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)
def body(self, master):
self.geometry('600x400')
columnspan = 5
row = 0
label = Label(master, text="AutoAssign project file setup window.")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.W)
#
# Set up the spectra
#
row += 1
label = Label(master, text="Spectrum type")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
label = Label(master, text="CCPN peak list")
label.grid(row=row, column=2, columnspan=2, sticky=Tkinter.W)
label = Label(master, text="Phase") # TODO What's this?
label.grid(row=row, column=4, sticky=Tkinter.W)
self.spectrumSelectWidget = {}
self.spectrumPhaseWidget = {}
for i in range(len(self.autoAssignProjectFile.defaultSpectra)):
row += 1
specType = self.autoAssignProjectFile.defaultSpectra[i][0]
if i == 0:
labelText = "%s (root)" % specType
else:
labelText = "%s" % specType
label = Label(master, text=labelText)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
self.spectrumSelectWidget[specType] = PulldownMenu(
master, entries=self.peakNameList)
self.spectrumSelectWidget[specType].grid(row=row,
column=2,
columnspan=2,
sticky=Tkinter.W)
self.spectrumPhaseWidget[specType] = Entry(master,
text="",
width=4)
self.spectrumPhaseWidget[specType].grid(row=row,
column=4,
sticky=Tkinter.W)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Set up the tolerances
#
row += 1
label = Label(master, text="Atom tolerances")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
toleranceAtoms = self.autoAssignProjectFile.toleranceAtoms
toleranceDefault = self.autoAssignProjectFile.toleranceDefault
self.toleranceWidget = {}
for i in range(0, len(toleranceAtoms), 2):
row += 1
for j in range(2):
curPos = i + j
if curPos == len(toleranceAtoms):
break
toleranceAtom = toleranceAtoms[curPos]
label = Label(master, text=toleranceAtom)
label.grid(row=row, column=2 * j, sticky=Tkinter.E)
self.toleranceWidget[toleranceAtom] = Entry(
master, text=str(toleranceDefault[curPos]), width=6)
self.toleranceWidget[toleranceAtom].grid(row=row,
column=1 + 2 * j,
sticky=Tkinter.W)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
row += 1
label = Label(
master,
text="Will save the peak files in the project file directory.",
fg='red')
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
texts = ['OK']
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=columnspan, column=0)
class HelpFrame(Frame):
def __init__(self,
parent,
width=70,
height=20,
xscroll=False,
yscroll=True,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
row = 0
texts = ('back', 'forward', 'load')
commands = (self.prevUrl, self.nextUrl, self.loadUrl)
self.buttons = ButtonList(self, texts=texts, commands=commands)
self.buttons.grid(row=row, column=0)
self.url_entry = Entry(self, returnCallback=self.loadUrl)
self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.createFindFrame(frame)
row = row + 1
self.grid_rowconfigure(row, weight=1)
self.help_text = ScrolledHtml(self,
width=width,
height=height,
xscroll=xscroll,
yscroll=yscroll,
startUrlCallback=self.startOpenUrl,
endUrlCallback=self.endOpenUrl,
enterLinkCallback=self.setLinkLabel,
leaveLinkCallback=self.setLinkLabel)
self.help_text.grid(row=row,
column=0,
columnspan=3,
sticky=Tkinter.NSEW)
row = row + 1
self.link_label = Label(self)
self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
button = memops.gui.Util.createDismissButton(self,
dismiss_cmd=self.close)
button.grid(row=row, column=2)
self.urls = []
self.current = -1
self.updateUrlList = True
self.setButtonState()
def close(self):
if (self.popup):
if (self.popup.modal):
self.popup.do_grab()
popup = self.parent
while (not hasattr(popup, 'top')):
popup = popup.parent
popup.close()
def createFindFrame(self, master):
frame = Frame(master)
frame.grid(row=0, column=0, sticky=Tkinter.W)
arrow = ToggleArrow(frame, callback=self.toggleFindFrame)
arrow.grid(row=0, column=0)
button = Button(frame, text='find:', command=self.findPhrase)
button.grid(row=0, column=1)
self.find_entry = Entry(frame,
width=20,
returnCallback=self.findPhrase)
self.find_entry.grid(row=0, column=2)
self.find_frame = frame = Frame(master)
