Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X

_

__eq__() (MDAnalysis.coordinates.base.Timestep method)
__getitem__() (MDAnalysis.coordinates.base.Timestep method)
__init__() (MDAnalysis.coordinates.base.Timestep method)
(MDAnalysis.selections.base.SelectionWriter method)
__iter__() (MDAnalysis.coordinates.base.Timestep method)
__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)
_compressed_formats (in module MDAnalysis.coordinates.__init__)
_fill_cache() (MDAnalysis.core.AtomGroup.AtomGroup method)
_forces (MDAnalysis.coordinates.base.Timestep attribute)
(MDAnalysis.coordinates.TRJ.Timestep attribute)
_frame_writers (in module MDAnalysis.coordinates.__init__)
_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)
_topology_coordinates_readers (in module MDAnalysis.coordinates.__init__)
_trajectory_readers (in module MDAnalysis.coordinates.__init__)
_trajectory_writers (in module MDAnalysis.coordinates.__init__)
_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)
Angle (class in MDAnalysis.core.Timeseries)
angle (MDAnalysis.core.AtomGroup.AtomGroup attribute)
angle() (in module MDAnalysis.lib.mdamath), [1]
angles (MDAnalysis.core.AtomGroup.Atom attribute), [1]
(MDAnalysis.core.AtomGroup.AtomGroup attribute)
(MDAnalysis.core.AtomGroup.Universe attribute)
(MDAnalysis.topology.tpr.obj.TPRTopology attribute)
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.PDB.PrimitivePDBWriter method)
(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)
atomelements (in module MDAnalysis.topology.tables)
AtomGroup (class in MDAnalysis.core.AtomGroup)
AtomKind (class in MDAnalysis.topology.tpr.obj)
atomnames (MDAnalysis.topology.tpr.obj.Atoms attribute)
AtomNeighborSearch (class in MDAnalysis.lib.NeighborSearch)
atomnumber (MDAnalysis.topology.tpr.obj.Atom attribute)
Atoms (class in MDAnalysis.topology.tpr.obj)
atoms (MDAnalysis.core.AtomGroup.AtomGroup attribute)
(MDAnalysis.topology.tpr.obj.Atoms attribute)
(MDAnalysis.topology.tpr.obj.TPRTopology attribute)

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)
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)
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)
CASelection (class in MDAnalysis.core.Selection)
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)
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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRZ.TRZReader method), [1]
(MDAnalysis.coordinates.TRZ.TRZWriter method), [1]
(MDAnalysis.coordinates.XTC.XTCReader method)
(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.PSA 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), [1]
ContactAnalysis1.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.GRO.GROWriter method)
(MDAnalysis.coordinates.LAMMPS.DCDWriter method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.Timestep method)
(MDAnalysis.coordinates.XTC.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.TRR.Timestep method)
(MDAnalysis.coordinates.XTC.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.PSA 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_trajectory() (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)
dihedral (MDAnalysis.core.AtomGroup.AtomGroup attribute)
dihedral() (in module MDAnalysis.lib.mdamath), [1]
dihedrals (MDAnalysis.core.AtomGroup.Atom attribute), [1]
(MDAnalysis.core.AtomGroup.AtomGroup attribute)
(MDAnalysis.core.AtomGroup.Universe attribute)
DIM (in module MDAnalysis.coordinates.xdrfile.libxdrfile2)
dimensions (MDAnalysis.coordinates.base.Timestep attribute)
(MDAnalysis.coordinates.DCD.Timestep attribute)
(MDAnalysis.coordinates.TRR.Timestep attribute)
(MDAnalysis.coordinates.TRZ.Timestep attribute), [1]
(MDAnalysis.coordinates.XTC.Timestep attribute)
(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)
Distance (class in MDAnalysis.core.Timeseries)
distance_array() (in module MDAnalysis.analysis.distances)
(in module MDAnalysis.lib.distances), [1]
(in module MDAnalysis.lib.parallel.distances)
distance_array_serial() (in module MDAnalysis.lib.parallel.distances)
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.Timestep attribute)
(MDAnalysis.coordinates.LAMMPS.DATAReader attribute)
(MDAnalysis.coordinates.TRR.TRRReader attribute)
(MDAnalysis.coordinates.TRR.Timestep attribute)
(MDAnalysis.coordinates.XTC.Timestep attribute)
(MDAnalysis.coordinates.XTC.XTCReader 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)

