def setData(self,hExchRateTableTags,i):
assignList = [['Id', 'ID',None],
['seqCode', 'Seq_ID',None],
['resLabel', 'Comp_ID',None],
['atomName', 'Atom_ID',None],
['atomType', 'Atom_type',None],
['value', 'Val',None],
['valueError', 'Val_err',0.0],
# ['valueMin', 'Val_min',None],
# ['valueMax', 'Val_max',0.0],
['details', 'Details',None],
['authorSeqCode', 'Author_seq_ID',None]
]
for (attrName,tagName,default) in assignList:
if hExchRateTableTags.has_key(tagName):
if hExchRateTableTags[tagName][i] != None:
setattr(self,attrName,hExchRateTableTags[tagName][i])
else:
setattr(self,attrName,default)
# For completeness...
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(self.seqCode)
def setAtomMembers(self, chainCode, seqCode, resLabel):
refAngle = self.cyanaLib.findAngle(resLabel, self.name)
if not refAngle:
print " Warning: no %s angle available for %s. Ignored." % (
self.name, resLabel)
return False
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.resLabel = resLabel
self.items.append(DyanaConstraintItem())
for atom in refAngle.atoms:
if atom.location:
curSeqCode = self.seqCode + atom.location
curResLabel = ""
else:
curSeqCode = self.seqCode
curResLabel = self.resLabel
self.items[-1].members.append(
DyanaConstraintMember(chainCode, curSeqCode, curResLabel,
atom.name))
return True
def setInfo(self, seqCode, atomName):
self.chainCode = defaultMolCode
self.resLabel = None
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.atomName = atomName
def __init__(self,parent,atomSerial,value,valueError,atomName,seqCode,verbose=False): self.atomSerial = returnInt(atomSerial,default=None,verbose=verbose) self.value = returnFloat(value,default=None,verbose=verbose) self.valueError = returnFloat(valueError,default=None,verbose=verbose) self.atomName = atomName (self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode) self.molCode = parent.defaultMolCode
def __init__(self,chainCode = None,seqCode = None, atomName = None, resLabel = None): self.chainCode = chainCode (self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode) self.atomName = atomName self.resLabel = resLabel self.defaultMolCode = defaultMolCode
def __init__(self,Id = None, chainCode = None,seqCode = None, atomName = None, resLabel = None): self.Id = Id self.fracVal = None self.chainCode = chainCode (self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode) self.atomName = atomName self.resLabel = resLabel
def __init__(self,Id,authorId,firstIndexId,authorFirstSeqCode = None,isWaterChain = False):
self.chainId = Id
self.authorId = authorId
self.firstIndexId = firstIndexId
self.isWaterChain = isWaterChain
(self.authorFirstSeqCode,self.authorFirstSeqInsertCode) = getSeqAndInsertCode(authorFirstSeqCode)
def setItemSpecificVars(self): (self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(self.seqCode) self.Id = self.parent.constraintNum self.targetAngle = self.value self.devAngle = self.error self.setAtomMembers()
def setValue(self, valueKey, values):
if len(values) == 1:
value = values[0]
if not self.parent.patt['emptyline'].search(value):
if valueKey == 'residue':
value = value.strip()
self.resLabel = value[0]
seqCodes = value[1:].split(',')
(self.seqCode,
self.seqInsertCode) = getSeqAndInsertCode(seqCodes[0])
if self.seqCode == None:
self.resLabel = value
# Can have multiple values - need to take care of that...
if len(seqCodes) > 1:
for seqCode in seqCodes[1:]:
self.otherSeqAndInsertCodes.append(
getSeqAndInsertCode(seqCode))
elif valueKey == 'atom':
self.atomName = value.strip()
elif valueKey == 'atomType':
self.atomType = value.strip()
elif valueKey == 'chemShift':
self.value = returnFloat(value)
elif valueKey == 'chemShiftError':
self.valueError = returnFloat(value)
elif valueKey == 'numAssignments':
self.numAssignments = returnInt(value)
else:
print " Warning: empty or invalid data field %s for Sparky chemical shift file." % valueKey
pass
def __init__(self, value, atomName, seqCode, spinSystemId, resLabel,
defaultMolCode):
self.value = returnFloat(value)
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = defaultMolCode
self.resLabel = resLabel
self.spinSystemId = spinSystemId
def setInfo(self,chainCode,seqCode,resLabel,atomName):
if chainCode != defaultMolCode:
self.chainCode = chainCode
else:
self.chainCode = concoordDefaultMolCode
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.resLabel = resLabel
self.atomName = atomName
def addStarInfo(self,constraintTableTags,i,position,tableTagNames):
self.chainCode = constraintTableTags[tableTagNames['chainCode'] % position][i]
if not self.chainCode:
self.chainCode = self.defaultMolCode
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(constraintTableTags[tableTagNames['seqCode'] % position][i])
self.atomName = constraintTableTags[tableTagNames['atomName'] % position][i]
self.resLabel = constraintTableTags[tableTagNames['resLabel'] % position][i]
def __init__(self, value, error, ambCode, atomSetName, atomName, seqCode,
molCode):
self.value = value
self.error = error
self.ambCode = ambCode
self.atomSetName = atomSetName
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = molCode
def __init__(self, value, atomName, seqCode, figOfMerit, resLabel, defaultMolCode, iCode = 'i'):
self.value = returnFloat(value)
self.valueError = 0.0
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = defaultMolCode
self.resLabel = resLabel
self.figOfMerit = figOfMerit
self.allValues = {iCode: self.value}
def __init__(self,value,valueError,atomName,atomType,seqCode,resLabel,molCode,ambCode = 0): self.value = value self.valueError = valueError self.atomName = atomName self.atomType = atomType (self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode) self.molCode = molCode self.resLabel = resLabel self.ambCode = ambCode
def setData(self, chemShiftTableTags, i):
# Values already formatted...
if self.parent.version == '2.1.1':
assignList = [
['Id', '_Atom_shift_assign_ID', None],
['seqCode', '_Residue_seq_code', None],
['resLabel', '_Residue_label', None],
['atomName', '_Atom_name', None],
['atomType', '_Atom_type', None],
['value', '_Chem_shift_value', None],
['valueError', '_Chem_shift_value_error', 0.0],
['ambCode', '_Chem_shift_ambiguity_code', 1],
['ambCode', '_Chem_shift_ambiguity_type',
1], # This apparently also occurs sometimes...
['authorSeqCode', '_Residue_author_seq_code', None]
]
else:
# TODO can get a lot more out...
assignList = [['Id', 'ID', None], ['seqCode', 'Seq_ID', None],
['backupSeqCode', 'Comp_index_ID', None],
['resLabel', 'Comp_ID', None],
['atomName', 'Atom_ID', None],
['atomType', 'Atom_type', None],
['value', 'Val', None],
['valueError', 'Val_err', 0.0],
['figOfMerit', 'Assign_fig_of_merit', None],
['ambCode', 'Ambiguity_code', 1],
['details', 'Details', None],
['authorSeqCode', 'Author_seq_ID', None]]
for (attrName, tagName, default) in assignList:
if chemShiftTableTags.has_key(tagName):
if chemShiftTableTags[tagName][i] != None:
setattr(self, attrName, chemShiftTableTags[tagName][i])
else:
setattr(self, attrName, default)
# Little hack - not sure what is best in the end...
if not self.seqCode and hasattr(
self, 'backupSeqCode') and self.backupSeqCode:
self.seqCode = self.backupSeqCode
# For completeness...
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(self.seqCode)
# This is a hack, is possible in older NMR-STAR files! Use resLabel as chain ID
if self.seqCode == None and hasattr(self,
'resLabel') and self.resLabel:
self.seqCode = 1
self.chainCode = self.resLabel
def __init__(self,parent,value,atomName,seqCode,resLabel,molCode):
self.value = value
self.atomName = atomName
#self.atomType = atomType
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = molCode
self.resLabel = resLabel
if not parent.chemShiftsBySeqCodeAndAtomName.has_key(self.seqCode):
parent.chemShiftsBySeqCodeAndAtomName[self.seqCode] = {}
parent.chemShiftsBySeqCodeAndAtomName[self.seqCode][self.atomName] = self
def __init__(self,
value,
atomName,
seqCode,
defaultMolCode,
unknownCode=0):
self.value = returnFloat(value)
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = defaultMolCode
self.unknownCode = returnInt(
unknownCode) # TODO: what is this one for?
