class WriteBmrbChemShiftDepPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'WriteBmrbChemShiftDep.html')
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.selectedFormats = []
self.defaultText = 'Select file'
self.chainDict = {}
self.chainList = []
self.shiftListDict = {}
self.shiftLists = []
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
if shiftList.measurements != ():
label = str(shiftList.serial) + ':' + str(shiftList.name)
self.shiftListDict[label] = shiftList
self.shiftLists.append(label)
if not self.shiftLists:
showError('Error', 'No shift lists available!')
return
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Write BMRB chemical shift deposition file',
modal=False,
transient=True)
def body(self, master):
row = 0
label = Label(master,
text="BMRB chemical shift deposition file writer.")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Shift lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftLists,
callback=self.setChainList,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Chains (only one per file):")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainListSelect = PulldownMenu(master, entries=self.chainList)
self.chainListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
self.setChainList(0, self.shiftLists[0])
row += 1
label = Label(master, text="Chemical shift deposition file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master,
text=self.defaultText,
command=self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = ['Write file']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def setChainList(self, shiftListIndex, shiftListLabel):
#
# Has to be done... very slow this.
#
shiftList = self.shiftListDict[shiftListLabel]
self.chainDict = {}
self.chainList = []
for shift in shiftList.measurements:
if shift.resonance:
rs = shift.resonance.resonanceSet
if rs:
atom = rs.findFirstAtomSet().findFirstAtom()
chain = atom.residue.chain
if chain not in self.chainDict.values():
label = chain.molSystem.code + ":'" + chain.code + "'"
self.chainDict[label] = chain
self.chainList.append(label)
self.chainListSelect.clearMenuItems()
if self.chainList:
self.chainListSelect.setup(self.chainList, 0)
def selectFile(self):
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
fileName = 'bmrb.csdep'
popup = FormatFilePopup(self,
file=fileName,
component='csdep',
format='bmrb')
if popup.fileSelected:
self.fileButton.config(text=popup.file)
popup.destroy()
def apply(self):
shiftListLabel = self.shiftListSelect.getSelected()
shiftList = self.shiftListDict[shiftListLabel]
try:
chainLabel = self.chainListSelect.getSelected()
chain = self.chainDict[chainLabel]
except:
showError(
"No chains",
"No chains were present or selected. Try running linkResonances first."
)
return False
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeBmrbChemShiftDeposition(self.guiParent, chain,
shiftList, fileName)
if fileCreated:
showInfo("Success",
"Succesfully wrote chemical shift deposition file")
else:
showError("Not written",
"Error writing file %s. File not written" % fileName)
return False
return True
class 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)
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)
class ConfirmSeqSpinSystemsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.spinSystems = []
self.spectrum = None
self.spectra = []
self.waiting = 0
self.shiftList = None
self.spinSystem = None
self.link = '-1'
BasePopup.__init__(self,
parent=parent,
title="Confirm Sequential Spin System",
**kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame)
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Shift List:')
label.grid(row=0, column=0, sticky='w')
self.shiftListPulldown = PulldownMenu(frame,
callback=self.setShiftList)
self.shiftListPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Sequential Link Type:')
label.grid(row=0, column=2, sticky='w')
entries = ['-1', '-1,+1', '+1']
self.linkPulldown = PulldownMenu(frame,
callback=self.setLink,
entries=entries,
do_initial_callback=False,
selected_index=entries.index(
self.link))
self.linkPulldown.grid(row=0, column=3, sticky='w')
row += 1
frame = LabelFrame(guiFrame, text='Link Atoms:')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
labels = ['C', 'CA', 'CB', 'CG', 'CD', 'H', 'HA', 'HB', 'HG', 'HD']
selected = ['CA', 'CB']
self.atomSelector = PartitionedSelector(frame,
objects=labels,
labels=labels,
selected=selected,
toggledBg='#808080',
callback=self.changeAtoms,
maxRowObjects=10)
self.atomSelector.grid(row=0, column=0, sticky='ew')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Predicted Residue Assignments')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = [
'#', 'Predicted\nResidue', 'Prob.', 'Links', 'CA', 'CA -1', 'CB',
'CB -1'
]
self.spinSystemMatrix = ScrolledMatrix(frame,
headingList=headingList,
callback=self.selectSpinSystem,
multiSelect=1)
self.spinSystemMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = ['Link Selected', 'Link All', 'Commit Assignment']
commands = [
self.linkSelectedSpinSystems, self.linkAllSpinSystems,
self.commitAssignments
]
buttonList = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url)
buttonList.grid(row=row, column=0, sticky='ew')
self.buttons = buttonList.buttons
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.ShiftList', ):
self.registerNotify(self.updateShiftLists, clazz, func)
for func in ('__init__', 'delete', 'setNmrChains', 'setResidue',
'setResonances', 'addResonance', 'removeResonance'):
self.registerNotify(self.updateSpinSystemsAfter,
'ccp.nmr.Nmr.ResonanceGroup', func)
self.updateShiftLists()
def setLink(self, index, name):
self.link = name
self.updateSpinSystemsAfter()
def updateButtons(self):
if len(self.spinSystemMatrix.currentObjects) > 1:
self.buttons[0].enable()
else:
self.buttons[0].disable()
if self.spinSystemMatrix.objectList:
self.buttons[1].enable()
else:
self.buttons[1].disable()
if self.spinSystem:
self.buttons[2].enable()
else:
self.buttons[2].disable()
def changeAtoms(self, *opt):
self.updateSpinSystemsAfter()
def getShiftListNames(self, shiftLists):
shiftListNames = []
for shiftList in shiftLists:
if not hasattr(shiftList, 'name'):
shiftList.name = "ShiftList " + str(shiftList.serial)
elif not shiftList.name:
shiftList.name = "ShiftList " + str(shiftList.serial)
shiftListNames.append(shiftList.name)
return shiftListNames
def updateShiftLists(self, *opt):
shiftLists = list(
self.nmrProject.findAllMeasurementLists(className='ShiftList'))
shiftListNames = self.getShiftListNames(shiftLists)
shiftList = None
index = -1
if shiftListNames:
if self.shiftList in shiftLists:
shiftList = self.shiftList
else:
shiftList = shiftLists[0]
index = shiftLists.index(shiftList)
self.shiftList = shiftList
self.shiftListPulldown.setup(shiftListNames, index)
def setShiftList(self, index, name=None):
shiftLists = list(
self.nmrProject.findAllMeasurementLists(className='ShiftList'))
if shiftLists:
self.shiftList = shiftLists[index]
else:
self.shiftList = None
self.updateSpinSystemsAfter()
def linkSelectedSpinSystems(self):
spinSystems = self.spinSystemMatrix.currentObjects
self.linkSpinSystems(spinSystems)
def linkAllSpinSystems(self):
spinSystems = self.spinSystemMatrix.objectList
self.linkSpinSystems(spinSystems)
def linkSpinSystems(self, spinSystems):
data = []
for spinSystem in spinSystems:
residue, p = self.getProbableResidue(spinSystem)
key = '%s%s%4.4d' % (residue.chain.molSystem.code,
residue.chain.code, residue.seqCode)
data.append([key, residue.seqCode, residue, spinSystem])
data.sort()
seqCodes = [x[1] for x in data]
residues = [x[2] for x in data]
spinSystems = [x[3] for x in data]
N = len(data)
for i in range(N):
if i > 0:
delta = seqCodes[i] - seqCodes[i - 1]
if delta == 1 and (residues[i].chain is residues[i - 1].chain):
ss = findConnectedSpinSystem(spinSystems[i], delta=-1)
if ss:
mergeSpinSystems(
ss,
spinSystems[i -
1]) # copy resonances across & delete
makeSeqSpinSystemLink(spinSystems[i - 1],
spinSystems[i],
delta=1)
if i < N - 1:
delta = seqCodes[i + 1] - seqCodes[i]
if delta == 1 and (residues[i].chain is residues[i + 1].chain):
ss = findConnectedSpinSystem(spinSystems[i], delta=1)
if ss:
mergeSpinSystems(
ss,
spinSystems[i +
1]) # copy resonances across & delete
makeSeqSpinSystemLink(spinSystems[i],
spinSystems[i + 1],
delta=1)
self.updateSpinSystemsAfter()
def commitAssignments(self):
merge = showYesNo('Query', 'Merge with any existing spin systems?',
self)
for spinSystem in self.spinSystemMatrix.currentObjects:
if not spinSystem.residue:
residue, p = self.getProbableResidue(spinSystem)
assignSpinSystemResidue(spinSystem, residue, warnMerge=merge)
def getProbableResidue(self, spinSystem):
residue = None
probability = 0.0
if spinSystem.residue:
return spinSystem.residue, 1.0
data = []
for residueProb in spinSystem.residueProbs:
data.append((residueProb.weight, residueProb.possibility))
data.sort()
if data:
residue, probability = data[-1]
return residue, probability
def getTentativeSpinSystems(self):
spinSystemsList = []
if self.project:
for spinSystem in self.nmrProject.sortedResonanceGroups():
if spinSystem.residueProbs and not spinSystem.residue:
#if spinSystem.residue:
residue, p = self.getProbableResidue(spinSystem)
key = '%s%s%4.4d' % (residue.chain.molSystem.code,
residue.chain.code, residue.seqCode)
spinSystemsList.append((key, spinSystem))
spinSystemsList.sort()
return [x[1] for x in spinSystemsList]
def updateSpinSystemsAfter(self, spinSystem=None):
if self.waiting:
return
else:
if spinSystem:
if not spinSystem.residueProbs:
return
if spinSystem.residue:
return
self.waiting = True
self.after_idle(self.updateSpinSystems)
def getHeadings(self):
headingList = ['#', 'Predicted\nResidue', 'Prob.', 'Links']
atoms = self.atomSelector.getSelected()
for atom in atoms:
headingList.append(atom)
if self.link == '-1':
headingList.append('%s -1' % atom)
headingList.append('D %s -1' % atom)
elif self.link == '+1':
headingList.append('%s +1' % atom)
headingList.append('D %s +1' % atom)
else:
headingList.append('%s -1' % atom)
headingList.append('D %s -1' % atom)
headingList.append('%s +1' % atom)
headingList.append('D %s +1' % atom)
return headingList
def addShiftData(self, spinSystem, datum):
prevSS, nextSS = self.getConnectedSpinSystems(spinSystem)
atoms = self.atomSelector.getSelected()
dict = {}
residue, p = self.getProbableResidue(spinSystem)
prevRes = residue.chain.findFirstResidue(seqCode=residue.seqCode - 1)
nextRes = residue.chain.findFirstResidue(seqCode=residue.seqCode + 1)
prevSS0 = None
nextSS0 = None
for ss in self.getTentativeSpinSystems():
if self.getProbableResidue(ss)[0] is prevRes:
prevSS0 = ss
if self.getProbableResidue(ss)[0] is nextRes:
nextSS0 = ss
if nextSS0 and prevSS0:
break
for atom in atoms:
resonances = []
resonancesPrev = []
resonancesNext = []
resonancesPrev0 = []
resonancesNext0 = []
for resonance0 in spinSystem.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonances.append(resonance0)
break
text = ''
if resonances:
text = self.getResonanceText(resonances)
datum.append(text)
if prevSS and ('-1' in self.link):
for resonance0 in prevSS.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonancesPrev.append(resonance0)
break
deltasPrev = []
if prevSS0 and resonancesPrev:
for resonance1 in prevSS0.sortedResonances():
for name1 in resonance1.assignNames:
if name1[:2] == atom:
shift1 = resonance1.findFirstShift(
parentList=self.shiftList)
