class DataFileImportFrame(Frame):
"""
TODO: should I also ask for sample conditions info with chemical shifts? Or do in ECI - possible? Check!
"""
# TODO should go where?
email = '*****@*****.**'
defaultSelectText = "Select file."
fontOkColor = 'green3'
fontCheckColor = 'orange3'
fontBadColor = 'red3'
fontDefaultColor = 'black'
def __init__(self, parent, basePopup, *args, **kw):
#
# Variable initialisation
#
self.fcWrapper = basePopup.fcWrapper
self.project = basePopup.project
self.basePopup = basePopup
# TODO necessary?
if self.project:
self.nmrProject = self.project.currentNmrProject
self.entry = self.project.currentNmrEntryStore.findFirstEntry()
if not self.entry:
self.entry = self.project.currentNmrEntryStore.newEntry(
name=self.project.name)
else:
self.nmrProject = None
self.sequenceCoordinatesLoaded = False
self.shiftsLoaded = False
self.linkResDone = False
self.currentShiftList = None
self.shiftListChainPairs = []
self.moleculeList = []
self.moleculeDict = {}
#
# Frame setup
#
Frame.__init__(self, parent, **kw)
self.grid_columnconfigure(1, weight=1)
self.grid_rowconfigure(1, weight=1)
options = ['Import', 'Deposition']
tabbedFrame = TabbedFrame(self,
options=options,
callback=self.selectTab)
tabbedFrame.grid(row=1, column=0, columnspan=2, sticky='nsew')
self.tabbedFrame = tabbedFrame
frameA, frameD = tabbedFrame.frames
#
# Main
#
frameA.grid_columnconfigure(0, weight=1)
#frameA.grid_columnconfigure(1, weight=1) # Change to 2 if want 2 columns
frameA.grid_rowconfigure(12, weight=1)
#frameA.grid_rowconfigure(12, weight=1)
row = 0
div = LabelDivider(
frameA,
text=
'Select the full coordinate file or a sequence file (with info for a single molecule).',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.sequenceCoordinatesImport = Button(
frameA,
text=self.defaultSelectText,
command=self.importSequenceOrCoords,
foreground=self.fontDefaultColor)
self.sequenceCoordinatesImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Select the molecule relevant for your chemical shift file.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.moleculeSelect = Label(
frameA,
text="None available yet - import valid file first",
foreground=self.fontBadColor)
self.moleculeSelect.grid(row=row, column=0, sticky='ew')
self.moleculeSelectRow = row
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text=
'Select a chemical shift file with values only for the above molecule.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.shiftImport = Button(frameA,
text=self.defaultSelectText,
command=self.importShifts,
foreground=self.fontDefaultColor)
self.shiftImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Consistency check between molecule and shift information.',
justify='center',
grid=(row, 0),
gridSpan=(2, 1))
row += 1
self.linkResCheckInfo = Label(frameA, text='')
self.linkResCheckInfo.grid(row=row, column=0, sticky='ew')
row += 1
div = Separator(frameA, grid=(row, 0), gridSpan=(1, 1))
row += 1
texts = ['Import new sequence', 'Import new set of shifts']
commands = [self.resetSequenceImport, self.resetShiftImport]
self.mainButtons = ButtonList(frameA, texts=texts, commands=commands)
self.mainButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.mainButtons.buttons[0].config(foreground=self.fontDefaultColor)
#print row
self.frameA = frameA
#
# Not in use...
#
#frameX.grid_columnconfigure(0, weight=1)
#frameX.grid_columnconfigure(1, weight=1)
#frameX.grid_rowconfigure(1, weight=1)
#frameX.grid_rowconfigure(3, weight=1)
#
# Deposition, is updated after each successful import run.
#
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(5, weight=1)
self.frameD = frameD
row = 0
div = LabelDivider(frameD,
text='Imported data.',
justify='center',
grid=(row, 0),
gridSpan=(1, 2))
row += 1
self.depositionImportText = "\nImported %d shift list(s) for a total of %d shifts.\n\nImported %d molecule(s) and %d chain(s).\n\nImported %d model(s) for a total of %d atom coordinates.\n\nLinked %.2f%% of imported NMR information to %d chain(s)."
