def __init__(self,
parent,
label,
entry='',
separator=': ',
label_width=20,
entry_width=60,
label_anchor=Tkinter.E,
show='',
isArray=False,
returnCallback=None,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
self.separator = separator
text = label + separator
self.label = Label(self,
text=text,
width=label_width,
anchor=label_anchor)
self.label.grid(row=0, column=0, sticky=Tkinter.EW)
self.entry = FloatEntry(self,
show=show,
width=entry_width,
isArray=isArray,
returnCallback=returnCallback)
self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
self.setEntry(entry)
class LabeledFloatEntry(Frame):
def __init__(self,
parent,
label,
entry='',
separator=': ',
label_width=20,
entry_width=60,
label_anchor=Tkinter.E,
show='',
isArray=False,
returnCallback=None,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
self.separator = separator
text = label + separator
self.label = Label(self,
text=text,
width=label_width,
anchor=label_anchor)
self.label.grid(row=0, column=0, sticky=Tkinter.EW)
self.entry = FloatEntry(self,
show=show,
width=entry_width,
isArray=isArray,
returnCallback=returnCallback)
self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
self.setEntry(entry)
def getLabel(self):
text = self.label.get()
n = text.find(self.separator)
if (n >= 0):
text = text[:n]
return text
def setLabel(self, text=''):
text = text + self.separator
self.label.set(text)
def getEntry(self):
return self.entry.get()
def setEntry(self, value=''):
self.entry.set(value)
def __init__(self,
parent,
label='',
world_region=None,
view_region=None,
orient=Tkinter.HORIZONTAL,
allow_resize=True,
width=20,
callback=None,
borderwidth=1,
show_text=True,
text_color='#000000',
text_decimals=2,
units_scroll=0.1,
pages_scroll=1.0,
menu_entries=None,
menu_callback=None,
min_thickness=None,
*args,
**kw):
self.menu_entries = menu_entries
self.myCallback = callback
Frame.__init__(self, parent, *args, **kw)
self.text_decimals = text_decimals
self.label = Label(self, text=label, width=4)
self.menu = PulldownMenu(self,
callback=menu_callback,
entries=menu_entries)
self.entry = FloatEntry(self,
width=6,
returnCallback=self.adjustScrollbar)
self.region_scrollbar = RegionScrollbar(self,
world_region=world_region,
view_region=view_region,
orient=orient,
allow_resize=allow_resize,
width=width,
callback=self.doCallback,
borderwidth=borderwidth,
show_text=show_text,
text_color=text_color,
text_decimals=text_decimals,
units_scroll=units_scroll,
pages_scroll=pages_scroll,
min_thickness=min_thickness)
self.gridAll()
def body(self, guiFrame):
self.geometry('500x500')
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='RDC protocol settings')
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.floatEntry = FloatEntry(self, returnCallback=self.setValue)
headingList = ['Parameter', 'Value', 'Description']
justifyList = ['center', 'center', 'left']
editWidgets = [None, self.floatEntry, None]
editGetCallbacks = [None, self.getValue, None]
editSetCallbacks = [None, self.setValue, None]
self.rdcMatrix = ScrolledMatrix(frame,
headingList=headingList,
justifyList=justifyList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=False,
initialRows=10,
passSelfToCallback=True,
callback=self.selectRdc)
self.rdcMatrix.grid(row=0, column=0, sticky='nsew')
self.rdcMatrix.refreshFunc = self.updateRdcSet
self.updateRdcSet()
def body(self, guiFrame):
self.noeClassChoice = None
self.spectrum = None
self.intensEntry = FloatEntry(self, returnCallback=self.setIntens, width=5)
self.targetEntry = FloatEntry(self, returnCallback=self.setTarget, width=5)
self.minEntry = FloatEntry(self, returnCallback=self.setMin, width=5)
self.maxEntry = FloatEntry(self, returnCallback=self.setMax, width=5)
row = 0
label = Label(guiFrame, text='Spectrum: ', grid=(row,0))
tipText = ''
self.spectrumPulldown = PulldownMenu(guiFrame,self.changeSpectrum, grid=(row,1))
row +=1
guiFrame.expandGrid(row, 1)
tipTexts = ['Lower bound of this intensity category. Values are relative to reference intensity.',
'Target restraint distance for this category',
'Lower bound distance for this category',
'Upper bound distance for this category']
headingList = ['Min. NOE\nIntensity','Target\nDist','Min\nDist','Max\nDist']
editWidgets = [self.intensEntry,self.targetEntry,self.minEntry,self.maxEntry]
editGetCallbacks = [self.getIntens,self.getTarget,self.getMin,self.getMax]
editSetCallbacks = [self.setIntens,self.setTarget,self.setMin,self.setMax]
self.noeClassMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
callback=self.selectClass,
tipTexts=tipTexts,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
deleteFunc=self.deleteClass,
grid=(row,0), gridSpan=(1,2))
row +=1
tipTexts = ['Add a new distance restraint category',
'Deleted selected restraint categor']
texts = ['Add Class','Delete Class']
commands = [self.addClass,self.deleteClass]
self.bottomButtons = UtilityButtonList(guiFrame, doClone=False, grid=(row,0),
gridSpan=(1,2), tipTexts=tipTexts,
commands=commands, texts=texts)
for func in ('__init__','delete','setName'):
self.registerNotify(self.updateSpectra, 'ccp.nmr.Nmr.Experiment', func)
self.registerNotify(self.updateSpectra, 'ccp.nmr.Nmr.DataSource', func)
self.updateSpectra()
self.update()
def update(self):
spec = self.peakList.dataSource.name
expt = self.peakList.dataSource.experiment.name
es = stringFromExperimentSpectrum(expt,spec)
self.specLabel.set('Spectrum: '+es)
self.listLabel.set('Peak List: List %d' % self.peakList.serial)
numDims = self.peakList.dataSource.numDim
self.numDims = numDims
self.dimLabel=numDims * ['']
self.adjustEntry=numDims * ['']
self.adjusts=numDims * [0]
for i in range(numDims):
self.dimLabel[i] = Label(self, text = "F%d" % (i+1) )
self.dimLabel[i].grid(row = i+2, column = 0, columnspan=1, sticky='w')
self.adjustEntry[i] = FloatEntry(self, text = "%f" % self.adjusts[i],
width=10, tipText='The referencing adjustment to add for this dimension')
self.adjustEntry[i].grid(row = i+2, column = 1, columnspan=2, sticky='w')
self.goButton .grid(row = i+3, column = 0, columnspan=1, sticky='nsew')
self.clearButton .grid(row = i+3, column = 1, columnspan=1, sticky='nsew')
self.cancelButton .grid(row = i+3, column = 2, columnspan=1, sticky='nsew')
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):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
class CloudHomologueAssignPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.molSystem = None
self.chain = None
self.assignment = None
self.scores = []
BasePopup.__init__(self, parent, title="Cloud Threader", **kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def update(self):
if self.assignment and self.scores:
self.assignButton.enable()
else:
self.assignButton.disable()
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def assignSpinSystems(self):
if self.assignment and self.scores:
if showWarning('Query','Are you sure?'):
threshold = self.thresholdEntry.get() or -4.0
i = 0
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=None)
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
i += 1
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=residue)
showWarning('Done','%d residues assigned' % i)
def getMolSystems(self):
names = []
for molSystem in self.project.molSystems:
if molSystem.chains:
names.append( '%s' % (molSystem.code) )
return names
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
def updateMolSystems(self, *opt):
names = self.getMolSystems()
if names:
if not self.molSystem:
self.molSystem = self.project.findFirstMolSystem(code=names[0])
self.molSysPulldown.setup(names, names.index(self.molSystem.code))
def getChains(self):
chains = []
if self.molSystem:
for chain in self.molSystem.chains:
chains.append( [chain.code, chain] )
return chains
def changeChain(self, i, name=None):
if not name:
i = self.chainPulldown.selected_index
chains = self.getChains()
if chains:
self.chain = chains[i][1]
def updateChains(self, *chain):
chains = self.getChains()
if chains:
names = [x[0] for x in chains]
if (not self.chain) or (self.chain.code not in names):
self.chain = chains[0][1]
self.chainPulldown.setup(names, names.index(self.chain.code) )
self.update()
def destroy(self):
for func in ('__init__','delete'):
Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
BasePopup.destroy(self)
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 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 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 body(self, guiFrame):
self.geometry('600x350')
project = self.project
analysisProject = self.analysisProject
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
frame = Frame(guiFrame, grid=(0,0))
label = Label(frame, text=' Window:', grid=(0,0))
self.windowPulldown = PulldownList(frame, grid=(0,1),
tipText='The window that will be printed out',
callback=self.selectWindow)
tipTexts = ['For the window pulldown, show all of the spectrum windows in the current project, irrespective of the active group',
'For the window pulldown, show only spectrum windows that are in the currently active window group']
self.whichWindows = RadioButtons(frame, grid=(0,2),
entries=ACTIVE_OPTIONS, tipTexts=tipTexts,
select_callback=self.updateWindows)
texts = [ 'Save Print File' ]
tipTexts = [ 'Save the printout to the specified file' ]
commands = [ self.saveFile ]
buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row,2),
commands=commands, texts=texts, tipTexts=tipTexts)
self.buttons = buttons
buttons.buttons[0].config(bg='#B0FFB0')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
options = ['Options', 'Spectra', 'Peak Lists', 'Region']
tipTexts = ['Optional settings for spectra', 'Optional settings for peak lists', 'Optional settings for the region']
tabbedFrame = TabbedFrame(guiFrame, options=options, tipTexts=tipTexts)
tabbedFrame.grid(row=row, column=0, columnspan=3, sticky='nsew')
self.tabbedFrame = tabbedFrame
optionFrame, spectrumFrame, peakListFrame, regionFrame = tabbedFrame.frames
optionFrame.expandGrid(0, 0)
getOption = lambda key, defaultValue: PrintBasic.getPrintOption(analysisProject, key, defaultValue)
setOption = lambda key, value: PrintBasic.setPrintOption(analysisProject, key, value)
self.printFrame = PrintFrame(optionFrame, getOption=getOption,
grid=(0,0), gridSpan=(1,1),
setOption=setOption, haveTicks=True,
doOutlineBox=False)
spectrumFrame.expandGrid(0, 0)
frame = Frame(spectrumFrame, grid=(0,0), gridSpan=(1,1))
frame.expandGrid(1,0)
self.overrideSpectrum = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0), sticky='w')
tipText = 'Change the settings of the selected spectra back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
self.posColorPulldown = PulldownList(self, callback=self.setPosColor)
self.negColorPulldown = PulldownList(self, callback=self.setNegColor)
headings = ['Spectrum', 'Pos. Contours\nDrawn', 'Neg. Contours\nDrawn', 'Positive\nColours', 'Negative\nColours']
tipTexts = ['Spectrum in window', 'Whether the positive contours should be drawn', 'Whether the negative contours should be drawn',
'Colour scheme for positive contours (can be a single colour)', 'Colour scheme for negative contours (can be a single colour)']
editWidgets = [ None, None, None, self.posColorPulldown, self.negColorPulldown]
editGetCallbacks = [ None, self.togglePos, self.toggleNeg, self.getPosColor, self.getNegColor]
editSetCallbacks = [ None, None, None, self.setPosColor, self.setNegColor]
self.spectrumTable = ScrolledMatrix(frame, headingList=headings,
tipTexts=tipTexts,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
peakListFrame.expandGrid(0, 0)
frame = Frame(peakListFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(1,0)
self.overridePeakList = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0))
tipText = 'Change the settings of the selected peak lists back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
colors = Color.standardColors
self.peakColorPulldown = PulldownList(self, callback=self.setPeakColor,
texts=[c.name for c in colors],
objects=[c.hex for c in colors],
colors=[c.hex for c in colors])
headings = [ 'Peak List', 'Symbols Drawn', 'Peak Font', 'Peak Colour']
self.fontMenu = FontList(self, mode='Print', extraTexts=[no_peak_text])
editWidgets = [ None, None, self.fontMenu, self.peakColorPulldown]
editGetCallbacks = [ None, self.togglePeaks, self.getPeakFont, self.getPeakColor ]
editSetCallbacks = [ None, None, self.setPeakFont, self.setPeakColor ]
self.peakListTable = ScrolledMatrix(frame, headingList=headings,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
regionFrame.expandGrid(0, 0)
frame = Frame(regionFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(3,0)
tipText = 'Use the specified override region when printing rather than the window values'
self.overrideButton = CheckButton(frame, text='Use override region when printing',
tipText=tipText,
callback=self.toggledOverride, grid=(0,0))
tipTexts = ('Use min and max to specify override region', 'Use center and width to specify override region')
self.use_entry = USE_ENTRIES[0]
self.useButtons = RadioButtons(frame, entries=USE_ENTRIES,
tipTexts=tipTexts,
select_callback=self.changedUseEntry,
grid=(1,0))
texts = ('Set Region from Window', 'Set Center from Window', 'Set Width from Window')
tipTexts = ('Set the override region to be the current window region',