deltas = []
for resonance2 in resonancesPrev:
shift2 = resonance2.findFirstShift(
parentList=self.shiftList)
if shift1 and shift2:
deltas.append(
abs(shift1.value - shift2.value))
if deltas:
deltas.sort()
deltasPrev.append('%.2f' % deltas[0])
break
if nextSS and ('+1' in self.link):
for resonance0 in nextSS.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonancesNext.append(resonance0)
break
deltasNext = []
if nextSS0 and resonancesNext:
for resonance1 in nextSS0.sortedResonances():
for name1 in resonance1.assignNames:
if name1[:2] == atom:
shift1 = resonance1.findFirstShift(
parentList=self.shiftList)
deltas = []
for resonance2 in resonancesNext:
shift2 = resonance2.findFirstShift(
parentList=self.shiftList)
if shift1 and shift2:
deltas.append(
abs(shift1.value - shift2.value))
if deltas:
deltas.sort()
deltasNext.append('%.2f' % deltas[0])
break
if self.link == '-1':
ppms = ''
diff = ''
if resonancesPrev:
ppms = self.getResonanceText(resonancesPrev)
diff = ','.join(deltasPrev)
datum.append(ppms)
datum.append(diff)
elif self.link == '+1':
ppms = ''
diff = ''
if resonancesNext:
ppms = self.getResonanceText(resonancesNext)
diff = ','.join(deltasNext)
datum.append(ppms)
datum.append(diff)
else:
ppms = ''
diff = ''
if resonancesPrev:
ppms = self.getResonanceText(resonancesPrev)
diff = ','.join(deltasPrev)
datum.append(ppms)
datum.append(diff)
ppms = ''
diff = ''
if resonancesNext:
ppms = self.getResonanceText(resonancesNext)
diff = ','.join(deltasNext)
datum.append(ppms)
datum.append(diff)
def updateSpinSystems(self):
textMatrix = []
objectList = []
colorMatrix = []
headingList = self.getHeadings()
for spinSystem in self.getTentativeSpinSystems():
residueText = None
residue, probability = self.getProbableResidue(spinSystem)
if residue:
residueText = '%d%s' % (residue.seqCode,
getResidueCode(residue))
links = []
color = '#D04040'
if findConnectedSpinSystem(spinSystem, delta=-1):
links.append('-1')
if findConnectedSpinSystem(spinSystem, delta=1):
links.append('+1')
if len(links) == 2:
color = '#40B040'
elif len(links) == 1:
color = '#B0B040'
datum = []
datum.append(spinSystem.serial)
datum.append(residueText)
datum.append(probability)
datum.append(' '.join(links))
self.addShiftData(spinSystem, datum)
colors = [None] * len(headingList)
colors[3] = color
objectList.append(spinSystem)
textMatrix.append(datum)
colorMatrix.append(colors)
if self.spinSystem not in objectList:
self.spinSystem = None
self.spinSystemMatrix.update(headingList=headingList,
objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
self.updateButtons()
self.waiting = False
def getResonanceText(self, resonances):
shifts = []
for resonance in resonances:
shift = resonance.findFirstShift(parentList=self.shiftList)
if shift:
shifts.append('%.2f' % shift.value)
return ','.join(shifts)
def getConnectedSpinSystems(self, spinSystem):
if self.link == '-1':
prevSS = findConnectedSpinSystem(spinSystem, delta=-1)
nextSS = None
elif self.link == '+1':
prevSS = None
nextSS = findConnectedSpinSystem(spinSystem, delta=1)
else:
prevSS = findConnectedSpinSystem(spinSystem, delta=-1)
nextSS = findConnectedSpinSystem(spinSystem, delta=1)
return prevSS, nextSS
def selectSpinSystem(self, object, row, col):
self.spinSystem = object
self.updateButtons()
def destroy(self):
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.ShiftList', ):
self.unregisterNotify(self.updateShiftLists, clazz, func)
for func in ('__init__', 'delete', 'setNmrChains', 'setResidue',
'setResonances', 'addResonance', 'removeResonance'):
self.unregisterNotify(self.updateSpinSystemsAfter,
'ccp.nmr.Nmr.ResonanceGroup', func)
BasePopup.destroy(self)
class EditSymmetryPopup(BasePopup):
def __init__(self, parent, project):
self.parent = parent
self.ccpnProject = project
self.hProject = project.currentHaddockProject
self.molPartner = None
self.molecules = []
self.symmetrySet = None
self.symmetryOp = None
self.symmetryCode = None
self.waiting = False
BasePopup.__init__(self, parent=parent, title='Symmetry Operations')
self.font = 'Helvetica 12'
self.setFont()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=0,column=0,sticky='ew')
frame.grid_columnconfigure(5, weight=1)
# Choose type of symmetry set to define or change (if allready present in the model)
self.molLabel = Label(frame, text='Symmetry Operator:')
self.molLabel.grid(row=0,column=2,sticky='w')
self.symmCodePulldown = PulldownMenu(frame, callback=self.setSymmCode, entries=['NCS','C2','C3','C5'], do_initial_callback=False)
self.symmCodePulldown.grid(row=0,column=3,sticky='w')
frame = LabelFrame(guiFrame, text='Symmetry Operations')
frame.grid(row=1,column=0,sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.molSysPulldown = PulldownMenu(self, callback=self.setMolSystem, do_initial_callback=False)
self.chainSelect = MultiWidget(self, CheckButton, callback=self.setChains, minRows=0, useImages=False)
self.segStartEntry = IntEntry(self, returnCallback=self.setSegStart, width=6)
self.segLengthEntry = IntEntry(self, returnCallback=self.setSegLength, width=6)
headings = ['#','Symmetry\noperator','Mol System','Chains','Start\nresidue','Segment\nlength']
editWidgets = [None, None, self.molSysPulldown, self.chainSelect, self.segStartEntry, self.segLengthEntry]
editGetCallbacks = [None, None, self.getMolSystem, self.getChains, self.getSegStart, self.getSegLength]
editSetCallbacks = [None, self.setSymmCode, self.setMolSystem, self.setChains, self.setSegStart, self.setSegLength]
self.symmetryMatrix = ScrolledMatrix(frame,headingList=headings,
callback=self.selectSymmetry,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.symmetryMatrix.grid(row=0,column=0,sticky='nsew')
texts = ['Add Symmetry Set','Remove Symmetry Set']
commands = [self.addSymmetrySet,self.removeSymmetrySet]
self.buttonList = createDismissHelpButtonList(guiFrame, texts=texts, commands=commands, expands=True)
self.buttonList.grid(row=2,column=0,sticky='ew')
self.updateMolPartners()
self.notify(self.registerNotify)
#Temporary report of parameters
print self.molSystem
print self.molecules
print self.symmetrySet
print self.symmetryOp
print self.symmetryCode
def getMolSystem(self, partner):
"""Select molecular system from list of molsystems stored in the project"""
names = []; index = -1
molSystem = partner.molSystem
molSystems = self.ccpnProject.sortedMolSystems()
if molSystems:
names = [ms.code for ms in molSystems]
if molSystem not in molSystems:
molSystem = molSystems[0]
index = molSystems.index(molSystem)
self.molSysPulldown.setup(names, index)
def getChains(self, partner):
names = []
values = []
molSystem = partner.molSystem
if molSystem:
for chain in molSystem.sortedChains():
names.append(chain.code)
if not partner.chains:
values.append(True)
elif partner.findFirstChain(chain=chain):
values.append(True)
else:
values.append(False)
self.chainSelect.set(values=values,options=names)
else:
showWarning('Warning','Set Mol System or ensemble first',parent=self)
self.symmetryMatrix.keyPressEscape()
def getSegLength(self, symmetryOp):
if symmetryOp and symmetryOp.segmentLength: self.segLengthEntry.set(symmetryOp.segmentLength)
def getSegStart(self):
pass
def setMolSystem(self, partner, name=None):
"""Get all molsystems as stored in the project as list"""
index = self.molSysPulldown.getSelectedIndex()
molSystems = self.ccpnProject.sortedMolSystems()
if molSystems:
molSystem = molSystems[index]
self.molPartner.molSystem = molSystem
chains = molSystem.sortedChains()
if (not self.molPartner.chains) and chains: setPartnerChains(self.molPartner,chains)
self.updateAllAfter()
def setChains(self, obj):
"""Get the list of chains for the selected molsystem"""
if self.molPartner and self.molPartner.molSystem:
if obj is not None:
chains = self.molPartner.molSystem.sortedChains()
values = self.chainSelect.get()
chains = [chains[i] for i in range(len(values)) if values[i]]
setPartnerChains(self.molPartner,chains)
self.symmetryMatrix.keyPressEscape()
self.updateAllAfter()
def setSegLength(self, event):
value = self.segLengthEntry.get() or 1
self.symmetryOp.segmentLength = value
def setSegStart(self):
pass
def setSymmCode(self, index, name=None):
self.symmetryCode = self.symmCodePulldown.getSelected()
def selectSymmetry(self, obj, row, col):
self.symmetryOp = obj
self.updateMolSysPulldown()
def notify(self, notifyFunc):
for func in ('__init__', 'delete', 'setSymmetryCode','setSegmentLength'):
notifyFunc(self.updateAllAfter, 'molsim.Symmetry.Symmetry', func)
for func in ('__init__', 'delete','setfirstSeqId'):
notifyFunc(self.updateAllAfter, 'molsim.Symmetry.Segment', func)
def addSymmetrySet(self):
if not self.ccpnProject.molSystems:
showWarning('Warning','No molecular systems present in CCPN project',parent=self)
return
molSystem = self.ccpnProject.findFirstMolSystem()
partner = self.hProject.newHaddockPartner(code=molSystem.code, molSystem=molSystem)
setPartnerChains(partner, molSystem.chains)
self.updateAllAfter()
def removeSymmetrySet(self):
pass
def updateAllAfter(self, obj=None):
if self.waiting: return
else:
self.waiting = True
self.after_idle(self.updateSymmetries,
self.updateMolPartners)
def updateMolPartners(self):
textMatrix = []
objectList = []
for partner in self.hProject.sortedHaddockPartners():
datum = [partner.code,
self.symmetryCode,
partner.molSystem.code,
','.join([c.chain.code for c in partner.chains]),
partner.autoHistidinePstate and 'Yes' or 'No',
partner.isDna and 'Yes' or 'No']
objectList.append(partner)
textMatrix.append(datum)
self.symmetryMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.updateMolSysPulldown()
def updateMolSysPulldown(self):
names = []
index = -1
partners = self.hProject.sortedHaddockPartners()
if partners:
if self.molPartner not in partners:
self.molPartner = partners[0]
names = ['Partner %s' % p.code for p in partners]
index = partners.index(self.molPartner)
else: self.molPartner = None
self.molSysPulldown.setup(names, index)
def updateSymmetries(self):
textMatrix = []; objectList = []
if self.symmetrySet:
for symmetryOp in self.symmetrySet.symmetries:
chains = []; segments = []
length = symmetryOp.segmentLength
for segment in symmetryOp.sortedSegments():
code = segment.chainCode
chain = self.molSystem.findFirstChain(code=code)
if chain:
chains.append(code)
seqId = segment.firstSeqId
residue1 = chain.findFirstResidue(seqId=seqId)
residue2 = chain.findFirstResidue(seqId=seqId+length-1)
segments.append('%s:%d-%d' % (code,residue1.seqCode,residue2.seqCode))
datum = [symmetryOp.serial, symmetryOp.symmetryCode, length, '\n'.join(chains), '\n'.join(segments)]
objectList.append(symmetryOp)
textMatrix.append(datum)
self.symmetryMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.waiting = False
def destroy(self):
self.notify(self.unregisterNotify)
BasePopup.destroy(self)
class SetupStructureCalcFrame(Frame):
def __init__(self, parent, application, *args, **kw):
self.parent = parent
self.molSystem = None
self.constraintSet = None
self.application = application
self.project = application.project
self.waiting = False
self.tableObj = None
Frame.__init__(self, parent=parent, **kw)
self.grid_columnconfigure(3, weight=1)
label = Label(self, text='Molecular system: ')
label.grid(row=0, column=0, sticky='nw')
self.molSysPulldown = PulldownMenu(
self,
self.changeMolSystem,
tipText='Select which molecular system to use in the calculation')
self.molSysPulldown.grid(row=0, column=1, sticky='nw')
