Important base classes are collected in MDAnalysis.coordinates.base.
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 some readers (such as PDB) 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 and PrimitivePDBReader, GROReader,
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Initialize a trajectory writer instance for filename.
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Changed in version 0.7.6: Added multiframe keyword. See also get_writer_for().
Helper functions:
Return the appropriate trajectory reader class for filename.
Automatic detection is disabled when an explicit format is provided.
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.
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Changed in version 0.7.6: Added multiframe keyword; the default None reflects the previous behaviour.
Returns the type of file filename.
The current heuristic simply looks at the filename extension but more complicated probes could be implemented here or in the individual packages (e.g. as static methods). filename can also be a stream, in which case filename.name is looked at for a hint to the format if format is not provided.
If format is supplied then it overrides the auto detection.
Convert the three triclinic box vectors to [A,B,C,alpha,beta,gamma].
Angles are in degrees.
See also
Definition of angles: http://en.wikipedia.org/wiki/Lattice_constant
Convert [A,B,C,alpha,beta,gamma] to a triclinic box representation.
Original code by Tsjerk Wassenaar posted on the Gromacs mailinglist.
If dimensions indicates a non-periodic system (i.e. all lengths 0) then null-vectors are returned.
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Returns : | numpy 3x3 array B, with B[0] = first box vector, B[1] = second vector, B[2] third box vector. |
Note
The first vector is always pointing along the X-axis i.e. parallel to (1,0,0).
Changed in version 0.7.6: Null-vectors are returned for non-periodic (or missing) unit cell.
Return the volume of the unitcell described by dimensions.
The volume is computed as det(x1,x2,x2) where the xi are the triclinic box vectors from triclinic_vectors().
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Returns : | numpy 3x3 array B, with B[0] = first box vector, B[1] = second vector, B[2] third box vector. |