def doExport(self):
if self.exportFileName:
chain = self.chainDict[self.chainSelect.getSelected()]
returnValue = self.autoAssignFormat.writeProject(
self.exportFileName, chain=chain, setTag=self.dateTimeFlag)
if not returnValue:
showError(
"No export file written",
"There were problems while exporting the %s project file."
% self.format)
else:
showInfo("File written", "File written successfully")
cdtsTag = "%s-%s" % (self.chainSelect.getSelected(),
self.dateTimeFlag)
if not cdtsTag in self.chainDateTimeSelect.entries:
if "<None>" in self.chainDateTimeSelect.entries:
self.chainDateTimeSelect.entries.pop(
self.chainDateTimeSelect.entries.index("<None>"))
self.chainDateTimeSelect.replace(
[cdtsTag] + self.chainDateTimeSelect.entries)
self.chainDateTimeStampDict[cdtsTag] = chain
else:
showError(
"No export file defined",
"Please define a name for the %s project file to export to." %
self.format)
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 timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials,
self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
self.run.status = 'failed'
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
self.run.status = 'completed'
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
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 apply(self):
shiftListLabel = self.shiftListSelect.getSelected()
shiftList = self.shiftListDict[shiftListLabel]
try:
chainLabel = self.chainListSelect.getSelected()
chain = self.chainDict[chainLabel]
except:
showError(
"No chains",
"No chains were present or selected. Try running linkResonances first."
)
return False
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeBmrbChemShiftDeposition(self.guiParent, chain,
shiftList, fileName)
if fileCreated:
showInfo("Success",
"Succesfully wrote chemical shift deposition file")
else:
showError("Not written",
"Error writing file %s. File not written" % fileName)
return False
return True
def storeSecondaryStructure(self):
if not self.chain:
return
getSpinSystem = self.nmrProject.findFirstResonanceGroup
newSpinSystem = self.nmrProject.newResonanceGroup
predDict = self.predictionDict.get(self.chain, {})
n = 0
for residue in predDict:
(ssCode, isReliable, probabilityDict) = predDict[residue]
if isReliable:
spinSystem = getSpinSystem(residue=residue)
if not spinSystem:
spinSystem = newSpinSystem(residue=residue,
ccpCode=residue.ccpCode)
spinSystem.secStrucCode = ssCode
n += 1
showInfo('Info',
'Stored secondary structure types for %d residues.' % n,
parent=self)
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 storeSecondaryStructure(self):
if not self.dangleChain:
return
getSpinSystem = self.nmrProject.findFirstResonanceGroup
newSpinSystem = self.nmrProject.newResonanceGroup
n = 0
for dangleResidue in self.dangleChain.dangleResidues:
ssCode = dangleResidue.secStrucCode
if not ssCode:
continue
residue = dangleResidue.residue
if not residue:
continue
spinSystem = getSpinSystem(residue=residue)
if not spinSystem:
spinSystem = newSpinSystem(residue=residue,
ccpCode=residue.ccpCode)
spinSystem.secStrucCode = ssCode
n += 1
showInfo('Info',
'Stored secondary structure types for %d residues.' % n,
parent=self)
def printStructure(self):
w = self.winfo_width()
h = self.winfo_height()
popup = PrintPopup(self,
width=w,
height=h,
title='Print Structure',
modal=True,
project=self.project,
getOption=self.getPrintOption,
setOption=self.setPrintOption)
outputHandler = popup.outputHandler
popup.destroy()
if (not outputHandler):
return
(x0, y0, x1, y1) = self.handler.getRegion()
try:
printHandler = PrintHandler.PrintHandler(outputHandler,
xRegion=(x0, x1),
yRegion=(y0, y1))
self.drawStructure(handler=printHandler)
file_name = outputHandler.file_name
printHandler.close(
) # clears file_name, hence first need to save, as above
showInfo('Wrote file',
'Successfully wrote file "%s"' % file_name,
parent=self)
except IOError, e:
showError('IO Error', str(e), parent=self)
def write_npc(self, pcsValues):
fileName = os.path.abspath(self.expPCSEntry.get())
with open(fileName, 'w') as o:
for key in sorted(pcsValues):
seq, atom = key
value = pcsValues[key]
line = "{0:<4d}{1:<2}{2:15.8f} 0.0\n".format(seq, atom, value)
o.write(line)
o.close()
showInfo("Wrote PCS", "Wrote experimental PCS to: {}".format(fileName))
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 showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def getSelected():
chemComp = frame.getSelectedChemComp()
if (chemComp):
if hasattr(chemComp,'chemComp'):
ccType = 'chemCompVar'
chemComp = chemComp.chemComp
else:
ccType = 'chemComp'
showInfo('ChemComp', 'Selected %s = (%s, %s)' % (ccType,chemComp.molType, chemComp.ccpCode), parent=root)
else:
showInfo('ChemComp', 'No chemComp selected', parent=root)
def openLicense(self):
licenseUrl = 'http://www.ccpn.ac.uk/license'
try:
import webbrowser
except ImportError:
showInfo('License Agreement',
'The CCPN License Agreement is available at %s' %
licenseUrl,
parent=self)
return
wb = webbrowser.get()
wb.open(licenseUrl)
def apply(self):
if self.frame.getSelectedChemComp():
return True
else:
showInfo(
'No selection',
'Please select a chemCompVar from the bottom half of the window, or press Cancel to quit.'
