5.20. 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.
See also
For trajectory formats:
DCDReader
,XTCReader
,TRRReader
,XYZReader
. For single frame formats:CRDReader
,PDBReader
andPrimitivePDBReader
,GROReader
,Parameters: - *filename* – filename of the input trajectory or coordinate file
- *permissive* – 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.
-
MDAnalysis.coordinates.core.
writer
(filename, n_atoms=None, **kwargs)[source]¶ Initialize a trajectory writer instance for filename.
Parameters: - *filename* – Output filename of the trajectory; the extension determines the format.
- *n_atoms* – The number of atoms in the output trajectory; can be ommitted for single-frame writers.
- *multiframe* –
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* –
Keyword arguments for the writer; all trajectory Writers accept at least
- start
- starting time [0]
- step
- step size in frames [1]
- delta
- 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.
Changed in version 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.
Automatic detection is disabled when an explicit format is provided.
-
MDAnalysis.coordinates.core.
get_writer_for
(filename=None, format='DCD', 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. The default is to return a dcd writer (format = ‘dcd’). If the filename is not provided or if it is something like a
cStringIO.StringIO
instance then the format argument must be used.Parameters: - *filename* – The filename for the trajectory is examined for its extension and the Writer is chosen accordingly.
- *format* – If no filename is supplied then the format can be explicitly set; possible values are “DCD”, “XTC”, “TRR”; “PDB”, “CRD”, “GRO”.
- *multiframe* –
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 isNone
.
Changed in version 0.7.6: Added multiframe keyword; the default
None
reflects the previous behaviour.