def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query',msg, parent=self):
self.purgeCingServer()
def removeResonance(self):
if self.resonance and self.spinSystem and (self.resonance in self.spinSystem.resonances):
if showOkCancel('Confirm','Really remove resonance from spin system?', parent=self):
self.spinSystem.codeScoreDict = {}
deassignResonance(self.resonance, clearAssignNames=False)
removeSpinSystemResonance(self.spinSystem, self.resonance)
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
def deleteExpSeries(self, *event):
if self.expSeries and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series?', parent=self):
self.expSeries.delete()
self.expSeries = None
self.conditionPoint = None
def transferChainAssignments(chainA, chainB):
"""Transfer any atomic assignments from one chain to another where possible.
.. describe:: Input
MolSystem.Chain, MolSystem.Chain
.. describe:: Output
None
"""
mapping = getChainResidueMapping(chainA, chainB)
for residueA, residueB in mapping:
if residueB:
resonancesB = getResidueResonances(residueB)
if resonancesB:
msg = 'Destination residue %s%d has assignments. Continue?.'
data = (residueB.seqCode, residueB.ccpCode)
if not showOkCancel('Warning', msg % data):
return
for residueA, residueB in mapping:
if residueA:
if residueB is None:
msg = 'Residue %d%s has no equivalent in destination chain'
data = (residueA.seqCode, residueA.ccpCode)
showWarning('Warning', msg % data)
else:
transferResidueAssignments(residueA, residueB)
def setJCoupling(self, index=None):
if not index:
atomNames = self.atomNames
index = couplingAtoms.index(atomNames)
else:
atomNames = couplingAtoms[index]
value = self.jCouplingEntry.get()
if self.residue and atomNames:
coupling = self.jCouplings[index]
if value is None:
if coupling:
if showOkCancel('Confirm',
'Really remove J coupling?',
parent=self):
coupling.delete()
else:
if not coupling:
self.setResidueJCoupling(self.measureJCouplingList,
self.residue,
atomNames,
value,
isSimulated=False)
else:
coupling.setValue(value)
def propagatePath(self):
dataStores = self.dataStoreTable.currentObjects
if self.dataStore and len(dataStores) > 1:
sourcePath = self.dataStore.dataUrl.url.dataLocation
if os.path.exists(sourcePath):
directory = sourcePath
elif os.path.exists(os.path.dirname(sourcePath)):
directory = os.path.dirname(sourcePath)
else:
directory = None
if not directory:
msg = 'Source directory does not exist'
showWarning('Failure', msg, parent=self)
return
msg = 'Transfer path "%s" to selection?' % directory
if showOkCancel('Confirm', msg, parent=self):
for dataStore in dataStores:
if dataStore is self.dataStore:
continue
if dataStore.dataUrl.url.dataLocation == directory:
continue
changeDataStoreUrl(dataStore, sourcePath)
def deleteConstraints(self):
if self.constrList and showOkCancel(
'Confirm', 'Really delete constraint list?', parent=self):
self.constrList.delete()
self.constrList = None
self.constrListButtons.buttons[0].disable()
self.constrListButtons.buttons[2].disable()
def deleteViolations(self):
if self.violList and showOkCancel(
'Confirm', 'Really delete violation list?', parent=self):
self.violList.delete()
self.violList = None
self.violListButtons.buttons[0].disable()
self.violListButtons.buttons[1].disable()
def deleteNodes(self):
if self.selectedNodes:
msg = 'Really delete %d selected nodes?' % len(self.selectedNodes)
if showOkCancel('Confirm', msg, parent=self):
for node in self.selectedNodes[:]:
node.delete()
self.selectedNodes = []
