def get_bound_resonances_of_isotope(resonance, isotope):
'''For a resonance, get all resonances of an
isotope type bound to this resonance.
'''
isotopeCode = '{}{}'.format(isotope.massNumber, isotope.chemElement.symbol)
# Use getBoundResonance to get from e.g. Cga to Hga* and not Hgb*
resonancesA = set(x for x in getBoundResonances(resonance, recalculate=True)
if x.isotopeCode == isotopeCode
and x.resonanceSet)
# get covalently bound atomSts
atoms = set()
for atomSet in resonance.resonanceSet.atomSets:
atoms.update(getBoundAtoms(atomSet.findFirstAtom()))
atomSets = set(a.atomSet for a in atoms if a.atomSet and \
a.chemAtom.chemElement is isotope.chemElement)
if resonancesA:
# remove covalently impossible resonances
resonanceSets = set(y for x in atomSets for y in x.resonanceSets)
resonancesA = set(x for x in resonancesA
if x.resonanceSet in resonanceSets)
if not resonancesA:
nmrProject = resonance.parent
# make new resonances for covanlently bound atoms
for atomSet in atomSets:
resonanceB = nmrProject.newResonance(isotopeCode=isotopeCode)
assignAtomsToRes([atomSet,], resonanceB)
resonancesA.add(resonanceB)
return resonancesA
def shiftx(structure, atomType=None):
from ccpnmr.analysis.core.StructureBasic import makePdbFromStructure
from ccpnmr.analysis.core.MoleculeBasic import makeResidueAtomSets, DEFAULT_ISOTOPES
from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes
memopsRoot = structure.root
nmrProject = memopsRoot.currentNmrProject
dataRepository = memopsRoot.findFirstRepository(name='userData')
projPath = dataRepository.url.dataLocation
tempDir = path.join(projPath, 'shiftx')
if not path.exists(tempDir):
mkdir(tempDir)
pdbFile = path.join(tempDir, 'shiftxInput.pdb')
outFile = path.join(tempDir, 'shiftxOutput.out')
exeFile = path.join(SHIFTX_DIR, 'shiftx')
chainDict = {}
shiftList = None
for model in structure.models:
makePdbFromStructure(pdbFile, structure, model=model, useOxt=True)
for coordChain in structure.sortedCoordChains():
chain = coordChain.chain
print 'CCPN SHIFTX executing for chain %s' % chain.code
cmd = '%s 1%s %s %s' % (exeFile, chain.code, pdbFile, outFile)
system(cmd)
fileHandle = open(outFile, 'r')
lines = fileHandle.readlines()
if chain not in chainDict:
chainDict[chain] = shiftData = {}
else:
shiftData = chainDict[chain]
for line in lines:
data = line.split()
if not data:
continue
first = data[0]
if first.upper() == 'NUM':
atomNames = data[2:]
elif first[0] == '-':
continue
elif first[0] == '*':
continue
elif first.isdigit(): # What to do with alt codes and inaccuracies? *10, 12A etc
seqCode = int(first)
resCode = data[1]
if seqCode not in shiftData:
shiftData[seqCode] = shiftDict = {}
else:
shiftDict = shiftData[seqCode]
for i, atomName in enumerate(atomNames):
if atomName not in shiftDict:
shiftDict[atomName] = []
shiftDict[atomName].append(float(data[i+2]))
for chain in chainDict:
print 'CCPN SHIFTX filling shift list for chain %s' % chain.code
shiftData = chainDict[chain]
if shiftData:
if not shiftList:
msCode = structure.molSystem.code
eId = structure.ensembleId
details = 'SHIFTX prediction for %s ensemble %d' % (msCode, eId)
shiftList = nmrProject.newShiftList(name='SHIFTX',
details=details,
isSimulated=True)
for residue in chain.sortedResidues():
shiftDict = shiftData.get(residue.seqCode)
if not shiftDict:
continue
getAtom = residue.findFirstAtom
for atomName in shiftDict:
atom = getAtom(name=atomName)
if not atom:
# Gly HA -> HA2, Ala HB - HB2, Val HG1 - HG12
atom = getAtom(name=atomName+'2')
if not atom:
continue
ppms = shiftDict[atomName]
ppm = sum(ppms)/float(len(ppms))
if ppm == 0.0: # Could actually be a real value...
