def body(self, master):
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
# get wild config iterations unless doExtraConfig=False
frame = ScrolledFrame(master,
doExtraConfig=False,
width=600,
height=300)
frame.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.parent_frame = frame.frame
self.edit_widget = None
self.keyList = getKeyList(self.metaclass, includeRoot=True)
self.createWidgets()
self.createBottomButtons(master)
self.setObject(self.object)
self.roleFuncs = {}
for name in self.metaclass.roleAllNames:
role = self.metaclass.elementDict[name]
if (self.showRole(role)):
# because of loop need role=role else all get bound to last role
f = lambda obj, role=role: self.setRoleValue(role)
self.roleFuncs[role] = f
if (self.editMode):
self.doRegisters()
class ChemCompAtomBondInfoPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(),'ChemCompAtomBondInfo.html')
def __init__(self, parent, chemCompInfo, chemCompAtoms, chemCompBonds):
self.chemCompInfo = chemCompInfo
self.chemCompAtoms = chemCompAtoms
self.chemCompBonds = chemCompBonds
self.obligatoryAtoms = []
for molTypeTuple in standardBackboneAtoms.keys():
if self.chemCompInfo[0][1] in molTypeTuple:
for atomName in standardBackboneAtoms[molTypeTuple]:
if atomName not in self.obligatoryAtoms:
self.obligatoryAtoms.append(atomName)
self.nonEntryAttributes = {
'chirality': (PulldownMenu,['R','S','unknown']),
'waterExchangeable': (CheckButton,False)
}
TemporaryBasePopup.__init__(self, parent=parent, title='ChemComp atom and bond creation', modal=False, transient=True)
def body(self, master):
#
# Popup window
#
self.columnspan = len(self.chemCompAtoms[0])
row = 0
label = Label(master, text= "Molecule type '%s', ccp code '%s'" % (self.chemCompInfo[0][1],self.chemCompInfo[1][1]))
label.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.EW)
#
# Warning message if necessary!
#
if self.obligatoryAtoms:
row += 1
label = Label(master, text= "Warning: have to define atoms: %s!" % string.join(self.obligatoryAtoms,', '), fg = 'red')
label.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.EW)
#
# Show top information...
#
row = row + 1
colNum = 0
self.frameWidth = 0
for chemCompAtomInfo in self.chemCompAtoms[0]:
attrName = chemCompAtomInfo[0]
label = Label(master, text = attrName, width = len(attrName) + 2)
label.grid(row=row, column=colNum, sticky=Tkinter.EW)
self.frameWidth += len(attrName) + 2
colNum += 1
#
# Separator
#
row += 1
separator = Separator(master, height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row = row, columnspan = self.columnspan, sticky = Tkinter.EW)
#
# Separate frame for info (have to be able to scroll)
#
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row,weight = 1)
for i in range(self.columnspan):
master.grid_columnconfigure(i,weight = 1)
self.atomFrame = ScrolledFrame(master, width = self.frameWidth, height = 300, doExtraConfig = False)
self.atomFrame.grid(row=row, column=0, columnspan = self.columnspan, sticky=Tkinter.NSEW)
self.atomFrameRow = row
self.atomFrameMaster = master
#
# Separator
#
row += 1
separator = Separator(master, height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row = row, columnspan = self.columnspan, sticky = Tkinter.EW)
#
# End bit...
#
row = row + 1
texts = [ 'OK', 'Update' ]
commands = [ self.ok, self.update ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = self.columnspan)
self.setupAtomFrame()
def setupAtomFrame(self,resetFrame = False, resetStatus = True):
frameRow = 0
self.atomWidgets = []
if resetFrame:
self.atomFrame = ScrolledFrame(self.atomFrameMaster, width = self.frameWidth, height = 300, doExtraConfig = False)
self.atomFrame.grid(row=self.atomFrameRow, column=0, columnspan = self.columnspan, sticky=Tkinter.NSEW)
frame = self.atomFrame.frame
#
# Make fake info at top for col length...
#
colNum = 0
for chemCompAtomInfo in self.chemCompAtoms[0]:
attrName = chemCompAtomInfo[0]
label = Label(frame, text = '', width = len(attrName) + 2)
label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW)