)
return False
def apply(self):
self.selectedFormats = self.formatListBox.getSelectedItems()
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeMappingFile(self.project,fileName,originalFormats = self.selectedFormats)
if fileCreated:
showInfo("Success","Succesfully wrote mapping file")
else:
showError("Not written","Error writing file %s. File not written" % fileName)
return False
return True
def apply(self):
selectedPeakLists = self.peakListBox.getSelectedItems()
for peakListLabel in selectedPeakLists:
self.peakLists.append(self.peakListDict[peakListLabel])
chemShiftList = self.shiftListDict[self.shiftListSelect.getSelected()]
if not chemShiftList:
chemShiftListName = askString("Enter chemical shift list name",
"New chemical shift list name", '',
self)
else:
chemShiftListName = chemShiftList.name
useAllContribs = self.useAllContribs.isSelected()
defaultShiftError = {}
for nucl in self.defaultShiftError.keys():
defaultShiftError[nucl] = returnFloat(
self.defaultShiftError[nucl].get())
listCreated = createChemShifts(self.peakLists,
guiParent=self.parent,
multiDialog=self.parent.multiDialog,
shiftList=chemShiftList,
useAllContribs=useAllContribs,
defaultShiftError=defaultShiftError,
shiftListName=chemShiftListName)
if listCreated:
showInfo(
"Success",
"Succesfully created a chemical shift list from peaklist(s)")
return True
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def importSequenceOrCoords(self):
dataTypes = ['sequence', 'coordinates']
fileTypes = self.createFileTypes(dataTypes)
if self.getFileName('Import sequence or coordinate file', fileTypes):
formatNameSuggestions = {}
for dataType in dataTypes:
tmpList = self.fcWrapper.determineFormatNamesForFile(
dataType, self.fileName)
if tmpList:
formatNameSuggestions[dataType] = tmpList
if not formatNameSuggestions:
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Let user select if multiple options, otherwise take default
#
if len(formatNameSuggestions) == 1 and len(formatNameSuggestions[
formatNameSuggestions.keys()[0]]) == 1:
dataType = formatNameSuggestions.keys()[0]
formatName = formatNameSuggestions[dataType][0]
if not showYesNo(
'File type detected',
'Reading as %s file in %s format. Is this correct?' %
(dataType, formatName),
parent=self):
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
else:
#
# Create a selection (hopefully user-understandable)
#
selectionList = []
selectionDict = {}
for dataType in dataTypes:
dataTypeString = dataType
if formatNameSuggestions.has_key(dataType):
formatNames = formatNameSuggestions[dataType]
formatNames.sort()
for formatName in formatNames:
selectionString = "%s file in %s format." % (
dataTypeString, formatName)
selectionList.append(selectionString)
selectionDict[selectionString] = (dataType,
formatName)
interaction = SelectionListPopup(self,
selectionList,
title='File format selection',
text='This is a:',
selectionDict=selectionDict,
dismissButton=True,
modal=True)
#
# Check if anything was selected...
#
dataType = formatName = None
if interaction.isSelected:
(dataType, formatName) = interaction.selection
else:
showWarning(
'Failure',
'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s'
% self.email,
parent=self)
return False
#
# Now read the file, need to do some field updates!
#
(fileRead, fileInformation) = self.fcWrapper.readFile(
dataType, formatName, self.fileName)
if not fileRead:
showWarning(
'Failure',
'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.'
% (fileInformation, self.email),
parent=self)
return False
(conversionInfo, conversionSuccess) = (
self.fcWrapper.formatConversion.conversionInfo,
self.fcWrapper.formatConversion.conversionSuccess)
if not conversionSuccess:
showWarning(
'Failure',
'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Set info if import worked OK
#
conversionLines = conversionInfo.split(": ")
showInfo("Import coordinate and/or sequence information",
":\n".join(conversionLines),
parent=self)
if dataType == 'sequence':
chains = self.fcWrapper.importReturns[dataType]
models = []
elif dataType == 'coordinates':
models = self.fcWrapper.importReturns[dataType]
chains = [
cChain.chain
for cChain in models[0].structureEnsemble.coordChains
]
self.sequenceCoordinatesImport.setText(
self.fileName) # TODO change color or something?