continue
atomSet = atom.atomSet
if not atomSet:
makeResidueAtomSets(residue)
atomSet = atom.atomSet
resonance = None
for resonanceSet in atomSet.resonanceSets:
resonances = list(resonanceSet.resonances)
if len(resonances) == 1:
resonance = resonances[0]
if not resonance:
isotopeCode = DEFAULT_ISOTOPES[atom.chemAtom.chemElement.symbol]
resonance = nmrProject.newResonance(isotopeCode=isotopeCode)
assignAtomsToRes([atomSet,], resonance)
if shiftList.findFirstMeasurement(resonance=resonance):
print residue.seqCode, residue.ccpCode, atom.name
else:
shift = shiftList.newShift(value=ppm, resonance=resonance)
print 'CCPN SHIFTX done'
return shiftList
def makeResidueAtomSetsEquivalent(residue):
"""Remake a residue's atom sets if they are found to be equivalent: e.g.
if an aromatic ring rotates quickly on the NMR timescale
.. describe:: Input
MolSystem.Residue
.. describe:: Output
None
"""
#chain = residue.chain
molType = residue.molResidue.molType
residueMapping = getResidueMapping(residue)
equivalent = {}
elementSymbolDict = {}
chemAtomSetDict = {}
for atom in residue.atoms:
chemAtom = atom.chemAtom
chemAtomSetDict[atom] = chemAtom
elementSymbol = chemAtom.elementSymbol
if chemAtom.chemAtomSet:
chemAtomSet = chemAtom.chemAtomSet
name = chemAtomSet.name
if chemAtomSet.isEquivalent is None: # i.e. not False, aromatic rotation
if equivalent.get(name) is None:
equivalent[name] = []
equivalent[name].append(atom)
elementSymbolDict[name] = chemAtom.elementSymbol
chemAtomSetDict[name] = chemAtomSet
for groupName in equivalent.keys():
atoms = equivalent[groupName]
if atoms[0].atomSet:
for atom in atoms[1:]:
if atom.atomSet is atoms[0].atomSet:
return
elementSymbol = elementSymbolDict[groupName]
chemAtomSet = chemAtomSetDict[groupName]
resonances = []
for atom in atoms:
# TBD more nested layers?
# delete ambiguous
name = makeGuiName(chemAtomSet.name, elementSymbol, molType)
atomSetMapping = residueMapping.findFirstAtomSetMapping(name=name)
if atomSetMapping:
atomSetMapping.delete()
# delete stereospecific
name = makeGuiName(atom.chemAtom.name, elementSymbol, molType)
atomSetMapping = residueMapping.findFirstAtomSetMapping(name=name)
if atomSetMapping:
atomSetMapping.delete()
# delete non-stereospecific
name = makeGuiName(makeNonStereoName(molType, atom.chemAtom.name),
elementSymbol, molType)
atomSetMapping = residueMapping.findFirstAtomSetMapping(name=name)
if atomSetMapping:
atomSetMapping.delete()
atomSet = atom.atomSet
if atomSet:
for resonanceSet in atomSet.resonanceSets:
resonances.extend(resonanceSet.resonances)
atomSet.delete()
elementSymbol = elementSymbolDict[groupName]
chemAtomSet = chemAtomSetDict[groupName]
# make single equivalent group
#makeAtomSet(,groupName,atoms,chemAtomSet,'simple')
atomSet = makeAtomSet(groupName, atoms, chemAtomSet, 'simple')
for resonance in resonances:
assignAtomsToRes([
atomSet,
], resonance)
def makeResidueAtomSetsNonEquivalent(residue):
"""Remake a residue's atom sets if they are found to be non-equivalent: e.g.