colNum += 1
#
# Now atom info...
#
for chemCompAtom in self.chemCompAtoms:
frameRow += 1
colNum = 0
self.atomWidgets.append([])
for chemCompAtomInfo in chemCompAtom:
attrName = chemCompAtomInfo[0]
if attrName == 'bondedAtoms':
bondedAtomText = ""
for otherAtom in chemCompAtomInfo[1]:
bondedAtomText += otherAtom[0][1] + ','
label = Label(frame, text = bondedAtomText[:-1])
label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW)
else:
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] == PulldownMenu:
self.atomWidgets[-1].append(PulldownMenu(frame, entries = widgetInfo[1], selected_index = widgetInfo[1].index(chemCompAtomInfo[1])))
elif widgetInfo[0] == CheckButton:
self.atomWidgets[-1].append(CheckButton(frame, selected = chemCompAtomInfo[1]))
else:
text = chemCompAtomInfo[1]
if not text:
text = ''
self.atomWidgets[-1].append(Entry(frame, text = text, width = 5))
self.atomWidgets[-1][-1].grid(row=frameRow, column=colNum)
colNum += 1
def update(self):
self.apply(checkAtoms = False)
self.setupAtomFrame()
def apply(self, checkAtoms = True):
atomNames = []
duplicateNames = []
if checkAtoms:
obligatoryAtoms = self.obligatoryAtoms[:]
for atomNum in range(0,len(self.chemCompAtoms)):
chemCompAtom = self.chemCompAtoms[atomNum]
widgets = self.atomWidgets[atomNum]
for widgetNum in range(0,len(widgets)):
attrName = chemCompAtom[widgetNum][0]
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] in [PulldownMenu,CheckButton]:
value = widgets[widgetNum].getSelected()
if widgetInfo[0] == CheckButton:
if value:
value = True
else:
value = False
else:
value = widgets[widgetNum].get()
if value == '':
value = None
chemCompAtom[widgetNum] = (attrName,value)
if attrName == 'name':
if value in atomNames:
if value not in duplicateNames:
duplicateNames.append(value)
else:
atomNames.append(value)
if checkAtoms:
if value in obligatoryAtoms:
obligatoryAtoms.pop(obligatoryAtoms.index(value))
if duplicateNames:
showWarning(self,"Duplicate atom names: %s - names have to be unique!" % string.join(duplicateNames,', '))
return False
if checkAtoms and obligatoryAtoms:
showWarning(self,"Obligatory atoms: %s still missing - please rename accordingly." % string.join(obligatoryAtoms,', '))
return False
return True
class SequenceChemCompSelect(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'SequenceChemCompSelect.html')
def __init__(self, parent, project, molName, createMoleculeDict,
localCreateMoleculeDict):
self.molName = molName
self.project = project
self.createMoleculeDict = createMoleculeDict
self.localCreateMoleculeDict = localCreateMoleculeDict
self.hasChanged = False
self.molecule = self.localCreateMoleculeDict[self.molName][0]
self.deleteText = 'Delete'
self.okText = 'OK'
self.startText = 'Insert at start'
self.endText = 'Append to end'
self.newMoleculeList = []
for molName in self.localCreateMoleculeDict.keys():
if molName != self.molName and not self.localCreateMoleculeDict[
molName][0]:
self.newMoleculeList.append(molName)
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Set chemComps for sequence',
modal=True,
transient=True)
def body(self, master):
self.geometry('700x500')
#
# Setup header
#
row = 0
label = Label(master, text='Original', width=10)
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text='Modify ChemCompVar', width=35)
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text='Status', width=20)
label.grid(row=row, column=2, sticky=Tkinter.EW)
label = Label(master, text='', width=5)
label.grid(row=row, column=3, sticky=Tkinter.EW)
row += 1
label = Label(master, text='code', width=10)
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text='ccpCode (molType): linking, descriptor',
width=35)
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Tkinter.Button(master,
text='Add new molecule',
command=self.addNewMolecule)
label.grid(row=row, column=2)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=3, sticky=Tkinter.EW)
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row, weight=1)
for i in range(4):
master.grid_columnconfigure(i, weight=1)
self.sequenceFrame = ScrolledFrame(master,
width=70,
height=300,
doExtraConfig=False)
self.sequenceFrame.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.sequenceFrameRow = row
self.sequenceFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=3, sticky=Tkinter.EW)
row += 1
texts = ['Change', 'Change and quit']
commands = [
self.updateMolDict, self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
self.setupSequenceFrame()
def setupSequenceFrame(self, resetFrame=False, resetStatus=True):
frameRow = 0
x = y = 0
if resetFrame:
self.sequenceFrame = ScrolledFrame(self.sequenceFrameMaster,
width=70,
height=300,
doExtraConfig=False)
self.sequenceFrame.grid(row=self.sequenceFrameRow,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
frame = self.sequenceFrame.frame
#
# Just use the first one as reference!
#
sequences = self.localCreateMoleculeDict[self.molName][1]
(self.origSequence, self.origSequenceList) = sequences[0]
if len(sequences) > 1:
multipleSequences = True
else:
multipleSequences = False
#
# Set info...
#
label = Label(frame, text='', width=10)
label.grid(row=frameRow, column=0, sticky=Tkinter.EW)
label = Label(frame, text='', width=35)
label.grid(row=frameRow, column=1, sticky=Tkinter.EW)
label = Label(frame, text='', width=20)
label.grid(row=frameRow, column=2, sticky=Tkinter.EW)
frameRow += 1
self.ccvButtons = []
if resetStatus or resetFrame:
self.statusList = []
self.moveStatus = {}
#
# Set up a list of status entries
#
statusEntries = [self.okText, self.deleteText]
for newMolName in self.newMoleculeList:
for appendCode in [self.startText, self.endText]:
statusEntries.append('%s of %s' % (appendCode, newMolName))
self.moveStatus[statusEntries[-1]] = (newMolName,
appendCode)
#
# Start creating all the objects...
#
for seqIndex in range(0, len(self.origSequenceList)):
(seqEl, ccHead, ccVar) = self.origSequenceList[seqIndex]
#
# Set the original sequence code info...
#
seqCode = seqEl.seqCode
if hasattr(seqEl, 'code3Letter') and seqEl.code3Letter:
seqText = seqEl.code3Letter
else:
seqText = seqEl.code1Letter
label = Label(frame, text="%s-%d" % (seqText, seqCode))
label.grid(row=frameRow, column=0, sticky=Tkinter.EW)
#
# Set the chemCompVar info
#
keywds = {}
if ccHead:
textCode = "%s (%s)" % (ccHead.ccpCode, ccHead.molType)
if ccVar:
textCode += ": %s,%s" % (ccVar.linking, ccVar.descriptor)
else:
textCode = 'Select chemCompVar for %s' % textCode
keywds['fg'] = 'red'
else:
textCode = 'Select chemCompVar'
keywds['fg'] = 'red'
self.ccvButtons.append(
Tkinter.Button(frame,
text=textCode,
command=lambda seqIndex=seqIndex: self.
selectChemCompVar(seqIndex),
**keywds))
self.ccvButtons[-1].grid(row=frameRow, column=1, sticky=Tkinter.EW)
#
# Set the selector...
#
if resetStatus or resetFrame:
self.statusList.append(
PulldownMenu(frame,
entries=statusEntries,
label_color='red'))
self.statusList[-1].grid(row=frameRow,
column=2,
sticky=Tkinter.EW)
frameRow += 1
return True
def addNewMolecule(self):
molFormat = 'newMolecule_%d'
if not hasattr(self, 'molNames'):
self.molNames = self.localCreateMoleculeDict.keys()
for i in range(0, 10):
newMolName = molFormat % (i + 1)
if newMolName not in self.molNames and not self.project.findFirstMolecule(
name=newMolName):
break
self.molNames.append(newMolName)
for statusPullDown in self.statusList:
for appendCode in [self.startText, self.endText]:
entryText = '%s of %s' % (appendCode, newMolName)
statusPullDown.append(entryText)
self.moveStatus[entryText] = (newMolName, appendCode)
def updateMolDict(self):
hasChanged = False
actualSeqIndex = 0
seqLength = len(self.origSequenceList)
origSequenceList = self.origSequenceList[:]
for seqIndex in range(0, seqLength):
(seqEl, ccHead, ccVar) = origSequenceList[seqIndex]
newStatus = self.statusList[seqIndex].getSelected()
if newStatus != self.okText:
hasChanged = True
if self.localCreateMoleculeDict == self.createMoleculeDict:
self.copyCreateMoleculeDict()
self.origSequenceList.pop(actualSeqIndex)
if newStatus != self.deleteText:
(moveToMoleculeName,
appendCode) = self.moveStatus[newStatus]
if not self.localCreateMoleculeDict.has_key(
moveToMoleculeName):
self.localCreateMoleculeDict[moveToMoleculeName] = [
None, [(None, [])]
]
sequences = self.localCreateMoleculeDict[
moveToMoleculeName][1]
for (tempSequence, tempSequenceList) in sequences:
if appendCode == self.startText:
tempSequenceList.insert(0, (seqEl, ccHead, ccVar))
elif appendCode == self.endText:
tempSequenceList.append((seqEl, ccHead, ccVar))
else:
actualSeqIndex += 1
#
# Check if changed and do some resets if so...
#
if hasChanged:
self.hasChanged = True
#
# Reset the linking if appropriate
#
for molName in self.localCreateMoleculeDict.keys():
if not self.localCreateMoleculeDict[molName][0]:
sequences = self.localCreateMoleculeDict[molName][1]
for (origSequence, origSequenceList) in sequences:
molTypes = []
for (seqEl, ccHead, ccVar) in origSequenceList:
if ccHead:
if ccHead.molType not in molTypes:
molTypes.append(ccHead.molType)
if len(molTypes) == 1 and molTypes[0] != 'other':
seqLength = len(origSequenceList)
for seqIndex in range(0, seqLength):
(seqEl, ccHead,
ccVar) = origSequenceList[seqIndex]
if ccVar:
if seqIndex == 0:
linking = 'start'
elif seqIndex == seqLength - 1:
linking = 'end'
else:
linking = 'middle'
if ccVar.linking != linking:
ccVar = ccHead.chemComp.findFirstChemCompVar(
descriptor=ccVar.descriptor,
linking=linking)
if ccVar:
origSequenceList[seqIndex] = (
seqEl, ccHead, ccVar)
self.setupSequenceFrame(resetFrame=True)
def selectChemCompVar(self, seqIndex):
hasChanged = False
(seqEl, ccHead, ccVar) = self.origSequenceList[seqIndex]
keywds = {}
if ccHead:
keywds['molTypeEntries'] = [ccHead.molType] # TODO HAS TO CHANGE!!
