Index

_

__getitem__() (MDAnalysis.coordinates.TRJ.NCDFReader method) __init__() (MDAnalysis.selections.base.SelectionWriter method) __iter__() (MDAnalysis.coordinates.TRJ.NCDFReader method) _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) _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) _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_readers_permissive (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_principalAxis() (MDAnalysis.core.AtomGroup.AtomGroup method) alignto() (in module MDAnalysis.analysis.align) all_get_indices() (MDAnalysis.KDTree.KDTree.KDTree method) all_get_radii() (MDAnalysis.KDTree.KDTree.KDTree method) all_search() (MDAnalysis.KDTree.KDTree.KDTree method) altLoc (MDAnalysis.core.AtomGroup.Atom attribute) Angle (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.topology.core) angle() (in module MDAnalysis.core.util) (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.topology.core.Angle method) angles (MDAnalysis.core.AtomGroup.Atom attribute), [1] angles() (MDAnalysis.topology.core.TopologyGroup method) anyopen() (in module MDAnalysis.core.util) ApplicationError (class in MDAnalysis.analysis.hole) (class in MDAnalysis.analysis.x3dna)

applyPBC() (in module MDAnalysis.core.distances) Arcball (class in MDAnalysis.core.transformations) arcball_nearest_axis() (in module MDAnalysis.core.transformations) asiterable() (in module MDAnalysis.core.util) asphericity() (MDAnalysis.core.AtomGroup.AtomGroup method) asUniverse() (in module MDAnalysis.core.AtomGroup) Atom (class in MDAnalysis.core.AtomGroup) (class in MDAnalysis.core.Timeseries) ATOM() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) atomelements (in module MDAnalysis.topology.tables) AtomGroup (class in MDAnalysis.core.AtomGroup) atomgroup_intersection() (MDAnalysis.topology.core.TopologyGroup method) AtomNeighborSearch (class in MDAnalysis.KDTree.NeighborSearch) atoms (MDAnalysis.core.AtomGroup.AtomGroup attribute)

B

BackboneSelection (class in MDAnalysis.core.Selection) backup_file() (in module MDAnalysis.analysis.gnm) BaseSelection (class in MDAnalysis.core.Selection) bbox() (MDAnalysis.core.AtomGroup.AtomGroup method) Bfactor2RMSF() (in module MDAnalysis.analysis.density) BfactorDensityCreator (class in MDAnalysis.analysis.density) bfactors (MDAnalysis.core.AtomGroup.AtomGroup attribute) Bond (class in MDAnalysis.core.Timeseries) (class in MDAnalysis.topology.core) bond() (MDAnalysis.core.AtomGroup.AtomGroup method)

bonded_atoms (MDAnalysis.core.AtomGroup.Atom attribute) bonds (MDAnalysis.core.AtomGroup.Atom attribute), [1] bonds() (MDAnalysis.topology.core.TopologyGroup method) box_volume() (in module MDAnalysis.coordinates.core) boxCheck() (in module MDAnalysis.core.distances) bsphere() (MDAnalysis.core.AtomGroup.AtomGroup method) build_residues() (in module MDAnalysis.topology.core) build_segments() (in module MDAnalysis.topology.core) build_topology() (MDAnalysis.core.AtomGroup.Universe method)

