class SaveLoadTab(object):
"""The tab that lets the user FileSelect
a file to open or to save.
"""
def __init__(self, parent, frame):
"""Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
"""
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.loadAndSaveButtons = None
self.fileselectionBox = None
self.body()
def body(self):
"""Setting up the body of this view."""
frame = self.frame
file_types = [FileType("pyc", ["*.pyc"])]
self.fileselectionBox = FileSelect(frame, multiSelect=False, file_types=file_types)
self.fileselectionBox.grid(row=0, column=0, columnspan=6, sticky="nsew")
texts = ["Load", "Save"]
commands = [self.loadDataFromPyc, self.saveDataToPyc]
self.loadAndSaveButtons = ButtonList(frame, commands=commands, texts=texts)
self.loadAndSaveButtons.grid(row=1, column=0, sticky="nsew")
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
def saveDataToPyc(self):
"""Save the data to the selected file."""
if self.guiParent.connector.results:
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.saveDataToPyc(fileName)
self.fileselectionBox.updateFileList()
else:
string = """There are no results to save, """ """the algorithm has not run yet."""
showWarning("No Results to Save", string, parent=self.guiParent)
def loadDataFromPyc(self):
"""Load the data from the selected file."""
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.loadDataFromPyc(fileName)
self.guiParent.resultsTab.update()
def body(self, guiParent):
row = 0
self.graph = ScrolledGraph(guiParent)
self.graph.grid(row=row, column=0, sticky='NSEW')
row += 1
texts = ['Draw graph', 'Goodbye']
commands = [self.draw, self.destroy]
buttons = ButtonList(guiParent, texts=texts, commands=commands)
buttons.grid(row=row, column=0, sticky='NSEW')
def createBottomButtons(self, parent):
if (self.editMode):
texts = []
commands = []
if (self.metaclass.parentRole):
texts.extend(['Parent', 'Siblings'])
commands.extend([self.gotoParent, self.showSiblings])
if (self.metaclass.parentRole.otherClass.parentRole):
texts.extend(['All'])
commands.extend([self.showAll])
texts.extend(['Delete', 'Close'])
commands.extend([self.deleteObject, self.close])
else:
texts = ['Create', 'Cancel']
commands = [self.createObject, self.close]
bottom_buttons = ButtonList(parent,
texts=texts,
commands=commands,
direction=Tkinter.HORIZONTAL,
expands=True)
bottom_buttons.grid(row=2, column=0, columnspan=2, sticky=Tkinter.EW)
class AssignMentTransferTab(object):
'''the tab in the GUI where assignments
can be transferred in bulk to the ccpn analysis
project. A difference is made between two types
of assignments:
1) spin systems to residues, which also
implies resonanceSets to atomSets.
2) resonances to peak dimensions.
The user is able to configure which assignments
should be transferred to the project.
Attributes:
guiParent: gui object this tab is part of.
frame: the frame in which this element lives.
dataModel(src.cython.malandro.DataModel): dataModel
object describing the assignment proposed by
the algorithm.
selectedSolution (int): The index of the solution/run
that is used asa the template to make the assignments.
resonanceToDimension (bool): True if resonances should
be assigned to peak dimensions. False if not.
spinSystemToResidue (bool): True if spin system to
residue assignment should be carried out.
minScore (float): The minimal score of a spin system
assignment to a residue to be allowed
to transfer this assignment to the project
intra (bool): True if intra-residual peaks should be
assigned.
sequential (bool): True if sequential peaks should be
assigned.
noDiagonal (bool): If True, purely diagonal peaks are
ignored during the transfer of assignments.
allSpectra (bool): If True, all spectra will be assigned.
If False, one specified spectrum will be assigned.
spectrum (src.cython.malandro.Spectrum): The spectrum
that should be assigned.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
# Buttons and fields,
# will be set in body():
self.peaksCheckButton = None
self.residuesCheckButton = None
self.intraCheckButton = None
self.sequentialCheckButton = None
self.noDiagonalCheckButton = None
self.spinSystemTypeSelect = None
self.minScoreEntry = None
self.solutionNumberEntry = None
self.spectrumSelect = None
self.spectraPullDown = None
self.assignedResidueStrategySelect = None
self.transferButton = None
# Settings that determine how assignments
# are transferred to the analysis project:
self.minScore = 80.0
self.dataModel = None
self.spectrum = None
self.selectedSolution = 1
self.body()
self.resonanceToDimension = True
self.spinSystemToResidue = True
self.intra = True
self.sequential = True
self.noDiagonal = True
self.allSpectra = True
self.spinSystemType = 0
self.strategy = 0
def body(self):
'''Describes the body of this tab. It consists
out of a number of radio buttons, check buttons
and number entries that allow the user to
indicate which assignments should be transferred.
'''
# self.frame.expandColumn(0)
self.frame.expandGrid(8, 0)
self.frame.expandGrid(8, 1)
typeOfAssignmentFrame = LabelFrame(
self.frame, text='type of assignment')
typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw')
# typeOfAssignmentFrame.expandGrid(0,5)
peakSelectionFrame = LabelFrame(
self.frame, text='which peaks to assign')
peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2)
spinSystemSelectionFrame = LabelFrame(self.frame,
text='Which spin-systems to use')
spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw')
tipText = 'What to do when a residue has already a spin system assigned to it.'
assignedResidueFrame = LabelFrame(self.frame,
text='if residue already has spin-system',
tipText=tipText)
assignedResidueFrame.grid(row=2, column=1, sticky='nesw')
spectrumSelectionFrame = LabelFrame(self.frame, text='spectra')
spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw')
row = 0
Label(typeOfAssignmentFrame,
text='Resonances to Peak Dimensions',
grid=(row, 0))
self.peaksCheckButton = CheckButton(typeOfAssignmentFrame,
selected=True,
grid=(row, 1))
row += 1
Label(typeOfAssignmentFrame,
text='SpinSystems to Residues',
grid=(row, 0))
self.residuesCheckButton = CheckButton(
typeOfAssignmentFrame, selected=True, grid=(row, 1))
row = 0
Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0))
self.intraCheckButton = CheckButton(
peakSelectionFrame, selected=True, grid=(row, 1))
row += 1
Label(peakSelectionFrame, text='Sequential', grid=(row, 0))
self.sequentialCheckButton = CheckButton(
peakSelectionFrame, selected=True, grid=(row, 1))
row += 1
Label(peakSelectionFrame,
text='Do not assign diagonal peaks',
grid=(row, 0))
self.noDiagonalCheckButton = CheckButton(
peakSelectionFrame, selected=True, grid=(row, 1))
entries = ['Only assigned spin systems',
'All that have a score of at least: ',
'User Defined',
'Solution number:']
tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.',
'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.',
"As defined in the lower row of buttons in the 'results' tab.",
'One of the single solutions of the annealing.']
self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame,
entries=entries, grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(4, 1),
tipTexts=tipTexts)
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minScoreEntry = FloatEntry(spinSystemSelectionFrame,
grid=(1, 1), width=7,
text=str(self.minScore),
returnCallback=self.changeMinScore,
tipText=tipText)
self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+')
self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame,
grid=(3, 1), width=7, text=1,
returnCallback=self.solutionUpdate,
tipText=tipText)
self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+')
#self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w')
entries = ['all spectra', 'only:']
tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.',
'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.']
self.spectrumSelect = RadioButtons(spectrumSelectionFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1), tipTexts=tipTexts)
self.spectraPullDown = PulldownList(spectrumSelectionFrame,
self.changeSpectrum,
grid=(1, 1), sticky='w')
entries = ['skip this residue',
'de-assign old spin system from residue',
'assign, but never merge',
'warn to merge']
tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances",
"De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.",
"Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.",
"Ask to merge individually for each spin system, this might result in clicking on a lot of popups."]
self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1),
tipTexts=tipTexts)
texts = ['Transfer Assignments']
commands = [self.transferAssignments]
self.transferButton = ButtonList(
self.frame, commands=commands, texts=texts)
self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
def update(self):
'''Update the nescesary elements in the
tab. Is called when the algorithm
has produced possible assignments.
The only thing that has to be updated
in practice in this tab is the pulldown
with spectra.
'''
self.dataModel = self.guiParent.connector.results
self.updateSpectra()
def setDataModel(self, dataModel):
'''Here the dataModel, which is the dataModel
containing the suggested assignments body
the algorithm, can be set.
'''
self.dataModel = dataModel
self.update()
def updateSpectra(self, *opt):
'''Updates the spectra shown in the spectra
pulldown. These are only the spectra that
were used by the algorithm. All other spectra
in the project are not relevant since for those
no simulated peaks have been matched to real
peaks.
'''
if not self.dataModel:
return
spectrum = self.spectrum
spectra = self.dataModel.getSpectra()
if spectra:
names = [spectrum.name for spectrum in spectra]
index = 0
if self.spectrum not in spectra:
self.spectrum = spectra[0]
else:
index = spectra.index(self.spectrum)
self.spectraPullDown.setup(names, spectra, index)
def changeSpectrum(self, spectrum):
'''Select a spectum to be assigned.'''
self.spectrum = spectrum
def solutionUpdate(self, event=None, value=None):
'''Select a solution. A solution is a
one to one mapping of spin systems
to residues produced by one run of
the algorithm.
args: event: event object, this is
one of the values the number
entry calls his callback
function with.
value: the index of the solution/run.
'''
if not self.dataModel:
return
Nsolutions = len(self.dataModel.chain.residues[0].solutions)
if value is None:
value = self.solutionNumberEntry.get()
if value == self.selectedSolution:
return
else:
self.selectedSolution = value
if value < 1:
self.solutionNumberEntry.set(1)
self.selectedSolution = 1
elif value > Nsolutions:
self.selectedSolution = Nsolutions
self.solutionNumberEntry.set(self.selectedSolution)
else:
self.solutionNumberEntry.set(self.selectedSolution)
def fetchOptions(self):
'''Fetches user set options from the gui in
one go and stores them in their corresponding
instance variables.
'''
self.resonanceToDimension = self.peaksCheckButton.get()
self.spinSystemToResidue = self.residuesCheckButton.get()
self.intra = self.intraCheckButton.get()
self.sequential = self.sequentialCheckButton.get()
self.noDiagonal = self.noDiagonalCheckButton.get()
self.spinSystemType = self.spinSystemTypeSelect.getIndex()
self.strategy = ['skip', 'remove', 'noMerge', None][
self.assignedResidueStrategySelect.getIndex()]
self.allSpectra = [True, False][self.spectrumSelect.getIndex()]
def changeMinScore(self, event=None):
'''Set the minimal score for which a spin system
to residue assignment gets transferred to the
ccpn analysis project.
'''
newMinScore = self.minScoreEntry.get()
if self.minScore != newMinScore:
if newMinScore <= 50.0:
self.minScore = 51.0
self.minScoreEntry.set(51.0)
elif newMinScore > 100.0:
self.minScore = 100.0
self.minScoreEntry.set(100.0)
else:
self.minScore = newMinScore
def transferAssignments(self):
'''Transfer assignments to project depending
on the settings from the GUI.
'''
self.fetchOptions()
if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue):
return
strategy = self.strategy
lookupSpinSystem = [self.getAssignedSpinSystem,
self.getBestScoringSpinSystem,
self.getUserDefinedSpinSystem,
self.getSelectedSolutionSpinSystem][self.spinSystemType]
residues = self.dataModel.chain.residues
spinSystemSequence = [lookupSpinSystem(res) for res in residues]
ccpnSpinSystems = []
ccpnResidues = []
# if self.spinSystemType == 0 it means that it for sure already
# assigned like this
if self.spinSystemToResidue and not self.spinSystemType == 0:
for spinSys, res in zip(spinSystemSequence, residues):
if spinSys and res:
ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup())
ccpnResidues.append(res.getCcpnResidue())
assignSpinSystemstoResidues(ccpnSpinSystems,
ccpnResidues,
strategy=strategy,
guiParent=self.guiParent)
if self.resonanceToDimension:
allSpectra = self.allSpectra
if self.intra:
for residue, spinSystem in zip(residues, spinSystemSequence):
if not spinSystem:
continue
intraLink = residue.getIntraLink(spinSystem)
for pl in intraLink.getPeakLinks():
peak = pl.getPeak()
if not allSpectra and peak.getSpectrum() is not self.spectrum:
continue
if not peak:
continue
resonances = pl.getResonances()
if self.noDiagonal and len(set(resonances)) < len(resonances):
continue
for resonance, dimension in zip(resonances, peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
assignResToDim(ccpnDimension, ccpnResonance)
if self.sequential:
for residue, spinSystemA, spinSystemB in zip(residues,
spinSystemSequence,
spinSystemSequence[1:]):
if not spinSystemA or not spinSystemB:
continue
link = residue.getLink(spinSystemA, spinSystemB)
for pl in link.getPeakLinks():
peak = pl.getPeak()
if not allSpectra and peak.getSpectrum() is not self.spectrum:
continue
if not peak:
continue
resonances = pl.getResonances()
if self.noDiagonal and len(set(resonances)) < len(resonances):
continue
for resonance, dimension in zip(resonances, peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
assignResToDim(ccpnDimension, ccpnResonance)
self.guiParent.resultsTab.update()
def getAssignedSpinSystem(self, residue):
'''Get the spinSystem that is assigned in the project
to a residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
ccpCode = residue.ccpCode
seqCode = residue.getSeqCode()
spinSystems = self.dataModel.getSpinSystems()[ccpCode]
ccpnResidue = residue.getCcpnResidue()
if ccpnResidue:
assignedResonanceGroups = ccpnResidue.getResonanceGroups()
if len(assignedResonanceGroups) > 1:
print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % (seqCode)
return
assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup()
if assignedResonanceGroup:
for spinSystem in spinSystems:
if spinSystem.getSerial() == assignedResonanceGroup.serial:
# Just checking to make sure, analysis project could
# have changed
if not self.skipResidue(residue, spinSystem):
return spinSystem
def getBestScoringSpinSystem(self, residue):
'''Get the spinSystem that scores the highest,
i.e. is assigned in most of the runs to the
given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
solutions = residue.solutions
weigth = 1.0 / len(solutions)
score, bestSpinSystem = max([(solutions.count(solution) * weigth * 100.0, solution) for solution in solutions])
if score >= self.minScore and not bestSpinSystem.getIsJoker() and not self.skipResidue(residue, bestSpinSystem):
return bestSpinSystem
return None
def getUserDefinedSpinSystem(self, residue):
'''Get the spinSystem that is defined by the user
(probably in the resultsTab) as the correct
assignment of the given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
userDefinedSpinSystem = residue.userDefinedSolution
if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker() and not self.skipResidue(residue, userDefinedSpinSystem):
return userDefinedSpinSystem
return None
def getSelectedSolutionSpinSystem(self, residue):
'''I a solution corresponding to one specific run
of the algorithm is defined, return which spinSystem
in that run got assigned to the given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
solutions = residue.solutions
spinSystem = solutions[self.selectedSolution - 1]
if not spinSystem.getIsJoker() and not self.skipResidue(residue, spinSystem):
return spinSystem
return None
def skipResidue(self, residue, spinSystem):
'''One strategy is to skip all residues that
already have a spin system assignment.
If that is the case determine whether to
skip the given residue.
args: residue (src.cython.malandro.Residue)
spinSystem (src.cython.malandro.SpinSystem)
return: boolean, True if residue should be skipped.
'''
if self.strategy == 0:
assignedGroups = residue.getCcpnResidue().getResonanceGroups()
assignedSerials = set([spinSys.serial for spinSys in assignedGroups])
if assignedSerials and spinSystem.getSerial() not in assignedSerials:
return True
return False
class ObjectTablePopup(BasePopup):
def __init__(self, parent, root, metaclass, onlyShow=False, *args, **kw):
self.root = root
self.metaclass = metaclass
self.onlyShow = onlyShow
BasePopup.__init__(self,
parent,
title='Browser for %s objects' % metaclass.name,
location='+50+50',
*args,
**kw)
def body(self, master):
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
self.table = ObjectTable(master, self.metaclass)
self.table.grid(row=0, column=0, sticky=Tkinter.NSEW)
if (self.onlyShow):
texts = ['Close']
commands = [self.close]
else:
texts = ['Ok', 'Cancel']
commands = [self.ok, self.close]
self.buttons = ButtonList(master,
texts=texts,
commands=commands,
direction=Tkinter.HORIZONTAL,
expands=True)
self.buttons.grid(row=1, column=0, sticky=Tkinter.EW)
self.selected = None
self.setObjects()
self.doRegisters()
def doRegisters(self):
# do not need '' since dealing with keys
#for func in ('', '__init__', 'delete'):
for func in ('__init__', 'delete'):
self.registerNotify(self.setObjects,
self.metaclass.qualifiedName(), func)
# unregisters dealt with by BasePopup
def apply(self):
selected = self.table.currentObject
if (not selected):
showError('No selection', "No object selected", parent=self)
return False
self.selected = selected
return True
def setObjects(self, *extra):
objects = getAllObjects(self.root, self.metaclass)
self.table.setObjects(objects)
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def __init__(self, parent, project, path = None,
molTypeEntries = None, chemCompEntries = None,
selectedChemComps = None, selectLinking = None,
*args, **kw):
Frame.__init__(self, parent, *args, **kw)
self.project = project
self.molTypeEntries = molTypeEntries
self.chemCompEntries = chemCompEntries
self.selectLinking = selectLinking
if (not path):
path = getDataPath()
self.path = path
# Check if all chemComps available locally
self.path_allChemComps = getChemCompArchiveDataDir()
if not os.path.exists(self.path_allChemComps):
self.path_allChemComps = None
self.chemCompInfoDict = {}
self.chemCompInfoList = []
self.chemCompDownload = False
self.chem_comps_shown = {}
for entry in chemCompList:
self.chemCompClasses[entry] = getattr(ccp.api.molecule.ChemComp, entry)
self.grid_columnconfigure(0, weight=1)
row = 0
if (molTypeEntries is None):
headerText = "Show residues (select molecular type(s)):"
else:
headerText = "Show %s residues:" % (str(molTypeEntries))
#
#
# TODO TODO: HERE need to do some niftier stuff for displaying!
#
#
headerTextWidget = Label(self, text = headerText)
headerTextWidget.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
if (molTypeEntries is None):
self.mol_type_buttons = CheckButtons(self, entries=molTypeList,
select_callback=self.updateTables)
self.mol_type_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
else:
self.mol_type_buttons = None
#
# The chemComps to display...
#
self.showLocalText = 'Show local'
self.showWebText = 'Show available via web'
self.display_buttons = CheckButtons(self, entries=[self.showLocalText,self.showWebText],
select_callback=self.updateTables,
selected = [self.showLocalText])
self.display_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
self.grid_rowconfigure(row, weight=2)
headings = ('number', 'show details', 'molType', 'ccpCode', 'code1Letter', 'cifCode', 'name')
editWidgets = 7 * [ None ]
editGetCallbacks = [ None, self.toggleShow, None, None, None, None, None ]
editSetCallbacks = 7 * [ None ]
self.chem_comp_table = ScrolledMatrix(self, headingList=headings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.chem_comp_table.grid(row=row, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = [ 'Show all in details window', 'Clear details window' ]
commands = [ self.showAll, self.showNone ]
buttons = ButtonList(self, texts=texts, commands=commands)
buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
separator = Separator(self,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
headerTextWidget = Label(self, text = "Select the residue variant:")
headerTextWidget.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
if (chemCompEntries is None):
self.chem_comp_buttons = CheckButtons(self, entries=chemCompList,
selected=('ChemComp',),
select_callback=self.updateChemCompVarTable)
self.chem_comp_buttons.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
else:
self.chem_comp_buttons = None
self.grid_rowconfigure(row, weight=1)
headings = ('number', 'molType', 'ccpCode', 'linking', 'descriptor', 'molecularMass', 'formula', 'nonStereoSmiles', 'stereoSmiles')
self.chem_comp_var_table = ScrolledMatrix(self, headingList=headings)
self.chem_comp_var_table.grid(row=row, column=0, sticky=Tkinter.NSEW)
self.chem_comp_var_headings = headings[1:]
if selectedChemComps:
for chemComp in selectedChemComps:
key = (chemComp.molType, chemComp.ccpCode)
self.chem_comps_shown[key] = 1
self.updateTables()
class AssignMentTransferTab(object):
'''the tab in the GUI where assignments
can be transferred in bulk to the ccpn analysis
project. A difference is made between two types
of assignments:
1) spin systems to residues, which also
implies resonanceSets to atomSets.
2) resonances to peak dimensions.
The user is able to configure which assignments
should be transferred to the project.
Attributes:
guiParent: gui object this tab is part of.
frame: the frame in which this element lives.
dataModel(src.cython.malandro.DataModel): dataModel
object describing the assignment proposed by
the algorithm.
selectedSolution (int): The index of the solution/run
that is used asa the template to make the assignments.
resonanceToDimension (bool): True if resonances should
be assigned to peak dimensions. False if not.
spinSystemToResidue (bool): True if spin system to
residue assignment should be carried out.
minScore (float): The minimal score of a spin system
assignment to a residue to be allowed
to transfer this assignment to the project
intra (bool): True if intra-residual peaks should be
assigned.
sequential (bool): True if sequential peaks should be
assigned.
noDiagonal (bool): If True, purely diagonal peaks are
ignored during the transfer of assignments.
allSpectra (bool): If True, all spectra will be assigned.
If False, one specified spectrum will be assigned.
spectrum (src.cython.malandro.Spectrum): The spectrum
that should be assigned.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
# Buttons and fields,
# will be set in body():
self.peaksCheckButton = None
self.residuesCheckButton = None
self.intraCheckButton = None
self.sequentialCheckButton = None
self.noDiagonalCheckButton = None
self.spinSystemTypeSelect = None
self.minScoreEntry = None
self.solutionNumberEntry = None
self.spectrumSelect = None
self.spectraPullDown = None
self.assignedResidueStrategySelect = None
self.transferButton = None
# Settings that determine how assignments
# are transferred to the analysis project:
self.minScore = 80.0
self.dataModel = None
self.spectrum = None
self.selectedSolution = 1
self.body()
self.resonanceToDimension = True
self.spinSystemToResidue = True
self.intra = True
self.sequential = True
self.noDiagonal = True
self.allSpectra = True
self.spinSystemType = 0
self.strategy = 0
def body(self):
'''Describes the body of this tab. It consists
out of a number of radio buttons, check buttons
and number entries that allow the user to
indicate which assignments should be transferred.
'''
# self.frame.expandColumn(0)
self.frame.expandGrid(8, 0)
self.frame.expandGrid(8, 1)
typeOfAssignmentFrame = LabelFrame(self.frame,
text='type of assignment')
typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw')
# typeOfAssignmentFrame.expandGrid(0,5)
peakSelectionFrame = LabelFrame(self.frame,
text='which peaks to assign')
peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2)
spinSystemSelectionFrame = LabelFrame(self.frame,
text='Which spin-systems to use')
spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw')
tipText = 'What to do when a residue has already a spin system assigned to it.'
assignedResidueFrame = LabelFrame(
self.frame,
text='if residue already has spin-system',
tipText=tipText)
assignedResidueFrame.grid(row=2, column=1, sticky='nesw')
spectrumSelectionFrame = LabelFrame(self.frame, text='spectra')
spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw')
row = 0
Label(typeOfAssignmentFrame,
text='Resonances to Peak Dimensions',
grid=(row, 0))
self.peaksCheckButton = CheckButton(typeOfAssignmentFrame,
selected=True,
grid=(row, 1))
row += 1
Label(typeOfAssignmentFrame,
text='SpinSystems to Residues',
grid=(row, 0))
self.residuesCheckButton = CheckButton(typeOfAssignmentFrame,
selected=True,
grid=(row, 1))
row = 0
Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0))
self.intraCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
row += 1
Label(peakSelectionFrame, text='Sequential', grid=(row, 0))
self.sequentialCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
row += 1
Label(peakSelectionFrame,
text='Do not assign diagonal peaks',
grid=(row, 0))
self.noDiagonalCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
entries = [
'Only assigned spin systems',
'All that have a score of at least: ', 'User Defined',
'Solution number:'
]
tipTexts = [
'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.',
'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.',
"As defined in the lower row of buttons in the 'results' tab.",
'One of the single solutions of the annealing.'
]
self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(4, 1),
tipTexts=tipTexts)
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minScoreEntry = FloatEntry(spinSystemSelectionFrame,
grid=(1, 1),
width=7,
text=str(self.minScore),
returnCallback=self.changeMinScore,
tipText=tipText)
self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+')
self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame,
grid=(3, 1),
width=7,
text=1,
returnCallback=self.solutionUpdate,
tipText=tipText)
self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+')
#self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w')
entries = ['all spectra', 'only:']
tipTexts = [
'Assign peaks in all the spectra that where selected before the annealing ran.',
'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'
]
self.spectrumSelect = RadioButtons(spectrumSelectionFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1),
tipTexts=tipTexts)
self.spectraPullDown = PulldownList(spectrumSelectionFrame,
self.changeSpectrum,
grid=(1, 1),
sticky='w')
entries = [
'skip this residue', 'de-assign old spin system from residue',
'assign, but never merge', 'warn to merge'
]
tipTexts = [
"Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances",
"De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.",
"Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.",
"Ask to merge individually for each spin system, this might result in clicking on a lot of popups."
]
self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1),
tipTexts=tipTexts)
texts = ['Transfer Assignments']
commands = [self.transferAssignments]
self.transferButton = ButtonList(self.frame,
commands=commands,
texts=texts)
self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
def update(self):
'''Update the nescesary elements in the
tab. Is called when the algorithm
has produced possible assignments.
The only thing that has to be updated
in practice in this tab is the pulldown
with spectra.
'''
self.dataModel = self.guiParent.connector.results
self.updateSpectra()
def setDataModel(self, dataModel):
'''Here the dataModel, which is the dataModel
containing the suggested assignments body
the algorithm, can be set.
'''
self.dataModel = dataModel
self.update()
def updateSpectra(self, *opt):
'''Updates the spectra shown in the spectra
pulldown. These are only the spectra that
were used by the algorithm. All other spectra
in the project are not relevant since for those
no simulated peaks have been matched to real
peaks.
'''
if not self.dataModel:
return
spectrum = self.spectrum
spectra = self.dataModel.getSpectra()
if spectra:
names = [spectrum.name for spectrum in spectra]
index = 0
if self.spectrum not in spectra:
self.spectrum = spectra[0]
else:
index = spectra.index(self.spectrum)
self.spectraPullDown.setup(names, spectra, index)
def changeSpectrum(self, spectrum):
'''Select a spectum to be assigned.'''
self.spectrum = spectrum
def solutionUpdate(self, event=None, value=None):
'''Select a solution. A solution is a
one to one mapping of spin systems
to residues produced by one run of
the algorithm.
args: event: event object, this is
one of the values the number
entry calls his callback
function with.
value: the index of the solution/run.
'''
if not self.dataModel:
return
Nsolutions = len(self.dataModel.chain.residues[0].solutions)
if value is None:
value = self.solutionNumberEntry.get()
if value == self.selectedSolution:
return
else:
self.selectedSolution = value
if value < 1:
self.solutionNumberEntry.set(1)
self.selectedSolution = 1
elif value > Nsolutions:
self.selectedSolution = Nsolutions
self.solutionNumberEntry.set(self.selectedSolution)
else:
self.solutionNumberEntry.set(self.selectedSolution)
def fetchOptions(self):
'''Fetches user set options from the gui in
one go and stores them in their corresponding
instance variables.
'''
self.resonanceToDimension = self.peaksCheckButton.get()
self.spinSystemToResidue = self.residuesCheckButton.get()
self.intra = self.intraCheckButton.get()
self.sequential = self.sequentialCheckButton.get()
self.noDiagonal = self.noDiagonalCheckButton.get()
self.spinSystemType = self.spinSystemTypeSelect.getIndex()
self.strategy = ['skip', 'remove', 'noMerge',
None][self.assignedResidueStrategySelect.getIndex()]
self.allSpectra = [True, False][self.spectrumSelect.getIndex()]
def changeMinScore(self, event=None):
'''Set the minimal score for which a spin system
to residue assignment gets transferred to the
ccpn analysis project.