keywds['selectedChemCompHeads'] = [ccHead]
if ccVar:
keywds['selectLinking'] = ccVar.linking
if hasattr(seqEl, 'code3Letter') and seqEl.code3Letter:
keywds['origCode'] = seqEl.code3Letter
else:
keywds['origCode'] = seqEl.code1Letter
popup = ChemCompSelectionPopup(self,
self.project,
chemCompEntries=['ChemCompVar'],
**keywds)
self.wait_window(popup)
if popup.frame.getSelectedChemComp():
newChemCompVar = popup.frame.getSelectedChemComp()
if not ccVar or ccVar != newChemCompVar:
if self.localCreateMoleculeDict == self.createMoleculeDict:
self.copyCreateMoleculeDict()
self.origSequenceList[seqIndex] = (
seqEl, newChemCompVar.chemComp.chemCompHead,
newChemCompVar)
hasChanged = True
if hasChanged:
self.setupSequenceFrame(resetStatus=False)
self.hasChanged = hasChanged
def copyCreateMoleculeDict(self):
self.localCreateMoleculeDict = {}
for molName in self.createMoleculeDict.keys():
self.localCreateMoleculeDict[molName] = [
self.createMoleculeDict[molName][0], []
]
for (sequence,
sequenceList) in self.createMoleculeDict[molName][1]:
self.localCreateMoleculeDict[molName][1].append(
(sequence, sequenceList[:]))
sequences = self.localCreateMoleculeDict[self.molName][1]
(self.origSequence, self.origSequenceList) = sequences[0]
def apply(self):
self.updateMolDict()
return True
class ProchiralStatusPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'ProchiralStatus.html')
def __init__(self, parent, chainList, chainAtomSetsDict):
self.chainList = chainList
self.chainAtomSetsDict = chainAtomSetsDict
self.resParentDict = {}
self.resParentList = []
self.resParentChainLabelDict = {}
self.resParentChainLabelList = {}
self.chainResonancesDict = {}
for resParent in self.chainAtomSetsDict.keys():
if isinstance(resParent, NmrConstraint.NmrConstraintStore):
strucGens = resParent.structureGenerations
strucGenSerials = [str(sg.serial) for sg in strucGens]
strucGenLabel = string.join(strucGenSerials, ',')
resParentLabel = "Constraint set %d (strucGens %s)" % (
resParent.serial, strucGenSerials)
else:
resParentLabel = "Nmr project %s" % resParent.name
self.resParentDict[resParentLabel] = resParent
self.resParentList.append(resParentLabel)
self.chainResonancesDict[resParent] = {}
self.resParentChainLabelDict[resParent] = {}
self.resParentChainLabelList[resParent] = []
for chain in self.chainList:
self.project = chain.root
if self.chainAtomSetsDict[resParent].has_key(
chain) and self.chainAtomSetsDict[resParent][chain]:
chainLabel = "Molecular system '%s':Chain '%s' (molecule '%s')" % (
chain.molSystem.code, chain.code, chain.molecule.name)
self.resParentChainLabelList[resParent].append(chainLabel)
self.resParentChainLabelDict[resParent][chainLabel] = chain
self.chainResonancesDict[resParent][chain] = []
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(
self,
parent=parent,
title="Project '%s': " % self.project.name +
'Set status prochiral atoms/resonances',
modal=False,
transient=True)
def body(self, master):
#
# Setup header
#
row = 0
label = Label(master, text='Select the resonance list:')
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text='Select the chain:')
label.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
self.resParentSelect = PulldownMenu(master,
entries=self.resParentList,
callback=self.setupResParentList,
do_initial_callback=False)
self.resParentSelect.grid(row=row, column=0, sticky=Tkinter.EW)
self.chainSelect = PulldownMenu(master,
entries=[],
callback=self.setupProchiralList,
do_initial_callback=False)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=2, sticky=Tkinter.EW)
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row, weight=1)
for i in range(2):
master.grid_columnconfigure(i, weight=1)
self.prochiralListFrame = ScrolledFrame(master,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
self.prochiralListFrameRow = row
self.prochiralListFrameMaster = master
row = row + 1
texts = ['Set all', 'Set chain']
commands = [
self.ok, self.setStereo
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
self.resParentSelect.callback(0, self.resParentList[0])
def setupResParentList(self, listIndex, resParentLabel):
resParent = self.resParentDict[resParentLabel]
self.resParent = resParent
self.chainSelect.setup(self.resParentChainLabelList[self.resParent], 0)
self.chainSelect.callback(
0, self.resParentChainLabelList[self.resParent][0])
def setupProchiralList(self, listIndex, chainLabel):
chain = self.resParentChainLabelDict[self.resParent][chainLabel]
self.chain = chain
self.prochiralListFrame.destroy()
self.prochiralListFrame = ScrolledFrame(self.prochiralListFrameMaster,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=self.prochiralListFrameRow,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