C

cached() (in module MDAnalysis.core.util) calc_angle() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) calc_angles() (in module MDAnalysis.core.distances) calc_bonds() (in module MDAnalysis.core.distances) calc_eucl_distance() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) calc_torsions() (in module MDAnalysis.core.distances) CalcRMSDRotationalMatrix() (in module MDAnalysis.core.qcprot) CASelection (class in MDAnalysis.core.Selection) 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 method) chargeUnit_factor (in module MDAnalysis.core.units) check_and_fix_long_filename() (MDAnalysis.analysis.hole.HOLE method) check_compatible() (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid method) check_same_atoms() (in module MDAnalysis.analysis.align) chi1_selection() (MDAnalysis.core.AtomGroup.Residue method) clear() (MDAnalysis.core.Timeseries.TimeseriesCollection method) clear_handlers() (in module MDAnalysis.core.log) close() (MDAnalysis.coordinates.base.IObase method) (MDAnalysis.coordinates.DCD.DCDWriter method) (MDAnalysis.coordinates.LAMMPS.DATAReader 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.core.util.NamedStream method) close_trajectory() (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) closeContactGNMAnalysis (class in MDAnalysis.analysis.gnm) closed (MDAnalysis.core.util.NamedStream attribute) 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.pymol.SelectionWriter method) (MDAnalysis.selections.vmd.SelectionWriter method) compose_matrix() (in module MDAnalysis.core.transformations) compute() (MDAnalysis.core.Timeseries.TimeseriesCollection method) concatenate_matrices() (in module MDAnalysis.core.transformations) CONECT() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) constants (in module MDAnalysis.core.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.core.util) conversion_factor (in module MDAnalysis.core.units) convert() (in module MDAnalysis.core.units) convert_aa_code() (in module MDAnalysis.core.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) 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) 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) 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) 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) 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) 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) 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) coord (MDAnalysis.core.AtomGroup.Universe attribute) CoordinateNeighborSearch (class in MDAnalysis.KDTree.NeighborSearch) coordinates() (MDAnalysis.core.AtomGroup.AtomGroup method) copy() (MDAnalysis.coordinates.base.Timestep method) (MDAnalysis.coordinates.DCD.Timestep method) (MDAnalysis.coordinates.LAMMPS.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.LAMMPS.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) CRDReader (class in MDAnalysis.coordinates.CRD) CRDWriter (class in MDAnalysis.coordinates.CRD) create() (in module MDAnalysis.core.log) create_vmd_surface() (MDAnalysis.analysis.hole.HOLE method) CRYST1() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method)

D

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.core.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) delta (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) 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.core.units) Dihedral (class in MDAnalysis.core.Timeseries)

dihedral() (in module MDAnalysis.core.util) (MDAnalysis.core.AtomGroup.AtomGroup method) dihedrals (MDAnalysis.core.AtomGroup.Atom attribute) DIM (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) dimensions (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.Timestep attribute) (MDAnalysis.coordinates.PDB.Timestep attribute) (MDAnalysis.coordinates.TRJ.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) dist() (in module MDAnalysis.analysis.distances) Distance (class in MDAnalysis.core.Timeseries) distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.core.distances) (in module MDAnalysis.core.parallel.distances) distance_array_serial() (in module MDAnalysis.core.parallel.distances) DMSReader (class in MDAnalysis.coordinates.DMS) doc() (MDAnalysis.core.__init__.Flags method) down() (MDAnalysis.core.transformations.Arcball method) drag() (MDAnalysis.core.transformations.Arcball method) dt (MDAnalysis.coordinates.base.Reader attribute) (MDAnalysis.coordinates.DCD.DCDReader attribute) (MDAnalysis.coordinates.LAMMPS.DATAReader attribute) (MDAnalysis.coordinates.LAMMPS.DCDReader 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) dump_contents() (MDAnalysis.topology.core.TopologyGroup method)

E

echo() (in module MDAnalysis.core.log) (MDAnalysis.core.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.core.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)

F

fasta2select() (in module MDAnalysis.analysis.align) FastCalcRMSDAndRotation() (in module MDAnalysis.core.qcprot) filename() (in module MDAnalysis.core.util) fileno() (MDAnalysis.core.util.NamedStream method) fixedwidth_bins() (in module MDAnalysis.core.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.core.util.NamedStream method) fmt (MDAnalysis.coordinates.GRO.GROWriter attribute) forces (MDAnalysis.core.AtomGroup.AtomGroup attribute) forceUnit_factor (in module MDAnalysis.core.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.core.util) FORTRANReader (class in MDAnalysis.core.util) fragment (MDAnalysis.core.AtomGroup.Atom 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.base.Reader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)