'''
newMinScore = self.minScoreEntry.get()
if self.minScore != newMinScore:
if newMinScore <= 50.0:
self.minScore = 51.0
self.minScoreEntry.set(51.0)
elif newMinScore > 100.0:
self.minScore = 100.0
self.minScoreEntry.set(100.0)
else:
self.minScore = newMinScore
def transferAssignments(self):
'''Transfer assignments to project depending
on the settings from the GUI.
'''
self.fetchOptions()
if not self.dataModel or (not self.resonanceToDimension
and not self.spinSystemToResidue):
return
strategy = self.strategy
lookupSpinSystem = [
self.getAssignedSpinSystem, self.getBestScoringSpinSystem,
self.getUserDefinedSpinSystem, self.getSelectedSolutionSpinSystem
][self.spinSystemType]
residues = self.dataModel.chain.residues
spinSystemSequence = [lookupSpinSystem(res) for res in residues]
ccpnSpinSystems = []
ccpnResidues = []
# if self.spinSystemType == 0 it means that it for sure already
# assigned like this
if self.spinSystemToResidue and not self.spinSystemType == 0:
for spinSys, res in zip(spinSystemSequence, residues):
if spinSys and res:
ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup())
ccpnResidues.append(res.getCcpnResidue())
assignSpinSystemstoResidues(ccpnSpinSystems,
ccpnResidues,
strategy=strategy,
guiParent=self.guiParent)
if self.resonanceToDimension:
allSpectra = self.allSpectra
if self.intra:
for residue, spinSystem in zip(residues, spinSystemSequence):
if not spinSystem:
continue
intraLink = residue.getIntraLink(spinSystem)
for pl in intraLink.getPeakLinks():
peak = pl.getPeak()
if not allSpectra and peak.getSpectrum(
) is not self.spectrum:
continue
if not peak:
continue
resonances = pl.getResonances()
if self.noDiagonal and len(
set(resonances)) < len(resonances):
continue
for resonance, dimension in zip(
resonances, peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
assignResToDim(ccpnDimension, ccpnResonance)
if self.sequential:
for residue, spinSystemA, spinSystemB in zip(
residues, spinSystemSequence, spinSystemSequence[1:]):
if not spinSystemA or not spinSystemB:
continue
link = residue.getLink(spinSystemA, spinSystemB)
for pl in link.getPeakLinks():
peak = pl.getPeak()
if not allSpectra and peak.getSpectrum(
) is not self.spectrum:
continue
if not peak:
continue
resonances = pl.getResonances()
if self.noDiagonal and len(
set(resonances)) < len(resonances):
continue
for resonance, dimension in zip(
resonances, peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
assignResToDim(ccpnDimension, ccpnResonance)
self.guiParent.resultsTab.update()
def getAssignedSpinSystem(self, residue):
'''Get the spinSystem that is assigned in the project
to a residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
ccpCode = residue.ccpCode
seqCode = residue.getSeqCode()
spinSystems = self.dataModel.getSpinSystems()[ccpCode]
ccpnResidue = residue.getCcpnResidue()
if ccpnResidue:
assignedResonanceGroups = ccpnResidue.getResonanceGroups()
if len(assignedResonanceGroups) > 1:
print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % (
seqCode)
return
assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup()
if assignedResonanceGroup:
for spinSystem in spinSystems:
if spinSystem.getSerial() == assignedResonanceGroup.serial:
# Just checking to make sure, analysis project could
# have changed
if not self.skipResidue(residue, spinSystem):
return spinSystem
def getBestScoringSpinSystem(self, residue):
'''Get the spinSystem that scores the highest,
i.e. is assigned in most of the runs to the
given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
solutions = residue.solutions
weigth = 1.0 / len(solutions)
score, bestSpinSystem = max([
(solutions.count(solution) * weigth * 100.0, solution)
for solution in solutions
])
if score >= self.minScore and not bestSpinSystem.getIsJoker(
) and not self.skipResidue(residue, bestSpinSystem):
return bestSpinSystem
return None
def getUserDefinedSpinSystem(self, residue):
'''Get the spinSystem that is defined by the user
(probably in the resultsTab) as the correct
assignment of the given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
userDefinedSpinSystem = residue.userDefinedSolution
if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker(
) and not self.skipResidue(residue, userDefinedSpinSystem):
return userDefinedSpinSystem
return None
def getSelectedSolutionSpinSystem(self, residue):
'''I a solution corresponding to one specific run
of the algorithm is defined, return which spinSystem
in that run got assigned to the given residue.
args: residue (src.cython.malandro.Residue)
return: spinSystem (src.cython.malandro.SpinSystem)
'''
solutions = residue.solutions
spinSystem = solutions[self.selectedSolution - 1]
if not spinSystem.getIsJoker() and not self.skipResidue(
residue, spinSystem):
return spinSystem
return None
def skipResidue(self, residue, spinSystem):
'''One strategy is to skip all residues that
already have a spin system assignment.
If that is the case determine whether to
skip the given residue.
args: residue (src.cython.malandro.Residue)
spinSystem (src.cython.malandro.SpinSystem)
return: boolean, True if residue should be skipped.
'''
if self.strategy == 0:
assignedGroups = residue.getCcpnResidue().getResonanceGroups()
assignedSerials = set(
[spinSys.serial for spinSys in assignedGroups])
if assignedSerials and spinSystem.getSerial(
) not in assignedSerials:
return True
return False
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
class CloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 50
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.peakListDict = {}
self.noesyPeakList = None
self.tocsyPeakList = None
self.noesy3dPeakList = None
self.hsqcPeakList = None
self.maxIntens = 37000000
self.resonances = None
self.origResonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.numClouds = 100
self.filePrefix = 'cloud_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
self.structure = None
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Resonance Clouds Analysis",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
self.adcAtomTypes = name
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
resonances = []
for constraint in self.distanceConstraintList.constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
startMdProcess(self.numClouds, self.distanceConstraintList,
resonances, self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def showPeaks(self):
self.guiParent.viewPeaks(peaks=self.noesyPeaks)
def showResonances(self):
pass
#self.guiParent.viewResonances(resonances=self.resonances)
def setupResonances(self):
if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList:
disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList,
self.tocsyPeakList, self.hsqcPeakList)
(self.origResonances, self.noesyPeaks,
null) = getCloudsResonanceList(self.guiParent.argumentServer,
hsqcPeakList=self.hsqcPeakList,
tocsy3dPeakList=self.tocsyPeakList,
noesy2dPeakList=self.noesyPeakList)
self.setButtonStates()
def setButtonStates(self):
if self.origResonances:
self.label03a.set('Resonances found: %d' %
(len(self.origResonances)))
if self.noesyPeaks:
self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks)))
if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList:
self.setupButtons.buttons[0].enable()
else:
self.setupButtons.buttons[0].disable()
if self.noesyPeaks:
self.setupButtons.buttons[1].enable()
else:
self.setupButtons.buttons[1].disable()
if self.origResonances:
self.setupButtons.buttons[2].enable()
else:
self.setupButtons.buttons[2].disable()
if self.noesyPeaks and self.origResonances:
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.midgeButtons.buttons[1].enable()
self.distConstrLabel.set(
'Distance constraints: %d' %
len(self.distanceConstraintList.constraints))
else:
self.distConstrLabel.set('Distance constraints:')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
'Anti-distance constraints: %d' %
len(self.antiDistConstraintList.constraints))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('Anti-distance constraints:')
self.midgeButtons.buttons[2].disable()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
def getNoesys(self):
names = []
spectra = getSpectraByType(self.project, '2dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
self.noesyPeakList = self.peakListDict[name]
self.setButtonStates()
def getTocsys(self):
names = []
spectra = getSpectraByType(self.project, '3dTOCSY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.tocsyPeakList:
self.tocsyPeakList = peakList
return names
def getNoesy3ds(self):
names = []
spectra = getSpectraByType(self.project, '3dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesy3dPeakList:
self.noesy3dPeakList = peakList
return names
def setTocsy(self, index, name=None):
if not name:
name = self.tocsyPulldown.getSelected()
self.tocsyPeakList = self.peakListDict[name]
self.setButtonStates()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
self.noesy3dPeakList = self.peakListDict[name]
self.setButtonStates()
def getHsqcs(self):
names = []
spectra = getSpectraByType(self.project, 'HSQC')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.hsqcPeakList:
self.hsqcPeakList = peakList
return names
def setHsqc(self, index, name=None):
if not name:
name = self.hsqcPulldown.getSelected()
self.hsqcPeakList = self.peakListDict[name]
self.setButtonStates()
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def getMaxIntens(self, obj):
self.maxIntensEntry.set(self.maxIntens)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def setMaxIntens(self, event):
value = self.maxIntensEntry.get()
if value is not None:
self.maxIntens = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
class BrowseStrucGenPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.strucGen = None
self.violList = None
self.constrList = None
self.waiting = 0
BasePopup.__init__(self,
parent=parent,
title="Structure Generation Runs",
**kw)
#self.geometry("+150+150")
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
strucGenFrame = LabelFrame(guiFrame, text='Generation Runs')
strucGenFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
strucGenFrame.grid_columnconfigure(0, weight=1)
strucGenFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=0)
#self.editDetailsEntry = Entry(self,text='',returnCallback = self.setDetails, width=12)
#editWidgets = [None, None, None, None, None, self.editDetailsEntry]
#editGetCallbacks = [None, None, None, None, None, self.getDetails]
#editSetCallbacks = [None, None, None, None, None, self.setDetails]
colHeadings = [
'#', 'Constraint\nLists', 'Violation\nLists', 'Structures',
'Fixed\nAtom Sets', 'Fixes\nResonance Sets', 'Chain\nStates',
'Database\nEntries', 'Resonance\nClouds'
]
editWidgets = [None, None, None, None, None, None, None, None, None]
editGetCallbacks = [
None, None, None, None, None, None, None, None, None
]
editSetCallbacks = [
None, None, None, None, None, None, None, None, None
]
self.structGenMatrix = ScrolledMatrix(
strucGenFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=3,
initialCols=6,
headingList=colHeadings,
callback=self.selectStructGenCell,
objectList=[],
textMatrix=[
[],
])
self.structGenMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Structures', 'Delete']
commands = [self.viewStructures, self.deleteStrucGen]
self.structGenButtons = ButtonList(strucGenFrame,
texts=texts,
expands=True,
commands=commands)
self.structGenButtons.grid(row=1, column=0, sticky='ew')
row += 1
constrFrame = LabelFrame(guiFrame, text='Constraint Lists')
constrFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
constrFrame.grid_columnconfigure(0, weight=1)
constrFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = [
'#', 'Type', 'Name', 'Constraints', 'Experiments', 'Details',
'Unit'
]
editWidgets = [None, None, None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None, None, None]
self.constrListMatrix = ScrolledMatrix(
constrFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=10,
headingList=colHeadings,
callback=self.selectConstrListCell,
objectList=[],
textMatrix=[
[],
])
self.constrListMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Constraints', 'Create List', 'Delete List']
commands = [
self.viewConstraints, self.createConstraints,
self.deleteConstraints
]
self.constrListButtons = ButtonList(constrFrame,
texts=texts,
expands=True,
commands=commands)
self.constrListButtons.grid(row=1, column=0, sticky='ew')
self.constrListButtons.buttons[1].disable()
row += 1
violFrame = LabelFrame(guiFrame, text='Violation Lists')
violFrame.grid(row=row, column=0, columnspan=1, sticky='nsew')
violFrame.grid_columnconfigure(0, weight=1)
violFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = [
'#',
'Violations',
'Structures',
'Details',
]
editWidgets = [None, None, None, None]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.violListMatrix = ScrolledMatrix(violFrame,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
initialRows=10,
headingList=colHeadings,
callback=self.selectViolListCell,
objectList=[],
textMatrix=[
[],
])
self.violListMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['View Violations', 'Delete List']
commands = [self.viewViolations, self.deleteViolations]
self.violListButtons = ButtonList(violFrame,
texts=texts,
expands=True,
commands=commands)
self.violListButtons.grid(row=1, column=0, sticky='ew')
row += 1
self.bottomButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, columnspan=1, sticky='ew')
self.update()
for func in ('__init__', 'delete', 'setName', 'setDetails', 'setUnit',
'setExperiments', 'addExperiment', 'removeExperiment'):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraintList',
'ccp.nmr.Nmr.DihedralConstraintList',
'ccp.nmr.Nmr.DistanceConstraintList',
'ccp.nmr.Nmr.HBondConstraintList',
'ccp.nmr.Nmr.JCouplingConstraintList',
'ccp.nmr.Nmr.RdcConstraintList'):
self.registerNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraint',
'ccp.nmr.Nmr.DihedralConstraint',
'ccp.nmr.Nmr.DistanceConstraint',
'ccp.nmr.Nmr.HBondConstraint',
'ccp.nmr.Nmr.JCouplingConstraint',
'ccp.nmr.Nmr.RdcConstraint'):
self.registerNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete', 'setChainStates', 'addChainState',
'removeChainState', 'addEntry', 'removeEntry',
'setResStructures', 'addResStructure', 'setEntries',
'removeResStructure', 'setStructures', 'addStructure',
'removeStructure'):
self.registerNotify(self.updateAfter,
'ccp.nmr.Nmr.StructureGeneration', func)
for func in ('__init__', 'delete', 'setDetails'):
for clazz in ('ccp.nmr.Nmr.ViolationList', ):
self.registerNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.Violation', ):
self.registerNotify(self.updateAfter, clazz, func)
def open(self):
self.updateAfter()
BasePopup.open(self)
def deleteViolations(self):
if self.violList and showOkCancel(
'Confirm', 'Really delete violation list?', parent=self):
self.violList.delete()
self.violList = None
self.violListButtons.buttons[0].disable()
self.violListButtons.buttons[1].disable()
def deleteConstraints(self):
if self.constrList and showOkCancel(
'Confirm', 'Really delete constraint list?', parent=self):
self.constrList.delete()
self.constrList = None
self.constrListButtons.buttons[0].disable()
self.constrListButtons.buttons[2].disable()
def createConstraints(self):
pass
def viewViolations(self):
self.guiParent.browseViolations()
popup = self.guiParent.popups['browse_violations']
popup.structGen = self.strucGen
popup.violList = self.violList
popup.updateAfter()
def viewConstraints(self):
self.guiParent.browseConstraints()
popup = self.guiParent.popups['browse_constraints']
popup.structGen = self.strucGen
popup.constrList = self.constrList
popup.updateAfter()
def viewStructures(self):
self.guiParent.editStructures()
popup = self.guiParent.popups['edit_structures']
popup.structGen = self.strucGen
popup.updateAfter()
def deleteStrucGen(self):
if self.strucGen and showOkCancel(
'Confirm', 'Really delete structure generation run?',
parent=self):
self.strucGen.delete()
self.strucGen = None
self.constrList = None
self.violist = None
self.structGenButtons.buttons[0].disable()
self.structGenButtons.buttons[1].disable()
def selectStructGenCell(self, strucGen, row, col):
self.strucGen = strucGen
if strucGen:
self.structGenButtons.buttons[1].enable()
if len(strucGen.molStructures) > 0:
self.structGenButtons.buttons[0].enable()
if self.constrList and (self.constrList.structureGeneration
is not self.strucGen):
self.constrList = None
self.updateConstrLists(self.strucGen)
def selectConstrListCell(self, constrList, row, col):
self.constrList = constrList
if constrList:
self.constrListButtons.buttons[0].enable()
self.constrListButtons.buttons[2].enable()
def selectViolListCell(self, violList, row, col):
self.violList = violList
if violList:
self.violListButtons.buttons[0].enable()
self.violListButtons.buttons[1].enable()
def updateAfter(self, object=None):
if self.waiting:
return
strucGen = None
name = object.className
if name == 'StructureGeneration':
self.waiting = True
self.after_idle(self.update)
return
elif name == 'ViolationList':
strucGen = object.structureGeneration
elif name == 'Violation':
strucGen = object.violationList.structureGeneration
elif name[-14:] == 'ConstraintList':
strucGen = object.structureGeneration
elif name[-10:] == 'Constraint':
strucGen = object.parentList.structureGeneration
if (object is None) or (strucGen is self.strucGen):
self.waiting = True
self.after_idle(self.update)
def destroy(self):
for func in ('__init__', 'delete', 'setName', 'setDetails', 'setUnit',
'setExperiments', 'addExperiment', 'removeExperiment'):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraintList',
'ccp.nmr.Nmr.DihedralConstraintList',
'ccp.nmr.Nmr.DistanceConstraintList',
'ccp.nmr.Nmr.HBondConstraintList',
'ccp.nmr.Nmr.JCouplingConstraintList',
'ccp.nmr.Nmr.RdcConstraintList'):
self.unregisterNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.ChemShiftConstraint',
'ccp.nmr.Nmr.DihedralConstraint',
'ccp.nmr.Nmr.DistanceConstraint',
'ccp.nmr.Nmr.HBondConstraint',
'ccp.nmr.Nmr.JCouplingConstraint',
'ccp.nmr.Nmr.RdcConstraint'):
self.unregisterNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete', 'setChainStates', 'addChainState',
'removeChainState', 'addEntry', 'removeEntry',
'setResStructures', 'addResStructure', 'setEntries',
'removeResStructure', 'setStructures', 'addStructure',
'removeStructure'):
self.unregisterNotify(self.updateAfter,
'ccp.nmr.Nmr.StructureGeneration', func)
for func in ('__init__', 'delete', 'setDetails'):
for clazz in ('ccp.nmr.Nmr.ViolationList', ):
self.unregisterNotify(self.updateAfter, clazz, func)
for func in (
'__init__',
'delete',
):
for clazz in ('ccp.nmr.Nmr.Violation', ):
self.unregisterNotify(self.updateAfter, clazz, func)
BasePopup.destroy(self)
def updateConstrLists(self, *opt):
strucGen = self.strucGen
objectList = []
textMatrix = []
if strucGen:
for constraintList in strucGen.constraintLists:
objectList.append(constraintList)
else:
textMatrix.append([])
for constrList in objectList:
datum = []
expText = ''
for e in constrList.experiments:
if expText:
expText += ' '
expText += e.name
datum.append(constrList.serial)
datum.append(constrList.className[0:-14])
datum.append(constrList.name)
datum.append(len(constrList.constraints))
datum.append(expText)
datum.append(constrList.details)
datum.append(constrList.unit)
textMatrix.append(datum)
if self.constrList:
self.constrListButtons.buttons[0].enable()
self.constrListButtons.buttons[2].enable()
else:
self.constrListButtons.buttons[0].disable()
self.constrListButtons.buttons[2].disable()
self.constrListMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateViolLists(self, *opt):
strucGen = self.strucGen
objectList = []
textMatrix = []
if strucGen:
for violationList in strucGen.violationLists:
objectList.append(violationList)
else:
textMatrix.append([])
for violationList in objectList:
datum = []
datum.append(violationList.serial)
datum.append(len(violationList.violations))
datum.append(len(violationList.molStructures))
datum.append(violationList.details)
textMatrix.append(datum)
if self.violList:
self.violListButtons.buttons[0].enable()
self.violListButtons.buttons[1].enable()
else:
self.violListButtons.buttons[0].disable()
self.violListButtons.buttons[1].disable()
self.violListMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def update(self):
objectList = []
textMatrix = []
project = self.project
for strucGen in self.nmrProject.structureGenerations:
objectList.append(strucGen)
if not objectList:
textMatrix.append([])
for strucGen in objectList:
datum = []
datum.append(strucGen.serial)
datum.append(len(strucGen.constraintLists))
datum.append(len(strucGen.violationLists))
datum.append(len(strucGen.molStructures))
datum.append(len(strucGen.fixedAtomSets))
datum.append(len(strucGen.fixedResonanceSets))
datum.append(len(strucGen.chainStates))
datum.append(len(strucGen.entries))
datum.append(len(strucGen.resStructures))
textMatrix.append(datum)
if not self.strucGen:
self.structGenButtons.buttons[0].disable()
self.structGenButtons.buttons[1].disable()
self.structGenMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.updateConstrLists()
self.updateViolLists()
self.waiting = False
class BrowsePeakGroupsPopup(BasePopup):
"""
**Display Groups of Peaks Linked by a Root Assignment**
This popup window is used to display the results of operations in Analysis that
generate grouped peaks, usually linked by virtue of a common 'root' assignment.
For example a selected set of peaks may be macthed to other peaks with
similar positions in a spectrum dimension, where each group corresponds
to a separate C-H or N-H position. For example the right-click
window menu option "Locate Peaks::Match multiple peaks" generates
such groupings to find rows or columns of peaks that share chemical shifts.
Whatever operation generated the groups, they are listed in ranked order in the
table; best scoring at the top. The number of peaks in the group and any common
assigment and position is also listed. The idea is that the groups are candidates
for some searh or macthing process that the user triggered. The best scoring
groups may be used to control the spectrum window display, thus displaying any
peak matches, by using [Display Groups in Strips] after selecting an approprate
window. This system is often used for NOESY experiments where resonances that are
close in space share common sets of peak positions; they are close to the same
set of other resonances.
"""
def __init__(self, parent, *args, **kw):
self.groups = []
self.variableDim = 1
self.windowPane = None
self.rulers = []
self.peakLists = []
self.orthogonalDict = {}
self.parent = parent
self.searchPeaks = []
BasePopup.__init__(self, parent, title= "Peak Groups", borderwidth=5, **kw)
def body(self, guiFrame):
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = LabelFrame(guiFrame, text='Matched Peak Groups')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
frame.grid(row=row, sticky='nsew')
headingList, tipTexts = self.getHeadingList()
self.scrolledMatrix = ScrolledMatrix(frame, initialRows=15, multiSelect=True,
headingList=headingList, tipTexts=tipTexts,
grid=(0,0), gridSpan=(1,3))
tipTexts = ['Remove the selected peak groups from the table',
'Show 1D positional ruler lines for the selected groups',
'Remove any ruler lines previously added for peak group',
'Display selected peak groups within strips of selected window']
texts = ['Remove\nGroups','Show\nRulers',
'Delete\nRulers','Display Groups\nIn Strips']
commands = [self.removeGroups,self.addRulers,
self.removeRulers,self.stripGroups]
self.buttons = ButtonList(frame, texts=texts, commands=commands, tipTexts=tipTexts)
self.buttons.grid(row=1, column=0, sticky='ew')
tipText = 'Selects the spectrum window in which to display strips & ruler lines'
label = Label(frame, text='Target window:', grid=(1,1))
self.windowPulldown = PulldownList(frame, callback=None,
grid=(1,2), tipText=tipText)
row+= 1
bottomButtons = UtilityButtonList(guiFrame, helpUrl=self.help_url, expands=True, doClone=False)
bottomButtons.grid(row = row, sticky = 'ew')
self.update()
for func in ('__init__', 'delete', 'setName'):
self.registerNotify(self.updateWindowsAfter, 'ccpnmr.Analysis.SpectrumWindow', func)
def open(self):
self.update()
BasePopup.open(self)
def updateWindowsAfter(self, opt=None):
self.after_idle(self.updateWindows)
def updateWindows(self):
if not self.groups:
self.windowPulldown.clear()
return
selected = self.windowPulldown.getText()
groups = self.scrolledMatrix.currentObjects or self.groups
self.orthogonalDict = {}
windowPane = self.windowPane
if windowPane and groups:
meanVarPos = 0.0
for peak in groups[0][2]:
meanVarPos += peak.sortedPeakDims()[self.variableDim].value
meanVarPos /= float(len(groups[0][2]))
xyz = []
for score, coords0, peaks in groups:
peak = peaks[0]
peakDims = peak.sortedPeakDims()
dimMapping = getPeakDimAxisMapping(peak, self.windowPane)
coords = list(coords0)
coords.insert(self.variableDim, meanVarPos)
posDict = {}
for i, peakDim in enumerate(peakDims):
posDict[peakDim] = coords[i]
pos = []
for axisPanel in windowPane.sortedAxisPanels():
peakDim = dimMapping[axisPanel.label]
pos.append( posDict[peakDim] )
xyz.append(pos)
windowZPlanes = findOrthogonalWindows(windowPane, xyz,
excludeQuery=False)
for windowPosition in windowZPlanes:
if windowPosition:
key, pane, xyz = windowPosition
self.orthogonalDict[key] = (pane, xyz)
xyPlaneKeys = self.orthogonalDict.keys()
xyPlaneKeys.sort()
if xyPlaneKeys:
index = min(self.windowPulldown.index, len(xyPlaneKeys)-1)
if selected in xyPlaneKeys:
index = xyPlaneKeys.index(selected)
self.windowPulldown.setup(xyPlaneKeys, xyPlaneKeys, index)
def removeGroups(self):
groups = self.scrolledMatrix.currentObjects
if groups:
newGroups = []
for group in self.groups:
if group not in groups:
newGroups.append(group)
self.update(groups=newGroups)
def stripGroups(self):
self.updateWindows()
name = self.windowPulldown.getText()
groups = self.scrolledMatrix.currentObjects
if groups and name and (name != '<None>'):
selected = self.windowPulldown.getText()
windowPane, positions = self.orthogonalDict[selected]
window = windowPane.spectrumWindow
N = len(positions)
msg = '%d positions selected. Really make %d strips in window %s'
if N > 10 and not showOkCancel('Warning', msg % (N,N,window.name ), parent=self):
return
displayStrips(self.parent, positions, orthoPositions=None,
spectrum=None, windowPane=windowPane)
# often fails first time...
self.update_idletasks()
displayStrips(self.parent, positions, orthoPositions=None,
spectrum=None, windowPane=windowPane)
def removeRulers(self):
for ruler in self.rulers:
if not ruler.isDeleted:
ruler.delete()
self.rulers = []
def addRulers(self):
groups = self.scrolledMatrix.currentObjects
if groups and self.windowPane:
positions = []
panelTypes = []
for peak in self.searchPeaks:
peakDim = peak.sortedPeakDims()[self.variableDim]
dimMapping = getPeakDimAxisMapping(peak, self.windowPane)
for axisPanel in self.windowPane.axisPanels:
if dimMapping[axisPanel.label] is peakDim:
positions.append(peakDim.value)
panelTypes.append(axisPanel.panelType)
break
color = '#808080'
for i in range(len(positions)):
ruler = createRuler(positions[i], panelTypes[i],
dashLength=3, gapLength=1,
color=color, remove=False)
self.rulers.append(ruler)
def update(self, groups=None, variableDim=None,
peakLists=None, searchPeaks=None):
self.removeRulers()
if groups is not None:
self.groups = groups
if variableDim is not None:
self.variableDim = variableDim
if peakLists:
self.peakLists = peakLists
spectrum = self.peakLists[0].dataSource
for spectrumWindow in self.analysisProject.spectrumWindows:
for windowPane in spectrumWindow.spectrumWindowPanes:
if isSpectrumInWindowPane(windowPane, spectrum):
if len(windowPane.axisPanels) == len(spectrum.dataDims):
self.windowPane = windowPane
break
self.searchPeaks = searchPeaks or []
objectList = []
textMatrix = []
for i, group in enumerate(self.groups):
(score,positions,peaks) = group
datum = ['%d' % (i+1),
'%f' % score,
'%d' % len(peaks)]
annotations = []
for j in range(len(peaks[0].peakDims)):
if j != self.variableDim:
annotation = ''
for peak in peaks:
peakDims = peak.sortedPeakDims()
peakDim = peakDims[j]
if peakDim.annotation:
if annotation and (annotation != peakDim.annotation):
annotation = '*'
else:
annotation = peakDim.annotation
annotations.append(annotation)
datum.append(' '.join(annotations))
for position in positions:
datum.append('%f' % position)
objectList.append(group)
textMatrix.append(datum)
headingList, tipTexts = self.getHeadingList()
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList,
headingList=headingList,
tipTexts=tipTexts)
self.updateWindows()
def getHeadingList(self):
tipTexts = ['The ranking of the peak group, comparing its score with others',
'The match score of the peak group',
'Number of peaks within the matched peak group',
'The root (usually amide) assignment, common to peaks in a group']
headingList = ['Rank','Score','Num\npeaks','Root\nAssignment']
if self.groups:
n = len( self.groups[0][2][0].peakDims )
for i in range(n):
if i != self.variableDim:
headingList.append( 'F%d position' % (i+1) )
tipTexts.append('Average location of the group in the F%d dimension' % (i+1))
else:
headingList.extend(['F1 position','F2 position'])
tipTexts.append('Average location of the group in the F1 dimension')
tipTexts.append('Average location of the group in the F2 dimension')
return headingList, tipTexts
def destroy(self):
for func in ('__init__', 'delete', 'setName'):
self.unregisterNotify(self.updateWindowsAfter, 'ccpnmr.Analysis.SpectrumWindow', func)
BasePopup.destroy(self)
def __init__(self,
parent,
objects=None,
attributes=None,
attributeHeadings=None,
attributeLabel='Attribute',
widgetClasses=None,
constructorArg=None,
constructorKw=None,
tableHeading='Dimension',
tableHeadingOffset=1,
callback=None,
attributeDirection=Tkinter.VERTICAL,
includeResetUpdate=True,
help_msg='',
help_url='',
*args,
**kw):
if (objects is None):
objects = []
if (attributes is None):
attributes = []
if (attributeHeadings is None):
attributeHeadings = {}
if (widgetClasses is None):
widgetClasses = {}
if (constructorArg is None):
constructorArg = {}
if (constructorKw is None):
constructorKw = {}
apply(Frame.__init__, (self, parent) + args, kw)
self.ndim = len(objects)
self.objects = objects
self.attributes = attributes
self.callback = callback
topFrame = Frame(self)
topFrame.grid(row=0, column=0, sticky=Tkinter.NSEW)
bottomFrame = Frame(self)
bottomFrame.grid(row=1, column=0, sticky=Tkinter.NSEW)
if (attributeLabel):
label = Label(topFrame, text=attributeLabel, relief=Tkinter.GROOVE)
label.grid(row=0, column=0, sticky=Tkinter.EW)
n = 0
for i in range(self.ndim):
text = tableHeading + ' ' + str(i + tableHeadingOffset)
label = Label(topFrame, text=text, relief=Tkinter.GROOVE)
if (attributeDirection == Tkinter.VERTICAL):
r = n
c = i + 1
else:
r = i + 1
c = n
label.grid(row=r, column=c, sticky=Tkinter.EW)
self.widgets = {}
for attr in self.attributes:
n = n + 1
text = attributeHeadings.get(attr, attr)
label = Label(topFrame, text=text, relief=Tkinter.GROOVE)
if (attributeDirection == Tkinter.VERTICAL):
r = n
c = 0
else:
r = 0
c = n
label.grid(row=r, column=c, sticky=Tkinter.EW)
self.widgets[attr] = self.ndim * [0]
for i in range(self.ndim):
arg = constructorArg.get(attr, ())
kw = constructorKw.get(attr, {})
self.widgets[attr][i] = widgetClasses[attr](topFrame, *arg,
**kw)
if (attributeDirection == Tkinter.VERTICAL):
r = n
c = i + 1
else:
r = i + 1
c = n
self.widgets[attr][i].grid(row=r, column=c, sticky=Tkinter.EW)
texts = []
commands = []
if (includeResetUpdate):
texts.extend(['Reset', 'Update'])
commands.extend([self.reset, self.update])
if (help_url or help_msg):
import memops.gui.HelpPopup
if (help_url):
help_cmd = lambda top=self.parent.top, url=help_url: memops.gui.HelpPopup.showHelpUrl(
top, url)
else:
help_cmd = lambda top=self.parent.top, message=help_msg: memops.gui.HelpPopup.showHelpText(
top, message)
texts.append('Help')
commands.append(help_cmd)
if (texts):
buttons = ButtonList(bottomFrame, texts=texts, commands=commands)
buttons.grid(row=0, column=0, sticky=Tkinter.EW)
self.reset()
class editResidueTypePopup(BasePopup):
'''
The main popup that is shown when the macro is loaded.