self.sequenceCoordinatesImport.configure(
foreground=self.fontOkColor)
self.sequenceCoordinatesLoaded = True
#
# Reset to list selector for further use
#
moleculeName = None
for chain in chains:
if chain in self.moleculeDict.values():
continue
numResidues = len(chain.residues)
if numResidues == 1:
residueText = "%s residue" % chain.findFirstResidue(
).ccpCode
else:
residueText = "%d residues" % numResidues
moleculeName = "%s (chain '%s', %s)" % (
chain.molecule.name, chain.code, residueText)
self.moleculeList.append(moleculeName)
self.moleculeDict[moleculeName] = chain
self.moleculeList.sort()
self.moleculeSelect.destroy()
if len(chains) == 1 and moleculeName:
selectedIndex = self.moleculeList.index(moleculeName)
else:
selectedIndex = 0
self.moleculeSelect = PulldownList(self.frameA,
texts=self.moleculeList,
index=selectedIndex,
sticky='ew')
self.moleculeSelect.grid(row=self.moleculeSelectRow, column=0)
#
# Now update Deposition tab
#
molecules = []
for chain in chains:
if not chain.molecule in molecules:
molecules.append(chain.molecule)
numCoords = 0
for model in models:
numCoords += len(model.coords)
self.updateDepositionImportLabel(molecules=len(molecules),
chains=len(chains),
models=len(models),
coordinates=numCoords)
# Add the molSystem to the entry!
if chains and not chains[0].molSystem == self.entry.molSystem:
self.entry.molSystem = chains[0].molSystem
self.updateAll()
def notYetImplemented(text=''):
if (text):
text = '"' + text + '" '
showInfo('Not Yet Implemented', text + 'not yet implemented')
class RegisterPopup(BasePopup):
"""
**Register User with CCPN**
The purpose of this dialog is to allow the user to register with CCPN.
This is mainly to allow CCPN to keep track of the number of users,
which is important for grant applications. This information is saved
both in a file on your computer but also in a private CCPN server
database if your computer is connected to the internet. (So unfortunately
you will need to register once for each computer you use.)
The required information: the user name, organisation and email address.
The other information stored on the CCPN server: the version number, the
first time and most recent time the server has been notifed.
If you are registered, then the server is notified every time a project is
opened or saved (if connected to the internet).
Click "Register Now" to register, or "Register Later" not to register.
"""
def __init__(self, parent, isModal=False, *args, **kw):
title = 'Project : Register with CCPN'
BasePopup.__init__(self,
parent=parent,
title=title,
modal=isModal,
**kw)
def body(self, guiFrame):
self.geometry('600x250+600+250')
analysisProfile = self.analysisProfile
userName = analysisProfile.userName
userOrganisation = analysisProfile.userOrganisation
userEmail = analysisProfile.userEmail
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(1, weight=1)
explainText = 'To keep track of our users and which versions are being used\n' \
'we would like you to register your details with us.\n' \
'Collating the number of users is important for grant applications.\n' \
'Please do not use accents in any of the information\n' \
'because Python does not handle it gracefully.'
row = 0
label = Label(guiFrame,
text=explainText,
grid=(row, 0),
gridSpan=(1, 2),
sticky='ew')
row += 1
licenseAgreeText = 'I agree to abide by the rules of the CCPN licensing agreement.'
self.agreeButton = CheckButton(guiFrame,
licenseAgreeText,
tipText=licenseAgreeText)
self.agreeButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
self.entryWidgets = []
for (text, value) in (('Name', userName),
('Organisation', userOrganisation), ('Email',
userEmail)):
label = Label(guiFrame, text=text + ':', grid=(row, 0))
entry = Entry(guiFrame,
text=value or '',
grid=(row, 1),
sticky='ew',
tipText='Your ' + text)
self.entryWidgets.append(entry)
row += 1
texts = ['Register Now', 'Read License', 'Register Later']
tipTexts = ['Register now', 'Read License', 'Register later']
commands = [self.register, self.openLicense, self.close]
buttons = UtilityButtonList(guiFrame,
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
commands=commands,
texts=texts,
tipTexts=tipTexts)
self.buttons = buttons
def openLicense(self):
licenseUrl = 'http://www.ccpn.ac.uk/license'
try:
import webbrowser
except ImportError:
showInfo('License Agreement',
'The CCPN License Agreement is available at %s' %
licenseUrl,
parent=self)
return
wb = webbrowser.get()
wb.open(licenseUrl)
def register(self):
if not self.agreeButton.get():
showError(
'License Agreement',
'Please tick the box indicating that you agree to the CCPN licensing terms and conditions.',
parent=self)
return
analysisProfile = self.analysisProfile
attrs = ('userName', 'userOrganisation', 'userEmail')
for n, entry in enumerate(self.entryWidgets):
attr = attrs[n]
value = entry.get().strip()
if not value:
showError('Blank value',
'%s is blank, value required' % attr[4:],
parent=self)
return
if attr == 'userEmail' and '@' not in value:
showError('Illegal email',
'Email must have "@" in it',
parent=self)
return
try:
setattr(analysisProfile, attr, value)
except Exception, e:
showError('Attribute setting',
'Error setting %s: %s' % (attr[4:], e),
parent=self)
return
analysisProfile.save()
try:
result = updateRegister(analysisProfile)
showInfo('Registering', result, parent=self)
self.close()
except Exception, e:
showError('Registering', str(e), parent=self)
def importShifts(self):
currentChain = self.getCurrentChain()
if not currentChain:
showWarning(
'Failure',
'Please first read in a sequence or coordinate file and select the molecule relevant for this shift list.',
parent=self)
return
elif self.currentShiftList:
shiftListChainPair = (self.currentShiftList, currentChain)
if shiftListChainPair in self.shiftListChainPairs:
showWarning(
'Failure',
"You already read in chemical shifts for this chain.\nPlease read in related shifts for the other chain(s), if present, or press the 'Import new set of shifts' button to read in a new set of shifts.",
parent=self)
return
dataType = 'shifts'
fileTypes = self.createFileTypes([dataType])
if self.getFileName('Import chemical shift file', fileTypes):
formatNameSuggestions = self.fcWrapper.determineFormatNamesForFile(
dataType, self.fileName)
if not formatNameSuggestions:
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Let user select if multiple options, otherwise take default
#
if len(formatNameSuggestions) == 1:
formatName = formatNameSuggestions[0]
if not showYesNo(
'File type detected',
'Reading as a chemical shift file in %s format. Is this correct?'
