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- Rfactor(pot, selection='all', normalize=False)
- R-factor (in percent) for an infinite number of randomly distributed
vectors.
The formula is based on Eq. 3 from Clore+Garrett, JACS 121, 9008 (1999):
R-factor = 100 [1/sqrt(2)] sqrt{ sum[(Di_calc - Di_obs)^2] / sum[Di_obs^2] }
where Di_calc and Di_obs are the ith calculated and observed RDC values,
respectively.
The selection argument can be used to choose a subset of restraints whose
atoms lie in selection.
If normalize is set to True, all values of Di_calc and Di_obs are divided by
sardcPot.SARDCPot_Restraint's Dmax in the above equation.
- addRestraints(rdc, restraints, useSign=True, useDist=False)
- Add XPLOR XDIPO or SARDC style restraints from a string.
One can specify the useSign argument to specify whether the RDC sign will be
significant in evaluating the energy. The useDist argument specifies whether
the 1/r^3 RDC dependence will be taken from the coordinates.
- analyze(potList)
- perform analysis of SARDCPot terms and return nicely formatted summary
- avecScale(pot)
- return pot.rdc.avectorScale()
- chi2(pot, selection='all')
- Compute the Chi^2 value for the specified restraints.
The optional selection argument can be used to choose a subset of
restraints whose atoms lie in selection.
- create_SARDCPot(name, file=0, useSign=True, useDist=False, restraints='', domainSel='not PSEUDO', tensor=None)
- Create an sardcPot.SARDCPot with given name, the filename of an RDC
assignment table and/or a string of assignments.
The file argument can optionally be a sequence of filenames.
domainSel is an atomSel.AtomSel which specifies atoms in an aligning
subunit.
If tensor is specified, it should be a <saTensor>.SATensor object.
One can specify the useSign argument to specify whether the RDC sign will be
significant in evaluating the energy. The useDist argument specifies whether
the 1/r^3 RDC dependence will be taken from the coordinates.
- makeTable(rdc)
- Return the assignment table (a string) corresponding to the
restraints associated with the specified sardcPot.SARDCPot.
- readRestraint(string, useSign, useDist)
- rmsd(pot, selection='all')
- Compute the RMSD value for the specified restraints.
The optional selection argument can be used to choose a subset of
restraints whose atoms lie in selection.
- saupeMatrix(pot, eIndex=None)
- given a SARDCPot term, return the associated Saupe matrix. If eIndex
is specified, return the Saupe matrix associated with the specified
ensemble member. NOT YET TESTED!
- writeNEF(rdc, name)
- Return a formatted NEF record for the restraints in the given SARDCPot
object as a string with the specified saveframe name.
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