterdynamics.SurvivalProbability attribute) (MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.x3dna.X3DNAtraj attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.DCDWriter attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter attribute) (MDAnalysis.selections.charmm.SelectionWriter attribute) (MDAnalysis.selections.gromacs.SelectionWriter attribute) (MDAnalysis.selections.jmol.SelectionWriter attribute) (MDAnalysis.selections.pymol.SelectionWriter attribute) (MDAnalysis.selections.vmd.SelectionWriter attribute) (MDAnalysis.topology.CRDParser.CRDParser attribute) (MDAnalysis.topology.DMSParser.DMSParser attribute) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser attribute) (MDAnalysis.topology.GMSParser.GMSParser attribute) (MDAnalysis.topology.GROParser.GROParser attribute) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser attribute) (MDAnalysis.topology.LAMMPSParser.DATAParser attribute) (MDAnalysis.topology.MOL2Parser.MOL2Parser attribute) (MDAnalysis.topology.PDBParser.PDBParser attribute) (MDAnalysis.topology.PDBQTParser.PDBQTParser attribute) (MDAnalysis.topology.PQRParser.PQRParser attribute) (MDAnalysis.topology.PSFParser.PSFParser attribute) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser attribute) (MDAnalysis.topology.TOPParser.TOPParser attribute) (MDAnalysis.topology.TPRParser.TPRParser attribute) (MDAnalysis.topology.XYZParser.XYZParser attribute) (MDAnalysis.topology.base.TopologyReader attribute) __version__ (in module MDAnalysis.version) _atoms (MDAnalysis.core.AtomGroup.AtomGroup attribute) _check_pdb_coordinates() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) _clear_caches() (MDAnalysis.core.AtomGroup.AtomGroup method) _fill_cache() (MDAnalysis.core.AtomGroup.AtomGroup method) _forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.Timestep attribute) _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) _init_unitcell() (MDAnalysis.coordinates.base.Timestep method) _pos (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.Timestep attribute) _rebuild_caches() (MDAnalysis.core.AtomGroup.AtomGroup method) _translate() (MDAnalysis.selections.base.SelectionWriter method) _update_frame() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) _velocities (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRJ.Timestep attribute) _write_head() (MDAnalysis.selections.base.SelectionWriter method) _write_pdb_bonds() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) _write_tail() (MDAnalysis.selections.base.SelectionWriter method) _write_timestep() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)

A

active_reader (MDAnalysis.coordinates.base.ChainReader attribute) addTimeseries() (MDAnalysis.core.Timeseries.TimeseriesCollection method) align_principal_axis() (MDAnalysis.core.AtomGroup.AtomGroup method) align_principalAxis() (MDAnalysis.core.AtomGroup.AtomGroup method) alignto() (in module MDAnalysis.analysis.align) altLoc (MDAnalysis.core.AtomGroup.Atom attribute) altLocs (MDAnalysis.core.AtomGroup.AtomGroup attribute) AltlocSelection (class in MDAnalysis.core.Selection) Angle (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.core.topologyobjects) angle (MDAnalysis.core.AtomGroup.AtomGroup attribute) angle() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.topologyobjects.Angle method) angles (MDAnalysis.core.AtomGroup.Atom attribute), [1] (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) (MDAnalysis.topology.tpr.obj.TPRTopology attribute) angles() (MDAnalysis.core.topologyobjects.TopologyGroup method) AngularDistribution (class in MDAnalysis.analysis.waterdynamics) anyopen() (in module MDAnalysis.lib.util) ApplicationError (class in MDAnalysis.analysis.hole) (class in MDAnalysis.analysis.x3dna) apply_PBC() (in module MDAnalysis.lib.distances), [1] Arcball (class in MDAnalysis.lib.transformations)

arcball_nearest_axis() (in module MDAnalysis.lib.transformations) as_Universe() (in module MDAnalysis.core.AtomGroup) asiterable() (in module MDAnalysis.lib.util) asphericity() (MDAnalysis.core.AtomGroup.AtomGroup method) atnr (MDAnalysis.topology.tpr.obj.Params attribute) Atom (class in MDAnalysis.core.AtomGroup) (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.topology.tpr.obj) ATOM() (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) atomelements (in module MDAnalysis.topology.tables) AtomGroup (class in MDAnalysis.core.AtomGroup) atomgroup_intersection() (MDAnalysis.core.topologyobjects.TopologyGroup method) AtomKind (class in MDAnalysis.topology.tpr.obj) atomnames (MDAnalysis.topology.tpr.obj.Atoms attribute) AtomNameSelection (class in MDAnalysis.core.Selection) AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch) atomnumber (MDAnalysis.topology.tpr.obj.Atom attribute) Atoms (class in MDAnalysis.topology.tpr.obj) atoms (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) (MDAnalysis.topology.tpr.obj.TPRTopology attribute) AtomTypeSelection (class in MDAnalysis.core.Selection)

B

BackboneSelection (class in MDAnalysis.core.Selection) backup_file() (in module MDAnalysis.analysis.gnm) BaseSelection (class in MDAnalysis.core.Selection) bBox (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bbox() (MDAnalysis.core.AtomGroup.AtomGroup method) bF (MDAnalysis.topology.tpr.obj.TpxHeader attribute) Bfactor2RMSF() (in module MDAnalysis.analysis.density) BfactorDensityCreator (class in MDAnalysis.analysis.density) bfactors (MDAnalysis.core.AtomGroup.AtomGroup attribute) bIr (MDAnalysis.topology.tpr.obj.TpxHeader attribute) Bond (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.core.topologyobjects) bond (MDAnalysis.core.AtomGroup.AtomGroup attribute)

bonded_atoms (MDAnalysis.core.AtomGroup.Atom attribute) bonds (MDAnalysis.core.AtomGroup.Atom attribute), [1] (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) (MDAnalysis.topology.tpr.obj.TPRTopology attribute) bonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) Box (class in MDAnalysis.topology.tpr.obj) box_volume() (in module MDAnalysis.lib.mdamath), [1] bsphere() (MDAnalysis.core.AtomGroup.AtomGroup method) bTop (MDAnalysis.topology.tpr.obj.TpxHeader attribute) build_residues() (in module MDAnalysis.topology.core) build_segments() (in module MDAnalysis.topology.core) build_topology() (MDAnalysis.core.AtomGroup.Universe method) bV (MDAnalysis.topology.tpr.obj.TpxHeader attribute) bX (MDAnalysis.topology.tpr.obj.TpxHeader attribute)

