def finaliseImport(self):
if not self.depositionImportNums[6]:
showWarning('Failure',
'Need connected molecule and shift information first')
return
if showYesNo(
"Save project and continue annotation",
"Are you sure you want to save this project and continue?",
parent=self):
if self.depositionImportNums[5] or showYesNo(
"No coordinates",
"No coordinates are available - are you sure you want to continue?",
parent=self):
showInfo("Project name",
"Your project will be saved in the %s directory." %
self.project.name,
parent=self)
self.project.saveModified()
#userData = self.project.findFirstRepository(name='userData')
#currentPath = userData.url.path
#currentProjectName = self.project.name
#projectDir = os.path.join(currentPath,currentProjectName)
eci = EntryCompletionGui(self.basePopup.root)
eci.initProject(self.project)
def deleteContourFile(self, *extra):
storedContours = self.getStoredContours()
if not storedContours:
return
if len(storedContours) == 1:
s = t = ''
else:
s = ' %d ' % len(storedContours)
t = 's'
if (showYesNo(
'Delete stored contour%s from project' % t,
'Are you sure you want to delete selected %sstored contour%s from the project?'
% (s, t),
parent=self)):
if (showYesNo(
'Delete underlying contour file%s on disk' % t,
'Do you also want to delete underlying contour file%s on disk (normally yes)?'
% t,
parent=self)):
for storedContour in storedContours:
path = storedContour.fullPath
try:
os.remove(path)
except:
print 'Warning: could not remove %s' % path
for storedContour in storedContours:
storedContour.delete()
def continueIfFileNameUsed(self, fileName):
result = True
storedContoursToDelete = []
for analysisSpectrum in self.analysisProject.analysisSpectra:
for storedContour in analysisSpectrum.storedContours:
if storedContour.fullPath == fileName:
storedContoursToDelete.append(storedContour)
if storedContoursToDelete:
if len(storedContoursToDelete) == 1:
s = ''
t = 's'
else:
s = 's'
t = ''
result = showYesNo('File used', 'Stored contour%s already use%s this fileName, and will be deleted: continue?' % (s, t), parent=self)
if result:
for storedContour in storedContoursToDelete:
try:
storedContour.delete()
except:
pass
return result
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 saveDataToPyc(self, fileName):
'''Pickle the data model and save it to file to
be use later. Since this storage method relies
on pickle, it is not guaranteed that the data
can be loaded in future versions of this macro.
'''
if self.results:
if not fileName[-4:] == '.pyc':
fileName = fileName + '.pyc'
if os.path.exists(fileName):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % fileName,
parent=self.GUI):
return
self.updateInfoText('Saving results...')
writeFile = open(fileName, 'wb')
cPickle.dump(self.results, writeFile, protocol=2)
writeFile.close()
self.updateInfoText('Results succesfully saved.')
else:
string = 'There are no results to save at the moment.'