self.node = None
def deleteChild(self, table):
object = table.currentObject
if (object):
if (showOkCancel(
'Delete object',
'Are you sure you want to delete selected object?',
parent=self)):
object.delete()
def deleteRun(self):
if self.run:
msg = 'Really delete calculation run %d?' % self.run.serial
if showOkCancel('Query', msg, parent=self):
self.run.delete()
self.run = None
self.updateAfter()
def deleteLinks(self):
if self.selectedLinks:
msg = 'Really delete %d selected links?' % len(self.selectedLinks)
if showOkCancel('Confirm', msg, parent=self):
for link in self.selectedLinks[:]:
link.delete()
self.selectedLinks = []
self.link = None
def setSpectrumMultiplet(self, spectrum, pattern):
prevPattern = getSpectrumMultipletPattern(spectrum)
if prevPattern and (prevPattern != pattern):
if showOkCancel('Query',
'Really change multiplet pattern?',
parent=self):
setSpectrumMultipletPattern(spectrum, pattern)
def deleteStrucGen(self):
if self.strucGen and showOkCancel(
'Confirm', 'Really delete structure generation run?',
parent=self):
self.strucGen.delete()
self.strucGen = None
self.constrList = None
self.violist = None
self.structGenButtons.buttons[0].disable()
self.structGenButtons.buttons[1].disable()
def deleteRun(self):
if self.dangleStore:
msg = 'Really delete DANGLE run "%s"?' % self.dangleStore.name
if showOkCancel('Confirm', msg, parent=self):
self.dangleStore.delete()
self.dangleStore = None
self.dangleChain = None
self.updatePredictionMatrix()
self.updateDangleStorePulldown()
def deleteMeasurements(self):
measurements = self.measurementsMatrix.currentObjects
if measurements:
className = self.measurementListB.className
if className == 'ShiftList':
msg = 'Really delete %s chemical shifts?' % len(measurements)
if not showOkCancel('Confirm', msg, parent=self):
return
untouched = set()
for shift in measurements:
for peakDim in shift.peakDims:
shiftList = peakDim.peak.peakList.dataSource.experiment.shiftList
if shiftList is self.measurementListB:
untouched.add(shift)
break
else:
shift.delete()
if untouched:
if len(untouched) > 1:
msg = 'Could not delete %d shifts because they are still assigned to peaks' % len(
untouched)
else:
msg = 'Could not delete shift because it is still assigned to peaks'
showWarning('Warning', msg, parent=self)
else:
msg = 'Really delete %d %s measurements?' % (len(measurements),
className[:-4])
if not showOkCancel('Confirm', msg, parent=self):
return
for measurement in measurements:
measurement.delete()
def deleteCloud(self):
if self.constraintSet and self.cloud and showOkCancel(
'Confirm', 'Really delete resonance cloud?', parent=self):
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
if clouds:
clouds.remove(self.cloud)
self.cloud = None
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=clouds)
self.updateAfter()
def deassignType(self):
if self.spinSystem:
residue = self.spinSystem.residue
if residue:
resText = '%d%s' % (residue.seqCode, residue.ccpCode)
msg = 'Spin system assigned to %s. Continue and deassign residue?'
if showOkCancel('Warning', msg % resText, parent=self):
assignSpinSystemResidue(self.spinSystem, None)
assignSpinSystemType(self.spinSystem, None)
else:
assignSpinSystemType(self.spinSystem,None)
def assign(self):
if self.spinSystem and self.ccpCode:
if self.spinSystem.residue and (self.spinSystem.residue.ccpCode != self.ccpCode):
resText = '%d%s' % (self.spinSystem.residue.seqCode, self.spinSystem.residue.ccpCode)
msg = 'Spin system is already assigned to %s. Continue?'