if an aromatic ring does not rotate quickly on the NMR timescale
.. describe:: Input
MolSystem.Residue
.. describe:: Output
None
"""
residueMapping = getResidueMapping(residue)
#chain = residue.chain
molType = residue.molResidue.molType
nonequivalent = {}
elementSymbolDict = {}
chemAtomSetDict = {}
for atom in residue.atoms:
chemAtom = atom.chemAtom
chemAtomSetDict[atom] = chemAtom
elementSymbol = chemAtom.elementSymbol
if chemAtom.chemAtomSet:
chemAtomSet = chemAtom.chemAtomSet
name = chemAtomSet.name
if chemAtomSet.isEquivalent is None: # i.e. not False, aromatic rotation
if nonequivalent.get(name) is None:
nonequivalent[name] = []
nonequivalent[name].append(atom)
elementSymbolDict[name] = chemAtom.elementSymbol
chemAtomSetDict[name] = chemAtomSet
for groupName in nonequivalent.keys():
atoms = nonequivalent[groupName]
atomSet = atoms[0].atomSet
if atomSet:
for atom in atoms[1:]:
if atom.atomSet is not atoms[0].atomSet:
return # already seperate
elementSymbol = elementSymbolDict[groupName]
chemAtomSet = chemAtomSetDict[groupName]
resonances = []
if atomSet:
for resonanceSet in atomSet.resonanceSets:
for resonance in resonanceSet.resonances:
resonances.append(resonance)
atomSet.delete()
name = makeGuiName(groupName, elementSymbol, molType)
atomSetMapping = residueMapping.findFirstAtomSetMapping(name=name)
if atomSetMapping:
atomSetMapping.delete()
atomSets = []
atomSetNames = []
for atom in atoms:
name = chemAtomSetDict[atom].name
atomSet = makeAtomSet(name, (atom, ), chemAtomSet, 'stereo')
atomSets.append(atomSet)
atomSetNames.append(name)
resonanceSet = None
for resonance in resonances:
resonanceSet = assignAtomsToRes(atomSets, resonance, resonanceSet)
for n, atom in enumerate(atoms):
name = chemAtomSetDict[atom].name
name2 = makeNonStereoName(molType, name, n)
makeGuiMultiAtomSet(residue, name2, atomSetNames, elementSymbol,
'nonstereo', chemAtomSet)
makeGuiMultiAtomSet(residue, groupName, atomSetNames, elementSymbol,
'ambiguous', chemAtomSet)
def duplicateResidueAssignments(residueA, residueB, experimentChains=None):
"""
Assign residueB to an equivalent set of resonances as residueA
Optional dictionary, keyed by experiment to specifiy which chain (should be parent of residueA
or residueB or None - for both) an experiment's peak assignments should go with.
.. describe:: Input
MolSystem.Residue, MolSystem.Residue, Dict of Nmr.Experiment:MolSystem.Chain (or None)
.. describe:: Output
None
"""
from ccpnmr.analysis.core.AssignmentBasic import assignResToDim
project = residueA.root
nmrProject = project.currentNmrProject
atomSetDict = {}
for atom in residueB.atoms:
atomSet = atom.atomSet
if atomSet:
atomSetDict[atomSet.name] = atomSet
if experimentChains is None:
experimentChains = {}
else:
for experiment in experimentChains:
chain = experimentChains[experiment]
molSystems = experiment.molSystems
if chain and chain.molSystem not in molSystems:
experiment.addMolSystem(chain.molSystem)
else:
if residueA.chain.molSystem not in molSystems:
experiment.addMolSystem(residueA.chain.molSystem)
if residueB.chain.molSystem not in molSystems:
experiment.addMolSystem(residueB.chain.molSystem)
resonancesA = getResidueResonances(residueA)
resonancesB = getResidueResonances(residueB)
resonancesDictA = {}
for resonance in resonancesA:
atomSetNames = [ass.name for ass in resonance.resonanceSet.atomSets]
atomSetNames.sort()
key = tuple(atomSetNames)
resonancesDictA[key] = resonancesDictA.get(key, []) + [
resonance,
]
resonancesDictB = {}
for resonance in resonancesB:
atomSetNames = [ass.name for ass in resonance.resonanceSet.atomSets]