showWarning('No results to save', string, parent=self.GUI)
def pressButton(self):
self.textWindow.setText('Button Pressed\n')
if showYesNo('Title','Prompt: Clear text window?'):
self.textWindow.clear()
return
def resetShiftImport(self):
doReset = True
if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Shifts not connected to sequence',
'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.',
parent=self):
self.connectShiftsSequence()
doReset = False
if doReset:
self.mainButtons.buttons[1].config(
foreground=self.fontDefaultColor)
self.shiftsLoaded = self.linkResDone = False
self.currentShiftList = None
self.shiftImport.setText(self.defaultSelectText)
self.shiftImport.configure(foreground=self.fontDefaultColor)
self.linkResCheckInfo.set("")
def deleteAxisUnit(self, *event):
axisUnit = self.getAxisUnit()
if (axisUnit):
if (showYesNo(
'Delete axis unit',
'Are you sure you want to delete axis unit "%s"?' %
axisUnit.unit, self)):
axisUnit.delete()
def deleteAxisType(self, *event):
axisType = self.getAxisType()
if axisType:
if (showYesNo(
'Delete axis type',
'Are you sure you want to delete axis type "%s"?' %
axisType.name, self)):
axisType.delete()
def commitAssignments(self):
merge = showYesNo('Query', 'Merge with any existing spin systems?',
self)
for spinSystem in self.spinSystemMatrix.currentObjects:
if not spinSystem.residue:
residue, p = self.getProbableResidue(spinSystem)
assignSpinSystemResidue(spinSystem, residue, warnMerge=merge)
def deletePanelType(self, *event):
panelType = self.getPanelType()
if (panelType):
if (showYesNo(
'Delete panel type',
'Are you sure you want to delete panel type "%s"?' %
panelType.name, self)):
panelType.delete()
def removePoint(self):
if self.object and (len(self.dataFitting.objects) > 2):
self.dataFitting.objects.remove(self.object)
if showYesNo('Query',
'Delete the corresponding %s?' %
(self.object.className),
parent=self):
self.object.delete()
self.updateAfter()
def checkSaving(self):
if not self.project:
return True
if isProjectModified(self.project):
if showYesNo('Save project', 'Save changes to project?', parent=self):
if not self.quitSaveProject():
return False
return True
def updateAll(self):
self.selectTab(self.tabbedFrame.selected)
if self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Connect shifts to sequence',
'You have to check whether the chemical shift information matches the sequence. Do you want to this now?',
parent=self):
self.connectShiftsSequence()
self.waiting = False
def closeProject(self, queryClose=True, querySave=True):
if queryClose:
if (not showYesNo('Close project', 'Close current project?')):
return False
if querySave:
if (not self.checkSaving()):
return False
self.destroyPopups()
self.initProject()
return True
def save(self):
filePrefix = self.fileEntry.get()
directory = self.dirSelect.getDirectory()
filePrefix = joinPath(directory, filePrefix)
fileName = filePrefix + '.tgz'
if os.path.exists(fileName):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % fileName,
parent=self):
return
includeBackups = self.backupCheck.isSelected()
includeData = self.dataCheck.isSelected()
packageProject(self.project, filePrefix, includeBackups, includeData)
def showAll(self):
loadAll = False
if self.chemCompDownload:
if (showYesNo('Show all variants','Are you sure you want to display all variants? This will also download the XML files for all chemComps that are not stored locally!')):
loadAll = True
else:
loadAll = True
if loadAll:
for key in self.chemCompInfoList:
self.chem_comps_shown[key] = 1
self.updateTables()
self.chemCompDownload = False
def quit(self):
if not showYesNo('Quit ' + self.programName, 'Quit ' + self.programName + '?'):
return
if self.project:
if not self.checkSaving():
return
self.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)
def _packageProject(memopsRoot):
"""Create a tar gzipped CCPN project from a MemopsRoot object"""
from memops.general.Io import saveProject, packageProject
repository = memopsRoot.findFirstRepository(name='userData')
if not repository:
return
projectPath = repository.url.path
parentDir, projectDir = os.path.split(projectPath)
writeable = os.access(parentDir, os.W_OK)
if not writeable:
msg = 'Directory %s does not have write access required to write temporary file.'