if showOkCancel('Warning', msg % resText, parent=self):
assignSpinSystemResidue(self.spinSystem,residue=None)
else:
return
if self.spinSystem.ccpCode != self.ccpCode:
assignSpinSystemType(self.spinSystem,self.ccpCode,'protein')
self.update()
def deleteSelected(self, event=None):
objs = self.selectedLinks + self.selectedNodes
if objs:
n1 = len(self.selectedNodes)
n2 = len(self.selectedLinks)
msg = 'Really delete %d selected objects?\n' % (n1 + n2)
msg += '(%d nodes, %d links)' % (n1, n2)
if showOkCancel('Confirm', msg, parent=self):
for obj in objs:
obj.delete()
self.selectedLinks = []
self.link = None
self.selectedNodes = []
self.node = None
def deleteClouds(self):
if self.names and self.name and showOkCancel(
'Confirm', 'Really remove selected clouds?'):
indices = []
for name in self.scrolledMatrix.currentObjects:
i = self.names.index(name)
indices.append(i)
indices.sort()
indices.reverse()
for i in indices:
self.clouds.pop(i)
self.rmsds.pop(i)
self.names.pop(i)
self.name = None
self.updateAfter()
def installUpdates(self):
if self.isGraphical and not showOkCancel(
'Confirmation', 'Continue with file upgrade?'):
return
if not self.server:
self.warningMessage('Warning', 'No accessible server')
return
if not self.installRoot:
self.warningMessage('Warning', 'No installation path')
return
updates = self.server.getSelectedUpdates()
if not updates:
self.warningMessage('Warning', 'No selected updates to install')
return
needMake = False
needMakeClean = False
needMakeLinks = False
for update in updates:
update.setInstallFromCache()
if update.fileName.endswith('.c'):
needMake = True
elif update.fileName.endswith('.h'):
needMake = needMakeClean = True
elif update.fileName == 'Makefile':
needMake = needMakeClean = needMakeLinks = True
#if not isWindowsOS():
if False: # 16 Nov 2010: do not even try to compile C code any more
self.compileCode(needMakeClean=needMakeClean,
needMake=needMake,
needMakeLinks=needMakeLinks)
if self.isGraphical and not self.isStandAlone:
self.warningMessage(
'Notice',
'All updates complete. You must restart Analysis for changes to take effect.'
)
def stripGroups(self):
self.updateWindows()
name = self.windowPulldown.getText()
groups = self.scrolledMatrix.currentObjects
if groups and name and (name != '<None>'):
selected = self.windowPulldown.getText()
windowPane, positions = self.orthogonalDict[selected]
window = windowPane.spectrumWindow
N = len(positions)
msg = '%d positions selected. Really make %d strips in window %s'
if N > 10 and not showOkCancel('Warning', msg % (N,N,window.name ), parent=self):
return
displayStrips(self.parent, positions, orthoPositions=None,
spectrum=None, windowPane=windowPane)
# often fails first time...
self.update_idletasks()
displayStrips(self.parent, positions, orthoPositions=None,
spectrum=None, windowPane=windowPane)
def deleteConditionPoint(self, *event):
if self.conditionPoint and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series point?', parent=self):
conditionSet = self.conditionPoint.sampleConditionSet
experiments = [e for e in conditionSet.experiments if e in self.expSeries.experiments]
for experiment in experiments:
self.expSeries.removeExperiment(experiment)
for experiment in experiments:
for expSeries in experiment.nmrExpSeries:
if self.conditionPoint.condition in self.expSeries.conditionNames:
break
else:
continue
break
else:
self.conditionPoint.delete()
self.conditionPoint = None
def deleteMeasurementList(self, *event):
if self.measurementList:
if (len(self.measurementList.experiments) >
0) and (self.measurementList.className == 'ShiftList'):
showWarning(
'Warning',
'Deletion of shift lists with associated experiments prohibited',
parent=self)
return
elif len(self.measurementList.measurements) > 0:
if showOkCancel('Confirm',
'List is not empty. Really delete?',
parent=self):
self.measurementList.delete()
self.measurementList = None
else:
return
else:
self.measurementList.delete()
self.measurementList = None
def makeStructureEnsemble(strucDict,
molSystem,
modelNames=None,
doWarnings=False,
checkTruncation=True,
fixAtomNames=True):