'Set the center of the override region to be the center of the current window region',
'Set the width of the override region to be the width of the current window region')
commands = (self.setRegionFromWindow, self.setCenterFromWindow, self.setWidthFromWindow)
self.setRegionButton = ButtonList(frame, texts=texts,
tipTexts=tipTexts,
commands=commands, grid=(2,0))
self.minRegionWidget = FloatEntry(self, returnCallback=self.setMinRegion, width=10)
self.maxRegionWidget = FloatEntry(self, returnCallback=self.setMaxRegion, width=10)
headings = MIN_MAX_HEADINGS
editWidgets = [ None, None, self.minRegionWidget, self.maxRegionWidget ]
editGetCallbacks = [ None, None, self.getMinRegion, self.getMaxRegion ]
editSetCallbacks = [ None, None, self.setMinRegion, self.setMaxRegion ]
self.regionTable = RegionScrolledMatrix(frame, headingList=headings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(3,0))
self.updateWindows()
self.updateAfter()
self.administerNotifiers(self.registerNotify)
class EditNoeClassesPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
BasePopup.__init__(self, parent=parent, title='NOE Distance Classes', **kw)
def body(self, guiFrame):
self.noeClassChoice = None
self.spectrum = None
self.intensEntry = FloatEntry(self, returnCallback=self.setIntens, width=5)
self.targetEntry = FloatEntry(self, returnCallback=self.setTarget, width=5)
self.minEntry = FloatEntry(self, returnCallback=self.setMin, width=5)
self.maxEntry = FloatEntry(self, returnCallback=self.setMax, width=5)
row = 0
label = Label(guiFrame, text='Spectrum: ', grid=(row,0))
tipText = ''
self.spectrumPulldown = PulldownMenu(guiFrame,self.changeSpectrum, grid=(row,1))
row +=1
guiFrame.expandGrid(row, 1)
tipTexts = ['Lower bound of this intensity category. Values are relative to reference intensity.',
'Target restraint distance for this category',
'Lower bound distance for this category',
'Upper bound distance for this category']
headingList = ['Min. NOE\nIntensity','Target\nDist','Min\nDist','Max\nDist']
editWidgets = [self.intensEntry,self.targetEntry,self.minEntry,self.maxEntry]
editGetCallbacks = [self.getIntens,self.getTarget,self.getMin,self.getMax]
editSetCallbacks = [self.setIntens,self.setTarget,self.setMin,self.setMax]
self.noeClassMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
callback=self.selectClass,
tipTexts=tipTexts,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
deleteFunc=self.deleteClass,
grid=(row,0), gridSpan=(1,2))
row +=1
tipTexts = ['Add a new distance restraint category',
'Deleted selected restraint categor']
texts = ['Add Class','Delete Class']
commands = [self.addClass,self.deleteClass]
self.bottomButtons = UtilityButtonList(guiFrame, doClone=False, grid=(row,0),
gridSpan=(1,2), tipTexts=tipTexts,
commands=commands, texts=texts)
for func in ('__init__','delete','setName'):
self.registerNotify(self.updateSpectra, 'ccp.nmr.Nmr.Experiment', func)
self.registerNotify(self.updateSpectra, 'ccp.nmr.Nmr.DataSource', func)
self.updateSpectra()
self.update()
def open(self):
self.updateSpectra()
self.update()
BasePopup.open(self)
def updateSpectra(self, *opt):
spectra = self.getSpectra()
if not spectra:
return
names = [self.getSpectrumName(x) for x in spectra]
if (not self.spectrum) or (self.spectrum not in spectra):
self.spectrum = spectra[0]
self.spectrumPulldown.setup(names, names.index(self.getSpectrumName(self.spectrum)) )
self.update()
def changeSpectrum(self, i, name):
self.spectrum = self.getSpectra()[i]
self.update()
def getSpectrumName(self,spectrum):
name = '%s:%s' % (spectrum.experiment.name,spectrum.name)
return name
def getSpectra(self):
spectra = set()
peakLists = getThroughSpacePeakLists(self.nmrProject)
for peakList in peakLists:
spectra.add(peakList.dataSource)
spectra = list(spectra)
spectra.sort()
return spectra
def selectClass(self, noeClass, row, col):
if noeClass:
self.noeClassChoice = (row, noeClass)
if len(self.noeClassMatrix.objectList) > 1:
self.bottomButtons.buttons[1].enable()
else:
self.bottomButtons.buttons[1].disable()
def addClass(self):
if self.spectrum:
noeClass = [0.0,6.0,0.0,6.0]
noeClasses = getIntensityDistanceTable(self.spectrum)
noeClasses.append(noeClass)
setSpectrumNoeDistanceClasses(self.spectrum, noeClasses)
self.update()
def deleteClass(self, *event):
if self.spectrum:
noeClasses = getIntensityDistanceTable(self.spectrum)
if self.noeClassChoice and (self.noeClassChoice[1] in noeClasses):
if len(noeClasses) > 1:
(i,noeClass) = self.noeClassChoice
noeClasses.remove(noeClass)
self.noeClassChoice = None
setSpectrumNoeDistanceClasses(self.spectrum, noeClasses)
self.update()
def setIntens(self, event):
if self.noeClassChoice:
val = self.intensEntry.get() or 0.0
self.noeClassChoice[1][0] = val
self.updateClass()
def getIntens(self, row):
if row:
self.intensEntry.set(row[0])
def setTarget(self, event):
if self.noeClassChoice:
val = self.targetEntry.get() or 0.0
self.noeClassChoice[1][1] = val
self.updateClass()
def getTarget(self, row):
if row:
self.targetEntry.set(row[1])
def setMin(self, event):
if self.noeClassChoice:
val = self.minEntry.get() or 0.0
self.noeClassChoice[1][2] = val
self.updateClass()
def getMin(self, row):
if row:
self.minEntry.set(row[2])
def setMax(self, event):
if self.noeClassChoice:
val = self.maxEntry.get() or 0.0
self.noeClassChoice[1][3] = val
self.updateClass()
def getMax(self, row):
if row:
self.maxEntry.set(row[3])
def getClasses(self):
noeClasses = []
if self.spectrum:
noeClasses = getIntensityDistanceTable(self.spectrum)
if noeClasses:
for i in range(len(noeClasses)):
(intens,target,minimum,maximum) = noeClasses[i]
if minimum > maximum:
(minimum,maximum) = (maximum,minimum)
minimum = min(target, minimum)
maximum = max(target, maximum)
intens = max(intens, 0.0)
noeClasses[i] = [intens,target,minimum,maximum]
noeClasses.sort()
noeClasses.reverse()
else:
noeClasses = []
if self.spectrum:
# default
noeClasses = getIntensityDistanceTable(self.spectrum)
return noeClasses
def updateClass(self):
if self.spectrum and self.noeClassChoice:
(i, noeClass) = self.noeClassChoice
noeClasses = getIntensityDistanceTable(self.spectrum)
noeClasses[i] = noeClass
setSpectrumNoeDistanceClasses(self.spectrum, noeClasses)
self.update()
def update(self):
textMatrix = []
objectList = self.getClasses()
if self.spectrum:
if self.noeClassChoice and (len(objectList) > 1):
self.bottomButtons.buttons[1].enable()
else:
self.bottomButtons.buttons[1].disable()
self.bottomButtons.buttons[0].enable()
else:
self.bottomButtons.buttons[0].disable()
self.bottomButtons.buttons[1].disable()
for (intens,target,minimum,maximum) in objectList:
datum = []
datum.append(intens)
datum.append(target)
datum.append(minimum)
datum.append(maximum)
textMatrix.append(datum)
self.noeClassMatrix.update(objectList=objectList,textMatrix=textMatrix)
if self.spectrum:
setSpectrumNoeDistanceClasses(self.spectrum,objectList)
def destroy(self):
for func in ('__init__','delete','setName'):
self.unregisterNotify(self.updateSpectra, 'ccp.nmr.Nmr.Experiment', func)
self.unregisterNotify(self.updateSpectra, 'ccp.nmr.Nmr.DataSource', func)
BasePopup.destroy(self)
def body(self, guiParent):
self.geometry("+150+150")
guiParent.grid_columnconfigure(0, weight=1)
self.master_frame = guiParent
units = ('ppm', 'point', 'Hz')
self.unit = 'ppm'
self.specLabel = Label(guiParent,
fg=self.titleColor,
grid=(0, 0),
sticky='ew')
self.peakLabel = Label(guiParent, grid=(0, 1), sticky='ew')
self.unit_frame = frame = Frame(guiParent,
grid=(1, 1),
gridSpan=(1, 2))
self.unitLabel = Label(frame, text='Current units: ', grid=(0, 0))
tipText = 'Selects which unit of measurement to display peak dimension positions with'
self.unitSelect = PulldownList(frame,
callback=self.changeUnit,
texts=units,
grid=(0, 1),
tipText=tipText)
self.heightLabel = Label(guiParent,
text='Height',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak height; the value of the spectrum point intensity (albeit often interpolated)'
self.heightEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.volumeLabel = Label(guiParent,
text='Volume',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak volume integral; normally a summation of data point values'
self.volumeEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.detailLabel = Label(guiParent,
text='Details',
borderwidth=2,
relief='groove')
tipText = 'A user-configurable textual comment for the peak, which appears an tables and occasionally on spectrum displays'
self.detailEntry = Entry(guiParent, borderwidth=1, tipText=tipText)
tipTexts = [
'Commits the specified values to update the peak and closes the popup',
]
texts = ['Update']
commands = [self.commit]
self.buttons = UtilityButtonList(guiParent,
texts=texts,
commands=commands,
doClone=False,
helpUrl=self.help_url,
tipTexts=tipTexts)
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()
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)
def update(self, peak=None, peakList=None):
# first destroy old labels and entries (saves grid hassles)
for label in self.dimensionLabels:
label.destroy()
for entry in self.dimensionEntries:
entry.destroy()
# now setup required data
if peak:
title = 'Edit Peak'
self.buttons.buttons[0].config(text='Update')
else:
title = 'Add Peak'
self.buttons.buttons[0].config(text='Add Peak')
self.setTitle(title)
self.peak = peak
self.peakList = peakList
if not peakList:
if peak:
self.peakList = peak.peakList
else:
return
peakList = self.peakList
spectrum = peakList.dataSource.name
self.numDims = peakList.dataSource.numDim
self.posn = self.numDims * [0]
self.dataDims = peakList.dataSource.sortedDataDims()
if self.peak:
serial = self.peak.serial
dims = self.peak.sortedPeakDims()
details = self.peak.details
if not details:
details = ''
if self.peak.annotation:
annotn = '%0.16s' % self.peak.annotation
else:
annotn = ''
heightIntensity = self.peak.findFirstPeakIntensity(
intensityType='height')
volumeIntensity = self.peak.findFirstPeakIntensity(
intensityType='volume')
if heightIntensity:
height = heightIntensity.value
else:
height = 0.0
if volumeIntensity:
volume = volumeIntensity.value
else:
volume = 0.0
for i in range(self.numDims):
peakDim = dims[i]
dataDimRef = peakDim.dataDimRef
if dataDimRef:
self.posn[i] = peakDim.position + (
peakDim.numAliasing * dataDimRef.dataDim.numPointsOrig)
else:
self.posn[i] = peakDim.position
else:
dict = peakList.__dict__.get('serialDict')
if dict is None:
serial = 1
else:
serial = dict.get('peaks', 0) + 1
height = 0.0
volume = 0.0
details = ''
annotn = ''
self.specLabel.set(
text='Experiment: %s Spectrum: %s PeakList: %d' %
(peakList.dataSource.experiment.name, spectrum, peakList.serial))
self.peakLabel.set(text='Peak: %d' % serial)
self.dimensionLabels = self.numDims * ['']
self.dimensionEntries = self.numDims * ['']
for i in range(self.numDims):
pos = self.posn[i]
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
pos = unit_converter[('point', self.unit)](
pos, getPrimaryDataDimRef(dataDim))
self.dimensionLabels[i] = Label(self.master_frame,
text='F%d' % (i + 1),
borderwidth=2,
relief='groove')
tipText = 'The peak position in dimension %d, in the specified units' % (
i + 1)
self.dimensionEntries[i] = FloatEntry(self.master_frame,
borderwidth=1,
text='%8.4f' % pos,
tipText=tipText)
self.heightEntry.set(text='%f' % height)
self.volumeEntry.set(text='%f' % volume)
self.detailEntry.set(text=details)
row = 0
self.specLabel.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
self.peakLabel.grid(row=row, column=0, sticky='nsew')
self.unit_frame.grid(row=row, column=1, columnspan=2, sticky='nsew')
for i in range(self.numDims):
row = row + 1
self.dimensionLabels[i].grid(row=row, column=0, sticky='nsew')
self.dimensionEntries[i].grid(row=row,
column=1,
columnspan=3,
sticky='e')
row = row + 1
self.heightLabel.grid(row=row, column=0, sticky='nsew')
self.heightEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.volumeLabel.grid(row=row, column=0, sticky='nsew')
self.volumeEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.detailLabel.grid(row=row, column=0, sticky='nsew')
self.detailEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.buttons.grid(row=row, column=0, columnspan=4, sticky='nsew')
class RegionSelector(Frame):
def __init__(self,
parent,
label='',
world_region=None,
view_region=None,
orient=Tkinter.HORIZONTAL,
allow_resize=True,
width=20,
callback=None,
borderwidth=1,
show_text=True,
text_color='#000000',
text_decimals=2,
units_scroll=0.1,
pages_scroll=1.0,
menu_entries=None,
menu_callback=None,
min_thickness=None,
*args,
**kw):
self.menu_entries = menu_entries
self.myCallback = callback
Frame.__init__(self, parent, *args, **kw)
self.text_decimals = text_decimals
self.label = Label(self, text=label, width=4)
self.menu = PulldownMenu(self,
callback=menu_callback,
entries=menu_entries)
self.entry = FloatEntry(self,
width=6,
returnCallback=self.adjustScrollbar)
self.region_scrollbar = RegionScrollbar(self,
world_region=world_region,
view_region=view_region,
orient=orient,
allow_resize=allow_resize,
width=width,
callback=self.doCallback,
borderwidth=borderwidth,
show_text=show_text,
text_color=text_color,
text_decimals=text_decimals,
units_scroll=units_scroll,
pages_scroll=pages_scroll,
min_thickness=min_thickness)
self.gridAll()
def gridAll(self):
col = 0
if (self.menu_entries and len(self.menu_entries) > 1):