showWarning('Warning', msg % parentDir)
return
currentProjName = memopsRoot.name
newProjName = '__%s' % currentProjName
newProjDir = os.path.join(parentDir, newProjName)
while os.path.exists(newProjDir):
msg = 'Filename %s exists. Overwrite?' % newProjDir
if showYesNo('Query', msg):
break
newProjName = '_' + newProjName
newProjDir = os.path.join(parentDir, newProjName)
try:
saveProject(memopsRoot, newPath=newProjDir, removeExisting=True, revertToOriginal=True)
packageProject(memopsRoot, filePrefix=newProjDir, userPath=newProjDir)
finally:
# reset project name
# need to use override since name is frozen
# wb104: 6 Feb 2014: should not need to do below any more because added revertToOriginal and userPath above
#memopsRoot.override = True
#memopsRoot.name = currentProjName
#memopsRoot.override = False
pass
return newProjDir + '.tgz'
def setDir(self):
directory = self.dir_entry.get()
if not directory:
showWarning('No directory',
'No directory specified, not setting backup directory',
parent=self)
return
if not os.path.abspath(directory):
directory = joinPath(os.getcwd(), directory)
if os.path.exists(directory):
if not os.path.isdir(directory):
showWarning('Path not directory',
'Path "%s" exists but is not a directory' %
directory,
parent=self)
return
else:
if showYesNo(
'Directory does not exist',
'Directory "%s" does not exist, should it be created?' %
directory,
parent=self):
os.mkdir(directory)
else:
showWarning(
'Directory not created',
'Directory "%s" not created so not setting backup directory'
% directory,
parent=self)
return
repository = self.project.findFirstRepository(name='backup')
if not repository:
showWarning(
'No backup repository',
'No backup repository found (something wrong somewhere)',
parent=self)
return
url = repository.url
if url.path != directory:
repository.url = Url(path=normalisePath(directory))
def apply(self):
returnValue = True
if self.importExportFlag == 'import':
returnValue = self.importExportFile(self.component) # If none, will do all components
if returnValue and self.project.molSystems:
if self.project.currentNmrProject.resonances or self.project.currentNmrProject.nmrConstraintStores:
runLinkResonances = showYesNo('Run linkResonances','You have a defined molecular system and NMR atom assignment information in your project. To connect this information to each other you have to run linkResonances. Do you want to run this program now?')
if runLinkResonances:
self.parent.linkResonances()
return returnValue
def quit(self):
msg = 'Quit ' + PROGRAM_NAME
if not showYesNo('Confirm', msg + '?', parent=self):
return
if self.project:
if not self.checkSaving():
return
self.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)
def quit(self):
if not hasattr(self.parent, 'project'):
if not showYesNo('Quit ' + self.programName, 'Quit ' + self.programName + '?'):
return
#if self.project:
# if not self.checkSaving():
# return
self.destroy()
# Only exit system of not inside another app
if not hasattr(self.parent, 'project'):
# Need the below code to fix the problem with Bash
# where the command line was getting screwed up on exit.
if os.name == 'posix':
os.system('stty sane')
sys.exit(0)
def go(self):
if showYesNo('Re-reference', "Are you sure?"):
for i in range(self.numDims):
self.adjusts[i] = self.adjustEntry[i].get()
for peak in self.peakList.peaks:
dims = peak.peakDims
for i, peakDim in enumerate(peak.sortedPeakDims()):
peakDim.position = peakDim.position + self.adjusts[i]
self.parent.parent.owner.peaksUpdate()
self.close()
def quit(self):
msg = 'Quit ' + self.programName
if not showYesNo('Confirm', msg + '?', parent=self):