"""Makes structure ensemble from a structure dictionary
[model][chainCode][resNum][atomName] = (x,y,z coords)
in a mol system. Options to supress warnings and thus
automatically link non-identical, but similar chains
or make a new chain if none is found,
NB chains and resides are those present in FIRST model
atoms are taken from all models,
and missing atoms are given x=y=z = 0.0; occupancy=0.0
.. describe:: Input
Dictionary, MolSystem.MolSystem, Boolean
.. describe:: Output
MolStructures.StructureEnsemble
"""
# Rasmus Fogh 20/6/2011: Changed to new MolStructure model
# Rasmus Fogh 4/5/2013:Added automatic name fixing: 2HB -> HB2
#
# Set up, and create structure ensemble
#
ll = sorted(strucDict.keys())
firstModelId = ll[0]
project = molSystem.root
ensembles = molSystem.sortedStructureEnsembles()
if ensembles:
eId = ensembles[-1].ensembleId + 1
else:
eId = 1
ensemble = project.newStructureEnsemble(molSystem=molSystem,
ensembleId=eId)
#models = []
#for m in strucDict.keys():
# models.append((m, ensemble.newModel()))
#
# record data list - for creating and processing records in reading order
#
recordDataList = []
recordDataDict = {}
coordResidues = {}
allMsResidues = {}
usedChains = []
failedAtoms = []
msAtomDict = {}
atomCheckDict = {}
systemAtoms = set()
chainsDict = strucDict[firstModelId]
# match or make chains
chCodes = list(chainsDict.keys())
chCodes.sort()
nOrigChCodes = len(chCodes)
for iChCode, chCode in enumerate(chCodes):
resDict = chainsDict[chCode]
seqIds = resDict.keys()
seqIds.sort()
chemComps = []
ccpCodes = []
seqIdsGood = []
# get list of good chemcomps
molTypes = set()
resNames = []
for seqId in seqIds:
ll = resDict[seqId].keys()
resName = resDict[seqId][ll[0]]['resName']
atomNames = [tt[0] for tt in ll]
chemComp = DataConvertLib.getBestChemComp(project, resName,
atomNames)
resNames.append(resName)
if chemComp:
chemComps.append(chemComp)
ccpCodes.append(chemComp.ccpCode)
seqIdsGood.append(seqId)
molTypes.add(chemComp.molType)
if not seqIdsGood:
msg = 'Could not find any matching CCPN ChemComps for sequence: '
msg += ' '.join(resNames)
showWarning('Structure Creation Failed', msg)
continue
#get matching MolSystem chains
seqIds = seqIdsGood
msChains, mappings = findMatchingChains(molSystem,
ccpCodes,
excludeChains=usedChains,
doWarning=doWarnings,
molTypes=molTypes)
nChains = len(msChains)
if nChains == 1:
msChain = msChains[0]
mapping = mappings[0]
elif nChains:
from memops.gui.DataEntry import askString
codes = [c.code for c in msChains]
msg = 'Structure chain %s matches %d \nCCPN chains' % (chCode,
nChains)
msg += ' equally well: %s\n' % (' '.join(codes), )
msg += 'Which CCPN chain should be linked to?'
if chCode in codes:
default = chCode
else:
default = codes[0]
choice = None
while choice not in codes:
choice = askString('Query', msg, default) or ''
choice = choice.strip()
index = codes.index(choice)
msChain = msChains[index]
mapping = mappings[index]
else:
msChain = None
if nChains:
nRes = len(mapping)
startPair = 0
endPair = nRes - 1
for i in range(nRes):
residueA, residueB = mapping[i]
if residueA and residueB:
startPair = i
break
for endTrunc in range(nRes):
j = endPair - endTrunc
residueA, residueB = mapping[j]
if residueA and residueB:
endPair = j
break
mismatch = []
for i in range(startPair, endPair + 1):
if None in mapping[i]:
mismatch.append(i)
break
if doWarnings:
if checkTruncation and ((endTrunc > 10) or (startPair > 10)):
msg = 'Structure truncated (Start:%s, End:%s) ' % (
startPair, endTrunc)
msg += 'compared to existing chain. Really link to chain %s?' % msChain.code
msg += ' (Otherwise a new chain will be made)'
if not showYesNo('Query', msg):
msChain = None
if mismatch and msChain is not None:
msg = 'Imperfect match: %s non-terminal mismatches, ' % len(
mismatch)
msg += 'compared to existing chain. Really link to chain %s?' % msChain.code
msg += ' (Otherwise a new chain will be made)'
if not showYesNo('Query', msg):
msChain = None
else:
if checkTruncation and (startPair or endTrunc):
print(
'WARNING, Structure truncated (Start:%s, End:%s) rel. to existing chain.'
