def getPeakResNames(self):
self.resNames = []
self.resLabels = []
origAssignName = self.rawPeak.assign[self.rawPeakDimIndex]
if origAssignName not in [None, '?', 'null', '']:
# Spin systems, not handled although in principle possible.
if origAssignName.count("{"):
pass
else:
# TODO Problems: No chain code, what if get for example 1CC5 for DNA or RNA? No label separator.
assignSearch = self.assignPatt.search(origAssignName)
if assignSearch:
if assignSearch.group(1):
chainCode = assignSearch.group(1)
else:
chainCode = defaultMolCode
self.resNames.append(
getResName(chainCode, assignSearch.group(2),
assignSearch.group(4)))
self.resLabels.append(assignSearch.group(3))
else:
print " No decomposition possible for %s assignment"
def getPeakResNames(self):
self.resNames = []
if self.rawPeak.assign:
# Have to do some interpretation of the assigns...
assign = self.rawPeak.assign[self.rawPeakDimIndex]
# Special handling for Montelione group
if '/' in assign:
addAssignStrings = assign.split('/')
assign = addAssignStrings.pop(0)
else:
addAssignStrings = []
if assign != '?':
# Ignore non-assigned peak dims
assignString = self.patt[self.format +
'LabelCodeName'].search(assign)
#
# In Sparky with K18,19HA-R20HN style assignments multiple resNames
# are possible here... making list of resNames to accomodate
#
if assignString:
self.resLabelCodes = assignString.group(1).split(',')
atomName = assignString.group(3)
else:
atomName = assign
for resLabelCode in self.resLabelCodes:
self.resNames.append(
getResName(defaultMolCode, resLabelCode, atomName))
# Add any other info (Montelione group again)
for addAssignString in addAssignStrings:
# This should always work in this case
assignString = self.patt[
self.format + 'LabelCodeName'].search(addAssignString)
resName = getResName(defaultMolCode, assignString.group(1),
assignString.group(3))
self.resNames.append(resName)
def getSinglePeakResName(self, assignName):
(residue, atomName) = assignName.split(self.peakFile.assignSep)
resLabel = residue[0]
seqCode = returnInt(residue[1:])
if atomName.count('|'):
(atomName, otherAtomName) = atomName.split('|')
self.resNames.append(getResName(defaultMolCode, seqCode, atomName))
def getPeakResNames(self):
if self.rawPeak.assignResNum[self.rawPeakDimIndex] != '':
(seqCode, seqInsertCode) = getSeqAndInsertCode(
self.rawPeak.assignResNum[self.rawPeakDimIndex])
self.resNames = [
getResName(' ',
seqCode,
self.rawPeak.assignAtom[self.rawPeakDimIndex],
seqInsertCode=seqInsertCode)
]
else:
self.resNames = []
def getPeakResNames(self):
self.resNames = []
if self.rawPeak.assign[self.rawPeakDimIndex] not in ['-']:
for assignment in [self.rawPeak.assign
] + self.rawPeak.ambiguousAssign:
(atomName,
seqCode) = assignment[self.rawPeakDimIndex].split('.')
self.resNames.append(
getResName(defaultMolCode, seqCode, atomName))
def getPeakResNames(self):
self.resNames = []
if hasattr(self.rawPeak, 'assign'):
if self.rawPeak.assign[self.rawPeakDimIndex] not in [
None, '?', 'null', '', '0'
]:
# TODO is this 'standard' felix type stuff?
(residueInfo, atomName) = string.split(
self.rawPeak.assign[self.rawPeakDimIndex], ':')
(residueCode, seqCode) = string.split(residueInfo, '_')
self.resNames.append(
getResName(defaultMolCode, seqCode, atomName))
def getSinglePeakResName(self, assignName):
(seqCode, atomName) = assignName.split(tagSep)
self.resNames.append(getResName(defaultMolCode, seqCode, atomName))
def duplicateResonances(nmrConstraintStore,format,mappingDict):
#
# Check which resonances have to be copied, and copy...
#
resonanceMappingDict = {}
copyResonances = []
resonanceDict = {}
copyConstraints = []
constrLinks = ['dihedralConstraints','chemShiftConstraints']
copyConstraintItems = {}
copyConstraintItemsList = []
#
# First determine which resonances are eligible for copying, and create a dictionary with resNames...
#
for resonance in nmrConstraintStore.sortedFixedResonances():
applData = resonance.findFirstApplicationData(application = format, keyword = assign_kw)
if applData:
resName = applData.value
resonanceDict[resName] = resonance
(chain,seqCode,spinSystemId,seqInsertCode,atomName) = getNameInfo(resName)
if mappingDict.has_key(chain):
copyResonances.append(resonance)