C

cached() (in module MDAnalysis.lib.util) calc_angle() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) calc_angles() (in module MDAnalysis.lib.distances), [1] calc_bonds() (in module MDAnalysis.lib.distances), [1] calc_dihedrals() (in module MDAnalysis.lib.distances), [1] calc_eucl_distance() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) CalcRMSDRotationalMatrix() (in module MDAnalysis.lib.qcprot) center_of_geometry() (MDAnalysis.core.AtomGroup.AtomGroup method) center_of_mass() (MDAnalysis.core.AtomGroup.AtomGroup method) CenterOfGeometry (class in MDAnalysis.core.Timeseries) centerOfGeometry() (MDAnalysis.core.AtomGroup.AtomGroup method) CenterOfMass (class in MDAnalysis.core.Timeseries) centerOfMass() (MDAnalysis.core.AtomGroup.AtomGroup method) centers() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) centroid() (MDAnalysis.core.AtomGroup.Atom method) (MDAnalysis.core.AtomGroup.AtomGroup method) ChainReader (class in MDAnalysis.coordinates.base) charge (MDAnalysis.core.AtomGroup.Atom attribute) charges (MDAnalysis.core.AtomGroup.AtomGroup attribute) chargeUnit_factor (in module MDAnalysis.units) check_and_fix_long_filename() (MDAnalysis.analysis.hole.HOLE method) check_compatible() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) check_slice_indices() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) chi1_selection() (MDAnalysis.core.AtomGroup.Residue method) clear() (MDAnalysis.core.Timeseries.TimeseriesCollection method) clear_handlers() (in module MDAnalysis.lib.log) close() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRZ.TRZReader method), [1] (MDAnalysis.coordinates.TRZ.TRZWriter method), [1] (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.core.TrjReader method) (MDAnalysis.lib.util.NamedStream method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) closeContactGNMAnalysis (class in MDAnalysis.analysis.gnm) closed (MDAnalysis.lib.util.NamedStream attribute) cluster() (MDAnalysis.analysis.psa.PSAnalysis method) collect() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.x3dna.X3DNA method) comment() (MDAnalysis.selections.base.SelectionWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) compose_matrix() (in module MDAnalysis.lib.transformations) compute() (MDAnalysis.core.Timeseries.TimeseriesCollection method) concatenate_matrices() (in module MDAnalysis.lib.transformations) CONECT() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) ConfigReader (class in MDAnalysis.coordinates.DLPoly)

constants (in module MDAnalysis.units) contact_matrix() (in module MDAnalysis.analysis.distances) ContactAnalysis (class in MDAnalysis.analysis.contacts) ContactAnalysis1 (class in MDAnalysis.analysis.contacts) ContactAnalysis1.plot() (in module MDAnalysis.analysis.contacts) ContactAnalysis1.plot_qavg() (in module 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.Writer method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.coordinates.xdrfile.core.TrjWriter method) convert_forces_from_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_forces_to_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_length() (MDAnalysis.analysis.density.Density method) convert_pos_from_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_pos_to_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_time_from_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_time_to_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_velocities_from_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) convert_velocities_to_native() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) (MDAnalysis.topology.base.TopologyReader method) coord (MDAnalysis.core.AtomGroup.Universe attribute) coordinates() (MDAnalysis.core.AtomGroup.AtomGroup method) copy() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) copy_slice() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) correl() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) count_by_time() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) count_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) 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.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method)

D

D (MDAnalysis.analysis.psa.PSAnalysis attribute) DATAParser (class in MDAnalysis.topology.LAMMPSParser) DATAReader (class in MDAnalysis.coordinates.LAMMPS) DCDReader (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) DCDWriter (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.LAMMPS) decompose_matrix() (in module MDAnalysis.lib.transformations) DEFAULT_ACCEPTORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) DEFAULT_DONORS (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) default_ignore_residues (MDAnalysis.analysis.hole.HOLE attribute) define_unpack_real() (in module MDAnalysis.topology.tpr.utils) delta (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] Density (class in MDAnalysis.analysis.density) Density() (MDAnalysis.analysis.density.BfactorDensityCreator method) density_from_PDB() (in module MDAnalysis.analysis.density) density_from_Universe() (in module MDAnalysis.analysis.density) densityUnit_factor (in module MDAnalysis.units) dihe (MDAnalysis.topology.tpr.obj.TPRTopology attribute) Dihedral (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.core.topologyobjects) dihedral (MDAnalysis.core.AtomGroup.AtomGroup attribute) dihedral() (in module MDAnalysis.lib.mdamath), [1] (MDAnalysis.core.topologyobjects.Dihedral method) dihedrals (MDAnalysis.core.AtomGroup.Atom attribute), [1] (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) dihedrals() (MDAnalysis.core.topologyobjects.TopologyGroup method) DIM (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute), [1] (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.core.Timestep attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) discrete_frechet() (in module MDAnalysis.analysis.psa) dist() (in module MDAnalysis.analysis.distances) dist_mat_to_vec() (in module MDAnalysis.analysis.psa) Distance (class in MDAnalysis.core.Timeseries)

distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances), [1] 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_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) dt (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) dump_contents() (MDAnalysis.core.topologyobjects.TopologyGroup method)

E

echo() (in module MDAnalysis.lib.log) (MDAnalysis.lib.log.ProgressMeter method) END() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) ENDMDL() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) environment variable PATH, [1] ERRORCODE (in module MDAnalysis.coordinates.xdrfile.statno) ERRORSYMBOLS (in module MDAnalysis.coordinates.xdrfile.statno) euler_from_quaternion() (in module MDAnalysis.lib.transformations) exdr3DX (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrCLOSE (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrDOUBLE (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrENDOFFILE (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrFILENOTFOUND (in module MDAnalysis.coordinates.xdrfile.libxdrfile2)

exdrFLOAT (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrHEADER (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrINT (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrMAGIC (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrNOMEM (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrOK (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrSTRING (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) exdrUINT (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) expect() (MDAnalysis.core.Selection.SelectionParser method) export() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) ExtendedPDBParser (class in MDAnalysis.topology.ExtendedPDBParser) extract_box_info() (in module MDAnalysis.topology.tpr.utils)