self.menu.grid(row=0, column=col, sticky=Tkinter.EW)
col = col + 1
else:
self.menu.grid_forget()
self.label.grid(row=0, column=col, sticky=Tkinter.EW)
col = col + 1
self.entry.grid(row=0, column=col, sticky=Tkinter.EW)
self.grid_columnconfigure(col, weight=0)
col = col + 1
self.region_scrollbar.grid(row=0, column=col, sticky=Tkinter.NSEW)
self.grid_columnconfigure(col, weight=1)
col = col + 1
self.grid_columnconfigure(col, weight=0)
def setMinThickness(self, min_thickness):
self.region_scrollbar.setMinThickness(min_thickness)
def setMenuEntries(self, menu_entries):
self.menu_entries = menu_entries
self.menu.replace(menu_entries)
self.gridAll()
def getMenuEntry(self):
return self.menu.getSelected()
def adjustScrollbar(self, *event):
try:
x = float(self.entry.get())
except:
showError('Entry error', 'Need to enter float in scrollbar box')
self.setEntry()
return
(v0, v1) = self.region_scrollbar.view_region
d = 0.5 * (v1 - v0)
self.region_scrollbar.setViewRegion(x - d, x + d, do_callback=True)
def doCallback(self, view_region):
if (self.myCallback):
self.myCallback(view_region)
#print 'doCallback', view_region
self.setEntry(view_region)
def setEntry(self, view_region=None):
if (not view_region):
view_region = self.region_scrollbar.view_region
(v0, v1) = view_region
x = 0.5 * (v0 + v1)
s = formatDecimals(x, decimals=self.text_decimals)
self.entry.set(s)
def __getattr__(self, name):
# dispatch everything not defined by RegionSelector to scrollbar widget
try:
return getattr(self.__dict__['region_scrollbar'], name)
except:
raise AttributeError, "RegionSelector instance has no attribute '%s'" % name
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def body(self, guiFrame):
self.geometry('600x350')
guiFrame.expandGrid(0, 0)
tipTexts = ['', '', '', '']
options = [
'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions',
'Region Peak Find'
]
tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0))
frameA, frameB, frameC, frameD = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
# Find Params
frameA.expandGrid(2, 0)
row = 0
label = LabelFrame(frameA,
text='Extrema to search for:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(0, 1)
entries = ['positive and negative', 'positive only', 'negative only']
tipTexts = [
'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima',
]
self.extrema_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
label = LabelFrame(frameA,
text='Nearby points to check:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(None, 1)
entries = ['+-1 in at most one dim', '+-1 allowed in any dim']
tipTexts = [
'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region',
]
self.adjacent_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
labelFrame = LabelFrame(frameA,
text='Other parameters:',
grid=(row, 0),
gridSpan=(1, 2))
labelFrame.expandGrid(5, 2)
frow = 0
label = Label(labelFrame,
text='Scale relative to contour levels:',
grid=(frow, 0),
sticky='e')
tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible'
self.scale_entry = FloatEntry(labelFrame,
grid=(frow, 1),
tipText=tipText,
returnCallback=self.apply,
width=10)
self.scale_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Exclusion buffer around peaks (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking'
self.buffer_entry = IntEntry(labelFrame,
returnCallback=self.apply,
grid=(frow, 1),
width=10,
tipText=tipText)
self.buffer_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Extra thickness in orthogonal dims (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals'
self.thickness_entry = IntEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.thickness_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Minimum drop factor (0.0-1.0):',
grid=(frow, 0),
sticky='e')
tipText = ''
self.drop_entry = FloatEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.drop_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Volume method:',
grid=(frow, 0),
sticky='e')
tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"'
self.method_menu = PulldownList(labelFrame,
texts=PeakBasic.PEAK_VOLUME_METHODS,
grid=(frow, 1),
callback=self.apply,
tipText=tipText)
# Spectrum widths
frameB.expandGrid(1, 1)
label = Label(frameB, text='Spectrum: ')
label.grid(row=0, column=0, sticky='e')
tipText = 'The spectrum which determines the widths being shown'
self.expt_spectrum = PulldownList(frameB,
tipText=tipText,
callback=self.setSpectrumProperties)
self.expt_spectrum.grid(row=0, column=1, sticky='w')
self.editLinewidthEntry = FloatEntry(self,
text='',
returnCallback=self.setLinewidth,
width=10)
self.editBoxwidthEntry = FloatEntry(self,
text='',
returnCallback=self.setBoxwidth,
width=10)
tipTexts = [
'The number of the spectrum dimension to which the settings apply',
'The nuclear isotope measures in the spectrum dimension',
'The smallest value for the linewidth of a peak for it to be picked',
'The size of the spectrum region to perform the volume integral over'
]
headingList = [
'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth'
]
editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth]
editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth]
editWidgets = [
None, None, self.editLinewidthEntry, self.editBoxwidthEntry
]
self.spectrumMatrix = ScrolledMatrix(frameB,
initialRows=6,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectCell,
tipTexts=tipTexts)
self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew')
# Diagonal Exclusions
frameC.expandGrid(0, 0)
tipTexts = [
'The isotope as measures on the axis of a spectrum window',
'The distance from the homonuclear diagonal line within which no peak picking can occur'
]
self.exclusionEntry = FloatEntry(self,
text='',
returnCallback=self.setExclusion,
width=10)
headingList = ['Isotope', 'Diagonal Exclusion (ppm)']
editSetCallbacks = [None, self.setExclusion]
editGetCallbacks = [None, self.getExclusion]
editWidgets = [None, self.exclusionEntry]
self.isotopeMatrix = ScrolledMatrix(frameC,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
grid=(0, 0),
tipTexts=tipTexts)
# Region peak find
self.regionFindPeakList = None
self.regionCondition = None
self.regionConditions = []
self.regionCol = 1
row = 0
label = Label(frameD, text='Peak List: ', grid=(0, 0))
tipText = 'Selects which peak list to perform region-wide peak picking for'
self.regionPeakListPulldown = PulldownList(
frameD,
callback=self.changeRegionPeakList,
grid=(0, 1),
tipText=tipText)
row += 1
frameD.expandGrid(row, 1)
self.regionEntry = FloatEntry(self,
text='',
returnCallback=self.setRegion,
width=10)
self.conditionMenu = PulldownList(self,
texts=('include', 'exclude'),
callback=self.setCondition)
tipTexts = [
'Whether to include or exclude the states region from region-wide peak picking',
]
headingList = ['Condition']
editSetCallbacks = [None]
editGetCallbacks = [None]
editWidgets = [self.conditionMenu]
self.regionFindMatrix = ScrolledMatrix(
frameD,
headingList=headingList,
callback=self.selectRegionCell,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(row, 0),
gridSpan=(1, 2))
row += 1
tipTexts = [
'Sets the currently selected region row to cover the whole spectrum',
'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas',
'Remove the selected region specification',
'Go to the panel for setting the parameters that control how peaks extrema are picked',
'Using the stated regions and parameters, perform region-wide peak picking'
]
texts = [
'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params',
'Find Peaks!'
]
commands = [
self.wholeRegion, self.addCondition, self.deleteCondition,
self.adjustParams, self.regionFindPeaks
]
buttons = ButtonList(frameD,
texts=texts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
buttons.buttons[4].config(bg='#B0FFB0')
utilButtons = UtilityButtonList(tabbedFrame.sideFrame,
grid=(0, 0),
helpUrl=self.help_url,
sticky='e')
self.dataDim = None
self.setParamsEntries()
self.updateSpectrum()
self.setIsotopeProperties()
self.updateRegionPeakLists()
self.administerNotifiers(self.registerNotify)
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 EditPeakFindParamsPopup(BasePopup):
"""
** Peak Settings and Non-Interactive Peak Finding **
The purpose of this dialog is to allow the user to select settings for
finding and integrating peaks, and also to be able to find peaks in an
arbitrary region that is specified in a table rather than via a spectrum
window.
** Find Parameters tab **
This can be used to specify how peak finding works.
First of all, you can search for just positive peaks, just negative
peaks or both, and the default is that it is just positive peaks.
However, this is further filtered by what the contour levels are.
If there are no positive contour levels for a given spectrum then
positive peaks are not found even if this dialog says they can be,
and similarly if there are no negative contour levels for a given
spectrum then negative peaks are not found even if this dialog says
they can be.
The peak finding algorithm looks for local extrema (maximum for
positive peaks and minima for negative peaks). But on a grid there
are various ways to define what you mean by an extremum. Suppose
you are trying to determine if point p is a maximum (similar
considerations apply for minimum). You would want the intensity
at all nearby points to be less than or equal to the intensity at p.
You can just check points that are just +- one point from p in each
dimension, or you can also check "diagonal" points. For
example, if you are looking at point p = (x, y) in 2D, then the
former would mean checking the four points (x-1, y), (x+1, y)
(x, y-1) and (x, y+1), whereas for the latter you would also have
to check (x-1, y-1), (x-1, y+1), (x+1, y-1) and (x+1, y+1). In
N dimensions the "diagonal" method involves checking 3^N-1 points
whereas the "non-diagonal" method involves checking only 2N points.
In general the "non-diagonal" method is probably the one to use,
and it is the default.
Peaks are only found above (for positive peaks) or below (for negative
peaks) some threshold. By default this is determined by the contour level
for the spectrum. For positive peaks the threshold is the minimum
positive contour level, and for negative peaks the threshold is the
maximum negative contour level. However these levels can be scaled up
(or down) using the "Scale relative to contour levels" option (default
value 1). For example, if you have drawn the contour levels low to
show a bit of noise, but do not want the noise picked as peaks, then
you could select a scale of 2 (or whatever) to increase the threshold.
The "Exclusion buffer around peaks" is so that in crowded regions you
do not get too many peaks near one location. By default the exclusion
buffer is 1 point in each dimension, but this can be increased to make
the algorithm find fewer peaks.
By default the peak finding only looks at the orthogonal region that
is displayed in the given window where peak finding is taking place.
Sometimes it looks like a peak should be found because in x, y you
can see an extremum, but unless it is also an extremum in the orthogonal
dimensions it is not picked. You can widen out the points being
examined in the orthogonal dimensions by using the "Extra thickness in
orthogonal dims" option, which is specified in points.
The "Minimum drop factor" is by what factor the intensity needs to drop
from its extreme value for there to be considered to be a peak. This
could help remove sinc wiggle peaks, for example. The default is that
the drop factor is 0, which in effect means that there is no condition.
The "Volume method" is what is used to estimate the volume of peaks that
are found. The default is "box sum", which just looks at a fixed size
box around the peak centre and sums the intensities in that. The size
of the box is set in the table in the Spectrum Widths tab. The
"truncated box sum" is the same as "box sum" except that the summing
stops in a given direction when (if) the intensities start increasing.
The "parabolic" fit fits a quadratic equation in each dimension to the
intensity at the peak centre and ad +- 1 points and then uses the
equivalent Gaussian fit to estimate the volume.
** Spectrum Widths **
This can be used to specify minimum linewidths (in Hz) for there to be
considered a peak to exist in the peak finding algorithm. It is also
where the Boxwidth for each dimension in each spectrum is specified.
** Diagonal Exclusions **
This can be used to exclude peaks from being found in regions near
the diagonal (so in homonuclear experiments). The exclusion region
is specified in ppm and is independent of spectrum.
** Region Peak Find **
This can be used to find peaks non-interactively (so not having to
control shift drag inside a spectrum window). The region being
analysed is specified in the table. There are two types of conditions
that can be specified, "include" for regions that should be included
and "exclude" for regions that should be excluded. The regions are
specified in ppm.
The "Whole Region" button will set the selected row in the table to be
the entire fundamental region of the spectrum.
The "Add Region" button adds an extra row to the table, and the "Delete
Region" button removes the selected row.
The "Adjust Params" button goes to the Find Parameters tab.
The "Find Peaks!" button does the peak finding.