entries = ('search forwards', 'search backwards')
self.direction_buttons = PulldownMenu(frame, entries=entries)
self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5)
self.forwards_entries = entries = ('wrap search', 'stop at end')
self.backwards_entries = ('wrap search', 'stop at beginning')
self.wrap_buttons = PulldownMenu(frame, entries=entries)
self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5)
self.direction_buttons.callback = self.setWrapText
entries = ('case insensitive', 'case sensitive')
self.case_buttons = PulldownMenu(frame, entries=entries)
self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5)
entries = ('literal search', 'regex search')
self.pattern_buttons = PulldownMenu(frame, entries=entries)
self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5)
self.countVar = Tkinter.IntVar()
def setWrapText(self, entry_ind, entry):
if (entry_ind == 0):
entries = self.forwards_entries
else:
entries = self.backwards_entries
self.wrap_buttons.replace(
entries, selected_index=self.wrap_buttons.getSelectedIndex())
def findPhrase(self, *extra):
phrase = self.find_entry.get()
if (not phrase):
showError('No find phrase', 'Enter phrase in entry box.')
return
if (self.direction_buttons.getSelectedIndex() == 0):
forwards = 1
backwards = 0
else:
forwards = 0
backwards = 1
if (self.case_buttons.getSelectedIndex() == 0):
nocase = 1
else:
nocase = 0
if (self.pattern_buttons.getSelectedIndex() == 0):
exact = 1
regexp = 0
else:
exact = 0
regexp = 1
start = self.help_text.tag_nextrange(Tkinter.SEL, '1.0')
if (start):
start = start[0]
if (forwards):
start = '%s+1c' % start
else:
start = '%s-1c' % start
else:
start = Tkinter.CURRENT
if (self.wrap_buttons.getSelectedIndex() == 0):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp)
elif (forwards):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex=Tkinter.END)
else:
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex='1.0')
if (match):
self.help_text.see(match)
self.help_text.setSelection(
match, '%s+%dc' % (match, self.countVar.get()))
self.help_text.tag_config(Tkinter.SEL, background='gray70')
else:
showInfo('No match', 'No match found for phrase.')
def toggleFindFrame(self, isClosed):
if (isClosed):
self.find_frame.grid_forget()
else:
self.find_frame.grid(row=1, column=0, sticky=Tkinter.W)
def setButtonState(self):
n = len(self.urls)
if ((n >= 2) and (self.current > 0)):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[0].config(state=state)
if ((n >= 2) and (self.current < (n - 1))):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[1].config(state=state)
def setLinkLabel(self, url=''):
self.link_label.set(url)
def loadUrl(self, *extra):
url = self.url_entry.get()
if (url):
if (url.find(':') == -1):
if (url[:2] != '//'):
url = '//' + url
url = 'http:' + url
self.showUrl(url, forceLoad=True)
def newUrl(self, url):
self.current = self.current + 1
self.urls[self.current:] = [[url, 0.0]]
self.setButtonState()
#print 'newUrl', self.current, self.urls
def prevUrl(self):
if (self.current > 0): # True if called via button
(url, offset) = self.urls[self.current - 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current - 1
self.setButtonState()
#print 'prevUrl', self.current, self.urls
def nextUrl(self):
if (self.current < (len(self.urls) - 1)): # True if called via button
(url, offset) = self.urls[self.current + 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current + 1
self.setButtonState()
#print 'nextUrl', self.current, self.urls
def showText(self, message, popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.setState(Tkinter.NORMAL) # so that can add text
self.help_text.clear() # clear existing text
self.help_text.append(message)
self.help_text.setState(Tkinter.DISABLED) # make text read-only
self.open()
def startOpenUrl(self, yview):
if (self.urls):
self.urls[self.current][1] = yview[0]
def endOpenUrl(self, url):
#print 'endOpenUrl', url, self.updateUrlList
self.url_entry.set(url)
if (self.updateUrlList):
self.newUrl(url)
self.setLinkLabel()
self.open()
def showUrl(self,
url,
offset=None,
forceLoad=False,
allowModifyPath=True,
popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.openUrl(url,