label = Label(self, text='Constraint Set: ')
label.grid(row=0, column=2, sticky='nw')
self.constraintSetPulldown = PulldownMenu(
self,
self.changeConstraintSet,
tipText='Select which set of restraints to use in the calculation')
self.constraintSetPulldown.grid(row=0, column=3, sticky='nw')
self.shiftListPulldown = PulldownMenu(
parent,
callback=self.setShiftList,
do_initial_callback=False,
tipText='select the shift list to use in the calculation')
tipTexts = [
'The type of ccp object used in the calculation',
'The identifier for the input data',
'A toggle whether to use the data',
'Whether to filter violated restraints',
'Whether to keep CCPN assignments (otherwise new restraint assignments will be used)',
'Whether the restraints are overly anbiguous and need refining',
'The shift list to use for shift-peak matching'
]
headingList = [
'Input Class', 'Id', 'Use?', 'Filter\nViolated',
'Keep\nAssignments?', 'Ambiguous\nProtocol', 'Shift List'
]
editWidgets = [
None, None, None, None, None, None, self.shiftListPulldown
]
editGetCallbacks = [
None, None, self.toggleUse, self.toggleFilterViol,
self.toggleKeepAssign, self.toggleAmbig, self.getShiftList
]
editSetCallbacks = [
None, None, None, None, None, None, self.setShiftList
]
self.grid_rowconfigure(1, weight=1)
self.scrolledMatrix = ScrolledMatrix(self,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True,
tipTexts=tipTexts,
callback=self.selectCell)
self.scrolledMatrix.grid(row=1, column=0, columnspan=4, sticky='nsew')
self.scrolledMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
#texts = ['','','']
#commands = [None,None,None]
#self.bottomButtons = ButtonList(self, texts=texts, expands=True, commands=commands)
#self.bottomButtons.grid(row=2, column=0, columnspan=4, sticky='ew')
self.updateMolSystems()
self.updateConstraintSets()
notify = self.application.registerNotify
for func in ('__init__', 'delete'):
notify(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notify(self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem',
func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete', 'setName'):
notify(self.updateAfter, 'ccp.nmr.Nmr.Experiment', func)
notify(self.updateAfter, 'ccp.nmr.Nmr.DataSource', func)
def doEditMarkExtraRules(self, obj, row, col):
className = obj.className
if className == 'PeakList':
if col == 5:
return False
elif className == 'DistanceConstraintList':
if col in (4, 6):
return False
else:
if col in (4, 5, 6):
return False
return True
def toggleUse(self, obj):
bool = not obj.setupStructureCalcFrameDict['use']
obj.setupStructureCalcFrameDict['use'] = bool
self.updateAfter()
def toggleFilterViol(self, obj):
bool = not obj.setupStructureCalcFrameDict['filter']
obj.setupStructureCalcFrameDict['filter'] = bool
self.updateAfter()
def toggleKeepAssign(self, obj):
bool = not obj.setupStructureCalcFrameDict['preserve']
obj.setupStructureCalcFrameDict['preserve'] = bool
self.updateAfter()
def toggleAmbig(self, obj):
bool = not obj.setupStructureCalcFrameDict['ambig']
obj.setupStructureCalcFrameDict['ambig'] = bool
self.updateAfter()
def selectCell(self, obj, row, col):
self.tableObj = obj
def getShiftList(self, peakList):
names = []
index = -1
shiftLists = getShiftLists(self.project.currentNmrProject)
if shiftLists:
shiftList = peakList.dataSource.experiment.shiftList
if shiftList not in shiftLists:
shiftList = shiftLists[0]
names = [sl.name or str(sl.serial) for sl in shiftLists]
index = shiftLists.index(shiftList)
print "getShiftList", names, index
self.shiftListPulldown.setup(names, index)
def setShiftList(self, index, name=None):
print "setShiftList", index, name
if not name:
index = self.shiftListPulldown.getSelectedIndex()
shiftList = getShiftLists(self.project.currentNmrProject)[index]
self.tableObj.setupStructureCalcFrameDict['shiftList'] = shiftList
self.updateAfter()
def updateMolSystems(self, *opt):
names = []
index = -1
molSystems = self.getMolSystems()
if molSystems:
names = [ms.code for ms in molSystems]
if self.molSystem not in molSystems:
self.molSystem = molSystems[0]
index = molSystems.index(self.molSystem)
self.molSysPulldown.setup(names, index)
def getMolSystems(self):
molSystems = []
if self.project:
for molSystem in self.project.molSystems:
if molSystem.chains:
molSystems.append(molSystem)
return molSystems
def getTableObjects(self):
objs = []
if self.project:
objs = getThroughSpacePeakLists(self.project)
if self.constraintSet:
objs.extend(list(self.constraintSet.constraintLists))
return objs
def updateConstraintSets(self, obj=None):
names = []
index = -1
if self.project and self.project.currentNmrProject:
constraintSets = self.project.currentNmrProject.sortedNmrConstraintStores(
)
if constraintSets:
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
names = [str(cs.serial) for cs in constraintSets]
index = constraintSets.index(self.constraintSet)
names.append('<None>')
self.constraintSetPulldown.setup(names, index)
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
self.updateAfter()
def changeConstraintSet(self, i, name):
if name == '<None>':
self.constraintSet = None
else:
self.constraintSet = self.project.currentNmrProject.sortedNmrConstraintStores(
)[i]
self.updateAfter()
def update(self):
textMatrix = []
objectList = []
#headingList = ['Input Class','Use?','Filter\nViolated',
# 'Keep\nAssignments?','Ambigous\nProtocol','Shift List']
for obj in self.getTableObjects():
if not hasattr(obj, 'setupStructureCalcFrameDict'):
obj.setupStructureCalcFrameDict = dict = {}
dict['use'] = True
dict['filter'] = True
dict['preserve'] = False
dict['ambig'] = False
dict['shiftList'] = None
new = True
else:
dict = obj.setupStructureCalcFrameDict
new = False
className = obj.className
if className == 'PeakList':
spectrum = obj.dataSource
experiment = spectrum.experiment
shiftList = dict['shiftList'] or experiment.shiftList
if shiftList:
shiftListName = shiftList.name
else:
shiftListName = '<None>'
if new and (self.molSystem not in experiment.molSystems):
dict['use'] = False
ident = '%s:%s:%d' % (experiment.name, spectrum.name,
obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = dict['filter'] and 'Yes' or 'No'
preserved = dict['preserve'] and 'Yes' or 'No'
ambig = None
elif className == 'DistanceConstraintList':
shiftListName = None
if new:
dict['filter'] = True
dict['ambig'] = False
ident = '%s:%d' % (obj.name or '', obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = dict['filter'] and 'Yes' or 'No'
preserved = None
ambig = dict['ambig'] and 'Yes' or 'No'
else:
shiftListName = None
if new:
dict['filter'] = False
dict['ambig'] = False
ident = '%s:%d' % (obj.name or '', obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = None
preserved = None
ambig = None
datum = [
className, ident, used, filtered, preserved, ambig,
shiftListName
]
textMatrix.append(datum)
objectList.append(obj)
self.waiting = False
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList)
def getAriaData(self):
if not self.project:
showWarning('Failure', 'No active project', parent=self)
return
if not self.molSystem:
showWarning('Failure', 'No molecular system selected', parent=self)
return
if len(self.molSystem.chains) > 1:
code = self.molSystem.findFirstChain().code
code = askString('Multiple chains',
'Enter chain code:',
code,
parent=self)
chain = self.molSystem.findFirstChain(code=code)
else:
chain = self.molSystem.findFirstChain()
peakData = []
dihedrals = []
ambigs = []
unambigs = []
jCouplings = []
for obj in self.scrolledMatrix.objectList:
opts = obj.setupStructureCalcFrameDict
if not opts['use']:
continue
className = obj.className
key = getObjectKeyString(obj)
if className == 'PeakList':
shiftList = opts['shiftList']
if not shiftList:
continue
datum = {
'shifts': {
KEY_ID: getObjectKeyString(shiftList)
},
'peaks': {
KEY_ID: key
},
'use_assignments': opts['preserve'],
'trust_assigned_peaks': opts['filter']
}
peakData.append(datum)
elif className == 'DistanceConstraintList':
if opts['ambig']:
ambigs.append({
KEY_ID: key,
'filter_contributions': opts['filter']
})
else:
unambigs.append({
KEY_ID: key,
'filter_contributions': opts['filter']
})
elif className == 'JCouplingConstraintList':
jCouplings.append({KEY_ID: key})
elif className == 'DihedralConstraintList':
dihedrals.append({KEY_ID: key})
projFileName = os.path.join(self.project.url.path, self.project.path)
dict = {
KEY_GENERAL: {
'project_name': self.project.name
},
KEY_CCPN: {
'filename': projFileName
},
KEY_MOLECULAR_SYSTEM: {
KEY_ID: getObjectKeyString(chain)
},
KEY_NOES: peakData,
KEY_DIHEDRALS: dihedrals,
KEY_DISTANCES_AMBIG: ambigs,
KEY_DISTANCES_UNAMBIG: unambigs,
KEY_JCOUPLINGS: jCouplings
}
return dict
def updateAll(self):
self.project = self.application.project
self.updateMolSystems()
self.updateConstraintSets()
self.updateAfter()
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def destroy(self):
notify = self.application.unregisterNotify
for func in ('__init__', 'delete'):
notify(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notify(self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem',
func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete', 'setName'):
notify(self.updateAfter, 'ccp.nmr.Nmr.Experiment', func)
notify(self.updateAfter, 'ccp.nmr.Nmr.DataSource', func)
Frame.destroy(self)
class EditSymmetryPopup(BasePopup):
def __init__(self, parent, project):
self.parent = parent
self.project = project
self.singleMolecule = True
self.molSystem = None
self.molecules = []
self.symmetrySet = None
self.symmetryOp = None
self.waiting = False
BasePopup.__init__(self, parent=parent, title='Symmetry Operations')
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=0, column=0, sticky='ew')
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='MolSystem:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
self.molLabel = Label(frame, text='Molecule:')
self.molLabel.grid(row=0, column=2, sticky='w')
self.moleculePulldown = PulldownMenu(frame,
callback=self.selectMolecule)
self.moleculePulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Same Molecule Symmetry:')
label.grid(row=0, column=4, sticky='w')
self.molSelect = CheckButton(frame, callback=self.toggleSingleMolecule)
self.molSelect.grid(row=0, column=5, sticky='w')
self.molSelect.set(self.singleMolecule)
frame = LabelFrame(guiFrame, text='Symmetry Operations')
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.symmCodePulldown = PulldownMenu(self,
callback=self.setSymmCode,
do_initial_callback=False)
self.segLengthEntry = IntEntry(self,
returnCallback=self.setSegLength,
width=6)
self.setChainMulti = MultiWidget(self,
CheckButton,
callback=self.setChains,
minRows=0,
useImages=False)
self.setSegmentMulti = MultiWidget(self,
IntEntry,
callback=self.setSegments,
minRows=0,
useImages=False)
editWidgets = [
None, self.symmCodePulldown, self.segLengthEntry,
self.setChainMulti, self.setSegmentMulti
]
editGetCallbacks = [
None, self.getSymmCode, self.getSegLength, self.getChains,
self.getSegments
]
editSetCallbacks = [
None, self.setSymmCode, self.setSegLength, self.setChains,
self.setSegments
]
headings = [
'#', 'Symmetry\nType', 'Segment\nLength', 'Chains',
'Segment\nPositions'
]
self.symmetryMatrix = ScrolledMatrix(frame,
headingList=headings,
callback=self.selectSymmetry,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.symmetryMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['Add Symmetry Op', 'Remove Symmetrey Op']