'''
def __init__(self, parent, *args, **kw):
self.font = 'Helvetica 10'
self.sFont = 'Helvetica %d'
self.project = parent.project
self.guiParent = parent
self.chemCompDict = {}
self.createChemCompDict()
self.waiting = False
BasePopup.__init__(self,
parent,
title="Residue Type Probabilities",
**kw)
def open(self):
self.updateAfter()
BasePopup.open(self)
def body(self, guiFrame):
'''Describes where all the GUI element are.'''
self.geometry('400x500')
guiFrame.expandGrid(0, 0)
tableFrame = Frame(guiFrame)
tableFrame.grid(
row=0,
column=0,
sticky='nsew',
)
tableFrame.expandGrid(0, 0)
buttonFrame = Frame(guiFrame)
buttonFrame.grid(
row=1,
column=0,
sticky='nsew',
)
headingList = ['Spinsystem Number', 'Assignment', 'Residue Type Probs']
self.table = ScrolledMatrix(tableFrame,
headingList=headingList,
callback=self.updateSpinSystemSelection,
multiSelect=True)
self.table.grid(row=0, column=0, sticky='nsew')
texts = ['Add Prob']
commands = [self.addProb]
self.AddProbButton = ButtonList(buttonFrame,
commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=0, sticky='nsew')
texts = ['Remove Prob']
commands = [self.removeProb]
self.AddProbButton = ButtonList(buttonFrame,
commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=2, sticky='nsew')
selectCcpCodes = sorted(self.chemCompDict.keys())
tipText = 'select ccpCode'
self.selectCcpCodePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
grid=(0, 1),
tipText=tipText)
selectCcpCodes = ['All Residue Types']
tipText = 'select ccpCode'
self.selectCcpCodeRemovePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
index=0,
grid=(0, 3),
tipText=tipText)
self.updateTable()
def updateSpinSystemSelection(self, obj, row, col):
'''Called after selectin a row in the table.'''
self.updateRemoveCcpCodePullDown()
def updateRemoveCcpCodePullDown(self):
'''Updates the pulldown showing all current residueTypeProbs
for a resonanceGroup that can be removed.
'''
removeCcpCodes = []
for spinSystem in self.table.currentObjects:
removeCcpCodes.extend([
typeProp.possibility.ccpCode
for typeProp in spinSystem.getResidueTypeProbs()
])
removeCcpCodes = ['All Residue Types'] + list(set(removeCcpCodes))
self.selectCcpCodeRemovePulldown.setup(texts=removeCcpCodes,
objects=removeCcpCodes,
index=0)
def getSpinSystems(self):
'''Get resonanceGroups (spin systems) in the project.'''
return self.nmrProject.resonanceGroups
def addProb(self):
'''Add the residue type selected in the selectCcpCodePulldown
as an residueTypeProb.
'''
ccpCode = self.selectCcpCodePulldown.object
for spinSystem in self.table.currentObjects:
if ccpCode not in [
typeProp.possibility.ccpCode
for typeProp in spinSystem.getResidueTypeProbs()
]:
chemComp = self.chemCompDict.get(ccpCode)
spinSystem.newResidueTypeProb(possibility=chemComp)
self.updateTable()
self.updateRemoveCcpCodePullDown()
def removeProb(self):
'''Removes the residueTypeProb selected in the
selectCcpCodeRemovePulldown from the selected resonanceGroup.
'''
ccpCode = self.selectCcpCodeRemovePulldown.object
for spinSystem in self.table.currentObjects:
residueTypeProbs = spinSystem.getResidueTypeProbs()
for typeProb in residueTypeProbs:
if ccpCode == 'All Residue Types' or ccpCode == typeProb.possibility.ccpCode:
typeProb.delete()
self.updateTable()
self.updateRemoveCcpCodePullDown()
def createChemCompDict(self):
'''Make a list of all amino acid types present in any of the
molecular chains present in the project.
'''
chains = self.getChains()
for chain in chains:
for residue in chain.sortedResidues():
if residue.ccpCode not in self.chemCompDict:
self.chemCompDict[
residue.ccpCode] = residue.chemCompVar.chemComp
def getChains(self):
'''Get all molecular chains stored in the project.'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateTable(self):
'''Update the whole table.'''
objectList = []
data = []
for spinSystem in self.getSpinSystems():
objectList.append(spinSystem)
residueTypeProbs = spinSystem.getResidueTypeProbs()
spinSystemInfo = self.getStringDescriptionOfSpinSystem(spinSystem)
probString = ''
for typeProp in residueTypeProbs:
probString += typeProp.possibility.ccpCode + ' '
data.append([spinSystem.serial, spinSystemInfo, probString])
self.table.update(objectList=objectList, textMatrix=data)
def getStringDescriptionOfSpinSystem(self, spinsys):
'''Get a simple identifier for the assignment status of a
resonanceGroup.
'''
spinSystemInfo = ''
if spinsys.residue:
spinSystemInfo += str(
spinsys.residue.seqCode) + ' ' + spinsys.residue.ccpCode
elif spinsys.residueProbs:
for residueProb in spinsys.residueProbs:
res = residueProb.possibility
spinSystemInfo += '{} {}? /'.format(res.seqCode, res.ccpCode)
spinSystemInfo = spinSystemInfo[:-1]
elif spinsys.ccpCode:
spinSystemInfo += spinsys.ccpCode
return spinSystemInfo
class CingFrame(NmrCalcRunFrame):
def __init__(self, parent, application, *args, **kw):
project = application.project
self.nmrProject = nmrProject = application.nmrProject
if project:
calcStore = project.findFirstNmrCalcStore(name=APP_NAME, nmrProject=nmrProject) or \
project.newNmrCalcStore(name=APP_NAME, nmrProject=nmrProject)
else:
calcStore = None
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.serverDone = False
NmrCalcRunFrame.__init__(self, parent, project, calcStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureTable.grid_forget()
self.structureButtons.grid_forget()
self.ensemblePulldown.grid_forget()
self.modelButtons.grid_forget()
self.modelPulldown.grid_forget()
frame = self.inputTabs.frames[0]
frame.grid_rowconfigure(0, weight=0)
frame.grid_rowconfigure(1, weight=1)
label = Label(frame, text='Ensemble: ', grid=(0, 0))
self.structurePulldown = PulldownList(
frame,
callback=self.changeStructure,
grid=(0, 1),
tipText='The structure ensemble coordinates to submit')
tipTexts = [
'Conformational model number', 'Whether analyse this model'
]
headingList = ['Model', 'Use']
editWidgets = [None, None]
editGetCallbacks = [None, self.toggleModel]
editSetCallbacks = [
None,
None,
]
self.modelTable = ScrolledMatrix(frame,
grid=(1, 0),
gridSpan=(1, 2),
callback=self.selectStructModel,
multiSelect=True,
tipTexts=tipTexts,
editWidgets=editWidgets,
initialRows=2,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
tipTexts = [
'Activate the selected models so that they will be consedered in the analysis',
'Deactivate the selected models so that they will not be considered in the analysis'
]
texts = ['Activate Selected', 'Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame,
texts=texts,
commands=commands,
grid=(2, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1, 0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0, 0))
frame.expandGrid(None, 2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
self.iCingBaseUrlPulldown = PulldownList(
frame,
texts=URLS,
objects=URLS,
index=0,
grid=(srow, 1),
tipText='Web location of iCING server to use')
srow += 1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(
frame,
bd=1,
text='',
grid=(srow, 1),
width=50,
tipText='Name of file to store compressed CING results in')
self.setZipFileName()
button = Button(frame,
text='Choose File',
bd=1,
sticky='ew',
command=self.chooseZipFile,
grid=(srow, 2),
tipText='Select file to overwrite with CING results')
srow += 1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(
frame,
bd=1,
text='',
grid=(srow, 1),
width=50,
tipText='Web location where CING results will be posted')
button = Button(frame,
text='View Results HTML',
bd=1,
sticky='ew',
command=self.viewHtmlResults,
grid=(srow, 2),
tipText='Open the HTML CING results in a web browser')
srow += 1
tipTexts = [
'Submit the CCPN project to the CING server',
'Determin whether the iCING job is complete, pending or has failed',
'Remove all trace of the last submissionfrom the iCING server',
'Download the compressed CING results, including HTML'
]
texts = [
'Submit Project!', 'Check Run Status', 'Purge Server Result',
'Download Results'
]
commands = [
self.runCingServer, self.checkStatus, self.purgeCingServer,
self.downloadResults
]
self.buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
grid=(srow, 0),
gridSpan=(1, 3),
tipTexts=tipTexts)
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1, 0))
frame.expandGrid(1, 1)
label = Label(frame, text='Chain: ')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Select the molecular system chain to consider')
self.chainPulldown.grid(row=0, column=1, sticky='w')
headingList = ['#', 'Residue', 'Linking', 'Decriptor', 'Use?']
tipTexts = [
'Sequence number', 'Residue type code',
'In-chain connectivity of residue',
'Protonation and steriochemical state',
'Whether to consider the residue in the analysis'
]
editWidgets = [None, None, None, None, None]
editGetCallbacks = [None, None, None, None, self.toggleResidue]
editSetCallbacks = [
None,
None,
None,
None,
None,
]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew')
tipTexts = [
'Use the selected residues in the analysis',
'Do not use the selected residues in the analysis'
]
texts = ['Activate Selected', 'Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame,
texts=texts,
commands=commands,
tipTexts=tipTexts)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(calcStore)
self.administerNotifiers(application.registerNotify)
def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query', msg, parent=self):
self.purgeCingServer()
def getServerUrl(self, baseUrl):
iCingUrl = os.path.join(baseUrl, 'icing/icing/serv/iCingServlet')
return iCingUrl
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structureData = self.getStructureData()
if not structureData:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
if not structureData.models:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueData = self.getResidueData()
if not (residueData and residueData.residues):
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.run.status = 'pending'
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(
self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.run.status = 'failed'
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(
iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(
credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID,
self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY,
self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
#run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials,
self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
self.run.status = 'failed'
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
self.run.status = 'completed'
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials,
self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials,
self.getServerUrl(url))
if results:
showInfo('Info', 'iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info', 'Purge failed')
self.update()
def chooseZipFile(self):
fileTypes = [
FileType('Zip', ['*.zip']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
file=self.resultFileEntry.get(),
title='Results zip file location',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def setZipFileName(self):
if self.project:
zipFile = '%s_CING_report.zip' % self.project.name
self.resultFileEntry.set(zipFile)
else:
self.resultFileEntry.set('CING_report.zip')
def selectStructModel(self, model, row, col):
self.model = model
def selectResidue(self, residue, row, col):
self.residue = residue
def getResidueData(self):
chain = self.chain.chain
chainCode = chain.code
msCode = chain.molSystem.code
dataObj = self.run.findFirstData(className=RESIDUE_DATA,
ioRole='input',
molSystemCode=msCode,
chainCode=chainCode,
name=APP_NAME)
if not dataObj:
dataObj = self.run.newMolResidueData(molSystemCode=msCode,
chainCode=chainCode,
ioRole='input',
name=APP_NAME)
# if not dataObj.residueSeqIds:
seqIds = [r.seqId for r in self.chain.sortedResidues()]
dataObj.residueSeqIds = seqIds
return dataObj
def getStructureData(self):
eId = self.structure.ensembleId
msCode = self.structure.molSystem.code
dataObj = self.run.findFirstData(className=STRUCTURE_DATA,
molSystemCode=msCode,
ensembleId=eId,
ioRole='input',
name=APP_NAME)
if not dataObj:
dataObj = self.run.newStructureEnsembleData(ioRole='input',
molSystemCode=msCode,
ensembleId=eId,
name=APP_NAME)
# if not dataObj.modelSerials:
serials = [m.serial for m in self.structure.sortedModels()]
dataObj.modelSerials = serials
for dataObjB in self.run.findAllData(className=STRUCTURE_DATA,
name=APP_NAME,
ioRole='input'):
if dataObjB is not dataObj:
dataObjB.delete()
return dataObj
def deactivateResidues(self):
if self.run and self.chain:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
for residue in self.residueMatrix.currentObjects:
seqId = residue.seqId
if seqId in seqIds:
seqIds.remove(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def activateResidues(self):
if self.run and self.chain:
for residue in self.residueMatrix.currentObjects:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
for residue in self.residueMatrix.currentObjects:
seqId = residue.seqId
if seqId not in seqIds:
seqIds.add(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def activateModels(self):
if self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
for model in self.modelTable.currentObjects:
serial = model.serial
if serial not in serials:
serials.add(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def disableModels(self):
if self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
for model in self.modelTable.currentObjects:
serial = model.serial
if serial in serials:
serials.remove(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def toggleModel(self, *opt):
if self.model and self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
serial = self.model.serial
if serial in serials:
serials.remove(serial)
else:
serials.add(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def toggleResidue(self, *opt):
if self.residue and self.run:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
seqId = self.residue.seqId
if seqId in seqIds:
seqIds.remove(seqId)
else:
seqIds.add(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def updateResidues(self):
if self.residue and (self.residue.topObject is not self.structure):
self.residue = None
textMatrix = []
objectList = []
colorMatrix = []
if self.chain:
resDataObj = self.getResidueData()
selectedRes = set(resDataObj.residues)
chainCode = self.chain.code
for residue in self.chain.sortedResidues():
msResidue = residue.residue
if msResidue in selectedRes:
colors = [None, None, None, None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None, None, None, None]
use = 'No'
datum = [
residue.seqCode,
msResidue.ccpCode,
msResidue.linking,
msResidue.descriptor,
use,
]
textMatrix.append(datum)
objectList.append(residue)
colorMatrix.append(colors)
self.residueMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def updateChains(self):
index = 0
names = []
chains = []
chain = self.chain
if self.structure:
chains = self.structure.sortedCoordChains()
names = [chain.code for chain in chains]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
self.changeChain(chain)
self.chainPulldown.setup(names, chains, index)
def updateStructures(self):
index = 0
names = []
structures = []
structure = self.structure
if self.run:
structures0 = [(s.ensembleId, s)
for s in self.project.structureEnsembles]
structures0.sort()
for eId, structure0 in structures0:
name = '%s:%s' % (structure0.molSystem.code, eId)
structures.append(structure0)
names.append(name)
if structures:
if structure not in structures:
structure = structures[-1]
index = structures.index(structure)
if self.structure is not structure:
self.changeStructure(structure)
self.structurePulldown.setup(names, structures, index)
def updateModels(self, obj=None):
textMatrix = []
objectList = []
colorMatrix = []
if self.structure and self.run:
strucDataObj = self.getStructureData()
selectedSerials = set(strucDataObj.modelSerials)
for model in self.structure.sortedModels():
if model.serial in selectedSerials:
colors = [None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None]
use = 'No'
datum = [model.serial, use]
textMatrix.append(datum)
objectList.append(model)
colorMatrix.append(colors)
self.modelTable.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def changeStructure(self, structure):
if self.project and (self.structure is not structure):
self.project.currentEstructureEnsemble = structure
self.structure = structure
if self.run:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
serials2 = set([m.serial for m in structure.models])
serials = list(serials & serials2)
serials.sort()
dataObj.modelSerials = serials
dataObj.ensembleId = structure.ensembleId
dataObj.molSystemCode = structure.molSystem.code
# Could clean up residue data if required
# prob OK to have haning around in case structure
# changes back
#for dataObj in self.run.findAllData(className=RESIDUE_DATA,
# ioRole='input',
# molSystemCode=msCode,
# name=APP_NAME)
# dataObj.delete()
self.updateModels()
self.updateChains()
def changeChain(self, chain):
if self.project and (self.chain is not chain):
self.chain = chain
self.updateResidues()
#def chooseValidScript(self):
#
# # Prepend default Cyana file extension below
# fileTypes = [ FileType('Python', ['*.py']), ]
# popup = FileSelectPopup(self, file_types = fileTypes,
# title='Python file', dismiss_text='Cancel',
# selected_file_must_exist = True)
# fileName = popup.getFile()
# self.validScriptEntry.set(fileName)
# popup.destroy()
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = nmrProject = project.currentNmrProject
calcStore = project.findFirstNmrCalcStore(name='CING', nmrProject=nmrProject) or \
project.newNmrCalcStore(name='CING', nmrProject=nmrProject)
else:
calcStore = None
if not self.project:
return
self.setZipFileName()
if not self.project.currentNmrProject:
name = self.project.name
self.nmrProject = self.project.newNmrProject(name=name)
else:
self.nmrProject = self.project.currentNmrProject
self.update(calcStore)
def update(self, calcStore=None):
NmrCalcRunFrame.update(self, calcStore)
run = self.run
urls = URLS
index = 0
if run:
userId = getRunTextParameter(run, iCingRobot.FORM_USER_ID)
accessKey = getRunTextParameter(run, iCingRobot.FORM_ACCESS_KEY)
if userId and accessKey:
self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId),
(iCingRobot.FORM_ACCESS_KEY,
accessKey)]
url = getRunTextParameter(run, ICING_BASE_URL)
if url:
htmlUrl = getRunTextParameter(run, HTML_RESULTS_URL)
self.iCingBaseUrl = url
self.resultsUrl = htmlUrl # May be None
self.resultUrlEntry.set(self.resultsUrl)
if self.iCingBaseUrl and self.iCingBaseUrl not in urls:
index = len(urls)
urls.append(self.iCingBaseUrl)
self.iCingBaseUrlPulldown.setup(urls, urls, index)
self.updateButtons()
self.updateStructures()
self.updateModels()
self.updateChains()
def updateButtons(self, event=None):
buttons = self.buttonBar.buttons
if self.project and self.run:
buttons[0].enable()
if self.resultsUrl and self.serverCredentials:
buttons[1].enable()
buttons[2].enable()
buttons[3].enable()
else:
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
else:
buttons[0].disable()
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
class CalcHeteroNoePopup(BasePopup):
"""
**Calculate Heteronuclear NOE Values From Peak Intensities**
The purpose of this popup window is to calculate the heteronuclear NOE for
amide resonances based upon a comparison of the peak intensities in spectra
that derive from an NOE saturated experiment and an unsaturated (reference)
experiment. The basic idea of this tool is that three peak lists are chosen,
two of which are for heteronuclear NOE experiments (H,N axes); unsaturated
reference and saturated, and one which is the source of assignments and peak
locations. This last "Assignment" peak list may be the same as one of the NOE
peak lists, but may also be entirely separate.
The "Assignment" peak list is used to specify which peak assignments and
locations should be used for the calculation of the heteronuclear NOE values,
and thus can be used to specify only a subset of the resonances for
measurement. For example, it is common to copy an HQSC peak list for use as
the "Assignment" peak list but remove overlapped and NH2 peaks so that the NOE
values are only calculated for separated backbone amides. The calculation
process involves taking each of these assigned peaks and finding peaks with
the same assignment in the NOE peak lists, or if that fails finding peaks with
a similar position (within the stated tolerances); new peaks may be picked if
the "Pick new peaks?" option is set.
The first "Peak Lists & Settings" tab allows the user to choose the peak lists
and various options that will be used in the peak-finding and NOE calculation.
The "Peaks" table allows the peaks from each of the three peak list selections
to be displayed when one of the "Show" buttons is clicked. The [Separate Peak
Table] function allows these peaks to be displayed in the main, separate `Peak
Lists`_ table, which has many more peak manipulation options. The options
below the table may be used to locate selected peaks within the spectrum
window displays.
The second "Peak Intensity Comparison" tab is where the heteronuclear NOE
values are actually calculated. Assuming that two NOE experiment peak lists
have been chosen and that some of their peaks match the assigned peak
positions then the peak intensities are extracted and NOE values automatically
calculated when the tab is opened. Although, a refresh of the table can be
forced with [Find Matching Peaks] at the bottom
If pairs of NOE saturated and reference peaks are found then the actual
heteronuclear NOE value is displayed as the "Intensity Ratio" in the last,
rightmost, column of the table. To store these values as a NOE measurement
list; so that the data can be saved in the CCPN project without need for
recalculation, the [Create Hetero NOE List] function can be used. The results
are then available to view at any time via the `Measurement Lists`_ table.
**Caveats & Tips**
Erroneous peak intensity comparisons may be removed with the [Remove Pairs]
function, but its is common to curate the "Assign" peak list first and
avoid tidying afterwards.
The "Closeness score" can be used to find peak positions where the compared
NOE peaks are unexpectedly far from one another.