forceLoad=forceLoad,
allowModifyPath=allowModifyPath)
if (offset is not None):
self.help_text.yview(Tkinter.MOVETO, str(offset))
def body(self, master):
#
# Peaklist setup
#
self.peakListDict = {}
for experiment in self.project.currentNmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
for peakList in dataSource.sortedPeakLists():
peakListLabel = "%s:%s:%d:%s" % (
experiment.name, dataSource.name, peakList.serial,
peakList.name)
self.peakListDict[peakListLabel] = peakList
peakListLabels = self.peakListDict.keys()
peakListLabels.sort()
#
# chemical shift list setup
#
self.shiftListDict = {}
self.shiftListDict['None'] = None
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
shiftListLabel = "%d:%s" % (shiftList.serial, shiftList.name)
self.shiftListDict[shiftListLabel] = shiftList
shiftListLabels = self.shiftListDict.keys()
shiftListLabels.sort()
row = 0
label = Label(master, text="Generation of chemical shift list")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Peak lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.peakListBox = ScrolledListbox(master,
width=50,
height=5,
selectmode=Tkinter.MULTIPLE,
initial_list=peakListLabels)
self.peakListBox.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use existing shift list:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master, entries=shiftListLabels)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use multiple assignments:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.useAllContribs = CheckButton(master)
self.useAllContribs.grid(row=row, column=1, sticky=Tkinter.W)
#
# Setup the default shift error per nucleus
#
self.defaultShiftError = {}
for (nucl, text, defValue) in [('1H', 'proton', '0.002'),
('13C', 'carbon', '0.1'),
('15N', 'nitrogen', '0.1')]:
row += 1
label = Label(master, text="Default %s shift error:" % text)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.defaultShiftError[nucl] = Entry(master, text=defValue)
self.defaultShiftError[nucl].grid(row=row,
column=1,
sticky=Tkinter.W)
row += 1
texts = ['Create shift list']
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)
class CloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 50
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.peakListDict = {}
self.noesyPeakList = None
self.tocsyPeakList = None
self.noesy3dPeakList = None
self.hsqcPeakList = None
self.maxIntens = 37000000
self.resonances = None
self.origResonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.numClouds = 100
self.filePrefix = 'cloud_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
self.structure = None
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Resonance Clouds Analysis",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
self.adcAtomTypes = name
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
resonances = []
for constraint in self.distanceConstraintList.constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
startMdProcess(self.numClouds, self.distanceConstraintList,
resonances, self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def showPeaks(self):
self.guiParent.viewPeaks(peaks=self.noesyPeaks)
def showResonances(self):
pass
#self.guiParent.viewResonances(resonances=self.resonances)
def setupResonances(self):
if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList:
disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList,
self.tocsyPeakList, self.hsqcPeakList)
(self.origResonances, self.noesyPeaks,
null) = getCloudsResonanceList(self.guiParent.argumentServer,
hsqcPeakList=self.hsqcPeakList,
tocsy3dPeakList=self.tocsyPeakList,
noesy2dPeakList=self.noesyPeakList)
self.setButtonStates()
def setButtonStates(self):
if self.origResonances:
self.label03a.set('Resonances found: %d' %
(len(self.origResonances)))
if self.noesyPeaks:
self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks)))
if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList:
self.setupButtons.buttons[0].enable()
else:
self.setupButtons.buttons[0].disable()
if self.noesyPeaks:
self.setupButtons.buttons[1].enable()
else:
self.setupButtons.buttons[1].disable()
if self.origResonances:
self.setupButtons.buttons[2].enable()
else:
self.setupButtons.buttons[2].disable()
if self.noesyPeaks and self.origResonances:
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.midgeButtons.buttons[1].enable()
self.distConstrLabel.set(
'Distance constraints: %d' %
len(self.distanceConstraintList.constraints))
else:
self.distConstrLabel.set('Distance constraints:')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
'Anti-distance constraints: %d' %
len(self.antiDistConstraintList.constraints))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('Anti-distance constraints:')
self.midgeButtons.buttons[2].disable()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
def getNoesys(self):
names = []
spectra = getSpectraByType(self.project, '2dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
self.noesyPeakList = self.peakListDict[name]
self.setButtonStates()
def getTocsys(self):
names = []
spectra = getSpectraByType(self.project, '3dTOCSY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.tocsyPeakList:
self.tocsyPeakList = peakList
return names
def getNoesy3ds(self):
names = []
spectra = getSpectraByType(self.project, '3dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesy3dPeakList:
self.noesy3dPeakList = peakList
return names
def setTocsy(self, index, name=None):
if not name:
name = self.tocsyPulldown.getSelected()
self.tocsyPeakList = self.peakListDict[name]
self.setButtonStates()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
self.noesy3dPeakList = self.peakListDict[name]
self.setButtonStates()
def getHsqcs(self):
names = []
spectra = getSpectraByType(self.project, 'HSQC')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.hsqcPeakList:
self.hsqcPeakList = peakList
return names
def setHsqc(self, index, name=None):
if not name:
name = self.hsqcPulldown.getSelected()
self.hsqcPeakList = self.peakListDict[name]
self.setButtonStates()
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def getMaxIntens(self, obj):
self.maxIntensEntry.set(self.maxIntens)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def setMaxIntens(self, event):
value = self.maxIntensEntry.get()
if value is not None:
self.maxIntens = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
def body(self, master):
self.geometry('600x400')
#
# Quick check
#
if not self.chains:
showError("No chains","No chains available - cannot use export/import cycle.")
self.destroy()
#
# Set it all up
#
columnspan = 2
row = 0
label = Label(master, text= "AutoAssign export/import cycle.")
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
label = Label(master, fg = 'red', text= "Popup to export %s data from the CCPN data model,\nrun %s, then re-import the output." % (self.format,self.format))
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Set up export file info
#
row += 1
label = Label(master, text= "Export menu (using date/time label '%s')" % self.dateTimeFlag)
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
(chainList,self.chainDict) = createSelection(self.chains)
label = Label(master, text= "Select chain to export:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainSelect = PulldownMenu(master,entries = chainList)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(master, text= "Export %s project file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectExportFileButton = Tkinter.Button(master, text = 'Select export file', command = (lambda : self.selectExportProjectFile()))
self.selectExportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.exportButton = Tkinter.Button(master, text = 'Export', command = (lambda : self.doExport()))
self.exportButton.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Set up import file info
#
row += 1
label = Label(master, text= "Re-import menu")
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
#
# Select the right chain with the right date/time flag...
#
label = Label(master, text= "Select chain with correct date/time flag:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainDateTimeSelect = PulldownMenu(master,entries = self.chainDateTimeStamps)
self.chainDateTimeSelect.grid(row=row, column=1, sticky=Tkinter.W)