return
# turn off the daemon!
self.taskDaemon.alive = False
if self.project:
if not self.checkSaving():
return
self.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)
def saveText(self):
fileSelectPopup = FileSelectPopup(
self,
file_types=[
FileType('Text', ['*.txt', '*.out', '*.text']),
FileType('All', ['*'])
],
title='Select text output save file')
fileName = fileSelectPopup.getFile()
if fileName:
writeFile = 1
if os.path.exists(fileName):
if not showYesNo('Overwrite file',
'Overwrite existing file %s?' % fileName):
writeFile = 0
if writeFile:
fout = open(fileName, 'w')
fout.write(self.text.text_area.getText())
fout.close()
def resetSequenceImport(self):
doReset = True
if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Shifts not connected to sequence',
'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.',
parent=self):
self.connectShiftsSequence()
doReset = False
if doReset:
self.mainButtons.buttons[0].config(
foreground=self.fontDefaultColor)
self.sequenceCoordinatesLoaded = self.shiftsLoaded = self.linkResDone = False
self.sequenceCoordinatesImport.setText(self.defaultSelectText)
self.sequenceCoordinatesImport.configure(
foreground=self.fontDefaultColor)
self.moleculeSelect.destroy()
self.moleculeSelect = Label(
self.frameA,
text="None available yet - import valid file first",
foreground=self.fontBadColor)
self.moleculeSelect.grid(row=self.moleculeSelectRow,
column=0,
sticky='ew')
self.shiftImport.setText(self.defaultSelectText)
self.shiftImport.configure(foreground=self.fontDefaultColor)
self.linkResCheckInfo.set("")
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 getOutputHandler(self, width, height, fonts=None):
if not fonts:
fonts = []
else:
fonts = list(fonts)
for n in range(len(fonts)):
if fonts[n] == 'Times':
fonts[n] = 'Times-Roman'
self.setOptionValues()
if not self.file_name:
showError('No file', 'No file specified', parent=self)
return None
if os.path.exists(self.file_name):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % self.file_name,
parent=self):
return None
if (self.paper_type == Output.other_paper_type):
paper_size = self.other_size + [self.other_unit]
else:
paper_size = paper_sizes[self.paper_type]
output_scaling = self.scaling / 100.0
font = 'Times-Roman'
border_text = {}
for decoration in self.border_decoration:
if (decoration == 'Time & date'):
location = 'se'
text = time.ctime(time.time())
elif (decoration == 'File name'):
location = 'sw'
text = self.file_name
else:
continue # should not be here
border_text[location] = (text, font, 12)
if (self.title):
location = 'n'
border_text[location] = (self.title, font, 18)
if font not in fonts:
fonts.append(font)
outputHandler = PrintHandler.getOutputHandler(
self.file_name,
width,
height,
output_scaling=output_scaling,
paper_size=paper_size,
paper_orientation=self.paper_orientation,
output_style=self.output_style,
output_format=self.output_format,
border_text=border_text,
fonts=fonts,
do_outline_box=self.doOutlineBox)
return outputHandler
def runDangle(self):
chain = self.chain
shiftList = self.shiftList
if (not chain) or (not shiftList):
showError('Cannot Run DANGLE',
'Please specify a chain and a shift list.',
parent=self)
return
# check if there is a DangleChain available
self.checkDangleStore()
dangleStore = self.dangleStore
if not dangleStore:
return
dangleChain = dangleStore.findFirstDangleChain(chain=chain)
if dangleChain:
data = (chain.code, dangleChain.shiftList.serial)
msg = 'Predictions for Chain %s using Shift List %d already exist.\nReplace data?' % data
if not showYesNo('Replace Data', msg, parent=self):
return
else:
self.dangleChain = dangleChain
dangleChain.shiftList = shiftList
else:
self.dangleChain = dangleStore.newDangleChain(chain=chain,
shiftList=shiftList)
#dangleStore.packageLocator.repositories[0].url.dataLocation = '/home/msc51/ccpn/NexusTestGI'
#dangleStore.packageName = 'cambridge.dangle'
repository = dangleStore.packageLocator.repositories[0]
array = dangleStore.packageName.split('.')
path = os.path.join(repository.url.dataLocation, *array)
path = os.path.join(path, dangleStore.name,
chain.code) # Dangle_dir/dangleStoreName/chainCode
if not os.path.exists(path):
os.makedirs(path)
self.dangleDir = path
inputFile = os.path.join(self.dangleDir, 'dangle_cs.inp')
if os.path.isfile(inputFile):
os.unlink(inputFile)
outputFile = os.path.join(self.dangleDir, 'danglePred.txt')
if os.path.isfile(outputFile):
os.unlink(outputFile)
numShift = self.makeDangleInput(inputFile, chain, shiftList)
if not os.path.isfile(inputFile):
msg = 'No DANGLE input has been generated.\nPlease check shift lists.'