F

fasta2select() (in module MDAnalysis.analysis.align) FastCalcRMSDAndRotation() (in module MDAnalysis.lib.qcprot) fep_state (MDAnalysis.topology.tpr.obj.TpxHeader attribute) fgen (MDAnalysis.topology.tpr.obj.TpxHeader attribute) file_tag (MDAnalysis.topology.tpr.obj.TpxHeader attribute) FileFormatWarning filename (MDAnalysis.analysis.psa.PSAnalysis attribute) filename() (in module MDAnalysis.lib.util) fileno() (MDAnalysis.lib.util.NamedStream method) FinishTimeException fit_exponential_decay() (in module MDAnalysis.analysis.polymer) fit_to_reference() (MDAnalysis.analysis.psa.Path method) fixedwidth_bins() (in module MDAnalysis.lib.util) Flag (class in MDAnalysis.core.__init__) Flags (class in MDAnalysis.core.__init__) flags (in module MDAnalysis.core.__init__) flagsDocs (class in MDAnalysis.core.__init__) flush() (MDAnalysis.lib.util.NamedStream method)

fmt (MDAnalysis.coordinates.GRO.GROWriter attribute) force (MDAnalysis.core.AtomGroup.Atom attribute) forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute) forceUnit_factor (in module MDAnalysis.units) FORTRAN_format_regex (in module MDAnalysis.lib.util) FORTRANReader (class in MDAnalysis.lib.util) fragment (MDAnalysis.core.AtomGroup.Atom attribute) fragments (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) frame (MDAnalysis.coordinates.base.ChainReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) frames (MDAnalysis.analysis.psa.PDBToBinaryTraj attribute) from_coordinates() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) from_indices() (MDAnalysis.core.topologyobjects.TopologyGroup class method) from_timestep() (MDAnalysis.coordinates.base.Timestep class method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.xdrfile.TRR.Timestep method) (MDAnalysis.coordinates.xdrfile.XTC.Timestep method) ftupd (in module MDAnalysis.topology.tpr.setting) fudgeQQ (MDAnalysis.topology.tpr.obj.Params attribute) functype (MDAnalysis.topology.tpr.obj.Params attribute) fver (MDAnalysis.topology.tpr.obj.TpxHeader attribute) fver_err() (in module MDAnalysis.topology.tpr.utils)

G

generate_grid() (in module MDAnalysis.analysis.gnm) generate_kirchoff() (MDAnalysis.analysis.gnm.GNMAnalysis method) generate_output() (MDAnalysis.analysis.gnm.GNMAnalysis method) generate_paths() (MDAnalysis.analysis.psa.PSAnalysis method) generate_streamlines() (in module MDAnalysis.visualization.streamlines) generate_streamlines_3d() (in module MDAnalysis.visualization.streamlines_3D) generate_table() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) get_atom_mass() (in module MDAnalysis.topology.core) get_bfactors() (MDAnalysis.coordinates.PDBQT.PDBQTReader method) get_charges() (MDAnalysis.coordinates.PQR.PQRReader method) get_conversion_factor() (in module MDAnalysis.units) get_coord_axes() (in module MDAnalysis.analysis.psa) get_distance_array() (MDAnalysis.analysis.contacts.ContactAnalysis method) get_forces() (MDAnalysis.core.AtomGroup.AtomGroup 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_occupancy() (MDAnalysis.coordinates.PDBQT.PDBQTReader method) get_pairwise_distances() (MDAnalysis.analysis.psa.PSAnalysis method) get_parser_for() (in module MDAnalysis.topology.core) get_path_metric_func() (in module MDAnalysis.analysis.psa) get_paths() (MDAnalysis.analysis.psa.PSAnalysis method) get_positions() (MDAnalysis.core.AtomGroup.AtomGroup method) get_radii() (MDAnalysis.coordinates.PQR.PQRReader method) get_reader_for() (in module MDAnalysis.coordinates.core)

get_structure() (in module MDAnalysis.coordinates.pdb.extensions) get_velocities() (MDAnalysis.core.AtomGroup.AtomGroup method) get_writer_for() (in module MDAnalysis.coordinates.core) getconstrain() (MDAnalysis.lib.transformations.Arcball method) GMSParser (class in MDAnalysis.topology.GMSParser) 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 (class in MDAnalysis.analysis.density) GROParser (class in MDAnalysis.topology.GROParser) GROReader (class in MDAnalysis.coordinates.GRO) group() (MDAnalysis.analysis.leaflet.LeafletFinder method) groups() (MDAnalysis.analysis.leaflet.LeafletFinder method) groups_iter() (MDAnalysis.analysis.leaflet.LeafletFinder method) GROWriter (class in MDAnalysis.coordinates.GRO) guess_angles() (in module MDAnalysis.topology.core) guess_atom_charge() (in module MDAnalysis.topology.core) guess_atom_element() (in module MDAnalysis.topology.core) guess_atom_mass() (in module MDAnalysis.topology.core) guess_atom_type() (in module MDAnalysis.topology.core) guess_bonds() (in module MDAnalysis.topology.core) (MDAnalysis.core.AtomGroup.AtomGroup method) guess_cpoint() (MDAnalysis.analysis.hole.HOLEtraj method) guess_dihedrals() (in module MDAnalysis.topology.core) guess_format() (in module MDAnalysis.lib.util) guess_improper_dihedrals() (in module MDAnalysis.topology.core)

H

has_forces (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) has_positions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) has_valid_coordinates() (MDAnalysis.coordinates.base.Writer method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) has_velocities (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) hasmethod() (in module MDAnalysis.lib.util) hausdorff() (in module MDAnalysis.analysis.psa) hausdorff_avg() (in module MDAnalysis.analysis.psa) hausdorff_neighbors() (in module MDAnalysis.analysis.psa) hausdorff_pair (MDAnalysis.analysis.psa.PSAPair attribute) hausdorff_pairs (MDAnalysis.analysis.psa.PSAnalysis attribute) hausdorff_wavg() (in module MDAnalysis.analysis.psa) HEADER() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)

helanal_main() (in module MDAnalysis.analysis.helanal) helanal_trajectory() (in module MDAnalysis.analysis.helanal) HistoryReader (class in MDAnalysis.coordinates.DLPoly) HOLE (class in MDAnalysis.analysis.hole) HOLE_MAX_LENGTH (MDAnalysis.analysis.hole.HOLE attribute) HOLEtraj (class in MDAnalysis.analysis.hole) HoomdXMLParser (class in MDAnalysis.topology.HoomdXMLParser) HydrogenBondAnalysis (class in MDAnalysis.analysis.hbonds.hbond_analysis) HydrogenBondAutoCorrel (class in MDAnalysis.analysis.hbonds.hbond_autocorrel) HydrogenBondLifetimes (class in MDAnalysis.analysis.waterdynamics) hydroxyl() (in module MDAnalysis.analysis.nuclinfo)