% (startPair, endTrunc))
if mismatch:
print 'WARNING, Imperfect match: %s non-terminal mismatches' % len(
mismatch)
if not msChain:
# no matching chain - make new one
# use existing chain code from PDB file if possible
sysChainCode = chCode.strip()
if not sysChainCode or molSystem.findFirstChain(code=sysChainCode):
sysChainCode = nextChainCode(molSystem)
if molTypes == set(('DNA', )) and iChCode <= nOrigChCodes:
# check for special case:
# double stranded DNA with a single chain code
oneLetterCodes = [cc.code1Letter for cc in chemComps]
if None not in oneLetterCodes:
# All ChemComps are (variants of) Std bases.
# Not sure certain, but this should mostly work.
nCodes = len(oneLetterCodes)
halfway, remainder = divmod(nCodes, 2)
if not remainder:
# even number of codes
resMap = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G'}
for ii in range(halfway):
if oneLetterCodes[ii] != resMap[oneLetterCodes[
-1 - ii]]:
break
else:
# the second half is the reverse complement of the first half.
# treat as two separate DNA chains
# Move second half to a new chain, and remove from this chain.
newChCode = chCode
while newChCode in chCodes:
newChCode = chr(ord(newChCode) + 1)
newResDict = chainsDict[newChCode] = {}
for ii in range(halfway, nCodes):
iix = seqIds[ii]
newResDict[iix] = resDict[iix]
del resDict[iix]
# put both chains on end of list for later (re)processing
chCodes.append(chCode)
chCodes.append(newChCode)
continue
codes = (molSystem.code, sysChainCode)
msg = 'Structure residue sequence (chain %s) not in molecular system. ' % chCode
msg += 'Make new molecular system %s chain (%s) for this sequence?' % codes
if not doWarnings or (not molSystem.chains) or (
doWarnings and showOkCancel('Confirm', msg)):
atomNames = resDict[seqIds[0]].keys()
molType = chemComps[0].molType
ccpCodes0 = []
startNum = resDict[seqIds[0]][atomNames[0]]['seqCode']
project = molSystem.root
molecule = makeMolecule(project, molType, [])
for i in range(len(seqIds)):
chemComp = chemComps[i]
if (chemComp.molType != molType) or (
i and (seqIds[i] != seqIds[i - 1] + 1)):
newMolResidues = addMolResidues(molecule,
molType,
ccpCodes0,
startNum=startNum)
# set seqCodes and seqInsertCodes
xSeqIds = seqIds[i - len(newMolResidues):i]
for j, x in enumerate(xSeqIds):
rr = newMolResidues[j]
for dummy in resDict[x]:
# future-safe of getting a random atomDict for seqId x
dd = resDict[x][dummy]
break
rr.seqCode = dd['seqCode']
rr.seqInsertCode = dd['insertCode']
ccpCodes0 = [
chemComp.ccpCode,
]
molType = chemComp.molType
startNum = seqIds[i]
else:
ccpCodes0.append(chemComp.ccpCode)
if ccpCodes0:
addMolResidues(molecule,
molType,
ccpCodes0,
startNum=startNum)
msChain = makeChain(molSystem, molecule, code=sysChainCode)
resMapping = {}
for i, residue in enumerate(msChain.sortedResidues()):
