7.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD

Read and write coordinates in CHARMM CARD coordinate format (suffix “crd”). The CHARMM “extended format” is handled automatically.

class MDAnalysis.coordinates.CRD.CRDReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]

CRD reader that implements the standard and extended CRD coordinate formats

Changed in version 0.11.0: Now returns a ValueError instead of FormatError. Frames now 0-based instead of 1-based.

Writer(filename, **kwargs)[source]

Returns a CRDWriter for filename.

Parameters:

filename (str) – filename of the output CRD file

Return type:

CRDWriter

units = {'length': 'Angstrom', 'time': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.coordinates.CRD.CRDWriter(filename, **kwargs)[source]

CRD writer that implements the CHARMM CRD coordinate format.

It automatically writes the CHARMM EXT extended format if there are more than 99,999 atoms.

Requires the following attributes to be present: - resids - resnames - names - chainIDs - tempfactors

Changed in version 0.11.0: Frames now 0-based instead of 1-based

Changed in version 2.2.0: CRD extended format can now be explicitly requested with the extended keyword

Changed in version 2.6.0: Files are now written in wt mode, and keep extensions, allowing for files to be written under compressed formats

Parameters:

  • filename (str or NamedStream) – name of the output file or a stream

  • extended (bool (optional)) –

    By default, noextended CRD format is used [False]. However, extended CRD format can be forced by specifying extended =True. Note that the extended format is always used if the number of atoms exceeds 99,999, regardless of the setting of extended.

    Added in version 2.2.0.

units = {'length': 'Angstrom', 'time': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

write(selection, frame=None)[source]

Write selection at current trajectory frame to file.

Parameters:

  • selection (AtomGroup) – group of atoms to be written

  • frame (int (optional)) – Move the trajectory to frame frame; by default, write the current frame.