I

iatoms (MDAnalysis.topology.tpr.obj.Ilist attribute) id (MDAnalysis.core.AtomGroup.Atom attribute) (MDAnalysis.core.AtomGroup.Segment attribute) ik (MDAnalysis.topology.tpr.obj.Ilist attribute) Ilist (class in MDAnalysis.topology.tpr.obj) impr (MDAnalysis.topology.tpr.obj.TPRTopology attribute) improper (MDAnalysis.core.AtomGroup.AtomGroup attribute) improper() (MDAnalysis.core.topologyobjects.ImproperDihedral method) ImproperDihedral (class in MDAnalysis.core.topologyobjects) impropers (MDAnalysis.core.AtomGroup.Atom attribute), [1] (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.Universe attribute) index (MDAnalysis.core.AtomGroup.Atom attribute) indices (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.topologyobjects.TopologyObject attribute) InnerProduct() (in module MDAnalysis.lib.qcprot)

interaction_types (in module MDAnalysis.topology.tpr.setting) InteractionKind (class in MDAnalysis.topology.tpr.obj) interpolated (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute) InterRDF (class in MDAnalysis.analysis.rdf) IObase (class in MDAnalysis.coordinates.base) iparams (MDAnalysis.topology.tpr.obj.Params attribute) is_anchor (MDAnalysis.core.AtomGroup.Universe attribute) is_guessed (MDAnalysis.core.topologyobjects.TopologyObject attribute) is_keyword() (in module MDAnalysis.core.Selection) is_periodic() (MDAnalysis.coordinates.TRJ.NCDFWriter method) isstream() (in module MDAnalysis.lib.util) iterable() (in module MDAnalysis.lib.util)

J

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

K

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

kv2dict() (in module MDAnalysis.topology.tables)

L

lamb (MDAnalysis.topology.tpr.obj.TpxHeader attribute) LAMMPSDataConverter (class in MDAnalysis.topology.LAMMPSParser) LeafletFinder (class in MDAnalysis.analysis.leaflet) length() (MDAnalysis.core.topologyobjects.Bond method)

lengthUnit_factor (in module MDAnalysis.units) load() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.psa.PSAnalysis method) load_new() (MDAnalysis.core.AtomGroup.Universe method) load_offsets() (MDAnalysis.coordinates.xdrfile.core.TrjReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)

M

m (MDAnalysis.topology.tpr.obj.Atom attribute) major_pair() (in module MDAnalysis.analysis.nuclinfo) make_anchor() (MDAnalysis.core.AtomGroup.Universe method) make_density() (MDAnalysis.analysis.density.Density method) make_whole() (in module MDAnalysis.lib.mdamath), [1] mass (MDAnalysis.core.AtomGroup.Atom attribute) masses (in module MDAnalysis.topology.tables) (MDAnalysis.core.AtomGroup.AtomGroup attribute) matrix() (MDAnalysis.lib.transformations.Arcball method) matrix_id (MDAnalysis.analysis.psa.PSAPair attribute) mB (MDAnalysis.topology.tpr.obj.Atom attribute) MDAnalysis.analysis.align (module) MDAnalysis.analysis.base (module) MDAnalysis.analysis.contacts (module) MDAnalysis.analysis.density (module) MDAnalysis.analysis.distances (module) MDAnalysis.analysis.gnm (module) MDAnalysis.analysis.hbonds.hbond_analysis (module) MDAnalysis.analysis.hbonds.hbond_autocorrel (module) MDAnalysis.analysis.helanal (module) MDAnalysis.analysis.hole (module) MDAnalysis.analysis.leaflet (module) MDAnalysis.analysis.lineardensity (module) MDAnalysis.analysis.nuclinfo (module) MDAnalysis.analysis.polymer (module) MDAnalysis.analysis.psa (module) MDAnalysis.analysis.rdf (module) MDAnalysis.analysis.rms (module) MDAnalysis.analysis.waterdynamics (module) MDAnalysis.analysis.x3dna (module) MDAnalysis.coordinates.__init__ (module) MDAnalysis.coordinates.base (module) MDAnalysis.coordinates.core (module) MDAnalysis.coordinates.CRD (module) MDAnalysis.coordinates.DCD (module) MDAnalysis.coordinates.DLPoly (module) MDAnalysis.coordinates.DMS (module) MDAnalysis.coordinates.GMS (module) MDAnalysis.coordinates.GRO (module) MDAnalysis.coordinates.INPCRD (module) MDAnalysis.coordinates.LAMMPS (module) MDAnalysis.coordinates.MOL2 (module) MDAnalysis.coordinates.PDB (module) MDAnalysis.coordinates.pdb.extensions (module) MDAnalysis.coordinates.PDBQT (module) MDAnalysis.coordinates.PQR (module) MDAnalysis.coordinates.TRJ (module) MDAnalysis.coordinates.TRR (module) MDAnalysis.coordinates.TRZ (module) MDAnalysis.coordinates.xdrfile.core (module) MDAnalysis.coordinates.xdrfile.libxdrfile2 (module) MDAnalysis.coordinates.xdrfile.statno (module) MDAnalysis.coordinates.xdrfile.TRR (module) MDAnalysis.coordinates.xdrfile.XTC (module) MDAnalysis.coordinates.XTC (module) MDAnalysis.coordinates.XYZ (module) MDAnalysis.core.__init__ (module) MDAnalysis.core.AtomGroup (module) MDAnalysis.core.Selection (module) MDAnalysis.core.Timeseries (module) MDAnalysis.core.topologyobjects (module) MDAnalysis.exceptions (module) MDAnalysis.lib (module) MDAnalysis.lib._distances (module) MDAnalysis.lib._distances_openmp (module)