.. _`Peak Lists`: EditPeakListsPopup.html
.. _`Measurement Lists`: EditMeasurementListsPopup.html
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.peakPairs = []
self.intensityType = 'height'
self.selectedPair = None
self.assignPeakList = None
self.refPeakList = None
self.satPeakList = None
self.displayPeakList = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Data Analysis : Heteronuclear NOE", **kw)
def body(self, guiFrame):
self.geometry('700x700')
guiFrame.expandGrid(0,0)
options = ['Peak Lists & Settings','Peak Intensity Comparison']
tabbedFrame = TabbedFrame(guiFrame, options=options, callback=self.changeTab)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
row = 0
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_columnconfigure(3, weight=1)
frameA.grid_columnconfigure(5, weight=1)
frameA.grid_rowconfigure(5, weight=1)
tipText = 'Number of reference peaks (no saturation)'
self.peaksALabel = Label(frameA, text='Number of Ref Peaks: ', tipText=tipText)
self.peaksALabel.grid(row=1,column=0,columnspan=2,sticky='w')
tipText = 'Number of NOE saturation peaks'
self.peaksBLabel = Label(frameA, text='Number of Sat Peaks: ', tipText=tipText)
self.peaksBLabel.grid(row=1,column=2,columnspan=2,sticky='w')
tipText = 'Number of peaks in assigned list'
self.peaksCLabel = Label(frameA, text='Number of Assign Peaks: ', tipText=tipText)
self.peaksCLabel.grid(row=1,column=4,columnspan=2,sticky='w')
tipText = 'Selects which peak list is considered the NOE intensity reference (no saturation)'
specALabel = Label(frameA, text='Ref Peak List: ')
specALabel.grid(row=0,column=0,sticky='w')
self.specAPulldown = PulldownList(frameA, callback=self.setRefPeakList, tipText=tipText)
self.specAPulldown.grid(row=0,column=1,sticky='w')
tipText = 'Selects which peak list is considered as NOE saturated.'
specBLabel = Label(frameA, text='Sat Peak List: ')
specBLabel.grid(row=0,column=2,sticky='w')
self.specBPulldown = PulldownList(frameA, callback=self.setSatPeakList, tipText=tipText)
self.specBPulldown.grid(row=0,column=3,sticky='w')
tipText = 'Selects a peak list with assignments to use as a positional reference'
specCLabel = Label(frameA, text='Assignment Peak List: ')
specCLabel.grid(row=0,column=4,sticky='w')
self.specCPulldown = PulldownList(frameA, callback=self.setAssignPeakList, tipText=tipText)
self.specCPulldown.grid(row=0,column=5,sticky='w')
frame0a = Frame(frameA)
frame0a.grid(row=2,column=0,columnspan=6,sticky='nsew')
frame0a.grid_columnconfigure(9, weight=1)
tipText = '1H ppm tolerance for matching assigned peaks to reference & NOE saturation peaks'
tolHLabel = Label(frame0a, text='Tolerances: 1H')
tolHLabel.grid(row=0,column=0,sticky='w')
self.tolHEntry = FloatEntry(frame0a,text='0.02', width=6, tipText=tipText)
self.tolHEntry .grid(row=0,column=1,sticky='w')
tipText = '15N ppm tolerance for matching assigned peaks to reference & NOE saturation peaks'
tolNLabel = Label(frame0a, text=' 15N')
tolNLabel .grid(row=0,column=2,sticky='w')
self.tolNEntry = FloatEntry(frame0a,text='0.1', width=6, tipText=tipText)
self.tolNEntry .grid(row=0,column=3,sticky='w')
tipText = 'Whether to peak new peaks in reference & NOE saturated lists (at assignment locations)'
label = Label(frame0a, text=' Pick new peaks?', grid=(0,4))
self.pickPeaksSelect = CheckButton(frame0a, tipText=tipText,
grid=(0,5), selected=True)
tipText = 'Whether to assign peaks in the peaks in the reference & NOE saturation lists, if not already assigned'
label = Label(frame0a, text=' Assign peaks?')
label.grid(row=0,column=6,sticky='w')
self.assignSelect = CheckButton(frame0a, tipText=tipText)
self.assignSelect.set(1)
self.assignSelect.grid(row=0,column=7,sticky='w')
tipText = 'Whether to consider peak height or volume in the heteronuclear NOE calculation'
intensLabel = Label(frame0a, text=' Intensity Type:')
intensLabel .grid(row=0,column=8,sticky='w')
self.intensPulldown = PulldownList(frame0a, texts=['height','volume'],
callback=self.setIntensityType,
tipText=tipText)
self.intensPulldown.grid(row=0,column=9,sticky='w')
divider = LabelDivider(frameA, text='Peaks', grid=(3,0),
gridSpan=(1,6))
tipTexts = ['Show the selected intensity reference peaks in the below table',
'Show the selected NOE saturation peaks in the below table',
'Show the selected assigned peak list in the below table',
'Show the displayed peaks in a separate peak table, where assignments etc. may be adjusted']
texts = ['Show Ref Peaks','Show Sat Peaks',
'Show Assign Peaks', 'Separate Peak Table']
commands = [self.viewRefPeakList, self.viewSatPeakList,
self.viewAssignPeakList, self.viewSeparatePeakTable]
self.viewPeaksButtons = ButtonList(frameA, expands=True, tipTexts=tipTexts,
texts=texts, commands=commands)
self.viewPeaksButtons.grid(row=4,column=0,columnspan=6,sticky='nsew')
self.peakTable = PeakTableFrame(frameA, self.guiParent, grid=(5,0),
gridSpan=(1,6))
self.peakTable.bottomButtons1.grid_forget()
self.peakTable.bottomButtons2.grid_forget()
#self.peakTable.topFrame.grid_forget()
self.peakTable.topFrame.grid(row=2, column=0, sticky='ew')
# Next tab
frameB.expandGrid(0,0)
tipTexts = ['Row number',
'Assignment annotation for NOE saturation peak',
'Assignment annotation for reference peak (no saturation)',
'1H chemical shift of NOE saturation peak',
'1H chemical shift of reference peak',
'15N chemical shift of NOE saturation peak',
'15N chemical shift of reference peak',
'The separation between compared peaks: square root of the sum of ppm differences squared',
'The intensity if the NOE saturation peak',
'The intensity of the reference peak (no saturation)',
'Ratio of peak intensities: saturated over reference',
'Residue(s) for reference peak']
colHeadings = ['#','Sat Peak','Ref Peak','1H shift A',
'1H shift B','15N shift A','15N shift B',
'Closeness\nScore','Intensity A','Intensity B',
'Intensity\nRatio','Residue']
self.scrolledMatrix = ScrolledMatrix(frameB, multiSelect=True,
headingList=colHeadings,
callback=self.selectCell,
tipTexts=tipTexts,
grid=(0,0),
deleteFunc=self.removePair)
tipTexts = ['Force a manual update of the table; pair-up NOE saturation and reference peaks according to assigned peak positions',
'Remove the selected rows of peak pairs',
'Show peaks corresponding to the selected row in a table',
'Save the Heteronuclear NOE values in the CCPN project as a data list']
texts = ['Refresh Table','Remove Pairs',
'Show Peak Pair','Create Hetero NOE List']
commands = [self.matchPeaks,self.removePair,
self.showPeakPair,self.makeNoeList]
self.pairButtons = ButtonList(frameB, tipTexts=tipTexts, grid=(1,0),
texts=texts, commands=commands)
bottomButtons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url)
bottomButtons.grid(row=0, column=0, sticky='e')
self.updatePulldowns()
self.updateAfter()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete','setName'):
for clazz in ('ccp.nmr.Nmr.DataSource', 'ccp.nmr.Nmr.Experiment',):
notifyFunc(self.updatePulldowns, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updatePulldowns,'ccp.nmr.Nmr.PeakList', func)
for func in ('__init__', 'delete','setAnnotation','setFigOfMerit'):
notifyFunc(self.updatePeaks, 'ccp.nmr.Nmr.Peak', func)
for func in ('setAnnotation','setPosition','setNumAliasing'):
notifyFunc(self.updatePeakChild, 'ccp.nmr.Nmr.PeakDim', func)
for func in ('__init__', 'delete', 'setValue'):
notifyFunc(self.updatePeakChild, 'ccp.nmr.Nmr.PeakIntensity', func)
def changeTab(self, index):
if index == 1:
self.matchPeaks()
def open(self):
self.updatePulldowns()
self.updateAfter()
BasePopup.open(self)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def updatePulldowns(self, *obj):
index0 = 0
index1 = 0
index2 = 0
names, peakLists = self.getPeakLists()
if names:
if self.refPeakList not in peakLists:
self.refPeakList = peakLists[0]
if self.satPeakList not in peakLists:
self.satPeakList = peakLists[0]
if self.assignPeakList not in peakLists:
self.assignPeakList = peakLists[0]
index0 = peakLists.index(self.refPeakList)
index1 = peakLists.index(self.satPeakList)
index2 = peakLists.index(self.assignPeakList)
self.specAPulldown.setup(names, peakLists, index0)
self.specBPulldown.setup(names, peakLists, index1)
self.specCPulldown.setup(names, peakLists, index2)
def updatePeakChild(self,peakChild):
if self.waiting:
return
self.updatePeaks(peakChild.peak)
def updatePeaks(self, peak):
if self.waiting:
return
if peak.peakList in (self.refPeakList,self.satPeakList,self.assignPeakList):
if peak.isDeleted and (peak.peakList in (self.refPeakList,self.satPeakList) ):
for peaks in self.peakPairs:
if peak in peaks:
self.peakPairs.remove(peaks)
if self.selectedPair is peaks:
self.selectedPair = None
self.updateAfter()
return
self.updateAfter()
def setIntensityType(self, intensityType):
self.intensityType = intensityType
self.updateAfter()
def viewRefPeakList(self):
if self.refPeakList:
self.updatePeakTable(self.refPeakList)
def viewSatPeakList(self):
if self.satPeakList:
self.updatePeakTable(self.satPeakList)
def viewAssignPeakList(self):
if self.assignPeakList:
self.updatePeakTable(self.assignPeakList)
def viewSeparatePeakTable(self):
if self.displayPeakList:
self.guiParent.editPeakList(peakList=self.displayPeakList)
def setRefPeakList(self, refPeakList):
if self.displayPeakList is self.refPeakList:
self.updatePeakTable(refPeakList)
self.refPeakList = refPeakList
self.updateViewButtons()
self.updateAfter()
def setSatPeakList(self, satPeakList):
if self.displayPeakList is self.satPeakList:
self.updatePeakTable(satPeakList)
self.satPeakList = satPeakList
self.updateViewButtons()
self.updateAfter()
def setAssignPeakList(self, assignPeakList):
if self.displayPeakList is self.assignPeakList:
self.updatePeakTable(assignPeakList)
self.assignPeakList = assignPeakList
self.updateViewButtons()
self.updateAfter()
def getPeakListName(self, peakList):
if peakList:
spectrum = peakList.dataSource
experiment = spectrum.experiment
name = '%s:%s:%d' % (experiment.name, spectrum.name, peakList.serial)
else:
name = '<None>'
return name
def getPeakLists(self):
names = []
peakLists = []
for experiment in self.nmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
if dataSource.numDim == 2:
dimsN = findSpectrumDimsByIsotope(dataSource,'15N')
dimsH = findSpectrumDimsByIsotope(dataSource,'1H')
if len(dimsN) == 1 and len(dimsH) == 1:
for peakList in dataSource.sortedPeakLists():
name = self.getPeakListName(peakList)
names.append( name )
peakLists.append(peakList)
return names, peakLists
def showPeakPair(self):
if self.selectedPair:
self.guiParent.viewPeaks(self.selectedPair)
def selectCell(self, object, row, col):
self.selectedPair = object
if self.selectedPair:
self.pairButtons.buttons[1].enable()
self.pairButtons.buttons[2].enable()
else:
self.pairButtons.buttons[1].disable()
self.pairButtons.buttons[2].disable()
def removePair(self, *event):
pairs = self.scrolledMatrix.currentObjects
if pairs:
for pair in pairs:
self.peakPairs.remove(pair)
self.selectedPair = None
self.updateAfter()
def matchPeaks(self):
# assign relative to reference
if self.assignPeakList and self.assignPeakList.peaks and self.refPeakList and self.satPeakList:
tolH = float( self.tolHEntry.get() )
tolN = float( self.tolNEntry.get() )
pickNewPeaks = self.pickPeaksSelect.get()
doAssign = self.assignSelect.get()
dimH = findSpectrumDimsByIsotope(self.assignPeakList.dataSource,'1H' )[0]
dimHA = findSpectrumDimsByIsotope(self.refPeakList.dataSource,'1H' )[0]
dimHB = findSpectrumDimsByIsotope(self.satPeakList.dataSource,'1H' )[0]
dimN = 1-dimH
dimNA = 1-dimHA
dimNB = 1-dimHB
tolerancesA = [0,0]
tolerancesA[dimHA] = tolH
tolerancesA[dimNA] = tolN
tolerancesB = [0,0]
tolerancesB[dimHB] = tolH
tolerancesB[dimNB] = tolN
self.peakPairs = matchHnoePeaks(self.assignPeakList,self.refPeakList,
self.satPeakList,tolerancesA,tolerancesB,
pickNewPeaks,doAssign)
self.updateAfter()
def makeNoeList(self):
if self.refPeakList is self.satPeakList:
showWarning('Same Peak List',
'Ref Peak List and Sat Peak List cannot be the same',
parent=self)
return
if self.peakPairs:
s1 = self.refPeakList.dataSource
s2 = self.satPeakList.dataSource
noiseRef = getSpectrumNoise(s1)
noiseSat = getSpectrumNoise(s2)
es = '%s-%s' % (s1.experiment.name,s2.experiment.name)
if len(es) > 50:
es = 'Expt(%d)-Expt(%d)' % (s1.experiment.serial,s2.experiment.serial)
noeList = self.nmrProject.newNoeList(unit='None',name='Hetero NOE list for %s' % es)
noeList.setExperiments([s1.experiment,])
if s1.experiment is not s2.experiment:
noeList.addExperiment( s2.experiment )
# TBD: sf, noeValueType, refValue, refDescription
resonancePairsSeen = set()
for (peakA,peakB) in self.peakPairs: # peakA is sat
intensA = getPeakIntensity(peakA,self.intensityType)
intensB = getPeakIntensity(peakB,self.intensityType)
value = float(intensA)/intensB
error = abs(value) * sqrt((noiseSat/intensA)**2 + (noiseRef/intensB)**2)
resonances = tuple(self.getPeakResonances(peakA))
frozenResonances = frozenset(resonances)
if len(resonances) < 2:
pl = peakA.peakList
sp = pl.dataSource
msg = 'Skipping %s:%s:%d peak %d it has too few resonances assigned'
data = (sp.experiment.name, sp.name, pl.serial, peakA.serial)
showWarning('Warning',msg % data, parent=self)
elif len(resonances) > 2:
pl = peakA.peakList
sp = pl.dataSource
resonanceText = ' '.join([makeResonanceGuiName(r) for r in resonances])
msg = 'Skipping %s:%s:%d peak %d it has too many resonances assigned (%s)'
data = (sp.experiment.name, sp.name, pl.serial, peakA.serial, resonanceText)
showWarning('Warning', msg % data, parent=self)
elif frozenResonances not in resonancePairsSeen:
resonancePairsSeen.add(frozenResonances)
noeList.newNoe(value=value,resonances=resonances,peaks=[peakA,peakB],error=error)
else:
resonanceText = ' '.join([makeResonanceGuiName(r) for r in resonances])
msg = 'Skipping duplicate entry for resonances %s' % resonanceText
showWarning('Warning', msg, parent=self)
self.parent.editMeasurements(measurementList=noeList)
def getPeakResonances(self,peak):
resonances = []
for peakDim in peak.sortedPeakDims():
for contrib in peakDim.sortedPeakDimContribs():
resonances.append(contrib.resonance)
return resonances
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def updateViewButtons(self):
if self.refPeakList:
self.viewPeaksButtons.buttons[0].enable()
else:
self.viewPeaksButtons.buttons[0].disable()
if self.satPeakList:
self.viewPeaksButtons.buttons[1].enable()
else:
self.viewPeaksButtons.buttons[1].disable()
if self.assignPeakList:
self.viewPeaksButtons.buttons[2].enable()
else:
self.viewPeaksButtons.buttons[2].disable()
def updatePeakTable(self, peakList):
if peakList is not self.displayPeakList:
self.displayPeakList = peakList
self.peakTable.update(peaks=peakList.sortedPeaks())
def update(self):
if self.refPeakList:
self.peaksALabel.set( 'Number of Ref Peaks: %d' % len(self.refPeakList.peaks) )
else:
self.peaksALabel.set( 'Number of Ref Peaks: %d' % 0 )
if self.satPeakList:
self.peaksBLabel.set( 'Number of Sat Peaks: %d' % len(self.satPeakList.peaks) )
else:
self.peaksBLabel.set( 'Number of Sat Peaks: %d' % 0 )
if self.assignPeakList:
self.peaksCLabel.set( 'Number of Assign Peaks: %d' % len(self.assignPeakList.peaks) )
else:
self.peaksCLabel.set( 'Number of Assign Peaks: %d' % 0 )
if self.refPeakList and self.satPeakList and self.assignPeakList:
if self.refPeakList is self.satPeakList:
self.pairButtons.buttons[0].disable()
else:
self.pairButtons.buttons[0].enable()
else:
self.pairButtons.buttons[0].disable()
if self.selectedPair:
self.pairButtons.buttons[1].enable()
self.pairButtons.buttons[2].enable()
else:
self.pairButtons.buttons[1].disable()
self.pairButtons.buttons[2].disable()
if self.peakPairs:
self.pairButtons.buttons[3].enable()
dsA = self.peakPairs[0][0].peakList.dataSource
dsB = self.peakPairs[0][1].peakList.dataSource
dimHA = findSpectrumDimsByIsotope(dsA,'1H')[0]
dimHB = findSpectrumDimsByIsotope(dsB,'1H')[0]
dimNA = findSpectrumDimsByIsotope(dsA,'15N')[0]
dimNB = findSpectrumDimsByIsotope(dsB,'15N')[0]
else:
self.pairButtons.buttons[3].disable()
objectList = []
textMatrix = []
i = 0
for (peakA,peakB) in self.peakPairs:
i += 1
peakDimsA = peakA.sortedPeakDims()
peakDimsB = peakB.sortedPeakDims()
ppm0 = peakDimsA[dimHA].value
ppm1 = peakDimsB[dimHB].value
ppm2 = peakDimsA[dimNA].value
ppm3 = peakDimsB[dimNB].value
d0 = abs(ppm0-ppm1)
d1 = abs(ppm2-ppm3)
intensA = getPeakIntensity(peakA,self.intensityType)
intensB = getPeakIntensity(peakB,self.intensityType)
datum = []
datum.append( i )
datum.append( getPeakAnnotation(peakA, doPeakDims=False) )
datum.append( getPeakAnnotation(peakB, doPeakDims=False) )
datum.append( ppm0 )
datum.append( ppm1 )
datum.append( ppm2 )
datum.append( ppm3 )
datum.append( sqrt((d0*d0)+(d1*d1)) )
datum.append( intensA )
datum.append( intensB )
if intensB:
datum.append( float(intensA)/intensB )
else:
datum.append( None )
seqCodes = ','.join(['%s' % seqCode for seqCode in getPeakSeqCodes(peakB)])
datum.append(seqCodes)
objectList.append( (peakA,peakB) )
textMatrix.append( datum )
if not objectList:
textMatrix.append([])
self.scrolledMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.waiting = False
class MidgePopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 15
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.ratioHD = 0.9
self.peakListDict = {}
self.peakListDict3d = {}
self.noesyPeakList = None
self.noesy3dPeakList = None
self.carbonLabel = 0
self.nitrogenLabel = 1
self.noesyPeakList1 = None
self.noesyPeakList2 = None
self.noesyPeakList3 = None
self.noesyPeakList3d = None
self.resonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.adcAtomTypes = None
self.structure = None
BasePopup.__init__(self,
parent,
title="Relaxation Matrix Optimisation",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
def setCarbonLabel(self, boolean):
self.carbonLabel = boolean
def setNitrogenLabel(self, boolean):
self.nitrogenLabel = boolean
def update(self):
if self.resonances and (
(self.noesyPeaks and self.noesyPeakList1 and self.noesyPeakList2
and self.noesyPeakList3) or self.noesyPeakList3d):
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.distConstrLabel.set(
str(len(self.distanceConstraintList.constraints)))
self.midgeButtons.buttons[1].enable()
else:
self.distConstrLabel.set('')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
str(len(self.antiDistConstraintList.constraints)))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('')
self.midgeButtons.buttons[2].disable()
if self.resonances:
self.numResonancesLabel.set(str(len(self.resonances)))
else:
self.numResonancesLabel.set('')
if self.noesyPeaks:
self.numPeaksLabel.set(str(len(self.noesyPeaks)))
else:
self.numPeaksLabel.set('')
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['<None>', 'HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
if name == '<None>':
name = None
self.adcAtomTypes = name
def getResonances(self):
resonanceDict = {}
if self.noesyPeaks:
for peak in self.noesyPeaks:
for peakDim in peak.peakDims:
for contrib in peakDim.peakDimContribs:
resonanceDict[contrib.resonance] = 1
# TBD: Set resonance.name for typing
self.resonances = resonanceDict.keys()
def getPeaks(self):
if self.noesyPeakList:
self.noesyPeaks = self.noesyPeakList.sortedPeaks()
def calculateDistances(self):
resonances = list(self.resonances)
resDict = {}
for resonance in resonances:
resDict[resonance.serial] = resonance
ratioHD = self.ratioHDEntry.get() or self.ratioHD
tmix1 = self.tmix1Entry.get() or 60
tmix2 = self.tmix2Entry.get() or 120
tmix3 = self.tmix3Entry.get() or 200
data = [(tmix1, self.noesyPeakList1), (tmix2, self.noesyPeakList2),
(tmix3, self.noesyPeakList3)]
data.sort()
mixingTimes = [x[0] for x in data]
peakLists = [x[1] for x in data]
# get a clean, symmetric and normalised NOE matrix
noeMatrix = getNoeMatrixFromPeaks(self.noesyPeaks,
resonances,
peakLists,
mixingTimes,
ratioHD=ratioHD,
analysis=self.guiParent)
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList, resonances = optimiseRelaxation(
resonances,
noeMatrix,
self.mixTime,
self.specFreq,
self.corrTime,
self.leakRate,
self.carbonLabel,
self.nitrogenLabel,
maxIter=self.maxIter)
#constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList and self.noesyPeakList:
constraintHead = self.distanceConstraintList.nmrConstraintStore
if self.adcAtomTypes:
adcDict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
allowedAtomTypes = adcDict[self.adcAtomTypes]
print "Making ADCs"
self.antiDistConstraintList = makeNoeAdcs(
resonances[:],
self.noesyPeakList.dataSource,
constraintHead,
allowedAtomTypes=allowedAtomTypes)
print "Done ADCs"
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
item = constraint.findFirstItem()
resonances = list(item.resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setOrigData(distance)
self.update()
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def getNoesys3d(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
if spectrum.numDim != 3:
continue
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict3d[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def getNoesys(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
if name == '<None>':
self.noesyPeakList = None
else:
self.noesyPeakList = self.peakListDict[name]
self.getPeaks()
self.getResonances()
self.update()
def setNoesy1(self, index, name=None):
if not name:
name = self.tmix1Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList1 = self.peakListDict[name]
else:
self.noesyPeakList1 = None
self.update()
def setNoesy2(self, index, name=None):
if not name:
name = self.tmix2Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList2 = self.peakListDict[name]
else:
self.noesyPeakList2 = None
self.update()
def setNoesy3(self, index, name=None):
if not name:
name = self.tmix3Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList3 = self.peakListDict[name]
else:
self.noesyPeakList3 = None
self.update()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
if name != '<None>':
self.noesyPeakList3d = self.peakListDict3d[name]
self.noesyPeaks = self.noesyPeakList3d.sortedPeaks()
else:
self.noesyPeakList3d = None
self.noesyPeaks = []
self.getResonances()
self.update()
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
class editResidueTypePopup(BasePopup):
'''
The main popup that is shown when the macro is loaded.
'''
def __init__(self, parent, *args, **kw):
self.font = 'Helvetica 10'
self.sFont = 'Helvetica %d'
self.project = parent.project
self.guiParent = parent
self.chemCompDict = {}
self.createChemCompDict()
self.waiting = False
BasePopup.__init__(self, parent,
title="Residue Type Probabilities", **kw)
def open(self):
self.updateAfter()
BasePopup.open(self)
def body(self, guiFrame):
'''Describes where all the GUI element are.'''
self.geometry('400x500')
guiFrame.expandGrid(0, 0)
tableFrame = Frame(guiFrame)
tableFrame.grid(row=0, column=0, sticky='nsew', )
tableFrame.expandGrid(0, 0)
buttonFrame = Frame(guiFrame)
buttonFrame.grid(row=1, column=0, sticky='nsew', )
headingList = ['Spinsystem Number', 'Assignment', 'Residue Type Probs']
self.table = ScrolledMatrix(tableFrame, headingList=headingList,
callback=self.updateSpinSystemSelection,
multiSelect=True)
self.table.grid(row=0, column=0, sticky='nsew')
texts = ['Add Prob']
commands = [self.addProb]
self.AddProbButton = ButtonList(buttonFrame, commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=0, sticky='nsew')
texts = ['Remove Prob']
commands = [self.removeProb]
self.AddProbButton = ButtonList(buttonFrame, commands=commands,
texts=texts)
self.AddProbButton.grid(row=0, column=2, sticky='nsew')
selectCcpCodes = sorted(self.chemCompDict.keys())
tipText = 'select ccpCode'
self.selectCcpCodePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
grid=(0, 1),
tipText=tipText)
selectCcpCodes = ['All Residue Types']
tipText = 'select ccpCode'
self.selectCcpCodeRemovePulldown = PulldownList(buttonFrame,
texts=selectCcpCodes,
index=0,
grid=(0, 3),
tipText=tipText)
self.updateTable()
def updateSpinSystemSelection(self, obj, row, col):
'''Called after selectin a row in the table.'''
self.updateRemoveCcpCodePullDown()
def updateRemoveCcpCodePullDown(self):
'''Updates the pulldown showing all current residueTypeProbs
for a resonanceGroup that can be removed.
'''
removeCcpCodes = []
for spinSystem in self.table.currentObjects:
removeCcpCodes.extend([typeProp.possibility.ccpCode for typeProp in spinSystem.getResidueTypeProbs()])
removeCcpCodes = ['All Residue Types'] + list(set(removeCcpCodes))
self.selectCcpCodeRemovePulldown.setup(texts=removeCcpCodes,
objects=removeCcpCodes,
index=0)
def getSpinSystems(self):
'''Get resonanceGroups (spin systems) in the project.'''
return self.nmrProject.resonanceGroups
def addProb(self):
'''Add the residue type selected in the selectCcpCodePulldown
as an residueTypeProb.
'''
ccpCode = self.selectCcpCodePulldown.object
for spinSystem in self.table.currentObjects:
if ccpCode not in [typeProp.possibility.ccpCode for typeProp in spinSystem.getResidueTypeProbs()]:
chemComp = self.chemCompDict.get(ccpCode)
spinSystem.newResidueTypeProb(possibility=chemComp)
self.updateTable()
self.updateRemoveCcpCodePullDown()
def removeProb(self):
'''Removes the residueTypeProb selected in the
selectCcpCodeRemovePulldown from the selected resonanceGroup.
'''
ccpCode = self.selectCcpCodeRemovePulldown.object
for spinSystem in self.table.currentObjects:
residueTypeProbs = spinSystem.getResidueTypeProbs()
for typeProb in residueTypeProbs:
if ccpCode == 'All Residue Types' or ccpCode == typeProb.possibility.ccpCode:
typeProb.delete()
self.updateTable()
self.updateRemoveCcpCodePullDown()
def createChemCompDict(self):
'''Make a list of all amino acid types present in any of the
molecular chains present in the project.
'''
chains = self.getChains()
for chain in chains:
for residue in chain.sortedResidues():
if residue.ccpCode not in self.chemCompDict:
self.chemCompDict[residue.ccpCode] = residue.chemCompVar.chemComp
def getChains(self):
'''Get all molecular chains stored in the project.'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateTable(self):
'''Update the whole table.'''
objectList = []
data = []
for spinSystem in self.getSpinSystems():
objectList.append(spinSystem)
residueTypeProbs = spinSystem.getResidueTypeProbs()
spinSystemInfo = self.getStringDescriptionOfSpinSystem(spinSystem)
probString = ''
for typeProp in residueTypeProbs:
probString += typeProp.possibility.ccpCode + ' '
data.append([spinSystem.serial, spinSystemInfo, probString])
self.table.update(objectList=objectList, textMatrix=data)
def getStringDescriptionOfSpinSystem(self, spinsys):
'''Get a simple identifier for the assignment status of a
resonanceGroup.