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)
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.PSA attribute)
filename() (in module MDAnalysis.lib.util)
fileno() (MDAnalysis.lib.util.NamedStream method)
FinishTimeException
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.XTC.Timestep attribute)
(MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)
(MDAnalysis.core.AtomGroup.AtomGroup attribute)
forceUnit_factor (in module MDAnalysis.units)
format (MDAnalysis.coordinates.base.IObase attribute)
(MDAnalysis.coordinates.xdrfile.core.TrjReader attribute)
(MDAnalysis.coordinates.xdrfile.core.TrjWriter attribute)
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.TRR.TRRReader attribute)
(MDAnalysis.coordinates.TRZ.Timestep attribute)
(MDAnalysis.coordinates.XTC.XTCReader attribute)
(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)
(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)
frechet_names (in module MDAnalysis.analysis.psa)
from_coordinates() (MDAnalysis.coordinates.base.Timestep class method)
(MDAnalysis.coordinates.DCD.Timestep method)
(MDAnalysis.coordinates.TRR.Timestep method)
(MDAnalysis.coordinates.XTC.Timestep method)
(MDAnalysis.coordinates.xdrfile.TRR.Timestep method)
(MDAnalysis.coordinates.xdrfile.XTC.Timestep method)
from_timestep() (MDAnalysis.coordinates.base.Timestep class method)
(MDAnalysis.coordinates.DCD.Timestep method)
(MDAnalysis.coordinates.TRR.Timestep method)
(MDAnalysis.coordinates.XTC.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.PSA 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.PDB.PDBReader method)
(MDAnalysis.coordinates.PDBQT.PDBQTReader method)
get_charges() (MDAnalysis.coordinates.PQR.PQRReader method)
get_conversion_factor() (in module MDAnalysis.units)
get_distance_array() (MDAnalysis.analysis.contacts.ContactAnalysis method)
get_forces() (MDAnalysis.core.AtomGroup.AtomGroup method)
get_matching_atoms() (in module MDAnalysis.analysis.align)
get_occupancy() (MDAnalysis.coordinates.PDB.PrimitivePDBReader method)
(MDAnalysis.coordinates.PDBQT.PDBQTReader method)
get_parser_for() (in module MDAnalysis.topology.core)
get_path_metric_func() (in module MDAnalysis.analysis.psa)
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)
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.XTC.Timestep attribute)
(MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)
has_positions (MDAnalysis.coordinates.base.Timestep attribute)
(MDAnalysis.coordinates.DCD.Timestep attribute)
(MDAnalysis.coordinates.XTC.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.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.XTC.Timestep attribute)
(MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)
hasmethod() (in module MDAnalysis.lib.util)
hausdorff() (in module MDAnalysis.analysis.psa)
hausdorff_names (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)
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)
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)
IObase (class in MDAnalysis.coordinates.base)
iparams (MDAnalysis.topology.tpr.obj.Params attribute)
is_anchor (MDAnalysis.core.AtomGroup.Universe attribute)
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

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)
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.PSA method)
load_new() (MDAnalysis.core.AtomGroup.Universe method)
load_offsets() (MDAnalysis.coordinates.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)
(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)
(MDAnalysis.coordinates.xdrfile.core.TrjReader 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)
mB (MDAnalysis.topology.tpr.obj.Atom attribute)
MDAnalysis.analysis.align (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.nuclinfo (module)
MDAnalysis.analysis.psa (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._distances (module)
MDAnalysis.lib.distances (module)
MDAnalysis.lib.log (module)
MDAnalysis.lib.mdamath (module)
MDAnalysis.lib.NeighborSearch (module)
MDAnalysis.lib.parallel (module)
MDAnalysis.lib.parallel.distances (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.TRR.TRRReader attribute)
(MDAnalysis.coordinates.TRR.Timestep attribute)
(MDAnalysis.coordinates.TRZ.TRZReader attribute), [1]
(MDAnalysis.coordinates.TRZ.Timestep attribute)
(MDAnalysis.coordinates.XTC.Timestep attribute)
(MDAnalysis.coordinates.XTC.XTCReader 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.TRR.TRRReader attribute)
(MDAnalysis.coordinates.TRZ.TRZReader attribute), [1]
(MDAnalysis.coordinates.XTC.XTCReader attribute)
(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)
next() (MDAnalysis.coordinates.DCD.DCDReader method)
(MDAnalysis.coordinates.LAMMPS.DCDReader method)
(MDAnalysis.coordinates.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader 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]
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