MDAnalysis.lib.distances (module) MDAnalysis.lib.log (module) MDAnalysis.lib.mdamath (module) MDAnalysis.lib.NeighborSearch (module) MDAnalysis.lib.qcprot (module) MDAnalysis.lib.transformations (module) MDAnalysis.lib.util (module) MDAnalysis.selections.base (module) MDAnalysis.selections.charmm (module) MDAnalysis.selections.gromacs (module) MDAnalysis.selections.jmol (module) MDAnalysis.selections.pymol (module) MDAnalysis.selections.vmd (module) MDAnalysis.topology.__init__ (module) MDAnalysis.topology.base (module) MDAnalysis.topology.core (module) MDAnalysis.topology.CRDParser (module) MDAnalysis.topology.DLPolyParser (module) MDAnalysis.topology.DMSParser (module) MDAnalysis.topology.ExtendedPDBParser (module) MDAnalysis.topology.GMSParser (module) MDAnalysis.topology.GROParser (module) MDAnalysis.topology.HoomdXMLParser (module) MDAnalysis.topology.LAMMPSParser (module) MDAnalysis.topology.MOL2Parser (module) MDAnalysis.topology.PDBParser (module) MDAnalysis.topology.PDBQTParser (module) MDAnalysis.topology.PQRParser (module) MDAnalysis.topology.PrimitivePDBParser (module) MDAnalysis.topology.PSFParser (module) MDAnalysis.topology.tables (module) MDAnalysis.topology.TOPParser (module) MDAnalysis.topology.tpr (module) MDAnalysis.topology.tpr.obj (module) MDAnalysis.topology.tpr.setting (module) MDAnalysis.topology.tpr.utils (module) MDAnalysis.topology.TPRParser (module) MDAnalysis.topology.XYZParser (module) MDAnalysis.units (module) MDAnalysis.version (module) MDAnalysis.visualization.streamlines (module) MDAnalysis.visualization.streamlines_3D (module) mean() (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) mean_std() (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) MeanSquareDisplacement (class in MDAnalysis.analysis.waterdynamics) Merge() (in module MDAnalysis.core.AtomGroup) min_radius() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) minor_pair() (in module MDAnalysis.analysis.nuclinfo) MissingDataWarning MODEL() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) MOL2Parser (class in MDAnalysis.topology.MOL2Parser) molb_natoms_mol (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nmol (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nposres_xA (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_nposres_xB (MDAnalysis.topology.tpr.obj.Molblock attribute) molb_type (MDAnalysis.topology.tpr.obj.Molblock attribute) Molblock (class in MDAnalysis.topology.tpr.obj) MoleculeKind (class in MDAnalysis.topology.tpr.obj) moltypes (MDAnalysis.topology.tpr.obj.Mtop attribute) moment_of_inertia() (MDAnalysis.core.AtomGroup.AtomGroup method) momentOfInertia() (MDAnalysis.core.AtomGroup.AtomGroup method) Mtop (class in MDAnalysis.topology.tpr.obj) MultiPDBWriter (class in MDAnalysis.coordinates.PDB)

N

n_atoms (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.XYZ.XYZReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.core.TrjReader attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute) N_Avogadro (in module MDAnalysis.units) n_frames (MDAnalysis.coordinates.TRJ.TRJReader attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.core.TrjReader attribute) n_residues (MDAnalysis.core.AtomGroup.AtomGroup attribute) n_segments (MDAnalysis.core.AtomGroup.AtomGroup attribute) name (MDAnalysis.core.AtomGroup.Atom attribute) NamedStream (class in MDAnalysis.lib.util) names (MDAnalysis.core.AtomGroup.AtomGroup attribute) natoms (MDAnalysis.topology.tpr.obj.TpxHeader attribute) NCDFReader (class in MDAnalysis.coordinates.TRJ) NCDFWriter (class in MDAnalysis.coordinates.TRJ) ndo_int() (in module MDAnalysis.topology.tpr.utils) ndo_ivec() (in module MDAnalysis.topology.tpr.utils) ndo_real() (in module MDAnalysis.topology.tpr.utils) ndo_rvec() (in module MDAnalysis.topology.tpr.utils) nearest_neighbors (MDAnalysis.analysis.psa.PSAnalysis attribute) (MDAnalysis.analysis.psa.PSAPair attribute) newname (MDAnalysis.analysis.psa.PDBToBinaryTraj attribute) next() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.lib.transformations.Arcball method)

ngtc (MDAnalysis.topology.tpr.obj.TpxHeader attribute) nmolblock (MDAnalysis.topology.tpr.obj.Mtop attribute) nmoltype (MDAnalysis.topology.tpr.obj.Mtop attribute) NoDataError, [1] norm() (in module MDAnalysis.lib.mdamath), [1] normal() (in module MDAnalysis.lib.mdamath), [1] npaths (MDAnalysis.analysis.psa.PSAPair attribute) nr (MDAnalysis.topology.tpr.obj.Atoms attribute) (MDAnalysis.topology.tpr.obj.Ilist attribute) nres (MDAnalysis.topology.tpr.obj.Atoms attribute) ntypes (MDAnalysis.topology.tpr.obj.Params attribute) NucleicBackboneSelection (class in MDAnalysis.core.Selection) NucleicSelection (class in MDAnalysis.core.Selection) NucleicSugarSelection (class in MDAnalysis.core.Selection) NullHandler (class in MDAnalysis.lib.log) number (MDAnalysis.core.AtomGroup.Atom attribute) (MDAnalysis.topology.tpr.obj.TpxHeader attribute) 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 (MDAnalysis.core.AtomGroup.AtomGroup attribute) occupancy (MDAnalysis.core.AtomGroup.Atom attribute) omega_selection() (MDAnalysis.core.AtomGroup.Residue method) open_trajectory() (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.TRZ.TRZReader method), [1] (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.core.TrjReader method) openany() (in module MDAnalysis.lib.util)

optimize_cutoff() (in module MDAnalysis.analysis.leaflet) order_list() (in module MDAnalysis.analysis.gnm) OtherWriter() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) output_exists() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method)

P

pack_into_box() (MDAnalysis.core.AtomGroup.AtomGroup method) packIntoBox() (MDAnalysis.core.AtomGroup.AtomGroup method) pair_id (MDAnalysis.analysis.psa.PSAPair attribute) Params (class in MDAnalysis.topology.tpr.obj) parse() (MDAnalysis.core.Selection.SelectionParser method) (MDAnalysis.topology.CRDParser.CRDParser method) (MDAnalysis.topology.DMSParser.DMSParser method) (MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser method) (MDAnalysis.topology.GMSParser.GMSParser method) (MDAnalysis.topology.GROParser.GROParser method) (MDAnalysis.topology.HoomdXMLParser.HoomdXMLParser method) (MDAnalysis.topology.LAMMPSParser.DATAParser method) (MDAnalysis.topology.MOL2Parser.MOL2Parser method) (MDAnalysis.topology.PDBParser.PDBParser method) (MDAnalysis.topology.PDBQTParser.PDBQTParser method) (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PSFParser.PSFParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) (MDAnalysis.topology.TOPParser.TOPParser method) (MDAnalysis.topology.TPRParser.TPRParser method) (MDAnalysis.topology.XYZParser.XYZParser method) parse_FORTRAN_format() (MDAnalysis.lib.util.FORTRANReader method) parse_residue() (in module MDAnalysis.lib.util) partner() (MDAnalysis.core.topologyobjects.Bond method) PATH, [1] Path (class in MDAnalysis.analysis.psa) path (MDAnalysis.analysis.psa.Path attribute) path_select (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) paths (MDAnalysis.analysis.psa.PSAnalysis attribute) 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) PDBToBinaryTraj (class in MDAnalysis.analysis.psa) PDBWriter (class in MDAnalysis.coordinates.PDB) perform_fit() (MDAnalysis.analysis.polymer.PersistenceLength method) PersistenceLength (class in MDAnalysis.analysis.polymer) phase_as() (in module MDAnalysis.analysis.nuclinfo) phase_cp() (in module MDAnalysis.analysis.nuclinfo) phi_selection() (MDAnalysis.core.AtomGroup.Residue method) place() (MDAnalysis.lib.transformations.Arcball method) plot() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.polymer.PersistenceLength method) (MDAnalysis.analysis.psa.PSAnalysis method) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) plot3D() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) plot_annotated_heatmap() (MDAnalysis.analysis.psa.PSAnalysis method) plot_nearest_neighbors() (MDAnalysis.analysis.psa.PSAnalysis method)

