6.26. Reading trajectory with Chemfiles — `MDAnalysis.coordinates.chemfiles`¶

Classes to read and write files using the chemfiles library. This library provides C++ implementation of multiple formats readers and writers, the full list if available here.

6.26.1. Classes¶

class MDAnalysis.coordinates.chemfiles.ChemfilesReader(filename, chemfiles_format='', **kwargs)[source]¶

Coordinate reader using chemfiles.

The file format to used is guessed based on the file extension. If no matching format is found, a ChemfilesError is raised. It is also possible to manually specify the format to use for a given file.

New in version 1.0.0.

Parameters

filename (chemfiles.Trajectory or str) – the chemfiles object to read or filename to read
chemfiles_format (str (optional)) – if filename was a string, use the given format name instead of guessing from the extension. The list of supported formats and the associated names is available in chemfiles documentation.
**kwargs (dict) – General reader arguments.

class MDAnalysis.coordinates.chemfiles.ChemfilesWriter(filename, n_atoms=0, mode='w', chemfiles_format='', topology=None, **kwargs)[source]¶

Coordinate writer using chemfiles.

The file format to used is guessed based on the file extension. If no matching format is found, a ChemfilesError is raised. It is also possible to manually specify the format to use for a given file.

Chemfiles support writting to files with varying number of atoms if the underlying format support it. This is the case of most of text-based formats.

New in version 1.0.0.

Parameters

filename (str) – filename of trajectory file.
n_atoms (int) – number of atoms in the trajectory to write. This value is not used and can vary during trajectory, if the underlying format support it
mode (str (optional)) – file opening mode: use ‘a’ to append to an existing file or ‘w’ to create a new file
chemfiles_format (str (optional)) –
use the given format name instead of guessing from the extension. The list of supported formats and the associated names is available in chemfiles documentation.
topology (Universe or AtomGroup (optional)) – use the topology from this AtomGroup or Universe to write all the timesteps to the file
**kwargs (dict) – General writer arguments.

class MDAnalysis.coordinates.chemfiles.ChemfilesPicklable(path, mode='r', format='')[source]¶

Chemfiles file object (read-only) that can be pickled.

This class provides a file-like object (as returned by chemfiles.Trajectory) that, unlike standard Python file objects, can be pickled. Only read mode is supported.

When the file is pickled, path, mode, and format of the file handle are saved. On unpickling, the file is opened by path with mode, and saved format. This means that for a successful unpickle, the original file still has to be accessible with its filename.

Note

Can only be used with reading (‘r’) mode. Upon pickling, the current frame is reset. universe.trajectory[i] has to be used to return to its original frame.

Parameters

filename (str) – a filename given a text or byte string.
mode ('r' , optional) – only ‘r’ can be used for pickling.
format ('', optional) – guessed from the file extension if empty.

Example

f = ChemfilesPicklable(XYZ, 'r', '')
print(f.read())
f.close()

can also be used as context manager:

with ChemfilesPicklable(XYZ) as f:
    print(f.read())

6.26. Reading trajectory with Chemfiles — MDAnalysis.coordinates.chemfiles¶

6.26.1. Classes¶

6.26. Reading trajectory with Chemfiles — `MDAnalysis.coordinates.chemfiles`¶