G

generate_grid() (in module MDAnalysis.analysis.gnm) generate_kirchoff() (MDAnalysis.analysis.gnm.GNMAnalysis method) generate_output() (MDAnalysis.analysis.gnm.GNMAnalysis 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.PDB.PrimitivePDBReader method) (MDAnalysis.coordinates.PDBQT.PDBQTReader method) get_charges() (MDAnalysis.coordinates.PQR.PQRReader method) get_conversion_factor() (in module MDAnalysis.core.units) get_distance_array() (MDAnalysis.analysis.contacts.ContactAnalysis method) get_forces() (MDAnalysis.core.AtomGroup.AtomGroup method) get_indices() (MDAnalysis.KDTree.KDTree.KDTree method) get_occupancy() (MDAnalysis.coordinates.PDB.PrimitivePDBReader method) (MDAnalysis.coordinates.PDBQT.PDBQTReader method) get_parser_for() (in module MDAnalysis.topology.core) get_positions() (MDAnalysis.core.AtomGroup.AtomGroup method) get_radii() (MDAnalysis.coordinates.PQR.PQRReader method) (MDAnalysis.KDTree.KDTree.KDTree 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() (in module MDAnalysis.selections.base)

get_writer_for() (in module MDAnalysis.coordinates.core) getconstrain() (MDAnalysis.core.transformations.Arcball method) GNMAnalysis (class in MDAnalysis.analysis.gnm) greedy_splitext() (in module MDAnalysis.core.util) Grid (class in MDAnalysis.analysis.density) 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) guess_cpoint() (MDAnalysis.analysis.hole.HOLEtraj method) guess_format() (in module MDAnalysis.coordinates.core) (in module MDAnalysis.topology.core) guess_improper_torsions() (in module MDAnalysis.topology.core) guess_torsions() (in module MDAnalysis.topology.core)

H

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) hasmethod() (in module MDAnalysis.core.util) HEADER() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) helanal_main() (in module MDAnalysis.analysis.helanal) helanal_trajectory() (in module MDAnalysis.analysis.helanal) HOLE (class in MDAnalysis.analysis.hole)

HOLE_MAX_LENGTH (MDAnalysis.analysis.hole.HOLE attribute) HOLEtraj (class in MDAnalysis.analysis.hole) HydrogenBondAnalysis (class in MDAnalysis.analysis.hbonds.hbond_analysis) HydrogenBondAutoCorrel (class in MDAnalysis.analysis.hbonds.hbond_autocorrel) hydroxyl() (in module MDAnalysis.analysis.nuclinfo)

I

id (MDAnalysis.core.AtomGroup.Atom attribute) (MDAnalysis.core.AtomGroup.Segment attribute) improper() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.topology.core.Improper_Torsion method) Improper_Torsion (class in MDAnalysis.topology.core) impropers (MDAnalysis.core.AtomGroup.Atom attribute) InnerProduct() (in module MDAnalysis.core.qcprot) interpolated (MDAnalysis.analysis.density.Density attribute) (MDAnalysis.analysis.density.Grid attribute)

IObase (class in MDAnalysis.coordinates.base) is_guessed (MDAnalysis.topology.core.Bond attribute) is_periodic() (MDAnalysis.coordinates.TRJ.NCDFWriter method) isstream() (in module MDAnalysis.core.util) iterable() (in module MDAnalysis.core.util)

J

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

K

KDTree (class in MDAnalysis.KDTree.KDTree) keys() (MDAnalysis.topology.core.TopologyDict method)

kinetic_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) kv2dict() (in module MDAnalysis.topology.tables)

L

LeafletFinder (class in MDAnalysis.analysis.leaflet) length() (MDAnalysis.topology.core.Bond method) lengthUnit_factor (in module MDAnalysis.core.units) list_search() (MDAnalysis.KDTree.KDTree.KDTree method)

load() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) (MDAnalysis.analysis.density.Density method) (MDAnalysis.analysis.density.Grid 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