self.depositionImportLoc = (row, 0)
# These used for setting text above...
self.depositionImportNums = [0, 0, 0, 0, 0, 0, 0.0, 0]
self.importedShiftLists = []
self.connectedChains = []
self.depositionImportLabel = Label(frameD,
text=self.depositionImportText %
tuple(self.depositionImportNums),
foreground=self.fontBadColor)
self.depositionImportLabel.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameD, text="")
label.grid(row=row, column=0, sticky='ew')
#
# Finalize the import part, proceed to ECI.
#
row += 1
div = LabelDivider(
frameD,
text=
'Import completed, save project and start Entry Completion Interface.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.eciStart = Button(frameD,
text="Finalise import",
command=self.finaliseImport,
foreground=self.fontBadColor)
self.eciStart.grid(row=row, column=0, sticky='ew')
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)
#
# File type determination and import
#
def createFileTypes(self, dataTypes):
fileTypes = [FileType('all', ['*'])]
for dataType in dataTypes:
formatNames = fileTypeDict[dataType].keys()
formatNames.sort()
for formatName in formatNames:
if formatName in self.fcWrapper.formatNameLists[dataType]:
fileTypes.append(
FileType(formatName,
fileTypeDict[dataType][formatName]))
return fileTypes
def getFileName(self, title, fileTypes):
fileSelectPopup = FileSelectPopup(
self,
file_types=fileTypes,
title=title,
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
)
self.fileName = fileSelectPopup.getFile()
if not self.fileName:
showWarning('Failure',
'Please select an existing file.',
parent=self)
return False
return True
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 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()
#
# Updaters
#
def selectTab(self, index):
funcsDict = {
0: (self.updateMain, ),
1: (self.updateCoordinates, ),
2: (self.updateDeposition, )
}
for func in funcsDict[index]:
func()
def updateMain(self):
pass
def updateCoordinates(self):
pass
def updateDeposition(self):
pass
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 getCurrentChain(self):
if len(self.moleculeList) == 1:
chain = self.moleculeDict.values()[0]
else:
try:
moleculeSelected = self.moleculeSelect.getText()
chain = self.moleculeDict[moleculeSelected]
except:
chain = None
return chain
def connectShiftsSequence(self):
if not self.linkResDone:
changeResetColor = False
#
# Get chain mapping and run linkResonances
#
chain = self.getCurrentChain()
forceChainMappings = self.fcWrapper.linkResonancesToSequence(
chain=chain)
self.fcWrapper.formatConversion.linkResonances(
forceChainMappings=forceChainMappings, guiParent=self)
#
# Get information about the linking process
#
# TODO Should only have an nmrProject (no restraint import, should be included?)
# In any case, is always the LAST info in numResonancesLinked info
numResonancesLinked = self.fcWrapper.formatConversion.numResonancesLinked
(origLinked, origUnlinked, linked,
unlinked) = (numResonancesLinked['origLinked'][-1],
numResonancesLinked['origUnlinked'][-1],
numResonancesLinked['linked'][-1],
numResonancesLinked['unlinked'][-1])
#
# Track number of new resonances, and reset for new import
#
if self.fcWrapper.formatConversion.allResonancesLinked:
status = 'All information matches (for all imports).'
foreground = self.fontOkColor
changeResetColor = True
else:
if origUnlinked - unlinked == self.fcWrapper.numNewResonances:
status = 'All information matches (for this import)'
foreground = self.fontOkColor
changeResetColor = True
else:
if origUnlinked != unlinked:
status = 'Not all information matches (for this and/or another import).'
foreground = self.fontCheckColor
changeResetColor = True
else:
status = 'No information matches (for this import).'