# TODO UPDATE THIS WHEN EXPORT BUTTON PRESSED AND GETTING OK FROM EXPORT ITSELF!
# Probably also need just a message if no importDateTimeStamp available...
row += 1
label = Label(master, text= "Import %s output file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectImportFileButton = Tkinter.Button(master, text = 'Select import file', command = (lambda : self.selectImportShiftFile()))
self.selectImportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.importButton = Tkinter.Button(master, text = 'Import', command = (lambda : self.doImport()))
self.importButton.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
buttons = createDismissHelpButtonList(master, texts=[], commands=[], help_url=self.help_url)
buttons.grid(row=row, columnspan = columnspan, column=0)
class RegionSelector(Frame):
def __init__(self,
parent,
label='',
world_region=None,
view_region=None,
orient=Tkinter.HORIZONTAL,
allow_resize=True,
width=20,
callback=None,
borderwidth=1,
show_text=True,
text_color='#000000',
text_decimals=2,
units_scroll=0.1,
pages_scroll=1.0,
menu_entries=None,
menu_callback=None,
min_thickness=None,
*args,
**kw):
self.menu_entries = menu_entries
self.myCallback = callback
Frame.__init__(self, parent, *args, **kw)
self.text_decimals = text_decimals
self.label = Label(self, text=label, width=4)
self.menu = PulldownMenu(self,
callback=menu_callback,
entries=menu_entries)
self.entry = FloatEntry(self,
width=6,
returnCallback=self.adjustScrollbar)
self.region_scrollbar = RegionScrollbar(self,
world_region=world_region,
view_region=view_region,
orient=orient,
allow_resize=allow_resize,
width=width,
callback=self.doCallback,
borderwidth=borderwidth,
show_text=show_text,
text_color=text_color,
text_decimals=text_decimals,
units_scroll=units_scroll,
pages_scroll=pages_scroll,
min_thickness=min_thickness)
self.gridAll()
def gridAll(self):
col = 0
if (self.menu_entries and len(self.menu_entries) > 1):
self.menu.grid(row=0, column=col, sticky=Tkinter.EW)
col = col + 1
else:
self.menu.grid_forget()
self.label.grid(row=0, column=col, sticky=Tkinter.EW)
col = col + 1
self.entry.grid(row=0, column=col, sticky=Tkinter.EW)
self.grid_columnconfigure(col, weight=0)
col = col + 1
self.region_scrollbar.grid(row=0, column=col, sticky=Tkinter.NSEW)
self.grid_columnconfigure(col, weight=1)
col = col + 1
self.grid_columnconfigure(col, weight=0)
def setMinThickness(self, min_thickness):
self.region_scrollbar.setMinThickness(min_thickness)
def setMenuEntries(self, menu_entries):
self.menu_entries = menu_entries
self.menu.replace(menu_entries)
self.gridAll()
def getMenuEntry(self):
return self.menu.getSelected()
def adjustScrollbar(self, *event):
try:
x = float(self.entry.get())
except:
showError('Entry error', 'Need to enter float in scrollbar box')
self.setEntry()
return
(v0, v1) = self.region_scrollbar.view_region
d = 0.5 * (v1 - v0)
self.region_scrollbar.setViewRegion(x - d, x + d, do_callback=True)
def doCallback(self, view_region):
if (self.myCallback):
self.myCallback(view_region)
#print 'doCallback', view_region
self.setEntry(view_region)
def setEntry(self, view_region=None):
if (not view_region):
view_region = self.region_scrollbar.view_region
(v0, v1) = view_region
x = 0.5 * (v0 + v1)
s = formatDecimals(x, decimals=self.text_decimals)
self.entry.set(s)
def __getattr__(self, name):
# dispatch everything not defined by RegionSelector to scrollbar widget
try:
return getattr(self.__dict__['region_scrollbar'], name)
except:
raise AttributeError, "RegionSelector instance has no attribute '%s'" % name
def body(self, master):
#
# Popup window
#
self.widgets = []
row = 0
label = Label(master, text="ChemComp formula '%s'" % self.formula)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Number of bonds: %d" % self.bondNumber)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