showError('File Does Not Exist', msg, parent=self)
return
if numShift == 0:
msg = 'No shift data in input file.\nPerhaps shifts are not assigned.\nContinue prediction anyway?'
if not showYesNo('Empty DANGLE input', msg, parent=self):
return
rejectThresh = self.rejectPulldown.getObject()
# Use the Reference info from the main installation
# location must be absolute because DANGLE could be run from anywhere
location = os.path.dirname(dangleModule.__file__)
progressBar = ProgressBar(self)
self.update_idletasks()
dangle = Dangle(location,
inputFile=inputFile,
outputDir=self.dangleDir,
reject=rejectThresh,
angleOnly=False,
progressBar=progressBar,
writePgm=False)
#self.dangleDir = '/home/msc51/nexus/gItest/DanglePred/'
#outputFile = '/home/msc51/nexus/gItest/DanglePred/danglePred.txt'
predictions = dangle.predictor.predictions
gleScores = dangle.predictor.gleScores
self.readPredictions(predictions, gleScores)
self.updatePredictionMatrix()
def findMatchingChain(molSystem,
ccpCodes,
excludeChains=None,
molTypes=None,
doWarning=True):
"""* * * Deprecated in light of findMathcingChains() * * *
Find the mol system chain that best matches the input ccpCodes
(like three letter codes). Useful for trying to match structures
to existing molecular data. Optional argument to specify which
chains cannot be matched.
.. describe:: Input
MolSystem.MolSystem, List of Strings (MolSystem.MolResidue.ccpCodes),
List of MolSystem.Chains
.. describe:: Output
Tuple of (MolSystem.Chain, Int (index of first matching ccpCode),
Int (first matching MolSystem.Residue.seqId))
"""
print("DEPRECATED, function findMatchingChain should not be used")
chains = []
for chain in molSystem.sortedChains():
if excludeChains and (chain in excludeChains):
continue
sequence = []
if not chain.residues:
continue
chains.append(chain)
residues = []
for residue in chain.sortedResidues():
molType = residue.molType
if molTypes and (molType not in molTypes):
break
residues.append((residue.seqId, residue))
else:
residues.sort()
for residue in residues:
sequence.append(residue[1].ccpCode)
len0 = len(sequence)
len1 = len(ccpCodes)
if len0 < len1:
continue
elif len0 == len1:
if sequence == ccpCodes:
mapping = [(i, residues[i][1]) for i in range(len0)]
return chain, mapping
else:
misMatch = 0
for i in range(len0):
if (ccpCodes[i]
is not None) and (ccpCodes[i] != sequence[i]):
misMatch = 1
break
if misMatch:
continue
else:
mapping = [(i, residues[i][1]) for i in range(len0)]
return chain, mapping
else:
d = len0 - len1
for x in range(d + 1):
misMatch = 0
for i in range(len1):
if (ccpCodes[i] is not None) and (ccpCodes[i] !=
sequence[i + x]):
misMatch = 1
break
if misMatch:
continue
else:
mapping = [(i, residues[i + x][1])
for i in range(len1)]
return chain, mapping
scoreList = []
bestMapping = None
bestScore = 0
bestChain = None
for chain in chains:
mapping, score = getSequenceResidueMapping(chain, ccpCodes)
scoreList.append((score, chain, mapping))
if scoreList:
scoreList.sort()
bestScore, bestChain, bestMapping = scoreList[-1]
chain = None
if bestScore and (bestScore / float(len(bestChain.residues)) > 2.0):
chain = bestChain
if chain.molecule.molType in (
CARBOHYDRATE_MOLTYPE): # DNA & RNA now hopefully fine to align
chain = None
if doWarning:
msg = 'Residue sequence matches an existing chain, but not exactly. '
msg += 'Really link to chain %s? (Otherwise a new chain will be made)' % chain.code
if not showYesNo('Query', msg):
chain = None
return chain, bestMapping