"""
def __init__(self, parent, *args, **kw):
self.spectrum = None
BasePopup.__init__(self,
parent=parent,
title='Peak : Peak Finding',
**kw)
def body(self, guiFrame):
self.geometry('600x350')
guiFrame.expandGrid(0, 0)
tipTexts = ['', '', '', '']
options = [
'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions',
'Region Peak Find'
]
tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0))
frameA, frameB, frameC, frameD = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
# Find Params
frameA.expandGrid(2, 0)
row = 0
label = LabelFrame(frameA,
text='Extrema to search for:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(0, 1)
entries = ['positive and negative', 'positive only', 'negative only']
tipTexts = [
'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima',
]
self.extrema_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
label = LabelFrame(frameA,
text='Nearby points to check:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(None, 1)
entries = ['+-1 in at most one dim', '+-1 allowed in any dim']
tipTexts = [
'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region',
]
self.adjacent_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
labelFrame = LabelFrame(frameA,
text='Other parameters:',
grid=(row, 0),
gridSpan=(1, 2))
labelFrame.expandGrid(5, 2)
frow = 0
label = Label(labelFrame,
text='Scale relative to contour levels:',
grid=(frow, 0),
sticky='e')
tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible'
self.scale_entry = FloatEntry(labelFrame,
grid=(frow, 1),
tipText=tipText,
returnCallback=self.apply,
width=10)
self.scale_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Exclusion buffer around peaks (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking'
self.buffer_entry = IntEntry(labelFrame,
returnCallback=self.apply,
grid=(frow, 1),
width=10,
tipText=tipText)
self.buffer_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Extra thickness in orthogonal dims (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals'
self.thickness_entry = IntEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.thickness_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Minimum drop factor (0.0-1.0):',
grid=(frow, 0),
sticky='e')
tipText = ''
self.drop_entry = FloatEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.drop_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Volume method:',
grid=(frow, 0),
sticky='e')
tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"'
self.method_menu = PulldownList(labelFrame,
texts=PeakBasic.PEAK_VOLUME_METHODS,
grid=(frow, 1),
callback=self.apply,
tipText=tipText)
# Spectrum widths
frameB.expandGrid(1, 1)
label = Label(frameB, text='Spectrum: ')
label.grid(row=0, column=0, sticky='e')
tipText = 'The spectrum which determines the widths being shown'
self.expt_spectrum = PulldownList(frameB,
tipText=tipText,
callback=self.setSpectrumProperties)
self.expt_spectrum.grid(row=0, column=1, sticky='w')
self.editLinewidthEntry = FloatEntry(self,
text='',
returnCallback=self.setLinewidth,
width=10)
self.editBoxwidthEntry = FloatEntry(self,
text='',
returnCallback=self.setBoxwidth,
width=10)
tipTexts = [
'The number of the spectrum dimension to which the settings apply',
'The nuclear isotope measures in the spectrum dimension',
'The smallest value for the linewidth of a peak for it to be picked',
'The size of the spectrum region to perform the volume integral over'
]
headingList = [
'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth'
]
editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth]
editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth]
editWidgets = [
None, None, self.editLinewidthEntry, self.editBoxwidthEntry
]
self.spectrumMatrix = ScrolledMatrix(frameB,
initialRows=6,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectCell,
tipTexts=tipTexts)
self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew')
# Diagonal Exclusions
frameC.expandGrid(0, 0)
tipTexts = [
'The isotope as measures on the axis of a spectrum window',
'The distance from the homonuclear diagonal line within which no peak picking can occur'
]
self.exclusionEntry = FloatEntry(self,
text='',
returnCallback=self.setExclusion,
width=10)
headingList = ['Isotope', 'Diagonal Exclusion (ppm)']
editSetCallbacks = [None, self.setExclusion]
editGetCallbacks = [None, self.getExclusion]
editWidgets = [None, self.exclusionEntry]
self.isotopeMatrix = ScrolledMatrix(frameC,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
grid=(0, 0),
tipTexts=tipTexts)
# Region peak find
self.regionFindPeakList = None
self.regionCondition = None
self.regionConditions = []
self.regionCol = 1
row = 0
label = Label(frameD, text='Peak List: ', grid=(0, 0))
tipText = 'Selects which peak list to perform region-wide peak picking for'
self.regionPeakListPulldown = PulldownList(
frameD,
callback=self.changeRegionPeakList,
grid=(0, 1),
tipText=tipText)
row += 1
frameD.expandGrid(row, 1)
self.regionEntry = FloatEntry(self,
text='',
returnCallback=self.setRegion,
width=10)
self.conditionMenu = PulldownList(self,
texts=('include', 'exclude'),
callback=self.setCondition)
tipTexts = [
'Whether to include or exclude the states region from region-wide peak picking',
]
headingList = ['Condition']
editSetCallbacks = [None]
editGetCallbacks = [None]
editWidgets = [self.conditionMenu]
self.regionFindMatrix = ScrolledMatrix(
frameD,
headingList=headingList,
callback=self.selectRegionCell,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(row, 0),
gridSpan=(1, 2))
row += 1
tipTexts = [
'Sets the currently selected region row to cover the whole spectrum',
'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas',
'Remove the selected region specification',
'Go to the panel for setting the parameters that control how peaks extrema are picked',
'Using the stated regions and parameters, perform region-wide peak picking'
]
texts = [
'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params',
'Find Peaks!'
]
commands = [
self.wholeRegion, self.addCondition, self.deleteCondition,
self.adjustParams, self.regionFindPeaks
]
buttons = ButtonList(frameD,
texts=texts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
buttons.buttons[4].config(bg='#B0FFB0')
utilButtons = UtilityButtonList(tabbedFrame.sideFrame,
grid=(0, 0),
helpUrl=self.help_url,
sticky='e')
self.dataDim = None
self.setParamsEntries()
self.updateSpectrum()
self.setIsotopeProperties()
self.updateRegionPeakLists()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
# Many more needed here, esp on the AnalysisProject prams
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.DataSource',
func)
notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.Experiment',
func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.PeakList',
func)
for clazz in ('Experiment', 'DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateSpectrumTable, 'ccp.nmr.Nmr.%s' % clazz,
func)
for func in ('setPeakFindBoxWidth', 'setPeakFindMinLineWidth'):
notifyFunc(self.updateSpectrumTable,
'ccpnmr.Analysis.AnalysisDataDim', func)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def updateSpectrum(self, spectrum=None):
if not spectrum:
spectrum = self.spectrum
spectra = self.parent.getSpectra()
if spectra:
if spectrum not in spectra:
spectrum = spectra[0]
index = spectra.index(spectrum)
names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra]
else:
index = 0
names = []
self.expt_spectrum.setup(names, spectra, index)
self.setSpectrumProperties(spectrum)
def updateNotifier(self, *extra):
self.updateSpectrum()
def setLinewidth(self, *event):
value = self.editLinewidthEntry.get()
if value is not None:
PeakFindParams.setPeakFindMinLinewidth(self.dataDim, value)
self.setSpectrumProperties(self.dataDim.dataSource)
def getLinewidth(self, dataDim):
if dataDim:
self.editLinewidthEntry.set(
PeakFindParams.getPeakFindMinLinewidth(self.dataDim))
def setBoxwidth(self, *event):
value = self.editBoxwidthEntry.get()
if value is not None:
PeakFindParams.setPeakFindBoxwidth(self.dataDim, value)
self.setSpectrumProperties(self.dataDim.dataSource)
def getBoxwidth(self, dataDim):
if dataDim:
self.editBoxwidthEntry.set(
PeakFindParams.getPeakFindBoxwidth(self.dataDim))
def selectCell(self, object, row, col):
self.dataDim = object
def setExclusion(self, *extra):
isotope = self.isotopeMatrix.currentObject
if not isotope:
return
value = self.exclusionEntry.get()
if value is not None:
setIsotopeExclusion(isotope, value)
self.setIsotopeProperties()
def getExclusion(self, isotope):
value = getIsotopeExclusion(isotope)
self.exclusionEntry.set(value)
def setParamsEntries(self):
project = self.project
params = PeakFindParams.getPeakFindParams(project)
self.scale_entry.set(params['scale'])
self.buffer_entry.set(params['buffer'])
self.thickness_entry.set(params['thickness'])
self.drop_entry.set(params['drop'])
volumeMethod = params['volumeMethod']
if volumeMethod == 'parabolic fit':
volumeMethod = PeakBasic.PEAK_VOLUME_METHODS[0]
self.method_menu.set(params['volumeMethod'])
if (params['nonadjacent']):
n = 1
else:
n = 0
self.adjacent_buttons.setIndex(n)
have_high = params['haveHigh']
have_low = params['haveLow']
if (have_high and have_low):
n = 0
elif (have_high):
n = 1
else:
n = 2
self.extrema_buttons.setIndex(n)
def apply(self, *extra):
params = {}
params['scale'] = self.scale_entry.get()
params['buffer'] = self.buffer_entry.get()
params['thickness'] = self.thickness_entry.get()
params['drop'] = self.drop_entry.get()
params['volumeMethod'] = self.method_menu.getText()
n = self.adjacent_buttons.getIndex()
if (n == 0):
nonadjacent = False
else:
nonadjacent = True
params['nonadjacent'] = nonadjacent
n = self.extrema_buttons.getIndex()
if (n == 0):
have_high = True
have_low = True
elif (n == 1):
have_high = True
have_low = False
elif (n == 2):
have_high = False
have_low = True
params['haveHigh'] = have_high
params['haveLow'] = have_low
project = self.project
try:
PeakFindParams.setPeakFindParams(project, params)
except Implementation.ApiError, e:
showError('Parameter error', e.error_msg, parent=self)
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
class PopupTemplate(BasePopup):
def __init__(self, parent, project=None, *args, **kw):
self.project = project
self.parent = parent
self.objects = self.getObjects()
self.object = None
BasePopup.__init__(self, parent=parent, title='Popup Template', **kw)
self.updateObjects()
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 floatEntryReturn(self, event):
value = self.floatEntry.get()
self.textWindow.setText('%s\n' % value)
def selectObject(self, object, row, col):
self.object = object
def getKeywords(self, object):
if object :
values = object.keywords
self.multiWidget.set(values)
def setKeywords(self, event):
values = self.multiWidget.get()
self.object.keywords = values
self.updateObjects()
def getNumber(self, object):
if object :
self.intEntry.set(object.quantity)
def setNumber(self, event):
value = self.intEntry.get()
self.object.quantity = value
self.updateObjects()
def toggleFrame1(self, isHidden):
if isHidden:
self.scrolledMatrix.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel2.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame2(self, isHidden):
if isHidden:
self.scrolledGraph.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame3(self, isHidden):
if isHidden:
self.scrolledCanvas.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel2.arrowOff()
def valueRampCallback(self, value):
self.textWindow.setText('%s\n' % value)
def checkRadioButtons(self, value):
self.textWindow.setText('%s\n' % value)
def selectPulldown(self, index, name):
self.textWindow.setText('%d, %s\n' % (index, name))
def toggleSelector(self, value):
self.textWindow.setText('%s\n' % value)
def changedCheckButtons(self, values):
self.textWindow.setText(','.join(values) + '\n')
def getObjects(self):
objects = []
objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) )
objects.append( Fruit('Orange', '#FF8000',4 ) )
objects.append( Fruit('Banana', '#FFF000',5 ) )
objects.append( Fruit('Pinapple','#FFD000',9 ) )
objects.append( Fruit('Kiwi', '#008000',12) )
objects.append( Fruit('Lime', '#00FF00',2 ) )
objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) )
objects.append( Fruit('Pear', '#408000',6 ) )
objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) )
objects.append( Fruit('Plumb', '#800080',7 ) )
return objects
def updateObjects(self, event=None):
textMatrix = []
objectList = []
colorMatrix = []
for object in self.objects:
datum = []
datum.append( object.name )
datum.append( None )
datum.append( object.quantity )
datum.append( ','.join(object.keywords) )
colors = [None, object.color, None, None]
textMatrix.append(datum)
objectList.append(object)
colorMatrix.append(colors)
if self.check.get():
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList)
else:
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix)
def selectFile(self):
fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = fileSelectPopup.getFile()
self.textWindow.setText('File Selected: %s\n' % fileName)
def showWarning(self, eventObject):
self.textWindow.setText('Text Entry Return Pressed\n')
showWarning('Warning Title','Warning Message')
return
def pressButton(self):
self.textWindow.setText('Button Pressed\n')
if showYesNo('Title','Prompt: Clear text window?'):
self.textWindow.clear()
return
def quit(self):
BasePopup.destroy(self)
class AnnealingSettingsTab(object):
'''This class describes the tab in the GUI where the user
can change setting that govern the monte carlo / annleaing
procedure. This also includes which information from the ccpn
analysis project is used and which information is
ignored. This includes:
* present sequential assignments
* tentative assignments
* amino acid type information
* whether to include untyped spin systems
* assignments to peak dimensions
ALso the chain can be selected here.
Furthermore the user can set the temperature
regime of the annealing, the amount of times the procedure
is repeated to obtain statistics. The fraction of peaks
that is left out in each run to diversify the results,
the treshhold score for amino acid typing and the treshhold
collabelling for a peak to be expected.
'''
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.minIsoFrac = 0.1
self.leavePeaksOutFraction = 0.0
self.minTypeScore = 1.0
self.chain = None
self.amountOfRepeats = 10
self.amountOfSteps = 10000
self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022,
0.033, 0.050, 0.075, 0.113,
0.170, 0.256, 0.384, 0.576,
0.864, 1.297, 1.946, 2.919,
4.378, 6.568, 9.852, 14.77,
22.16, 33.25]
self.energyDataSets = [[]]
self.residues = []
self.body()
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def runCalculations(self):
'''Run all calculations. Also triggers the disabling of
some buttons and fields.
'''
self.startButton.disable()
self.disableIllegalButtonsAfterPrecalculations()
self.guiParent.connector.runAllCalculations()
self.startButton.configure(text='More runs')
self.startButton.enable()
def disableIllegalButtonsAfterPrecalculations(self):
'''Disable buttons and field the user can not alter
any longer after the model is set up and the
'pre-calculations' have finished.
This is done because this part of the calculation
should only be run once. All settings that would
be changed after this point will not have any influence.
'''
illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry,
self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck,
self.useTypeCheck, self.useDimensionalAssignmentsCheck,
self.useTentativeCheck]
for illegalButton in illegalButtons:
illegalButton.configure(state='disabled')
self.molPulldown.disable()
def getChainName(self, chain):
'''Get the name for a chain.
args: chain: ccpn analysis
chain object
returns: chain name
'''
return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType)
def getChains(self):
'''Get all chains present in the project.
returns: list of ccpn analysis chain objects
'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateChains(self, *opt):
'''Updates the list of chains if a new one is added
to or deleted from the project. Updates the
pull down list where a chain can be selected.
'''
index = 0
texts = []
chains = self.getChains()
chain = self.chain
if chains:
if chain not in chains:
chain = chains[0]
texts = [self.getChainName(c) for c in chains]
index = chains.index(chain)
else:
chain = None
self.molPulldown.setup(texts, chains, index)
if chain is not self.chain:
self.chain = chain
def changeMolecule(self, chain):
'''Select a molecular chain.'''
