def convertAtomNameByType(self, assign):
(chain, seqId, codedAtomName) = assign.split('.')
(typeCode, resType, atomName) = codedAtomName.split(':')
newAssign = None
# Warning: this is slightly dangerous because molType not defined - could in principle find wrong chemComp (Wim 080207)
targetChemComp = self.project.findFirstChemComp(ccpCode=resType)
if targetChemComp:
namingSystem = targetChemComp.findFirstNamingSystem(
name=self.namingSystemName)
if namingSystem:
searchDict = {'sysName': atomName}
chemAtomSysName = findChemAtomSysName(namingSystem, searchDict)
newAtomName = chemAtomSysName.atomName
#print chemAtomSysName,atomName,newAtomName
newCodedAtomName = ':'.join((typeCode, resType, newAtomName), )
newAssign = '.'.join((chain, seqId, newCodedAtomName), )
#if assign != newAssign:
#print '\tNote: changed %s %s %s %s to %s' % (chain,resType,seqId,atomName,newAtomName)
return newAssign
def findMatchingAtom(self,residue,atomName):
atom = residue.findFirstAtom(name = atomName)
if not atom:
# Rough search but should be OK for bb atoms
namingSystem = residue.chemCompVar.chemComp.findFirstNamingSystem(name = 'XPLOR')
chemAtomSysName = findChemAtomSysName(namingSystem,{'sysName': atomName})
atom = residue.findFirstAtom(name = chemAtomSysName.atomName)
return atom
def setRawDistanceConstraintItemMembers(self):
#
# Expand the information... is necessary for Concoord (only handles individual atoms)
#
atomNameLists = []
for i in range(0, 2):
atomNameLists.append([])
resonanceToAtom = self.ccpInfo[i][3]
chemAtomOrigName = self.ccpInfo[i][2]
if resonanceToAtom.chemAtomSet:
chemAtomOrSet = resonanceToAtom.chemAtomSet
else:
chemAtomOrSet = resonanceToAtom.chemAtom
if chemAtomOrSet:
chemCompVar = resonanceToAtom.getResidue().chemCompVar
namingSystem = chemCompVar.chemComp.findFirstNamingSystem(
name=self.namingSystemName)
if namingSystem:
chemAtomSysName = findChemAtomSysName(
namingSystem, {'sysName': chemAtomOrigName})
else:
chemAtomSysName = None
if chemAtomSysName:
chemAtom = chemCompVar.findFirstChemAtom(
name=chemAtomSysName.atomName,
subType=chemAtomSysName.atomSubType)
else:
chemAtom = chemCompVar.findFirstChemAtom(
name=chemAtomOrigName)
if not chemAtom:
chemAtomSetSysName = findChemAtomSetSysName(
namingSystem, {'sysName': chemAtomOrigName})
if chemAtomSetSysName:
chemAtomSet = chemCompVar.findFirstChemAtomSet(
name=chemAtomSetSysName.atomName,
subType=chemAtomSetSysName.atomSubType)
else:
chemAtomSet = chemCompVar.findFirstChemAtomSet(
name=chemAtomOrigName)
if chemAtomSet:
(chainCode, seqCode, spinSystemId, seqInsertCode,
atomName) = getNameInfo(self.resSetNames[i])
if chemAtomSet.chemAtomSets:
chemAtomSets = list(chemAtomSet.chemAtomSets)
else:
chemAtomSets = [chemAtomSet]
for chemAtomSet in chemAtomSets:
chemAtomSysNames = self.getChemAtomSysNamesFromSet(
chemAtomSet, chemCompVar, findIupac=1)
for chemAtomSysName in chemAtomSysNames:
if chemAtomSysName:
atomNameLists[-1].append(
getResName(
chainCode,
seqCode,
chemAtomSysName,
seqInsertCode=seqInsertCode))
else:
print " Error: problems with decompressing Concoord name %s - sysNames missing for %s" % (
self.resSetNames[i], chemAtomSet.name)
else:
print " Error: can't decompress Concoord name %s" % self.resSetNames[
i]
#
# If no names use default
#
if not atomNameLists[-1]:
atomNameLists[-1].append(self.resSetNames[i])
#
# Now write them one by one...
#
itemResonances = getResonancesFromPairwiseConstraintItem(self.item)
for resSetName0 in atomNameLists[0]:
# TODO: bit risky this one! What if original names (eg GLU-) are being used?!
resonance = itemResonances[0]
resLabel0 = resonance.resonanceSet.findFirstAtomSet(
).findFirstAtom().residue.molResidue.chemComp.ccpCode.upper()
(chainCode0, seqCode0, spinSystemId0, seqInsertCode0,
atomName0) = getNameInfo(resSetName0)
if atomName0 == allResidueAtoms_kw:
print " Error: not handling residue level constraints for %s." % self.format
continue
for resSetName1 in atomNameLists[1]:
# TODO: bit risky this one! What if original names (eg GLU-) are being used?!
resonance = itemResonances[1]
resLabel1 = resonance.resonanceSet.findFirstAtomSet(
).findFirstAtom().residue.molResidue.chemComp.ccpCode.upper()
(chainCode1, seqCode1, spinSystemId1, seqInsertCode1,
atomName1) = getNameInfo(resSetName1)
if atomName1 == allResidueAtoms_kw:
print " Error: not handling residue level constraints for %s." % self.format
continue
#
# Now set all items and members...
#
self.rawConstraint.items.append(self.rawConstraintItemClass())
self.rawConstraintItem = self.rawConstraint.items[-1]
self.rawConstraintItem.members.append(
self.rawConstraintItemMemberClass())
self.rawConstraintItem.members[-1].setInfo(
chainCode0, seqCode0, resLabel0, atomName0)
self.rawConstraintItem.members.append(
self.rawConstraintItemMemberClass())
self.rawConstraintItem.members[-1].setInfo(
chainCode1, seqCode1, resLabel1, atomName1)