foreground = self.fontBadColor
otherUnlinked = (origUnlinked -
self.fcWrapper.numNewResonances)
notLinked = unlinked - otherUnlinked
status += "\nUnable to link %d out of %d imported shifts (%.2f%%)." % (
notLinked, self.fcWrapper.numNewResonances,
(notLinked * 100.0) / self.fcWrapper.numNewResonances)
self.linkResCheckInfo.set("Status: %s" % status)
self.linkResCheckInfo.config(foreground=foreground)
self.linkResDone = True
#
# Change the color of the reset button to indicate OK to do next one
#
if changeResetColor:
self.mainButtons.buttons[0].config(foreground=self.fontOkColor)
self.updateDepositionImportLabel(
shiftList=None,
percentageLinked=(linked * 100.0 / (unlinked + linked)),
connectedChain=chain)
def updateDepositionImportLabel(self,
shiftList=None,
molecules=0,
chains=0,
models=0,
coordinates=0,
percentageLinked=None,
connectedChain=None):
if shiftList and shiftList not in self.importedShiftLists:
self.importedShiftLists.append(shiftList)
self.depositionImportNums[0] += 1
shifts = 0
for shiftList in self.importedShiftLists:
shifts += len(shiftList.measurements)
self.depositionImportNums[1] += shifts
self.depositionImportNums[2] += molecules
self.depositionImportNums[3] += chains
self.depositionImportNums[4] += models
self.depositionImportNums[5] += coordinates
if percentageLinked != None:
self.depositionImportNums[6] = percentageLinked
if connectedChain and connectedChain not in self.connectedChains:
self.depositionImportNums[7] += 1
self.connectedChains.append(connectedChain)
self.depositionImportLabel.destroy()
finalForeground = self.fontBadColor
if self.depositionImportNums[0] == 0 and self.depositionImportNums[
2] == 0:
# Nothing imported
foreground = self.fontBadColor
elif self.depositionImportNums[6]:
# Linked shifts available - TODO base this on % of shifts linked?
foreground = self.fontOkColor
if self.depositionImportNums[5]:
finalForeground = self.fontOkColor
else:
finalForeground = self.fontCheckColor
else:
# Intermediate state
foreground = self.fontCheckColor
self.depositionImportLabel = Label(self.frameD,
text=self.depositionImportText %
tuple(self.depositionImportNums),
foreground=foreground)
self.depositionImportLabel.grid(row=self.depositionImportLoc[0],
column=self.depositionImportLoc[1],
sticky='ew')
self.eciStart.configure(foreground=finalForeground)
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 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 destroy(self):
Frame.destroy(self)
#
# Instructions
#
def showMainInstructions(self):
popup = getPopup(self)
message = """Use this tab to import the chemical shifts and the coordinate and/or sequence information for your molecular chains.
The imported chemical shift file should contain information for only *one* molecular chain to make it easier to connect the molecule information to the chemical shift information. You therefore have to select a single chain for each shift list from the dropdown menu that will appear after you imported a coordinate or sequence file.
For example, when using sequence files for a dimer, import the information for the chemical shifts for each chain separately:
1. Import the sequence for the first molecular chain.
2. Import a chemical shift file with shifts only for this molecular chain.
3. Reset using the 'Import new sequence' button
4. Import the sequence for the second molecular chain
5. Import a chemical shift file with shifts only for this second chain
Alternatively, it is possible to read in the molecule information from a full coordinate file:
1. Import a coordinate file with all molecular information, including coordinates.
2. Select a molecular chain.
3. Import a chemical shift file with shifts only for the selected molecular chain.
4. Go back to step 2. if necessary.
You can also import multiple sets of chemical shifts (e.g. for the sample in different conditions). In this case, you have to import all chemical shift information that belongs together for all molecular chains, then press the 'Import new set of shifts' button.
Notes:
1. This application always creates a new CCPN project. It is not possible to import files into existing projects.
2. If your chemical shift file contains information for multiple chains, you have to edit it manually to split up the information per chain.