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges(fromChain=True)
def updateStepEntry(self, event=None):
'''Update the value and entry that sets the amount of
steps per temperature point.
'''
value = self.NAStepEntry.get()
if value == self.amountOfSteps:
return
if value < 1:
self.NAStepEntry.set(1)
self.amountOfSteps = 1
else:
self.amountOfSteps = value
self.NAStepEntry.set(value)
def updateRepeatEntry(self, event=None):
'''Update the value and entry of that sets
the amount of times the whole annealing
procedure is repeated in order
to obtain statistics.
'''
value = self.repeatEntry.get()
if value == self.amountOfRepeats:
return
if value < 1:
self.repeatEntry.set(1)
self.amountOfRepeats = 1
else:
self.amountOfRepeats = value
self.repeatEntry.set(value)
def updateMinTypeScoreEntry(self, event=None):
'''Updates the value and the entry for the
treshhold value for amino acid typing.
'''
value = self.minTypeScoreEntry.get()
if value == self.minTypeScore:
return
if value < 0:
self.minTypeScoreEntry.set(0.0)
self.minTypeScore = 0.0
elif value > 100:
self.minTypeScoreEntry.set(100.0)
self.minTypeScore = 100.0
else:
self.minTypeScoreEntry.set(value)
self.minTypeScore = value
def updateMinLabelEntry(self, event=None):
'''Updates the minimum colabelling fraction
for which a peak is expected to be present
in the spectra.
'''
value = self.minLabelEntry.get()
if value == self.minIsoFrac:
return
if value < 0:
self.minIsoFrac = 0.0
self.minLabelEntry.set(0.0)
elif value > 1:
self.minIsoFrac = 1.0
self.minLabelEntry.set(1.0)
else:
self.minIsoFrac = value
self.minLabelEntry.set(value)
def updateLeavePeaksOutEntry(self, event=None):
'''Updates the value and entry of the fraction
of peaks that should be left out in each
run in order to diversify the results.
'''
value = self.leaveOutPeaksEntry.get()
if value == self.leavePeaksOutFraction:
return
if value < 0:
self.leavePeaksOutFraction = 0.0
self.leaveOutPeaksEntry.set(0.0)
elif value > 1:
self.leavePeaksOutFraction = 1.0
self.leaveOutPeaksEntry.set(1.0)
else:
self.leavePeaksOutFraction = value
self.leaveOutPeaksEntry.set(value)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def addEnergyPoint(self, energy, time):
'''Adds a point to the graph that shows the progress
of the annealling procedure.
args: energy: the y-value
time: the x-value
'''
point = (time, energy * -1)
# This means one run has finished
if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1):
self.energyDataSets.append([point])
else:
self.energyDataSets[-1].append(point)
colors = colorSeries
Ncolors = len(colors)
NdataSets = len(self.energyDataSets)
colorList = (NdataSets / Ncolors) * colors + \
colors[:NdataSets % Ncolors]
self.energyPlot.update(dataSets=self.energyDataSets,
dataColors=colorList)
# Forcing the graph to draw, eventhough calculations
# are still running. Only do this with high numbers of
# steps, otherwise drawing takes longer than annealling.
if self.amountOfSteps >= 100000:
self.energyPlot.draw()
def __init__(self, guiParent, ccpnProject=None, **kw):
self.guiParent = guiParent
self.project = ccpnProject
self.spectrum = None
self.peakMode = 0
if ccpnProject:
self.nmrProject = ccpnProject.currentNmrProject
else:
self.nmrProject = None
Frame.__init__(self, guiParent, **kw)
self.expandGrid(0,0)
options = ['Peak Picking',] #,'About Auremol' 'NOE assignment','Homology Modelling',]
self.tabbedFrame = TabbedFrame(self, options=options)
self.tabbedFrame.grid(row=0,column=0,sticky='nsew')
frameA = self.tabbedFrame.frames[0]
#frameC.grid_columnconfigure(0, weight=1)
#frameC.grid_rowconfigure(0, weight=1)
#frameD.grid_columnconfigure(0, weight=1)
#frameD.grid_rowconfigure(0, weight=1)
#
# Frame A
#
frameA.expandGrid(2,0)
frameA.expandGrid(3,0)
frameA.expandGrid(4,0)
frameA.expandGrid(5,0)
frame = Frame(frameA, grid=(0,0))
frame.expandGrid(0,4)
label = Label(frame, text='Spectrum:', grid=(0,0))
self.spectrumPulldown = PulldownList(frame, self.changeSpectrum, grid=(0,1))
label = Label(frame, text=' Use Peak Sign:', grid=(0,2))
self.peakModePulldown = PulldownList(frame, self.changePeakMode, texts=PEAK_MODES,
objects=[0,1,2], grid=(0,3))
frame = Frame(frameA, grid=(1,0))
frame.expandGrid(0,4)
label = Label(frame, text='Integration Depth (Relative to max):', grid=(1,0))
self.segLevelEntry = FloatEntry(frame, text=0.1, grid=(1,1), width=8)
label = Label(frame, text='Threshold (Threshold only):', grid=(1,3))
self.thresholdEntry = IntEntry(frame, text=100000, grid=(1,4), width=8)
label = Label(frame, text='Keep Peaks (Adaptive only):', grid=(1,5))
self.keepPeakEntry = IntEntry(frame, text=4000, grid=(1,6), width=8)
texts = ['Threshold\nPeak Pick','Adaptive\nPeak Pick']
commands = [self.pickThreshold, self.pickAdaptive]
self.buttons = ButtonList(frameA, texts=texts, commands=commands,
grid=(2,0), sticky='NSEW')
frame = Frame(frameA, grid=(3,0))
frame.expandGrid(0,0)
frame = Frame(frameA, grid=(4,0))
frame.expandGrid(0,0)
frame = Frame(frameA, grid=(5,0))
frame.expandGrid(0,0)
#
# About
"""
frameB.expandGrid(4,0)
label = Label(frameB, text='References', font='Helvetica 12 bold')
label.grid(row=0, column=0, sticky='w')
text =
* Gronwald W, Brunner K, Kirchhofer R, Nasser A, Trenner J, Ganslmeier B,
Riepl H, Ried A, Scheiber J, Elsner R, Neidig K-P, Kalbitzer HR
AUREMOL, a New Program for the Automated Structure Elucidation of Biological Macromolecules
Bruker Reports 2004; 154/155: 11-14
* Ried A, Gronwald W, Trenner JM, Brunner K, Neidig KP, Kalbitzer HR
Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling,
transverse relaxation and chemical shift anisotrophy
J Biomol NMR. 2004 Oct;30(2):121-31
* Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE)
J Biomol NMR. 2002 Aug;23(4):271-87
* Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR
RFAC, a program for automated NMR R-factor estimation
J Biomol NMR. 2000 Jun;17(2):137-51
label = Label(frameB, text=text)
label.grid(row=1, column=0, sticky='w')
"""
#
# Frame C
#
#
# Frame D
#
self.updateAll()
class MeccanoPopup(BasePopup):
def __init__(self, parent, project, *args, **kw):
self.alignMedium = None
self.chain = None
self.constraint = None
self.constraintSet = None
self.molSystem = None
self.project = project
self.run = None
self.shiftList = None
self.tensor = None
BasePopup.__init__(self, parent=parent, title='MECCANO', *args, **kw)
self.curateNotifiers(self.registerNotify)
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 close(self):
self.updateRunParams()
BasePopup.close(self)
def destroy(self):
self.updateRunParams()
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateConstraintSetsAfter, 'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
for func in ('__init__', 'delete','setName','setConditionState'):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraintList',
'ccp.nmr.NmrConstraint.DihedralConstraintList',
'ccp.nmr.NmrConstraint.DistanceConstraintList',
'ccp.nmr.NmrConstraint.HBondConstraintList',
'ccp.nmr.NmrConstraint.JCouplingConstraintList',
'ccp.nmr.NmrConstraint.RdcConstraintList'):
notifyFunc(self.updateConstraintListsAfter, clazz, func)
for func in ('__init__', 'delete',):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraint',
'ccp.nmr.NmrConstraint.DihedralConstraint',
'ccp.nmr.NmrConstraint.DistanceConstraint',
'ccp.nmr.NmrConstraint.HBondConstraint',
'ccp.nmr.NmrConstraint.JCouplingConstraint',
'ccp.nmr.NmrConstraint.RdcConstraint'):
notifyFunc(self.updateConstraintsAfter, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateShiftListsAfter,'ccp.nmr.Nmr.ShiftList', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateMolSystemsAfter,'ccp.molecule.MolSystem.MolSystem', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateChainsAfter,'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete','setDynamicAlignment',
'setStaticAlignment','setName','setDetails'):
notifyFunc(self.updateAlignMediaAfter,'ccp.nmr.NmrConstraint.ConditionState', func)
def updateAlignMediaAfter(self, alignMedium):
if alignMedium.nmrConstraintStore is self.constraintSet:
self.after_idle(self.updateAlignMedia)
if alignMedium is self.alignMedium:
self.after_idle(self.updateTensors)
def updateConstraintSetsAfter(self, constraintSet):
self.after_idle(self.updateConstraintSets)
def updateShiftListsAfter(self, shiftList):
self.after_idle(self.updateShiftLists)
def updateMolSystemsAfter(self, molSystem):
self.after_idle(self.updateMolSystems)
def updateChainsAfter(self, chain):
self.after_idle(self.updateChains)
def updateConstraintsAfter(self, constraint):
if constraint.parent.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def updateConstraintListsAfter(self, constraintList):
if constraintList.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def runMeccano(self):
#
#
# Input checks first
#
#
warning = ''
if not self.molSystem:
warning += 'No molecular system selected\n'
if not self.chain:
warning += 'No chain selected\n'
if not self.constraintSet:
warning += 'No selected constraint set\n'
else:
constraintLists = [cl for cl in self.constraintSet.constraintLists if cl.useForMeccano]
if not constraintLists:
warning += 'No constraint lists selected for use\n'
first, last = self.updateResidueRanges()
if (last-first) < 2:
warning += 'Too few peptide planes selected\n'
if warning:
showWarning('Cannot run MECCANO','Encountered the following problems:\n' + warning)
return
if not self.run:
self.run = self.makeSimRun()
self.updateRunParams()
if self.toggleCopyShifts.get() and self.shiftList:
shiftList = self.run.findFirstOutputMeasurementList(className='ShiftList')
if not shiftList:
shiftList = self.project.currentNmrProject.newShiftList(name='Meccano Input')
self.run.setOutputMeasurementLists([shiftList,])
shiftDict = {}
for shift in shiftList.shifts:
shiftDict[shift.resonance] = shift
for shift in self.shiftList.shifts:
resonance = shift.resonance
resonanceSet = resonance.resonanceSet
if resonanceSet:
atom = resonanceSet.findFirstAtomSet().findFirstAtom()
if (atom.name == 'C') and (atom.residue.molResidue.molType == 'protein'):
shift2 = shiftDict.get(resonance)
if shift2:
shift2.value = shift.value
shift2.error = shift.error
else:
shiftList.newShift(resonance=resonance, value=shift.value, error=shift.error)
#
#
# Accumulate data from CCPN data model & GUI
#
#
# Sequence
residues = self.chain.sortedResidues()
residueDict = {}
seqData = []
for residue in residues:
molResidue = residue.molResidue
code1Letter = molResidue.chemComp.code1Letter
if not code1Letter:
msg = 'Encountered non-standard residue type: %s'
showWarning('Cannot run MECCANO', msg % residue.ccpCode)
return
seqCode = residue.seqCode
seqData.append((seqCode, code1Letter))
residueDict[seqCode] = residue.chemCompVar.chemComp.code3Letter
# Media, RDCs & Dihedrals
rdcLists = []
dihedralLists = []
for constraintList in constraintLists:
if constraintList.className == 'RdcConsraintList':
if constraintList.conditionState:
rdcLists.append(constraintList)
elif constraintList.className == 'DihedralConstraintList':
dihedralLists.append(dihedralLists)
f = PI_OVER_180
mediaData = []
for constraintList in rdcLists:
medium = constraintList.conditionState
dynamicTensor = medium.dynamicAlignment
staticTensor = medium.staticAlignment
if not (dynamicTensor or staticTensor):
continue
if dynamicTensor:
dynamicTensorData = ['Dynamic', dynamicTensor.aAxial, dynamicTensor.aRhombic,
f*dynamicTensor.alpha, f*dynamicTensor.beta, f*dynamicTensor.gamma]
if staticTensor:
staticTensorData = ['Static', staticTensor.aAxial, staticTensor.aRhombic,
f*staticTensor.alpha, f*staticTensor.beta, f*staticTensor.gamma]
if not dynamicTensor:
dynamicTensorData = staticTensorData
elif not staticTensor:
staticTensorData = dynamicTensorData
rdcData = []
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
resonanceA, resonanceB = [fr.resonance for fr in items[0].resonances]
resonanceSetA = resonanceA.resonanceSet
if not resonanceSetA:
continue
resonanceSetB = resonanceB.resonanceSet
if not resonanceSetB:
continue
resNameA = getResonanceName(resonanceA)
resNameB = getResonanceName(resonanceB)
residueA = resonanceSetA.findFirstAtomSet().findFirstAtom().residue
residueB = resonanceSetB.findFirstAtomSet().findFirstAtom().residue
seqA = residueA.seqCode
seqB = residueB.seqCode
value = restraint.targetValue
error = restraint.error
if error is None:
key = [resNameA,resNameB]
key.sort()
sigma = DEFAULT_ERRORS.get(tuple(key), 1.0)
rdcData.append([seqA, resNameA, seqB, resNameB, value, error])
mediaData.append((dynamicTensorData,staticTensorData,rdcData))
oneTurn = 360.0
dihedralDict = {}
for constraintList in dihedralLists:
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
item = items[0]
resonances = [fr.resonance for fr in item.resonances]
resonanceSets = [r.resonanceSet for r in resonances]
if None in resonanceSets:
continue
atoms = [rs.findFirstAtomSet().findFirstAtom() for rs in resonanceSets]
atomNames = [a.name for a in atoms]
if atomNames == PHI_ATOM_NAMES:
isPhi = True
elif atomNames == PSI_ATOM_NAMES:
isPhi = False
else:
continue
residue = atoms[2].residue
if residue.chain is not self.chain:
continue
if isPhi:
residuePrev = getLinkedResidue(residue, linkCode='prev')
if not residuePrev:
continue
atomC0 = residuePrev.findFirstAtom(name='C')
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atoms2 = [atomC0, atomN, atomCa, atomC]
else:
residueNext = getLinkedResidue(residue, linkCode='next')
if not residueNext:
continue
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atomN2 = residueNext.findFirstAtom(name='N')
atoms2 = [atomN, atomCa, atomC, atomN2]
if atoms != atoms2:
continue
value = item.targetValue
error = item.error
if error is None:
upper = item.upperLimit
lower = item.lowerLimit
if (upper is not None) and (lower is not None):
dUpper = angleDifference(value, lower, oneTurn)
dLower = angleDifference(upper, value, oneTurn)
error = max(dUpper, dLower)
elif lower is not None:
error = angleDifference(value, lower, oneTurn)
elif upper is not None:
error = angleDifference(upper, value, oneTurn)
else:
error = 30.0 # Arbitrary, but sensible for TALOS, DANGLE
seqCode = residue.seqCode
if not dihedralDict.has_key(seqCode):
dihedralDict[seqCode] = [None, None, None, None] # Phi, Psi, PhiErr, PsiErr
if isPhi:
dihedralDict[seqCode][0] = value
dihedralDict[seqCode][2] = error
else:
dihedralDict[seqCode][1] = value
dihedralDict[seqCode][3] = error
phipsiData = []
seqCodes = dihedralDict.keys()
seqCodes.sort()
for seqCode in seqCodes:
data = dihedralDict[seqCode]
if None not in data:
phi, psi, phiErr, psiErr = data
phipsiData.append((seqCode, phi, psi, phiErr, psiErr))
# User options
firstPPlaneFrag = self.firstResEntry.get() or 1
lastPPlaneFrag = self.lastResEntry.get() or 1
ppNbMin = self.numOptPlaneEntry.get() or 1
minValueBest = self.numOptHitsEntry.get() or 2
maxValueBest = self.maxOptStepEntry.get() or 5
strucData = Meccano.runFwd(firstPPlaneFrag, lastPPlaneFrag, ppNbMin,
minValueBest, maxValueBest, RAMACHANDRAN_DATABASE,
seqData, mediaData, phipsiData)
if strucData:
fileName = 'CcpnMeccanoPdb%f.pdb' % time.time()
fileObj = open(fileName, 'w')
ch = self.chain.pdbOneLetterCode.strip()
if not ch:
ch = self.chain.code[0].upper()
i = 1
for atomType, resNb, x, y, z in strucData:
resType = residueDict.get(resNb, '???')