omega_selection() (MDAnalysis.core.AtomGroup.Residue method)
open_trajectory() (MDAnalysis.coordinates.TRJ.TRJReader method)
(MDAnalysis.coordinates.TRR.TRRReader method)
(MDAnalysis.coordinates.TRZ.TRZReader method), [1]
(MDAnalysis.coordinates.XTC.XTCReader method)
(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.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader 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)
Params (class in MDAnalysis.topology.tpr.obj)
parse() (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)
PATH, [1]
Path (class in MDAnalysis.analysis.psa)
path (MDAnalysis.analysis.psa.Path attribute)
path_select (MDAnalysis.analysis.psa.Path attribute)
(MDAnalysis.analysis.psa.PSA attribute)
paths (MDAnalysis.analysis.psa.PSA attribute)
PDBParser (class in MDAnalysis.topology.PDBParser)
PDBQTParser (class in MDAnalysis.topology.PDBQTParser)
PDBQTReader (class in MDAnalysis.coordinates.PDBQT)
PDBQTWriter (class in MDAnalysis.coordinates.PDBQT)
PDBReader (class in MDAnalysis.coordinates.PDB)
PDBWriter (class in MDAnalysis.coordinates.PDB)
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.psa.PSA method)
(MDAnalysis.analysis.x3dna.X3DNA method)
(MDAnalysis.analysis.x3dna.X3DNAtraj method)
plot3D() (MDAnalysis.analysis.hole.HOLE method)
(MDAnalysis.analysis.hole.HOLEtraj 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.XTC.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)
prot_res (MDAnalysis.core.Selection.ProteinSelection attribute)
ProteinSelection (class in MDAnalysis.core.Selection)
PSA (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)
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.PSA attribute)
ref_select (MDAnalysis.analysis.psa.Path attribute)
(MDAnalysis.analysis.psa.PSA 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)
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.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader 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.PSA 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_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.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader method)
(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)
(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)
(MDAnalysis.coordinates.xdrfile.core.TrjReader method)
save_paths() (MDAnalysis.analysis.psa.PSA method)
save_result() (MDAnalysis.analysis.psa.PSA 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)
segments (MDAnalysis.core.AtomGroup.AtomGroup attribute)
select_atoms() (MDAnalysis.core.AtomGroup.AtomGroup method)
(MDAnalysis.core.AtomGroup.Universe method)
selectAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method)
(MDAnalysis.core.AtomGroup.Universe 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_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
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.TRR.TRRReader attribute)
(MDAnalysis.coordinates.TRR.Timestep attribute)
(MDAnalysis.coordinates.TRZ.Timestep attribute)
(MDAnalysis.coordinates.XTC.Timestep attribute)
(MDAnalysis.coordinates.XTC.XTCReader 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.TRR)
(class in MDAnalysis.coordinates.TRZ), [1]
(class in MDAnalysis.coordinates.XTC)
(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_path() (MDAnalysis.analysis.psa.Path method)
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.TRR.TRRReader attribute)
(MDAnalysis.coordinates.XTC.XTCReader 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.TRR.Timestep attribute)
(MDAnalysis.coordinates.XTC.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.TRR)
(class in MDAnalysis.coordinates.xdrfile.TRR)
TRRWriter (class in MDAnalysis.coordinates.TRR)
(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.topology.tpr.obj.Atoms attribute)
typeB (MDAnalysis.topology.tpr.obj.Atom attribute)
(MDAnalysis.topology.tpr.obj.Atoms attribute)
types (MDAnalysis.core.AtomGroup.AtomGroup attribute)

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.PSA attribute)
unit_types (in module MDAnalysis.units)
units (MDAnalysis.coordinates.base.IObase attribute)
(MDAnalysis.coordinates.xdrfile.core.TrjReader attribute)
(MDAnalysis.coordinates.xdrfile.core.TrjWriter attribute)
Universe (class in MDAnalysis.core.AtomGroup)
universe (MDAnalysis.core.AtomGroup.Atom attribute)
(MDAnalysis.core.AtomGroup.AtomGroup attribute)
universes (MDAnalysis.analysis.psa.PSA 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)
velocities (MDAnalysis.coordinates.base.Timestep attribute)
(MDAnalysis.coordinates.DCD.Timestep attribute)
(MDAnalysis.coordinates.XTC.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.TRR.Timestep attribute)
(MDAnalysis.coordinates.XTC.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.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRWriter method)
(MDAnalysis.coordinates.XTC.XTCWriter 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.TRR.TRRReader method)
(MDAnalysis.coordinates.XTC.XTCReader 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)
(class in MDAnalysis.coordinates.XTC)
XTCWriter (class in MDAnalysis.coordinates.xdrfile.XTC)
(class in MDAnalysis.coordinates.XTC)
XYZParser (class in MDAnalysis.topology.XYZParser)
XYZReader (class in MDAnalysis.coordinates.XYZ)
XYZWriter (class in MDAnalysis.coordinates.XYZ)