commands = [self.addSymmOp, self.removeSymmOp]
buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
buttonList.grid(row=2, column=0, sticky='ew')
self.updateMolSystems()
self.updateMolecules()
self.updateSymmetriesAfter()
self.notify(self.registerNotify)
def open(self):
self.updateMolSystems()
self.updateMolecules()
self.updateSymmetriesAfter()
BasePopup.open(self)
def notify(self, notifyFunc):
for func in ('__init__', 'delete', 'setSymmetryCode',
'setSegmentLength'):
notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Symmetry',
func)
for func in ('__init__', 'delete', 'setfirstSeqId'):
notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Segment',
func)
def getSymmCode(self, symmetryOp):
"""Get allowed symmetry operators from the model"""
symmetryOpCodes = symmetryOp.parent.metaclass.container.getElement(
'SymmetryOpCode').enumeration
index = 0
if symmetryOp.symmetryCode in symmetryOpCodes:
index = symmetryOpCodes.index(symmetryOp.symmetryCode)
self.symmCodePulldown.setup(symmetryOpCodes, index)
def getSegLength(self, symmetryOp):
if symmetryOp and symmetryOp.segmentLength:
self.segLengthEntry.set(symmetryOp.segmentLength)
def getChains(self, symmetryOp):
chains = []
for chain in self.molSystem.chains:
if chain.residues:
if chain.molecule in self.molecules: chains.append(chain.code)
chains.sort()
values = []
for chain in chains:
if symmetryOp.findFirstSegment(chainCode=chain):
values.append(True)
else:
values.append(False)
self.setChainMulti.set(values=values, options=chains)
def getSegments(self, symmetryOp):
values = []
names = []
if symmetryOp:
for segment in symmetryOp.sortedSegments():
names.append(segment.chainCode)
values.append(segment.firstSeqId)
n = len(values)
self.setSegmentMulti.maxRows = n
self.setSegmentMulti.minRows = n
self.setSegmentMulti.set(values=values, options=names)
def setSymmCode(self, index, name=None):
"""Set the symmetry code as NCS,C2,C3,C4,C5,C6"""
if self.symmetryOp:
symmCode = self.symmCodePulldown.getSelected()
self.symmetryOp.symmetryCode = symmCode
def setSegLength(self, event):
value = self.segLengthEntry.get() or 1
self.symmetryOp.segmentLength = value
def setChains(self, obj):
if self.symmetryOp and obj:
codes = self.setChainMulti.options
segment = self.symmetryOp.findFirstSegment()
values = self.setChainMulti.get()
if segment: seqId0 = segment.firstSeqId
else: seqId0 = 1
for i in range(len(values)):
segment = self.symmetryOp.findFirstSegment(chainCode=codes[i])
if segment and not values[i]: segment.delete()
elif values[i] and not segment:
chain = self.molSystem.findFirstChain(code=codes[i])
residue = chain.findFirstResidue(seqid=seqId0)
if residue: seqId = seqId0
else:
residue = chain.sortedResidues()[0]
seqId = residue.seqId
residue2 = chain.findFirstResidue(
seqid=seqId + self.symmetryOp.segmentLength)
if not residue2:
residue2 = chain.sortedResidues()[-1]
self.symmetryOp.segmentLength = (residue2.seqId -
seqId) + 1
segment = self.symmetryOp.newSegment(chainCode=codes[i],
firstSeqId=seqId)
self.symmetryMatrix.keyPressEscape()
def setSegments(self, obj):
if self.symmetryOp and obj:
segments = self.symmetryOp.sortedSegments()
values = self.setSegmentMulti.get()
for i in range(len(values)):
seqCode = values[i]
chain = self.molSystem.findFirstChain(
code=segments[i].chainCode)
residue = chain.findFirstResidue(seqCode=seqCode)
if residue: seqId = residue.seqId
if segments[i].firstSeqId != seqId:
segments[i].delete()
segments[i] = self.symmetryOp.newSegment(
chainCode=chain.code, firstSeqId=seqId)
self.symmetryMatrix.keyPressEscape()
def selectSymmetry(self, obj, row, col):
self.symmetryOp = obj
def addSymmOp(self):
if self.molSystem:
if not self.symmetrySet:
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet(
)
if not self.symmetrySet:
objGen = self.project.newMolSystemSymmetrySet
self.symmetrySet = objGen(symmetrySetId=1,
molSystem=self.molSystem)
segLen = len(self.molSystem.findFirstChain().residues)
symmetry = self.symmetrySet.newSymmetry(segmentLength=segLen)
def removeSymmOp(self):
if self.symmetryOp: self.symmetryOp.delete()
def toggleSingleMolecule(self, boolean):
self.singleMolecule = not boolean
self.updateMolSystems()
self.updateMolecules()
def setMolecules(self, molecules):
self.molecules = molecules
if self.symmetrySet:
for symmetryOp in self.symmetrySet.symmetries:
for segment in symmetryOp.segments:
chain = self.molSystem.findFirstChain(
code=segment.chainCode)
if chain and (chain.molecule not in molecules):
segment.delete()
def selectMolecule(self, index, name):
self.setMolecules(self.getMolecules()[index])
self.updateSymmetries()
def getMolecules(self):
counts = {}
moleculesList = []
for chain in self.molSystem.chains:
molecule = chain.molecule
counts[molecule] = counts.get(molecule, 0) + 1
molecules = counts.keys()
if self.singleMolecule:
for molecule in counts:
if counts[molecule] > 1: moleculesList.append([
molecule,
])
elif molecules:
molecules = counts.keys()
n = len(molecules)
moleculesList.append([
molecules[0],
])
if n > 1:
moleculesList.append([
molecules[1],
])
moleculesList.append([molecules[0], molecules[1]])
if n > 2:
moleculesList.append([
molecules[2],
])
moleculesList.append([molecules[1], molecules[2]])
moleculesList.append(
[molecules[0], molecules[1], molecules[2]])
if n > 3:
moleculesList.append([
molecules[3],
])
moleculesList.append([molecules[0], molecules[3]])
moleculesList.append([molecules[1], molecules[3]])
moleculesList.append([molecules[2], molecules[3]])
moleculesList.append(
[molecules[0], molecules[1], molecules[3]])
moleculesList.append(
[molecules[0], molecules[2], molecules[3]])
moleculesList.append(
[molecules[1], molecules[2], molecules[3]])
moleculesList.append(
[molecules[0], molecules[1], molecules[2], molecules[3]])
return moleculesList
def updateMolecules(self):
names = []
index = -1
moleculesList = self.getMolecules()
if moleculesList:
if self.molecules not in moleculesList:
self.setMolecules(moleculesList[0])
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet(
)
index = moleculesList.index(self.molecules)
names = []
for molecules in moleculesList:
names.append(','.join([mol.name for mol in molecules]))
else:
self.molecules = []
self.moleculePulldown.setup(names, index)
def selectMolSystem(self, index, name):
self.molSystem = self.getMolSystems()[index]
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet()
self.updateSymmetries()
def getMolSystems(self):
molSystems = []
for molSystem in self.project.sortedMolSystems():
n = len(molSystem.chains)
if self.singleMolecule and (n > 1): molSystems.append(molSystem)
elif n > 0: molSystems.append(molSystem)
return molSystems
def updateMolSystems(self):
names = []
index = -1
molSystems = self.getMolSystems()
if molSystems:
if self.molSystem not in molSystems: self.molSystem = molSystems[0]
index = molSystems.index(self.molSystem)
names = [ms.code for ms in molSystems]
else:
self.molSystem = None
self.molSystemPulldown.setup(names, index)
def updateSymmetriesAfter(self, obj=None):
if self.waiting: return
else:
self.waiting = True
self.after_idle(self.updateSymmetries)
def updateSymmetries(self):
textMatrix = []
objectList = []
if self.symmetrySet:
for symmetryOp in self.symmetrySet.symmetries:
chains = []
segments = []
length = symmetryOp.segmentLength
for segment in symmetryOp.sortedSegments():
code = segment.chainCode
chain = self.molSystem.findFirstChain(code=code)
if chain:
chains.append(code)
seqId = segment.firstSeqId
residue1 = chain.findFirstResidue(seqId=seqId)
residue2 = chain.findFirstResidue(seqId=seqId +
length - 1)
segments.append(
'%s:%d-%d' %
(code, residue1.seqCode, residue2.seqCode))
datum = [
symmetryOp.serial, symmetryOp.symmetryCode, length,
'\n'.join(chains), '\n'.join(segments)
]
objectList.append(symmetryOp)
textMatrix.append(datum)
self.symmetryMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = False
def destroy(self):
self.notify(self.unregisterNotify)
BasePopup.destroy(self)
class ProchiralStatusPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'ProchiralStatus.html')
def __init__(self, parent, chainList, chainAtomSetsDict):
self.chainList = chainList
self.chainAtomSetsDict = chainAtomSetsDict
self.resParentDict = {}
self.resParentList = []
self.resParentChainLabelDict = {}
self.resParentChainLabelList = {}
self.chainResonancesDict = {}
for resParent in self.chainAtomSetsDict.keys():
if isinstance(resParent, NmrConstraint.NmrConstraintStore):
strucGens = resParent.structureGenerations
strucGenSerials = [str(sg.serial) for sg in strucGens]
strucGenLabel = string.join(strucGenSerials, ',')
resParentLabel = "Constraint set %d (strucGens %s)" % (
resParent.serial, strucGenSerials)
else:
resParentLabel = "Nmr project %s" % resParent.name
self.resParentDict[resParentLabel] = resParent
self.resParentList.append(resParentLabel)
self.chainResonancesDict[resParent] = {}
self.resParentChainLabelDict[resParent] = {}
self.resParentChainLabelList[resParent] = []
for chain in self.chainList:
self.project = chain.root
if self.chainAtomSetsDict[resParent].has_key(
chain) and self.chainAtomSetsDict[resParent][chain]:
chainLabel = "Molecular system '%s':Chain '%s' (molecule '%s')" % (
chain.molSystem.code, chain.code, chain.molecule.name)
self.resParentChainLabelList[resParent].append(chainLabel)
self.resParentChainLabelDict[resParent][chainLabel] = chain
self.chainResonancesDict[resParent][chain] = []
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(
self,
parent=parent,
title="Project '%s': " % self.project.name +
'Set status prochiral atoms/resonances',
modal=False,
transient=True)
def body(self, master):
#
# Setup header
#
row = 0
label = Label(master, text='Select the resonance list:')
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text='Select the chain:')
label.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
self.resParentSelect = PulldownMenu(master,
entries=self.resParentList,
callback=self.setupResParentList,
do_initial_callback=False)
self.resParentSelect.grid(row=row, column=0, sticky=Tkinter.EW)
self.chainSelect = PulldownMenu(master,
entries=[],
callback=self.setupProchiralList,
do_initial_callback=False)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=2, sticky=Tkinter.EW)
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row, weight=1)
for i in range(2):
master.grid_columnconfigure(i, weight=1)
self.prochiralListFrame = ScrolledFrame(master,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
self.prochiralListFrameRow = row
self.prochiralListFrameMaster = master
row = row + 1
texts = ['Set all', 'Set chain']
commands = [
self.ok, self.setStereo
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
self.resParentSelect.callback(0, self.resParentList[0])
def setupResParentList(self, listIndex, resParentLabel):
resParent = self.resParentDict[resParentLabel]
self.resParent = resParent
self.chainSelect.setup(self.resParentChainLabelList[self.resParent], 0)
self.chainSelect.callback(
0, self.resParentChainLabelList[self.resParent][0])
def setupProchiralList(self, listIndex, chainLabel):
chain = self.resParentChainLabelDict[self.resParent][chainLabel]
self.chain = chain
self.prochiralListFrame.destroy()
self.prochiralListFrame = ScrolledFrame(self.prochiralListFrameMaster,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=self.prochiralListFrameRow,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
