mdtraj.Trajectory¶

class mdtraj.Trajectory(xyz, topology, time=None, unitcell_lengths=None, unitcell_angles=None)¶

Container object for a molecular dynamics trajectory

A Trajectory represents a collection of one or more molecular structures, generally (but not necessarily) from a molecular dynamics trajectory. The Trajectory stores a number of fields describing the system through time, including the cartesian coordinates of each atoms (xyz), the topology of the molecular system (topology), and information about the unitcell if appropriate (unitcell_vectors, unitcell_length, unitcell_angles).

A Trajectory should generally be constructed by loading a file from disk. Trajectories can be loaded from (and saved to) the PDB, XTC, TRR, DCD, binpos, NetCDF or MDTraj HDF5 formats.

Trajectory supports fancy indexing, so you can extract one or more frames from a Trajectory as a separate trajectory. For example, to form a trajectory with every other frame, you can slice with traj[::2].

Trajectory uses the nanometer, degree & picosecond unit system.

See also

mdtraj.load: High-level function that loads files and returns an md.Trajectory

Examples

>>> # loading a trajectory
>>> import mdtraj as md
>>> md.load('trajectory.xtc', top='native.pdb')
<mdtraj.Trajectory with 1000 frames, 22 atoms at 0x1058a73d0>

>>> # slicing a trajectory
>>> t = md.load('trajectory.h5')
>>> print(t)
<mdtraj.Trajectory with 100 frames, 22 atoms>
>>> print(t[::2])
<mdtraj.Trajectory with 50 frames, 22 atoms>

>>> # calculating the average distance between two atoms
>>> import mdtraj as md
>>> import numpy as np
>>> t = md.load('trajectory.h5')
>>> np.mean(np.sqrt(np.sum((t.xyz[:, 0, :] - t.xyz[:, 21, :])**2, axis=1)))

Attributes

n_framesint: Number of frames in the trajectory
n_atomsint: Number of atoms in the trajectory
n_residuesint: Number of residues (amino acids) in the trajectory
timenp.ndarray, shape=(n_frames,): The simulation time corresponding to each frame, in picoseconds
timestepfloat: Timestep between frames, in picoseconds
topologymd.Topology: Topology of the system, describing the organization of atoms into residues, bonds, etc
topmd.Topology: Alias for self.topology, describing the organization of atoms into residues, bonds, etc
xyznp.ndarray, shape=(n_frames, n_atoms, 3): Cartesian coordinates of each atom in each simulation frame
unitcell_vectors{np.ndarray, shape=(n_frames, 3, 3), None}: The vectors that define the shape of the unit cell in each frame
unitcell_lengths{np.ndarray, shape=(n_frames, 3), None}: Lengths that define the shape of the unit cell in each frame.
unitcell_angles{np.ndarray, shape=(n_frames, 3), None}: Angles that define the shape of the unit cell in each frame.

Methods

`atom_slice`(atom_indices[, inplace])	Create a new trajectory from a subset of atoms
`center_coordinates`([mass_weighted])	Center each trajectory frame at the origin (0,0,0).
`image_molecules`([inplace, anchor_molecules, …])	Recenter and apply periodic boundary conditions to the molecules in each frame of the trajectory.
`join`(other[, check_topology, …])	Join two trajectories together along the time/frame axis.
`load`(filenames, **kwargs)	Load a trajectory from disk
`make_molecules_whole`([inplace, sorted_bonds])	Only make molecules whole
`openmm_boxes`(frame)	OpenMM-compatable box vectors of a single frame.
`openmm_positions`(frame)	OpenMM-compatable positions of a single frame.
`remove_solvent`([exclude, inplace])	Create a new trajectory without solvent atoms
`restrict_atoms`(**kwargs)	DEPRECATED: restrict_atoms was replaced by atom_slice and will be removed in 2.0
`save`(filename, **kwargs)	Save trajectory to disk, in a format determined by the filename extension
`save_amberrst7`(filename[, force_overwrite])	Save trajectory in AMBER ASCII restart format
`save_binpos`(filename[, force_overwrite])	Save trajectory to AMBER BINPOS format
`save_dcd`(filename[, force_overwrite])	Save trajectory to CHARMM/NAMD DCD format
`save_dtr`(filename[, force_overwrite])	Save trajectory to DESMOND DTR format
`save_gro`(filename[, force_overwrite, precision])	Save trajectory in Gromacs .gro format
`save_gsd`(filename[, force_overwrite])	Save trajectory to HOOMD GSD format
`save_hdf5`(filename[, force_overwrite])	Save trajectory to MDTraj HDF5 format
`save_lammpstrj`(filename[, force_overwrite])	Save trajectory to LAMMPS custom dump format
`save_lh5`(filename[, force_overwrite])	Save trajectory in deprecated MSMBuilder2 LH5 (lossy HDF5) format.
`save_mdcrd`(filename[, force_overwrite])	Save trajectory to AMBER mdcrd format
`save_netcdf`(filename[, force_overwrite])	Save trajectory in AMBER NetCDF format
`save_netcdfrst`(filename[, force_overwrite])	Save trajectory in AMBER NetCDF restart format
`save_pdb`(filename[, force_overwrite, bfactors])	Save trajectory to RCSB PDB format
`save_tng`(filename[, force_overwrite])	Save trajectory to Gromacs TNG format
`save_trr`(filename[, force_overwrite])	Save trajectory to Gromacs TRR format
`save_xtc`(filename[, force_overwrite])	Save trajectory to Gromacs XTC format
`save_xyz`(filename[, force_overwrite])	Save trajectory to .xyz format.
`slice`(key[, copy])	Slice trajectory, by extracting one or more frames into a separate object
`smooth`(width[, order, atom_indices, inplace])	Smoothen a trajectory using a zero-delay Buttersworth filter.
`stack`(other[, keep_resSeq])	Stack two trajectories along the atom axis
`superpose`(reference[, frame, atom_indices, …])	Superpose each conformation in this trajectory upon a reference

