Index

_

__init__() (mdtraj.formats.AmberNetCDFRestartFile method) (mdtraj.formats.AmberRestartFile method) (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.PDBTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method) (mdtraj.reporters.DCDReporter method) (mdtraj.reporters.HDF5Reporter method) (mdtraj.reporters.NetCDFReporter method) (mdtraj.Topology method) (mdtraj.Trajectory method) (mdtraj.utils.timing method)

A

add_atom() (mdtraj.Topology method) add_bond() (mdtraj.Topology method) add_chain() (mdtraj.Topology method) add_residue() (mdtraj.Topology method) AmberNetCDFRestartFile (class in mdtraj.formats) AmberRestartFile (class in mdtraj.formats)

application() (mdtraj.formats.HDF5TrajectoryFile property) ArcTrajectoryFile (class in mdtraj.formats) atom() (mdtraj.Topology method) atom_slice() (mdtraj.Trajectory method) atoms() (mdtraj.Topology property) atoms_by_name() (mdtraj.Topology method)

B

baker_hubbard() (in module mdtraj) BINPOSTrajectoryFile (class in mdtraj.formats)

bonds() (mdtraj.Topology property) box_vectors_to_lengths_and_angles() (in module mdtraj.utils)

C

center_coordinates() (mdtraj.Trajectory method) chain() (mdtraj.Topology method) chains() (mdtraj.Topology property) check_random_state() (in module mdtraj.utils) chemical_shifts_ppm() (in module mdtraj) chemical_shifts_shiftx2() (in module mdtraj) chemical_shifts_spartaplus() (in module mdtraj) close() (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.PDBTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method) (mdtraj.reporters.DCDReporter method) (mdtraj.reporters.HDF5Reporter method) (mdtraj.reporters.NetCDFReporter method) closed() (mdtraj.formats.PDBTrajectoryFile property) compute_angles() (in module mdtraj) compute_center_of_mass() (in module mdtraj)

compute_chi1() (in module mdtraj) compute_chi2() (in module mdtraj) compute_chi3() (in module mdtraj) compute_chi4() (in module mdtraj) compute_contacts() (in module mdtraj) compute_dihedrals() (in module mdtraj) compute_directors() (in module mdtraj) compute_displacements() (in module mdtraj) compute_distances() (in module mdtraj) compute_drid() (in module mdtraj) compute_dssp() (in module mdtraj) compute_gyration_tensor() (in module mdtraj) compute_inertia_tensor() (in module mdtraj) compute_J3_HN_C() (in module mdtraj) compute_J3_HN_CB() (in module mdtraj) compute_J3_HN_HA() (in module mdtraj) compute_neighbors() (in module mdtraj) compute_nematic_order() (in module mdtraj) compute_omega() (in module mdtraj) compute_phi() (in module mdtraj) compute_psi() (in module mdtraj) compute_rdf() (in module mdtraj) compute_rg() (in module mdtraj) constraints() (mdtraj.formats.HDF5TrajectoryFile property) copy() (mdtraj.Topology method) create_disulfide_bonds() (mdtraj.Topology method) create_standard_bonds() (mdtraj.Topology method)

D

DCDReporter (class in mdtraj.reporters) DCDTrajectoryFile (class in mdtraj.formats) delete_atom_by_index() (mdtraj.Topology method) density() (in module mdtraj)

describeNextReport() (mdtraj.reporters.DCDReporter method) (mdtraj.reporters.HDF5Reporter method) (mdtraj.reporters.NetCDFReporter method) dipole_moments() (in module mdtraj) DTRTrajectoryFile (class in mdtraj.formats)

E

ensure_type() (in module mdtraj.utils)

F

find_molecules() (mdtraj.Topology method) flush() (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method)

forcefield() (mdtraj.formats.HDF5TrajectoryFile property) from_dataframe() (mdtraj.Topology class method) from_openmm() (mdtraj.Topology class method)

