Index

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__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

acylindricity() (in module mdtraj) AmberNetCDFRestartFile (class in mdtraj.formats)

AmberRestartFile (class in mdtraj.formats) ArcTrajectoryFile (class in mdtraj.formats) asphericity() (in module mdtraj)

B

baker_hubbard() (in module mdtraj)

BINPOSTrajectoryFile (class in mdtraj.formats) box_vectors_to_lengths_and_angles() (in module mdtraj.utils)

C

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) 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)

D

DCDReporter (class in mdtraj.reporters) DCDTrajectoryFile (class in mdtraj.formats)

density() (in module mdtraj) dipole_moments() (in module mdtraj) DTRTrajectoryFile (class in mdtraj.formats)

E

ensure_type() (in module mdtraj.utils)

G

GroTrajectoryFile (class in mdtraj.formats)

H

HDF5Reporter (class in mdtraj.reporters)

HDF5TrajectoryFile (class in mdtraj.formats)

I

ilen() (in module mdtraj.utils) 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)

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) 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

MDCRDTrajectoryFile (class in mdtraj.formats)

N

NetCDFReporter (class in mdtraj.reporters)

NetCDFTrajectoryFile (class in mdtraj.formats)

O

open() (in module mdtraj)

P

PDBTrajectoryFile (class in mdtraj.formats)

principal_moments() (in module mdtraj)

R

reindex_dataframe_by_atoms() (in module mdtraj) relative_shape_antisotropy() (in module mdtraj)

rmsd() (in module mdtraj) rmsf() (in module mdtraj) rotation_matrix_from_quaternion() (in module mdtraj.utils)

S

shrake_rupley() (in module mdtraj) squareform() (in module mdtraj.geometry)

static_dielectric() (in module mdtraj) superpose() (mdtraj.Trajectory method)

T

thermal_expansion_alpha_P() (in module mdtraj) timing (class in mdtraj.utils)

Topology (class in mdtraj) Trajectory (class in mdtraj) TRRTrajectoryFile (class in mdtraj.formats)

U

uniform_quaternion() (in module mdtraj.utils)

W

wernet_nilsson() (in module mdtraj)

X

XTCTrajectoryFile (class in mdtraj.formats)

XYZTrajectoryFile (class in mdtraj.formats)