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- analyzePr(tagPairDist, PrRef=None, idClosest=False)
- Return string with formatted Pr, and a report of the constituent
distances and weights. If Pr is specified, the reference Pr is also
reported. If idClosest=True, the identities of the non-tag atoms giving
rise to the close distances are output.
- createTags(restraints, nonTagSel, numRotamers=None, resname='R1', tagCoordFilename=None, paraAtomname=None, outSegidPref='', tagInfo=None, tagSim=None, verbose=False)
- Read in conformer PSF and coordinates.
Create a tagSimulation.TagSimulation containing nonTagSel with
tags attached at all attachment points specified by the pairs of
selections in restraints. If nonTagSel is None, then it is read from the
database entry for the given resname. If the database is not populated,
then the value is set to the module-global variable nonTagSelDefault.
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 string which is not used by this
function. In cases where the segid is not important to specify,
the selections can be given as residue numbers (ints in int or
string form).
Tags are added using the tagTool module.
numRotamers: number of rotamer conformations. A value of None
specifies that all conformations in the rotamer library
are used.
The tag identity is specified in the following parameters:
resname - the name of the tag residue.
outSegidPref- all created tags will have begin with this string.
Returns a tagTool.TagTool instance containing information on the added
and attached tag conformers.
tagCoordFilename is passed as the coordsFilename to tagTool.updateDBentry
paraAtomname is also passed to tagTool.updateDBentry.
If the tagInfo argument is not specified, a tagTool.TagTool is
created and a tagTool.TagInfo object is created by calling the
associated addAtoms() method. Otherwise, the specified tagInfo argument
is used for this purpose. If tagInfo is specified, tagSim should also be
specified as a simulation.Simulation containing attached tag atoms.
- readWeights(term, stringOrFilename, potName='[a-zA-Z]*')
- Read rotamer weights from PDB comment lines from the input PDB string
or PDB filename into the energy term.
Returns True if weights are read, and False otherwise.
- selectionMaybeSegidResid(input, segidWildcard=False)
- Return an atom selection string given an input value.
Input is first checked to be of the form SEGID:RESID or simply RESID, in
which case the return value is f"segid {SEGID} and resid {RESID}", or
f"resid {RESID}", respectively. If input takes neither of these forms, it
is simply returned.
If segidWildcard is True, the segid (if present) is replaced with SEGID*.
This is necessay to select all the tag atoms (which have segids which
match this glob.
- setParaAtomRadiusDistanceSigmoidWidth(pot, tagEntries, paraAtomRadius, default_paraAtomRadius, distanceSigmoidWidth, default_distanceSigmoidWidth)
- pot is a deerPot.DEERPot or tagPairPot.TagPairPot
object. Set the paraAtomRadius and distanceSigmoidWidth parameters for
tag atoms based on this rule: the first non-None value of the explicit
parameter value (paraAtomRadius or distanceSigmoidWidth), followed by the
value in the appropriate element of tagEntries, followed by the default
value.
- setProbWidth(pot, tagEntries, probWidth, default_probWidth=None)
- pot is a deerPot.DEERPot or tagPairPot.TagPairPot
object. This function sets the width of the probabilty density
distribution of a single rotamer contribution for each restraint
based on this rule: the first non-None value of the explicit
parameter value (probWidth argument), followed by the value in the
appropriate element of tagEntries, followed by the default value.
- setWeights(pot, weights=None)
- pot is a deerPot.DEERPot object. This function sets the ensemble
populations specifed in the weights argument for all restraints in pot,
which must have length at least equal to the number of rotamers.
- sortRotamersByIWeight(term)
- Sort the rotamers by intrinsic weight, either the fixed values, or
values encoded in aWeights.AWeights coordinates.
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