plot_qavg() (MDAnalysis.analysis.contacts.ContactAnalysis1 method) pos (MDAnalysis.core.AtomGroup.Atom attribute) position (MDAnalysis.core.AtomGroup.Atom attribute) positions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute) potential_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) PQRParser (class in MDAnalysis.topology.PQRParser) PQRReader (class in MDAnalysis.coordinates.PQR) PQRWriter (class in MDAnalysis.coordinates.PQR) precision (MDAnalysis.topology.tpr.obj.TpxHeader attribute) pressure (MDAnalysis.coordinates.TRZ.Timestep attribute) pressure_tensor (MDAnalysis.coordinates.TRZ.Timestep attribute) PrimitivePDBParser (class in MDAnalysis.topology.PrimitivePDBParser) PrimitivePDBReader (class in MDAnalysis.coordinates.PDB) PrimitivePDBWriter (class in MDAnalysis.coordinates.PDB) principal_axes() (MDAnalysis.core.AtomGroup.AtomGroup method) principalAxes() (MDAnalysis.core.AtomGroup.AtomGroup method) process() (MDAnalysis.topology.tpr.obj.InteractionKind method) profiles (MDAnalysis.analysis.hole.HOLE attribute) (MDAnalysis.analysis.hole.HOLEtraj attribute) (MDAnalysis.analysis.x3dna.X3DNA attribute) (MDAnalysis.analysis.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) psa_pairs (MDAnalysis.analysis.psa.PSAnalysis attribute) PSAnalysis (class in MDAnalysis.analysis.psa) PSAPair (class in MDAnalysis.analysis.psa) pseudo_dihe_baseflip() (in module MDAnalysis.analysis.nuclinfo) PSFParser (class in MDAnalysis.topology.PSFParser) psi_selection() (MDAnalysis.core.AtomGroup.Residue method) ptype (MDAnalysis.topology.tpr.obj.Atom attribute)

Q

q (MDAnalysis.topology.tpr.obj.Atom attribute) qarray() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) qB (MDAnalysis.topology.tpr.obj.Atom attribute)

qN() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) quaternion_imag() (in module MDAnalysis.lib.transformations) quaternion_real() (in module MDAnalysis.lib.transformations)

R

r_cov (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) radii (MDAnalysis.core.AtomGroup.AtomGroup attribute) radius (MDAnalysis.core.AtomGroup.Atom attribute) radius_of_gyration() (MDAnalysis.core.AtomGroup.AtomGroup method) radiusOfGyration() (MDAnalysis.core.AtomGroup.AtomGroup method) RangeSelection (class in MDAnalysis.core.Selection) read() (MDAnalysis.lib.util.FORTRANReader method) read_DATA_timestep() (MDAnalysis.topology.LAMMPSParser.DATAParser method) read_tpxheader() (in module MDAnalysis.topology.tpr.utils) read_trr() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_trr_n_frames() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_trr_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc_n_frames() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) readable() (MDAnalysis.lib.util.NamedStream method) Reader (class in MDAnalysis.coordinates.base) reader() (in module MDAnalysis.coordinates.core) realpath() (in module MDAnalysis.lib.util) ref_frame (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) ref_select (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) reflection_from_matrix() (in module MDAnalysis.lib.transformations) register() (MDAnalysis.core.__init__.Flags method) rel (MDAnalysis.topology.tpr.obj.Box attribute) remap_angles() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_bonds() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_dihe() (MDAnalysis.topology.tpr.obj.MoleculeKind method) remap_impr() (MDAnalysis.topology.tpr.obj.MoleculeKind method) REMARK() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) remark_max_length (MDAnalysis.coordinates.PDB.PrimitivePDBWriter attribute) remove_anchor() (MDAnalysis.core.AtomGroup.Universe method) reppow (MDAnalysis.topology.tpr.obj.Params attribute)

resample() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) resample_factor() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) reset() (MDAnalysis.lib.util.NamedStream method) resid (MDAnalysis.core.AtomGroup.Atom attribute) resids (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.ResidueGroup attribute) Residue (class in MDAnalysis.core.AtomGroup) residue (MDAnalysis.core.AtomGroup.Atom attribute) ResidueGroup (class in MDAnalysis.core.AtomGroup) ResidueNameSelection (class in MDAnalysis.core.Selection) residues (MDAnalysis.core.AtomGroup.AtomGroup attribute) resind (MDAnalysis.topology.tpr.obj.Atom attribute) resname (MDAnalysis.core.AtomGroup.Atom attribute) resnames (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.ResidueGroup attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) resnum (MDAnalysis.core.AtomGroup.Atom attribute) resnums (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.ResidueGroup attribute) rewind() (MDAnalysis.coordinates.base.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.TRJ.TRJReader method) (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) rms_fit_trj() (in module MDAnalysis.analysis.align) RMSD (class in MDAnalysis.analysis.rms) rmsd (MDAnalysis.analysis.rms.RMSD attribute) rmsd() (in module MDAnalysis.analysis.rms) RMSF (class in MDAnalysis.analysis.rms) rmsf (MDAnalysis.analysis.rms.RMSF attribute), [1] rotate() (MDAnalysis.core.AtomGroup.AtomGroup method) rotateby() (MDAnalysis.core.AtomGroup.AtomGroup 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.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 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.psa.PSAnalysis method) (MDAnalysis.analysis.psa.Path 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) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) run_hole() (MDAnalysis.analysis.hole.HOLEtraj method) run_pairs_analysis() (MDAnalysis.analysis.psa.PSAnalysis method) run_x3dna() (MDAnalysis.analysis.x3dna.X3DNAtraj method)