atomSetNames.sort()
key = tuple(atomSetNames)
resonancesDictB[key] = resonancesDictB.get(key, []) + [
resonance,
]
transfers = []
pureTransfer = True
for key in resonancesDictA.keys():
resonances1 = resonancesDictA[key]
resonances2 = resonancesDictB.get(key, [])
atomSets = []
for atomSetName in key:
if atomSetDict.has_key(atomSetName):
atomSets.append(atomSetDict[atomSetName])
if len(atomSets) == len(
key
): # If we find all equiv atom sets in destination (not always true if different res type)
# Duplications of resonances is only done if needed at a per atomSet level
doDuplicate = False
contribs = set()
for resonance1 in resonances1:
contribs.update(resonance1.peakDimContribs)
if contribs:
for contrib in contribs:
experiment = contrib.peakDim.peak.peakList.dataSource.experiment
if experimentChains.get(
experiment, residueB.chain
) is not residueB.chain: # Not a plain transfer
doDuplicate = True
pureTransfer = False
break
else: # All orphans
for experiment in experimentChains:
if experimentChains[experiment] is not residueB.chain:
doDuplicate = True
pureTransfer = False
break
if doDuplicate: # Not a plain transfer Need to make new resonances
while len(resonances2) < len(resonances1):
resonances2.append(None)
for i, resonance1 in enumerate(resonances1):
resonance2 = resonances2[i]
peakDimContribs = list(resonance1.peakDimContribs)
if peakDimContribs:
for peakDimContrib in peakDimContribs:
peakDim = peakDimContrib.peakDim
experiment = peakDim.peak.peakList.dataSource.experiment
chainB = experimentChains.get(experiment)
if chainB is None: # Duplication on this peak
if resonance2 is None:
resonance2 = nmrProject.newResonance(
isotopeCode=resonances1[0].isotopeCode)
assignAtomsToRes(atomSets, resonance2)
resonances2[i] = resonance2
assignResToDim(peakDim,
resonance2,
doWarning=False)
elif chainB is residueB.chain: # Transfer this peak
if resonance2 is None:
resonance2 = nmrProject.newResonance(
isotopeCode=resonances1[0].isotopeCode)
assignAtomsToRes(atomSets, resonance2)
resonances2[i] = resonance2
assignResToDim(peakDim,
resonance2,
doWarning=False)
for peakContrib in peakDimContrib.peakContribs:
if len(peakContrib.peakDimContribs) < 2:
peakContrib.delete()
if not peakDimContrib.isDeleted:
peakDimContrib.delete()
else:
if resonance2 is None:
resonance2 = nmrProject.newResonance(
isotopeCode=resonances1[0].isotopeCode)
assignAtomsToRes(atomSets, resonance2)
resonances2[i] = resonance2
else:
# Plain transfer, move existing resonances to different atoms
transfers.append((resonances1, atomSets))
# Transfer original spin system to destination residue
# to keep existing links and attrs (pure transfers only)
spinSystem = nmrProject.findFirstResonanceGroup(residue=residueA)
if spinSystem and pureTransfer:
spinSystem.residue = residueB
spinSystem.ccpCode = residueB.ccpCode
spinSystem.chains = [
residueB.chain,
]
# Clear all resonance to spinSystem links first so
# that assigniment can pickup the original spin system
for resonances, atomSets in transfers:
for resonance in resonances:
resonance.resonanceGroup = None
for resonances, atomSets in transfers:
for resonance in resonances:
assignAtomsToRes(atomSets, resonance)
def assignResonances(resonances, atomToResonanceMap, molSystem, ccpnShiftList,
AnalysisProject, nmrConstraintStore):
print "assigning resonances"
atomTupleDict = {}
resonanceDict = {}
fixedResonanceDict = {}
cingFixedResonanceDict = {}
for cingResonance in resonances:
ccpnResidueArray = cingResonance.atom.residue.typeIdentifier.translate(
'CCPN').split()
ccpnResidueName = ccpnResidueArray[1]
if cingResonance.stereo == True:
### find the ccpnResonance from which the cingResonance originated and assign it.
ringAtoms = [
'CD1', 'CD2', 'CE1', 'CE2', 'HD1', 'HD2', 'HE1', 'HE2'
]
ccpnRealAtomName = cingResonance.atom.typeIdentifier.translate(
'CCPN')
if ccpnResidueName == 'Phe' and ccpnRealAtomName in ringAtoms:
ccpnRealAtomName = ccpnRealAtomName[:2] + "*"
if ccpnResidueName == 'Tyr' and ccpnRealAtomName in ringAtoms:
ccpnRealAtomName = ccpnRealAtomName[:2] + "*"
ccpnMappingAtomName = ccpnRealAtomName[0] + ccpnRealAtomName[
1:].lower()
if len(ccpnRealAtomName) == 1:
ccpnMappingAtomName = ccpnRealAtomName
else:
ccpnMappingAtomName = ccpnRealAtomName[0] + ccpnRealAtomName[
1:].lower()
ccpnChainCode = molSystem.findFirstChain(
code=cingResonance.atom.chainId)
ccpnResNum = cingResonance.atom.sequenceId
ccpnResidue = molSystem.findFirstChain().findFirstResidue(
seqCode=ccpnResNum)
ccpnResidueMapping = AnalysisProject.findFirstChainMapping(
molSystemCode=molSystem.code,
chainCode=cingResonance.atom.chainId).findFirstResidueMapping(
seqId=ccpnResidue.seqId)
ccpnAtomMapping = ccpnResidueMapping.findFirstAtomSetMapping(
name=ccpnMappingAtomName)
atomTuple = (ccpnChainCode, ccpnResidue.seqId, ccpnRealAtomName)
if atomTuple not in atomTupleDict:
atomTupleDict[atomTuple] = cingResonance
resonance = atomToResonanceMap[atomTuple]
assignAtomsToRes(ccpnAtomMapping.atomSets, resonance)
# except KeyError:
# pass
else:
### find the ccpnResonance from which the cingResonance originated and assign it.
ringAtoms = [
'CD1', 'CD2', 'CE1', 'CE2', 'HD1', 'HD2', 'HE1', 'HE2'
]
ccpnRealAtomName = cingResonance.atom.typeIdentifier.translate(
'CCPN')
if ccpnResidueName == 'Phe' and ccpnRealAtomName in ringAtoms:
ccpnRealAtomName = ccpnRealAtomName[:2] + "*"
if ccpnResidueName == 'Tyr' and ccpnRealAtomName in ringAtoms:
ccpnRealAtomName = ccpnRealAtomName[:2] + "*"
ccpnChainCode = molSystem.findFirstChain(
code=cingResonance.atom.chainId)
ccpnResNum = cingResonance.atom.sequenceId
ccpnResidue = molSystem.findFirstChain().findFirstResidue(
seqCode=ccpnResNum)
atomTuple = (ccpnChainCode, ccpnResidue.seqId, ccpnRealAtomName)
if atomTuple not in atomTupleDict:
atomTupleDict[atomTuple] = cingResonance
for atomTuple in atomTupleDict:
cingResonance = atomTupleDict[atomTuple]
try:
resonance = atomToResonanceMap[atomTuple]
shift = ccpnShiftList.newShift(value=cingResonance.value,
resonance=resonance)
if resonance is not None:
resonanceDict[cingResonance] = resonance
fixedResonance = getFixedResonance(nmrConstraintStore,
resonance)
fixedResonanceDict[resonance] = fixedResonance
cingFixedResonanceDict[cingResonance.atom] = fixedResonance
except KeyError:
pass
return {
"resonanceDict": resonanceDict,
"fixedResonanceDict": fixedResonanceDict,
"cingFixedResonanceDict": cingFixedResonanceDict
}
print "Resonances assigned"
def storeDihedralConstraints(self):
if not self.dangleChain:
return
# make a new dihedralConstraintList
head = self.constraintSet
if not head:
head = self.project.newNmrConstraintStore(
nmrProject=self.nmrProject)
self.constraintSet = head
chain = self.dangleChain.chain
shiftList = self.dangleChain.shiftList
name = 'DANGLE Chain %s:%s ShiftList %d' % (
chain.molSystem.code, chain.code, shiftList.serial)
constraintList = head.newDihedralConstraintList(name=name,
measureListSerials=[
shiftList.serial,
])
# traverse the sequence and make appropriate constraint objects
residues = chain.sortedResidues()
for residue in residues:
# Ensure we have atomSets etc
getResidueMapping(residue)
residueList = [(dr.residue.seqCode, dr.residue, dr)
for dr in self.dangleChain.dangleResidues]
residueList.sort()
cnt = 0
for seqCode, residue, dangleResidue in residueList:
phi = dangleResidue.phiValue
psi = dangleResidue.psiValue
if (phi is None) and (psi is None):
continue