def addStarInfo(self,constraintTableTags,i,position,tableTagNames):
# Tag can be missing in 2.1.1 files...
if constraintTableTags.has_key(tableTagNames['chainCode'] % position):
self.chainCode = constraintTableTags[tableTagNames['chainCode'] % position][i]
else:
self.chainCode = None
if not self.chainCode:
self.chainCode = self.defaultMolCode
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(constraintTableTags[tableTagNames['seqCode'] % position][i])
self.atomName = constraintTableTags[tableTagNames['atomName'] % position][i]
self.resLabel = constraintTableTags[tableTagNames['resLabel'] % position][i]
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 __init__(self, seqCode, *args, **keywds):
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.formatCode = None
self.atomNames = []
self.hasCisPeptideBond = False
self.bonds = {}
self.setResidueCode(*args)
self.setFormatSpecific(*args, **keywds)
self.secStrucInfo = None
def setData(self,nodeMembersTableTags,i,tableTagNames):
self.Id = nodeMembersTableTags[tableTagNames['memberID']][i]
if tableTagNames.has_key('fracVal'):
self.fracVal = nodeMembersTableTags[tableTagNames['fracVal']][i]
self.chainCode = nodeMembersTableTags[tableTagNames['chainCode']][i]
if not self.chainCode:
self.chainCode = defaultMolCode
self.resLabel = nodeMembersTableTags[tableTagNames['resLabel']][i]
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(nodeMembersTableTags[tableTagNames['seqCode']][i])
self.atomName = nodeMembersTableTags[tableTagNames['atomName']][i]
if tableTagNames.has_key('chemCompID'):
self.chemCompID = nodeMembersTableTags[tableTagNames['chemCompID']][i]
def apply(self):
self.chainDict = {}
for ccpChainLabel in self.ccpChainLabelDict.keys():
chain = self.ccpChainLabelDict[ccpChainLabel]
selection = self.formatChainMenu[ccpChainLabel].getSelected()
if selection != 'Do not link':
chainDictKey = (ccpChainLabel, selection)
(formatChainCode,
seqCodesList) = self.localFormatChainDict[chainDictKey]
selectedItems = self.ccpCodeLow[
ccpChainLabel].getSelectedItems()
if not selectedItems:
showError(
"No sequence ID selected",
"Please select a sequence ID on the left side for chain %s!"
% ccpChainLabel)
return False
ccpCodeLow = returnInt(
self.ccpChainSeqIdDict[ccpChainLabel][selectedItems[0]])
(formatChainSeqCodeLow, seqInsertCode) = getSeqAndInsertCode(
self.formatChainCodeLow[ccpChainLabel].getSelectedItems()
[0])
exportSeqCodesList = seqCodesList[:]
for (tempSeqCode, tempSeqInsertCode) in seqCodesList:
if tempSeqCode == formatChainSeqCodeLow and tempSeqInsertCode == seqInsertCode:
break
else:
exportSeqCodesList.pop(0)
self.chainDict[chain] = [
formatChainCode, ccpCodeLow, exportSeqCodesList
]
return True
def setData(self, t1RelaxTableTags, i):
assignList = [['Id', 'ID', None], ['seqCode', 'Seq_ID', None],
['resLabel', 'Comp_ID', None],
['atomName', 'Atom_ID', None],
['atomType', 'Atom_type', None],
['tauEValue', 'Tau_e_val', None],
['tauEError', 'Tau_e_val_fit_err', 0.0],
['authorSeqCode', 'Author_seq_ID', None]]
for (attrName, tagName, default) in assignList:
if t1RelaxTableTags.has_key(tagName):
if t1RelaxTableTags[tagName][i] != None:
setattr(self, attrName, t1RelaxTableTags[tagName][i])
else:
setattr(self, attrName, default)
# For completeness...
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(self.seqCode)
def __init__(self,
value,
atomName,
seqCode,
spinSystemId,
peakId,
resLabel,
defaultMolCode,
iCode='i'):
self.value = returnFloat(value)
self.valueError = 0.0
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = defaultMolCode
self.resLabel = resLabel
self.allValues = {iCode: self.value}
self.spinSystemId = spinSystemId
self.peakId = peakId
def __init__(self,
value,
atomName,
seqCode,
spinSystemId,
stripId,
resLabel,
defaultMolCode,
infoCode=None,
prevSpinSystemId=None):
self.value = returnFloat(value)
self.atomName = atomName
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(seqCode)
self.molCode = defaultMolCode
self.resLabel = resLabel
self.spinSystemId = spinSystemId
self.prevSpinSystemId = prevSpinSystemId
self.stripId = stripId
self.infoCode = infoCode
def setData(self,nodeMembersTableTags,i,tableTagNames):
self.Id = nodeMembersTableTags[tableTagNames['memberID']][i]
if tableTagNames.has_key('fracVal'):
self.fracVal = nodeMembersTableTags[tableTagNames['fracVal']][i]
self.chainCode = nodeMembersTableTags[tableTagNames['chainCode']][i]
if not self.chainCode:
self.chainCode = defaultMolCode
self.resLabel = nodeMembersTableTags[tableTagNames['resLabel']][i]
(self.seqCode,self.seqInsertCode) = getSeqAndInsertCode(nodeMembersTableTags[tableTagNames['seqCode']][i])
# This is a hack, is possible in NMR-STAR file from CNS/XPLOR data!
if self.seqCode == None and self.chainCode:
self.seqCode = 1
self.atomName = nodeMembersTableTags[tableTagNames['atomName']][i]
if tableTagNames.has_key('chemCompID'):
self.chemCompID = nodeMembersTableTags[tableTagNames['chemCompID']][i]
def setAtomMembers(self,constraintTableTags,i,tableTagNames):