#
# TODO: also handle case one resonance, two atomSets!?!?
#
frameRow = 0
x = y = 0
frame = self.prochiralListFrame.frame
self.resonanceObjects = {}
self.resonanceLabelDict = {}
#
# Reuse previous settings...
#
if len(self.chainResonancesDict[self.resParent][chain]) == len(
self.chainAtomSetsDict[self.resParent][chain]):
usePreviousSettings = True
else:
usePreviousSettings = False
for i in range(0, len(self.chainAtomSetsDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
isStereo = False
hasResonances = False
isValidCase = False
resonances = []
if usePreviousSettings and self.chainResonancesDict[
self.resParent][chain][i]:
resonances = self.chainResonancesDict[
self.resParent][chain][i][3]
isStereo = self.chainResonancesDict[
self.resParent][chain][i][0]
hasResonances = True
isValidCase = True
else:
for atomSet in atomSetGroup:
resonanceSets = atomSet.sortedResonanceSets()
if resonanceSets:
hasResonances = True
for resonanceSet in resonanceSets:
for resonance in resonanceSet.sortedResonances():
if resonance not in resonances:
resonances.append(resonance)
if len(resonanceSets) == 1:
isValidCase = True
if len(resonanceSet.atomSets) == 1:
isStereo = True
else:
# Case only one resonance but stereo assigned
resonances.append(0)
if len(resonances) == 1:
# Case only one resonance, not stereo assigned
resonances.append(None)
#
# Set up only for valid cases
#
if hasResonances and isValidCase:
if not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(
[isStereo, False, False, resonances])
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
rowspan = 2
checkButton = CheckButton(
frame,
selected=isStereo,
callback=lambda status=isStereo, fr=frameRow, item=i, setup
=False: self.toggleResonances(status, fr, item, setup))
checkButton.grid(row=frameRow,
rowspan=rowspan,
column=0,
sticky=Tkinter.EW)
label = Label(frame, text=ccpCode, width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=1,
sticky=Tkinter.E)
label = Label(frame, text=str(seqCode), width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=2,
sticky=Tkinter.W)
#
# Set up the atom names
#
for j in range(0, len(atomSetGroup)):
atomSet = atomSetGroup[j]
label = Label(frame, text=atomSet.name)
label.grid(row=frameRow + j,
column=3,
sticky=Tkinter.E,
ipadx=4)
#
# Set up the resonances
#
self.resonanceObjects[frameRow] = {
True: [[], []],
False: [[], []]
}
resonanceLabelList = []
for resonance in resonances:
if not resonance:
resonanceLabel = 'unknown'
else:
if hasattr(resonance, 'shifts') and resonance.shifts:
shiftLabel = " (shifts: "
for shift in resonance.sortedShifts():
shiftLabel += "%.2f, " % shift.value
shiftLabel = shiftLabel[:-2] + ")"
else:
shiftLabel = ""
resonanceLabel = "'%d.%s'%s" % (
seqCode, resonance.name, shiftLabel)
self.resonanceLabelDict[resonanceLabel] = resonance
resonanceLabelList.append(resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow, column=4, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(separator)
separator = CrossLine(frame,
height=20,
width=30,
canvas_bg=frame['bg'],
color='dimgray')
self.resonanceObjects[frameRow][False][0].append(separator)
resonanceList = PulldownMenu(
frame,
entries=resonanceLabelList,
callback=lambda selInd=x, selItem=y, fr=frameRow, item=i:
self.setProchiralLabels(selInd, selItem, fr, item),
do_initial_callback=False,
label_color='red')
resonanceList.grid(row=frameRow, column=5, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(resonanceList)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[0],
fg='dimgray')
self.resonanceObjects[frameRow][False][0].append(
resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + 1, column=4)
self.resonanceObjects[frameRow][True][1].append(separator)
self.resonanceObjects[frameRow][False][1].append(None)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='red')
resonanceLabel.grid(row=frameRow + 1,
column=5,
sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][1].append(resonanceLabel)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='dimgray')
self.resonanceObjects[frameRow][False][1].append(
resonanceLabel)
if not isStereo:
checkButton.callback(isStereo, setup=True)
separator = Separator(frame, height=1)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + rowspan,
columnspan=6,
sticky=Tkinter.EW)
frameRow += rowspan + 1
elif not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(None)
return True
def setProchiralLabels(self, selInd, selItem, fr, item):
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][False][0][1].set(resonanceLabel)
selInd = not selInd
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][True][1][1].set(resonanceLabel)
self.resonanceObjects[fr][False][1][1].set(resonanceLabel)
self.chainResonancesDict[self.resParent][
self.chain][item][2] = not self.chainResonancesDict[
self.resParent][self.chain][item][2]
self.chainResonancesDict[self.resParent][self.chain][item][3].reverse()
def toggleResonances(self, status, frameRow, item, setup):
if not setup:
self.chainResonancesDict[self.resParent][
self.chain][item][0] = status
self.chainResonancesDict[self.resParent][
self.chain][item][1] = not self.chainResonancesDict[
self.resParent][self.chain][item][1]
for i in range(0, len(self.resonanceObjects[frameRow])):
#
# Remove other widgets from grid
#
rpds = self.resonanceObjects[frameRow][not status][i]
for rpd in rpds:
if rpd:
rpd.grid_forget()
#
# Set current widgets
#
rpds = self.resonanceObjects[frameRow][status][i]
for j in range(0, len(rpds)):
rpd = rpds[j]
if rpd:
keywds = {}
if j == 1:
keywds['sticky'] = Tkinter.W
if j == 0:
if not status:
keywds['rowspan'] = 2
rpd.grid(row=frameRow + i, column=4 + j, **keywds)
def setStereo(self, chain=None):
if not chain:
chain = self.chain
if self.chainResonancesDict[self.resParent][chain]:
for i in range(
0, len(self.chainResonancesDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
(stereoStatus, stereoStatusChanged, resChanged, resonances
) = self.chainResonancesDict[self.resParent][chain][i]
if stereoStatusChanged or (stereoStatus and resChanged):
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
atomText = "%s/%s" % (atomSetGroup[0].name,
atomSetGroup[1].name)
if stereoStatusChanged:
if stereoStatus:
stereoText = "non-stereospecific to stereospecific."
else:
stereoText = "stereospecific to non-stereospecific."
print " Warning: Changed '%s.%d' prochiral resonances for atoms %s from %s" % (
ccpCode, seqCode, atomText, stereoText)
self.chainResonancesDict[
self.resParent][chain][i][1] = False
self.chainResonancesDict[
self.resParent][chain][i][2] = False
if stereoStatus:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[0]:
resonanceSet.removeAtomSet(atomSetGroup[1])
if resonances[1]:
if not resonances[0]:
# Remove right atom set if only one resonance...
resonanceSet.removeAtomSet(atomSetGroup[0])
else:
# Only create a new resonance set if two resonances present!
resonanceSet.removeResonance(resonances[1])
if isinstance(
self.resParent,
NmrConstraint.NmrConstraintStore):
newResonanceSet = self.resParent.newFixedResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
newResonanceSet = self.resParent.newResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
if resonances[0]:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[1]:
atomSetGroup[1].findFirstResonanceSet(
).delete()
resonanceSet.addResonance(resonances[1])
resonanceSet.addAtomSet(atomSetGroup[1])
elif resonances[1]:
resonanceSet = atomSetGroup[1].resonanceSets[0]
resonanceSet.addAtomSet(atomSetGroup[0])
elif stereoStatus and resChanged:
print " Warning: Changed resonance assignment for '%s.%d' stereospecifically assigned atoms %s." % (
ccpCode, seqCode, atomText)
self.chainResonancesDict[
self.resParent][chain][i][2] = False
resonanceSets = []
for i in range(0, 2):
if atomSetGroup[i].resonanceSets:
resonanceSets.append(
atomSetGroup[i].findFirstResonanceSet())
else:
resonanceSets.append(None)
for i in range(0, 2):
resonanceSet = resonanceSets[i]
if resonanceSet:
resonanceSet.addAtomSet(atomSetGroup[not i])
resonanceSet.removeAtomSet(atomSetGroup[i])
def apply(self):
for chain in self.chainList:
self.setStereo(chain=chain)
return True
class EditResStructuresPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.structure = None
self.constraintSet = None
self.cloud = None
self.cloudRmsdDict = {}
self.strucRmsdDict = {}
self.waiting = False
BasePopup.__init__(self,
parent=parent,
title="Resonance Cloud Structures",
**kw)
def body(self, guiFrame):
row = 0
guiFrame.grid_columnconfigure(1, weight=1)
guiFrame.grid_rowconfigure(0, weight=0)
guiFrame.grid_rowconfigure(1, weight=1)
self.generationLabel = Label(guiFrame, text='Structure Generation:')
constraintSets = []
constraintSetNames = []
index = -1
for constraintSet in self.project.nmrConstraintStores:
index += 1
constraintSets.append(constraintSet)
constraintSetNames.append(str(constraintSet.serial))
self.constraintSet = constraintSet
self.constrSetPulldown = PulldownMenu(guiFrame,
self.changeConstraintSet,
constraintSetNames,
selected_index=index,
do_initial_callback=False)
self.generationLabel.grid(row=row, column=0, columnspan=1, sticky='e')
self.constrSetPulldown.grid(row=row,
column=1,
columnspan=1,
sticky='w')
strucLabel = Label(guiFrame, text='Comparison structure')
strucLabel.grid(row=row, column=2, sticky='e')
self.strucPulldown = PulldownMenu(guiFrame,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=False)
self.strucPulldown.grid(row=row, column=3, sticky='w')
sdTolLabel = Label(guiFrame, text='Tolerance (SDs):')
sdTolLabel.grid(row=row, column=4, sticky='e')
self.sdToleranceEntry = FloatEntry(guiFrame, text=2.0, width=6)
self.sdToleranceEntry.grid(row=row, column=5, stick='w')
row += 1
colHeadings = ['#', 'File name', 'RMSD to mean', 'RMSD to structure']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
initialRows=10,
headingList=colHeadings,
callback=self.selectCell,
objectList=[],
textMatrix=[
[],
])
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=6,
sticky='nsew')
row += 1
texts = [
'Calc\nRMSD', 'Make Cloud\nfrom structure', 'Delete', 'Delete\nbad'
]
commands = [
self.calcRmsd, self.makeStrucCloud, self.deleteCloud,
self.filterClouds
]
self.bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
expands=False,
commands=commands,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, columnspan=6, sticky='nsew')
self.update()
for func in ('__init__', 'delete'):
self.registerNotify(self.updateStructureGen,
'ccp.nmr.Nmr.StructureGeneration', func)
def open(self):
self.updateAfter()
BasePopup.open(self)
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.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
structures.append(structure)
self.structure = structures[index - 1]
def filterClouds(self):
if self.constraintSet:
sdTolerance = self.sdToleranceEntry.get() or 2.0
keptClouds = []
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
meanGroupRmsds = []
for cloud in clouds:
rmsd = self.cloudRmsdDict.get(cloud)
if rmsd is not None:
meanGroupRmsds.append(rmsd)
meanRmsd = 0.0
N = 0
for rmsd in meanGroupRmsds:
meanRmsd += rmsd
N += 1
if N > 0:
meanRmsd /= float(N)
sd = 0.0
for rmsd in meanGroupRmsds:
sd += (rmsd - meanRmsd) * (rmsd - meanRmsd)
if N > 0:
sd /= float(N - 1)
sd = sqrt(sd)
print meanRmsd, '+/-', sd
n = 0
for cloud in clouds:
rmsd = self.cloudRmsdDict.get(cloud)
if rmsd is None:
keptClouds.append(cloud)
elif abs(rmsd - meanRmsd) > (sdTolerance * sd):
print 'Cloud %s is bad' % (cloud)
else:
keptClouds.append(cloud)
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=keptClouds)
self.updateAfter()
def makeStrucCloud(self):
if self.structure:
serials = self.guiParent.application.getValues(
self.constraintSet, 'cloudsResonances')
pdbFileName = 'CloudForStructure.pdb'
#from ccpnmr.clouds.AtomCoordList import AtomCoordList
from ccpnmr.c.AtomCoordList import AtomCoordList
atomCoordList = AtomCoordList()
resDict = {}
hmass = 25
print "L1", len(serials)
for resonance in self.nmrProject.resonances:
resDict[resonance.serial] = resonance
print "L2", len(resDict)
resonances = []
for serial in serials:
if resDict.get(serial) is not None:
resonances.append(resDict[serial])
print "L3", len(resonances)
C = 0
for resonance in resonances:
resonanceSet = resonance.resonanceSet
if resonanceSet:
i = resonanceSet.sortedResonances().index(resonance)
atomSet = resonance.resonanceSet.sortedAtomSets()[i]
coords = getAtomSetCoords(atomSet, self.structure)
coord = coords[0]
atomCoordList.add(hmass, coord.x, coord.y, coord.z)
C += 1
print "L4", len(atomCoordList)
from ccpnmr.clouds.FilterClouds import writeTypedPdbCloud
writeTypedPdbCloud(atomCoordList, pdbFileName, resonances)
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
clouds.append(pdbFileName)
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=clouds)
self.updateAfter()
def calcRmsd(self):
if self.constraintSet:
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
from ccpnmr.clouds.FilterClouds import filterClouds
rmsds = filterClouds(clouds)
n = len(clouds)
for i in range(n):
cloud = clouds[i]
rmsd = rmsds[i]
self.cloudRmsdDict[cloud] = rmsd
self.updateAfter()
def changeConstraintSet(self, i, name):
project = self.project
if project.nmrConstraintStores:
constraintSet = project.nmrConstraintStores[i]
else:
constraintSet = None
if constraintSet is not self.constraintSet:
self.constraintSet = constraintSet
self.cloud = None
self.updateAfter()
def deleteCloud(self):
if self.constraintSet and self.cloud and showOkCancel(
'Confirm', 'Really delete resonance cloud?', parent=self):
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
if clouds:
clouds.remove(self.cloud)
self.cloud = None
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=clouds)
self.updateAfter()
def selectCell(self, cloud, row, col):
self.cloud = cloud
self.bottomButtons.buttons[1].enable()
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def getConstraintSetNames(self):
names = []
constraintSets = self.project.nmrConstraintStores
for set in constraintSets:
names.append('%d' % set.serial)
return names
def updateStructureGen(self, *opt):
project = self.project
constraintSets = self.project.sortedNmrConstraintStores
if constraintSets:
constraintSetNames = self.getConstraintSetNames()
# set defaults
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
self.cloud = None
i = constraintSets.index(self.constraintSet)
self.constrSetPulldown.setup(constraintSetNames, i)
else:
self.constraintSet = None
self.cloud = None
self.constrSetPulldown.setup([], -1)
def destroy(self):
for func in ('__init__', 'delete'):
self.unregisterNotify(self.updateStructureGen,
'ccp.nmr.Nmr.StructureGeneration', func)
BasePopup.destroy(self)
def update(self):
objectList = []
textMatrix = []
if self.constraintSet:
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
if clouds:
objectList = list(clouds)
i = 0
for cloud in objectList:
i += 1
datum = []
datum.append(i)
datum.append(cloud)
datum.append(self.cloudRmsdDict.get(cloud) or '-')
datum.append(self.strucRmsdDict.get(cloud) or '-')
textMatrix.append(datum)
if not self.cloud:
self.bottomButtons.buttons[1].disable()
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = False
class PredictKarplusPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.waiting = False
self.molSystem = None
self.residue = None
self.jCouplings = []
self.atomNames = []
self.measureJCouplingList = None
self.predictJCouplingList = None
self.coeffAtomNames = []
self.coefficients = {}
self.coefficient = None
for i in range(3):
self.coefficients[i] = {}
BasePopup.__init__(
self,
parent=parent,
title='Predict Karplus Coefficients from J Coupling',
**kw)
self.updateJCouplingLists()
self.updateMolSystems()
self.updateAfter()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1, minsize=500)
row = 0
frame = LabelFrame(guiFrame, text='General Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(1, weight=1)
label = Label(frame, text='Molecular System:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
self.changeMolSystem,
do_initial_callback=False)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Measured J coupling list:')
label.grid(row=0, column=2, sticky='w')
self.measureCouplingListPulldown = PulldownMenu(
frame, self.changeMeasureCouplingList)
self.measureCouplingListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Predicted J coupling list:')
label.grid(row=0, column=4, sticky='w')
self.predictCouplingListPulldown = PulldownMenu(
frame, self.changePredictCouplingList)
self.predictCouplingListPulldown.grid(row=0, column=5, sticky='w')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Angles & 3J Couplings')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Residue', 'Phi', 'Chi^2']
editWidgets = [None, None, None]
editGetCallbacks = [None, None, None]
editSetCallbacks = [None, None, None]
self.jCouplingEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setJCoupling())
i = 0
for names in couplingAtoms:
headingList.extend(
['Pred\nJ(%s,%s)' % names,
'Expt\nJ(%s,%s)' % names])
editWidgets.extend([None, self.jCouplingEntry])
editGetCallbacks.extend(
[None, lambda obj, i=i: self.getJCoupling(obj, i)])
editSetCallbacks.extend(
[None, lambda event, i=i: self.setJCoupling(i)])
i += 1
self.couplingMatrix = ScrolledMatrix(frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectJCoupling,
multiSelect=False)
self.couplingMatrix.grid(row=0, column=0, sticky='nsew')
self.couplingMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
row += 1
frame = LabelFrame(guiFrame, text='Karplus Coefficients')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Phase']
editWidgets = [
None,
]
editGetCallbacks = [
None,
]
editSetCallbacks = [
None,
]
self.coefficientEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setCoefficient())
for names in couplingAtoms:
headingList.append('J(%s,%s)' % names)
editWidgets.append(self.coefficientEntry)
editGetCallbacks.append(
lambda obj, n=names: self.getCoefficient(obj, n))
editSetCallbacks.append(
lambda event, n=names: self.setCoefficient(n))
headingList = [
'Phase', 'J(H,HA)', 'J(H,C)', 'J(H,CB)', 'J(C,HA)', 'J(C,C)',
'J(C,CB)'
]
self.coefficientMatrix = ScrolledMatrix(
frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectCoefficient,
maxRows=3,
multiSelect=False)
self.coefficientMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = []
commands = []
self.bottomButtons = UtilityButtonList(guiFrame,
commands=commands,
texts=texts,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, sticky='ew')
for func in ('__init__', 'delete', 'setValue', 'setError'):
for clazz in ('ccp.nmr.Nmr.JCoupling', ):
self.registerNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.JCouplingList', ):
self.registerNotify(self.updateJCouplingLists, clazz, func)
def getJCouplingLists(self, isSimulated=False):
jCouplingLists = self.nmrProject.findAllMeasurementLists(
className='JCouplingList', isSimulated=isSimulated)
return jCouplingLists
def updateJCouplingLists(self, *obj):
jCouplingLists = self.getJCouplingLists(isSimulated=False)
names = [
'%d:%s' % (jcl.serial, jcl.name or '') for jcl in jCouplingLists
]
names.append('<New>')
index = -1
if jCouplingLists:
if self.measureJCouplingList in jCouplingLists:
index = jCouplingLists.index(self.measureJCouplingList)
else:
self.measureJCouplingList = jCouplingLists[0]
index = 0
else:
self.measureJCouplingList = None
self.measureCouplingListPulldown.setup(names, index)
jCouplingLists = self.getJCouplingLists(isSimulated=True)
names = ['%d:%s' % (jcl.serial, jcl.name) for jcl in jCouplingLists]
names.append('<New>')
index = -1
if jCouplingLists:
if self.predictJCouplingList in jCouplingLists:
index = jCouplingLists.index(self.predictJCouplingList)