'''
spinSystemInfo = ''
if spinsys.residue:
spinSystemInfo += str(spinsys.residue.seqCode) + ' ' + spinsys.residue.ccpCode
elif spinsys.residueProbs:
for residueProb in spinsys.residueProbs:
res = residueProb.possibility
spinSystemInfo += '{} {}? /'.format(res.seqCode, res.ccpCode)
spinSystemInfo = spinSystemInfo[:-1]
elif spinsys.ccpCode:
spinSystemInfo += spinsys.ccpCode
return spinSystemInfo
def __init__(self, parent, dangleGui, project=None, *args, **kw):
self.guiParent = parent
self.dangleGui = dangleGui
self.dangleDir = None
self.dangleChain = None
self.dangleResidue = None
#self.outDir = OUTDIR
self.row = None
self.col = None
self.project = project
self.nmrProject = None
self.colorScheme = 'red'
self.chain = None
self.shiftList = None
self.dangleStore = False # Not None
self.constraintSet = None
self.ensemble = None
Frame.__init__(self, parent=parent)
self.grid_columnconfigure(0, weight=1)
self.grid_rowconfigure(1, weight=1)
row = 0
# TOP LEFT FRAME
frame = LabelFrame(self, text='Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.columnconfigure(5, weight=1)
label = Label(frame, text='Chain')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Choose the molecular system chain to make predictions for'
)
self.chainPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Shift List')
label.grid(row=0, column=2, sticky='w')
self.shiftListPulldown = PulldownList(
frame,
callback=self.changeShiftList,
tipText='Select the shift list to take input chemical shifts from')
self.shiftListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Max No. of Islands:')
label.grid(row=0, column=4, sticky='w')
sizes = range(10)
texts = [str(s) for s in sizes] + [
'Do not reject',
]
self.rejectPulldown = PulldownList(
frame,
texts=texts,
objects=sizes + [
None,
],
tipText=
'Select the maximum allowed number of disontinuous prediction islands'
)
self.rejectPulldown.set(DEFAULT_MAX_ISLANDS) # Actual value not index
self.rejectPulldown.grid(row=0, column=5, sticky='w')
label = Label(frame, text='Dangle Run:')
label.grid(row=1, column=0, sticky='w')
self.dangleStorePulldown = PulldownList(
frame,
callback=self.changeDangleStore,
tipText='Select a run number to store DANGLE results within')
self.dangleStorePulldown.grid(row=1, column=1, sticky='w')
label = Label(frame, text='Ensemble:')
label.grid(row=1, column=2, sticky='w')
self.ensemblePulldown = PulldownList(
frame,
callback=self.changeEnsemble,
tipText=
'Select the structure ensemble for superimposition of angle values on the GLE plots'
)
self.ensemblePulldown.grid(row=1, column=3, sticky='w')
label = Label(frame, text='Restraint Set:')
label.grid(row=1, column=4, sticky='w')
self.constrSetPulldown = PulldownList(
frame,
callback=self.changeConstraintSet,
tipText=
'Select the CCPN restraint set to store DANGLE dihedral angle restraints in'
)
self.constrSetPulldown.grid(row=1, column=5, sticky='w')
# TOP RIGHT FRAME
outerFrame = Frame(self)
outerFrame.grid(row=row, column=1, rowspan=2, sticky='nsew')
outerFrame.rowconfigure(0, weight=1)
outerFrame.columnconfigure(0, weight=1)
frame = LabelFrame(outerFrame, text='Global Likelihood Estimates')
frame.grid(row=0, column=0, sticky='nsew')
frame.rowconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
self.prevPlot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=180,
height=180,
bgColor=self.cget('bg'),
nullColor='#000000',
titleText='Previous',
xTicks=False,
yTicks=False,
xLabel='',
yLabel='',
showCoords=False)
self.prevPlot.grid(row=0, column=0, sticky='nsew')
self.prevPlot.getPlotColor = self.getPlotColor
self.nextPlot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=180,
height=180,
bgColor=self.cget('bg'),
nullColor='#000000',
titleText='Next',
xTicks=False,
yTicks=False,
xLabel='',
yLabel='',
showCoords=False)
self.nextPlot.grid(row=0, column=1, sticky='nsew')
self.nextPlot.getPlotColor = self.getPlotColor
self.plot = ViewRamachandranFrame(frame,
relief='sunken',
defaultPlot=False,
width=360,
height=360,
bgColor=self.cget('bg'),
nullColor='#000000')
self.plot.grid(row=1, column=0, columnspan=2, sticky='nsew')
self.plot.selectColor = '#FFB0B0'
self.plot.getPlotColor = self.getPlotColor
# BOTTOM RIGHT FRAME
frame = Frame(outerFrame)
frame.grid(row=1, column=0, sticky='nsew')
frame.rowconfigure(0, weight=1)
frame.columnconfigure(0, weight=1)
texts = ('Previous', ' Next ')
commands = (self.showPrevious, self.showNext)
tipTexts = [
'Show GLE plot of angle predictions for previous residue in chain',
'Show GLE plot of angle predictions for next residue in chain'
]
buttonList = ButtonList(frame, texts, commands, tipTexts=tipTexts)
buttonList.grid(row=0, column=0, sticky='nsew')
row += 1
# BOTTOM LEFT FRAME
frame = LabelFrame(self, text='Dihedral Angle Predictions')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.floatEntry = FloatEntry(self,
text='',
returnCallback=self.setFloatEntry,
width=10,
formatPlaces=9)
tipTexts = [
'Residue number in chain', 'Residue type code',
'Number of high scoring discontinuous angle predictions',
'Predicted secondary structure code',
'Predicted phi dihedral angle (CO-N-CA-CO)',
'Predicted psi dihedral angle (N-CA-CO-N)',
'Upper bound of phi angle prediction',
'Lower bound of phi angle prediction',
'Upper bound of psi angle prediction',
'Lower bound of phi angle prediction',
'Chemical shifts used in prediction'
]
headingList = [
'Res\nNum', 'Res\nType', 'No. of\nIslands', 'SS', 'Phi', 'Psi',
'Phi\nUpper', 'Phi\nLower', 'Psi\nUpper', 'Psi\nLower',
'Chemical Shifts'
]
editWidgets = [
None, None, None, None, self.floatEntry, self.floatEntry,
self.floatEntry, self.floatEntry, self.floatEntry, self.floatEntry
]
editGetCallbacks = [
None, None, None, None, self.getFloatEntry, self.getFloatEntry,
self.getFloatEntry, self.getFloatEntry, self.getFloatEntry,
self.getFloatEntry
]
editSetCallbacks = [
None, None, None, None, self.setFloatEntry, self.setFloatEntry,
self.setFloatEntry, self.setFloatEntry, self.setFloatEntry,
self.setFloatEntry
]
self.predictionMatrix = ScrolledMatrix(
frame,
headingList=headingList,
multiSelect=True,
callback=self.selectCell,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
# doubleCallback=self.loadGLEs)
self.predictionMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
tipTexts = [
'Remove the predictions for the selected residues',
'Run the DANGLE method to predict dihedral angles and secondary structure',
'Delete the DANGLE results stored under the current run number',
'Store the angle predictions and bounds in a new CCPN dihedral angle restraint list',
'Store the secondary structure predictions in the CCPN project'
]
texts = [
'Clear\nSelected', 'Run Prediction!', 'Delete\nCurrent Run',
'Commit\nRestraints', 'Commit\nSecondary Structure'
]
commands = [
self.clearSelected, self.runDangle, self.deleteRun,
self.storeDihedralConstraints, self.storeSecondaryStructure
]
self.buttonList = createDismissHelpButtonList(
self,
texts=texts,
commands=commands, # dismiss_text='Quit',
dismiss_cmd=self.dangleGui.quit,
help_url=self.dangleGui.help_url,
expands=True,
tipTexts=tipTexts)
self.buttonList.grid(row=row, column=0, columnspan=2, sticky='ew')
self.buttonList.buttons[1].config(bg='#C0FFFF')
self.updateProject(project)
self.notify(dangleGui.registerNotify)
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index-2
format = ['PDB','CCPN','CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get()
if not file:
showWarning('Failure','No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append( ('script',script) )
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [ FileType('CING', ['project.xml']),
FileType('All', ['*'])
]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Select CING project file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy,name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'PDB file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir,name,dummy = nTpath( fileName )
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CCPN project XML file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir,name,dummy = nTpath( fileName )
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CYANA fproject file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self ):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self ):
fName = self.projEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open( name=fName, status='old', verbose=False )
#end def
def initPdb(self ):
fName = self.pdbEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open( self.nameEntry.get(), status='new' )
self.project.initPDB( pdbFile=fName, convention = 'PDB' )
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:',geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:',geometry
sys.exit(0) # remove later
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
def body(self, guiFrame):
row = 0
col = 0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu(guiFrame)
self.menuBar.grid(row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col = 0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes)
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew')
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = [
'old', 'new from PDB', 'new from CCPN', 'new from CYANA'
]
self.projOptionsSelect = RadioButtons(frame,
selected_index=0,
entries=self.projectOptions,
direction='vertical',
select_callback=self.updateGui)
self.projOptionsSelect.grid(row=srow,
column=0,
rowspan=len(self.projectOptions),
columnspan=2,
sticky='w')
if self.options.name:
text = self.options.name
else:
text = ''
# end if
self.projEntry = Entry(frame,
bd=1,
text=text,
returnCallback=self.updateGui)
self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame,
bd=1,
command=self.chooseOldProjectFile,
text='browse')
projButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow, column=2, sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame,
bd=1,
command=self.choosePdbFile,
text='browse')
pdbButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow, column=2, sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame,
bd=1,
command=self.chooseCcpnFile,
text='browse')
ccpnButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow, column=2, sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame,
bd=1,
command=self.chooseCyanaFile,
text='browse')
cyanaButton.grid(row=srow, column=3, sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow, column=0, sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow, column=2, sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.openProjectButton = Button(frame,
command=self.openProject,
text='Open Project',
**actionButtonAttributes)
self.openProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid(row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame,
height=11,
width=70,
borderwidth=0,
relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.closeProjectButton = Button(frame,
command=self.closeProject,
text='Close Project',
**actionButtonAttributes)
self.closeProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row += 1
col = 0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow, column=0, sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1, sticky='nw')
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow, column=2, sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1, sticky='nw')
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1, sticky='nw')
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1, sticky='nw')
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1, sticky='nw')
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,
column=2,
columnspan=3,
sticky='ew')
scriptButton = Button(frame,
bd=1,
command=self.chooseValidScript,
text='browse')
scriptButton.grid(row=srow, column=5, sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow, column=0, sticky='nw')
self.rangesEntry = Entry(frame, text='')
self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation', 'View Results', 'Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row += 0
col = 1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame,
text='Miscellaneous',
**labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1, minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow, column=0, sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1, sticky='nw')
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1, sticky='nw')
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1, sticky='nw')
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1, sticky='nw')
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1, sticky='nw')
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow, column=3, sticky='ew')
script2Button = Button(frame,
bd=1,
command=self.chooseMiscScript,
text='browse')
script2Button.grid(row=srow, column=4, sticky='ew')
srow += 1
texts = ['Export', 'Run Script']
commands = [None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row += 1
col = 0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index - 2
format = ['PDB', 'CCPN', 'CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry,
self.cyanaEntry][i].get()
if not file:
showWarning('Failure', 'No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append(('script', script))
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [FileType('CING', ['project.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Select CING project file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy, name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='PDB file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir, name, dummy = nTpath(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CCPN project XML file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir, name, dummy = nTpath(fileName)
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CYANA fproject file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self):
fName = self.projEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open(name=fName,
status='old',
verbose=False)
#end def
def initPdb(self):
fName = self.pdbEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open(self.nameEntry.get(), status='new')
self.project.initPDB(pdbFile=fName, convention='PDB')
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [
self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry,
self.nameEntry
]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(
sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:', geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:', geometry
sys.exit(0) # remove later
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
options = ['Parameters','Restraints','Alignment Media & Tensors','About Meccano']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
frameA, frameB, frameC, frameD = tabbedFrame.frames
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_rowconfigure(13, weight=1)
frameB.grid_columnconfigure(1, weight=1)
frameB.grid_rowconfigure(1, weight=1)
frameC.grid_columnconfigure(0, weight=1)
frameC.grid_rowconfigure(1, weight=1)
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(0, weight=1)
texts = ['Run MECCANO!']
commands = [self.runMeccano]
bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts,
commands=commands, expands=True)
bottomButtons.grid(row=1, column=0, sticky='ew')
if not Meccano:
bottomButtons.buttons[0].disable()
# Parameters
row = 0
label = Label(frameA, text='Calculation Run:')
label.grid(row=row,column=0,sticky='w')
self.runPulldown = PulldownList(frameA, callback=self.selectRun)
self.runPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Shift List (for CO):')
label.grid(row=row,column=0,sticky='w')
self.shiftListPulldown = PulldownList(frameA, callback=self.selectShiftList)
self.shiftListPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Keep Copy of Used Shifts:')
label.grid(row=row,column=0,sticky='w')
self.toggleCopyShifts = CheckButton(frameA)
self.toggleCopyShifts.grid(row=row,column=1,sticky='w')
self.toggleCopyShifts.set(True)
row += 1
label = Label(frameA, text='Molecular System:')
label.grid(row=row,column=0,sticky='w')
self.molSystemPulldown = PulldownList(frameA, callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Chain:')
label.grid(row=row,column=0,sticky='w')
self.chainPulldown = PulldownList(frameA, callback=self.selectChain)
self.chainPulldown.grid(row=row,column=1,sticky='w')
self.chainPulldown.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='First Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.firstResEntry = IntEntry(frameA, text=None, width=8)
self.firstResEntry.grid(row=row,column=1,sticky='w')
self.firstResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Last Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.lastResEntry = IntEntry(frameA, text=None, width=8)
self.lastResEntry.grid(row=row,column=1,sticky='w')
self.lastResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Max Num Optimisation Steps:')
label.grid(row=row,column=0,sticky='w')
self.maxOptStepEntry = IntEntry(frameA, text=500, width=8)
self.maxOptStepEntry.grid(row=row,column=1,sticky='w')
self.maxOptStepEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Num Optimisation Peptide Planes:')
label.grid(row=row,column=0,sticky='w')
self.numOptPlaneEntry = IntEntry(frameA, text=2, width=8)
self.numOptPlaneEntry.grid(row=row,column=1,sticky='w')
self.numOptPlaneEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Min Num Optimisation Hits:')
label.grid(row=row,column=0,sticky='w')
self.numOptHitsEntry = IntEntry(frameA, text=5, width=8)
self.numOptHitsEntry.grid(row=row,column=1,sticky='w')
self.numOptHitsEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='File Name Prefix:')
label.grid(row=row,column=0,sticky='w')
self.pdbFileEntry = Entry(frameA, text='Meccano', width=8)
self.pdbFileEntry.grid(row=row,column=1,sticky='w')
self.pdbFileEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write Output File (.out):')
label.grid(row=row,column=0,sticky='w')
self.toggleWriteOutFile = CheckButton(frameA)
self.toggleWriteOutFile.grid(row=row,column=1,sticky='w')
self.toggleWriteOutFile.set(False)
self.toggleWriteOutFile.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write PDB File (.pdb):')
label.grid(row=row,column=0,sticky='w')
self.toggleWritePdbFile = CheckButton(frameA)
self.toggleWritePdbFile.grid(row=row,column=1,sticky='w')
self.toggleWritePdbFile.set(True)
self.toggleWritePdbFile.bind('<Leave>', self.updateRunParams)
if not Meccano:
row += 1
label = Label(frameA, text='The Meccano executable is not available (it needs to be compiled)', fg='red')
label.grid(row=row,column=0,columnspan=2,sticky='w')
# Restraints
label = Label(frameB, text='Constraint Set:')
label.grid(row=0,column=0,sticky='w')
self.constraintSetPulldown = PulldownList(frameB, callback=self.selectConstraintSet)
self.constraintSetPulldown.grid(row=0,column=1,sticky='w')
self.alignMediumPulldown= PulldownList(self, callback=self.setAlignMedium)
headingList = ['#','List Type','Use?','Alignment\nMedium','Num\nRestraints']
editWidgets = [None,None,None,self.alignMediumPulldown,None]
editGetCallbacks = [None,None,self.toggleUseRestraints,self.getAlignMedium,None]
editSetCallbacks = [None,None,None,self.setAlignMedium,None]
self.restraintMatrix = ScrolledMatrix(frameB,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=None,
multiSelect=True)
self.restraintMatrix.grid(row=1,column=0,columnspan=2,sticky='nsew')
# Alignment Media
div = LabelDivider(frameC,text='Alignment Media')
div.grid(row=0,column=0,sticky='ew')
self.mediumNameEntry = Entry(self, returnCallback=self.setMediumName)
self.mediumDetailsEntry = Entry(self, returnCallback=self.setMediumDetails)
headingList = ['#','Name','Details','Static Tensor','Dynamic Tensor']
editWidgets = [None, self.mediumNameEntry, self.mediumDetailsEntry, None, None]
editGetCallbacks = [None, self.getMediumName, self.getMediumDetails, None, None]
editSetCallbacks = [None, self.setMediumName, self.setMediumDetails, None, None]
self.mediaMatrix = ScrolledMatrix(frameC,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAlignMedium,
multiSelect=True)
self.mediaMatrix.grid(row=1,column=0,sticky='nsew')
texts = ['Add Alignment medium','Remove Alignment Medium']
commands = [self.addAlignMedium,self.removeAlignMedium]
buttonList = ButtonList(frameC, texts=texts, commands=commands, expands=True)
buttonList.grid(row=2,column=0,sticky='nsew')
self.editAxialEntry = FloatEntry(self, returnCallback=self.setAxial)
self.editRhombicEntry = FloatEntry(self, returnCallback=self.setRhombic)
self.editAlphaEulerEntry = FloatEntry(self, returnCallback=self.setEulerAlpha)
self.editBetaEulerEntry = FloatEntry(self, returnCallback=self.setEulerBeta)
self.editGammaEulerEntry = FloatEntry(self, returnCallback=self.setEulerGamma)
div = LabelDivider(frameC,text='Alignment Tensors')
div.grid(row=3,column=0,sticky='ew')
headingList = ['Type', u'Axial (\u03B6)',u'Rhombic (\u03B7)',
u'Euler \u03B1',u'Euler \u03B2',u'Euler \u03B3']
editWidgets = [None,self.editAxialEntry,
self.editRhombicEntry,self.editAlphaEulerEntry,
self.editBetaEulerEntry,self.editGammaEulerEntry]
editSetCallbacks = [None,self.setAxial,self.setRhombic,
self.setEulerAlpha,self.setEulerBeta,self.setEulerGamma]
editGetCallbacks = [None,self.getAxial,self.getRhombic,
self.getEulerAlpha,self.getEulerBeta,self.getEulerGamma]
self.tensorMatrix = ScrolledMatrix(frameC, maxRows=2,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectTensor,
multiSelect=True)
self.tensorMatrix.grid(row=4,column=0,sticky='nsew')
texts = ['Add Static Tensor','Add Dynamic Tensor','Remove Tensor']
commands = [self.addStaticTensor,self.addDynamicTensor,self.removeTensor]
buttonList = ButtonList(frameC,texts=texts, commands=commands, expands=True)
buttonList.grid(row=5,column=0,sticky='ew')
# About
label = Label(frameD, text='About Meccano...')
label.grid(row=0,column=0,sticky='w')
#
self.geometry('500x400')
self.updateShiftLists()
self.updateMolSystems()
self.updateResidueRanges()
self.updateConstraintSets()
self.updateAlignMedia()
self.updateRuns()
def body(self, guiFrame):
row = 0
col = 0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu(guiFrame)
self.menuBar.grid(row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col = 0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes)
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew')
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = [
'old', 'new from PDB', 'new from CCPN', 'new from CYANA'
]
self.projOptionsSelect = RadioButtons(frame,
selected_index=0,
entries=self.projectOptions,
direction='vertical',
select_callback=self.updateGui)
self.projOptionsSelect.grid(row=srow,
column=0,
rowspan=len(self.projectOptions),
columnspan=2,
sticky='w')
if self.options.name:
text = self.options.name
else:
text = ''
# end if
self.projEntry = Entry(frame,
bd=1,
text=text,
returnCallback=self.updateGui)
self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame,
bd=1,
command=self.chooseOldProjectFile,
text='browse')
projButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow, column=2, sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame,
bd=1,
command=self.choosePdbFile,
text='browse')
pdbButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow, column=2, sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame,
bd=1,
command=self.chooseCcpnFile,
text='browse')
ccpnButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow, column=2, sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame,
bd=1,
command=self.chooseCyanaFile,
text='browse')
cyanaButton.grid(row=srow, column=3, sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow, column=0, sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow, column=2, sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.openProjectButton = Button(frame,
command=self.openProject,
text='Open Project',
**actionButtonAttributes)
self.openProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid(row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame,
height=11,
width=70,
borderwidth=0,
relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.closeProjectButton = Button(frame,
command=self.closeProject,
text='Close Project',
**actionButtonAttributes)
self.closeProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row += 1
col = 0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow, column=0, sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1, sticky='nw')
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow, column=2, sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1, sticky='nw')
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1, sticky='nw')
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1, sticky='nw')
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1, sticky='nw')
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,
column=2,
columnspan=3,
sticky='ew')
scriptButton = Button(frame,
bd=1,
command=self.chooseValidScript,
text='browse')
scriptButton.grid(row=srow, column=5, sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow, column=0, sticky='nw')
self.rangesEntry = Entry(frame, text='')
self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation', 'View Results', 'Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row += 0
col = 1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame,
text='Miscellaneous',
**labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1, minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow, column=0, sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1, sticky='nw')
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1, sticky='nw')
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1, sticky='nw')
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1, sticky='nw')
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1, sticky='nw')
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow, column=3, sticky='ew')
script2Button = Button(frame,
bd=1,
command=self.chooseMiscScript,
text='browse')
script2Button.grid(row=srow, column=4, sticky='ew')
srow += 1
texts = ['Export', 'Run Script']
commands = [None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row += 1
col = 0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
class HelpFrame(Frame):
def __init__(self,
parent,
width=70,
height=20,
xscroll=False,
yscroll=True,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
row = 0
texts = ('back', 'forward', 'load')
commands = (self.prevUrl, self.nextUrl, self.loadUrl)
self.buttons = ButtonList(self, texts=texts, commands=commands)
self.buttons.grid(row=row, column=0)
self.url_entry = Entry(self, returnCallback=self.loadUrl)
self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.createFindFrame(frame)
row = row + 1
self.grid_rowconfigure(row, weight=1)
self.help_text = ScrolledHtml(self,
width=width,
height=height,
xscroll=xscroll,
yscroll=yscroll,
startUrlCallback=self.startOpenUrl,
endUrlCallback=self.endOpenUrl,
enterLinkCallback=self.setLinkLabel,
leaveLinkCallback=self.setLinkLabel)
self.help_text.grid(row=row,
column=0,
columnspan=3,
sticky=Tkinter.NSEW)
row = row + 1
self.link_label = Label(self)
self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
button = memops.gui.Util.createDismissButton(self,
dismiss_cmd=self.close)
button.grid(row=row, column=2)
self.urls = []
self.current = -1
self.updateUrlList = True
self.setButtonState()
def close(self):
if (self.popup):
if (self.popup.modal):
self.popup.do_grab()
popup = self.parent
while (not hasattr(popup, 'top')):
popup = popup.parent
popup.close()
def createFindFrame(self, master):
frame = Frame(master)
frame.grid(row=0, column=0, sticky=Tkinter.W)
arrow = ToggleArrow(frame, callback=self.toggleFindFrame)
arrow.grid(row=0, column=0)
button = Button(frame, text='find:', command=self.findPhrase)
button.grid(row=0, column=1)
self.find_entry = Entry(frame,
width=20,
returnCallback=self.findPhrase)
self.find_entry.grid(row=0, column=2)
self.find_frame = frame = Frame(master)
entries = ('search forwards', 'search backwards')
self.direction_buttons = PulldownMenu(frame, entries=entries)
self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5)
self.forwards_entries = entries = ('wrap search', 'stop at end')
self.backwards_entries = ('wrap search', 'stop at beginning')
self.wrap_buttons = PulldownMenu(frame, entries=entries)
self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5)
self.direction_buttons.callback = self.setWrapText
entries = ('case insensitive', 'case sensitive')
self.case_buttons = PulldownMenu(frame, entries=entries)
self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5)
entries = ('literal search', 'regex search')
self.pattern_buttons = PulldownMenu(frame, entries=entries)
self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5)
self.countVar = Tkinter.IntVar()
def setWrapText(self, entry_ind, entry):
if (entry_ind == 0):
entries = self.forwards_entries
else:
entries = self.backwards_entries
self.wrap_buttons.replace(
entries, selected_index=self.wrap_buttons.getSelectedIndex())
def findPhrase(self, *extra):
phrase = self.find_entry.get()
if (not phrase):
showError('No find phrase', 'Enter phrase in entry box.')
return
if (self.direction_buttons.getSelectedIndex() == 0):
forwards = 1
backwards = 0
else:
forwards = 0
backwards = 1
if (self.case_buttons.getSelectedIndex() == 0):
nocase = 1
else:
nocase = 0
if (self.pattern_buttons.getSelectedIndex() == 0):
exact = 1
regexp = 0
else:
exact = 0
regexp = 1
start = self.help_text.tag_nextrange(Tkinter.SEL, '1.0')
if (start):
start = start[0]
if (forwards):
start = '%s+1c' % start
else:
start = '%s-1c' % start
else:
start = Tkinter.CURRENT
if (self.wrap_buttons.getSelectedIndex() == 0):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp)
elif (forwards):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex=Tkinter.END)
else:
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex='1.0')
if (match):
self.help_text.see(match)
self.help_text.setSelection(
match, '%s+%dc' % (match, self.countVar.get()))
self.help_text.tag_config(Tkinter.SEL, background='gray70')
else:
showInfo('No match', 'No match found for phrase.')
def toggleFindFrame(self, isClosed):
if (isClosed):
self.find_frame.grid_forget()
else:
self.find_frame.grid(row=1, column=0, sticky=Tkinter.W)
def setButtonState(self):
n = len(self.urls)
if ((n >= 2) and (self.current > 0)):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[0].config(state=state)
if ((n >= 2) and (self.current < (n - 1))):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[1].config(state=state)
def setLinkLabel(self, url=''):
self.link_label.set(url)
def loadUrl(self, *extra):
url = self.url_entry.get()
if (url):
if (url.find(':') == -1):
if (url[:2] != '//'):
url = '//' + url
url = 'http:' + url
self.showUrl(url, forceLoad=True)
def newUrl(self, url):
self.current = self.current + 1
self.urls[self.current:] = [[url, 0.0]]
self.setButtonState()
#print 'newUrl', self.current, self.urls
def prevUrl(self):
if (self.current > 0): # True if called via button
(url, offset) = self.urls[self.current - 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current - 1
self.setButtonState()
#print 'prevUrl', self.current, self.urls
def nextUrl(self):
if (self.current < (len(self.urls) - 1)): # True if called via button
(url, offset) = self.urls[self.current + 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current + 1
self.setButtonState()
#print 'nextUrl', self.current, self.urls
def showText(self, message, popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.setState(Tkinter.NORMAL) # so that can add text
self.help_text.clear() # clear existing text
self.help_text.append(message)
self.help_text.setState(Tkinter.DISABLED) # make text read-only
self.open()
def startOpenUrl(self, yview):
if (self.urls):
self.urls[self.current][1] = yview[0]
def endOpenUrl(self, url):
#print 'endOpenUrl', url, self.updateUrlList
self.url_entry.set(url)
if (self.updateUrlList):
self.newUrl(url)
self.setLinkLabel()
self.open()
def showUrl(self,
url,
offset=None,
forceLoad=False,
allowModifyPath=True,
popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.openUrl(url,
forceLoad=forceLoad,
allowModifyPath=allowModifyPath)
if (offset is not None):
self.help_text.yview(Tkinter.MOVETO, str(offset))
class CingFrame(NmrSimRunFrame):
def __init__(self, parent, application, *args, **kw):
project = application.project
simStore = project.findFirstNmrSimStore(application=APP_NAME) or \
project.newNmrSimStore(application=APP_NAME, name=APP_NAME)
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.nmrProject = application.nmrProject
self.serverDone = False
NmrSimRunFrame.__init__(self, parent, project, simStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureFrame.grid_forget()
tab = self.tabbedFrame.frames[0]
frame = Frame(tab, grid=(1,0))
frame.expandGrid(2,1)
div = LabelDivider(frame, text='Structures', grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Ensemble: ', grid=(1,0))
self.structurePulldown = PulldownList(frame, callback=self.changeStructure, grid=(1,1))
headingList = ['Model','Use']
editWidgets = [None,None]
editGetCallbacks = [None,self.toggleModel]
editSetCallbacks = [None,None,]
self.modelTable = ScrolledMatrix(frame, grid=(2,0), gridSpan=(1,2),
callback=self.selectStructModel,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame, texts=texts, commands=commands, grid=(3,0), gridSpan=(1,2))
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1,0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0,0))
frame.expandGrid(None,2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
urls = [DEFAULT_URL,]
self.iCingBaseUrlPulldown = PulldownList(frame, texts=urls, objects=urls, index=0, grid=(srow,1))
srow +=1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
self.setZipFileName()
button = Button(frame, text='Choose File', bd=1, sticky='ew',
command=self.chooseZipFile, grid=(srow, 2))
srow +=1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
button = Button(frame, text='View Results HTML', bd=1, sticky='ew',
command=self.viewHtmlResults, grid=(srow, 2))
srow +=1
texts = ['Submit Project!', 'Check Run Status',
'Purge Server Result', 'Download Results']
commands = [self.runCingServer, self.checkStatus,
self.purgeCingServer, self.downloadResults]
self.buttonBar = ButtonList(frame, texts=texts, commands=commands,
grid=(srow, 0), gridSpan=(1,3))
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1,0))
frame.expandGrid(1,1)
label = Label(frame, text='Chain: ')
label.grid(row=0,column=0,sticky='w')
self.chainPulldown = PulldownList(frame, callback=self.changeChain)
self.chainPulldown.grid(row=0,column=1,sticky='w')
headingList = ['#','Residue','Linking','Decriptor','Use?']