# Use below functions because residues may not be sequentially numbered
prevRes = getLinkedResidue(residue, 'prev')
nextRes = getLinkedResidue(residue, 'next')
if (prevRes is None) or (nextRes is None):
continue
C__1 = prevRes.findFirstAtom(name='C') # C (i-1)
N_0 = residue.findFirstAtom(name='N') # N (i)
CA_0 = residue.findFirstAtom(name='CA') # CA(i)
C_0 = residue.findFirstAtom(name='C') # N (i)
N_1 = nextRes.findFirstAtom(name='N') # C (i+1)
# get fixedResonances
fixedResonances = []
for atom in (C__1, N_0, CA_0, C_0, N_1):
atomSet = atom.atomSet
if atomSet.resonanceSets:
resonance = atomSet.findFirstResonanceSet(
).findFirstResonance()
else:
# make new resonance
if not atom.chemAtom:
print 'no chem atom'
ic = atom.chemAtom.elementSymbol
if (ic == 'C'):
ic = '13' + ic
elif (ic == 'N'):
ic = '15' + ic
resonance = self.nmrProject.newResonance(isotopeCode=ic)
assignAtomsToRes([
atomSet,
], resonance)
fixedResonances.append(getFixedResonance(head, resonance))
# make dihedralConstraints
phiResonances = (fixedResonances[0], fixedResonances[1],
fixedResonances[2], fixedResonances[3])
phiConstraint = constraintList.newDihedralConstraint(
resonances=phiResonances)
psiResonances = (fixedResonances[1], fixedResonances[2],
fixedResonances[3], fixedResonances[4])
psiConstraint = constraintList.newDihedralConstraint(
resonances=psiResonances)
# make constraint items
if phi is not None:
phiConstraint.newDihedralConstraintItem(
targetValue=phi,
upperLimit=dangleResidue.phiUpper,
lowerLimit=dangleResidue.phiLower)
cnt += 1
if psi is not None:
psiConstraint.newDihedralConstraintItem(
targetValue=psi,
upperLimit=dangleResidue.psiUpper,
lowerLimit=dangleResidue.psiLower)
cnt += 1
showInfo('Success',
'DANGLE has generated %d dihedral restraints.' % cnt,
parent=self)
def makeRandomCoilShiftList(molSystems):
"""
Make a synthetic chemical shift list using random coil values,
adjusting protein backbone values for sequence where approprate.
.. describe:: Input
MolSystem.MolSystem
.. describe:: Output
Nmr.ShiftList
"""
from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes
from ccpnmr.analysis.core.MoleculeBasic import DEFAULT_ISOTOPES, getRandomCoilShift
project = list(molSystems)[0].root
done = set()
nmr = project.currentNmrProject
shiftList = nmr.newShiftList(isSimulated=True, unit='ppm', name='Random coil')
resonanceDict = {}
for molSystem in molSystems:
for chain in molSystem.sortedChains():
if chain.molecule in done:
continue
done.add(chain.molecule)
residues = chain.sortedResidues()
n = len(residues)
for i, residue in enumerate(residues):
context = [None] * 5
for k, j in enumerate(range(i-2, i+3)):
if 0 <= j < n:
context[k] = residues[j]
atomSets = set()
for atom in residue.atoms:
atomSet = atom.atomSet
if atomSet:
atomSets.add(atomSet)
for atomSet in atomSets:
atom = atomSet.findFirstAtom()
chemAtom = atom.chemAtom
value = getRandomCoilShift(chemAtom, context)
if value is not None:
resonanceSet = atomSet.findFirstResonanceSet()
if resonanceSet:
resonances = list(resonanceSet.resonances)
index = list(resonanceSet.atomSets).index(atomSet)
resonance = resonances[min(index, len(resonances)-1)]
else:
isotope = DEFAULT_ISOTOPES.get(atom.chemAtom.elementSymbol)
if isotope is None:
continue
resonance = nmr.newResonance(isotopeCode=isotope)
resonanceSet = assignAtomsToRes((atomSet,), resonance)
resonanceDict[resonance] = value
for resonance in resonanceDict:
value = resonanceDict[resonance]
shift = shiftList.newShift(value=value, resonance=resonance)
return shiftList
def getCouplingAtomResonances(nmrProject, residue, atomNames, makeNew=True):
"""
Get resonances that correspond to two named atoms in a given residue context
- could include sequential neighbours. A prerequisite for accessign the Jcoupling
etc for those atoms.