% formatName,
parent=self):
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
else:
#
# Create a selection (hopefully user-understandable)
#
selectionList = []
selectionDict = {}
formatNameSuggestions.sort()
for formatName in formatNameSuggestions:
selectionString = "chemical shift file in %s format." % (
formatName)
selectionList.append(selectionString)
selectionDict[selectionString] = formatName
interaction = SelectionListPopup(self,
selectionList,
title='File format selection',
text='This is a:',
selectionDict=selectionDict,
dismissButton=True,
modal=True)
#
# Check if anything was selected...
#
formatName = None
if interaction.isSelected:
formatName = interaction.selection
else:
showWarning(
'Failure',
'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s'
% self.email,
parent=self)
return False
#
# Now read the file, need to do some field updates! Also make sure to re-use shift list for other molecules...
#
(fileRead, fileInformation) = self.fcWrapper.readFile(
dataType,
formatName,
self.fileName,
addKeywords={'measurementList': self.currentShiftList})
if not fileRead:
showWarning(
'Failure',
'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.'
% (fileInformation, self.email),
parent=self)
return False
(conversionInfo, conversionSuccess) = (
self.fcWrapper.formatConversion.conversionInfo,
self.fcWrapper.formatConversion.conversionSuccess)
if not conversionSuccess:
showWarning(
'Failure',
'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Set info if import worked OK
#
conversionLines = conversionInfo.split(": ")
showInfo("Import chemical shift information",
":\n".join(conversionLines),
parent=self)
self.shiftImport.setText(
self.fileName) # TODO change color or something?
self.shiftImport.configure(foreground=self.fontOkColor)
self.shiftsLoaded = True
self.shiftsFormatName = formatName
shiftList = self.fcWrapper.importReturns[dataType]
if not self.currentShiftList:
self.currentShiftList = shiftList
self.shiftListChainPairs.append(
(self.currentShiftList, currentChain))
self.updateDepositionImportLabel(shiftList=shiftList)
if not shiftList in self.entry.measurementLists:
print shiftList
self.entry.addMeasurementList(shiftList)
print self.entry.measurementLists
self.updateAll()
def showVersion(self):
showInfo('Version', 'Version ' + self.versionInfo, parent=self)
def writeFile(self,format,tasks):
self.updateAcqProcParsWidget()
self.updateAcqProcPars()
#
# Get or set up format classes
#
if self.formatObjectDict[self.format]:
formatObject = self.formatObjectDict[self.format]
else:
formatLabel = allFormatsDict[self.format]
formatModule = __import__('ccpnmr.format.converters.%sFormat' % formatLabel,{},{},['%sFormat' % formatLabel])
formatClass = getattr(formatModule,'%sFormat' % formatLabel)
formatObject = formatClass(self.project,self.guiParent,verbose = 1)
self.formatObjectDict[self.format] = formatObject
# Bit cumbersome... is there a better way to define writeFile, ... ?
dataDimRefs = self.getDataDimRefs(format)
for task in tasks:
parFile = None
addKeywds = {'dataDimRefs': dataDimRefs}
if format == self.nmrPipe:
if task == 'conversion':
function = 'writeProcPars'
self.fileName = self.buttons[0].__getitem__('text')
outputFile = self.buttons[1].__getitem__('text')
addKeywds['outputFile'] = outputFile
elif task == 'processing':
function = 'writeProcScript'
self.fileName = self.buttons[2].__getitem__('text')
inputFile = self.buttons[1].__getitem__('text')
outputFile = self.buttons[3].__getitem__('text')
addKeywds['outputFile'] = outputFile
addKeywds['inputFile'] = inputFile
if format == self.azara:
if task == 'processingPars':
function = 'writeProcPars'
self.fileName = self.buttons[0].__getitem__('text')
elif task == 'processingScript':
function = 'writeProcScript'
self.fileName = self.buttons[1].__getitem__('text')
inputFile = self.buttons[0].__getitem__('text')
outputFile = self.buttons[2].__getitem__('text')
parFile = self.buttons[3].__getitem__('text')
addKeywds['outputFile'] = outputFile
addKeywds['inputFile'] = inputFile
addKeywds['parFile'] = parFile
# Write for each task in list
exportFunc = getattr(formatObject,function)
if exportFunc(self.fileName, **addKeywds):
showInfo("Success","Successfully exported file:\n%s." % self.fileName,self)
else:
showError("Error","Error while exporting file:\n%s." % self.fileName,self)
def importExportFile(self,checkComponent):
returnFlag = True
importFuncs = []
for component in self.components:
#
# Pass if no info...
#
if not self.IOkeywords[component]:
continue
#
# If component passed in, only do that one
#
if checkComponent and checkComponent != component:
continue
else:
#
# Otherwise, if import, then only do so if checkButton is pressed
#
if self.importExportFlag == 'import' and not self.component:
if not self.checkButton.has_key(component):
continue
elif not self.checkButton[component].isSelected():
continue
#
# Get or set up format classes
#
if self.formatObjectDict[self.format]:
formatObject = self.formatObjectDict[self.format]
else:
formatClass = getattr(self.formatModule,'%sFormat' % self.formatLabel)
#
# ...and create the format class instance
#
formatObject = formatClass(self.project,self.guiParent,verbose = 0)
self.formatObjectDict[self.format] = formatObject
#
# Add input keyword information...
#
addArgs = []
addKeywds = {}
inputValid = True
if self.widgets[component]:
for inputKeyWord in self.widgets[component].keys():
(widgetInfo,selectionDict) = self.widgetInfo[component][inputKeyWord]
value = getIoInfo(self.widgets[component][inputKeyWord],widgetInfo,self.project,selectionDict)
#
# File name is a special case...
#
if inputKeyWord in ('fileName','fileNames'):
self.fileName = self.fileNames = False
if value == widgetInfo[3]:
setattr(self,inputKeyWord,None)
else:
if inputKeyWord == 'fileName':
self.fileName = value
else:
self.fileNames = self.decomposeMultipleFileText(value)
addArgs.append(getattr(self,inputKeyWord))
elif value != None:
# Do not set as keyword for FileButtons that haven't been set!
if widgetInfo[0] not in ('FileButton','FileMultiButton','DirButton') or widgetInfo[3] != value:
if widgetInfo[0] == 'FileMultiButton':
addKeywds[inputKeyWord] = self.decomposeMultipleFileText(value)
else:
addKeywds[inputKeyWord] = value
else:
if self.IOkeywords[component][inputKeyWord][1]:
showWarning("Error","Nothing selected for %s writing, mandatory input %s!" % (component,inputKeyWord),self)
inputValid = False
break
if not inputValid:
break
#
# exportFunctions
#
if self.importExportFlag == 'export' and self.exportFunc[component]:
for exportFuncLine in self.exportFunc[component]:
if exportFuncLine == 'return':
return
if type(exportFuncLine) == type(''):
eval(exportFuncLine)
else:
exportFuncLine()
#
# First check if a file name was selected?
# Here add other checks for mandatory input to function?
#
if hasattr(self,'fileNames') and self.fileNames == False and not self.fileName:
showWarning("Error","Please select a valid file name.",self)
elif hasattr(self,'fileName') and self.fileName == False and not self.fileNames:
showWarning("Error","Please select valid file names.",self)
else:
#
# Do the read/write
#
rwFunc = getattr(formatObject,self.function[component])
returnValue = None
if self.threading:
curThread = Thread(target = rwFunc,args = addArgs,kwargs = addKeywds)
curThread.start()
curThread.join()
if curThread and curThread.returnValue:
returnValue = curThread.returnValue
else:
returnValue = rwFunc(*addArgs,**addKeywds)
#
# Do some prep here...
#
fileNameText = ""
if hasattr(self,'fileNames'):
if self.fileNames == False:
(tPathName,tFileName) = os.path.split(self.fileName)
fileNameText = " file with name: %s." % tFileName
else:
fileNameText = " multiple files."
#
# Now show popup and set info depending on return value
#
if returnValue:
conversionSuccess = True
if formatObject.convertCount.keys():
conversionSuccess = False
for convertMainObj in formatObject.convertCount.keys():
conversionInfo = formatObject.convertCount[convertMainObj]
if conversionInfo[1].keys():
for convertSubObj in conversionInfo[1].keys():
if conversionInfo[1][convertSubObj]:
conversionSuccess = True
break
elif conversionInfo[0]:
conversionSuccess = True
if conversionSuccess:
break
convertInfoString = formatObject.getConvertCountString(startIndent = "")
if conversionSuccess:
if fileNameText:
showInfo("Success","Successfully %sed %s\n\n%s" % (self.importExportFlag,fileNameText,convertInfoString),self)
returnFlag = True
if self.importExportFlag == 'import':
# TODO: this is a hack... needs to be more sophisticated than this (format selection,
# even format dependent on particular resonance (!?!?!)
if component != 'sequence':
self.guiParent.resonanceFormat = self.format
if self.importFunc[component]:
for importFunc in self.importFunc[component]:
if importFunc not in importFuncs:
importFuncs.append(importFunc)
else:
if fileNameText:
showInfo("Not finished","The %s did not finish correctly for %s\n\n%s" % (self.importExportFlag,fileNameText,convertInfoString),self)
elif self.winfo_exists():
if fileNameText:
showError("Error","Error while %sing %s" % (self.importExportFlag,fileNameText),self)