line = PDB_FORMAT % ('ATOM',i,'%-3s' % atomType,'',resType,ch,resNb,'',x,y,z,1.0,1.0)
i += 1
fileObj.close()
ensemble = getStructureFromFile(self.molSystem, fileName)
if not self.toggleWritePdbFile.get():
os.unlink(fileName)
self.run.outputEnsemble = ensemble
self.run = None
self.updateRuns()
def getMediumName(self, alignMedium):
self.mediumNameEntry.set(alignMedium.name)
def getMediumDetails(self, alignMedium):
self.mediumDetailsEntry.set(alignMedium.details)
def setMediumName(self, event):
value = self.mediumNameEntry.get()
self.alignMedium.name = value or None
def setMediumDetails(self, event):
value = self.mediumDetailsEntry.get()
self.alignMedium.details = value or None
def setAlignMedium(self, alignMedium):
if self.constraintSet:
self.constraintSet.conditionState = alignMedium
def getAlignMedium(self, constraintList):
media = self.getAlignmentMedia()
names = [am.name for am in media]
if constraintList.conditionState in media:
index = media.index(constraintList.conditionState)
else:
index = 0
self.alignMediumPulldown.setup(names, media, index)
def toggleUseRestraints(self, constraintList):
bool = constraintList.useForMeccano
bool = not bool
if bool and (not constraintList.conditionState) \
and (constraintList.className == 'RdcConsraintList'):
msg = 'Cannot use RDC restraint list for Meccano '
msg += 'unless it is first associated with an amigment medium'
showWarning('Warning', msg, parent=self)
else:
constraintList.useForMeccano = bool
self.updateConstraintLists()
def addStaticTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.staticAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def addDynamicTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.dynamicAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def removeTensor(self):
if self.alignMedium and self.tensor:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = None
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = None
self.updateAlignMediaAfter(self.alignMedium)
def addAlignMedium(self):
if self.constraintSet:
medium = self.constraintSet.newConditionState()
medium.name = 'Align Medium %d' % medium.serial
def removeAlignMedium(self):
if self.alignMedium:
self.alignMedium.delete()
def updateTensor(self, aAxial=None, aRhombic=None, alpha=None, beta=None, gamma=None):
aAxial = aAxial or self.tensor.aAxial
aRhombic = aRhombic or self.tensor.aRhombic
alpha = alpha or self.tensor.alpha
beta = beta or self.tensor.beta
gamma = gamma or self.tensor.gamma
tensor = Implementation.SymmTracelessMatrix(aAxial=aAxial,
aRhombic=aRhombic,
alpha=alpha,beta=beta,
gamma=gamma)
if self.alignMedium:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = tensor
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = tensor
self.tensor = tensor
def setAxial(self, event):
value = self.editAxialEntry.get()
self.updateTensor(aAxial=value)
self.updateTensors()
def setRhombic(self, event):
value = self.editRhombicEntry.get()
self.updateTensor(aRhombic=value)
self.updateTensors()
def setEulerAlpha(self, event):
value = self.editAlphaEulerEntry.get()
self.updateTensor(alpha=value)
self.updateTensors()
def setEulerBeta(self, event):
value = self.editBetaEulerEntry.get()
self.updateTensor(beta=value)
self.updateTensors()
def setEulerGamma(self, event):
value = self.editGammaEulerEntry.get()
self.updateTensor(gamma=value)
self.updateTensors()
def getAxial(self, tensor):
value = tensor.aAxial
self.editAxialEntry.set(value)
def getRhombic(self, tensor):
value = tensor.aRhombic
self.editRhombicEntry.set(value)
def getEulerAlpha(self, tensor):
value = tensor.alpha
self.editAlphaEulerEntry.set(value)
def getEulerBeta(self, tensor):
value = tensor.beta
self.editBetaEulerEntry.set(value)
def getEulerGamma(self, tensor):
value = tensor.gamma
self.editGammaEulerEntry.set(value)
def selectTensor(self, tensor, row, col):
self.tensor = tensor
def selectAlignMedium(self, alignMedium, row, col):
self.alignMedium = alignMedium
self.updateTensors()
def getAlignmentMedia(self):
if self.constraintSet:
return self.constraintSet.sortedConditionStates()
else:
return []
def updateAlignMedia(self):
textMatrix = []
objectList = []
if self.constraintSet:
objectList = self.getAlignmentMedia()
for conditionState in objectList:
staticTensor = None
dyamicTensor = None
tensor = conditionState.dynamicAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
dyamicTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
tensor = conditionState.staticAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
staticTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
datum = [conditionState.serial,
conditionState.name,
conditionState.details,
dyamicTensor,
staticTensor]
textMatrix.append(datum)
if dyamicTensor or staticTensor:
if not self.alignMedium:
self.alignMedium = conditionState
self.mediaMatrix.update(textMatrix=textMatrix, objectList=objectList)
if self.alignMedium:
self.mediaMatrix.selectObject(self.alignMedium)
def updateTensors(self):
textMatrix = []
objectList = []
conditionState = self.alignMedium
if conditionState:
tensor = conditionState.dynamicAlignment
if tensor:
datum = ['Dynamic', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
tensor = conditionState.staticAlignment
if tensor:
datum = ['Static', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
self.tensorMatrix.update(textMatrix=textMatrix, objectList=objectList)
def getMolSystems(self):
molSystems = []
for molSystem in self.project.sortedMolSystems():
if molSystem.chains:
molSystems.append(molSystem)
return molSystems
def updateMolSystems(self, *notifyObj):
index = 0
names = []
molSystems = self.getMolSystems()
molSystem = self.molSystem
if molSystems:
if molSystem not in molSystems:
molSystem = molSystems[0]
index = molSystems.index(molSystem)
names = [ms.code for ms in molSystems]
else:
self.molSystem = None
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
self.molSystemPulldown.setup(texts=names, objects=molSystems, index=index)
def selectMolSystem(self, molSystem):
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
def updateChains(self, *notifyObj):
index = 0
names = []
chains = []
chain = self.chain
if self.molSystem:
chains = [c for c in self.molSystem.sortedChains() if c.residues]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
names = [c.code for c in chains]
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
self.chainPulldown.setup(texts=names, objects=chains, index=index)
def selectChain(self, chain):
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
def updateResidueRanges(self):
first = self.firstResEntry.get()
last = self.lastResEntry.get()
if self.chain:
residues = self.chain.sortedResidues()
firstSeq = residues[0].seqCode
lastSeq = residues[-2].seqCode
if first < firstSeq:
first = firstSeq
if last == first:
last = lastSeq
elif last > lastSeq:
last = lastSeq
if first > last:
last, first = first, last
self.firstResEntry.set(first)
self.lastResEntry.set(last)
return first, last
def getConstraintSets(self):
constraintSets = []
nmrProject = self.project.currentNmrProject
for constraintSet in nmrProject.sortedNmrConstraintStores():
for constraintList in constraintSet.constraintLists:
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintSets.append(constraintSet)
break
return constraintSets
def updateConstraintSets(self, *notifyObj):
index = 0
names = []
constraintSets = self.getConstraintSets()
constraintSet = self.constraintSet
if constraintSets:
if constraintSet not in constraintSets:
constraintSet = constraintSets[0]
index = constraintSets.index(constraintSet)
names = ['%d' % cs.serial for cs in constraintSets]
if constraintSet is not self.constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
self.constraintSetPulldown.setup(texts=names, objects=constraintSets, index=index)
def selectConstraintSet(self, constraintSet):
if self.constraintSet is not constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
def getConstraintLists(self):
constraintLists = []
if self.constraintSet:
for constraintList in self.constraintSet.sortedConstraintLists():
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintLists.append(constraintList)
return constraintLists
def updateConstraintLists(self, *notifyObj):
textMatrix = []
objectList = self.getConstraintLists()
for constraintList in objectList:
if not hasattr(constraintList, 'useForMeccano'):
if constraintList.conditionState \
or (constraintList.className != 'RdcConstraintList'):
bool = True
else:
bool = False
constraintList.useForMeccano = bool
if constraintList.conditionState:
alignMedium = constraintList.conditionState.name
else:
alignMedium = None
datum = [constraintList.serial,
constraintList.className[:-14],
constraintList.useForMeccano and 'Yes' or 'No',
alignMedium,
len(constraintList.constraints)]
textMatrix.append(datum)
self.restraintMatrix.update(textMatrix=textMatrix, objectList=objectList)
def selectConstraint(self, obj, row, column):
if self.constraint is not obj:
self.constraint = obj
def getSimStore(self):
simStore = self.project.findFirstNmrSimStore(name='meccano')
if not simStore:
simStore = self.project.newNmrSimStore(name='meccano')
return simStore
def getRuns(self):
runs = [None, ]
if self.molSystem and self.constraintSet:
simStore = self.getSimStore()
runs += simStore.sortedRuns()
return runs
def updateRuns(self, *notifyObj):
index = 0
names = ['<New>']
runs = self.getRuns()
run = self.run
if runs:
if run not in runs:
run = runs[0]
index = runs.index(run)
names += [r.serial for r in runs if r]
if run is not self.run:
self.updateConstraintSets()
self.updateMolSystems()
self.updateShiftLists()
self.runPulldown.setup(names, runs, index)
def updateRunParams(self, event=None):
if self.run and self.molSystem and self.constraintSet:
simRun = self.run
simRun.inputConstraintStore = self.constraintSet
simRun.molSystem = self.molSystem
if self.shiftList:
simRun.setInputMeasurementLists([self.shiftList,])
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
def makeSimRun(self, template=None):
simStore = self.getSimStore()
if template:
molSystem = template.molSystem
constraintSet = template.inputConstraintStore
shiftList = template.findFirstInputMeasurementList(className='ShiftList')
protocol = template.annealProtocol
else:
molSystem = self.molSystem
constraintSet = self.constraintSet
shiftList = self.shiftList
protocol = self.annealProtocol
simRun = simStore.newRun(annealProtocol=protocol,
molSystem=molSystem,
inputConstraintStore=protocol)
if shiftList:
simRun.addInputMeasurementList(shiftList)
if template:
for param in template.runParameters:
simRun.newRunParameter(code=param.code,
id=param.id,
booleanValue=param.booleanValue,
floatValue=param.floatValue,
intValue=param.intValue,
textValue=param.textValue)
else:
if self.chain:
chainCode = self.chain.code
else:
chaincode = 'A'
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
simRun.newRunParameter(code='ChainCode', id=1,
textValue=chainCode)
return simRun
def selectRun(self, simRun):
if self.run is not simRun:
if simRun:
if simRun.outputEnsemble:
msg = 'Selected run has already been used to generate a structure.'