S

save() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.rms.RMSD method) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) save_offsets() (MDAnalysis.coordinates.xdrfile.core.TrjReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader 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) scale_from_matrix() (in module MDAnalysis.lib.transformations) search() (MDAnalysis.lib.NeighborSearch.AtomNeighborSearch method) seek() (MDAnalysis.lib.util.NamedStream method) seekable() (MDAnalysis.lib.util.NamedStream method) segid (MDAnalysis.core.AtomGroup.Atom attribute) segids (MDAnalysis.core.AtomGroup.AtomGroup attribute) (MDAnalysis.core.AtomGroup.ResidueGroup attribute) (MDAnalysis.core.AtomGroup.SegmentGroup attribute) Segment (class in MDAnalysis.core.AtomGroup) SegmentGroup (class in MDAnalysis.core.AtomGroup) SegmentNameSelection (class in MDAnalysis.core.Selection) segments (MDAnalysis.core.AtomGroup.AtomGroup attribute) select_atoms() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.Universe method) select_bonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) selectAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.Universe method) selectBonds() (MDAnalysis.core.topologyobjects.TopologyGroup method) SelectionError, [1] SelectionParser (class in MDAnalysis.core.Selection) SelectionWarning, [1] SelectionWriter (class in MDAnalysis.selections.base) (class in MDAnalysis.selections.charmm) (class in MDAnalysis.selections.gromacs) (class in MDAnalysis.selections.jmol) (class in MDAnalysis.selections.pymol) (class in MDAnalysis.selections.vmd) self_distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.lib.distances), [1] seq2str() (in module MDAnalysis.analysis.hole) sequence() (MDAnalysis.core.AtomGroup.AtomGroup method) serials (MDAnalysis.core.AtomGroup.AtomGroup attribute) set() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) (MDAnalysis.core.AtomGroup.SegmentGroup method) set_altLoc() (MDAnalysis.core.AtomGroup.AtomGroup method) set_altLocs() (MDAnalysis.core.AtomGroup.AtomGroup method) set_bfactor() (MDAnalysis.core.AtomGroup.AtomGroup method) set_bfactors() (MDAnalysis.core.AtomGroup.AtomGroup method) set_charge() (MDAnalysis.core.AtomGroup.AtomGroup method) set_charges() (MDAnalysis.core.AtomGroup.AtomGroup method) set_forces() (MDAnalysis.core.AtomGroup.AtomGroup method) set_mass() (MDAnalysis.core.AtomGroup.AtomGroup method) set_masses() (MDAnalysis.core.AtomGroup.AtomGroup method) set_name() (MDAnalysis.core.AtomGroup.AtomGroup method) set_names() (MDAnalysis.core.AtomGroup.AtomGroup method) set_occupancies() (MDAnalysis.core.AtomGroup.AtomGroup method)

set_positions() (MDAnalysis.core.AtomGroup.AtomGroup method) set_radii() (MDAnalysis.core.AtomGroup.AtomGroup method) set_radius() (MDAnalysis.core.AtomGroup.AtomGroup method) set_resid() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resids() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resname() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resnames() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resnum() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resnums() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_segid() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.SegmentGroup method) set_segids() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.SegmentGroup method) set_serial() (MDAnalysis.core.AtomGroup.AtomGroup method) set_serials() (MDAnalysis.core.AtomGroup.AtomGroup method) set_type() (MDAnalysis.core.AtomGroup.AtomGroup method) set_types() (MDAnalysis.core.AtomGroup.AtomGroup method) set_velocities() (MDAnalysis.core.AtomGroup.AtomGroup method) setaxes() (MDAnalysis.lib.transformations.Arcball method) setconstrain() (MDAnalysis.lib.transformations.Arcball method) shape (MDAnalysis.core.Timeseries.Timeseries attribute) shape_parameter() (MDAnalysis.core.AtomGroup.AtomGroup method) shapeParameter() (MDAnalysis.core.AtomGroup.AtomGroup method) shear_from_matrix() (in module MDAnalysis.lib.transformations) SIMPLE2_RAD (in module MDAnalysis.analysis.hole) size (MDAnalysis.topology.tpr.obj.Box attribute) sizes() (MDAnalysis.analysis.leaflet.LeafletFinder method) skip_timestep (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] SloppyPDBIO (class in MDAnalysis.coordinates.pdb.extensions) SloppyStructureBuilder (class in MDAnalysis.coordinates.pdb.extensions) solve() (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) sorted_profiles_iter() (MDAnalysis.analysis.hole.HOLE method) (MDAnalysis.analysis.hole.HOLEtraj method) (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) speedUnit_factor (in module MDAnalysis.units) split() (MDAnalysis.core.AtomGroup.AtomGroup method) sqnorm() (in module MDAnalysis.analysis.psa) start_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) std() (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) stop_logging() (in module MDAnalysis) (in module MDAnalysis.lib.log) stp() (in module MDAnalysis.lib.mdamath), [1] StreamWarning StringSelection (class in MDAnalysis.core.Selection) SUPPORTED_VERSIONS (in module MDAnalysis.topology.tpr) (in module MDAnalysis.topology.tpr.setting) SurvivalProbability (class in MDAnalysis.analysis.waterdynamics)

T

table (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) TABLE_ATOMELEMENTS (in module MDAnalysis.topology.tables) TABLE_MASSES (in module MDAnalysis.topology.tables) tell() (MDAnalysis.lib.util.NamedStream method) temperature (MDAnalysis.coordinates.TRZ.Timestep attribute) time (MDAnalysis.coordinates.base.ChainReader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) Timeseries (class in MDAnalysis.core.Timeseries) timeseries (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) timeseries() (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) TimeseriesCollection (class in MDAnalysis.core.Timeseries) Timestep (class in MDAnalysis.coordinates.base) (class in MDAnalysis.coordinates.DCD) (class in MDAnalysis.coordinates.TRJ) (class in MDAnalysis.coordinates.TRZ), [1] (class in MDAnalysis.coordinates.xdrfile.TRR) (class in MDAnalysis.coordinates.xdrfile.XTC) (class in MDAnalysis.coordinates.xdrfile.core) timesteps (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) timesteps_by_type() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) timeUnit_factor (in module MDAnalysis.units) TITLE() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) to_indices() (MDAnalysis.core.topologyobjects.TopologyGroup method) to_path() (MDAnalysis.analysis.psa.Path method) topDict (MDAnalysis.core.topologyobjects.TopologyGroup attribute) TopologyDict (class in MDAnalysis.core.topologyobjects) TopologyGroup (class in MDAnalysis.core.topologyobjects) TopologyObject (class in MDAnalysis.core.topologyobjects) TopologyReader (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.AtomGroup.AtomGroup method)