#
# Then determine which constraint/items have to be copied (all resonances have to have the same chainCode!!)
#
for resonance in copyResonances:
#
# Constraints
#
for constrLink in constrLinks:
for constr in getattr(resonance,constrLink):
copyConstraint = 1
for otherRes in constr.resonances:
if otherRes not in copyResonances:
copyConstraint = 0
break
if copyConstraint and constr not in copyConstraints:
j = 0
constrKey = (constr.parent.serial,constr.serial)
for j in range(0,):
if constrKey < (copyConstraints[j].parent.serial,copyConstraints[j].serial):
copyConstraints.insert(j,constr)
break
listLen = len(copyConstraints)
if j == (listLen - 1) or listLen == 0:
copyConstraints.append(constr)
#
# ConstraintItems
#
for constrItem in resonance.sortedPairwiseConstraintItems():
copyConstraintItem = 1
for otherRes in constrItem.resonances:
if otherRes not in copyResonances:
copyConstraintItem = 0
break
if copyConstraintItem:
if not copyConstraintItems.has_key(constrItem.constraint):
copyConstraintItems[constrItem.constraint] = []
j = 0
constrKey = (constrItem.constraint.parent.serial,constrItem.constraint.serial)
for j in range(0,len(copyConstraintItemsList)):
if constrKey < (copyConstraintItemsList[j].parent.serial,copyConstraintItemsList[j].serial):
copyConstraintItemsList.insert(j,constrItem.constraint)
break
listLen = len(copyConstraintItemsList)
#print constrKey, j, listLen
if j == (listLen - 1) or listLen == 0:
copyConstraintItemsList.append(constrItem.constraint)
if constrItem not in copyConstraintItems[constrItem.constraint]:
copyConstraintItems[constrItem.constraint].append(constrItem)
#
# Now copy the resonances or find an existing resonance...
#
for resonance in copyResonances:
applData = resonance.findFirstApplicationData(application = format, keyword = assign_kw)
applDataClass = applData.__class__
resName = applData.value
(chain,seqCode,spinSystemId,seqInsertCode,atomName) = getNameInfo(resName)
resonanceMappingDict[resonance] = {}
resonance.removeApplicationData(applData)
newValue = getResName(mappingDict[chain][0],seqCode,atomName,seqInsertCode = seqInsertCode)
resonance.addApplicationData(applDataClass(application = format, keyword = assign_kw, value = newValue))
for i in range(1,len(mappingDict[chain])):
newChainCode = mappingDict[chain][i]
newResName = getResName(newChainCode,seqCode,atomName,seqInsertCode = seqInsertCode)
if resonanceDict.has_key(newResName):
newResonance = resonanceDict[newResName]
print " Using existing resonance %s..." % newResName
else:
print " Creating new resonance %s..." % newResName
newResonance = nmrConstraintStore.newFixedResonance(isotopeCode = resonance.isotopeCode)
resonanceDict[newResName] = newResonance
copyResonanceInfo(resonance,newResonance,toResName = newResName)
applData = newResonance.findFirstApplicationData(application = format, keyword = assign_kw)
applDataClass = applData.__class__
newResonance.removeApplicationData(applData)
newResonance.addApplicationData(applDataClass(application = format, keyword = assign_kw, value = newResName))
#
# Constraints and constraint items have to be deleted and recreated later...
#
for constrLink in constrLinks:
for constr in getattr(newResonance,constrLink):
constr.delete()
for constrItem in newResonance.pairwiseConstraintItems:
constrItem.delete()
resonanceMappingDict[resonance][newChainCode] = newResonance
#
# Loop over the 'new' chain codes...
#
print
print "########################## "
print "# Duplicating resonances # "
print "########################## "
print
for i in range(1,len(mappingDict[chain])):
newChainCode = mappingDict[chain][i]
#
# Copy the relevant dihedral constraints...
#
for constraint in copyConstraints:
print " Copying constraint %d.%d" % (constraint.parent.serial,constraint.serial)
print " Resonances %s" % ', '.join([getResNameText(res) for res in constraint.resonances])
(newResonances, oldToNewResonanceDict) = getMappedResonances(constraint,resonanceMappingDict,newChainCode)
print " to %s" % ', '.join([getResNameText(res) for res in newResonances])
newConstr = constraint.__class__(constraint.parent,resonances = newResonances)
copyAttributeInfo(constraint,newConstr)
for constrItem in constraint.sortedItems():
newConstrItem = constrItem.__class__(newConstr, upperLimit = 1.0, lowerLimit = 0.0)
copyAttributeInfo(constrItem,newConstrItem)
print
#
# ..and the constraints from the relevant constraintItems...
#
for constraint in copyConstraintItemsList:
print " Copying constraint %d.%d" % (constraint.parent.serial,constraint.serial)
newConstr = constraint.__class__(constraint.parent)
copyAttributeInfo(constraint,newConstr)
if hasattr(constraint,'weight'):
newConstr.weight = constraint.weight
for constrItem in constraint.sortedItems():
print " Copying item with resonances %s" % ', '.join([getResNameText(res) for res in constrItem.resonances])
if constrItem in copyConstraintItems[constraint]:
(newResonances, oldToNewResonanceDict) = getMappedResonances(constrItem,resonanceMappingDict,newChainCode)
else:
newResonances = constrItem.resonances
oldToNewResonanceDict = {}
print " to %s" % ', '.join([getResNameText(res) for res in newResonances])
newConstrItem = constrItem.__class__(newConstr,resonances = newResonances)
if constrItem.className in ('DistanceConstraintItem', 'HBondConstraintItem', 'JCouplingConstraintItem', 'RdcConstraintItem'):
firstResonance = constrItem.firstResonance
if oldToNewResonanceDict:
firstResonance = oldToNewResonanceDict[firstResonance]
newConstrItem.firstResonance = firstResonance
copyAttributeInfo(constrItem,newConstrItem)
print
print "###################### "
print "# End of duplication # "
print "###################### "
print
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)