def calcQshift(project):
"""Calculate per residue Q factors between assignment and shiftx results
"""
if project is None:
nTmessage("calcQshift: no project defined")
return None
# end if
if not project.molecule:
nTmessage("calcQshift: no molecule defined")
return None
# end if
nTdetail("==> Calculating Q-factors for chemical shift")
for res in project.molecule.allResidues():
atms = res.allAtoms()
bb = NTlist()
heavy = NTlist()
protons = NTlist()
for a in atms:
if a.isBackbone():
bb.append(a)
if a.isProton():
protons.append(a)
else:
heavy.append(a)
# end for
result = project.validationData.getResult(res, constants.SHIFTX_KEY, QshiftxResult())
if result is None:
nTmessage("calcQshift: error setting QshiftResult for residue %s", res)
return None
# end if
result[QshiftxResult.ALL_ATOMS] = _calcQshift(project, atms)
result[QshiftxResult.BACKBONE] = _calcQshift(project, bb)
result[QshiftxResult.HEAVY_ATOMS] = _calcQshift(project, heavy)
result[QshiftxResult.PROTONS] = _calcQshift(project, protons)
# LEGACY
qshiftDict = legacyQshiftDict()
for k in [QshiftxResult.ALL_ATOMS, QshiftxResult.BACKBONE, QshiftxResult.HEAVY_ATOMS, QshiftxResult.PROTONS]:
qshiftDict[k] = result[k]
qshiftDict["residue"] = res
res.Qshift = qshiftDict
def save(self, path = None):
"""
Create a SML file
Return self or None on error
Sort the list on id before saving, to preserve (original) order from save to restore.
"""
# sort the list on id number
NTsort( self, byItem='id', inplace=True)
if not path:
path = self.objectPath
if self.SMLhandler.toFile(self, path) != self:
nTerror('%s.save: failed creating "%s"' % (self.__CLASS__, path))
return None
#end if
# restore original sorting
if self._byItem:
NTsort( self, byItem=self._byItem, inplace=True)
nTdetail('==> Saved %s to "%s"', self, path)
return self