msg += 'A new run will be setup based on the selection.'
showWarning('Warning',msg)
simRun = self.makeSimRun(template=simRun)
molSystem = simRun.molSystem
constraintSet = simRun.inputConstraintStore
shiftList = simRun.findFirstInputMeasurementList(className='ShiftList')
if molSystem and (self.molSystem is not molSystem):
self.molSystem = molSystem
self.updateMolSystems()
if constraintSet and (self.constraintSet is not constraintSet):
self.constraintSet = constraintSet
self.updateConstraintSets()
if shiftList and (self.shiftList is not shiftList):
self.shiftList = shiftList
self.updateShiftLists()
firstPepPlane = simRun.findFirstrunParameter(code='FirstPepPlane')
lastPepPlane = simRun.findFirstrunParameter(code='LastPepPlane')
maxOptSteps = simRun.findFirstrunParameter(code='MaxOptSteps')
numOptPlanes = simRun.findFirstrunParameter(code='NumOptPlanes')
minOptHits = simRun.findFirstrunParameter(code='MinOptHits')
chainCode = simRun.findFirstrunParameter(code='ChainCode')
if firstPepPlane is not None:
self.firstResEntry.set(firstPepPlane.intValue or 0)
if lastPepPlane is not None:
self.lastResEntry.set(lastPepPlane.intValue or 0)
if maxOptSteps is not None:
self.maxOptStepEntry.set(maxOptSteps.intValue or 0)
if numOptPlanes is not None:
self.numOptPlaneEntry.set(numOptPlanes.intValue or 0)
if minOptHits is not None:
self.numOptHitsEntry.set(minOptHits.intValue or 0)
if chainCode is not None:
chainCode = chainCode.textValue or 'A'
if self.molSystem:
chain = self.molSystem.findFirsChain(code=chainCode)
if chain:
self.selectChain(chain)
self.run = simRun
def updateShiftLists(self, *notifyObj):
index = 0
names = []
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
shiftLists = [(sl.serial, sl) for sl in shiftLists]
shiftLists.sort()
shiftLists = [x[1] for x in shiftLists]
shiftList = self.shiftList
if shiftLists:
if shiftList not in shiftLists:
shiftList = shiftLists[0]
index = shiftLists.index(shiftList)
names = ['%d'% sl.serial for sl in shiftLists]
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftListPulldown.setup(texts=names, objects=shiftLists, index=index)
def selectShiftList(self, shiftList):
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftList = shiftList
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):
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()
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
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)
class EditExperimentSeriesPopup(BasePopup):
"""
**Setup Experiment Series for Chemical Shift and Intensity Changes**
The purpose of this popup is to setup ordered groups of experiments that are
related by the variation in some condition or parameter, but otherwise the
kind of experiment being run is the same. For example the user could setup
experiments for a temperature series, ligand binding titration or relaxation
rate measurement.
The layout is divided into two tables. The upper table shows all of the series
that are known to the current project and the lower table shows all of the
experiments or planes that comprise the selected series. These series relate
to both groups of separate experiments (and hence spectra) and also single
experiment where one dimension is not for NMR frequency but rather a "sampled"
dimension and thus effectively combines many experiments (e.g. for different
T1 values) as different planes. A stack of effectively 2D experiments combined
in this manner is typically referred to as pseudo-3D. - The experiment is 3D
but there are only two NMR dimensions.
Series which are stacks of planes in a single experiment entity are
automatically detected and entered into the table once they are loaded. Series
that are constructed from multiple, separate experiments however must be setup
by the user. To setup a new series of this kind [Add Series] makes a new,
empty NMR series. Next the user should change the "Parameter varied" column to
specify what type of thing is varied between the different experiments. The
user then adds experiments into this series with the [Add Series Point]
function at the bottom. Once the points have been added to the series the name
of the experiment for each point may be changed. Initially, arbitrary
experiments appear for the series points, so these almost always have to be
adjusted.
Once a stacked-plane experiment or series of experiments is setup, the user
next sets (or checks) the value of the parameter associated with each point in
the lower table. When loading stacked-plane experiments these values may come
though automatically, if they are present in the spectrum header or parameter
file. Given a completed NMR series specification the user may then extract the
relevant data from the series using one of the analysis tools like `Follow
Intensity Changes`_ or `Follow Shift Changes`_.
**Caveats & Tips**
Make sure the "Parameter Varied" for a given NMR series is appropriate to the
type of analysis being performed. Many tools that extract T1 or Kd
measurements for example look for specific types of series.
The "Set/Unset Ref Plane" function is only used in certain kinds of series
such as those that use trains of CPMG pulses.
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.expSeries = None
self.conditionPoint = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Experiment : NMR Series", **kw)
def body(self, guiFrame):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
#for func in ('__init__', 'delete','setName'):
for func in ('__init__', 'delete','setName','setConditionNames',
'addConditionName','removeConditionName'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.NmrExpSeries', func)
for func in ('__init__', 'delete','setName'):
notifyFunc(self.updateExperiments,'ccp.nmr.Nmr.Experiment', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateDataDim,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete','setCondition','setUnit','setValue','setError'):
notifyFunc(self.updateConditionsAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('__init__', 'delete','setCondition'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('setConditionVaried', 'setPointErrors',
'addPointError', 'removePointError',
'setPointValues','addPointValue',
'removePointValue','setUnit'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateColorSchemes,'ccpnmr.AnalysisProfile.ColorScheme', func)
def open(self):
self.updateAfter()
BasePopup.open(self)
def updateColorSchemes(self, scheme=None):
index = 0
prevScheme = self.colorSchemePulldown.getObject()
schemes = getHueSortedColorSchemes(self.analysisProfile)
schemes = [s for s in schemes if len(s.colors) > 1]
colors = [list(s.colors) for s in schemes]
if schemes:
names = [s.name for s in schemes]
if prevScheme in schemes:
index = schemes.index(prevScheme)
else:
names = []
self.colorSchemePulldown.setup(names, schemes, index, colors)
def autoColorSpectra(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
scheme = self.colorSchemePulldown.getObject()
if scheme:
colors = scheme.colors
else:
colors = ['#FF0000','#00FF00','#0000FF']
cdict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionName = list(self.expSeries.conditionNames)[0]
expList = []
for sampleCondition in cdict.get(conditionName, []):
expList.append( (sampleCondition.value, sampleCondition.parent.experiments) )
expList.sort()
m = len(expList)-1.0
c = len(colors)-1
for i, (value, experiments) in enumerate(expList):
p = c*i/m
j = int(p)
r1, g1, b1 = Color.hexToRgb(colors[j])
r2, g2, b2 = Color.hexToRgb(colors[min(c,j+1)])
f2 = p-j
f1 = 1.0-f2
r = (r1*f1)+(r2*f2)
g = (g1*f1)+(g2*f2)
b = (b1*f1)+(b2*f2)
hexColor = Color.hexRepr(r,g,b)
for experiment in experiments:
for spectrum in experiment.dataSources:
if spectrum.dataType == 'processed':
analysisSpec = getAnalysisSpectrum(spectrum)
if analysisSpec.posColors:
analysisSpec.posColors = [hexColor,]
elif analysisSpec.negColors:
analysisSpec.negColors = [hexColor,]
def getUnusedExperiments(self):
sampleExperiments = getSampledDimExperiments(self.nmrProject)
experiments = []
for experiment in self.nmrProject.sortedExperiments():
if experiment in sampleExperiments:
continue
if self.expSeries and (self.expSeries.className != 'Experiment'):
if experiment in self.expSeries.experiments:
continue
experiments.append(experiment)
return experiments
def conditionTableShow(self, object, row, col):
if type(object) is type(()):
dataDim, index = object
refPlane = dataDim.analysisDataDim.refSamplePlane
if refPlane == index:
return False
if col == 1:
return False
return True
def setSampledReferencePlane(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
if self.conditionPoint:
dataDim, point = self.conditionPoint
analysisDataDim = dataDim.analysisDataDim
refPoint = analysisDataDim.refSamplePlane
if refPoint == point:
analysisDataDim.refSamplePlane = None
else:
analysisDataDim.refSamplePlane = point
self.updateAfter()
def checkAddSampleCondition(self, experiment):
conditionSet = getExperimentConditionSet(experiment)
conditionName = self.expSeries.conditionNames[0]
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
sampleConditions = condDict.get(conditionName, [])
units = [sc.unit for sc in sampleConditions if sc.unit]
if units:
sortList = list(set(units))
sortList.sort(key = lambda u:units.count(u))
unit = sortList[-1]
else:
unit = CONDITION_UNITS_DICT[conditionName][0]
condition = conditionSet.findFirstSampleCondition(condition=conditionName)
if not condition:
condition = conditionSet.newSampleCondition(condition=conditionName,
unit=unit, value=0.0, error=0.0)
def addConditionPoint(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
experiments = self.getUnusedExperiments()
if not experiments:
showWarning('Warning','No experiments available', parent=self)
return
experiment = experiments[0]
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
self.checkAddSampleCondition(experiment)
self.updateAfter()
def deleteConditionPoint(self, *event):
if self.conditionPoint and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series point?', parent=self):
conditionSet = self.conditionPoint.sampleConditionSet
experiments = [e for e in conditionSet.experiments if e in self.expSeries.experiments]
for experiment in experiments:
self.expSeries.removeExperiment(experiment)
for experiment in experiments:
for expSeries in experiment.nmrExpSeries:
if self.conditionPoint.condition in self.expSeries.conditionNames:
break
else:
continue
break
else:
self.conditionPoint.delete()
self.conditionPoint = None
def selectConditionPoint(self, object, row, col):
if object:
self.conditionPoint = object
self.updateButtons()
def selectExpSeries(self, object, row, col):
if object:
self.expSeries = object
self.checkExperimentConditionsConsistent()
self.updateConditions()
def checkExperimentConditionsConsistent(self):
if self.expSeries.className != 'Experiment':
for experiment in self.expSeries.experiments:
self.checkAddSampleCondition(experiment)
def getUnits(self):
units = []
if self.expSeries:
if self.expSeries.className == 'Experiment':
conditionName = getExperimentSampledDim(self.expSeries).conditionVaried
else:
conditionName = self.expSeries.conditionNames[0]
units = CONDITION_UNITS_DICT.get(conditionName)
if not units:
units = ['?',]
return units
def getUnit(self, sampleCondition):
index = -1
units = self.getUnits()
if units:
if sampleCondition:
if type(sampleCondition) is type(()):
dataDim, index = sampleCondition
unit = dataDim.unit
else:
unit = sampleCondition.unit
if unit not in units:
unit = units[0]
index = units.index(unit)
self.unitPulldown.setup(units,units,index)
def setUnit(self, obj):
name = self.unitPulldown.getObject()
if self.conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
dataDim.setUnit(name)
else:
self.conditionPoint.setUnit(name)
def getConditionNames(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
names = ['delay time','mixing time','num delays','pulsing frequency','gradient strength']
else:
names = CONDITION_UNITS_DICT.keys()
names.sort()
return names
def setConditionName(self, obj):
name = self.conditionNamesPulldown.getObject()
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
dataDim.conditionVaried = name
else:
self.expSeries.setConditionNames([name,])
def getConditionName(self, expSeries):
index = 0
names = self.getConditionNames()
if names:
if expSeries:
if expSeries.className == 'Experiment':
name = getExperimentSampledDim(expSeries).conditionVaried
else:
name = expSeries.conditionNames[0]
if name:
index = names.index(name)
else:
index = 0
self.conditionNamesPulldown.setup(names,names,index)
def getName(self, expSeries):
if expSeries :
self.nameEntry.set(expSeries.name)
def setName(self, event):
text = self.nameEntry.get()
if text and text != ' ':
self.expSeries.setName( text )
def getValue(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
value = dataDim.pointValues[index]
else:
value = conditionPoint.value
self.valueEntry.set(value)
def setValue(self, event):
value = self.valueEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
values = list(dataDim.pointValues)
values[index] = value
dataDim.setPointValues(values)
else:
self.conditionPoint.setValue( value )
def getError(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
if index < len(dataDim.pointErrors):
error = dataDim.pointValues[index]
else:
error = 0.0
else:
error = conditionPoint.error
self.errorEntry.set(error)
def setError(self, event):
value = self.errorEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
pointErrors = dataDim.pointErrors
if pointErrors:
values = list(pointErrors)
else:
values = [0.0] * dataDim.numPoints
values[index] = value
dataDim.setPointErrors(values)
else:
self.conditionPoint.setError( value )
def getDetails(self, expSeries):
if expSeries :
self.detailsEntry.set(expSeries.details)
def setDetails(self, event):
text = self.detailsEntry.get()
if text and text != ' ':
self.expSeries.setDetails( text )
def addExpSeries(self):
expSeries = self.nmrProject.newNmrExpSeries(conditionNames=['delay time',])
def deleteExpSeries(self, *event):
if self.expSeries and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series?', parent=self):
self.expSeries.delete()
self.expSeries = None
self.conditionPoint = None
def getExperiments(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
return [self.expSeries,]