resMapping[i] = residue
# TBD deal with HETATMs, proper Molecule name,
# store CCPN xml as non-standard naming system?
else:
continue
else:
# msChain is not None
sysChainCode = msChain.code
resMapping = {}
for i, residue in mapping:
resMapping[i] = residue
usedChains.append(msChain)
atomNamesList = []
msResidues = []
for j, seqId in enumerate(seqIds):
atomNames = [tt[0] for tt in resDict[seqId].keys()]
if fixAtomNames:
# change names to get right naming system.
for ii, name in enumerate(atomNames):
if name[0] in '123':
atomNames[ii] = name[1:] + name[0]
atomNamesList.append(atomNames)
msResidue = resMapping.get(j)
msResidues.append(msResidue)
namingSystem = DataConvertLib.getBestNamingSystem(
msResidues, atomNamesList)
coordChain = ensemble.newChain(code=sysChainCode)
#ensemble.override = True
#
# Done making chain - start adding residues to chain
#
for j, seqId in enumerate(seqIds):
msResidue = msResidues[j]
if not msResidue: # Structure is bigger
continue
resName = ccpCodes[j]
ccpCode = msResidue.ccpCode
if doWarnings:
if resName != ccpCode:
msg = 'Residue names [%s,%s] don\'t match\nin'
msg += ' loaded molecular system\nchain %s position %d'
data = (resName, ccpCode, chCode, seqId)
showWarning('Warning', msg % data)
continue
if msResidue is None:
msg = 'No equivalent molecular system residue'
msg += '\nfor PDB chain %s residue %d'
showWarning('Warning', msg % (chCode, seqId))
continue
coordResidue = coordChain.newResidue(
seqCode=msResidue.seqCode,
seqInsertCode=msResidue.seqInsertCode,
seqId=msResidue.seqId)
coordResidues[(chCode, seqId)] = coordResidue
allMsResidues[(chCode, seqId)] = msResidue
#
# Now make atoms
#
for atomKey, coordDict in resDict[seqId].items():
atomName, altLoc = atomKey
key = '%s:%s:%s' % (atomName, msResidue, namingSystem)
if key in msAtomDict:
systemAtom = msAtomDict.get(key)
else:
systemAtom = DataConvertLib.findMatchingMolSystemAtom(
atomName,
msResidue,
namingSystem,
systemAtoms,
fixAtomNames=fixAtomNames)
msAtomDict[key] = systemAtom
if (systemAtom is None) or atomCheckDict.get(
(systemAtom, altLoc)):
#print '### failing', atomName
failedAtoms.append(
'%s %d %s %4s' %
(chCode, seqId, msResidue.ccpCode, atomName))
continue
systemAtoms.add(systemAtom)
#print '### adding', atomName, systemAtom.name
atomCheckDict[(systemAtom, altLoc)] = True
tt = (coordDict.get('recordId'), (chCode, seqId, atomKey),
coordResidue, systemAtom.name, coordDict)
recordDataList.append(tt)
recordDataDict[(chCode, seqId, atomKey)] = tt
#
# Finished getting data for reading order from first model
#
# Now loop over other models and add new atoms to existing residues
# ignoring new residues and chains, to cater for varying atom presence
#
for modelInd, chainsDict in sorted(strucDict.items()[1:]):
for chCode, resDict in sorted(chainsDict.items()):
for seqId, atomDict in sorted(resDict.items()):
coordResidue = coordResidues.get((chCode, seqId))
msResidue = allMsResidues.get((chCode, seqId))
if coordResidue is None or msResidue is None:
continue
for atomKey, coordDict in atomDict.items():
tt = recordDataDict.get((chCode, seqId, atomKey))
if tt is None:
# new atom, make new record
atomName, altLoc = atomKey
key = '%s:%s:%s' % (atomName, msResidue, namingSystem)
if key in msAtomDict:
systemAtom = msAtomDict.get(key)
else:
systemAtom = DataConvertLib.findMatchingMolSystemAtom(
atomName,
msResidue,
namingSystem,
systemAtoms,
fixAtomNames=fixAtomNames)
msAtomDict[key] = systemAtom
if (systemAtom is None) or atomCheckDict.get(
(systemAtom, altLoc)):
failedAtoms.append(
'%s %d %s %4s' %
(chCode, seqId, msResidue.ccpCode, atomName))
continue
print '### NBNB add extra atom:', (chCode, seqId,
atomKey)
systemAtoms.add(systemAtom)
atomCheckDict[(systemAtom, altLoc)] = True
tt = (coordDict.get('recordId'), (chCode, seqId,
atomKey),
coordResidue, systemAtom.name, coordDict)
recordDataList.append(tt)