"""
showHelpText(self, message, popup=popup)
def showFormats(self):
popup = getPopup(self)
message = """For chemical shifts, the following formats are recognised:
*** Auremol ***
section_sequenzdefinition
_Residue_seq_code
_Atom_num_code
_Residue_label
_Atom_name
_Atom_type
_Atom_alias
_Atom_equivalent
_Atom_CSA
1 1 MET HN H - - 8.95
1 2 MET N N - - 157.00
1 3 MET CA C - - 40.00
*** Autoassign ***
AA HN N15 CO-1 CA-1 CB-1 HA-1 CO CA CB HA
A31 8.14 121.4 51.3 19.6 (GS178 115.HSQC)
D32 8.88 122.9 51.3 19.5 55.4 39.6 (GS271 22.HSQC)
*** CNS ***
do ( store1 = 53.13218 ) ( resid 78 and name CA )
do ( store1 = 0.7356673 ) ( resid 15 and name HD1# )
do ( store1 = 120.5381 ) ( resid 8 and name N )
do ( store1 = 121.1414 ) ( resid 78 and name N )
*** Cosmos ***
CS_VALUES 3
C_ALA 176.6
CA_ALA 51.66
CB_ALA 17.26
END
*** CSI ***
# A HA CA CO CB Consensus
#
1 MET 0 C 0 C NA 0 C 0 C
2 GLY 0 C 0 C NA 0 C 0 C
*** MARS ***
H N CO-1 CA CA-1
PR_2 8.900 123.220 170.540 55.080 54.450
PR_4 8.320 115.340 175.920 - 55.080
*** MONTE ***
1 102.544 8.211 45.853 54.925 0.000 18.069 180.112
2 103.276 8.580 45.334 54.154 0.000 35.650 175.087
3 103.997 7.407 45.165 0.000 0.000 0.000 0.000
*** NMR-STAR ***
data_test
save_shifts1
_Saveframe_category assigned_chemical_shifts
loop_
_Atom_shift_assign_ID
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 1 ASP CA C 52.000 0.02 1
2 1 ASP HA H 4.220 0.02 1
stop_
save_
*** NMRVIEW ***
2.CG1 18.549 0
2.CG2 18.844 0
2.HG1# 0.800 0
2.HG2# 0.723 0
3.HG2 2.298 0
3.HG1 2.298 0
*** PIPP ***
RES_ID 1
RES_TYPE MET
SPIN_SYSTEM_ID 1
CA 55.9920
CB 33.1470
HA 4.1141
HB# 2.0492
HG# 2.4250
END_RES_DEF
*** PISTACHIO ***
1 1 GLY C C 172.621 1.000 0
2 1 GLY CA C 44.308 1.000 0
3 2 SER N N 122.241 1.000 0
*** PRONTO ***
Spin system HN HA Other:
1: Val-1 3.76 HB: 1.945, HG1: 0.770, HG2: 0.608
2: Ile-2 8.80 4.26 HB: 1.526, HG1: 1.278, HG2: 0.728, HD: 0.918
*** SHIFTX ***
NUM RES HA H N CA CB C
--- --- ------ ------ -------- ------- ------- --------
2 T 4.4161 8.1749 111.0443 61.8324 70.3867 172.5362
3 Y 4.9022 9.0239 120.2106 56.0493 41.4218 173.0761
NUM RES H HA HB HB2 HB3 HD1 HD2 HD21 HD22 HD3 HE HE1 HE2 HE21 HE22 HE3 HG HG1 HG12 HG13 HG2 HG3 HZ
2 T 8.17 4.42 4.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.21 0.00 0.00
3 Y 9.02 4.90 0.00 2.22 2.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
*** SPARKY ***
Group Atom Nuc Shift SDev Assignments
R2 CA 13C 56.539 0.003 3
R2 CB 13C 30.808 0.009 3
*** TALOS ***
VARS RESID RESNAME PHI PSI DPHI DPSI DIST COUNT CLASS
FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %2d %s
1 Q 9999.000 9999.000 0.000 0.000 0.000 0 None
2 N -85.000 124.000 23.000 28.000 85.920 10 Good
***XEASY/CYANA:
1 117.803 0.000 N 1
2 8.208 0.002 HN 1
3 56.508 0.055 CA 1
4 999.000 0.000 HA 1
5 29.451 0.004 CB 1
"""
showHelpText(self, message, popup=popup)
def updatePhiPsi(self):
# labels='outliers', ''
if not self.structure:
return
model = self.model
ccpCode = self.ccpCode
residueSel = self.residue
labelMode = self.labelMode
getValue = self.plot.getIntensityValue
ccpCode = self.ccpCode
if self.residue:
ccpCode = self.residue.residue.ccpCode
self.plot.setAminoAcid(ccpCode)
phiPsiAccept = []
plotObjects = []
resLabels = []
colors = []
if self.colorScheme:
scheme = list(self.colorScheme.colors)
else:
scheme = ['#800000','#008000','#000080']
nCols = len(scheme)
nCore = 0
nAllowed = 0
nDisallowed = 0
colorFrame = self.colorFrame
colorLabels = self.colorLabels
structure = self.structure
if structure == 'All':
structures = self.getStructures()
nstructures = len(structures)