else:
return self.nmrProject.sortedExperiments()
def getExperiment(self, sampleCondition):
index = 0
names = []
if self.conditionPoint and (type(self.conditionPoint) != type(())):
index = 0
experiment = self.conditionPoint.parent.findFirstExperiment()
experiments = self.getUnusedExperiments()
name = experiment.name
names = [name] + [e.name for e in experiments]
experiments = [experiment,] + experiments
self.experimentPulldown.setup(names,experiments,index)
def setExperiment(self, obj):
experiment = self.experimentPulldown.getObject()
if self.conditionPoint and (type(self.conditionPoint) != type(())):
conditionSet = getExperimentConditionSet(experiment)
if conditionSet is not self.conditionPoint.parent:
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
unit = self.conditionPoint.unit
if not unit:
unit = CONDITION_UNITS_DICT[self.expSeries.conditionNames[0]]
condition = self.conditionPoint.condition
experiments = set(self.expSeries.experiments)
for experiment0 in self.conditionPoint.parent.experiments:
if experiment0 in experiments:
experiments.remove(experiment0)
self.expSeries.experiments = experiments
value = self.conditionPoint.value
error = self.conditionPoint.error
self.conditionPoint.delete()
self.conditionPoint = conditionSet.findFirstSampleCondition(condition=condition)
if self.conditionPoint:
self.conditionPoint.unit = unit
self.updateAfter()
else:
self.conditionPoint = conditionSet.newSampleCondition(condition=condition,unit=unit,
value=value,error=error)
def updateDataDim(self, sampledDataDim):
experiment = sampledDataDim.dataSource.experiment
self.updateExperiments(experiment)
def updateExperiments(self, experiment):
experiments = self.getExperiments()
names = [e.name for e in experiments]
self.experimentPulldown.setup(names, experiments,0)
if getExperimentSampledDim(experiment):
self.updateAfter()
elif self.expSeries:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.updateConditionsAfter()
elif experiment in self.expSeries.experiments:
self.updateConditionsAfter()
def updateConditionsAfter(self, sampleCondition=None):
if self.waitingConditions:
return
if sampleCondition:
experiments = sampleCondition.sampleConditionSet.experiments
for experiment in experiments:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
elif experiment in self.expSeries.experiments:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
else:
self.waitingConditions = True
self.after_idle(self.updateConditions)
def updateConditions(self):
self.updateButtons()
objectList = []
textMatrix = []
colorMatrix = []
nCols = len(self.conditionPointsMatrix.headingList)
defaultColors = [None] * nCols
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
analysisDataDim = getAnalysisDataDim(dataDim)
conditionVaried = dataDim.conditionVaried
expName = self.expSeries.name
unit = dataDim.unit
pointValues = dataDim.pointValues
pointErrors = dataDim.pointErrors
refPlane = analysisDataDim.refSamplePlane
for i in range(dataDim.numPoints):
if i < len(pointErrors):
error = pointErrors[i]
else:
error = None
pointText = ':%3d' % (i+1)
if i == refPlane:
datum = ['* Ref Plane *',
expName+pointText,
None,
None,
None]
colorMatrix.append(['#f08080'] * nCols)
else:
datum = [conditionVaried ,
expName+pointText,
pointValues[i],
error,
unit]
colorMatrix.append(defaultColors)
textMatrix.append(datum)
objectList.append((dataDim, i))
else:
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionNames = self.expSeries.conditionNames
for conditionName in conditionNames:
for sampleCondition in condDict.get(conditionName, []):
datum = [sampleCondition.condition,
' '.join([e.name for e in sampleCondition.parent.experiments]),
sampleCondition.value,
sampleCondition.error,
sampleCondition.unit]
textMatrix.append(datum)
objectList.append(sampleCondition)
colorMatrix.append(defaultColors)
self.conditionPointsMatrix.update(objectList=objectList,
colorMatrix=colorMatrix,
textMatrix=textMatrix)
self.waitingConditions = 0
def updateAfter(self, object=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def updateButtons(self):
if self.expSeries is None:
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].disable()
elif self.expSeries.className == 'Experiment':
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].enable()
else:
self.seriesButtons.buttons[1].enable()
self.seriesButtons.buttons[2].enable()
self.conditionPointsButtons.buttons[0].enable()
self.conditionPointsButtons.buttons[2].disable()
if self.conditionPoint is None:
self.conditionPointsButtons.buttons[1].disable()
else:
self.conditionPointsButtons.buttons[1].enable()
def update(self):
self.updateButtons()
objectList = []
textMatrix = []
for experiment in getSampledDimExperiments(self.nmrProject):
getExperimentConditionSet(experiment)
sampledDim = getExperimentSampledDim(experiment)
datum = [None,
experiment.name,
1,
sampledDim.conditionVaried,
sampledDim.numPoints]
textMatrix.append(datum)
objectList.append(experiment)
for expSeries in self.nmrProject.sortedNmrExpSeries():
experiments = expSeries.experiments
conditionSets = len([e.sampleConditionSet for e in experiments if e.sampleConditionSet])
datum = [expSeries.serial,
expSeries.name or ' ',
len(experiments),
','.join(expSeries.conditionNames),
conditionSets]
textMatrix.append(datum)
objectList.append(expSeries)
self.seriesMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.updateConditions()
self.waiting = False
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
class EditPeakPopup(BasePopup):
"""
**Edit Position, Intensity & Details for a Peak**
This popup window provides an means of editing peak information as an
alternative to editing values in the main peak tables. This popup is also used
to specify parameters for when a new peak is explicitly added to a peak list
using a tabular display.
The user can specify the position of the peak's dimensions in ppm, Hz or data
point units. Also, the user can adjust the height and volume peak intensity
values and a textual "Details" field, ,which can carry the user's comments
about the peak.
When editing an existing peak, no changes are made to the peak until the
[Update] button is pressed. Likewise for a new peak the [Add Peak] button
commits the changes. If the popup window is closed before the changes are
committed then the entire editing or peak addition operation is cancelled.
"""
def __init__(self, parent, peak=None, peakList=None, *args, **kw):
self.titleColor = '#000080'
self.numDims = 0
self.peak = peak
kw['borderwidth'] = 6
BasePopup.__init__(self, parent=parent, title='Edit Peak', **kw)
self.registerNotify(self.deletedPeak, 'ccp.nmr.Nmr.Peak', 'delete')
for func in ('setAnnotation', 'setDetails', 'setFigOfMerit'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.Peak', func)
for func in ('setAnnotation', 'setPosition', 'setNumAliasing'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakDim', func)
for func in ('__init__', 'delete', 'setValue'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakIntensity',
func)
self.dimensionLabels = []
self.dimensionEntries = []
self.update(self.peak, peakList)
def body(self, guiParent):
self.geometry("+150+150")
guiParent.grid_columnconfigure(0, weight=1)
self.master_frame = guiParent
units = ('ppm', 'point', 'Hz')
self.unit = 'ppm'
self.specLabel = Label(guiParent,
fg=self.titleColor,
grid=(0, 0),
sticky='ew')
self.peakLabel = Label(guiParent, grid=(0, 1), sticky='ew')
self.unit_frame = frame = Frame(guiParent,
grid=(1, 1),
gridSpan=(1, 2))
self.unitLabel = Label(frame, text='Current units: ', grid=(0, 0))
tipText = 'Selects which unit of measurement to display peak dimension positions with'
self.unitSelect = PulldownList(frame,
callback=self.changeUnit,
texts=units,
grid=(0, 1),
tipText=tipText)
self.heightLabel = Label(guiParent,
text='Height',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak height; the value of the spectrum point intensity (albeit often interpolated)'
self.heightEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.volumeLabel = Label(guiParent,
text='Volume',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak volume integral; normally a summation of data point values'
self.volumeEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.detailLabel = Label(guiParent,
text='Details',
borderwidth=2,
relief='groove')
tipText = 'A user-configurable textual comment for the peak, which appears an tables and occasionally on spectrum displays'
self.detailEntry = Entry(guiParent, borderwidth=1, tipText=tipText)
tipTexts = [
'Commits the specified values to update the peak and closes the popup',
]
texts = ['Update']
commands = [self.commit]
self.buttons = UtilityButtonList(guiParent,
texts=texts,
commands=commands,
doClone=False,
helpUrl=self.help_url,
tipTexts=tipTexts)
def open(self):
self.updatePeak()
BasePopup.open(self)
def updatePeak(self, object=None):
peak = None
if object:
if object.className == 'Peak':
peak = object
elif object.className == 'PeakDim':
peak = object.peak
elif object.className == 'PeakIntensity':
peak = object.peak
if (peak is None) or (peak is self.peak):
self.update(peak=self.peak)
def update(self, peak=None, peakList=None):
# first destroy old labels and entries (saves grid hassles)
for label in self.dimensionLabels:
label.destroy()
for entry in self.dimensionEntries:
entry.destroy()
# now setup required data
if peak:
title = 'Edit Peak'
self.buttons.buttons[0].config(text='Update')
else:
title = 'Add Peak'
self.buttons.buttons[0].config(text='Add Peak')
self.setTitle(title)
self.peak = peak
self.peakList = peakList
if not peakList:
if peak:
self.peakList = peak.peakList
else:
return
peakList = self.peakList
spectrum = peakList.dataSource.name
self.numDims = peakList.dataSource.numDim
self.posn = self.numDims * [0]
self.dataDims = peakList.dataSource.sortedDataDims()
if self.peak:
serial = self.peak.serial
dims = self.peak.sortedPeakDims()
details = self.peak.details
if not details:
details = ''
if self.peak.annotation:
annotn = '%0.16s' % self.peak.annotation
else:
annotn = ''
heightIntensity = self.peak.findFirstPeakIntensity(
intensityType='height')
volumeIntensity = self.peak.findFirstPeakIntensity(
intensityType='volume')
if heightIntensity:
height = heightIntensity.value
else:
height = 0.0
if volumeIntensity:
volume = volumeIntensity.value
else:
volume = 0.0
for i in range(self.numDims):
peakDim = dims[i]
dataDimRef = peakDim.dataDimRef
if dataDimRef:
self.posn[i] = peakDim.position + (
peakDim.numAliasing * dataDimRef.dataDim.numPointsOrig)
else:
self.posn[i] = peakDim.position
else:
dict = peakList.__dict__.get('serialDict')
if dict is None:
serial = 1
else:
serial = dict.get('peaks', 0) + 1
height = 0.0
volume = 0.0
details = ''
annotn = ''
self.specLabel.set(
text='Experiment: %s Spectrum: %s PeakList: %d' %
(peakList.dataSource.experiment.name, spectrum, peakList.serial))
self.peakLabel.set(text='Peak: %d' % serial)
self.dimensionLabels = self.numDims * ['']
self.dimensionEntries = self.numDims * ['']
for i in range(self.numDims):
pos = self.posn[i]
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
pos = unit_converter[('point', self.unit)](
pos, getPrimaryDataDimRef(dataDim))
self.dimensionLabels[i] = Label(self.master_frame,
text='F%d' % (i + 1),
borderwidth=2,
relief='groove')
tipText = 'The peak position in dimension %d, in the specified units' % (
i + 1)
self.dimensionEntries[i] = FloatEntry(self.master_frame,
borderwidth=1,
text='%8.4f' % pos,
tipText=tipText)
self.heightEntry.set(text='%f' % height)
self.volumeEntry.set(text='%f' % volume)
self.detailEntry.set(text=details)
row = 0
self.specLabel.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
self.peakLabel.grid(row=row, column=0, sticky='nsew')
self.unit_frame.grid(row=row, column=1, columnspan=2, sticky='nsew')
for i in range(self.numDims):
row = row + 1
self.dimensionLabels[i].grid(row=row, column=0, sticky='nsew')
self.dimensionEntries[i].grid(row=row,
column=1,
columnspan=3,
sticky='e')
row = row + 1
self.heightLabel.grid(row=row, column=0, sticky='nsew')
self.heightEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.volumeLabel.grid(row=row, column=0, sticky='nsew')
self.volumeEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.detailLabel.grid(row=row, column=0, sticky='nsew')
self.detailEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.buttons.grid(row=row, column=0, columnspan=4, sticky='nsew')
def changeUnit(self, unit):
posDisp = self.numDims * [None]
for i in range(self.numDims):
posDisp[i] = float(self.dimensionEntries[i].get())
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
posDisp[i] = unit_converter[(self.unit, 'point')](
posDisp[i], getPrimaryDataDimRef(dataDim))
self.unit = unit
if self.unit != 'point':
for i in range(self.numDims):
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
posDisp[i] = unit_converter[('point', self.unit)](
posDisp[i], getPrimaryDataDimRef(dataDim))
for i in range(self.numDims):
value = posDisp[i]
if value is None:
self.dimensionEntries[i].set('None')
else:
self.dimensionEntries[i].set('%8.4f' % posDisp[i])
def commit(self):
posDisp = self.numDims * [0]
for i in range(self.numDims):
posDisp[i] = float(self.dimensionEntries[i].get())
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
self.posn[i] = unit_converter[(self.unit, 'point')](
posDisp[i], getPrimaryDataDimRef(dataDim))
else:
self.posn[i] = posDisp[i]
if self.peak:
movePeak(self.peak, self.posn)
else:
self.peak = pickPeak(self.peakList, self.posn)
height = self.heightEntry.get()
volume = self.volumeEntry.get()
setManualPeakIntensity(self.peak, height, intensityType='height')
setManualPeakIntensity(self.peak, volume, intensityType='volume')
details = self.detailEntry.get() or None
self.peak.setDetails(details)
self.close()
def deletedPeak(self, peak):
if self.peak is peak:
self.close()
def destroy(self):
self.unregisterNotify(self.deletedPeak, 'ccp.nmr.Nmr.Peak', 'delete')
for func in ('setAnnotation', 'setDetails', 'setFigOfMerit'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.Peak', func)
for func in ('setAnnotation', 'setPosition', 'setNumAliasing'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakDim', func)
for func in ('__init__', 'delete', 'setValue'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakIntensity',
func)
BasePopup.destroy(self)