def setSpectrum(self, *event):
if self.currentObject:
text = self.spectrumEntry.get()
if text and text != ' ':
for data in self.scrolledMatrix.objectList:
if data is self.currentObject:
continue
if (data.specName
== text) and (data.exptName
== self.currentObject.exptName):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
elif (self.experiment) and (
self.experiment.findFirstDataSource(name=text)):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
self.currentObject.specName = text
self.update()
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def clusterSelectedPeaks(self):
peaks0 = self.parent.currentPeaks
peaks = []
for peak in peaks0:
if peak.peakList in self.peakLists:
peaks.append(peak)
if not peaks:
showWarning('Cluster Failure',
'No peaks selected from active peak lists',
parent=self)
return
if not self.multiplet:
showWarning('Cluster Failure',
'No multiplet pattern selected',
parent=self)
return
cluster = makeMultipletPeakCluster(peaks, self.multiplet,
self.windowPane)
if cluster:
self.clusterMatrix.selectObject(cluster)
def setAtomTypeDefault(self):
if self.scheme:
atomName = askString(
'Query',
'Specify atom name to set\ndefault abundance for',
'H',
parent=self)
if not atomName:
return
atomLabels = []
for chemCompLabel in self.scheme.chemCompLabels:
if chemCompLabel.molType == self.molType:
for isotopomer in chemCompLabel.isotopomers:
# Multiple because of isotopes and subTypes
atomLabels += isotopomer.findAllAtomLabels(
name=atomName)
if atomLabels:
for atomLabel in atomLabels:
isotope = atomLabel.isotope
weight = self.defaultAbun.get(isotope,
100.0 * isotope.abundance)
atomLabel.weight = weight
else:
data = (atomName, self.scheme.name)
msg = 'Atom name %s does not match any atoms in %s scheme isotopomers' % data
showWarning('Failure', msg)
def sendRequest(url, fields, files):
"""Function to send form fields and files to a given URL.
"""
contentType, bodyData = encodeForm(fields, files)
headerDict = {'User-Agent': 'anonymous',
'Content-Type': contentType,
'Content-Length': str(len(bodyData))
}
request = urllib2.Request(url, bodyData, headerDict)
response = urlOpen(request)
if not response:
return
jsonTxt = response.read()
result = _processResponse(jsonTxt)
if result.get(RESPONSE_EXIT_CODE) != RESPONSE_SUCCESS:
msg = 'Request not successful. Action was: %s' % fields
msg += ' Response was: %s' % jsonTxt
showWarning('Failure', msg)
return
return result
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 purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials, self.getServerUrl(url))
if results:
showInfo('Info','iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info','Purge failed')
self.update()
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 importPdbCoords(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB coordinates file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = PseudoPdbFormat(self.project, self, verbose=True)
pdbObj.readCoordinates(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return pdbObj
def importFastaSeq(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('Fasta', ['*.fsa']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import Fasta sequence file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
fastaObj = FastaFormat(self.project, self, verbose=True)
fastaObj.readSequence(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return fastaObj
def importNmrStar31(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('STAR', ['*.str']),
FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import NMR-STAR 3.1 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
nmrStarObj = NmrStarFormat(self.project, self, verbose=True)
nmrStarObj.readProject(fileName, minimalPrompts=True, version='3.1')
self.eciFrame.updateAll()
return nmrStarObj
def importPdb(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB 3.20 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = ReadPdb(fileName, self.project, 'PDB_'+ name, self)
self.eciFrame.updateAll()
return pdbObj
def setResidueScheme(molLabel, molResidue, scheme):
"""Descrn: Link a given input residue to a standard set of itotopomers
specified in a given labelling scheme. The residue labelling
is only set within a given molLabel instance and so may
correspond to only one component of a mixture.