G

get_times() (mdtraj.formats.DTRTrajectoryFile method)

GroTrajectoryFile (class in mdtraj.formats) guess_anchor_molecules() (mdtraj.Topology method)

H

HDF5Reporter (class in mdtraj.reporters)

HDF5TrajectoryFile (class in mdtraj.formats)

I

ilen() (in module mdtraj.utils) image_molecules() (mdtraj.Trajectory method) import_() (in module mdtraj.utils)

in_units_of() (in module mdtraj.utils) insert_atom() (mdtraj.Topology method) isothermal_compressability_kappa_T() (in module mdtraj) iterload() (in module mdtraj)

J

join() (in module mdtraj) (mdtraj.Topology method) (mdtraj.Trajectory method)

K

kabsch_sander() (in module mdtraj)

L

LAMMPSTrajectoryFile (class in mdtraj.formats) lengths_and_angles_to_box_vectors() (in module mdtraj.utils) LH5TrajectoryFile (class in mdtraj.formats) load() (in module mdtraj) (mdtraj.Trajectory static method) load_arc() (in module mdtraj) load_binpos() (in module mdtraj) load_dcd() (in module mdtraj) load_dtr() (in module mdtraj) load_frame() (in module mdtraj) load_hdf5() (in module mdtraj)

load_hoomdxml() (in module mdtraj) load_lammpstrj() (in module mdtraj) load_lh5() (in module mdtraj) load_netcdf() (in module mdtraj) load_pdb() (in module mdtraj) load_prmtop() (in module mdtraj) load_trr() (in module mdtraj) load_xml() (in module mdtraj) load_xtc() (in module mdtraj) load_xyz() (in module mdtraj) lprmsd() (in module mdtraj)

M

make_molecules_whole() (mdtraj.Trajectory method)

MDCRDTrajectoryFile (class in mdtraj.formats)

N

n_atoms() (mdtraj.Topology property) (mdtraj.Trajectory property) n_bonds() (mdtraj.Topology property) n_chains() (mdtraj.Topology property) (mdtraj.Trajectory property)

n_frames() (mdtraj.Trajectory property) n_residues() (mdtraj.Topology property) (mdtraj.Trajectory property) NetCDFReporter (class in mdtraj.reporters) NetCDFTrajectoryFile (class in mdtraj.formats)

O

offsets (mdtraj.formats.TRRTrajectoryFile attribute) (mdtraj.formats.XTCTrajectoryFile attribute)

open() (in module mdtraj) openmm_boxes() (mdtraj.Trajectory method) openmm_positions() (mdtraj.Trajectory method)

P

parse_box() (mdtraj.formats.LAMMPSTrajectoryFile method)

PDBTrajectoryFile (class in mdtraj.formats) positions() (mdtraj.formats.PDBTrajectoryFile property)

R

randomState() (mdtraj.formats.HDF5TrajectoryFile property) read() (mdtraj.formats.AmberNetCDFRestartFile method) (mdtraj.formats.AmberRestartFile method) (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method) read_as_traj() (mdtraj.formats.AmberNetCDFRestartFile method) (mdtraj.formats.AmberRestartFile method) (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method)

reference() (mdtraj.formats.HDF5TrajectoryFile property) reindex_dataframe_by_atoms() (in module mdtraj) remove_solvent() (mdtraj.Trajectory method) report() (mdtraj.reporters.DCDReporter method) (mdtraj.reporters.HDF5Reporter method) (mdtraj.reporters.NetCDFReporter method) residue() (mdtraj.Topology method) residues() (mdtraj.Topology property) restrict_atoms() (mdtraj.Trajectory method) rmsd() (in module mdtraj) rmsf() (in module mdtraj) root() (mdtraj.formats.HDF5TrajectoryFile property) rotation_matrix_from_quaternion() (in module mdtraj.utils)

