5.18. Common functions for coordinate reading — MDAnalysis.coordinates.core

Important base classes are collected in MDAnalysis.coordinates.base.

MDAnalysis.coordinates.core.reader(filename, **kwargs)[source]

Provide a trajectory reader instance for filename.

This function guesses the file format from the extension of filename and it will throw a TypeError if the extension is not recognized.

In most cases, no special keyword arguments are necessary. For PDB readers it might be useful to set the permissive = True flag to select a simpler but faster reader.

All other keywords are passed on to the underlying Reader classes; see their documentation for details.

Parameters:
  • filename (str or tuple) – filename (or tuple of filenames) of the input coordinate file
  • permissive (bool) – If set to True, a reader is selected that is more tolerant of the input (currently only implemented for PDB). [False]
  • kwargs – Keyword arguments for the selected Reader class.
Returns:

  • A Reader object
  • .. SeeAlso (: For trajectory formats: DCDReader,) – XTCReader, TRRReader, XYZReader. For single frame formats: CRDReader, PDBReader and PrimitivePDBReader, GROReader,

MDAnalysis.coordinates.core.writer(filename, n_atoms=None, **kwargs)[source]

Initialize a trajectory writer instance for filename.

filename : str
Output filename of the trajectory; the extension determines the format.
n_atoms : int, optional
The number of atoms in the output trajectory; can be ommitted for single-frame writers.
multiframe : bool, optional
True: write a trajectory with multiple frames; False only write a single frame snapshot; None first try to get a multiframe writer and then fall back to single frame [None]
kwargs : optional

Keyword arguments for the writer; all trajectory Writers accept at least

start
starting time [0]
step
step size in frames [1]
dt
length of time between two frames, in ps [1.0]

Some readers accept additional arguments, which need to be looked up in the documentation of the reader.

Returns:
  • A Writer object
  • .. SeeAlso (: DCDWriter for DCD) – trajectories or XTCWriter and TRRWriter for Gromacs.
  • .. versionchanged (: 0.7.6) – Added multiframe keyword. See also get_writer_for().

Helper functions:

MDAnalysis.coordinates.core.get_reader_for(filename, permissive=False, format=None)[source]

Return the appropriate trajectory reader class for filename.

Parameters:
  • filename (str) – filename of the input trajectory or coordinate file
  • permissive (bool) – If set to True, a reader is selected that is more tolerant of the input (currently only implemented for PDB). [False]
  • kwargs – Keyword arguments for the selected Reader class.
Returns:

Return type:

A Reader object

Notes

Automatic detection is disabled when an explicit format is provided.

MDAnalysis.coordinates.core.get_writer_for(filename=None, format=None, multiframe=None)[source]

Return an appropriate trajectory or frame writer class for filename.

The format is determined by the format argument or the extension of filename. If format is provided, it takes precedence over The extension of filename.

Parameters:
  • filename (str) – If no format is supplied, then the filename for the trajectory is examined for its extension and the Writer is chosen accordingly.
  • format (str) – Explicitly set a format.
  • multiframe (bool) – True: write multiple frames to the trajectory; False: only write a single coordinate frame; None: first try trajectory (multi frame writers), then the single frame ones. Default is None.
Returns:

Return type:

A Writer object

Raises:
  • ValueError – The format could not be deduced from filename or an unexpected value was provided for the multiframe argument.
  • TypeError – No writer got found for the required format.
  • .. versionchanged (: 0.7.6) – Added multiframe keyword; the default None reflects the previous behaviour.
  • .. versionchanged (: 0.14.0) – Removed the default value for the format argument. Now, the value provided with the format parameter takes precedence over the extension of filename. A ValueError is raised if the format cannot be deduced from filename.