#
# TODO: also handle case one resonance, two atomSets!?!?
#
frameRow = 0
x = y = 0
frame = self.prochiralListFrame.frame
self.resonanceObjects = {}
self.resonanceLabelDict = {}
#
# Reuse previous settings...
#
if len(self.chainResonancesDict[self.resParent][chain]) == len(
self.chainAtomSetsDict[self.resParent][chain]):
usePreviousSettings = True
else:
usePreviousSettings = False
for i in range(0, len(self.chainAtomSetsDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
isStereo = False
hasResonances = False
isValidCase = False
resonances = []
if usePreviousSettings and self.chainResonancesDict[
self.resParent][chain][i]:
resonances = self.chainResonancesDict[
self.resParent][chain][i][3]
isStereo = self.chainResonancesDict[
self.resParent][chain][i][0]
hasResonances = True
isValidCase = True
else:
for atomSet in atomSetGroup:
resonanceSets = atomSet.sortedResonanceSets()
if resonanceSets:
hasResonances = True
for resonanceSet in resonanceSets:
for resonance in resonanceSet.sortedResonances():
if resonance not in resonances:
resonances.append(resonance)
if len(resonanceSets) == 1:
isValidCase = True
if len(resonanceSet.atomSets) == 1:
isStereo = True
else:
# Case only one resonance but stereo assigned
resonances.append(0)
if len(resonances) == 1:
# Case only one resonance, not stereo assigned
resonances.append(None)
#
# Set up only for valid cases
#
if hasResonances and isValidCase:
if not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(
[isStereo, False, False, resonances])
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
rowspan = 2
checkButton = CheckButton(
frame,
selected=isStereo,
callback=lambda status=isStereo, fr=frameRow, item=i, setup
=False: self.toggleResonances(status, fr, item, setup))
checkButton.grid(row=frameRow,
rowspan=rowspan,
column=0,
sticky=Tkinter.EW)
label = Label(frame, text=ccpCode, width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=1,
sticky=Tkinter.E)
label = Label(frame, text=str(seqCode), width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=2,
sticky=Tkinter.W)
#
# Set up the atom names
#
for j in range(0, len(atomSetGroup)):
atomSet = atomSetGroup[j]
label = Label(frame, text=atomSet.name)
label.grid(row=frameRow + j,
column=3,
sticky=Tkinter.E,
ipadx=4)
#
# Set up the resonances
#
self.resonanceObjects[frameRow] = {
True: [[], []],
False: [[], []]
}
resonanceLabelList = []
for resonance in resonances:
if not resonance:
resonanceLabel = 'unknown'
else:
if hasattr(resonance, 'shifts') and resonance.shifts:
shiftLabel = " (shifts: "
for shift in resonance.sortedShifts():
shiftLabel += "%.2f, " % shift.value
shiftLabel = shiftLabel[:-2] + ")"
else:
shiftLabel = ""
resonanceLabel = "'%d.%s'%s" % (
seqCode, resonance.name, shiftLabel)
self.resonanceLabelDict[resonanceLabel] = resonance
resonanceLabelList.append(resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow, column=4, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(separator)
separator = CrossLine(frame,
height=20,
width=30,
canvas_bg=frame['bg'],
color='dimgray')
self.resonanceObjects[frameRow][False][0].append(separator)
resonanceList = PulldownMenu(
frame,
entries=resonanceLabelList,
callback=lambda selInd=x, selItem=y, fr=frameRow, item=i:
self.setProchiralLabels(selInd, selItem, fr, item),
do_initial_callback=False,
label_color='red')
resonanceList.grid(row=frameRow, column=5, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(resonanceList)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[0],
fg='dimgray')
self.resonanceObjects[frameRow][False][0].append(
resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + 1, column=4)
self.resonanceObjects[frameRow][True][1].append(separator)
self.resonanceObjects[frameRow][False][1].append(None)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='red')
resonanceLabel.grid(row=frameRow + 1,
column=5,
sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][1].append(resonanceLabel)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='dimgray')
self.resonanceObjects[frameRow][False][1].append(
resonanceLabel)
if not isStereo:
checkButton.callback(isStereo, setup=True)
separator = Separator(frame, height=1)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + rowspan,
columnspan=6,
sticky=Tkinter.EW)
frameRow += rowspan + 1
elif not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(None)
return True
