Python: module chemShiftTools
Tools for converting from various chemical shift formats to that used by
the Xplor-NIH potential terms.
Functions |
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- convertFromPipp(restraints, segid=None, ambiguousGlyHA=False, verbose=False)
- Parse the given string restraint table and split it into tables for each
supported atom type present. If segid is not specified, then the
selection omits a segid selection.
- convertFromTalos(restraints, segid=None, ambiguousGlyHA=False, verbose=False)
- Parse the given string restraint table and split it into tables for each
supported atom type present. If segid is not specified, then the
selection omits a segid selection.
- convertRestraints(restraints, format, saveSet=None, segid=None, ambiguousGlyHA=False, returnDict=False, outFormat='XPLOR', verbose=False)
- Convert restraints to Xplor-NIH native format.
The format of this string can be 'plain' (internal Xplor-NIH format),
'TALOS', 'PIPP', or 'NMRSTAR'. The saveSet argument can be specified to
choose a specific set of chemical shifts from a NMRSTAR table.
The segid argument can be used to add a segment name to each restraint.
If ambiguousGlyHA is True, HA1 and HA2 stereo specific chemical
shifts will be made ambiguous.
For outFormat="XPLOR", the return value is a string of lines of the form:
assign (selection) val err
unless returnDict=True, in which case, a dictionary is returned with
the keys atom names, and the values (possibly mutiline) strings of assign
lines.
For outFormat="tuples", a list of tuples of ( "sel str", shift, err ) is
returned, with the err element possibly missing.
- nameConvertType(name)
- Given an atom name, return a tuple consisting of the corresponding
Sparta atom type and a possibly converted atom name
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