class WriteBmrbChemShiftDepPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'WriteBmrbChemShiftDep.html')
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.selectedFormats = []
self.defaultText = 'Select file'
self.chainDict = {}
self.chainList = []
self.shiftListDict = {}
self.shiftLists = []
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
if shiftList.measurements != ():
label = str(shiftList.serial) + ':' + str(shiftList.name)
self.shiftListDict[label] = shiftList
self.shiftLists.append(label)
if not self.shiftLists:
showError('Error', 'No shift lists available!')
return
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Write BMRB chemical shift deposition file',
modal=False,
transient=True)
def body(self, master):
row = 0
label = Label(master,
text="BMRB chemical shift deposition file writer.")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Shift lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftLists,
callback=self.setChainList,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Chains (only one per file):")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainListSelect = PulldownMenu(master, entries=self.chainList)
self.chainListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
self.setChainList(0, self.shiftLists[0])
row += 1
label = Label(master, text="Chemical shift deposition file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master,
text=self.defaultText,
command=self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = ['Write file']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def setChainList(self, shiftListIndex, shiftListLabel):
#
# Has to be done... very slow this.
#
shiftList = self.shiftListDict[shiftListLabel]
self.chainDict = {}
self.chainList = []
for shift in shiftList.measurements:
if shift.resonance:
rs = shift.resonance.resonanceSet
if rs:
atom = rs.findFirstAtomSet().findFirstAtom()
chain = atom.residue.chain
if chain not in self.chainDict.values():
label = chain.molSystem.code + ":'" + chain.code + "'"
self.chainDict[label] = chain
self.chainList.append(label)
self.chainListSelect.clearMenuItems()
if self.chainList:
self.chainListSelect.setup(self.chainList, 0)
def selectFile(self):
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
fileName = 'bmrb.csdep'
popup = FormatFilePopup(self,
file=fileName,
component='csdep',
format='bmrb')
if popup.fileSelected:
self.fileButton.config(text=popup.file)
popup.destroy()
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
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.clearMenuItems()
self.chainSelect.entries = self.chainLabelList
self.chainSelect.addMenuItems()
#
# 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'):
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