def setProchiralLabels(self, selInd, selItem, fr, item):
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][False][0][1].set(resonanceLabel)
selInd = not selInd
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][True][1][1].set(resonanceLabel)
self.resonanceObjects[fr][False][1][1].set(resonanceLabel)
self.chainResonancesDict[self.resParent][
self.chain][item][2] = not self.chainResonancesDict[
self.resParent][self.chain][item][2]
self.chainResonancesDict[self.resParent][self.chain][item][3].reverse()
def toggleResonances(self, status, frameRow, item, setup):
if not setup:
self.chainResonancesDict[self.resParent][
self.chain][item][0] = status
self.chainResonancesDict[self.resParent][
self.chain][item][1] = not self.chainResonancesDict[
self.resParent][self.chain][item][1]
for i in range(0, len(self.resonanceObjects[frameRow])):
#
# Remove other widgets from grid
#
rpds = self.resonanceObjects[frameRow][not status][i]
for rpd in rpds:
if rpd:
rpd.grid_forget()
#
# Set current widgets
#
rpds = self.resonanceObjects[frameRow][status][i]
for j in range(0, len(rpds)):
rpd = rpds[j]
if rpd:
keywds = {}
if j == 1:
keywds['sticky'] = Tkinter.W
if j == 0:
if not status:
keywds['rowspan'] = 2
rpd.grid(row=frameRow + i, column=4 + j, **keywds)
def setStereo(self, chain=None):
if not chain:
chain = self.chain
if self.chainResonancesDict[self.resParent][chain]:
for i in range(
0, len(self.chainResonancesDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
(stereoStatus, stereoStatusChanged, resChanged, resonances
) = self.chainResonancesDict[self.resParent][chain][i]
if stereoStatusChanged or (stereoStatus and resChanged):
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
atomText = "%s/%s" % (atomSetGroup[0].name,
atomSetGroup[1].name)
if stereoStatusChanged:
if stereoStatus:
stereoText = "non-stereospecific to stereospecific."
else:
stereoText = "stereospecific to non-stereospecific."
print " Warning: Changed '%s.%d' prochiral resonances for atoms %s from %s" % (
ccpCode, seqCode, atomText, stereoText)
self.chainResonancesDict[
self.resParent][chain][i][1] = False
self.chainResonancesDict[
self.resParent][chain][i][2] = False
if stereoStatus:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[0]:
resonanceSet.removeAtomSet(atomSetGroup[1])
if resonances[1]:
if not resonances[0]:
# Remove right atom set if only one resonance...
resonanceSet.removeAtomSet(atomSetGroup[0])
else:
# Only create a new resonance set if two resonances present!
resonanceSet.removeResonance(resonances[1])
if isinstance(
self.resParent,
NmrConstraint.NmrConstraintStore):
newResonanceSet = self.resParent.newFixedResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
newResonanceSet = self.resParent.newResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
if resonances[0]:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[1]:
atomSetGroup[1].findFirstResonanceSet(
).delete()
resonanceSet.addResonance(resonances[1])
resonanceSet.addAtomSet(atomSetGroup[1])
elif resonances[1]:
resonanceSet = atomSetGroup[1].resonanceSets[0]
resonanceSet.addAtomSet(atomSetGroup[0])
elif stereoStatus and resChanged:
print " Warning: Changed resonance assignment for '%s.%d' stereospecifically assigned atoms %s." % (
ccpCode, seqCode, atomText)
self.chainResonancesDict[
self.resParent][chain][i][2] = False
resonanceSets = []
for i in range(0, 2):
if atomSetGroup[i].resonanceSets:
resonanceSets.append(
atomSetGroup[i].findFirstResonanceSet())
else:
resonanceSets.append(None)
for i in range(0, 2):
resonanceSet = resonanceSets[i]
if resonanceSet:
resonanceSet.addAtomSet(atomSetGroup[not i])
resonanceSet.removeAtomSet(atomSetGroup[i])
def apply(self):
for chain in self.chainList:
self.setStereo(chain=chain)
return True
class GroupChemShiftsPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'GroupChemShifts.html')
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 setChainLabels(self, molSysLabel, molSysList):
#
# Set up chain information
#
chainLabelList = []
chainLabelDict = {}
chainLabelShiftListDict = {}
self.molSysRelationDict[molSysLabel] = [
chainLabelList, chainLabelDict, chainLabelShiftListDict
]
chains = []
for molSys in molSysList:
chains.extend(list(molSys.sortedChains()))
chainLabel = 'All chains'
if self.setShiftListLabels(chainLabel, chains,
self.molSysRelationDict[molSysLabel][2]):
