Trajectory File

This module defines a base class for format specific trajectory classes.

class TrajFile(filename, mode='r')

A base class for trajectory file classes:

• DCDFile

Open filename for reading (default, mode="r"), writing (mode="w"), or appending (mode="r+" or mode="a"). Binary mode option will be appended automatically.

close()

Close trajectory file.

getAtoms()

Returns associated/selected atoms.

getCoords()

Returns a copy of reference coordinates for (selected) atoms.

getCoordsets(indices=None)

Returns coordinate sets at given indices. indices may be an integer, a list of ordered integers or None. None returns all coordinate sets. If a list of indices is given, unique numbers will be selected and sorted. That is, this method will always return unique coordinate sets in the order they appear in the trajectory file. Shape of the coordinate set array is (n_sets, n_atoms, 3).

getFilename(absolute=False)

Returns relative path to the current file. For absolute path, pass absolute=True argument.

getFirstTimestep()

Returns first timestep value.

getFrame(index)

Returns frame at given index.

getFrameFreq()

Returns timesteps between frames.

getLinked()

Returns linked AtomGroup instance, or None if a link is not established.

getTimestep()

Returns timestep size.

getTitle()

Returns title of the ensemble.

getWeights()

Returns a copy of weights of (selected) atoms.

goto(n)

Go to the frame at index n. n=0 will rewind the trajectory to the beginning, same as calling reset() method. n=-1 will go to the last frame. Frame n will not be parsed until one of next() or nextCoordset() methods is called.

hasUnitcell()

Returns True if trajectory has unitcell data.

isLinked()

Returns True if trajectory is linked to an AtomGroup instance.

iterCoordsets()

Yield coordinate sets for (selected) atoms. Reference coordinates are not included. Iteration starts from the next frame in line.

link(*ag)

Link, return, or unlink an AtomGroup instance. When a link to ag is established, coordinates of new frames parsed from the trajectory file will be set as the coordinates of ag and this will update coordinates of all selections and atom subsets pointing to it. At link time, if ag does not have any coordinate sets and reference coordinates of the trajectory is set, reference coordinates of the trajectory will be passed to ag. To break an established link, pass None argument, or to return the linked atom group instance, call with no arguments.

Warning

Every time a frame is parsed from the trajectory, all coordinate sets present in the linked AtomGroup will be overwritten.

next()

Returns next coordinate set in a Frame instance. Note that when atoms are set for the trajectory, this method will return the same frame instance after updating its coordinates.

nextCoordset()

Returns next coordinate set.

nextIndex()

Returns the index of the next frame.

numAtoms()

Returns number of atoms.

numCoordsets()

Returns number of frames.

numFixed()

Returns number of fixed atoms.

numFrames()

Returns number of frames.

numSelected()

Returns number of selected atoms. A subset of atoms can be selected by passing a selection to setAtoms().

reset()

Go to first frame at index 0. First frame will not be parsed until one of next() or nextCoordset() methods is called.

setAtoms(atoms)

Set atoms or specify a selection of atoms to be considered in calculations and coordinate requests. When a selection is set, corresponding subset of coordinates will be considered in, for example, alignments and RMSD calculations. Setting atoms also allows some functions to access atomic data when needed. For example, Trajectory and Frame instances become suitable arguments for writePDB(). Passing None as atoms argument will deselect atoms. Note that setting atoms does not change the reference coordinates of the trajectory. To change the reference, use setCoords() method.

setCoords(coords)

Set coords as the trajectory reference coordinate set. coords must be an object with getCoords() method, or a Numpy array with suitable data type, shape, and dimensionality.

setTitle(title)

Set title of the ensemble.

setWeights(weights)

Set atomic weights.

skip(n)

Skip n frames. n must be a positive integer. Skipping some frames will only change the next frame index (nextIndex()) Next frame will not be parsed until one of next() or nextCoordset() methods is called.