editWidgets = [None,None,None,None,None]
editGetCallbacks = [None,None,None,None,self.toggleResidue]
editSetCallbacks = [None,None,None,None,None,]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky = 'nsew')
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame, texts=texts, commands=commands,)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(simStore)
self.administerNotifiers(application.registerNotify)
def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query',msg, parent=self):
self.purgeCingServer()
def getServerUrl(self, baseUrl):
iCingUrl = os.path.join(baseUrl, 'icing/serv/iCingServlet')
return iCingUrl
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structure = self.structure
if not structure:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
ensembleText = getModelsString(run)
if not ensembleText:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueText = getResiduesString(structure)
if not residueText:
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID, self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY, self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials, self.getServerUrl(url))
if results:
showInfo('Info','iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info','Purge failed')
self.update()
def chooseZipFile(self):
fileTypes = [ FileType('Zip', ['*.zip']), ]
popup = FileSelectPopup(self, file_types=fileTypes, file=self.resultFileEntry.get(),
title='Results zip file location', dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def setZipFileName(self):
zipFile = '%s_CING_report.zip' % self.project.name
self.resultFileEntry.set(zipFile)
def selectStructModel(self, model, row, col):
self.model = model
def selectResidue(self, residue, row, col):
self.residue = residue
def deactivateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = False
self.updateResidues()
def activateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = True
self.updateResidues()
def activateModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model not in self.run.inputStructures:
self.run.addInputStructure(model)
self.updateModels()
def disableModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model in self.run.inputStructures:
self.run.removeInputStructure(model)
self.updateModels()
def toggleModel(self, *opt):
if self.model and self.run:
if self.model in self.run.inputStructures:
self.run.removeInputStructure(self.model)
else:
self.run.addInputStructure(self.model)
self.updateModels()
def toggleResidue(self, *opt):
if self.residue:
self.residue.useInCing = not self.residue.useInCing
self.updateResidues()
def updateResidues(self):
if self.residue and (self.residue.topObject is not self.structure):
self.residue = None
textMatrix = []
objectList = []
colorMatrix = []
if self.chain:
chainCode = self.chain.code
for residue in self.chain.sortedResidues():
msResidue = residue.residue
if not hasattr(residue, 'useInCing'):
residue.useInCing = True
if residue.useInCing:
colors = [None, None, None, None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None, None, None, None]
use = 'No'
datum = [residue.seqCode,
msResidue.ccpCode,
msResidue.linking,
msResidue.descriptor,
use,]
textMatrix.append(datum)
objectList.append(residue)
colorMatrix.append(colors)
self.residueMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def updateChains(self):
index = 0
names = []
chains = []
chain = self.chain
if self.structure:
chains = self.structure.sortedCoordChains()
names = [chain.code for chain in chains]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
self.changeChain(chain)
self.chainPulldown.setup(names, chains, index)
def updateStructures(self):
index = 0
names = []
structures = []
structure = self.structure
if self.run:
model = self.run.findFirstInputStructure()
if model:
structure = model.structureEnsemble
structures0 = [(s.ensembleId, s) for s in self.project.structureEnsembles]
structures0.sort()
for eId, structure in structures0:
name = '%s:%s' % (structure.molSystem.code, eId)
structures.append(structure)
names.append(name)
if structures:
if structure not in structures:
structure = structures[-1]
index = structures.index(structure)
self.changeStructure(structure)
self.structurePulldown.setup(names, structures, index)
def updateModels(self):
textMatrix = []
objectList = []
colorMatrix = []
if self.structure and self.run:
used = self.run.inputStructures
for model in self.structure.sortedModels():
if model in used:
colors = [None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None]
use = 'No'
datum = [model.serial,use]
textMatrix.append(datum)
objectList.append(model)
colorMatrix.append(colors)
self.modelTable.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def changeStructure(self, structure):
if self.project and (self.structure is not structure):
self.project.currentEstructureEnsemble = structure
self.structure = structure
if self.run:
self.run.inputStructures = structure.sortedModels()
self.updateModels()
self.updateChains()
def changeChain(self, chain):
if self.project and (self.chain is not chain):
self.chain = chain
self.updateResidues()
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('Python', ['*.py']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title='Python file', dismiss_text='Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
simStore = project.findFirstNmrSimStore(application='CING') or \
project.newNmrSimStore(application='CING', name='CING')
else:
simStore = None
if not self.project:
return
self.setZipFileName()
if not self.project.currentNmrProject:
name = self.project.name
self.nmrProject = self.project.newNmrProject(name=name)
else:
self.nmrProject = self.project.currentNmrProject
self.update(simStore)
def update(self, simStore=None):
NmrSimRunFrame.update(self, simStore)
run = self.run
urls = [DEFAULT_URL,]
index = 0
if run:
userId = getRunParameter(run, iCingRobot.FORM_USER_ID)
accessKey = getRunParameter(run, iCingRobot.FORM_ACCESS_KEY)
if userId and accessKey:
self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId),
(iCingRobot.FORM_ACCESS_KEY, accessKey)]
url = getRunParameter(run, ICING_BASE_URL)
if url:
htmlUrl = getRunParameter(run, HTML_RESULTS_URL)
self.iCingBaseUrl = url
self.resultsUrl = htmlUrl # May be None
self.resultUrlEntry.set(self.resultsUrl)
if self.iCingBaseUrl and self.iCingBaseUrl not in urls:
index = len(urls)
urls.append(self.iCingBaseUrl)
self.iCingBaseUrlPulldown.setup(urls, urls, index)
self.updateButtons()
self.updateStructures()
self.updateModels()
self.updateChains()
def updateButtons(self, event=None):
buttons = self.buttonBar.buttons
if self.project and self.run:
buttons[0].enable()
if self.resultsUrl and self.serverCredentials:
buttons[1].enable()
buttons[2].enable()
buttons[3].enable()
else:
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
else:
buttons[0].disable()
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
class SaveLoadTab(object):
'''The tab that lets the user FileSelect
a file to open or to save.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.loadAndSaveButtons = None
self.fileselectionBox = None
self.body()
def body(self):
'''Setting up the body of this view.'''
frame = self.frame
file_types = [FileType('pyc', ['*.pyc'])]
self.fileselectionBox = FileSelect(frame,
multiSelect=False,
file_types=file_types)
self.fileselectionBox.grid(row=0,
column=0,
columnspan=6,
sticky='nsew')
texts = ['Load', 'Save']
commands = [self.loadDataFromPyc, self.saveDataToPyc]
self.loadAndSaveButtons = ButtonList(frame,
commands=commands,
texts=texts)
self.loadAndSaveButtons.grid(row=1, column=0, sticky='nsew')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
def saveDataToPyc(self):
'''Save the data to the selected file.'''
if self.guiParent.connector.results:
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.saveDataToPyc(fileName)
self.fileselectionBox.updateFileList()
else:
string = ('''There are no results to save, '''
'''the algorithm has not run yet.''')
showWarning('No Results to Save', string, parent=self.guiParent)
def loadDataFromPyc(self):
'''Load the data from the selected file.'''
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.loadDataFromPyc(fileName)
self.guiParent.resultsTab.update()
class RepositoryFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Repository'] = self
# get a port proxy instance
# this should probably belong to the repository directly
# or else should belong in a dictionary in the main gui
# layer when it can be picked up easily
# FIXME JMCI
# need to work out how to get a number of these!
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=0)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=0, minsize=10)
self.grid_rowconfigure(5, weight=1, minsize=10)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
# widgets for view when no data
self.noDataWidgets = []
self.noRepLabel = Label(self, text='No repository currently selected.')
self.noDataWidgets.append(self.noRepLabel)
# widgets for view when current repository set
self.dataWidgets = []
self.repTitle = Label(self, text='Repository:', font='Helvetica16')
self.dataWidgets.append(self.repTitle)
#self.repLabel = Label(self,text='All Projects in Repository')
#self.dataWidgets.append(self.repLabel)
self.repTree = Tree(self, doubleCallback=self.goto_project_tab)
self.dataWidgets.append(self.repTree)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'],
select_callback=self.set_refresh,
selected_index=sel)
# need to decide whether this is static or not
r_button_texts = [
'Add to Basket', ' Import ', ' Export ', ' Refresh ',
'Properties'
]
r_button_cmds = [
self.tmpCall, self.import_project, self.export_project,
self.drawFrame, self.goto_project_tab
]
self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds)
self.dataWidgets.append(self.rep_button_list)
self.filterFrame = FilterFrame(self, self.basePopup, text='Filter')
self.dataWidgets.append(self.filterFrame)
baskets = ('basket1', 'basket2', 'basket3')
self.basketSelect = PulldownList(self, self.tmpCall, baskets)
self.dataWidgets.append(self.basketSelect)
basketElements = ('1ay3', '1ay7')
self.basketList = ScrolledListbox(self, basketElements, 25, 18)
self.dataWidgets.append(self.basketList)
b_button_texts = ['Remove from Basket', 'New Basket']
b_button_cmds = [self.tmpCall, self.tmpCall]
self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds)
self.dataWidgets.append(self.b_button_list)
# draw if not automatically refreshing
if sel == 1:
self.drawFrame()
# set up a loop
self.refresh()
def drawFrame(self):
if self.basePopup.repList.currentRepository == None:
for widget in self.dataWidgets:
widget.grid_remove()
self.noRepLabel.grid(row=1, column=1, sticky='n')
else:
self.repository = self.basePopup.repList.currentRepository
for widget in self.noDataWidgets:
widget.grid_remove()
# Column headers
# want to have a general admin panel; current repository, button to change, info
# about login and so on
self.repTitle.set('Repository: ' + self.repository.user + '@' +
self.repository.name + ' ( ' +
self.repository.connect + ' )')
self.repTitle.grid(row=1, column=1, sticky='w')
# self.repLabel.grid(row=2, column=1, sticky='w')
# Repository block
#grid and update
self.repTree.grid(row=3, column=1, rowspan=3, sticky='nsew')
self.updateRepTree()
self.autoRefreshSwitchLabel.grid(row=6,
column=1,
padx=10,
sticky='w')
self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e')
# the buttons for functionality in repository area
self.rep_button_list.grid(row=7, column=1, padx=3, sticky='ew')
# filter frame
self.filterFrame.grid(row=3, column=2, stick='nsew')
# list of baskest. Will callback to change current basket
self.basketSelect.grid(row=4, column=2, padx=10, stick='w')
# lists projects per basket
self.basketList.grid(row=5,
rowspan=2,
column=2,
padx=10,
stick='nsew')
self.b_button_list.grid(row=7, column=2, padx=5, stick='ew')
def openLink(self, node):
tree = node.tree
par = node.object
# this should be associated with the repository object
request = getList()
# FIXME JMCI
# 1. Potentially need to traverse up the node tree
# 2. Currently there is bug in expansion/contraction
# 3. Search needs to work off proxy method (not off
# generated stubs
# pass the parent name for now. may need other criteria later
h1 = {'name': par.__str__()}
h2 = {'project': h1}
wsstr_in = WSString(h2)
request._arg0 = 'org.pimslims.applet.server.ProjectVersionBean'
request._arg1 = 'getListWithFields'
request._arg2 = wsstr_in.str
# get the response
response = self.port.getList(request)
# currently we just get a list of numbers. May want to send
# all the fields for every object too to cut down on db calls
wsstr_out = WSString(response._return)
ss = wsstr_out.getStruct()
for hm in ss:
print 'handling ', hm, ', ', hm['status'].__str__()
#if hm['status'].__str__() == 'AVAILABLE':
icon = 'text-x-generic'
#else:
# icon='emblem-readonly'
pv = par.__str__() + '::' + hm['versionTag'].__str__()
obj = pv
text = hm['versionTag'].__str__()
callback = None
tree.add(node, obj, text, icon, callback)
def set_refresh(self, text):
print 'setting refresh ', text
if text == 'on':
self.autoRefresh = True
else:
self.autoRefresh = False
def refresh(self):
if self.autoRefresh:
print 'refreshing frame ', time.time()
self.drawFrame()
self.after(5000, self.refresh)
# FIME JMCI
# it would probably be a good idea to have a method that allowed
# a user to unlock a given project version. Would need to check
# permissions very carefully, though
def unlock_project_version(self):
pass
def goto_project_tab(self, node=None):
if node is None:
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
pv = node.object.__str__()
print 'GOTO PROJECT ', pv, ', ', node, ', ', node.object
pat = re.compile('::')
matcher = pat.search(pv, 0)
name = pv[0:matcher.start()]
versionTag = pv[matcher.end():]
print 'GOTO PROJECT ', name, ', ', versionTag
#versionTag = node.object.__str__()
#name = node.parent.object.__str__()
#print node.__dict__
#print node.parent.__dict__
self.basePopup.repList.currentRepository.currentProjectName = name
self.basePopup.repList.currentRepository.currentVersionTag = versionTag
# this is going to have to be keyed on a natural key that then
# gets set into the criteria of a ws query
# hack for now. build in later. Essentially, we have to handle two
# cases; that of a specific projectVersion request and that of a
# request on a project alone. Probably the best behaviour would be
# for the project-only request to default to the latest trunk
# version of the project and the most elegent way of triggering
# this would probably be to have this as a property of the project
# returned in the main hash from Project.getFields().
self.basePopup.tabbedFrame.select(1)
if self.basePopup.frameShortcuts.has_key('Project'):
self.basePopup.frameShortcuts['Project'].drawFrame()
def import_project(self):
# FIXME JMCI
# need to preserve the current status. Take default from the
# Wms layer
rootDir = self.basePopup.repList.current_import_dir
fileSelectPopup = FileSelectPopup(self, None, rootDir)
new_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_import_dir = new_project_dir
print 'in import project with directory', new_project_dir
idx = new_project_dir.rfind('/')
new_project_name = new_project_dir[idx + 1:]
print 'in import project with project', new_project_name
# FIXME
# need to set the project version number somewhere. For now set to none
# and this gets picked up and set to a default 1.1 later
self.repository.import_project(new_project_name, None, new_project_dir)
self.drawFrame()
def export_project(self):
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
name = node.parent.object.__str__()
versionTag = node.object.__str__()[len(name) + 2:]
# need to preserve the current status. Take a default from the
# Wms layer
rootDir = self.basePopup.repList.current_export_dir
# This should be obtained from a query box. Hard code for now
fileSelectPopup = FileSelectPopup(self, None, rootDir)
exp_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_export_dir = exp_project_dir
self.repository.export_project(name, versionTag, exp_project_dir)
def disconnectRepository(self):
# do we need to formally break a connection and destroy the session?
# yes we probably should.
# need an "are you sure" dialog box
# need to protect
self.repository.repList.repositories.remove(self.repository)
self.grid_remove()
for ff in self.guiParent.guiParent.parent.frames[0].children.values():
ff.drawFrame()
def tmpCall(self):
return
# This will need a separate call to the WS with an additional
# criterion (picking up the checkout version)
def updateRepTree(self):
texts = []
icons = []
parents = []
callbacks = []
objects = []
# OK, this would be a good point to access the list
# this should be associated with the repository object
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
request = getList()
# these are actually static
request._arg0 = 'org.pimslims.applet.server.ProjectBean'
request._arg1 = 'getList'
request._arg2 = ''
# get the response
response = port.getList(request)
# this is a hack at present. It needs to be written properly
wsstr = WSString(response._return)
ss = wsstr.getStruct()
for strg in ss:
texts.append(strg)
icons.append('folder')
parents.append(None)
objects.append(strg)
callbacks.append(self.openLink)
print 'UPDATE ', ss
print 'UPDATE ', len(ss)
if len(ss) > 0:
print 'UPDATE: updating '
self.repTree.update(parents, objects, texts, icons, callbacks)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
class WorkflowFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.basePopup.frameShortcuts['Workflow'] = self
#self.registerNotify=basePopup.registerNotify
#self.unregisterNotify=basePopup.unregisterNotify
Frame.__init__(self, guiParent)
self.grid_rowconfigure(0, weight=0)
self.grid_rowconfigure(1, weight=0, minsize=100)
self.grid_rowconfigure(2, weight=1)
self.grid_rowconfigure(3, weight=0, minsize=30)
self.grid_columnconfigure(0, weight=0)
self.grid_columnconfigure(1, weight=1)
self.grid_columnconfigure(2, weight=0)
# build up the body.
self.lcA = LinkChart(self, background='#8080B0', height=110)
self.lcB = LinkChart(self, background='#8080B0')
lcButtonOpts=['Load','Save','Clear','New Protocol']
lcButtonCmds=[self.tmpCall,self.tmpCall,self.tmpCall,self.tmpCall]
self.lcButtons = ButtonList(self, lcButtonOpts, lcButtonCmds)
# hack for now. This should come from db of meta-tasks
self.expts=['Test1','Test2','ARIA','CING','ISD']
# needs custom version
self.filter = FilterFrame(self, self.basePopup, text='Filter')
# no bean udnerneath for now so mock up nodes
self.wfTree = Tree(self, width=35)
wfButtonOpts=['Load','Save']
wfButtonCmds=[self.tmpCall,self.tmpCall]
self.wfButtons = ButtonList(self, wfButtonOpts, wfButtonCmds)
self.drawFrame()
def drawFrame(self):
# hack the WF Tree for now. just get is looking OK
texts=['JMCI WF 1','JMCI WF 2']
icons=[]
parents=[]
callbacks=[]
objects=['JMCI WF 1','JMCI WF 2']
for text in texts:
icons.append('list-add')
callbacks.append(None)
parents.append(None)
self.wfTree.update(parents, objects, texts, icons, callbacks)
self.lcA.grid(row=1, column=1, padx=5, pady=5, sticky='new')
self.lcB.grid(row=2, column=1, padx=5, pady=5, sticky='nsew')
self.lcButtons.grid(row=3, column=1, padx=5, pady=5, sticky='ew')
self.filter.grid(row=1, column=2, sticky='new')
self.wfTree.grid(row=2, column=2, padx=5, pady=5, sticky='nsew')
self.wfButtons.grid(row=3, column=2, padx=5, pady=5, sticky='ew')
self.nodes = []
x = 0
for expt in self.expts:
node = PrototypeNode(self.lcA, title=expt, width=38,
updateFunc=None, resizeable=False, shape='SQUARE',
coords=(50+x*90, 50), object=None)
x += 1
self.lcA.draw()
self.lcB.draw()
def tmpCall(self):
pass
def administerNotifiers(self, notifyFunc):
for func in ('__init__','delete','setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
if not self.nmrProject:
self.nmrProject = project.newNmrProject(name=project.name)
if not self.project:
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
class PeakSeparatorGui(BasePopup):
"""
**Separate Merged Peaks Using Peak Models**
The Peak Separator code uses a Markov Chain Monte Carlo search which, using
idealised peak shapes, attempts to deconvolve overlapped peak regions into
their separate constituent peaks.
This routine is also suitable for accurately fitting model shapes to single
peaks in order to calculate precise intensities.
**Options Peak Separator Parameters**
*Min. Number of peaks* is by default set to one, it is not possible to set
this to a value less than one.
*Max. Number of peaks* is by default set to one, increasing this value allows
the search routine to fit more models. The best fit may be found with fewer than
the maximum number models. Higher numbers slow the routine, and setting this
value to 0 allows the routine to (effectively) fit unlimited peaks.
*Only pick positive peaks*. If you are not interested in negative peaks, removing
the possibility of fitting negative peaks can reduce search time.
*Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian
peak model.
**Options Region**
*Peak List* choose which peak list newly picked peaks should be added to. Peaks
picked using this method will have their details appended with 'PeakSepartor'
so you know where they came from.
*Region Table* shows which area of the current spectrum is about to be searched.
*Add Region*. Once an area of spectra has been highlighted clicking this button
will pass it's details on to the Peak Separator.
*Reset All* will reset all search parameters.
*Separate Peaks* will run the Peak Separator code with your current settings. This
may take a few minutes to run, depending on the size of the spectral region being
searched, the number of peaks being fitted and the speed of your machine. Please
wait while this completes.
After a successful Peak Separation run, the found peaks will be added to the
selected peak list. These peaks intensties (volume) have been found using the
peak model selected.
**Advanced Settings Tab**
*Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value
results in longer execution, but possibly higher quality results. The default
setting is deemed sensible for the majority of runs.
*Line Width* offers a finer degree of control over maximum and minimum peak widths
for each dimension. The default values are *very* stupid and could do with
re-checking for each experiment.
*Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick
*every* peak in your peak list, try this option - but note that this may take
a very long time!
"""
def __init__(self, parent, programName='Peak Separator', **kw):
self.parent = parent
self.programName = programName
self.versionInfo = 'Version 0.2'
self.help_url = 'http://www.ccpn.ac.uk/'
self.window = None
self.waiting = False
self.rootWindow = None
# just used for display - PeakSeparator will not see this
self._minSigmaHz = None
self._maxSigmaHz = None
self.customSigma = False
self.rePickPeakList = False
self._sampleStartPpm = None
self._sampleEndPpm = None
try:
self.project = parent.project
except:
pass
self.params = PeakSeparatorParams()
BasePopup.__init__(self,
parent=parent,
title=programName,
location='+100+100',
**kw)
if not self.analysisProject:
print '&&& init: No analysis project found ...'
try:
if parent.argumentServer:
self.argServer = parent.argumentServer
else:
print '&&& init: No argument server found...'
except:
print '&&& init: Test'
###########################################################################
def body(self, guiFrame):
self.geometry('450x500')
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
options = ['Peak Separator', 'Advanced Settings']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
buttons = UtilityButtonList(tabbedFrame.sideFrame,
helpUrl=self.help_url)
buttons.grid(row=0, column=0, sticky='e')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
#
# FrameA : Main Settings
#
frameA.grid_columnconfigure(1, weight=1)
row = 0 # Label row
row += 1
div = LabelDivider(frameA, text='Peak Separator Parameters')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Min. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Minimum number of peaks to find (must be > 0)')
self.minPeaksEntry.grid(row=row, column=1, sticky='n')
self.minPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Max. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Maximum number of peaks to find (0 is unlimited - not recommended)')
self.maxPeaksEntry.grid(row=row, column=1, sticky='n')
self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Only pick positive peaks:')
label.grid(row=row, column=0, sticky='w')
entries = ['False', 'True']
self.posPeaksButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Search for both positive and negative intensity peaks',
'Limit search to only positive peaks'
])
self.posPeaksButtons.grid(row=row, column=1, sticky='n')
row += 1
label = Label(frameA, text='Peak Model:')
label.grid(row=row, column=0, sticky='w')
### G/L Mixture works, but volume calculation involves Gamma function
# entries = ['Gaussian', 'Lorentzian', 'G/L Mixture']
entries = ['Gaussian', 'Lorentzian']
self.shapeButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Choose a Gaussian model peak shape to fit to peaks',
'Choose a Lorentzian model peak shape to fit to peaks'
])
self.shapeButtons.grid(row=row, column=1, sticky='n')
row += 1
div = LabelDivider(frameA,
text='Region',
tipText='Region that search will limit itself to')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Peak List:')
label.grid(row=row, column=0, sticky='nw')
self.peakListPulldown = PulldownList(
frameA,
callback=self.setManuallyPickPeakList,
tipText='Select which peak list new peaks are to be added to')
self.peakListPulldown.grid(row=row, column=1, sticky='nw')
# tricky scrolled matrix
row += 1
self.regionTable = None
frameA.grid_rowconfigure(row, weight=1)
headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size')
self.editDimEntry = IntEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Dimension number')
self.editStartEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area lower bound')
self.editEndEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area upper bound')
editWidgets = [
self.editDimEntry, self.editStartEntry, self.editEndEntry, None
]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.regionTable = ScrolledMatrix(frameA,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=5)
self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew')
# Run Button
row += 1
texts = ['Add Region']
commands = [self.updateFromRegion]
self.addResetButtons = ButtonList(
frameA,
texts=texts,
commands=commands,
tipTexts=['Add selected specrtral region'])
self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameA,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
#
# FrameB : Further Settings
#
frameB.grid_columnconfigure(0, weight=1)
row = 0
div = LabelDivider(frameB, text='Rate:')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text='Rate of MCMC step size change')
label.grid(row=row, column=0, columnspan=1, sticky='w')
self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \
tipText='Rate effects speed of run, smaller values take longer but may produce better results')
self.rateEntry.grid(row=row, column=1, sticky='n')
self.rateEntry.bind('<Leave>', self.applyChange, '+')
self.rateEntry.set(self.params.rate)
# tricky scrolled matrix for line width
row += 2
div = LabelDivider(frameB, text='Line Width (Hz):')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text="Descr.")
label.grid(row=row, rowspan=2, column=0, sticky='w')
row += 1
self.lineWidthTable = None
frameB.grid_rowconfigure(row, weight=1)
lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)')
self.editMinSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Minimum line width (Hz)')
self.editMaxSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Maximum line width (Hz)')
# self.editDimEntry is also from regionTable
initialWidthRows = 4
editLineWidthWidgets = [
None, self.editMinSigmaEntry, self.editMaxSigmaEntry
]
editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax]
editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax]
self.lineWidthTable = ScrolledMatrix(
frameB,
headingList=lineWidthHeadings,
multiSelect=False,
editWidgets=editLineWidthWidgets,
editGetCallbacks=editLineWidthGetCallbacks,
editSetCallbacks=editLineWidthSetCallbacks,
initialRows=initialWidthRows)
self.lineWidthTable.grid(row=row,
column=0,
columnspan=2,
sticky='nsew')
# option to 'repick' exisiting peak list
row += initialWidthRows
div = LabelDivider(frameB, text='(optional - repick entire peak list)')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
self.repickListPulldown = PulldownList(
frameB,
callback=self.setRePickPeakList,
tipText=
'Select which peak list to repick (new peaks will be put into a new peak list)'
)
self.repickListPulldown.grid(row=row, column=0, sticky='nw')
texts = ['Repick Peak List']
commands = [self.runRepickPeaks]
self.runButton = ButtonList(
frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Repick selected peak list into a new peak list.'])
self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
div = LabelDivider(frameB)
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.setWidgetEntries()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.Experiment', 'setName')
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.DataSource', 'setName')
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
###########################################################################
# update parameters from PS Region
def updateFromRegion(self):
if not self.params.peakList:
print '&&& update from region: Need a peak list'
return
if (self.argServer.parent.currentRegion) == None:
showError('No Region',
'Please select a peak region to be separated')
return
self.rePickPeakList = False
getRegionParams(self.params, argServer=self.argServer)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# update parameters from PS PeakList
def updateFromPeakList(self):
if not self.params.peakList:
print '&&& update from peakList: Need a peak list'
return
getPeakListParams(self.params)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# Run the C library!
def runPeakSeparator(self):
""" run the peak separator """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
# SeparatePeakRoutine(self.params, self.params.peakList, routine='pymc' )
SeparatePeakRoutine(self.params,
self.params.peakList,
routine='bayesys')
def runRepickPeaks(self):
""" Run the Peak Separator on entire chosen peak list """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
SeparatePeaksInPeakList(self.params)
###########################################################################
def setWidgetEntries(self):
### Page One widgets
self.minPeaksEntry.set(self.params.minAtoms)
self.maxPeaksEntry.set(self.params.maxAtoms)
if self.params.positivePeaks == 1:
self.posPeaksButtons.set('True') # only pick pos peaks
else:
self.posPeaksButtons.set('False')
# do something fancy if different shapes for each dim!
n = self.params.peakShape - 3 # shape is only 3, 4, (5)
self.shapeButtons.setIndex(n)
if self.project is not None:
self.updatePeakListList()
self.updateSpectrumWindow()
if self.params.sampleStart and self.params.peakList:
if not self.rePickPeakList:
objectList = []
textMatrix = []
if len(self.params.samplePpmStart) != self.params.Ndim: return
for i in range(self.params.Ndim):
dim_entry = []
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self.params.samplePpmStart[i])
dim_entry.append('%7.3f' % self.params.samplePpmEnd[i])
dim_entry.append('%3d' % self.params.sampleSize[i])
textMatrix.append(dim_entry)
self.regionTable.update(textMatrix=textMatrix,
objectList=objectList)
### Page Two widgets
self.rateEntry.set(self.params.rate)
if self.params.peakList and self.params.Ndim:
textMatrix = []
objectList = []
for i in range(self.params.Ndim):
if self.params.isFreqDim[i]:
dim_entry = []
objectList.append(i)
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self._minSigmaHz[i])
dim_entry.append('%7.3f' % self._maxSigmaHz[i])
textMatrix.append(dim_entry)
self.lineWidthTable.update(textMatrix=textMatrix,
objectList=objectList)
def applyChange(self, *event):
""" Upon change, add settings to params """
# Page One apply changes
self.params.minAtoms = self.minPeaksEntry.get()
self.params.maxAtoms = self.maxPeaksEntry.get()
if self.posPeaksButtons.get() == 'True': # asked only pick pos peaks
self.params.positivePeaks = 1
else:
self.params.positivePeaks = 0
# do something fancy if different shapes for each dim!
n = self.shapeButtons.getIndex() # shape is only 3, 4, (5)
self.params.peakShape = n + 3
# Page Two apply changes
self.params.rate = float(self.rateEntry.get())
self.updateSigmaParams()
###########################################################################
# Peak list functions provide PeakSeparator some inherited params
def getPeakListList(self):
""" given a spectrum, get list of peak lists """
project = self.project
peakLists = []
for experiment in self.nmrProject.experiments:
for spectrum in experiment.dataSources:
for peakList in spectrum.peakLists:
peakLists.append([
'%s:%s:%d' %
(experiment.name, spectrum.name, peakList.serial),
peakList
])
peakLists.sort()
return peakLists
def updatePeakListList(self):
""" set the peaklist list in the pulldown menu """
peakListData = self.getPeakListList()
index = -1
names = []
peakList = self.params.peakList
if peakListData:
names = [x[0] for x in peakListData]
peakLists = [x[1] for x in peakListData]
if peakList not in peakLists:
peakList = peakLists[0]
index = peakLists.index(peakList)
else:
peakList = None
peakLists = []
if peakList is not self.params.peakList:
self.params.peakList = peakList
self.peakListPulldown.setup(names, peakLists, index)
self.repickListPulldown.setup(names, peakLists, index)
def setRePickPeakList(self, peakList):
""" Set the peak list to be repicked (and hit a Flag) """
self.rePickPeakList = True
self.setPeakList(peakList)
def setManuallyPickPeakList(self, peakList):
""" Set the peak list to add new peaks to (and hit a Flag) """
self.rePickPeakList = False
self.setPeakList(peakList)
def setPeakList(self, peakList):
""" Sets the Peak List """
if peakList is not self.params.peakList:
self.params.peakList = peakList
# # interrogate the peak list and get all the usefull parameters out
self.updateFromPeakList()
self.updateSpectrumWindow()
self.setWidgetEntries()
###########################################################################
# TBD I suspect this is for matching region with peak list, but may be obsolete now
def getSpectrumWindowList(self):
""" get list of windows which spectrum could be in """
windows = {}
if self.params.peakList:
views = getSpectrumViews(self.params.peakList.dataSource)
for view in views:
windows[view.spectrumWindowPane.spectrumWindow] = None
return [[w.name, w] for w in windows.keys()]
def updateSpectrumWindow(self):
""" update the spectrum window """
windowData = self.getSpectrumWindowList()
index = -1
names = []
window = self.rootWindow
if windowData:
names = [x[0] for x in windowData]
windows = [x[1] for x in windowData]
if window not in windows:
window = windows[0]
index = windows.index(window)
else:
window = None
windows = []
if window is not self.rootWindow:
self.rootWindow = window
###########################################################################
# get and set sigma stuff
def setSigmaMin(self, dim):
value = self.editMinSigmaEntry.get()
self._minSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMin(self, dim):
if dim is not None:
self.editMinSigmaEntry.set(self._minSigmaHz[dim])
def setSigmaMax(self, dim):
value = self.editMaxSigmaEntry.get()
self._maxSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMax(self, dim):
if dim is not None:
self.editMaxSigmaEntry.set(self._maxSigmaHz[dim])
def updateSigmaParams(self, dim=None):
""" updateSigmaParams Just updates the parameters (params obj) for sigma values.