recordDataDict[(chCode, seqId, atomKey)] = tt
#
# Finished getting data for reading order
#
# sort by recordId. If not set - or if duplicate recordId
# will sort by full key.
recordDataList.sort()
#
nAtoms = len(recordDataList)
#
# Create atoms
#
for tt in recordDataList:
recordId, fullKey, coordResidue, atomName, coordDict = tt
# make coordAtom
coordResidue.newAtom(name=atomName, altLocationCode=fullKey[2][1])
#
# set data for all models
#
kk = 0
for modelInd, chainsDict in sorted(strucDict.items()):
#create model
model = ensemble.newModel()
if modelNames:
model.name = modelNames[kk]
kk += 1
# set up for data reading
coordinates = [0.0] * (3 * nAtoms
) # NB deliberate this is 0.0, not None
# There might be atoms missing in other models
occupancies = [1.0] * nAtoms
bFactors = [0.0] * nAtoms
ii = 0
jj = 0
hasOccupancies = False
hasBFactors = False
for tt in recordDataList:
recordId, fullKey, coordResidue, atomName, coordDict = tt
resDict = chainsDict.get(fullKey[0])
if resDict:
atomDict = resDict.get(fullKey[1])
if atomDict:
coordDict = atomDict.get(fullKey[2])
#try:
# xxx = atomDict[fullKey[2]]
# coordDict = xxx
#except:
# print '###', atomDict.keys(), tt
if coordDict:
# get data for model
coordinates[jj] = coordDict['x']
jj += 1
coordinates[jj] = coordDict['y']
jj += 1
coordinates[jj] = coordDict['z']
jj += 1
occupancy = coordDict.get('occupancy', 1.0)
if occupancy != 1.0:
occupancies[ii] = occupancy
hasOccupancies = True
bFactor = coordDict.get('bFactor', 0.0)
if bFactor != 0.0:
bFactors[ii] = bFactor
hasBFactors = True
ii += 1
else:
# This atom not found in this model
# Just leave default values, set occupancy to 0
# and increment indices
# NBNB this leaves coordinates as 0.0 NBNBNB
occupancies[ii] = 0.0
hasOccupancies = True
ii += 1
jj += 3
# fill data into model
model.setSubmatrixData('coordinates', coordinates)
if hasOccupancies:
model.setSubmatrixData('occupancies', occupancies)
if hasBFactors:
model.setSubmatrixData('bFactors', bFactors)
# final validity check
try:
ensemble.checkAllValid()
except:
ensemble.delete()
return
# reset switches
#ensemble.override = False
if failedAtoms:
ll = sorted(set(failedAtoms))
ll = [x for x in ll if not ('Q' in x[-5:] or '*' in x[-5:])]
#skipAtoms = (' HT1', ' HT2', ' HT3', ' 1HT', ' 2HT', ' 3HT', ' OXT',
# ' OT1', ' OT2', ' 1H', ' 2H', ' 3H')
#ll = [x for x in failedAtoms
# if 'Q' not in x
# and not [x.endswith(y) for y in skipAtoms]]
if ll:
print(
'## WARNING %s failed atoms. Unique, non-pesudo atoms are:' %
len(failedAtoms), ', '.join(ll))
if failedAtoms and doWarnings:
msg = 'No equivalent molecular system atoms for PDB atoms: %s'
showWarning('Warning', msg % (' '.join(failedAtoms)))
if not ensemble.coordChains:
ensemble.delete()
ensemble = None
return ensemble
def getLatestRelease(self):
# assumes is in correct directory (so far)
# fetches latest release
# returns name of release file (not full path, just file name)
ss = ''
use_precompiled = False
try:
from ccpnmr.analysis.Version import platform, bits, arch, built_by
if built_by == 'ccpn':
if platform == 'linux':
ss = '_%s%s' % (platform, bits)
use_precompiled = True
elif platform == 'darwin':
if arch != 'ppc':
arch = 'intel'
ss = '_%s' % arch
use_precompiled = True
except:
pass
self.use_precompiled = use_precompiled
