Index

_

__init__() (mdtraj.formats.AmberNetCDFRestartFile method) (mdtraj.Topology method) (mdtraj.Trajectory 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.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 attribute) ArcTrajectoryFile (class in mdtraj.formats) atom() (mdtraj.Topology method) atom_slice() (mdtraj.Trajectory method) atoms (mdtraj.Topology attribute) atoms_by_name() (mdtraj.Topology method)

B

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

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

C

center_coordinates() (mdtraj.Trajectory method) chain() (mdtraj.Topology method) chains (mdtraj.Topology attribute) 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 attribute) 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_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 attribute) 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) 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 attribute) 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) 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 attribute) (mdtraj.Trajectory attribute) n_bonds (mdtraj.Topology attribute) n_chains (mdtraj.Topology attribute) (mdtraj.Trajectory attribute)

n_frames (mdtraj.Trajectory attribute) n_residues (mdtraj.Topology attribute) (mdtraj.Trajectory attribute) 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 attribute)

R

randomState (mdtraj.formats.HDF5TrajectoryFile attribute) 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 attribute) 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 attribute) restrict_atoms() (mdtraj.Trajectory method) rmsd() (in module mdtraj) root (mdtraj.formats.HDF5TrajectoryFile attribute) 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 attribute)

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

U

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

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

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 attribute) XYZTrajectoryFile (class in mdtraj.formats)