If dim is None, do this for each dim
"""
dataDimRefs = self.params.dataDimRefs
if not dataDimRefs: return
if not self.params.minSigma or len(
self.params.minSigma) != self.params.Ndim:
self.params.minSigma = [0.] * self.params.Ndim
if not self.params.maxSigma or len(
self.params.maxSigma) != self.params.Ndim:
self.params.maxSigma = [0.] * self.params.Ndim
def updateSigmaParam(dim, dataDimRefs):
""" Convert and update sigma for dim """
if self.params.isFreqDim[dim]:
# note factor of two!
self.params.minSigma[dim] = self.rHz2pnt(
self._minSigmaHz[dim], dataDimRefs[dim]) / 2.
self.params.maxSigma[dim] = self.rHz2pnt(
self._maxSigmaHz[dim], dataDimRefs[dim]) / 2.
else:
self.params.minSigma[dim] = 1.0
self.params.maxSigma[dim] = 1.0
if dim:
updateSigmaParam(dim, dataDimRefs)
else:
for dim in range(self.params.Ndim):
updateSigmaParam(dim, dataDimRefs)
# utility functions for sigma values
def pnt2rHz(self, point, dataDimRef):
""" Point to relative Hz frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert point, dataDimRef
sigmaBase = pnt2hz(0, dataDimRef)
sigmaHz = pnt2hz(point, dataDimRef)
return abs(sigmaHz - sigmaBase)
def rHz2pnt(self, freq, dataDimRef):
""" Relative Hz to point frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert freq, dataDimRef
sigmaBase = hz2pnt(0, dataDimRef)
sigmaPoint = hz2pnt(freq, dataDimRef)
return abs(sigmaPoint - sigmaBase)
def initSigmaParams(self):
""" Set some initial default values for sigma """
self._minSigmaHz = []
self._maxSigmaHz = []
if self.params.Ndim:
for dim in range(self.params.Ndim):
self._minSigmaHz.append(6.)
self._maxSigmaHz.append(28.)
###########################################################################
def updateAll(self):
self.updateSpectrumWindow()
self.updatePeakListList()
self.waiting = False
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateAll)
class UpdatePopup(BasePopup, UpdateAgent):
def __init__(self,
parent,
serverLocation=UPDATE_SERVER_LOCATION,
serverDirectory=UPDATE_DIRECTORY,
dataFile=UPDATE_DATABASE_FILE,
exitOnClose=False):
self.exitOnClose = exitOnClose
UpdateAgent.__init__(self,
serverLocation,
serverDirectory,
dataFile,
isStandAlone=exitOnClose)
self.fileUpdate = None
if exitOnClose:
quitFunc = sys.exit
else:
quitFunc = None
BasePopup.__init__(self,
parent=parent,
title='CcpNmr Software Updates',
quitFunc=quitFunc)
def body(self, guiParent):
self.geometry('600x300')
guiParent.grid_columnconfigure(1, weight=1)
url = ''
if self.server:
url = self.server.url
label = Label(guiParent, text='Server location: %s' % url)
label.grid(row=0, column=0, sticky='w', columnspan=2)
label = Label(guiParent,
text='Installation root: %s%s' %
(self.installRoot, os.sep))
label.grid(row=1, column=0, sticky='w', columnspan=2)
editWidgets = [None] * 5
editGetCallbacks = [None, self.toggleSelected, None, None, None]
editSetCallbacks = [None] * 5
guiParent.grid_rowconfigure(2, weight=1)
headingList = [
'File', 'Install?', 'Date', 'Relative Path', 'Priority', 'Comments'
]
self.scrolledMatrix = ScrolledMatrix(guiParent,
headingList=headingList,
highlightType=0,
editWidgets=editWidgets,
callback=self.selectCell,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.scrolledMatrix.grid(row=2, column=0, columnspan=2, sticky='nsew')
if self.exitOnClose:
txt = 'Quit'
cmd = sys.exit
else:
txt = 'Close'
cmd = self.close
texts = ['Refresh List', 'Select All', 'Install Selected', txt]
commands = [self.updateFiles, self.selectAll, self.install, cmd]
self.buttonList = ButtonList(guiParent,
texts=texts,
commands=commands,
expands=True)
self.buttonList.grid(row=3, column=0, columnspan=2, sticky='ew')
if self.server:
for fileUpdate in self.server.fileUpdates:
fileUpdate.isSelected = False
#self.update()
# need self.updateFiles, not just self.update
# because otherwise the 2.0.5 to 2.0.6 upgrades do not work
# (self.server not set on first pass so need call to updateFiles here)
self.updateFiles()
def toggleSelected(self, fileUpdate):
boolean = fileUpdate.isSelected
fileUpdate.isSelected = not boolean
self.update()
def install(self):
if self.server:
self.installUpdates()
self.updateFiles()
def selectAll(self):
if self.server:
for fileUpdate in self.scrolledMatrix.objectList:
fileUpdate.isSelected = True
self.update()
def selectCell(self, object, row, col):
self.fileUpdate = object
def updateButtons(self):
buttons = self.buttonList.buttons
if self.server:
selected = False
if self.server and self.server.fileUpdates:
for fileUpdate in self.scrolledMatrix.objectList:
if fileUpdate.isSelected:
selected = True
break
buttons[1].enable()
else:
buttons[1].disable()
if selected:
buttons[2].enable()
buttons[2].config(bg='#A0FFA0')
else:
buttons[2].disable()
buttons[2].config(bg=buttons[1].cget('bg'))
else:
for button in buttons[:-1]:
button.disable()
def updateFiles(self):
if self.server:
if not self.server.fileUpdates:
self.server.getFileUpdates()
for fileUpdate in self.server.fileUpdates:
fileUpdate.isSelected = False
self.update()
def update(self):
self.updateButtons()
self.fileUpdate = None
textMatrix = []
objectList = []
colorMatrix = []
if self.server:
for fileUpdate in self.server.fileUpdates:
if fileUpdate.getIsUpToDate():
continue
color = [None, '#A04040', None, None, None]
yesNo = 'No'
if fileUpdate.isSelected:
color = [None, '#A0FFA0', None, None, None]
yesNo = 'Yes'
datum = []
datum.append(fileUpdate.fileName)
datum.append(yesNo)
datum.append(fileUpdate.date)
datum.append(fileUpdate.filePath + os.sep)
datum.append(fileUpdate.priority)
datum.append(fileUpdate.details)
colorMatrix.append(color)
textMatrix.append(datum)
objectList.append(fileUpdate)
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList,
colorMatrix=colorMatrix)
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 __init__(self,
parent,
initial_list=None,
width=60,
height=5,
xscroll=True,
yscroll=True,
addDeleteButtons=False,
selectmode=Tkinter.BROWSE,
exportselection=0,
select_callback=None,
double_callback=None,
list_background='white',
*args,
**kw):
if (initial_list is None):
initial_list = []
apply(Frame.__init__, (self, parent) + args, kw)
self.selectmode = selectmode
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
listbox = Tkinter.Listbox(self,
width=width,
height=height,
background=list_background,
selectmode=selectmode,
exportselection=exportselection)
listbox.grid(row=0, column=0, sticky=Tkinter.NSEW)
if (xscroll):
xscrollbar = Tkinter.Scrollbar(self, orient=Tkinter.HORIZONTAL)
xscrollbar.config(command=listbox.xview)
listbox.config(xscrollcommand=xscrollbar.set)
xscrollbar.grid(row=1, column=0, sticky=Tkinter.EW)
if (yscroll):
yscrollbar = Tkinter.Scrollbar(self, orient=Tkinter.VERTICAL)
yscrollbar.config(command=listbox.yview)
listbox.config(yscrollcommand=yscrollbar.set)
yscrollbar.grid(row=0, column=1, sticky=Tkinter.NS)
if addDeleteButtons:
texts = ['Add item', 'Delete selected']
commands = [self.addItem, self.deleteItems]
buttons = ButtonList(self, texts=texts, commands=commands)
buttons.grid(row=1, columnspan=2, sticky=Tkinter.EW)
# bind frame, not listbox, because listbox with focus has
# activation which means in particular that get underlining
self.bind('<Enter>', self.enterCallback)
self.bind('<KeyPress>', self.keypressCallback)
self.listbox = listbox
self.setItems(initial_list)
self.setSelectCallback(select_callback)
self.setDoubleCallback(double_callback)
self.size = self.listbox.size # otherwise get Frame size called
class ResultsTab(object):
def __init__(self, parent, frame):
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.selectedLinkA = None
self.selectedLinkB = None
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLink = None
self.dataModel = self.guiParent.connector.results
self.body()
def body(self):
frame = self.frame
self.resultsResidueNumber = 1
frame.expandGrid(5, 0)
resultTopFrame = LabelFrame(frame, text='Which results to show')
resultTopFrame.grid(row=0, column=0, sticky='ew')
self.resultsResidueNumber = 3
texts = [' < ']
commands = [self.resultsPrevResidue]
self.resultsPreviousButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsPreviousButton.grid(row=0, column=1, sticky='nsew')
tipText = 'The Number of the residue in the sequence to display results for'
self.resultsResidueNumberEntry = IntEntry(
resultTopFrame,
grid=(0, 2),
width=7,
text=3,
returnCallback=self.resultsUpdateAfterEntry,
tipText=tipText)
#self.resultsResidueNumberEntry.bind('<Leave>', self.resultsUpdateAfterEntry, '+')
texts = [' > ']
commands = [self.resultsNextResidue]
self.resultsNextButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsNextButton.grid(row=0, column=3, sticky='nsew')
selectCcpCodes = ['residue'] + AMINO_ACIDS
self.resultsSelectedCcpCode = 'residue'
tipText = 'Instead of going through the sequence residue by residue, jump directly to next amino acid of a specific type.'
resultsSelectCcpCodeLabel = Label(
resultTopFrame,
text='Directly jump to previous/next:',
grid=(0, 4))
self.resultsSelectCcpCodePulldown = PulldownList(
resultTopFrame,
callback=self.resultsChangeSelectedCcpCode,
texts=selectCcpCodes,
index=selectCcpCodes.index(self.resultsSelectedCcpCode),
grid=(0, 5),
tipText=tipText)
self.selectedSolution = 1
runLabel = Label(resultTopFrame, text='run:')
runLabel.grid(row=0, column=6)
texts = [' < ']
commands = [self.resultsPrevSolution]
self.resultsPreviousSolutionButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsPreviousSolutionButton.grid(row=0, column=7, sticky='nsew')
tipText = 'If you ran the algorithm more than once, you can select the solution given by the different runs.'
self.resultsSolutionNumberEntry = IntEntry(
resultTopFrame,
grid=(0, 8),
width=7,
text=1,
returnCallback=self.solutionUpdateAfterEntry,
tipText=tipText)
#self.resultsSolutionNumberEntry.bind('<Leave>', self.solutionUpdateAfterEntry, '+')
texts = [' > ']
commands = [self.resultsNextSolution]
self.resultsNextSolutionButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsNextSolutionButton.grid(row=0, column=9, sticky='nsew')
self.energyLabel = Label(resultTopFrame, text='energy:')
self.energyLabel.grid(row=0, column=10)
texts = ['template for puzzling']
commands = [self.adoptSolution]
self.adoptButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.adoptButton.grid(row=0, column=11, sticky='nsew')
# LabelFrame(frame, text='Spin Systems')
resultsSecondFrame = Frame(frame)
resultsSecondFrame.grid(row=2, column=0, sticky='nsew')
resultsSecondFrame.grid_columnconfigure(0, weight=1)
resultsSecondFrame.grid_columnconfigure(1, weight=1)
resultsSecondFrame.grid_columnconfigure(2, weight=1)
resultsSecondFrame.grid_columnconfigure(3, weight=1)
resultsSecondFrame.grid_columnconfigure(4, weight=1)
headingList = ['#', '%']
tipTexts = [
'Spinsystem number {} indicates serial of the spinsystem. If the spinsystem was already assigned to a residue, the residue number is shown aswell',
'percentage of the solutions that connected this spinsystem to this residue'
]
editWidgets = [None, None, None]
self.displayResultsTables = []
self.residueLabels = []
for i in range(5):
label = Label(resultsSecondFrame, text='residue')
label.grid(row=0, column=i)
#editGetCallbacks = [createCallbackFunction(i)]*3
displayResultsTable = ScrolledMatrix(
resultsSecondFrame,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts,
callback=self.selectSpinSystemForTable,
passSelfToCallback=True)
displayResultsTable.grid(row=2, column=i, sticky='nsew')
displayResultsTable.sortDown = False
self.residueLabels.append(label)
self.displayResultsTables.append(displayResultsTable)
# LabelFrame(frame, text='Sequence Fragment')
resultsFirstFrame = Frame(resultsSecondFrame)
resultsFirstFrame.grid(row=1, column=0, sticky='ew', columnspan=5)
resultsFirstFrame.grid_rowconfigure(0, weight=1)
resultsFirstFrame.grid_rowconfigure(1, weight=1)
resultsFirstFrame.grid_columnconfigure(0, weight=1)
texts = [
' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ',
' res 4 ', ' links ', ' res 5 '
]
commands = [
lambda: self.selectRelativeResidue(1, True),
lambda: self.selectLink(1, True),
lambda: self.selectRelativeResidue(2, True),
lambda: self.selectLink(2, True),
lambda: self.selectRelativeResidue(3, True),
lambda: self.selectLink(3, True),
lambda: self.selectRelativeResidue(4, True),
lambda: self.selectLink(4, True),
lambda: self.selectRelativeResidue(5, True)
]
self.sequenceButtons = ButtonList(resultsFirstFrame,
commands=commands,
texts=texts)
self.sequenceButtons.grid(row=0, column=0, sticky='nsew')
for n, button in enumerate(self.sequenceButtons.buttons):
if n % 2:
button.grid(column=n, sticky='ns')
self.sequenceButtons.grid_columnconfigure(n, weight=0)
else:
self.sequenceButtons.grid_columnconfigure(n, uniform=2)
spacer = Spacer(resultsFirstFrame)
spacer.grid(row=1, column=0, sticky='nsew')
texts = [
' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ',
' res 4 ', ' links ', ' res 5 '
]
commands = commands = [
lambda: self.selectRelativeResidue(1, False),
lambda: self.selectLink(1, False),
lambda: self.selectRelativeResidue(2, False),
lambda: self.selectLink(2, False),
lambda: self.selectRelativeResidue(3, False),
lambda: self.selectLink(3, False),
lambda: self.selectRelativeResidue(4, False),
lambda: self.selectLink(4, False),
lambda: self.selectRelativeResidue(5, False)
]
self.sequenceButtonsB = ButtonList(resultsFirstFrame,
commands=commands,
texts=texts)
self.sequenceButtonsB.grid(row=2, column=0, sticky='nsew')
for n, button in enumerate(self.sequenceButtonsB.buttons):
if n % 2:
button.grid(column=n, sticky='ns')
self.sequenceButtonsB.grid_columnconfigure(n, weight=0)
else:
self.sequenceButtonsB.grid_columnconfigure(n, uniform=2)
frame.grid_rowconfigure(3, weight=2)
resultsThirdFrame = Frame(frame)
resultsThirdFrame.grid(row=3, column=0, sticky='nsew')
resultsThirdFrame.grid_rowconfigure(0, weight=1)
resultsThirdFrame.grid_columnconfigure(0, weight=1)
tabbedFrameB = TabbedFrame(resultsThirdFrame,
options=['Peaks', 'Spin System'],
callback=self.toggleTab,
grid=(0, 0))
#self.tabbedFrameB = tabbedFrame
PeakFrame, SpinSystemFrame = tabbedFrameB.frames
SpinSystemFrame.grid_rowconfigure(0, weight=1)
PeakFrame.grid_rowconfigure(1, weight=1)
SpinSystemFrame.grid_columnconfigure(0, weight=1)
PeakFrame.grid_columnconfigure(0, weight=1)
headingList = [
'residue', 'assigned to in project', 'user defined sequence',
'selected annealing result', '%'
]
tipTexts = [None, None, None, None, None]
editWidgets = [None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None]
self.spinSysTable = ScrolledMatrix(SpinSystemFrame,
headingList=headingList,
editWidgets=editWidgets,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.spinSysTable.grid(row=0, column=0, sticky='nsew')
buttonFrameinPeakFrame = Frame(PeakFrame)
buttonFrameinPeakFrame.grid(sticky='ew')
self.findButton = Button(
buttonFrameinPeakFrame,
text=' Go to Peak ',
borderwidth=1,
padx=2,
pady=1,
command=self.findPeak,
tipText='Locate the currently selected peak in the specified window'
)
self.findButton.grid(row=0, column=0, sticky='e')
label = Label(buttonFrameinPeakFrame, text='in window:')
label.grid(row=0, column=1, sticky='w')
self.windowPulldown = PulldownList(
buttonFrameinPeakFrame,
callback=self.selectWindowPane,
tipText='Choose the spectrum window for locating peaks or strips')
self.windowPulldown.grid(row=0, column=2, sticky='w')
self.assignSelectedPeaksButton = Button(
buttonFrameinPeakFrame,
text='Assign Resonances to Peak(s)',
borderwidth=1,
padx=2,
pady=1,
command=self.assignSelectedPeaks,
tipText=
'Assign resonances to peak dimensions, this of course only works when the peak is found in the spectrum.'
)
self.assignSelectedPeaksButton.grid(row=0, column=3, sticky='ew')
self.assignSelectedSpinSystemsToResiduesButton = Button(
buttonFrameinPeakFrame,
text='Assign Spinsystems to Residues',
borderwidth=1,
padx=2,
pady=1,
command=self.assignSelectedSpinSystemsToResidues,
tipText='Assign spinsystems to residues')
self.assignSelectedSpinSystemsToResiduesButton.grid(row=0,
column=4,
sticky='ew')
headingList = [
'#', 'spectrum', 'Dim1', 'Dim2', 'Dim3', 'c.s. dim1', 'c.s. dim2',
'c.s. dim3', 'colabelling'
]
tipTexts = [
'Peak number, only present when the peak was actually found in the spectrum.',
'Name of the spectrum',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Chemical Shift', 'Chemical Shift', 'Chemical Shift',
'Colabbeling fraction over all nuclei that are on the magnetization transfer pathway during the experiment that gave rise to the peak, including visited nuclei that were not measured in any of the peak dimensions'
]
#editWidgets = [None, None, None, None, None, None, None, None, None]
editGetCallbacks = [
None, None, None, None, None, None, None, None, None
]
#editGetCallbacks = [self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak]
editSetCallbacks = [
None, None, None, None, None, None, None, None, None
]
self.displayPeakTable = ScrolledMatrix(PeakFrame,
headingList=headingList,
multiSelect=True,
tipTexts=tipTexts)
#editWidgets=editWidgets, multiSelect=True,
# editGetCallbacks=editGetCallbacks,
# editSetCallbacks=editSetCallbacks,
# tipTexts=tipTexts)
self.displayPeakTable.grid(row=1, column=0, sticky='nsew')
self.windowPane = None
self.updateWindows()
def selectSpinSystemForTable(self, spinSystem, row, column, table):
table_number = self.displayResultsTables.index(table)
self.selectSpinSystem(table_number, spinSystem)
@lockUntillResults
def showResults(self):
self.updateResultsTable()
@lockUntillResults
def selectLink(self, number, topRow):
if topRow:
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLinkA = number
self.selectedLinkB = None
else:
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLinkA = None
self.selectedLinkB = number
self.updateButtons()
self.updateLink()
@lockUntillResults
def selectRelativeResidue(self, number, topRow):
if topRow:
self.selectedResidueA = number
self.selectedResidueB = None
self.selectedLinkA = None
self.selectedLinkB = None
else:
self.selectedResidueA = None
self.selectedResidueB = number
self.selectedLinkA = None
self.selectedLinkB = None
self.updateButtons()
self.updateLink()
def updateLink(self):
'''
Checks for any selected link (self.selectedLinkA or self.selectedLinkB) and calls
updatePeakTable with the correct residue Object and spinsystem Objects.
'''
number = self.selectedLinkA or self.selectedLinkB or self.selectedResidueA or self.selectedResidueB
if not number:
self.emptyPeakTable()
return
dataModel = self.dataModel
resNumber = self.resultsResidueNumber
chain = dataModel.chain
residues = chain.residues
solutionNumber = self.selectedSolution - 1
if self.selectedResidueA:
res = residues[resNumber - 4 + number]
spinSystem = res.solutions[solutionNumber]
self.selectedLink = None
if res and spinSystem:
self.selectedLink = res.getIntraLink(spinSystem)
#self.updatePeakTableIntra(res, spinSystem)
self.updateSpinSystemTable(spinSystem)
elif self.selectedResidueB:
res = residues[resNumber - 4 + number]
spinSystem = res.userDefinedSolution
self.selectedLink = None
if res and spinSystem:
self.selectedLink = res.getIntraLink(spinSystem)
#self.updatePeakTableIntra(res, spinSystem)
self.updateSpinSystemTable(spinSystem)
elif self.selectedLinkA:
resA = residues[resNumber - 4 + number]
resB = residues[resNumber - 3 + number]
spinSystemA = resA.solutions[solutionNumber]
spinSystemB = resB.solutions[solutionNumber]
self.selectedLink = None
if resA and spinSystemA and spinSystemB:
self.selectedLink = resA.getLink(spinSystemA, spinSystemB)
#self.updatePeakTable(resA, spinSystemA, spinSystemB)
# and resA.userDefinedSolution and resB.userDefinedSolution:
elif self.selectedLinkB:
resA = residues[resNumber - 4 + number]
resB = residues[resNumber - 3 + number]
spinSystemA = resA.userDefinedSolution
spinSystemB = resB.userDefinedSolution
self.selectedLink = None
if resA and spinSystemA and spinSystemB:
self.selectedLink = resA.getLink(spinSystemA, spinSystemB)
#self.updatePeakTable(resA, spinSystemA, spinSystemB)
self.updatePeakTable()
def emptyPeakTable(self):
self.displayPeakTable.update(objectList=[],
textMatrix=[],
colorMatrix=[])
def updatePeakTable(self):
'''
Updates the peak table to show the peaks that are found for a sequencial pair of
spinsystems A and B. If there is not a linkobject found for spinsystems A and B the
table is emptied. Also sets the selected peak to None.