ncolorLabels = len(colorLabels)
n = nstructures - ncolorLabels
if n > 0:
for i in range(n):
label = Label(colorFrame, grid=(0,i+ncolorLabels+1))
colorLabels.append(label)
for i, structure0 in enumerate(structures):
text = 'Structure %d' % structure0.ensembleId
label = colorLabels[i]
label.set(text)
color = scheme[i % nCols]
label.config(bg=color)
if color == '#000000':
label.config(fg='#FFFFFF')
else:
label.config(fg='#000000')
colorFrame.grid(row=self.colorRow, column=0)
else:
structures = [structure]
colorFrame.grid_forget()
for structure0 in structures:
if model:
models = [model,]
else:
models = list(structure0.models)
nModels = len(models)
for chain in structure0.coordChains:
for residue in chain.residues:
sysResidue = residue.residue
sysCode = getResidueCode(sysResidue)
resLabel = '%d%s' % (sysResidue.seqCode,sysCode)
if sysResidue.molResidue.molType != 'protein':
continue
if residue and residueSel and (residue.residue is not residueSel.residue):
continue
if ccpCode and (sysCode != ccpCode):
continue
for model0 in models:
phi, psi = getResiduePhiPsi(residue, model=model0)
if None in (phi,psi):
continue
value = getValue(phi,psi)
if nModels == 1:
resLabels.append(resLabel)
else:
resLabels.append( '%s:%d' % (resLabel, model0.serial) )
doLabel = False
if value < 6.564e-5:
if labelMode == LABEL_MODES[1]:
doLabel = True
nDisallowed += 1
elif value < 0.000821:
nAllowed += 1
else:
nCore += 1
if labelMode == LABEL_MODES[0]:
doLabel = False
elif labelMode == LABEL_MODES[2]:
doLabel = True
if structure == 'All':
ind = structures.index(structure0)
else:
ind = model0.serial - 1
colors.append(scheme[ind % nCols])
plotObjects.append((residue, model0))
phiPsiAccept.append((phi,psi,doLabel))
spotSize = self.spotSizePulldown.getObject()
nRes = 0.01*float(nDisallowed+nAllowed+nCore)
if nRes:
self.regionLabel.set(REGION_TEXT % (nCore/nRes,nAllowed/nRes,nDisallowed/nRes))
else:
self.regionLabel.set(REGION_TEXT % (0.0, 0.0, 0.0))
self.plot.cirRadius = spotSize
self.plot.updateObjects(phiPsiAccept, plotObjects, resLabels, colors)
class PulldownList(Frame):
# if using indentation then should use list as stack only
# in other words only delete or insert at end
# There is a 1:1 correspondance between the ordered lists of texts and
# list of objects
# categories is the category name for each text/object
# objects with the same category will go under a submenu
# of that name
def __init__(self, parent, callback=None, texts=None, objects=None,
categories=None, colors=None, index=0, prefix='', indent='',
initCallback=False, forceCallback=False, numbering=False,
arrowLine='#602000', arrowFill='#B05848', labelColor='#501000',
menuBg='#F0F0FF', sticky='w', docKey=None, tipText=None,
categoriesLast=True, *args, **kw):
Frame.__init__(self, parent, sticky=sticky, docKey=docKey, tipText=tipText, createToolTip=True, *args, **kw)
self.callback = callback
self.texts = texts or []
self.objects = objects or []
self.categories = categories or []
self.colors = colors or []
self.prefix = prefix
self.indent = indent
self.initCallback = initCallback
self.numbering = numbering
self.arrowLine = arrowLine
self.arrowFill = arrowFill
self.labelColor = labelColor
self.active = True
self.categoriesLast = categoriesLast
# Current selection
self.index = None
self.object = NullText
self.rows = []
self.bg = self.cget('bg')
self.label = Label(self, foreground=labelColor)
self.canvas = Canvas(self, width=12, height=12, background=self.bg)
self.menu = Menu(self.canvas, tearoff=False, bg=menuBg, relief='solid',
borderwidth=1, activeborderwidth=1)