Inputs: LabeledMolecule.MolLabel, Molecule.molResidue,
ChemCompLabel.LabelingScheme
Output: LabeledMolecule.ResLabel
"""
chemComp = molResidue.chemComp
chemCompLabel = scheme.findFirstChemCompLabel(chemComp=chemComp)
if (not chemCompLabel) or not chemCompLabel.isotopomers:
data = (chemComp.molType, chemComp.ccpCode, scheme.name)
msg = 'No isotopomer information found for %s %s in labelling scheme %s' % data
showWarning('Failure', msg)
return
resLabel = molLabel.findFirstResLabel(resId=molResidue.serial)
if resLabel:
for oldFraction in resLabel.resLabelFractions:
oldFraction.delete()
else:
resLabel = molLabel.newResLabel(resId=molResidue.serial)
# Weight 1.0 is he default in any case
# Isotopomer serial zero means standard set
resLabel.newResLabelFraction(schemeName=scheme.name,
weight=1.0, isotopomerSerial=0)
return resLabel
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 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 get(self):
# TBD: str below is used to convert unicode to string
# (in Tcl/Tk 8.5 it looks like everything is unicode)
###s = str(Tkinter.Entry.get(self).strip())
s = Tkinter.Entry.get(self).strip().encode('utf-8')
if (self.isArray):
if (self.maxCharsPerLine):
s = s.replace(self.joiner, self.separator)
if (s):
value = re.split(self.array_re, s)
else:
value = []
if (self.strToVal):
value = map(self.strToVal, value)
elif (self.strToVal):
if (s):
try:
value = self.strToVal(s)
except:
value = None
showWarning('Error',
'Could not convert value to required type')
else:
value = None
else:
value = s
return value
def checkDangleStore(self):
if not self.dangleStore:
N = len(self.project.dangleStores) + 1
name = askString('Request',
'Dangle Run Name:',
'Run%d' % N,
parent=self)
if not name:
return None
for character in whitespace:
if character in name:
showWarning('Failure',
'Name cannot contain whitespace',
parent=self)
return None
if self.project.findFirstDangleStore(name=name):
showWarning('Failure', 'Name already used', parent=self)
return None
self.dangleStore = self.project.newDangleStore(name=name)
self.updateDangleStorePulldown()
def iCingFetch(credentials, url, iCingUrl, zipFileName):
"""Fetch a CCPn project from an job on iCing server associated with given credentials.
"""
response = iCingProjectName(credentials, iCingUrl)
if not response:
msg = 'Fetch not possible'
showWarning('Warning', msg)
return
entryId = response.get(RESPONSE_RESULT)
baseUrl, resultUrl, logUrl, zipUrl = getResultUrls(credentials, entryId, url)
#print "Base URL", baseUrl
#print "Results URL:", resultUrl
#print "Log URL:", logUrl
#print "Zip URL:", zipUrl
response = urlOpen(logUrl)
if response:
logText = response.read()
response = urlOpen(zipUrl)
if response:
file = open(zipFileName, 'wb')
file.write(response.read())
file.close()
return logText
def selectRun(self, simRun):
if self.run is not simRun:
if simRun:
if simRun.outputEnsemble:
msg = 'Selected run has already been used to generate a structure.'
msg += 'A new run will be setup based on the selection.'
showWarning('Warning',msg)
simRun = self.makeSimRun(template=simRun)
molSystem = simRun.molSystem
constraintSet = simRun.inputConstraintStore
shiftList = simRun.findFirstInputMeasurementList(className='ShiftList')
if molSystem and (self.molSystem is not molSystem):
self.molSystem = molSystem
self.updateMolSystems()
if constraintSet and (self.constraintSet is not constraintSet):
self.constraintSet = constraintSet
self.updateConstraintSets()
if shiftList and (self.shiftList is not shiftList):
self.shiftList = shiftList
self.updateShiftLists()
firstPepPlane = simRun.findFirstrunParameter(code='FirstPepPlane')
lastPepPlane = simRun.findFirstrunParameter(code='LastPepPlane')
maxOptSteps = simRun.findFirstrunParameter(code='MaxOptSteps')
numOptPlanes = simRun.findFirstrunParameter(code='NumOptPlanes')
minOptHits = simRun.findFirstrunParameter(code='MinOptHits')
chainCode = simRun.findFirstrunParameter(code='ChainCode')
if firstPepPlane is not None:
self.firstResEntry.set(firstPepPlane.intValue or 0)
if lastPepPlane is not None:
self.lastResEntry.set(lastPepPlane.intValue or 0)
if maxOptSteps is not None:
self.maxOptStepEntry.set(maxOptSteps.intValue or 0)
if numOptPlanes is not None:
self.numOptPlaneEntry.set(numOptPlanes.intValue or 0)
if minOptHits is not None:
self.numOptHitsEntry.set(minOptHits.intValue or 0)
if chainCode is not None:
chainCode = chainCode.textValue or 'A'
if self.molSystem:
chain = self.molSystem.findFirsChain(code=chainCode)
if chain:
self.selectChain(chain)
self.run = simRun
def warnChempCompLabelFailure(ccpCode,molType,scheme):
"""Descrn: Display a general warning for not being able to find a chemComplLabel
Inputs: Word, Word, ChemCompLabel.LabelingScheme, MolSystem.Atom
Output: None
"""
data = (ccpCode,molType,scheme.name)
msg = 'Could not find chemp comp labelling information for %s(%s) in scheme %s'
showWarning('Failure',msg % data)
def shouldChangeDir(self, directory):
shouldNotChange = self.isProjectDirectory(directory)
if shouldNotChange:
showWarning('Warning',
'Cannot save project inside a project directory',
parent=self)
return not shouldNotChange
def wrapperFunction(self, *args, **kwargs):
if self.guiParent.connector.results:
function(self, *args, **kwargs)
else:
string = 'There are no results since the annealing did not run yet.'