#
# Show relevant attributes...
#
for chemCompAttrInfo in self.chemCompInfo:
row = row + 1
attrName = chemCompAttrInfo[0]
label = Label(master, text=attrName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] == PulldownMenu:
self.widgets.append(
PulldownMenu(master,
entries=widgetInfo[1],
selected_index=widgetInfo[1].index(
chemCompAttrInfo[1])))
elif widgetInfo[0] == CheckButton:
self.widgets.append(
CheckButton(master, selected=widgetInfo[1]))
else:
text = chemCompAttrInfo[1]
if not text:
text = ''
self.widgets.append(Entry(master, text=text))
self.widgets[-1].grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=2)
def setSelected(self, value):
PulldownMenu.setSelectedIndex(self, self.booleanToIndex[value])
def body(self, master):
#
# Popup window
#
row = 0
if self.headerLines:
for headerLine in self.headerLines:
label = Label(master, text=headerLine)
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Residue type '%s'" % self.ccpCode)
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
row = row + 1
matchNameString = "[%s]" % self.matchName
if self.matchInfoPopup:
label = Label(master, text="%s:" % self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
button = Tkinter.Button(
master,
text=matchNameString,
command=lambda: self.matchInfoPopup(self, self.matchName),
fg='blue')
button.grid(row=row, column=1, columnspan=2)
else:
label = Label(master, text="%s:" % self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
label = Label(master, text=matchNameString, fg='blue')
label.grid(row=row, column=1, columnspan=2)
if self.shifts:
row = row + 1
label = Label(master, text="(shifts: %s ppm)" % self.shifts)
label.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Pick atom:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.menu = PulldownMenu(master, entries=self.chemAtomList)
self.menu.grid(row=row, column=1, columnspan=2, ipadx=20)
row = row + 1
label = Label(master, text="Propagate\nmapping to:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.propagateMenu = PulldownMenu(master,
entries=self.propagateList,
selected_index=self.selectedIndex)
self.propagateMenu.grid(row=row, column=1, columnspan=2)
row = row + 1
texts = ['OK', 'Show all atoms']
commands = [
self.ok, self.showAllAtoms
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Do not link',
dismiss_cmd=self.doNotLink,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
class AtomSelectPopup(TemporaryBasePopup):
def __init__(self,
parent,
matchName,
chemAtomList,
chemAtomDict,
propagateList,
ccpCode,
shifts,
matchType='Resonance',
matchInfoPopup=None,
selectedIndex=4,
title='Select resonance atom match',
helpUrl='AtomSelect.html',
headerLines=None,
modal=False):
self.help_url = joinPath(getHelpUrlDir(), helpUrl)
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.chemAtomOrSets = None
self.propagate = None
self.matchName = matchName
self.matchType = matchType
self.matchInfoPopup = matchInfoPopup
self.chemAtomList = chemAtomList
self.chemAtomDict = chemAtomDict
self.propagateList = propagateList
self.ccpCode = ccpCode
self.shifts = shifts
self.guiParent = parent
self.headerLines = headerLines
self.selectedIndex = selectedIndex
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(self,
parent=parent,
title=title,
modal=modal,
transient=True)
def showAllAtoms(self):
self.chemAtomList = self.chemAtomDict.keys()
self.chemAtomList.sort()
self.menu.replace(self.chemAtomList)
def body(self, master):
#
# Popup window
#
row = 0
if self.headerLines:
for headerLine in self.headerLines:
label = Label(master, text=headerLine)
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Residue type '%s'" % self.ccpCode)
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
row = row + 1
matchNameString = "[%s]" % self.matchName
if self.matchInfoPopup:
label = Label(master, text="%s:" % self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
button = Tkinter.Button(
master,
text=matchNameString,
command=lambda: self.matchInfoPopup(self, self.matchName),
fg='blue')
button.grid(row=row, column=1, columnspan=2)
else:
label = Label(master, text="%s:" % self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
label = Label(master, text=matchNameString, fg='blue')