if use_precompiled:
extension = 'tgz'
else:
extension = 'tar.gz'
fileName = 'analysis%s%s%s.%s' % (
self.server.version, self.server.minor_version, ss, extension)
self.releaseFile = None
addr = 'http://' + joinPath(self.httpServer, self.homeDir,
self.httpDir, fileName)
try:
url = urllib.urlopen(addr)
except:
self.server.parent.warningMessage('Download failed',
'Could not connect to %s' % addr)
return
data = url.read()
url.close()
destFile = joinPath(self.baseDir, self.releaseDir, fileName)
try:
fp = open(destFile, 'wb')
except:
self.server.parent.warningMessage(
'Saving release failed',
'Could not save release to %s' % destFile)
fp.write(data)
fp.close()
self.releaseFile = fileName
if self.server.parent.isGraphical:
if showOkCancel(
'Query',
'Can CCPN log your IP address for its statistics? No other information will be taken'
):
self.logDownload()
else:
print 'CCPN is logging your IP address for its statistics. No other information will be taken'
self.logDownload()
def installLatestRelease(self):
if self.server:
msg = 'Current version is %s - ' % self.version + \
'You must upgrade to version %s to get updates. ' % self.server.version + \
'Continue with automatic upgrade to the latest major release? ' + \
'(Old version will not be deleted from disk)'
if self.isGraphical and not showOkCancel('Confirmation', msg):
return
if not self.server:
self.warningMessage('Warning', 'No accessible server')
return
if not self.installRoot:
self.warningMessage('Warning', 'No installation path')
return
releaseUpdate = ReleaseUpdate(self.server, self.installRoot,
self.version)
success = releaseUpdate.installRelease()
if success:
self.server.parent.version = self.server.version
if success and self.isGraphical:
self.server.getFileUpdates()
if self.server.fileUpdates and showOkCancel(
'Confirmation',
'Also install any updates to new release?'):
wasGraphical = self.isGraphical
self.isGraphical = False
self.installNewUpdates()
for fileUpdate in self.server.getSelectedUpdates():
print 'Updated %s in %s' % (fileUpdate.fileName,
fileUpdate.filePath)
self.isGraphical = wasGraphical
if hasattr(self, 'parent'):
if not self.isStandAlone:
self.warningMessage(
'Notice',
'Release update complete. Program will exit. Restart for changes to take effect.'
)
parent = self.parent
# parent.project does not exist in some contexts (e.g. updateCheck)
if hasattr(parent, 'project') and parent.project:
if not parent.checkSaving():
return
parent.destroy()
# Need the below code to fix the problem with Bash
# where the commend line was getting screwed up on exit.
if os.name == 'posix':
os.system('stty sane')
sys.exit(0)
else:
if not self.isStandAlone:
self.warningMessage(
'Notice',
'Release update complete. You must restart for changes to take effect.'
)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structure = self.structure
if not structure:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
ensembleText = getModelsString(run)
if not ensembleText:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueText = getResiduesString(structure)
if not residueText:
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID, self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY, self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