S

save() (mdtraj.Trajectory method) save_amberrst7() (mdtraj.Trajectory method) save_binpos() (mdtraj.Trajectory method) save_dcd() (mdtraj.Trajectory method) save_dtr() (mdtraj.Trajectory method) save_gro() (mdtraj.Trajectory method) save_hdf5() (mdtraj.Trajectory method) save_lammpstrj() (mdtraj.Trajectory method) save_lh5() (mdtraj.Trajectory method) save_mdcrd() (mdtraj.Trajectory method) save_netcdf() (mdtraj.Trajectory method) save_netcdfrst() (mdtraj.Trajectory method) save_pdb() (mdtraj.Trajectory method) save_tng() (mdtraj.Trajectory method) save_trr() (mdtraj.Trajectory method) save_xtc() (mdtraj.Trajectory method) save_xyz() (mdtraj.Trajectory method) seek() (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method)

select() (mdtraj.Topology method) select_atom_indices() (mdtraj.Topology method) select_expression() (mdtraj.Topology method) select_pairs() (mdtraj.Topology method) set_chain_names() (mdtraj.formats.PDBTrajectoryFile class method) shrake_rupley() (in module mdtraj) slice() (mdtraj.Trajectory method) smooth() (mdtraj.Trajectory method) squareform() (in module mdtraj.geometry) stack() (mdtraj.Trajectory method) static_dielectric() (in module mdtraj) subset() (mdtraj.Topology method) superpose() (mdtraj.Trajectory method), [1]

T

tell() (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method) thermal_expansion_alpha_P() (in module mdtraj) time() (mdtraj.Trajectory property)

timestep() (mdtraj.Trajectory property) timing (class in mdtraj.utils) title() (mdtraj.formats.HDF5TrajectoryFile property) to_bondgraph() (mdtraj.Topology method) to_dataframe() (mdtraj.Topology method) to_fasta() (mdtraj.Topology method) to_openmm() (mdtraj.Topology method) top() (mdtraj.Trajectory property) Topology (class in mdtraj) topology() (mdtraj.formats.HDF5TrajectoryFile property) (mdtraj.formats.LH5TrajectoryFile property) (mdtraj.formats.PDBTrajectoryFile property) (mdtraj.Trajectory property) Trajectory (class in mdtraj) TRRTrajectoryFile (class in mdtraj.formats)

U

uniform_quaternion() (in module mdtraj.utils) unitcell_angles() (mdtraj.formats.PDBTrajectoryFile property) (mdtraj.Trajectory property)

unitcell_lengths() (mdtraj.formats.PDBTrajectoryFile property) (mdtraj.Trajectory property) unitcell_vectors() (mdtraj.Trajectory property) unitcell_volumes() (mdtraj.Trajectory property)

W

wernet_nilsson() (in module mdtraj) write() (mdtraj.formats.AmberNetCDFRestartFile method) (mdtraj.formats.AmberRestartFile method) (mdtraj.formats.ArcTrajectoryFile method) (mdtraj.formats.BINPOSTrajectoryFile method) (mdtraj.formats.DCDTrajectoryFile method) (mdtraj.formats.DTRTrajectoryFile method) (mdtraj.formats.GroTrajectoryFile method) (mdtraj.formats.HDF5TrajectoryFile method) (mdtraj.formats.LAMMPSTrajectoryFile method) (mdtraj.formats.LH5TrajectoryFile method) (mdtraj.formats.MDCRDTrajectoryFile method) (mdtraj.formats.NetCDFTrajectoryFile method) (mdtraj.formats.PDBTrajectoryFile method) (mdtraj.formats.TRRTrajectoryFile method) (mdtraj.formats.XTCTrajectoryFile method) (mdtraj.formats.XYZTrajectoryFile method)

write_box() (mdtraj.formats.LAMMPSTrajectoryFile method)

X

XTCTrajectoryFile (class in mdtraj.formats)

xyz() (mdtraj.Trajectory property) XYZTrajectoryFile (class in mdtraj.formats)