#
# TODO: this is rather nasty: assuming it's DIANA if dihedral angle name given.
# should really be checking type... leave this for now
#
chainCode = constraintTableTags[tableTagNames['chainCode'] % tableTagNames['position'][0]][i]
if not chainCode:
chainCode = defaultMolCode
# Can only handle real numbers here - no insert codes allowed...
(seqCode,seqInsertCode) = getSeqAndInsertCode(constraintTableTags[tableTagNames['seqCode'] % tableTagNames['position'][0]][i])
resLabel = constraintTableTags[tableTagNames['resLabel'] % tableTagNames['position'][0]][i]
refAngle = self.cyanaLib.findAngle(resLabel,self.name)
self.nodes.append(NmrStarDihedralConstraintItem())
if refAngle:
for atom in refAngle.atoms:
if atom.location:
curSeqCode = seqCode + atom.location
curResLabel = ""
else:
curSeqCode = seqCode
curResLabel = resLabel
self.setAtomMember(self.nodes[-1],chainCode,curSeqCode,atom.name,curResLabel)
else:
print " Error: no reference angle found for name %s..." % self.name
for i in range(4):
curSeqCode = seqCode
curResLabel = resLabel
self.setAtomMember(self.nodes[-1],chainCode,curSeqCode,'',curResLabel)
def setData(self, orderParamTableTags, i):
if self.parent.version == '2.1.1':
assignList = [
['Id', 'SET', i + 1],
['seqCode', '_Residue_seq_code', None],
['resLabel', '_Residue_label', None],
['atomName', '_Atom_name', None],
['s2Value', '_S2_value', None],
['s2Error', '_S2_value_fit_error', 0.0],
['tauEValue', '_Tau_e_value', None],
['tauEError', '_Tau_e_value_fit_error', 0.0],
]
else:
assignList = [['Id', 'ID', None], ['seqCode', 'Seq_ID', None],
['resLabel', 'Comp_ID', None],
['atomName', 'Atom_ID', None],
['atomType', 'Atom_type', None],
['tauEValue', 'Tau_e_val', None],
['tauEError', 'Tau_e_val_fit_err', 0.0],
['authorSeqCode', 'Author_seq_ID', None]]
for (attrName, tagName, default) in assignList:
if orderParamTableTags.has_key(tagName):
if orderParamTableTags[tagName][i] != None:
setattr(self, attrName, orderParamTableTags[tagName][i])
else:
setattr(self, attrName, default)
elif tagName == 'SET':
setattr(self, attrName, default)
# For completeness...
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(self.seqCode)
def setData(self, chemShiftTableTags, i):
# Values already formatted...
if self.parent.version == '2.1.1':
assignList = [['Id', '_Atom_shift_assign_ID', None],
['seqCode', '_Residue_seq_code', None],
['resLabel', '_Residue_label', None],
['atomName', '_Atom_name', None],
['atomType', '_Atom_type', None],
['value', '_Chem_shift_value', None],
['valueError', '_Chem_shift_value_error', 0.0],
['ambCode', '_Chem_shift_ambiguity_code', 1],
['authorSeqCode', '_Residue_author_seq_code', None]]
else:
# TODO can get a lot more out...
assignList = [['Id', 'ID', None], ['seqCode', 'Seq_ID', None],
['resLabel', 'Comp_ID', None],
['atomName', 'Atom_ID', None],
['atomType', 'Atom_type', None],
['value', 'Val', None],
['valueError', 'Val_err', 0.0],
['figOfMerit', 'Assign_fig_of_merit', None],
['ambCode', 'Ambiguity_code', 1],
['details', 'Details', None],
['authorSeqCode', 'Author_seq_ID', None]]
for (attrName, tagName, default) in assignList:
if chemShiftTableTags.has_key(tagName):
if chemShiftTableTags[tagName][i] != None:
setattr(self, attrName, chemShiftTableTags[tagName][i])
else:
setattr(self, attrName, default)
# For completeness...
(self.seqCode, self.seqInsertCode) = getSeqAndInsertCode(self.seqCode)