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- genPSF(pdbFilename)
- Generate PSF info from CafeMol-style PDB file.
It is normal to see this message:
%PATCH-ERR: dihedral 1P 1S 2P 2S not found
- loadNinfoNonBonded(filename, selection='not pseudo')
- Read the spcified ninfo file for non-bonded parameters required
by <pair12_10PotTools>.create_Pair12_10Pot
- nonBondToDistanceRestraints(filenameOrString, types=['basepair'], pmErr=2, selection='not pseudo')
- Given the ninfo filename, generate distance restraints from the
nonbonded terms specified by types. The noePot.NOEPot restraint +/-
error is specified by the pmErr argument. The selection argument can be
used to specify restraints for a subset of loaded atoms.
A string of NOEPot restraints is returned, which can be loaded by
NOEPot.addRestraints().
- readCovalentParams(ninfoFilename, verbose=False, selection='not PSEUDO')
- Read BOND, ANGL and DIHE parameters from the specified ninfo file.
Default NONBonded parameters are also added so that the VDW and RepelPot
terms do not crash if invoked.
This function must be called after a PSF is initialized, and has a side
effect: if an angle has an energy scale (force constant) of 0, that angle
wil be removed.
- validateAtomIDs(pdbFilename)
- Check that atom id field in the input CafeMol PDB file are the same as
in the current PSF.
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