#
# TODO: this might not be the best way to handle this!!
#
if returnFlag:
if self.importExportFlag == 'import':
if importFuncs:
for importFuncLine in importFuncs:
if type(importFuncLine) == type(''):
eval(importFuncLine)
else:
importFuncLine()
if hasattr(self.guiParent,'setMenuState'):
self.guiParent.setMenuState()
return returnFlag
def saveFile(self):
windowPane = self.windowPulldown.getObject()
if not windowPane:
return
axisPanels = windowPane.sortedAxisPanels()
aspectRatio = self.getPrintAspectRatio()
pixelWidth = self.totalSize(axisPanels[0])
pixelHeight = aspectRatio*self.totalSize(axisPanels[1])
unitWidth = self.totalOverrideRegion(axisPanels[0])
unitHeight = self.totalOverrideRegion(axisPanels[1])
printFrame = self.printFrame
isOverrideSpectrumSelected = self.overrideSpectrum.isSelected()
if isOverrideSpectrumSelected:
spectrumWindowViews = self.spectrumTable.objectList
# alternatively, spectrumWindowViews = windowPane.spectrumWindowViews
analysisSpectra = set()
for spectrumWindowView in spectrumWindowViews:
spectrumWindowView.printPositive = PrintBasic.getPrintOption(spectrumWindowView, 'PositiveOn', spectrumWindowView.isPosVisible)
spectrumWindowView.printNegative = PrintBasic.getPrintOption(spectrumWindowView, 'NegativeOn', spectrumWindowView.isNegVisible)
analysisSpectra.add(spectrumWindowView.analysisSpectrum)
for analysisSpectrum in analysisSpectra:
analysisSpectrum.printPositiveColors = PrintBasic.getPrintOption(analysisSpectrum, 'PositiveColors', analysisSpectrum.posColors)
analysisSpectrum.printNegativeColors = PrintBasic.getPrintOption(analysisSpectrum, 'NegativeColors', analysisSpectrum.negColors)
isOverridePeakListSelected = self.overridePeakList.isSelected()
if isOverridePeakListSelected:
windowPeakLists = self.peakListTable.objectList
analysisPeakLists = set()
for windowPeakList in windowPeakLists:
windowPeakList.printPeaks = PrintBasic.getPrintOption(windowPeakList, 'PeaksOn', windowPeakList.isSymbolDrawn)
if windowPeakList.isAnnotationDrawn:
default = windowPeakList.analysisPeakList.analysisSpectrum.font
else:
default = no_peak_text
windowPeakList.printFont = PrintBasic.getPrintOption(windowPeakList, 'PeakFont', default)
analysisPeakLists.add(windowPeakList.analysisPeakList)
for analysisPeakList in analysisPeakLists:
analysisPeakList.printColor = PrintBasic.getPrintOption(analysisPeakList, 'PeakColor', analysisPeakList.symbolColor)
xrr = axisPanels[0].findFirstAxisRegion().region
dxx = abs(xrr[0]-xrr[1])
yrr = axisPanels[1].findFirstAxisRegion().region
dyy = abs(yrr[0]-yrr[1])
try:
outputHandler = printFrame.getOutputHandler(pixelWidth, pixelHeight, unitWidth, unitHeight, fonts=printNames)
if not outputHandler:
return
analysisProject = self.analysisProject
major_minor_dict = {}
spacing_choice = PrintBasic.getPrintOption(analysisProject, 'SpacingChoice', spacing_choices[0])
if spacing_choice != spacing_choices[0]:
for attr in ('XMajor', 'XMinor', 'XDecimal',
'YMajor', 'YMinor', 'YDecimal',):
val = PrintBasic.getPrintOption(analysisProject, attr, None)
if val is not None:
major_minor_dict[attr] = val
tick_length_choice = PrintBasic.getPrintOption(analysisProject, 'TickLengthChoice', tick_length_choices[0])
if tick_length_choice != tick_length_choices[0]:
for attr in ('TickMajor', 'TickMinor'):
val = PrintBasic.getPrintOption(analysisProject, attr, None)
if val is not None:
major_minor_dict[attr] = val
windowDraw = WindowDraw(self.parent, windowPane)