self.menu.images = [] # Photoimage has to remain referenced
self.setup(self.texts, self.objects, index,
self.colors, self.categories)
self.label.bind( "<Button-1>", self._labelClick)
self.menu.bind( "<Leave>", self._leave)
self.canvas.bind("<Button-1>", self._canvasClick)
self.canvas.bind("<Configure>", self._resizeCallback)
self.grid_columnconfigure(0, weight=1)
self.label.grid(row=0, column=0, sticky='w')
self.canvas.grid(row=0, column=1, sticky='w', padx=2)
#
# Retrieval
#
def get(self):
return (self.getText(),self.getObject())
def getSelected(self):
return self.get()
def getObject(self):
return self._fetch(self.index, self.objects)
def getText(self):
return self._fetch(self.index, self.texts)
def getSelectedIndex(self):
return self.index
#
# Setting selected
#
def set(self, item, doCallback=False):
# Works with an object or a text
index = None
if item in self.texts:
index = list(self.texts).index(item)
elif item in self.objects:
index = list(self.objects).index(item)
if index is not None:
self.setIndex(index, doCallback=doCallback)
def setSelected(self, item, doCallback=False):
self.set(item, doCallback=doCallback)
def setIndex(self, index, doCallback=False):
self.index = index
if self.objects:
obj = self.objects[index]
if obj is not self.object:
self.object = obj
if (doCallback or self.initCallback) and self.texts and self.callback:
self.callback(obj)
self._updateLabel()
#
# Bulk configuration
#
def clear(self):
self.setup([], [], 0)
def setup(self, texts, objects, index, colors=None, categories=None):
self.texts = texts
nTexts = len(texts)
if not objects:
objects = texts
while len(objects) < nTexts:
objects.append(None)
self.objects = objects
if colors is None:
self.colors = [None] * nTexts
else:
while len(colors) < nTexts:
colors.append(None)
self.colors = colors
if categories is None:
self.categories = [None] * nTexts
else:
while len(categories) < nTexts:
categories.append(None)
self.categories = categories
self._setMenuItems()
self.setIndex(index or 0)
#
# In-place/minor configuration
#
def insert(self, index, text, object=None, color=None,
category=None, select=False):
index = max(0, min(len(self.texts),index))
self.texts.insert(index, text)
self.objects.insert(index, object)
self.colors.insert(index, color)
self.categories.insert(index, category)
self._setMenuItems()
if select:
self.setIndex(index)
def append(self, text, object=None, color=None, category=None, select=False):
self.insert(len(self.texts), text, object=None,
color=None, category=None, select=False)
def delete(self, index, howMany=1):
if index < 0:
return
elif index >= len(self.texts):
return
end = min(index+howMany,len(self.texts))
self._clearMenu()
del self.texts[index:end]
del self.objects[index:end]
del self.colors[index:end]
del self.categories[index:end]
self._setMenuItems()
index = min(len(self.texts)-1,self.index)
self.setIndex(index)
def disable(self):
self.label.config(foreground='#808080')
self.active = False
self._resizeCallback()
def enable(self):
self.label.config(foreground=self.labelColor)
self.active = True
self._resizeCallback()
#
# Internal methods
#
def _leave(self, event):
# look for widget under event, if it is a Menu do not popdown
# this often seems to throw exceptions deep in Tk so use try/except
try:
widget = self.menu.winfo_containing(event.x_root, event.y_root)
if not isinstance(widget, Menu):
self._popdown()
except:
""" The problem with the below approach is that when moving to a submenu
the menu produces a leaving event which can easily be outside that menu,
which causes an unintended popdown.