else:
self.predictJCouplingList = jCouplingLists[0]
index = 0
else:
self.predictJCouplingList = None
self.predictCouplingListPulldown.setup(names, index)
def changeMeasureCouplingList(self, index, name):
if name == '<New>':
self.measureJCouplingList = None
else:
jCouplingLists = self.getJCouplingLists()
jCouplingList = jCouplingLists[index]
if jCouplingList is not self.measureJCouplingList:
self.measureJCouplingList = jCouplingList
if self.predictJCouplingList is self.measureJCouplingList:
for jCouplingList2 in jCouplingLists:
if self.measureJCouplingList is not jCouplingList2:
self.predictJCouplingList = jCouplingList2
break
else:
self.predictJCouplingList = None
self.updateAfter()
def changePredictCouplingList(self, index, name):
if name == '<New>':
self.predictJCouplingList = None
self.updateAfter()
else:
jCouplingLists = self.getJCouplingLists()
jCouplingList = jCouplingLists[index]
if jCouplingList is not self.predictJCouplingList:
self.predictJCouplingList = jCouplingList
if self.predictJCouplingList is self.measureJCouplingList:
for jCouplingList2 in jCouplingLists:
if self.predictJCouplingList is not jCouplingList2:
self.measureJCouplingList = jCouplingList2
break
else:
self.measureJCouplingList = None
self.updateAfter()
def doEditMarkExtraRules(self, obj, row, col):
i = (col - 3) / 2
if i > -1:
atoms = couplingAtoms[i]
residue = obj[0]
for atomName in atoms:
if not residue.findFirstAtom(name=atomName):
return False
return True
def open(self):
self.updateMolSystems()
BasePopup.open(self)
def selectJCoupling(self, object, row, col):
self.residue = object[0]
self.jCouplings = object[1:]
def selectCoefficient(self, object, row, col):
self.coefficient = object
def getCoefficient(self, object, atomNames):
self.coeffAtomNames = atomNames
coefficient = self.coefficients[object].get(atomNames)
self.coefficientEntry.set(coefficient)
def setCoefficient(self, atomNames=None):
if not atomNames:
atomNames = self.coeffAtomNames
value = self.coefficientEntry.get()
if atomNames and (self.coefficient is not None):
self.coefficients[self.coefficient][atomNames] = value
#print self.coefficient, atomNames, value
self.updateCoefficients()
def getJCoupling(self, object, index):
atomNames = couplingAtoms[index]
self.atomNames = atomNames
coupling = object[index + 1]
if not coupling:
residue = object[0]
coupling = self.getResidueJCoupling(self.measureJCouplingList,
residue, atomNames)
if coupling:
value = coupling.value
else:
value = None
self.jCouplingEntry.set(value)
def setJCoupling(self, index=None):
if not index:
atomNames = self.atomNames
index = couplingAtoms.index(atomNames)
else:
atomNames = couplingAtoms[index]
value = self.jCouplingEntry.get()
if self.residue and atomNames:
coupling = self.jCouplings[index]
if value is None:
if coupling:
if showOkCancel('Confirm',
'Really remove J coupling?',
parent=self):
coupling.delete()
else:
if not coupling:
self.setResidueJCoupling(self.measureJCouplingList,
self.residue,
atomNames,
value,
isSimulated=False)
else:
coupling.setValue(value)
def getResidueJCoupling(self, jCouplingList, residue, atomNames):
if jCouplingList:
return getResidueJCoupling(jCouplingList, residue, atomNames)
def setResidueJCoupling(self,
jCouplingList,
residue,
atomNames,
value,
isSimulated=False):
if jCouplingList is None:
jCouplingList = self.nmrProject.newJCouplingList(
isSimulated=isSimulated)
if isSimulated:
self.predictJCouplingList = jCouplingList
else:
self.measureJCouplingList = jCouplingList
setResidueJCoupling(jCouplingList, self.residue, atomNames, value)
def updateMolSystems(self, *obj):
index = -1
names = []
molSystems = self.project.sortedMolSystems()
if molSystems:
if self.molSystem not in molSystems:
self.molSystem = molSystems[0]
names = [ms.code for ms in molSystems]
index = molSystems.index(self.molSystem)
self.molSystemPulldown.setup(names, index)
def changeMolSystem(self, index, name):
molSystems = self.project.sortedMolSystems()
if molSystems:
molSystem = molSystems[index]
else:
molSystem = None
if molSystem is not self.molSystem:
self.molSystem = molSystem
self.updateAfter()
def updateAfter(self, object=None):
current = False
if object and (object.className == 'JCoupling'):
for resonance in object.resonances:
resonanceSet = resonance.resonanceSet
if resonanceSet:
molSystem = resonanceSet.findFirstAtomSet().findFirstAtom(
).topObject
if molSystem is self.molSystem:
current = True
break
else:
current = True
if self.waiting or (not current):
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self):
textMatrix = []
objectList = []
if self.molSystem:
chains = self.molSystem.sortedChains()
if len(chains) > 1:
doChains = False
else:
doChains = True
for chain in chains:
if doChains:
chainCode = chain.code
else:
chainCode = ''
for residue in chain.sortedResidues():
name = '%s%d%s' % (chainCode, residue.seqCode,
getResidueCode(residue))
phi = 0.0
chiSq = 0.0
datum = [name, phi, chiSq]
object = [
residue,
]
for atomNames in couplingAtoms:
couplingM = self.getResidueJCoupling(
self.measureJCouplingList, residue, atomNames)
couplingP = self.getResidueJCoupling(
self.predictJCouplingList, residue, atomNames)
pred = None
expt = None
if couplingM:
expt = couplingM.value
if couplingP:
pred = couplingP.value
datum.append(pred)
datum.append(expt)
object.append(couplingM)
objectList.append(object)
textMatrix.append(datum)
self.couplingMatrix.update(textMatrix=textMatrix,
objectList=objectList)
self.updateCoefficients()
self.waiting = False
def updateCoefficients(self):
textMatrix = []
objectList = []
for i in range(3):
name = 'C%d' % i
datum = [
name,
]
for atomNames in couplingAtoms:
datum.append(self.coefficients[i].get(atomNames))
textMatrix.append(datum)
objectList.append(i)
self.coefficientMatrix.update(textMatrix=textMatrix,
objectList=objectList)
def destroy(self):
for func in ('__init__', 'delete', 'setValue', 'setError'):
for clazz in ('ccp.nmr.Nmr.JCoupling', ):
self.unregisterNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.JCouplingList', ):
self.unregisterNotify(self.updateJCouplingLists, clazz, func)
BasePopup.destroy(self)
class BacusPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.project = parent.project
self.hNoesy = None
self.nNoesy = None
self.cNoesy = None
self.shiftList = None
BasePopup.__init__(self, parent, title="BACUS control module", **kw)
def body(self, guiParent):
guiParent.grid_columnconfigure(0, weight=1)
row = 0
guiParent.grid_rowconfigure(row, weight=1)
inputFrame = LabelFrame(guiParent, text='Inputs:')
inputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
label = Label(inputFrame, text='NOESY:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.hNoesyPulldown = PulldownMenu(inputFrame,callback=self.setHNoesy)
self.hNoesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='15N NOESY:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.nNoesyPulldown = PulldownMenu(inputFrame,callback=self.setNNoesy)
self.nNoesyPulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='13C NOESY:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.cNoesyPulldown = PulldownMenu(inputFrame,callback=self.setCNoesy)
self.cNoesyPulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='Shift List:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.shiftListPulldown = PulldownMenu(inputFrame,callback=self.setShiftList)
self.shiftListPulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='2d BACUS executable:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.executableEntry = Entry(inputFrame, text='/home/tjs23/clouds/justin/SpiBacusMidge/bacus/bacus_tjs.exe')
self.executableEntry.grid(row=4, column=1, sticky=Tkinter.NW)
self.executableButton = Button(inputFrame, text='Choose file', command=self.chooseExecutable)
self.executableButton.grid(row=5, column=1, sticky=Tkinter.EW)
row += 1
outputFrame = LabelFrame(guiParent, text='Output:')
outputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
row += 1
texts = ['Run BACUS 2d','Run BACUS 3d']
commands = [self.runBacus,self.runBacus3d]
self.bottomButtons = createDismissHelpButtonList(guiParent,texts=texts,commands=commands,expands=0,help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
def chooseExecutable(self):
fileTypes = [FileType('Table', ['*.exe']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types = fileTypes,
title = 'Choose 2d BACUS executable', dismiss_text = 'Cancel',
selected_file_must_exist = False)
fileName = fileSelectPopup.getFile()
if fileName:
self.executableEntry.set(fileName)
def update(self):
# set defaults via pulldown callbacks
names = [self.getPeakListlabel(x) for x in self.gethNoesys()]
if names:
self.hNoesyPulldown.setup(names,0)
else:
self.hNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getNNoesys()]
if names:
self.nNoesyPulldown.setup(names,0)
else:
self.nNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getCNoesys()]
if names:
self.cNoesyPulldown.setup(names,0)
else:
self.cNoesyPulldown.setup([],-1)
names = ['Shift List %d' % x.serial for x in self.getShiftLists()]
if names:
self.shiftListPulldown.setup(names,0)
else:
self.shiftListPulldown.setup([],-1)
self.updateButtons()
def updateButtons(self):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
self.bottomButtons.buttons[1].enable()
else:
self.bottomButtons.buttons[1].disable()
if self.hNoesy and self.executableEntry.get() and self.shiftList:
self.bottomButtons.buttons[0].enable()
else:
self.bottomButtons.buttons[0].disable()
def runBacus3d(self, fileRoot='CCPN1'):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
run3dBacus(fileRoot,self.shiftList,self.cNoesy,self.nNoesy)
def runBacus(self, fileRoot='CCPN1'):
executable = self.executableEntry.get()
if self.hNoesy and self.shiftList and executable:
run2dBacus(fileRoot, executable, self.hNoesy, self.shiftList)
def getPeakListlabel(self, peakList):
return '%s:%s:%d' % (peakList.dataSource.experiment.name, peakList.dataSource.name, peakList.serial)
def getShiftLists(self):
shiftLists = []
if self.project:
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
return list(shiftLists)
def setShiftList(self, index, name=None):
shiftLists = self.getShiftLists()
if shiftLists:
self.shiftList = shiftLists[index]
else:
self.shiftList = None
def gethNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
if isotopes == ['1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getNNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['15N', '1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getCNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['13C', '1H', '1H']:
for peakList in spectrum.peakLists:
if 'NOE' in experiment.name.upper():
peakLists.insert(0, peakList)
else:
peakLists.append(peakList)
return peakLists
def setHNoesy(self, index, name=None):
peakLists = self.gethNoesys()
if peakLists:
self.hNoesy = peakLists[index]
else:
self.hNoesy = None
def setNNoesy(self, index, name=None):
peakLists = self.getNNoesys()
if peakLists:
self.nNoesy = peakLists[index]
else:
self.nNoesy = None
def setCNoesy(self, index, name=None):
peakLists = self.getCNoesys()
if peakLists:
self.cNoesy = peakLists[index]
else:
self.cNoesy = None
def destroy(self):
BasePopup.destroy(self)
class HcloudsMdPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.constraintSet = None
self.constrLists = [None] * 4
self.numClouds = 100
self.filePrefix = 't_intra_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
# 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="Hydrogen Cloud Molecular Dynamics",
**kw)
def body(self, guiFrame):
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
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Input constraints')
frame.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame.grid_columnconfigure(2, weight=1)
srow = 0
label = Label(frame, text='Constraint set:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.constraintSetPulldown = PulldownMenu(
frame,
callback=self.changeConstraintSet,
selected_index=0,
do_initial_callback=0)
self.constraintSetPulldown.grid(row=srow, column=1, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 1:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance1Pulldown = PulldownMenu(
frame,
callback=self.changeDistance1ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance1Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr1Label = Label(frame, text='Constraints: 0')
self.numConstr1Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 2:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance2Pulldown = PulldownMenu(
frame,
callback=self.changeDistance2ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance2Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr2Label = Label(frame, text='Constraints: 0')
self.numConstr2Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 3:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance3Pulldown = PulldownMenu(