PrintBasic.printWindow(windowDraw,
outputHandler,
printFrame.tick_location,
printFrame.tick_placement,
aspectRatio,
printFrame.tick_font,
major_minor_dict)
msg = 'Saved to file "%s"' % printFrame.file_name
showInfo('Success', msg, parent=self)
except IOError, e:
showError('IO Error', str(e), parent=self)
def storeDihedralConstraints(self):
if not self.dangleChain:
return
# make a new dihedralConstraintList
head = self.constraintSet
if not head:
head = self.project.newNmrConstraintStore(
nmrProject=self.nmrProject)
self.constraintSet = head
chain = self.dangleChain.chain
shiftList = self.dangleChain.shiftList
name = 'DANGLE Chain %s:%s ShiftList %d' % (
chain.molSystem.code, chain.code, shiftList.serial)
constraintList = head.newDihedralConstraintList(name=name,
measureListSerials=[
shiftList.serial,
])
# traverse the sequence and make appropriate constraint objects
residues = chain.sortedResidues()
for residue in residues:
# Ensure we have atomSets etc
getResidueMapping(residue)
residueList = [(dr.residue.seqCode, dr.residue, dr)
for dr in self.dangleChain.dangleResidues]
residueList.sort()
cnt = 0
for seqCode, residue, dangleResidue in residueList:
phi = dangleResidue.phiValue
psi = dangleResidue.psiValue
if (phi is None) and (psi is None):
continue
# Use below functions because residues may not be sequentially numbered
prevRes = getLinkedResidue(residue, 'prev')
nextRes = getLinkedResidue(residue, 'next')
if (prevRes is None) or (nextRes is None):
continue
C__1 = prevRes.findFirstAtom(name='C') # C (i-1)
N_0 = residue.findFirstAtom(name='N') # N (i)
CA_0 = residue.findFirstAtom(name='CA') # CA(i)
C_0 = residue.findFirstAtom(name='C') # N (i)
N_1 = nextRes.findFirstAtom(name='N') # C (i+1)
# get fixedResonances
fixedResonances = []
for atom in (C__1, N_0, CA_0, C_0, N_1):
atomSet = atom.atomSet
if atomSet.resonanceSets:
resonance = atomSet.findFirstResonanceSet(
).findFirstResonance()
else:
# make new resonance
if not atom.chemAtom:
print 'no chem atom'
ic = atom.chemAtom.elementSymbol
if (ic == 'C'):
ic = '13' + ic
elif (ic == 'N'):
ic = '15' + ic
resonance = self.nmrProject.newResonance(isotopeCode=ic)
assignAtomsToRes([
atomSet,
], resonance)
fixedResonances.append(getFixedResonance(head, resonance))
# make dihedralConstraints
phiResonances = (fixedResonances[0], fixedResonances[1],
fixedResonances[2], fixedResonances[3])
phiConstraint = constraintList.newDihedralConstraint(
resonances=phiResonances)
psiResonances = (fixedResonances[1], fixedResonances[2],
fixedResonances[3], fixedResonances[4])
psiConstraint = constraintList.newDihedralConstraint(
resonances=psiResonances)
# make constraint items
if phi is not None:
phiConstraint.newDihedralConstraintItem(
targetValue=phi,
upperLimit=dangleResidue.phiUpper,
lowerLimit=dangleResidue.phiLower)
cnt += 1
if psi is not None:
psiConstraint.newDihedralConstraintItem(
targetValue=psi,
upperLimit=dangleResidue.psiUpper,
lowerLimit=dangleResidue.psiLower)
cnt += 1
showInfo('Success',
'DANGLE has generated %d dihedral restraints.' % cnt,
parent=self)
class AddContourFilePopup(BasePopup):
"""
**Add Existing Contour Files to Project**
The purpose of this dialog is to allow the user to add pre-existing
contour files to the project. Contour files only depend on the spectrum
data so the same contour files can be used across multiple projects,
and that is the reason this dialog might be used.
See also: `Spectrum Contour Files`_, `Creating Contour Files`_.