self.molSysRelationDict[molSysLabel][0].append(chainLabel)
self.molSysRelationDict[molSysLabel][1][chainLabel] = chains
for chain in chains:
chainLabel = "'%s' (mol. '%s')" % (chain.code, chain.molecule.name)
if self.setShiftListLabels(
chainLabel, [chain],
self.molSysRelationDict[molSysLabel][2]):
self.molSysRelationDict[molSysLabel][0].append(chainLabel)
self.molSysRelationDict[molSysLabel][1][chainLabel] = [chain]
return self.molSysRelationDict[molSysLabel][0]
def setShiftListLabels(self, chainLabel, chains, chainLabelShiftListDict):
#
# Set up chemical shift list information (slooooww so done at start)
#
shiftLists = []
shiftListCount = {}
resonanceTracker = []
shiftListLabels = []
shiftListLabelsDict = {}
atomCount = 0
for chain in chains:
for residue in chain.residues:
for atom in residue.atoms:
atomCount += 1
if atom.atomSet:
for resonanceSet in atom.atomSet.resonanceSets:
for resonance in resonanceSet.resonances:
if resonance in resonanceTracker:
continue
resonanceTracker.append(resonance)
for shift in resonance.shifts:
if shift.parentList not in shiftLists:
shiftLists.append(shift.parentList)
shiftListCount[shift.parentList] = 0
shiftListCount[shift.parentList] += 1
for shiftList in shiftLists:
percentage = (shiftListCount[shift.parentList] * 100.0) / atomCount
shiftListLabel = "%d:%s (%.1f%%)" % (shiftList.serial,
shiftList.name, percentage)
shiftListLabels.append(shiftListLabel)
shiftListLabelsDict[shiftListLabel] = shiftList
chainLabelShiftListDict[chainLabel] = [
shiftListLabels, shiftListLabelsDict
]
return shiftListLabels
def body(self, master):
#
# Setup header
#
row = 0
self.columnSpan = 3
label = Label(
master,
text=
'Select molecular system, chains and chemical shift list to be analyzed:'
)
label.grid(row=row,
column=0,
columnspan=self.columnSpan,
sticky=Tkinter.EW)
row += 1
self.molSysSelect = PulldownMenu(master,
entries=self.molSysLabelList,
callback=self.setupChains)
self.molSysSelect.grid(row=row, column=0, sticky=Tkinter.W)
self.chainSelect = PulldownMenu(master,
entries=self.chainLabelList,
callback=self.setupShiftList)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftListLabels,
callback=self.setupPercentageFrame,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=2, sticky=Tkinter.W)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
master.grid_rowconfigure(row, weight=1)
for i in range(self.columnSpan):
master.grid_columnconfigure(i, weight=1)
self.percentageFrame = ScrolledFrame(master,
height=180,
doExtraConfig=False)
self.percentageFrame.grid(row=row,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
self.percentageFrameRow = row
self.percentageFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
master.grid_rowconfigure(row, weight=1)
self.resultsFrame = ScrolledFrame(master,
height=180,
doExtraConfig=False)
self.resultsFrame.grid(row=row,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
self.resultsFrameRow = row
self.resultsFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
texts = ['Recalculate', 'Write to file']
commands = [
self.recalc, self.writeFile
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
self.shiftListSelect.callback(0, self.shiftListLabels[0])
def setupChains(self, listIndex, molSysLabel):
molSystems = self.molSysLabelDict[molSysLabel]
if self.molSystems == molSystems:
return
self.molSystems = molSystems
self.chainLabelList = self.molSysRelationDict[molSysLabel][0]
self.chainLabelDict = self.molSysRelationDict[molSysLabel][1]
self.chainLabelShiftListDict = self.molSysRelationDict[molSysLabel][2]
if hasattr(self, 'chainSelect'):
self.chains = None
self.chainSelect.callback(0, self.chainLabelList[0])
def setupShiftList(self, listIndex, chainLabel):
chains = self.chainLabelDict[chainLabel]
if self.chains == chains:
return
self.chains = chains
#
# Reset the pulldown menu
#
if hasattr(self, 'chainSelect'):
self.chainSelect.replace(self.chainLabelList)
#
# Set up chemical shift lists
#
self.shiftListLabels = self.chainLabelShiftListDict[chainLabel][0]
self.shiftListLabelsDict = self.chainLabelShiftListDict[chainLabel][1]
if hasattr(self, 'percentageFrame'):
self.shiftList = None
self.shiftListLabel = None
self.setupPercentageFrame(0, self.shiftListLabels[0])
def setupPercentageFrame(self, listIndex, shiftListLabel):
if self.shiftListLabel == shiftListLabel:
return
self.shiftList = self.shiftListLabelsDict[shiftListLabel]
