| | |
- analyze(potlist)
- Perform analysis of TagPairPot terms.
- correlation(term)
- create_TagPairPot(instanceName, restraints=[], verbose=True, nonTagSel='not PSEUDO', paraAtomRadius=None, probWidth=None, distanceSigmoidWidth=None, varyWeights=False, minFrac=0.1, **kwargs)
- Create a tagPairPot.tagPairPot energy term using the specified
restraints. The restraints argument should be a list of
3-element sequences. The first two specify the atom selections of
the two tags, while the third specifies a P(r), either as a filename or as
a string containing the P(r); in either case the file contents or string
should contain lines in which the first two columns r and P(r),
respectively.
nonTagSel - selection for atoms which should be considered
in the computation of tag weight due to overlap.
paraAtomRadius: - radius of paramagnateic tag atom. If specified,
this value overrides that specified in the
tagCoord file. If neither is specified, it is set
to 3 angstroms.
distanceSigmoidWidth - parameter used to compute distance-based weight
based on tag atom distance to atoms in nonTagSel.
If specified, this value overrides that specified
in the tagCoord file. If neither is specified, it
is set to 3 angstroms.
probWidth - width of the distance distribution contribution
from a single pair of rotamers. If specified, this
value overrides that specified in the tagCoord
file. If neither is specified, it is set to
0.7 angstroms.
The created TagSimulation instance is held in the tagSimulation member.
The follow optional arguments are handled by
tagPairDistTools.createTags, and documented there:
numRotamers
resname
tagCoordFilename
paraAtomname
outSegidPref
The verbose argument can be a boolean, or an integer, where larger value
results in more verbose output.
- plotRestraints(pot, outFilename='tagPairRestraints')
- Observed is green, calculated is red
|