major_pair() (in module MDAnalysis.analysis.nuclinfo) make_density() (MDAnalysis.analysis.density.Density method) mass (MDAnalysis.core.AtomGroup.Atom attribute) masses (in module MDAnalysis.topology.tables) matrix() (MDAnalysis.core.transformations.Arcball method) 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.rms (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.DMS (module) MDAnalysis.coordinates.GRO (module) MDAnalysis.coordinates.LAMMPS (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.distances (module) MDAnalysis.core.log (module) MDAnalysis.core.parallel (module) MDAnalysis.core.parallel.distances (module) MDAnalysis.core.qcprot (module) MDAnalysis.core.Selection (module) MDAnalysis.core.Timeseries (module) MDAnalysis.core.transformations (module) MDAnalysis.core.units (module) MDAnalysis.core.util (module) MDAnalysis.KDTree.KDTree (module) MDAnalysis.KDTree.NeighborSearch (module) MDAnalysis.selections.base (module) MDAnalysis.selections.charmm (module) MDAnalysis.selections.gromacs (module) MDAnalysis.selections.pymol (module) MDAnalysis.selections.vmd (module) MDAnalysis.topology.__init__ (module) MDAnalysis.topology.core (module) MDAnalysis.topology.CRDParser (module) MDAnalysis.topology.DMSParser (module) MDAnalysis.topology.ExtendedPDBParser (module) MDAnalysis.topology.GROParser (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.TPRParser (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) 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) MODEL() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) momentOfInertia() (MDAnalysis.core.AtomGroup.AtomGroup method) MultiPDBWriter (class in MDAnalysis.coordinates.PDB)

N

N_Avogadro (in module MDAnalysis.core.units) name (MDAnalysis.core.AtomGroup.Atom attribute) NamedStream (class in MDAnalysis.core.util) names() (MDAnalysis.core.AtomGroup.AtomGroup method) NCDFReader (class in MDAnalysis.coordinates.TRJ) NCDFWriter (class in MDAnalysis.coordinates.TRJ) next() (MDAnalysis.coordinates.base.Reader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.PrimitivePDBReader method) (MDAnalysis.coordinates.TRR.TRRReader method) (MDAnalysis.coordinates.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.core.transformations.Arcball method) NoDataError norm() (in module MDAnalysis.core.util) normal() (in module MDAnalysis.core.util) NucleicBackboneSelection (class in MDAnalysis.core.Selection)

NucleicSelection (class in MDAnalysis.core.Selection) NucleicSugarSelection (class in MDAnalysis.core.Selection) NullHandler (class in MDAnalysis.core.log) numatoms (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.TRR.TRRReader attribute) (MDAnalysis.coordinates.TRZ.TRZReader attribute), [1] (MDAnalysis.coordinates.TRZ.Timestep attribute) (MDAnalysis.coordinates.XTC.XTCReader attribute) (MDAnalysis.coordinates.XYZ.XYZReader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute) (MDAnalysis.coordinates.xdrfile.core.TrjReader attribute) number (MDAnalysis.core.AtomGroup.Atom attribute) number_of_matches() (MDAnalysis.core.util.FORTRANReader method) numberOfAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method) numberOfResidues() (MDAnalysis.core.AtomGroup.AtomGroup method) numberOfSegments() (MDAnalysis.core.AtomGroup.AtomGroup method) numframes (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)

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.core.util) optimize_cutoff() (in module MDAnalysis.analysis.leaflet)

order_list() (in module MDAnalysis.analysis.gnm) OtherWriter() (MDAnalysis.coordinates.base.Reader method) (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

packIntoBox() (MDAnalysis.core.AtomGroup.AtomGroup method) parse() (MDAnalysis.topology.PQRParser.PQRParser method) (MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser method) parse_FORTRAN_format() (MDAnalysis.core.util.FORTRANReader method) parse_residue() (in module MDAnalysis.core.util) partner() (MDAnalysis.topology.core.Bond method) PATH, [1] 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.core.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.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.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) 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) principalAxes() (MDAnalysis.core.AtomGroup.AtomGroup 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.core.log) projection_from_matrix() (in module MDAnalysis.core.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) pseudo_dihe_baseflip() (in module MDAnalysis.analysis.nuclinfo) psi_selection() (MDAnalysis.core.AtomGroup.Residue method)

Q

qarray() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method) qN() (MDAnalysis.analysis.contacts.ContactAnalysis method) (MDAnalysis.analysis.contacts.ContactAnalysis1 method)

quaternion_imag() (in module MDAnalysis.core.transformations) quaternion_real() (in module MDAnalysis.core.transformations)