showWarning('Run Annealing first', string, parent=self.guiParent)
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def __init__(self, parent, project):
#
# Info for writing file...
#
self.groupText = {}
#
# Set up molSystem information
#
self.project = project
self.molSysList = list(project.sortedMolSystems())
self.molSystems = None
self.molSysLabelList = []
self.molSysLabelDict = {}
self.molSysRelationDict = {}
molSysLabel = 'All molSystems'
if self.setChainLabels(molSysLabel, self.molSysList):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = self.molSysList
for molSys in self.molSysList:
molSysLabel = '%s' % molSys.code
if self.setChainLabels(molSysLabel, [molSys]):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = [molSys]
if not self.molSysLabelList:
showWarning('Warning',
'No chemical shift lists available! Exiting...')
return
#
# Some initializing...
#
self.chains = None
self.shiftList = None
self.shiftListLabel = None
self.results = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Group chemical shift values',
modal=False,
transient=True)
def addSymmetrySet(self):
if not self.ccpnProject.molSystems:
showWarning('Warning','No molecular systems present in CCPN project',parent=self)
return
molSystem = self.ccpnProject.findFirstMolSystem()
partner = self.hProject.newHaddockPartner(code=molSystem.code, molSystem=molSystem)
setPartnerChains(partner, molSystem.chains)
self.updateAllAfter()
def checkValue(self, value):
if (self.minVal is not None) and (value < self.minVal):
showWarning('Value is less than minimum value (%s)' % self.minVal)
value = None
elif (self.maxVal is not None) and (value > self.maxVal):
showWarning('Value is greater than maximum value (%s)' % self.maxVal)
value = None
return value
def toggleTab(self, index):
if (index > 0) and not self.project:
showWarning('Warning', 'No active project', parent=self)
self.tabbedFrame.select(0)
return
frame = self.tabbedFrame.frames[index]
if hasattr(frame, 'printOutDocString'):
print frame.printOutDocString
# only print it once
del frame.printOutDocString
def saveSchemes(self):
schemes = [x for x in self.project.labelingSchemes if x.isModified]
if schemes:
for scheme in schemes:
scheme.save()
showInfo('Notice', 'Successfully saved %d schemes' % len(schemes))
self.updateSchemes()
else:
showWarning('Notice', 'No modified schemes to save')
def makeNewScheme(self):
name = askString('Input text', 'New Scheme Code:', '', parent=self)
if name:
scheme = self.project.findFirstLabelingScheme(name=name)
if scheme:
showWarning('Failure', 'Scheme name already in use')
else:
scheme = self.project.newLabelingScheme(name=name)
self.scheme = scheme
else:
showWarning('Failure', 'No name specified')
def saveDataToPyc(self):
"""Save the data to the selected file."""
if self.guiParent.connector.results:
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.saveDataToPyc(fileName)
self.fileselectionBox.updateFileList()
else:
string = """There are no results to save, """ """the algorithm has not run yet."""
showWarning("No Results to Save", string, parent=self.guiParent)
def toggleUseRestraints(self, constraintList):
bool = constraintList.useForMeccano
bool = not bool
if bool and (not constraintList.conditionState) \
and (constraintList.className == 'RdcConsraintList'):
msg = 'Cannot use RDC restraint list for Meccano '
msg += 'unless it is first associated with an amigment medium'
showWarning('Warning', msg, parent=self)
else:
constraintList.useForMeccano = bool
self.updateConstraintLists()
def checkPoint2(self):
'''Second of two checkpoints, is run before the annealing starts.