total_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) total_mass() (MDAnalysis.core.AtomGroup.AtomGroup method) totalCharge() (MDAnalysis.core.AtomGroup.AtomGroup method) totalMass() (MDAnalysis.core.AtomGroup.AtomGroup method) totaltime (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) tp (MDAnalysis.topology.tpr.obj.Atom attribute) TPRParser (class in MDAnalysis.topology.TPRParser) TPRTopology (class in MDAnalysis.topology.tpr.obj) TpxHeader (class in MDAnalysis.topology.tpr.obj) trajectory (MDAnalysis.core.AtomGroup.Universe attribute) transform() (MDAnalysis.core.AtomGroup.AtomGroup method) transform_RtoS() (in module MDAnalysis.lib.distances), [1] transform_StoR() (in module MDAnalysis.lib.distances), [1] translate() (MDAnalysis.core.AtomGroup.AtomGroup method) translation_from_matrix() (in module MDAnalysis.lib.transformations) triclinic_box() (in module MDAnalysis.lib.mdamath), [1] triclinic_dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) triclinic_vectors() (in module MDAnalysis.lib.mdamath), [1] TRJReader (class in MDAnalysis.coordinates.TRJ) TrjReader (class in MDAnalysis.coordinates.xdrfile.core) TrjWriter (class in MDAnalysis.coordinates.xdrfile.core) TRRReader (class in MDAnalysis.coordinates.xdrfile.TRR) TRRWriter (class in MDAnalysis.coordinates.xdrfile.TRR) truncate() (MDAnalysis.lib.util.NamedStream method) TRZReader (class in MDAnalysis.coordinates.TRZ), [1] TRZWriter (class in MDAnalysis.coordinates.TRZ), [1] ts (MDAnalysis.core.AtomGroup.AtomGroup attribute) type (MDAnalysis.core.AtomGroup.Atom attribute) (MDAnalysis.core.topologyobjects.TopologyObject attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) typeB (MDAnalysis.topology.tpr.obj.Atom attribute) (MDAnalysis.topology.tpr.obj.Atoms attribute) types (MDAnalysis.core.AtomGroup.AtomGroup attribute) types() (MDAnalysis.core.topologyobjects.TopologyGroup method)

U

u_fitted (MDAnalysis.analysis.psa.Path attribute) u_original (MDAnalysis.analysis.psa.Path attribute) u_reference (MDAnalysis.analysis.psa.Path attribute) (MDAnalysis.analysis.psa.PSAnalysis attribute) unique() (in module MDAnalysis.core.Selection) unit_types (in module MDAnalysis.units)

units (MDAnalysis.coordinates.base.IObase attribute) Universe (class in MDAnalysis.core.AtomGroup) universe (MDAnalysis.analysis.psa.PDBToBinaryTraj attribute) (MDAnalysis.core.AtomGroup.Atom attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute) universes (MDAnalysis.analysis.psa.PSAnalysis attribute) update() (MDAnalysis.analysis.leaflet.LeafletFinder method) (MDAnalysis.core.__init__.Flags method) (MDAnalysis.lib.log.ProgressMeter method)

V

v (MDAnalysis.topology.tpr.obj.Box attribute) value() (MDAnalysis.core.topologyobjects.Angle method) (MDAnalysis.core.topologyobjects.Bond method) (MDAnalysis.core.topologyobjects.Dihedral method) values() (MDAnalysis.core.topologyobjects.TopologyGroup method) velocities (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute) (MDAnalysis.core.AtomGroup.AtomGroup attribute)

velocity (MDAnalysis.core.AtomGroup.Atom attribute) ver_str (MDAnalysis.topology.tpr.obj.TpxHeader attribute) volume (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute) (MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)

W

water (in module MDAnalysis.units) WaterDipole (class in MDAnalysis.core.Timeseries) WaterOrientationalRelaxation (class in MDAnalysis.analysis.waterdynamics) wc_pair() (in module MDAnalysis.analysis.nuclinfo) which() (in module MDAnalysis.lib.util) wrap() (MDAnalysis.core.AtomGroup.AtomGroup method) writable() (MDAnalysis.lib.util.NamedStream method) write() (MDAnalysis.coordinates.base.Writer method) (MDAnalysis.coordinates.CRD.CRDWriter method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.GRO.GROWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.PDBWriter method) (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) (MDAnalysis.coordinates.PQR.PQRWriter method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.selections.base.SelectionWriter method) (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) write_all_timesteps() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) write_next_timestep() (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DCDWriter method) (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.TRJ.NCDFWriter method) (MDAnalysis.coordinates.XYZ.XYZWriter method) (MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method) (MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method) (MDAnalysis.coordinates.xdrfile.core.TrjWriter method) write_pdb() (in module MDAnalysis.coordinates.pdb.extensions)

write_preamble() (MDAnalysis.selections.charmm.SelectionWriter method) (MDAnalysis.selections.gromacs.SelectionWriter method) (MDAnalysis.selections.jmol.SelectionWriter method) (MDAnalysis.selections.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) write_selection() (MDAnalysis.analysis.leaflet.LeafletFinder method) (MDAnalysis.core.AtomGroup.AtomGroup method) write_simplerad2() (in module MDAnalysis.analysis.hole) write_trr() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) write_xtc() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) writePDB() (MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter method) writePSF() (MDAnalysis.topology.LAMMPSParser.LAMMPSDataConverter method) Writer (class in MDAnalysis.coordinates.base) writer() (in module MDAnalysis.coordinates.core) Writer() (MDAnalysis.coordinates.CRD.CRDReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GRO.GROReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.PDBReader method) (MDAnalysis.coordinates.PDB.PrimitivePDBReader method) (MDAnalysis.coordinates.PDBQT.PDBQTReader method) (MDAnalysis.coordinates.PQR.PQRReader method) (MDAnalysis.coordinates.TRJ.NCDFReader method) (MDAnalysis.coordinates.XYZ.XYZReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.core.TrjReader method)

X

X3DNA (class in MDAnalysis.analysis.x3dna) X3DNAtraj (class in MDAnalysis.analysis.x3dna) xdrfile_close() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) xdrfile_open() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) XTCReader (class in MDAnalysis.coordinates.xdrfile.XTC)

XTCWriter (class in MDAnalysis.coordinates.xdrfile.XTC) XYZParser (class in MDAnalysis.topology.XYZParser) XYZReader (class in MDAnalysis.coordinates.XYZ) XYZWriter (class in MDAnalysis.coordinates.XYZ)