R

r_cov (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis attribute) radii() (MDAnalysis.core.AtomGroup.AtomGroup method) radius (MDAnalysis.core.AtomGroup.Atom attribute) radiusOfGyration() (MDAnalysis.core.AtomGroup.AtomGroup method) read() (MDAnalysis.core.util.FORTRANReader method) read_trr() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_trr_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_trr_numframes() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) read_xtc_numframes() (in module MDAnalysis.coordinates.xdrfile.libxdrfile2) readable() (MDAnalysis.core.util.NamedStream method) Reader (class in MDAnalysis.coordinates.base) reader() (in module MDAnalysis.coordinates.core) realpath() (in module MDAnalysis.core.util) reflection_from_matrix() (in module MDAnalysis.core.transformations) register() (MDAnalysis.core.__init__.Flags method) REMARK() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) remark_max_length (MDAnalysis.coordinates.PDB.PrimitivePDBWriter 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.core.util.NamedStream method)

resid (MDAnalysis.core.AtomGroup.Atom attribute) resids() (MDAnalysis.core.AtomGroup.AtomGroup method) Residue (class in MDAnalysis.core.AtomGroup) residue (MDAnalysis.core.AtomGroup.Atom attribute) ResidueGroup (class in MDAnalysis.core.AtomGroup) resname (MDAnalysis.core.AtomGroup.Atom attribute) resnames() (MDAnalysis.core.AtomGroup.AtomGroup method) resnum (MDAnalysis.core.AtomGroup.Atom attribute) resnums() (MDAnalysis.core.AtomGroup.AtomGroup method) rewind() (MDAnalysis.coordinates.base.ChainReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader 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.base.Reader method) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader method) (MDAnalysis.coordinates.xdrfile.XTC.XTCReader method) (MDAnalysis.coordinates.xdrfile.core.TrjReader 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.align) (in module MDAnalysis.analysis.rms) rotate() (MDAnalysis.core.AtomGroup.AtomGroup method) rotateby() (MDAnalysis.core.AtomGroup.AtomGroup method) rotation_from_matrix() (in module MDAnalysis.core.transformations) rotation_matrix() (in module MDAnalysis.analysis.align) rotaxis() (in module MDAnalysis.core.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.rms.RMSD 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_results() (MDAnalysis.analysis.hbonds.hbond_autocorrel.HydrogenBondAutoCorrel method) save_table() (MDAnalysis.analysis.hbonds.hbond_analysis.HydrogenBondAnalysis method) scale_from_matrix() (in module MDAnalysis.core.transformations) search() (MDAnalysis.KDTree.KDTree.KDTree method) (MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method) (MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method) search_all() (MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method) (MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method) search_list() (MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method) (MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method) seek() (MDAnalysis.core.util.NamedStream method) seekable() (MDAnalysis.core.util.NamedStream method) segid (MDAnalysis.core.AtomGroup.Atom attribute) segids() (MDAnalysis.core.AtomGroup.AtomGroup method) Segment (class in MDAnalysis.core.AtomGroup) SegmentGroup (class in MDAnalysis.core.AtomGroup) selectAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.Universe method) selectBonds() (MDAnalysis.topology.core.TopologyGroup method) SelectionError SelectionParser (class in MDAnalysis.core.Selection) SelectionWarning SelectionWriter (class in MDAnalysis.selections.base) (class in MDAnalysis.selections.charmm) (class in MDAnalysis.selections.gromacs) (class in MDAnalysis.selections.pymol) (class in MDAnalysis.selections.vmd) self_distance_array() (in module MDAnalysis.analysis.distances) (in module MDAnalysis.core.distances) seq2str() (in module MDAnalysis.analysis.hole) sequence() (MDAnalysis.core.AtomGroup.AtomGroup method) set() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) (MDAnalysis.core.AtomGroup.SegmentGroup method) set_bfactor() (MDAnalysis.core.AtomGroup.AtomGroup method) set_charge() (MDAnalysis.core.AtomGroup.AtomGroup method) set_coords() (MDAnalysis.KDTree.KDTree.KDTree method) set_forces() (MDAnalysis.core.AtomGroup.AtomGroup method)