.. describe:: Input
Nmr.NmrProject, MolSystem.Residue, 2-List of Words (MolSystem.Atom.names), Boolean
.. describe:: Output
Nmr.Resonance, Nmr.Resonance
"""
# Add FindLinkedresidue calls here so not relying on seqCode
from ccpnmr.analysis.core.AssignmentBasic import assignAtomsToRes
atomNames = tuple(atomNames)
if 'C' in atomNames:
if 'H' in atomNames:
residueA = residueB = residue
else:
if 'C' == atomNames[0]:
residueA = residue.chain.findFirstResidue(
seqCode=residue.seqCode - 1)
residueB = residue
else:
residueA = residue
residueB = residue.chain.findFirstResidue(
seqCode=residue.seqCode - 1)
else:
residueA = residueB = residue
if not (residueA and residueB):
return None, None
atomA = residueA.findFirstAtom(name=atomNames[0])
atomB = residueB.findFirstAtom(name=atomNames[1])
resonanceA = None
resonanceB = None
if atomA and atomB:
atomSetA = atomA.atomSet
atomSetB = atomB.atomSet
if atomSetA and atomSetB:
resonanceSetsA = list(atomSetA.resonanceSets)
resonanceSetsB = list(atomSetB.resonanceSets)
if not resonanceSetsA:
if makeNew:
isotope = DEFAULT_ISOTOPES.get(
atomA.chemAtom.elementSymbol)
resonanceA = nmrProject.newResonance(isotopeCode=isotope)
resonanceSetA = assignAtomsToRes([
atomSetA,
], resonanceA)
else:
resonanceSetA = resonanceSetsA[0]
for resonanceSet in resonanceSetsA:
if len(resonanceSet.resonances) < len(
resonanceSetA.resonances):
resonanceSetA = resonanceSet
resonanceA = resonanceSetA.findFirstResonance()
if not resonanceSetsB:
if makeNew:
isotope = DEFAULT_ISOTOPES.get(
atomB.chemAtom.elementSymbol)
resonanceB = nmrProject.newResonance(isotopeCode=isotope)
resonanceSetB = assignAtomsToRes([
atomSetB,
], resonanceB)
else:
resonanceSetB = resonanceSetsB[0]
for resonanceSet in resonanceSetsB:
if len(resonanceSet.resonances) < len(
resonanceSetB.resonances):
resonanceSetB = resonanceSet
resonanceB = resonanceSetB.findFirstResonance()
return resonanceA, resonanceB
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if ((self.constrLists != [None] * 4) and (self.numClouds > 0)
and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
constraints = []
constraintStore = None
for dcl in self.constrLists:
if dcl:
constraintStore = dcl.nmrConstraintStore
constraints.extend(list(dcl.constraints))
resonances = []
for constraint in constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if fixedResonance.resonanceSerial is None:
resonance = newResonance(
self.guiParent.project,
isotopeCode=fixedResonance.isotopeCode)
resonance.setName(fixedResonance.name)
fixedResonance.setResonanceSerial(resonance.serial)
resDict[resonance.serial] = resonance
if fixedResonance.resonanceSet:
atomSets = list(
fixedResonance.resonanceSet.atomSets)
assignAtomsToRes(atomSets, resonance)
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
resonances, intraConstraintList = self.makeIntraConstraints(
resonances, constraintStore)
constraints.extend(list(intraConstraintList.constraints))
resonances, interConstraintList = self.makeInterConstraints(
resonances, constraintStore)
constraints.extend(list(interConstraintList.constraints))
startMdProcess(self.numClouds, constraints, resonances,
self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(constraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(constraintStore,
'cloudsResonances',
values=serials)