frame,
callback=self.changeDistance3ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance3Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr3Label = Label(frame, text='Constraints: 0')
self.numConstr3Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 4:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance4Pulldown = PulldownMenu(
frame,
callback=self.changeDistance4ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance4Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr4Label = Label(frame, text='Constraints: 0')
self.numConstr4Label.grid(row=srow, column=2, sticky=Tkinter.W)
row += 1
frame0 = LabelFrame(guiFrame, text='Cooling scheme')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
frame0.grid_rowconfigure(f0row, weight=1)
colHeadings = [
'Step', 'Initial\nTemp.', 'Final\nTemp.', 'Cooling\nSteps',
'MD Steps', 'MD Tau', 'Rep.\nScale'
]
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(
frame0,
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=f0row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f0row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame0,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = LabelFrame(guiFrame, text='Dynamics control')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(1, weight=1)
f1row = 0
label20 = Label(frame1, text='Number of clouds:')
label20.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = IntEntry(frame1,
text=1,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f1row, column=1, sticky=Tkinter.NW)
label21 = Label(frame1, text='Cloud file prefix:')
label21.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame1,
text='t_intra_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame1,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f1row,
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.update()
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.registerNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.registerNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
def getContraintSetNames(self):
names = []
constraintSets = self.project.currentNmrProject.nmrConstraintStores
for set in constraintSets:
names.append('%d' % set.serial)
return names
def changeConstraintSet(self, i, name):
project = self.project
if project.currentNmrProject.nmrConstraintStores:
constraintSet = project.currentNmrProject.sortedNmrConstraintStores(
)[i]
else:
constraintSet = None
if constraintSet is not self.constraintSet:
self.constraintSet = constraintSet
self.updateConstraintLists()
self.update()
def updateConstraintLists(self, *opt):
constrListData = self.getConstraintLists()
constrListNames = [x[0] for x in constrListData]
constraintLists = [x[1] for x in constrListData]
# copes with self.constraintSet being None
if constrListNames:
i = 0
for constraintList in self.constrLists:
if constraintList not in constraintLists:
if i == 0:
self.constrLists[i] = constraintLists[0]
else:
self.constrLists[i] = None
i += 1
constraintLists.append(None)
constrListNames.append('<None>')
self.distance1Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[0]))
self.distance2Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[1]))
self.distance3Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[2]))
self.distance4Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[3]))
else:
self.constrLists = [None] * 4
self.distance1Pulldown.setup([], -1)
self.distance2Pulldown.setup([], -1)
self.distance3Pulldown.setup([], -1)
self.distance4Pulldown.setup([], -1)
def updateConstraintSets(self, *opt):
project = self.project
constraintSets = list(project.currentNmrProject.nmrConstraintStores)
if constraintSets:
constraintSetNames = self.getContraintSetNames()
# set defaults
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
if self.constraintSet:
j = 0
for constraintList in self.constrLists:
if constraintList and (constraintList.nmrConstraintStore
is not self.constraintSet):
if self.constraintSet.constraintLists and j == 0:
self.constrLists[
j] = self.constraintSet.constraintLists[0]
else:
self.constrLists[j] = None
j += 1
else:
self.constrLists = [None] * 4
i = constraintSets.index(self.constraintSet)
self.constraintSetPulldown.setup(constraintSetNames, i)
else:
self.constraintSet = None
self.constrLists = [None] * 4
self.constraintSetPulldown.setup([], -1)
def getConstraintListName(self, constraintList):
if constraintList.name:
listName = ':%s' % (constraintList.name)
else:
listName = ''
name = '%d:%d:%s%s' % (constraintList.nmrConstraintStore.serial,
constraintList.serial,
constraintList.className[:-14], listName)
return name
def getConstraintLists(self):
constraintLists = []
if self.constraintSet:
for constraintList in self.constraintSet.constraintLists:
if constraintList.className == 'DistanceConstraintList':
name = self.getConstraintListName(constraintList)
constraintLists.append([name, constraintList])
return constraintLists
def changeDistance1ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 0)
def changeDistance2ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 1)
def changeDistance3ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 2)
def changeDistance4ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 3)
def changeDistanceConstraintList(self, i, name, listNum):
project = self.project
constraintLists = self.getConstraintLists()
if constraintLists and (i < 4):
self.constrLists[listNum] = constraintLists[i][1]
else:
self.constrLists[listNum] = None
self.update()
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if ((self.constrLists != [None] * 4) and (self.numClouds > 0)
and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
constraints = []
constraintStore = None
for dcl in self.constrLists:
if dcl:
constraintStore = dcl.nmrConstraintStore
constraints.extend(list(dcl.constraints))
resonances = []
for constraint in constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if fixedResonance.resonanceSerial is None:
resonance = newResonance(
self.guiParent.project,
isotopeCode=fixedResonance.isotopeCode)
resonance.setName(fixedResonance.name)
fixedResonance.setResonanceSerial(resonance.serial)
resDict[resonance.serial] = resonance
if fixedResonance.resonanceSet:
atomSets = list(
fixedResonance.resonanceSet.atomSets)
assignAtomsToRes(atomSets, resonance)
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
resonances, intraConstraintList = self.makeIntraConstraints(
resonances, constraintStore)
constraints.extend(list(intraConstraintList.constraints))
resonances, interConstraintList = self.makeInterConstraints(
resonances, constraintStore)
constraints.extend(list(interConstraintList.constraints))
startMdProcess(self.numClouds, constraints, 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(constraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(constraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def makeInterConstraints(self, resonances, constraintSet):
from ccpnmr.analysis.core.ConstraintBasic import getFixedResonance
from ccpnmr.analysis.core.AssignmentBasic import findConnectedSpinSystem
project = constraintSet.root
constraintList = constraintSet.newDistanceConstraintList()
constraintList.name = 'Seq connections'
resDict = {}
spinSystemDict = {}
for resonance in resonances:
resDict[resonance] = True
spinSystem = resonance.resonanceGroup
if spinSystem:
spinSystemDict[spinSystem] = None
spinSystems = spinSystemDict.keys()
for spinSystem in spinSystems:
nextSpinSystem = findConnectedSpinSystem(spinSystem, delta=1)
if nextSpinSystem:
ca = spinSystem.newAtoms.get('CA')
c = spinSystem.newAtoms.get('C')
n = nextSpinSystem.newAtoms.get('N')
if ca and c and n:
if resDict.get(ca) is None:
resonances.append(ca)
if resDict.get(c) is None:
resonances.append(c)
if resDict.get(n) is None:
resonances.append(n)
c_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.32,
upperLimit=1.35,
lowerLimit=1.29,
error=0.06)
# below based on angle constraints
ca_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=2.415,
upperLimit=2.513,
lowerLimit=2.316,
error=0.197)
frCa = getFixedResonance(constraintSet, ca)
frC = getFixedResonance(constraintSet, c)
frN = getFixedResonance(constraintSet, n)
item = ca_n.newDistanceConstraintItem(
resonances=[frCa, frN])
item = c_n.newDistanceConstraintItem(resonances=[frC, frN])
return resonances, constraintList
def makeIntraConstraints(self, resonances, constraintSet):
from ccpnmr.analysis.core.ConstraintBasic import getFixedResonance
project = constraintSet.root
constraintList = constraintSet.newDistanceConstraintList()
constraintList.name = 'Backbone intra'
dict = {}
for resonance in resonances:
if resonance.resonanceGroup and resonance.assignNames:
dict[resonance] = 1
resonance.resonanceGroup.newAtoms = {}
for resonance in dict.keys():
ss = resonance.resonanceGroup
if resonance.assignNames[0] == 'H':
for resonance2 in ss.resonances:
if dict.get(resonance2
) and resonance2.assignNames[0][:2] == 'HA':
ca = ss.newAtoms.get('CA')
if ca is None:
ca = project.newResonance(isotopeCode='13C',
assignNames=[
'CA',
])
resonances.append(ca)
c = ss.newAtoms.get('C')
if c is None:
c = project.newResonance(isotopeCode='13C',
assignNames=[
'C',
])
resonances.append(c)
n = ss.newAtoms.get('N')
if n is None:
n = project.newResonance(isotopeCode='15N',
assignNames=[
'N',
])
resonances.append(n)
ss.newAtoms['C'] = c
ss.newAtoms['CA'] = ca
ss.newAtoms['N'] = n
frCa = getFixedResonance(constraintSet, ca)
frC = getFixedResonance(constraintSet, c)
frN = getFixedResonance(constraintSet, n)
frH = getFixedResonance(constraintSet, resonance)
frha = getFixedResonance(constraintSet, resonance2)
h_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.01,
upperLimit=1.1,
lowerLimit=0.9,
error=0.2)
n_ca = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.465,
upperLimit=1.50,
lowerLimit=1.43,
error=0.07)
ca_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.525,
upperLimit=1.55,
lowerLimit=1.50,
error=0.05)
# below based on angle constraints
n_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=2.464,
upperLimit=2.572,
lowerLimit=2.356,
error=0.216)
item = h_n.newDistanceConstraintItem(
resonances=[frH, frN])
item = n_ca.newDistanceConstraintItem(
resonances=[frN, frCa])
item = ca_c.newDistanceConstraintItem(
resonances=[frCa, frC])
item = n_c.newDistanceConstraintItem(
resonances=[frN, frC])
if ss.newAtoms.get('CAHA') is None:
ca_ha = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
item = ca_ha.newDistanceConstraintItem(
resonances=[frC, frha])
ss.newAtoms['CAHA'] = 1
if resonance.assignNames[0][:2] == 'HA':
for resonance2 in ss.resonances:
if dict.get(resonance2
) and resonance2.assignNames[0][:2] == 'HB':
ca = ss.newAtoms.get('CA')
if ca is None:
ca = project.newResonance(isotopeCode='13C',
assignNames=[
'CA',
])
resonances.append(ca)
cb = ss.newAtoms.get('CB')
if cb is None:
cb = project.newResonance(isotopeCode='13C',
assignNames=[
'CB',
])
resonances.append(cb)
ss.newAtoms['CA'] = cb
ss.newAtoms['CB'] = ca
ss.newAtoms['CAHA'] = 1
frCA = getFixedResonance(constraintSet, ca)
frCB = getFixedResonance(constraintSet, cb)
frHA = getFixedResonance(constraintSet, resonance)
frHB = getFixedResonance(constraintSet, resonance2)
c_b = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
c_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.53,
upperLimit=1.56,
lowerLimit=1.51,
error=0.05)
item = c_b.newDistanceConstraintItem(
resonances=[frCB, frHB])
item = c_c.newDistanceConstraintItem(
resonances=[frCA, frCB])
if ss.newAtoms.get('CAHA') is None:
c_a = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
item = c_a.newDistanceConstraintItem(
resonances=[frCA, frHA])
ss.newAtoms['CAHA'] = 1
return resonances, constraintList
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 update(self):
self.updateConstraintSets()
self.updateConstraintLists()
if (self.constrLists != [None] * 4) and self.coolingScheme:
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
if self.constrLists[0]:
self.numConstr1Label.set('Constraints: ' +
str(len(self.constrLists[0].constraints)))
else:
self.numConstr1Label.set('Constraints: 0')
if self.constrLists[1]:
self.numConstr2Label.set('Constraints: ' +
str(len(self.constrLists[1].constraints)))
else:
self.numConstr2Label.set('Constraints: 0')
if self.constrLists[2]:
self.numConstr3Label.set('Constraints: ' +
str(len(self.constrLists[2].constraints)))
else:
self.numConstr3Label.set('Constraints: 0')
if self.constrLists[3]:
self.numConstr4Label.set('Constraints: ' +
str(len(self.constrLists[3].constraints)))
else:
self.numConstr4Label.set('Constraints: 0')
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 destroy(self):
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.unregisterNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.unregisterNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
BasePopup.destroy(self)
