MDTraj
Installation
New to Python
Examples
What’s New?
Trajectory Reference
Analysis Reference
Atom Selection Reference
Low-level API
OpenMM Reporters
MDTraj Utils
mdconvert
(
mdconvert-mdtraj
)
MDTraj HDF5 Format Specification
MDTraj
Index
Index
_
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A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
|
X
_
__init__() (mdtraj.formats.AmberNetCDFRestartFile method)
(mdtraj.formats.AmberRestartFile method)
(mdtraj.formats.ArcTrajectoryFile 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)
application (mdtraj.formats.HDF5TrajectoryFile attribute)
ArcTrajectoryFile (class in mdtraj.formats)
asphericity() (in module mdtraj)
atoms (mdtraj.Topology attribute)
B
baker_hubbard() (in module mdtraj)
bonds (mdtraj.Topology attribute)
box_vectors_to_lengths_and_angles() (in module mdtraj.utils)
C
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)
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_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 attribute)
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)
F
forcefield (mdtraj.formats.HDF5TrajectoryFile attribute)
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_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
n_atoms (mdtraj.formats.GroTrajectoryFile attribute)
(mdtraj.Trajectory attribute)
n_frames (mdtraj.Trajectory attribute)
n_residues (mdtraj.Trajectory attribute)
NetCDFReporter (class in mdtraj.reporters)
NetCDFTrajectoryFile (class in mdtraj.formats)
O
open() (in module mdtraj)
P
PDBTrajectoryFile (class in mdtraj.formats)
positions (mdtraj.formats.PDBTrajectoryFile attribute)
principal_moments() (in module mdtraj)
R
randomState (mdtraj.formats.HDF5TrajectoryFile attribute)
reference (mdtraj.formats.HDF5TrajectoryFile attribute)
reindex_dataframe_by_atoms() (in module mdtraj)
relative_shape_antisotropy() (in module mdtraj)
residues (mdtraj.Topology attribute)
rmsd() (in module mdtraj)
rmsf() (in module mdtraj)
root (mdtraj.formats.HDF5TrajectoryFile attribute)
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)
time (mdtraj.Trajectory attribute)
timestep (mdtraj.Trajectory attribute)
timing (class in mdtraj.utils)
title (mdtraj.formats.HDF5TrajectoryFile attribute)
top (mdtraj.Trajectory attribute)
Topology (class in mdtraj)
topology (mdtraj.formats.ArcTrajectoryFile attribute)
(mdtraj.formats.GroTrajectoryFile attribute)
(mdtraj.formats.HDF5TrajectoryFile attribute)
(mdtraj.formats.PDBTrajectoryFile attribute)
(mdtraj.Trajectory attribute)
Trajectory (class in mdtraj)
TRRTrajectoryFile (class in mdtraj.formats)
U
uniform_quaternion() (in module mdtraj.utils)
unitcell_angles (mdtraj.Trajectory attribute)
unitcell_lengths (mdtraj.Trajectory attribute)
unitcell_vectors (mdtraj.Trajectory attribute)
W
wernet_nilsson() (in module mdtraj)
X
XTCTrajectoryFile (class in mdtraj.formats)
xyz (mdtraj.Trajectory attribute)
XYZTrajectoryFile (class in mdtraj.formats)