"""
x = event.x
y = event.y
x1 = self.menu.winfo_width()
y1 = self.menu.winfo_height()
if (x<0) or (y<0) or (x>=x1) or (y>=y1):
self._popdown()
def _resizeCallback(self, *event):
if self.active:
fill = self.arrowFill
outline = self.arrowLine
else:
fill = '#808080'
outline = '#404040'
c = self.canvas
w = c.winfo_width() -1
h = c.winfo_height() -1
c.delete('all')
c.create_rectangle(0,0,10,2,
fill=fill, outline=outline)
c.create_polygon(0, 4, 0, 6, 5, 11, 10, 6, 10, 4,
fill=fill, outline=outline)
def _fetch(self, index, array):
if index is None:
return None
if index < 0:
index += len(array)
if index < 0:
return None
elif index >= len(array):
return None
else:
return array[index]
def _setMenuItems(self):
self._clearMenu()
self.menu.images = [] # Clear photoimages
if not self.texts and not self.menu.entrycget(1, 'label'):
item = {'kind': 'command',
'label': NullText,
'command': None }
self.menu.addMenuItem(item)
self.rows = [0]
return
topList = []
categoryDict = {}
catLast = self.categoriesLast
catList = []
for i in range(len(self.texts)):
text = self.texts[i]
color = self.colors[i]
category = self.categories[i]
if type(category) is SET_TYPE:
for altCat in category:
if altCat is None:
topList.append((i, text, color, None))
else:
if categoryDict.get(altCat) is None:
categoryDict[altCat] = []
if catLast:
catList.append((None, altCat, None, altCat))
else:
topList.append((None, altCat, None, altCat))
categoryDict[altCat].append((i, text, color))
elif category:
if categoryDict.get(category) is None:
categoryDict[category] = []
if catLast:
catList.append((None, category, None, category))
else:
topList.append((None, category, None, category))
categoryDict[category].append((i, text, color))
else:
topList.append((i, text, color, None))
if catLast:
catList.sort()
topList += catList
divider = False
row = 0
for index, text, color, cat in topList:
columnbreak = 0
if row and row % 36 == 0:
columnbreak = 1
if cat:
string = (self.indent * row) + self.prefix + text
items = []
rowB = 0
for index2, text2, color2 in categoryDict.get(cat, []):
columnbreakB = 0
if rowB and rowB % 36 == 0:
columnbreakB = 1
if self.numbering:
number = '%d%. ' % (index2+1)
else:
number = ''
string2 = number + self.prefix + text2
command = lambda n=index2: self.setIndex(n, True)
if color2:
image = self._makeColorTile(color2)
item2 = {'kind': 'command', 'accelerator': string2,
'command': command, 'image': image,
'columnbreak': columnbreakB}
else:
item2 = {'kind': 'command', 'label': string2,
'command': command, 'columnbreak': columnbreakB}
items.append(item2)
self.rows.append(row)
rowB += 1
if catLast and not divider:
divider = True
self.menu.add_separator()
item = {'kind':'cascade', 'label':string,
'submenu':items, 'columnbreak':columnbreak}
else:
if self.numbering:
number = '%d%. ' % (index+1)
else:
number = ''
string = (self.indent * row) + number + self.prefix + text
command = lambda n=index: self.setIndex(n, True)
if color:
image = self._makeColorTile(color)
item = {'kind': 'command', 'accelerator': string, 'command': command,
'image': image, 'columnbreak': columnbreak}
else:
item = {'kind': 'command', 'label': string,
'command': command, 'columnbreak': columnbreak}
self.menu.addMenuItem(item)
self.rows.append(row)
row += 1
def _clearMenu(self):
self.menu.delete(0, 'end')
self.index = 0
self.rows = []
def _popdown(self, *event):
self.menu.unpost()
def _labelClick(self, event):
if not self.active:
return
s = self.rows[self.index]
#x = event.x_root - event.x + 2 + self.label.winfo_width()
x = event.x_root - 2
y = event.y_root - event.y - max(0, s) * (self.label.winfo_height() + 1)
self.menu.post(x, y)
def _canvasClick(self, event):
if not self.active:
return
s = self.rows[self.index]
x = event.x_root - event.x + 2
y = event.y_root - event.y - max(0, s) * (self.label.winfo_height() + 1)
self.menu.post(x, y)
def _updateLabel(self):
if self.texts:
text = self.texts[self.index] or NullText
else:
text = NullText
self.label.set(text=text)
def _makeColorTile(self, color):
image = Tkinter.PhotoImage()
self.menu.images.append(image)
if type(color) == type([]):
colors = [ scaleColor(self.menu, c, 1.0) for c in color ]
else:
colors = [ scaleColor(self.menu, color, 1.0), ]
cols = max(8, len(colors))
for x in range(cols):
i = x % len(colors)
c = colors[i]
for y in range(16):
image.put('{%s %s}' % (c,c), to=(2*x,y))
return image
