perform analysis of NOEPot terms and return nicely formatted summary
- calcDeltaResid(r, deltaResidLR)
given an NOE restraint, determine the difference in the residue number of
the two atom selections. If the selections have differing segids,
deltaResid is set to deltaResidLR.
If a selection specifies atoms with differing residue IDs, -1 is returned.
- create_NOEPot(name, file='', esim=0, restraints='', splitRestraints=False, deltaResidLR=5, verbose=False)
Return an noePot.NOEPot instance.
The name of the potential is given by the argument name (a string).
Restraints are specified via an NOE assignment table (whose filename is
indicated in the file argument; a string), and/or via a string of such
assignments (restraints argument). The file argument can optionally be a
sequence of assignment table filenames. esim specifies an ensemble
If splitRestraints=True, the returned potential is a potList.PotList
with noePot.NOEPot instances corresponding to the following classes:
interresidue - sequential
interresidue - short range (1 < delta resid <= deltaResidLR)
interresidue - long range (delta resid > deltaResidLR)
The classes are arranged in the above order within the potList.PotList.
given an atomSel.AtomSel object, return the tuple
(segid,resid), if they are unique. If they are not unique return
given an noePot, generate the associated assignment
table. Return this as a string.
- repeated_restraints(noe, selstrings=True)
Find NOE restraints with similar selection pairs.
Return a list of the type:
[( (seli1, seli2), [(selj1, selj2), ...] ), ...]
where (selk1, selk2) is a pair of selection strings (if selstrings=True,
otherwise atomSel.AtomSel instances) associated with a restraint of the
input noe potential (a noePot.NOEPot instance). In the above example,
(seli1, seli2) has similar selection pairs [(selj1, selj2), ...] within the
noe restraint table. Two individual selections are considered similar if
they select at least one common atom.
- splitTable(noe, deltaResidLR)