self.shiftListLabel = shiftListLabel
#
# Reset chemical shift groups...
#
self.shiftGroupsList = []
for i in range(1, 10):
shiftGroupLabel = 'Group_%s' % i
self.shiftGroupsList.append(shiftGroupLabel)
#
# Reset the pulldown menu
#
if hasattr(self, 'shiftListSelect'):
if hasattr(self.shiftListSelect,
'entries') and tuple(self.shiftListLabels) != tuple(
self.shiftListSelect.entries): # HACK
# otherwise can get infinite recursion but even with above could
# if no self.shiftListLabels because of "None" entry in PulldownMenu
self.shiftListSelect.replace(self.shiftListLabels)
self.shiftListSelect.setSelected(shiftListLabel)
#
# Reset frame...
#
self.percentageFrame.destroy()
self.percentageFrame = ScrolledFrame(self.percentageFrameMaster,
height=180,
doExtraConfig=False)
self.percentageFrame.grid(row=self.percentageFrameRow,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
#
# Recalculate results
#
self.results = makeChemShiftSelections(self.parent, self.chains,
self.shiftList)
resultKeys = self.results.keys()
resultKeys.sort()
#
# Set up the information
#
frameRow = 0
frame = self.percentageFrame.frame
self.shiftGroupObjects = {}
for resultKey in resultKeys:
allAtoms = self.results[resultKey][0]
shiftAtoms = self.results[resultKey][1]
percentage = shiftAtoms * 100.0 / allAtoms
label = Label(frame, text=resultKey)
label.grid(row=frameRow, column=0, sticky=Tkinter.W)
label = Label(frame, text="%.1f%%" % percentage)
label.grid(row=frameRow, column=1, sticky=Tkinter.W)
label = Label(frame, text="(%d/%d)" % (shiftAtoms, allAtoms))
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
self.shiftGroupObjects[resultKey] = PulldownMenu(
frame, entries=self.shiftGroupsList)
self.shiftGroupObjects[resultKey].grid(row=frameRow,
column=3,
sticky=Tkinter.E)
frameRow += 1
return True
def recalc(self):
groups = {}
groupsInfo = {}
for resultKey in self.shiftGroupObjects:
group = self.shiftGroupObjects[resultKey].getSelected()
if not groups.has_key(group):
groups[group] = []
groupsInfo[group] = [0, 0]
(allAtoms, shiftAtoms) = self.results[resultKey]
groupsInfo[group][0] += allAtoms
groupsInfo[group][1] += shiftAtoms
groups[group].append(resultKey)
#
# Reset frame...
#
self.resultsFrame.destroy()
self.resultsFrame = ScrolledFrame(self.resultsFrameMaster,
height=180,
doExtraConfig=False)
self.resultsFrame.grid(row=self.resultsFrameRow,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
#
# Set info in lower frame
#
frameRow = 0
frame = self.resultsFrame.frame
groupKeys = groups.keys()
groupKeys.sort()
self.groupText = {}
for group in groupKeys:
percentage = groupsInfo[group][1] * 100.0 / groupsInfo[group][0]
label = Label(frame, text=group)
label.grid(row=frameRow, column=0, sticky=Tkinter.W)
label = Label(frame, text=groups[group][0])
label.grid(row=frameRow, column=1, sticky=Tkinter.W)
label = Label(frame, text="%.1f%%" % percentage)
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
label = Label(frame,
text="(%d/%d)" %
(groupsInfo[group][1], groupsInfo[group][0]))
label.grid(row=frameRow, column=3, sticky=Tkinter.W)
self.groupText[group] = "%-10s %-20s %8.1f%% (%d/%d)%s" % (
group, groups[group][0], percentage, groupsInfo[group][1],
groupsInfo[group][0], newline)
frameRow += 1
for otherResultKey in groups[group][1:]:
label = Label(frame, text=otherResultKey)
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
self.groupText[group] += "%-10s %-20s%s" % ('', otherResultKey,
newline)
frameRow += 1
return True
def writeFile(self):
filePopup = FormatFilePopup(self, component='text')
if filePopup.fileSelected:
groupKeys = self.groupText.keys()
groupKeys.sort()
fout = open(filePopup.file, 'w')
fout.write("Project: %s" % self.project.name + newline)
fout.write("Molsystems: %s" % self.molSysSelect.getSelected() +
newline)
fout.write("Chains: %s" % self.chainSelect.getSelected() + newline)
fout.write("Shiftlist: %s" % self.shiftListSelect.getSelected() +
newline * 2)
for group in groupKeys:
fout.write(self.groupText[group])
print "Wrote file %s..." % filePopup.file
def apply(self):
return True