__init__(xyz, topology, time=None, unitcell_lengths=None, unitcell_angles=None)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(xyz, topology[, time, …])	Initialize self.
`atom_slice`(atom_indices[, inplace])	Create a new trajectory from a subset of atoms
`center_coordinates`([mass_weighted])	Center each trajectory frame at the origin (0,0,0).
`image_molecules`([inplace, anchor_molecules, …])	Recenter and apply periodic boundary conditions to the molecules in each frame of the trajectory.
`join`(other[, check_topology, …])	Join two trajectories together along the time/frame axis.
`load`(filenames, **kwargs)	Load a trajectory from disk
`make_molecules_whole`([inplace, sorted_bonds])	Only make molecules whole
`openmm_boxes`(frame)	OpenMM-compatable box vectors of a single frame.
`openmm_positions`(frame)	OpenMM-compatable positions of a single frame.
`remove_solvent`([exclude, inplace])	Create a new trajectory without solvent atoms
`restrict_atoms`(**kwargs)	DEPRECATED: restrict_atoms was replaced by atom_slice and will be removed in 2.0
`save`(filename, **kwargs)	Save trajectory to disk, in a format determined by the filename extension
`save_amberrst7`(filename[, force_overwrite])	Save trajectory in AMBER ASCII restart format
`save_binpos`(filename[, force_overwrite])	Save trajectory to AMBER BINPOS format
`save_dcd`(filename[, force_overwrite])	Save trajectory to CHARMM/NAMD DCD format
`save_dtr`(filename[, force_overwrite])	Save trajectory to DESMOND DTR format
`save_gro`(filename[, force_overwrite, precision])	Save trajectory in Gromacs .gro format
`save_gsd`(filename[, force_overwrite])	Save trajectory to HOOMD GSD format
`save_hdf5`(filename[, force_overwrite])	Save trajectory to MDTraj HDF5 format
`save_lammpstrj`(filename[, force_overwrite])	Save trajectory to LAMMPS custom dump format
`save_lh5`(filename[, force_overwrite])	Save trajectory in deprecated MSMBuilder2 LH5 (lossy HDF5) format.
`save_mdcrd`(filename[, force_overwrite])	Save trajectory to AMBER mdcrd format
`save_netcdf`(filename[, force_overwrite])	Save trajectory in AMBER NetCDF format
`save_netcdfrst`(filename[, force_overwrite])	Save trajectory in AMBER NetCDF restart format
`save_pdb`(filename[, force_overwrite, bfactors])	Save trajectory to RCSB PDB format
`save_tng`(filename[, force_overwrite])	Save trajectory to Gromacs TNG format
`save_trr`(filename[, force_overwrite])	Save trajectory to Gromacs TRR format
`save_xtc`(filename[, force_overwrite])	Save trajectory to Gromacs XTC format
`save_xyz`(filename[, force_overwrite])	Save trajectory to .xyz format.
`slice`(key[, copy])	Slice trajectory, by extracting one or more frames into a separate object
`smooth`(width[, order, atom_indices, inplace])	Smoothen a trajectory using a zero-delay Buttersworth filter.
`stack`(other[, keep_resSeq])	Stack two trajectories along the atom axis
`superpose`(reference[, frame, atom_indices, …])	Superpose each conformation in this trajectory upon a reference

Attributes

`n_atoms`	Number of atoms in the trajectory
`n_chains`	Number of chains in the trajectory
`n_frames`	Number of frames in the trajectory
`n_residues`	Number of residues (amino acids) in the trajectory
`time`	The simulation time corresponding to each frame, in picoseconds
`timestep`	Timestep between frames, in picoseconds
`top`	Alias for self.topology, describing the organization of atoms into residues, bonds, etc
`topology`	Topology of the system, describing the organization of atoms into residues, bonds, etc
`unitcell_angles`	Angles that define the shape of the unit cell in each frame.
`unitcell_lengths`	Lengths that define the shape of the unit cell in each frame.
`unitcell_vectors`	The vectors that define the shape of the unit cell in each frame
`unitcell_volumes`	Volumes of unit cell for each frame.
`xyz`	Cartesian coordinates of each atom in each simulation frame