It is checked whether the precalculations already ran and whether
the list with acceptance constants is valid.
Returns True if it is safe to proceed. Returns False otherwise.
'''
if self.ranPreCalculations:
if self.GUI.annealingSettingsTab.updateAcceptanceConstantList():
return True
else:
string = '''Without running the pre-calculations,
the annealing can not run.
'''
showWarning('Run pre-calculations first', string, parent=self.GUI)
return False
def checkChain(self):
'''Checks whether a chain is configured
and whether this chain has residues.
'''
if not self.chain:
string = 'Setup a molecular chain in Molecule --> Molecules'
showWarning('No chain selected', string, parent=self.GUI)
return False
if not self.chain.residues:
string = '''The selected chain does not have residues,
set up the residues in
Molecule --> Molecules --> Sequences
'''
showWarning('No Residues', string, parent=self.GUI)
return False
return True
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 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()
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index-2
format = ['PDB','CCPN','CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get()
if not file:
showWarning('Failure','No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append( ('script',script) )
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
def loadDataFromPyc(self, fileName):
'''Load previously pickled data.
args: fileName: name of the file
'''
self.updateInfoText('Loading file...')
# TODO : fix this, getting these values from the GUI is ridiculous
self.project = self.GUI.project
self.nmrProject = self.GUI.nmrProject
results = None
fileExists = False
if os.path.exists(fileName):
fileExists = True
elif os.path.exists(fileName + '.pyc'):
fileName = fileName + '.pyc'
fileExists = True
if fileExists:
try:
with open(fileName, 'rb') as readFile:
results = cPickle.load(readFile)
except:
string = ('''Something went wrong when trying to '''
'''load the previously produced results. '''
'''Probably the file you try to '''
'''open is not of the correct type.''')
print string
showWarning('Can not open file', string, parent=self.GUI)
raise
if results:
if isinstance(results, DataModel):
self.results = results
self.updateInfoText('File loaded succesfully.')
self.updateInfoText(('''Re-connecting to object in '''
'''the ccpn analysis project...'''))
self.results.connectToProject(self.project,
self.nmrProject)
# TODO: this is not very nice
self.GUI.resultsTab.dataModel = self.results
self.updateInfoText('Done')
return
else:
string = (('''You are trying to open a file that '''
'''was not created using this macro.'''))
showWarning('Can not open file', string, parent=self.GUI)
else:
string = 'The file you selected does not exist.'
showWarning('No Such File', string, parent=self.GUI)
self.updateInfoText(' ')
def checkSpectraAndLabelling(self):
'''Check whether some spectra are selected by the user
and whether a reference experiment has been set
for this experiment (needed to simulate the spectra)
and if the user said the labelling scheme should
come automatically from the labelled sample,
the labelled mixture should be set.
'''
if not self.selectedSpectra:
string = 'Select one or more spectra.'
showWarning('No Spectra Selected', string, parent=self.GUI)
return False
for spec in self.selectedSpectra:
name = spec.ccpnSpectrum.experiment.name
if not spec.ccpnSpectrum.experiment.refExperiment:
string = name + (''' has no reference experiment, '''
'''go to Experiment --> Experiments --> '''
'''Experiment Types and select '''
'''a experiment type.''')
showWarning('No Reference Experiment',
string, parent=self.GUI)
return False
mixtures = spec.ccpnSpectrum.experiment.labeledMixtures
if spec.labellingScheme is True and not mixtures:
string = name + (''' is not connected to any labelled'''
''' sample.In order to determine the'''
''' labelling scheme automatically'''
''' from the experiment, this has to'''
''' be set. Go to'''
''' Menu-Modecule-Isotope Labelling'''
''' to do so.''')
showWarning('No Labelled Sample', string, parent=self.GUI)
return False
elif len(mixtures) > 1:
string = name + (''' is connected to more than one labelled'''
''' sample. This is physically impossible.'''
''' Go to Menu-Modecule-Isotope Labelling'''
''' if you want to change this.''')
showWarning('Multiple Labelled Samples for Spectrum',
string, parent=self.GUI)
return False
return True