set_mass() (MDAnalysis.core.AtomGroup.AtomGroup method) set_name() (MDAnalysis.core.AtomGroup.AtomGroup method) set_positions() (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_resname() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_resnum() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.ResidueGroup method) set_segid() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.core.AtomGroup.SegmentGroup method) set_type() (MDAnalysis.core.AtomGroup.AtomGroup method) set_velocities() (MDAnalysis.core.AtomGroup.AtomGroup method) setaxes() (MDAnalysis.core.transformations.Arcball method) setconstrain() (MDAnalysis.core.transformations.Arcball method) shape (MDAnalysis.core.Timeseries.Timeseries attribute) shapeParameter() (MDAnalysis.core.AtomGroup.AtomGroup method) shear_from_matrix() (in module MDAnalysis.core.transformations) SIMPLE2_RAD (in module MDAnalysis.analysis.hole) 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.core.units) split() (MDAnalysis.core.AtomGroup.AtomGroup method) start_logging() (in module MDAnalysis) std() (MDAnalysis.analysis.x3dna.X3DNA method) (MDAnalysis.analysis.x3dna.X3DNAtraj method) stop_logging() (in module MDAnalysis) stp() (in module MDAnalysis.core.util)

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.core.util.NamedStream method) temperature (MDAnalysis.coordinates.TRZ.Timestep attribute) time (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.base.Reader attribute) (MDAnalysis.coordinates.xdrfile.TRR.TRRReader 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.LAMMPS) (class in MDAnalysis.coordinates.PDB) (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.core.units) TITLE() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method) (MDAnalysis.coordinates.PDBQT.PDBQTWriter method) TopologyDict (class in MDAnalysis.topology.core) TopologyGroup (class in MDAnalysis.topology.core) TopologyObject (class in MDAnalysis.topology.core) 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) Torsion (class in MDAnalysis.topology.core)

torsion() (MDAnalysis.topology.core.Torsion method) torsions (MDAnalysis.core.AtomGroup.Atom attribute), [1] torsions() (MDAnalysis.topology.core.TopologyGroup method) total_energy (MDAnalysis.coordinates.TRZ.Timestep attribute) totalCharge() (MDAnalysis.core.AtomGroup.AtomGroup method) totalMass() (MDAnalysis.core.AtomGroup.AtomGroup method) totaltime (MDAnalysis.coordinates.base.Reader attribute) (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) TPRParser (class in MDAnalysis.topology.TPRParser) trajectory (MDAnalysis.core.AtomGroup.Universe attribute) transform() (MDAnalysis.core.AtomGroup.AtomGroup method) transform_RtoS() (in module MDAnalysis.core.distances) transform_StoR() (in module MDAnalysis.core.distances) translate() (MDAnalysis.core.AtomGroup.AtomGroup method) translation_from_matrix() (in module MDAnalysis.core.transformations) triclinic_box() (in module MDAnalysis.coordinates.core) triclinic_vectors() (in module MDAnalysis.coordinates.core) 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.core.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.core.TopologyObject attribute) types() (MDAnalysis.core.AtomGroup.AtomGroup method) (MDAnalysis.topology.core.TopologyGroup method)

U

unit_types (in module MDAnalysis.core.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) update() (MDAnalysis.analysis.leaflet.LeafletFinder method) (MDAnalysis.core.__init__.Flags method) (MDAnalysis.core.log.ProgressMeter method)

V

vecangle() (in module MDAnalysis.core.transformations) velocities (MDAnalysis.core.AtomGroup.AtomGroup attribute)

velocity (MDAnalysis.core.AtomGroup.Atom attribute) volume (MDAnalysis.coordinates.base.Timestep attribute) (MDAnalysis.coordinates.DCD.Timestep attribute) (MDAnalysis.coordinates.LAMMPS.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.core.units) WaterDipole (class in MDAnalysis.core.Timeseries) wc_pair() (in module MDAnalysis.analysis.nuclinfo) which() (in module MDAnalysis.core.util) writable() (MDAnalysis.core.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.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.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) Writer (class in MDAnalysis.coordinates.base) writer() (in module MDAnalysis.coordinates.core) Writer() (MDAnalysis.coordinates.base.Reader method) (MDAnalysis.coordinates.CRD.CRDReader method) (MDAnalysis.coordinates.DCD.DCDReader method) (MDAnalysis.coordinates.GRO.GROReader method) (MDAnalysis.coordinates.LAMMPS.DATAReader method) (MDAnalysis.coordinates.LAMMPS.DCDReader method) (MDAnalysis.coordinates.PDB.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) XYZReader (class in MDAnalysis.coordinates.XYZ) XYZWriter (class in MDAnalysis.coordinates.XYZ)