.. _`Spectrum Contour Files`: EditContourFilesPopup.html
.. _`Creating Contour Files`: CreateContourFilePopup.html
"""
def __init__(self, parent, *args, **kw):
self.spectrum = None
BasePopup.__init__(self,
parent=parent,
title='Add existing contour file',
**kw)
def body(self, master):
self.geometry('600x130')
master.grid_columnconfigure(1, weight=1)
for n in range(5):
master.grid_rowconfigure(n, weight=1)
row = 0
label = Label(master, text='Spectrum: ')
label.grid(row=row, column=0, sticky='e')
tipText = 'The spectrum for which the contour file is being added'
self.expt_spectrum = PulldownList(master,
callback=self.updateContourDir,
tipText=tipText)
self.expt_spectrum.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'The location of the directory where contour files are stored on disk'
label = Label(master, text='Contour dir: ')
label.grid(row=row, column=0, sticky='e')
self.dir_label = Label(master, text='', tipText=tipText)
self.dir_label.grid(row=row, column=1, sticky='w')
row = row + 1
label = Label(
master,
text=
'(file will be copied into Contour dir if it is not already in there)'
)
label.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'Browse for a file store contour data'
button = Button(master,
text='File name: ',
command=self.selectFile,
tipText=tipText)
button.grid(row=row, column=0, sticky='e')
tipText = 'Enter the name of the file to store contour data'
self.file_entry = Entry(master, tipText=tipText)
self.file_entry.grid(row=row, column=1, sticky='ew')
row = row + 1
texts = ['Add File']
commands = [self.addFile]
tipTexts = [
'Use the selected contour file in the current project, copying it to the contour directory if required',
]
self.buttons = UtilityButtonList(master,
texts=texts,
doClone=False,
tipTexts=tipTexts,
commands=commands,
helpUrl=self.help_url)
self.buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.curateNotifiers(self.registerNotify)
self.updateSpectrum()
def destroy(self):
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
for clazz in ('Experiment', 'DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateNotifier, 'ccp.nmr.Nmr.%s' % clazz, func)
def updateSpectrum(self, spectrum=None):
if not spectrum:
spectrum = self.spectrum
spectra = self.parent.getSpectra()
if spectra:
if spectrum not in spectra:
spectrum = spectra[0]
index = spectra.index(spectrum)
names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra]
else:
index = 0
names = []
self.expt_spectrum.setup(names, spectra, index)
self.updateContourDir(spectrum)
def updateNotifier(self, *extra):
self.updateSpectrum()
def updateContourDir(self, spectrum):
if spectrum is self.spectrum:
return
self.spectrum = spectrum
if spectrum:
path = spectrum.analysisSpectrum.contourDir.dataLocation
else:
path = ''
self.dir_label.set(path)
def selectFile(self):
spectrum = self.spectrum
if spectrum:
directory = spectrum.analysisSpectrum.contourDir.dataLocation
else:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory)
fileName = popup.getFile()
popup.destroy()
if fileName:
self.file_entry.set(fileName)
def addFile(self):
spectrum = self.spectrum
if not spectrum:
return
dataStore = spectrum.dataStore
if not dataStore:
showError('No dataStore',
'Spectrum does not have associated dataStore',
parent=self)
return
if not isinstance(dataStore, BlockedBinaryMatrix):
showError('No blockedBinaryMatrix',
'Spectrum dataStore is not a blockedBinaryMatrix',
parent=self)
return
if not dataStore.blockSizes:
showError('No blockSize',
'Spectrum dataStore does not have blockSize set',
parent=self)
return
blockSize = list(dataStore.blockSizes)
fileName = self.file_entry.get()
if not fileName:
showError('No filename', 'No filename given', parent=self)
return
fileName = normalisePath(fileName, makeAbsolute=True)
contourDir = spectrum.analysisSpectrum.contourDir.dataLocation
if fileName.startswith(contourDir):
path = fileName[len(contourDir) + 1:]
else:
path = os.path.basename(fileName)
if not os.path.exists(contourDir):
os.makedirs(contourDir)
print 'Copying %s to %s' % (fileName, contourDir)
shutil.copy(fileName, contourDir)
try:
header = getStoredContourHeader(fileName)
except Exception, e:
showError('File error', str(e), parent=self)
return
if header['ndim'] != spectrum.numDim:
showError(
'Number of dimensions',
'Number of dimensions in file (%d) does not match spectrum (%d)'
% (header['ndim'], spectrum.numDim),
parent=self)
return
dataDims = spectrum.sortedDataDims()
npoints = [x.numPoints for x in dataDims]
if header['npoints'] != npoints:
showError(
'Number of points',
'Number of points in file (%s) does not match spectrum (%s)' %
(header['npoints'], npoints),
parent=self)
return
if header['blockSize'] != blockSize:
showError('Block size',
'Block size in file (%s) does not match spectrum (%s)' %
(header['blockSize'], blockSize),
parent=self)
return
createStoredContour(spectrum, path, header['xdim'], header['ydim'])
showInfo('Added file',
'Successfully added stored contour file',
parent=self)
try:
(firstInt[i], lastInt[i]) = self.convertToPoints(spectrum, i, region[i])
except Exception, e:
showError('Invalid region', str(e), parent=self)
try:
#print 'about to saveSpectrumContours', fullPath, xdim, ydim, levels, firstInt, lastInt
saveSpectrumContours(spectrum, fullPath, xdim, ydim, levels, firstInt, lastInt,
mem_cache=self.parent.mem_cache)
except Exception, e:
showError('Save error', str(e), parent=self)
return
createStoredContour(spectrum, fileName, xdim, ydim)
showInfo('Created file', 'Successfully created stored contour file', parent=self)
def convertToPoints(self, spectrum, n, region):
(rMin, rMax) = region
dim = n + 1
dataDim = spectrum.findFirstDataDim(dim=dim)
if dataDim.className != 'SampledDataDim':
converter = UnitConverter.ppm2pnt
dataDimRef = ExperimentBasic.getPrimaryDataDimRef(dataDim)
(rMin, rMax) = (converter(rMax, dataDimRef), converter(rMin, dataDimRef))
rMin = max(1, rMin)
rMax = min(dataDim.numPoints, rMax)
rMin = rMin - 1
rMin = int(rMin+0.5)