'''
link = self.selectedLink
if not link:
self.emptyPeakTable()
else:
resA, resB = link.getResidues()
spinSystemA, spinSystemB = link.getSpinSystems()
data = []
objectList = []
peakLinks = link.getAllPeakLinks()
if not peakLinks:
self.emptyPeakTable()
return
maxDimenionality = max([
len(peakLink.getSimulatedPeak().getContribs())
for peakLink in peakLinks
])
for peakLink in peakLinks:
serial = None
realPeak = peakLink.getPeak()
simPeak = peakLink.getSimulatedPeak()
atomTexts = [None] * maxDimenionality
chemicalShifts = [None] * maxDimenionality
for simulatedPeakContrib in simPeak.getContribs():
atomName = simulatedPeakContrib.getAtomName()
#ccpCode = simulatedPeakContrib.getCcpCode()
dimNumber = simulatedPeakContrib.getDimNumber()
if resA is simulatedPeakContrib.getResidue():
spinSystemDescription = spinSystemA.getDescription(
noSerialWhenSeqCodeIsPresent=True)
else:
spinSystemDescription = spinSystemB.getDescription(
noSerialWhenSeqCodeIsPresent=True)
atomTexts[dimNumber -
1] = '%s %s' % (spinSystemDescription, atomName)
if realPeak:
serial = realPeak.getSerial()
for dim in realPeak.getDimensions():
chemicalShifts[dim.getDimNumber() -
1] = dim.getChemicalShift()
else:
shiftListSerial = simPeak.getSpectrum().getShiftListSerial(
)
for resonance, simulatedPeakContrib in zip(
peakLink.getResonances(), simPeak.getContribs()):
if resonance:
chemicalShifts[simulatedPeakContrib.getDimNumber()
- 1] = resonance.getChemicalShift(
shiftListSerial)
else:
chemicalShifts[simulatedPeakContrib.getDimNumber()
- 1] = '?'
data.append([serial, simPeak.getSpectrum().name] + atomTexts +
chemicalShifts + [simPeak.colabelling])
objectList.append(peakLink)
headingList = ['#', 'spectrum'] + [
'dim%s' % a for a in range(1, maxDimenionality + 1)
] + ['c.s. dim%s' % a
for a in range(1, maxDimenionality + 1)] + ['colabbeling']
self.displayPeakTable.update(objectList=objectList,
textMatrix=data,
headingList=headingList)
def findPeak(self):
if not self.windowPane:
return
selectedPeakLinks = self.displayPeakTable.currentObjects
if not selectedPeakLinks:
self.guiParent.updateInfoText('Please select a peak first.')
return
if len(selectedPeakLinks) > 1:
self.guiParent.updateInfoText('Can only go to one peak at a time.')
return
selectedPeakLink = selectedPeakLinks[0]
selectedPeak = selectedPeakLink.getPeak()
if selectedPeak:
ccpnPeak = selectedPeak.getCcpnPeak()
createPeakMark(ccpnPeak, lineWidth=2.0)
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPeak(ccpnPeak)
else:
simPeak = selectedPeakLink.getSimulatedPeak()
spectrum = simPeak.getSpectrum()
ccpnSpectrum = spectrum.getCcpnSpectrum()
view = getSpectrumWindowView(self.windowPane, ccpnSpectrum)
if not view:
self.guiParent.updateInfoText(
'This peak cannot be displayed in the window you chose.')
axisMappingByRefExpDimNumber = {}
for axisMapping in view.axisMappings:
refExpDimNumber = axisMapping.analysisDataDim.dataDim.expDim.refExpDim.dim
axisMappingByRefExpDimNumber[refExpDimNumber] = axisMapping
positionToGoTo = {}
markPosition = []
axisTypes = []
for resonance, contrib in zip(selectedPeakLink.getResonances(),
simPeak.getContribs()):
dimNumber = contrib.getDimNumber()
axisMapping = axisMappingByRefExpDimNumber.get(dimNumber)
label = axisMapping.label
if resonance:
axisType = axisMapping.axisPanel.axisType
chemicalShift = resonance.getChemicalShift()
positionToGoTo[label] = chemicalShift
markPosition.append(chemicalShift)
axisTypes.append(axisType)
# Not drawing a mark at this chemical shift, just hoovering to
# the good region in the spectrum
else:
ccpCode = contrib.getResidue().getCcpCode()
atomName = contrib.getAtomName()
medianChemicalShift = self.getMedianChemicalShift(
ccpCode, atomName)
if medianChemicalShift:
positionToGoTo[label] = medianChemicalShift
if positionToGoTo:
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPosition(positionToGoTo)
if markPosition:
createNonPeakMark(markPosition, axisTypes)
def assignSelectedPeaks(self):
selectedPeakLinks = self.displayPeakTable.currentObjects
for pl in selectedPeakLinks:
peak = pl.getPeak()
if peak:
for resonance, dimension in zip(pl.getResonances(),
peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
if ccpnResonance and ccpnDimension:
assignResToDim(ccpnDimension, ccpnResonance)
def assignSelectedSpinSystemsToResidues(self):
link = self.selectedLink
if link:
residues = link.getResidues()
spinSystems = link.getSpinSystems()
ccpnSpinSystems = []
ccpnResidues = []
for spinSys, res in zip(spinSystems, residues):
if spinSys and res:
ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup())
ccpnResidues.append(res.getCcpnResidue())
assignSpinSystemstoResidues(ccpnSpinSystems,
ccpnResidues,
guiParent=self.guiParent)
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updatePeakTable()
def getMedianChemicalShift(self, ccpCode, atomName):
nmrRefStore = self.project.findFirstNmrReferenceStore(
molType='protein', ccpCode=ccpCode)
chemCompNmrRef = nmrRefStore.findFirstChemCompNmrRef(
sourceName='RefDB')
chemCompVarNmrRef = chemCompNmrRef.findFirstChemCompVarNmrRef(
linking='any', descriptor='any')
if chemCompVarNmrRef:
chemAtomNmrRef = chemCompVarNmrRef.findFirstChemAtomNmrRef(
name=atomName)
if chemAtomNmrRef:
distribution = chemAtomNmrRef.distribution
maxIndex = max([
(value, index) for index, value in enumerate(distribution)
])[1]
return chemAtomNmrRef.refValue + chemAtomNmrRef.valuePerPoint * (
maxIndex - chemAtomNmrRef.refPoint)
return None
def selectWindowPane(self, windowPane):
if windowPane is not self.windowPane:
self.windowPane = windowPane
def updateWindows(self):
index = 0
windowPane = None
windowPanes = []
names = []
peakList = None
tryWindows = WindowBasic.getActiveWindows(self.project)
windowData = []
getName = WindowBasic.getWindowPaneName
for window in tryWindows:
for windowPane0 in window.spectrumWindowPanes:
# if WindowBasic.isSpectrumInWindowPane(windowPane0, spectrum):
windowData.append((getName(windowPane0), windowPane0))
windowData.sort()
names = [x[0] for x in windowData]
windowPanes = [x[1] for x in windowData]
if windowPanes:
if windowPane not in windowPanes:
windowPane = windowPanes[0]
index = windowPanes.index(windowPane)
else:
windowPane = None
self.selectWindowPane(windowPane)
self.windowPulldown.setup(names, windowPanes, index)
def selectSpinSystem(self, number, spinSystem):
res = self.dataModel.chain.residues[self.resultsResidueNumber - 3 +
number]
oldSpinSystemForResidue = res.userDefinedSolution
if oldSpinSystemForResidue and res.getSeqCode(
) in oldSpinSystemForResidue.userDefinedSolutions:
oldSpinSystemForResidue.userDefinedSolutions.remove(
res.getSeqCode())
res.userDefinedSolution = spinSystem
spinSystem.userDefinedSolutions.append(res.getSeqCode())
# self.updateSpinSystemTable(spinSystem)
self.updateLink()
self.updateButtons()
def updateSpinSystemTable(self, spinSystem):
if not spinSystem:
self.emptySpinSystemTable()
return
dataModel = self.dataModel
residues = dataModel.chain.residues
data = []
colorMatrix = []
for residue in spinSystem.allowedResidues:
oneRow = []
oneRowColor = []
string = str(residue.getSeqCode()) + ' ' + residue.getCcpCode()
oneRow.append(string)
resonanceGroup = spinSystem.getCcpnResonanceGroup()
ccpnResidue = residue.ccpnResidue
# Assigned in the project to this residue
if resonanceGroup and resonanceGroup.residue and resonanceGroup.residue is ccpnResidue:
oneRow.append('x')
else:
oneRow.append(None)
# The user selected this res for this spinsystem (could be more
# than one res for which this happens)
if residue.getSeqCode() in spinSystem.userDefinedSolutions:
oneRow.append('x')
else:
oneRow.append(None)
if residue.solutions[self.selectedSolution - 1] == spinSystem:
oneRow.append('x')
else:
oneRow.append(None)
if spinSystem.solutions:
percentage = spinSystem.solutions.count(
residue.getSeqCode()) / float(len(
spinSystem.solutions)) * 100.0
else:
percentage = 0
oneRow.append(int(percentage + 0.5))
color = pick_color_by_percentage(percentage)
oneRowColor = [color] * 5
data.append(oneRow)
colorMatrix.append(oneRowColor)
self.spinSysTable.update(objectList=data,
textMatrix=data,
colorMatrix=colorMatrix)
self.spinSysTable.sortDown = False
self.spinSysTable.sortLine(-1, noUpdate=True)
def emptySpinSystemTable(self):
self.spinSysTable.update(objectList=[], textMatrix=[], colorMatrix=[])
@lockUntillResults
def adoptSolution(self):
dataModel = self.dataModel
selectedSolution = self.selectedSolution
for res in dataModel.chain.residues:
spinSystem = res.solutions[selectedSolution - 1]
res.userDefinedSolution = spinSystem
spinSystem.userDefinedSolutions = [res.getSeqCode()]
self.updateLink()
self.updateButtons()
@lockUntillResults
def resultsPrevSolution(self):
if self.selectedSolution != 1:
self.selectedSolution = self.selectedSolution - 1
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
self.updateEnergy()
@lockUntillResults
def resultsNextSolution(self):
amountOfRepeats = len(self.dataModel.chain.residues[0].solutions)
if self.selectedSolution < amountOfRepeats:
self.selectedSolution = self.selectedSolution + 1
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
self.updateEnergy()
@lockUntillResults
def resultsPrevResidue(self):
residues = self.dataModel.chain.residues
#chainLength = len(residues)
new_value = self.resultsResidueNumber
if self.resultsSelectedCcpCode == 'residue':
if self.resultsResidueNumber != 3:
new_value = self.resultsResidueNumber - 1
else:
for res in residues:
if res.getSeqCode() == self.resultsResidueNumber:
break
elif res.getCcpCode() == self.resultsSelectedCcpCode:
new_value = res.getSeqCode()
if new_value < 3:
new_value = 3
if self.resultsResidueNumber != new_value:
self.resultsResidueNumber = new_value
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
@lockUntillResults
def resultsNextResidue(self):
residues = self.dataModel.chain.residues
chainLength = len(residues)
new_value = self.resultsResidueNumber
if self.resultsSelectedCcpCode == 'residue':
if self.resultsResidueNumber != chainLength - 2:
new_value = self.resultsResidueNumber + 1
else:
for res in residues[(self.resultsResidueNumber):]:
if res.getCcpCode() == self.resultsSelectedCcpCode:
new_value = res.getSeqCode()
if new_value > chainLength - 2:
new_value = chainLength - 2
break
if self.resultsResidueNumber != new_value:
self.resultsResidueNumber = new_value
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
def resultsChangeSelectedCcpCode(self, ccpCode):
self.resultsSelectedCcpCode = ccpCode
@lockUntillResults
def resultsUpdateAfterEntry(self, event=None):
'''
Update for entry of residue number in strip plots
'''
residues = self.dataModel.chain.residues
value = self.resultsResidueNumberEntry.get()
if value == self.resultsResidueNumber:
return
else:
self.resultsResidueNumber = value
if value < 3:
self.resultsResidueNumberEntry.set(3)
self.resultsResidueNumber = 3
elif value > len(residues) - 2:
self.resultsResidueNumber = len(residues) - 2
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
else:
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
@lockUntillResults
def solutionUpdateAfterEntry(self, event=None):
'''
Update for entry of residue number in strip plots
'''
Nsolutions = len(self.dataModel.chain.residues[0].solutions)
value = self.resultsSolutionNumberEntry.get()
if value == self.selectedSolution:
return
else:
self.selectedSolution = value
if value < 1:
self.resultsSolutionNumberEntry.set(1)
self.selectedSolution = 1
elif value > Nsolutions:
self.selectedSolution = Nsolutions
self.resultsSolutionNumberEntry.set(self.selectedSolution)
else:
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
def update(self):
self.updateLink()
self.updateResidueLabels()
self.updateResultsTable()
self.updateButtons()
self.updateButtons()
self.updateEnergy()
def updateResultsTable(self):
resNumber = self.resultsResidueNumber
dataModel = self.dataModel
chain = dataModel.chain
residues = chain.residues
resA = residues[resNumber - 3]
resB = residues[resNumber - 2]
resC = residues[resNumber - 1]
resD = residues[resNumber]
resE = residues[resNumber + 1]
resList = [resA, resB, resC, resD, resE]
tableList = self.displayResultsTables
for res, table in zip(resList, tableList):
ccpCode = res.ccpCode
spinSystemsWithThisCcpCode = dataModel.getSpinSystems()[ccpCode]
data = []
colorMatrix = []
objectList = []
jokers = []
realSpinSystems = []
for spinSys in spinSystemsWithThisCcpCode:
if spinSys.getIsJoker():
jokers.append(spinSys)
else:
realSpinSystems.append(spinSys)
for spinsys in realSpinSystems:
oneRow = []
oneRowColor = []
# self.getStringDescriptionOfSpinSystem(spinsys)
spinSystemInfo = spinsys.getDescription()
oneRow.append(spinSystemInfo)
assignmentPercentage = int(
float(res.solutions.count(spinsys)) / len(res.solutions) *
100.0)
oneRow.append(assignmentPercentage)
objectList.append(spinsys)
color = pick_color_by_percentage(assignmentPercentage)
oneRowColor = [color, color]
data.append(oneRow)
colorMatrix.append(oneRowColor)
if jokers:
oneRow = ['Joker']
NumberOfAssignmentsToJoker = 0
for spinSys in jokers:
NumberOfAssignmentsToJoker += res.solutions.count(spinSys)
assignmentPercentage = int(
float(NumberOfAssignmentsToJoker) / len(res.solutions) *
100.0)
oneRow.append(assignmentPercentage)
color = pick_color_by_percentage(assignmentPercentage)
oneRowColor = [color, color]
data.append(oneRow)
colorMatrix.append(oneRowColor)
objectList.append(jokers[0])
percentages = [datapoint[1] for datapoint in data]
tableData = sorted(zip(percentages, data, objectList, colorMatrix),
reverse=True)
percentage, data, objectList, colorMatrix = zip(*tableData)
table.update(objectList=objectList,
textMatrix=data,
colorMatrix=colorMatrix)
def updateResidueLabels(self):
resList = self.getCurrentlyDisplayedResidues()
labels = self.residueLabels
for residue, label in zip(resList, labels):
text = str(residue.getSeqCode()) + ' ' + residue.getCcpCode()
label.set(text)
def updateButtons(self):
self.updateButtonHighLights()
self.updateResultsTopRowButtons()
self.updateResultsBottomRowButtons()
def updateResultsTopRowButtons(self):
resList = self.getCurrentlyDisplayedResidues()
buttons = self.sequenceButtons.buttons[::2]
for button, res in zip(buttons, resList):
spinsys = res.solutions[self.selectedSolution - 1]
# str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': ' +
# spinsys.getDescription()
# self.getStringDescriptionOfSpinSystem(spinsys)
text = spinsys.getDescription(noSerialWhenSeqCodeIsPresent=False)
button.config(text=text)
def updateResultsBottomRowButtons(self):
resList = self.getCurrentlyDisplayedResidues()
buttons = self.sequenceButtonsB.buttons[::2]
for button, res in zip(buttons, resList):
if res.userDefinedSolution:
selectedSpinSystem = res.userDefinedSolution
text = selectedSpinSystem.getDescription(
noSerialWhenSeqCodeIsPresent=False)
if len(selectedSpinSystem.userDefinedSolutions) > 1:
# The red color signals that the spinssystem is used in
# more than 1 place in the sequence
button.config(text=text, bg=highLightRed)
else:
button.config(text=text)
else:
# str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': -'
text = '-'
button.config(text=text)
def updateButtonHighLights(self):
self.setAllButtonsToGrey()
if self.selectedResidueA:
buttons = [
self.sequenceButtons.buttons[0],
self.sequenceButtons.buttons[2],
self.sequenceButtons.buttons[4],
self.sequenceButtons.buttons[6],
self.sequenceButtons.buttons[8]
]
buttons[self.selectedResidueA - 1].config(bg=highLightYellow)
elif self.selectedResidueB:
buttons = [
self.sequenceButtonsB.buttons[0],
self.sequenceButtonsB.buttons[2],
self.sequenceButtonsB.buttons[4],
self.sequenceButtonsB.buttons[6],
self.sequenceButtonsB.buttons[8]
]
buttons[self.selectedResidueB - 1].config(bg=highLightYellow)
elif self.selectedLinkA:
buttons = [
self.sequenceButtons.buttons[1],
self.sequenceButtons.buttons[3],
self.sequenceButtons.buttons[5],
self.sequenceButtons.buttons[7]
]
buttons[self.selectedLinkA - 1].config(bg=highLightYellow)
elif self.selectedLinkB:
buttons = [
self.sequenceButtonsB.buttons[1],
self.sequenceButtonsB.buttons[3],
self.sequenceButtonsB.buttons[5],
self.sequenceButtonsB.buttons[7]
]
buttons[self.selectedLinkB - 1].config(bg=highLightYellow)
def updateEnergy(self):
text = 'energy: %s' % int(
self.dataModel.getEnergy(self.selectedSolution - 1) + 0.5)
self.energyLabel.set(text)
self.energyLabel.update()
def setAllButtonsToGrey(self):
for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons:
button.config(bg='grey83')
def setAllRedButtonsToGrey(self):
for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons:
if button.enableFg == highLightRed:
button.config(bg='grey83')
def getCurrentlyDisplayedResidues(self):
resNumber = self.resultsResidueNumber
residues = self.dataModel.chain.residues[resNumber - 3:resNumber + 2]
return residues
def toggleTab(self, index):
pass
class ProtocolFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.basePopup.frameShortcuts['Protocol'] = self
Frame.__init__(self, guiParent)
self.grid_rowconfigure(0, weight=0)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0)
self.grid_rowconfigure(3, weight=1)
self.grid_rowconfigure(4, weight=0, minsize=30)
self.grid_rowconfigure(5, weight=0, minsize=30)
self.grid_columnconfigure(0, weight=0)
self.grid_columnconfigure(1, weight=1)
self.grid_columnconfigure(2, weight=0)
# build up the body.
self.title = Label(self, font='Helvetica16')
self.details = Label(self)
initial_cols = ['Parameter', 'Type', 'Value']
self.pMatrix = ScrolledMatrix(self,
headingList=initial_cols,
initialRows=15)
editButtonOpts = ['Save', 'Clear', 'New Protocol', 'New Expt Type']
editButtonCmds = [
self.tmpCall, self.tmpCall, self.tmpCall, self.tmpCall
]
self.editButtons = ButtonList(self, editButtonOpts, editButtonCmds)
# needs custom version
self.filter = FilterFrame(self, self.basePopup, text='Filter')
# no bean udnerneath for now so mock up nodes
self.pTree = Tree(self, width=33)
pButtonOpts1 = ['Load', 'Save']
pButtonCmds1 = [self.tmpCall, self.tmpCall]
self.pButtons1 = ButtonList(self, pButtonOpts1, pButtonCmds1)
pButtonOpts2 = ['New', 'Delete']
pButtonCmds2 = [self.tmpCall, self.tmpCall]
self.pButtons2 = ButtonList(self, pButtonOpts2, pButtonCmds2)
self.openedLinks = {
'Test 1': ['ParSet 1', 'ParSet 2'],
'Test 2': ['Std Pars', 'Big Pars', 'Little Pars'],
'ARIA': ['default', 'complex'],
'CING': ['Std'],
'ISD': ['protein', 'DNA']
}
self.drawFrame()
def drawFrame(self):
# hack the WF Tree for now. just get is looking OK
texts = ['Test 1', 'Test 2', 'ARIA', 'CING', 'ISD']
icons = []
parents = []
callbacks = []
objects = ['Test 1', 'Test 2', 'ARIA', 'CING', 'ISD']
for text in texts:
icons.append('list-add')
callbacks.append(self.openLink)
parents.append(None)
self.pTree.update(parents, objects, texts, icons, callbacks)
self.title.set('Protocol: Std (ARIA)')
self.title.grid(row=1, column=1, padx=5, sticky='w')
self.details.set('Description: details about the exp type or protocol')
self.details.grid(row=2, column=1, padx=5, sticky='nw')
self.pMatrix.grid(row=3,
rowspan=2,
column=1,
padx=5,
pady=5,
sticky='ew')
self.editButtons.grid(row=5, column=1, padx=5, pady=5, sticky='ew')
self.filter.grid(row=1, column=2, rowspan=2, sticky='new')
self.pTree.grid(row=3, column=2, padx=5, pady=5, sticky='nsew')
self.pButtons1.grid(row=4, column=2, padx=5, sticky='ew')
self.pButtons2.grid(row=5, column=2, padx=5, sticky='ew')
matrix = []
objs = []
matrix.append(['Parameter1', 'String', 'foobar'])
objs.append('obj1')
matrix.append(['Parameter2', 'Number', '10'])
objs.append('obj2')
self.pMatrix.update(objectList=objs, textMatrix=matrix)
def tmpCall(self):
pass
def openLink(self, node):
tree = node.tree
par = node.object
print 'opening node "', par, '"'
print 'got series "', self.openedLinks[par], '"'
if len(self.openedLinks[par]) > 0:
for pv in self.openedLinks[par]:
icon = 'folder'
obj = par + '::' + pv
text = pv
callback = None
tree.add(node, obj, text, icon, callback)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
if not self.nmrProject:
self.nmrProject = project.newNmrProject(name=project.name)
if not self.project:
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
class UpdateAdministratorPopup(BasePopup, UpdateAgent):
def __init__(self,
parent,
serverLocation=UPDATE_SERVER_LOCATION,
serverDirectory=UPDATE_DIRECTORY,
dataFile=UPDATE_DATABASE_FILE):
UpdateAgent.__init__(self,
serverLocation,
serverDirectory,
dataFile,
admin=1)
self.fileTypes = [
FileType('Python', ['*.py']),
FileType('C', ['*.c']),
FileType('All', ['*'])
]
self.fileUpdate = None
BasePopup.__init__(self,
parent=parent,
title='CcpNmr Update Administrator',
quitFunc=self.quit)
def body(self, guiParent):
guiParent.grid_columnconfigure(3, weight=1)
self.commentsEntry = Entry(self)
self.priorityEntry = IntEntry(self)
row = 0
label = Label(guiParent, text='Server location:')
label.grid(row=row, column=0, sticky='w')
location = ''
uid = ''
httpDir = ''
subDir = ''
version = 'None'
if self.server:
location, uid, httpDir, subDir = self.server.identity
version = self.server.version or 'None'
self.serverEntry = Entry(guiParent, text=location)
self.serverEntry.grid(row=row, column=1, stick='w')
label = Label(guiParent, text='User ID:')
label.grid(row=row, column=2, sticky='w')
self.uidEntry = Entry(guiParent, text=uid)
self.uidEntry.grid(row=row, column=3, stick='w')
row += 1
label = Label(guiParent, text='HTTP directory:')
label.grid(row=row, column=0, sticky='w')
self.httpDirEntry = Entry(guiParent, text=httpDir)
self.httpDirEntry.grid(row=row, column=1, stick='w')
label = Label(guiParent, text='Sub-directory:')
label.grid(row=row, column=2, sticky='w')
self.subDirEntry = Entry(guiParent, text=subDir)
self.subDirEntry.grid(row=row, column=3, stick='w')
row += 1
self.localVerLabel = Label(guiParent,
text='Local version: %s' % self.version)
self.localVerLabel.grid(row=row, column=0, sticky='w')
self.serverLabel = Label(guiParent,
text='Server version: %s' % version)
self.serverLabel.grid(row=row, column=2, sticky='w')
row += 1
guiParent.grid_rowconfigure(row, weight=1)
headingList = [
'File',
'Location',
'Date',
'Priority',
'Comments',
'StoredAs',
]
editWidgets = [
None, None, None, self.priorityEntry, self.commentsEntry
]
editGetCallbacks = [
None, None, None, self.getPriority, self.getComments
]
editSetCallbacks = [
None, None, None, self.setPriority, self.setComments
]
self.scrolledMatrix = ScrolledMatrix(guiParent,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
callback=self.selectCell,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=4,
sticky='nsew')
row += 1
texts = [
'Add\nFiles', 'Remove\nFiles', 'Remove\nAll', 'Query\nServer',
'Commit\nSelected', 'Synchronise\nAll', 'Commit\nNew', 'Quit'
]
commands = [
self.addFile, self.removeFile, self.removeAll, self.queryFiles,
self.synchroniseSelected, self.synchroniseServer,
self.updateServer, self.quit
]
self.buttonList = ButtonList(guiParent,
texts=texts,
commands=commands,
expands=1)
self.buttonList.grid(row=row, column=0, columnspan=4, sticky='ew')
self.update()
def getPriority(self, fileUpdate):
if fileUpdate:
self.priorityEntry.set(fileUpdate.priority)
def setPriority(self, event):
i = self.priorityEntry.get()
if self.fileUpdate:
self.fileUpdate.priority = i
self.update()
def getComments(self, fileUpdate):
if fileUpdate:
self.commentsEntry.set(fileUpdate.details)
def setComments(self, event):
text = self.commentsEntry.get()
if self.fileUpdate:
self.fileUpdate.details = text
self.update()
def quit(self):
self.close()
self.destroy()
sys.exit()
def updateServer(self):
if self.server:
# Unly upload new updates
success = self.server.setFileUpdates()
self.serverLabel.set('Server version: %s' % self.server.version)
if success:
self.queryFiles()
def synchroniseSelected(self):
if self.server:
selectedUpdates = self.scrolledMatrix.currentObjects
if selectedUpdates:
# Refresh all selected updates
success = self.server.setFileUpdates(
fileUpdates=selectedUpdates, refresh=True)
self.serverLabel.set('Server version: %s' %
self.server.version)
if success:
self.queryFiles()
def synchroniseServer(self):
if self.server:
# Refresh all avaiable updates
success = self.server.setFileUpdates(refresh=True)
self.serverLabel.set('Server version: %s' % self.server.version)
if success:
self.queryFiles()
def queryFiles(self):
if self.server:
self.server.getFileUpdates()
self.update()
def addFile(self):
if self.server:
fileSelectPopup = FileSelectPopup(self,
title='Select Source File',
dismiss_text='Cancel',
file_types=self.fileTypes,
multiSelect=True,
selected_file_must_exist=True)
filePaths = fileSelectPopup.file_select.getFiles()
n = len(self.installRoot)
for filePath in filePaths:
if self.installRoot != filePath[:n]:
showWarning(
'Warning',
'Install root %s not found in file path %s' %
(self.installRoot, filePath))
continue
filePath = filePath[n + 1:]
if filePath:
dirName, fileName = splitPath(filePath)
if fileName[-3:] == '.py':
language = 'python'
else:
language = 'None'
fileUpdate = FileUpdate(self.server,
fileName,
dirName,
language,
isNew=True)
self.update()
def removeFile(self):
if self.fileUpdate:
self.fileUpdate.delete()
self.update()
def removeAll(self):
if self.server:
for fileUpdate in list(self.server.fileUpdates):
fileUpdate.delete()
self.update()
def selectAll(self):
if self.server:
for fileUpdate in self.server.fileUpdates:
fileUpdate.isSelected = 1
self.update()
def selectCell(self, object, row, col):
self.fileUpdate = object
self.updateButtons()
def updateButtons(self):
buttons = self.buttonList.buttons
if self.server:
buttons[0].enable()
buttons[3].enable()
buttons[4].enable()
else:
buttons[0].disable()
buttons[3].disable()
buttons[4].disable()
if self.server and self.server.fileUpdates:
buttons[2].enable()
else:
buttons[2].disable()
if self.fileUpdate:
buttons[1].enable()
else:
buttons[1].disable()
def update(self):
location = self.serverEntry.get()
uid = self.uidEntry.get()
httpDir = self.httpDirEntry.get()
subDir = self.subDirEntry.get()
if self.server:
if (location, uid, httpDir, subDir) != self.server.identity:
self.setServer(location)
self.updateButtons()
self.fileUpdate = None
textMatrix = []
objectList = []
colorMatrix = []
if self.server:
for fileUpdate in self.server.fileUpdates:
datum = []
datum.append(fileUpdate.fileName)
datum.append(fileUpdate.filePath)
datum.append(fileUpdate.date)
datum.append(fileUpdate.priority)
datum.append(fileUpdate.details)
datum.append(fileUpdate.storedAs)
textMatrix.append(datum)
objectList.append(fileUpdate)
if fileUpdate.isNew:
colorMatrix.append(5 * ['#B0FFB0'])
elif not fileUpdate.getIsUpToDate():
colorMatrix.append(5 * ['#FFB0B0'])
else:
colorMatrix.append(5 * [None])
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList,
colorMatrix=colorMatrix)