label.grid(row=row, column=1, columnspan=2)
if self.shifts:
row = row + 1
label = Label(master, text="(shifts: %s ppm)" % self.shifts)
label.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Pick atom:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.menu = PulldownMenu(master, entries=self.chemAtomList)
self.menu.grid(row=row, column=1, columnspan=2, ipadx=20)
row = row + 1
label = Label(master, text="Propagate\nmapping to:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.propagateMenu = PulldownMenu(master,
entries=self.propagateList,
selected_index=self.selectedIndex)
self.propagateMenu.grid(row=row, column=1, columnspan=2)
row = row + 1
texts = ['OK', 'Show all atoms']
commands = [
self.ok, self.showAllAtoms
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Do not link',
dismiss_cmd=self.doNotLink,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def apply(self):
selectionText = self.menu.getSelected()
if selectionText == '<None>':
return False
self.chemAtomOrSets = self.chemAtomDict[selectionText]
self.propagate = self.propagateMenu.getSelectedIndex()
return True
def doNotLink(self):
self.propagate = self.propagateMenu.getSelectedIndex()
self.close()
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
class MidgePopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 15
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.ratioHD = 0.9
self.peakListDict = {}
self.peakListDict3d = {}
self.noesyPeakList = None
self.noesy3dPeakList = None
self.carbonLabel = 0
self.nitrogenLabel = 1
self.noesyPeakList1 = None
self.noesyPeakList2 = None
self.noesyPeakList3 = None
self.noesyPeakList3d = None
self.resonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.adcAtomTypes = None
self.structure = None
BasePopup.__init__(self,
parent,
title="Relaxation Matrix Optimisation",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
def setCarbonLabel(self, boolean):
self.carbonLabel = boolean
def setNitrogenLabel(self, boolean):
self.nitrogenLabel = boolean
def update(self):
if self.resonances and (
(self.noesyPeaks and self.noesyPeakList1 and self.noesyPeakList2
and self.noesyPeakList3) or self.noesyPeakList3d):
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.distConstrLabel.set(
str(len(self.distanceConstraintList.constraints)))
self.midgeButtons.buttons[1].enable()
else:
self.distConstrLabel.set('')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
str(len(self.antiDistConstraintList.constraints)))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('')
self.midgeButtons.buttons[2].disable()
if self.resonances:
self.numResonancesLabel.set(str(len(self.resonances)))
else:
self.numResonancesLabel.set('')
if self.noesyPeaks:
self.numPeaksLabel.set(str(len(self.noesyPeaks)))
else:
self.numPeaksLabel.set('')
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['<None>', 'HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
if name == '<None>':
name = None
self.adcAtomTypes = name
def getResonances(self):
resonanceDict = {}
if self.noesyPeaks:
for peak in self.noesyPeaks:
for peakDim in peak.peakDims:
for contrib in peakDim.peakDimContribs:
resonanceDict[contrib.resonance] = 1
# TBD: Set resonance.name for typing
self.resonances = resonanceDict.keys()
def getPeaks(self):
if self.noesyPeakList:
self.noesyPeaks = self.noesyPeakList.sortedPeaks()
def calculateDistances(self):
resonances = list(self.resonances)
resDict = {}
for resonance in resonances:
resDict[resonance.serial] = resonance
ratioHD = self.ratioHDEntry.get() or self.ratioHD
tmix1 = self.tmix1Entry.get() or 60
tmix2 = self.tmix2Entry.get() or 120
tmix3 = self.tmix3Entry.get() or 200
data = [(tmix1, self.noesyPeakList1), (tmix2, self.noesyPeakList2),
(tmix3, self.noesyPeakList3)]
data.sort()
mixingTimes = [x[0] for x in data]
peakLists = [x[1] for x in data]
# get a clean, symmetric and normalised NOE matrix
noeMatrix = getNoeMatrixFromPeaks(self.noesyPeaks,
resonances,
peakLists,
mixingTimes,
ratioHD=ratioHD,
analysis=self.guiParent)
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList, resonances = optimiseRelaxation(
resonances,
noeMatrix,
self.mixTime,
self.specFreq,
self.corrTime,
self.leakRate,
self.carbonLabel,
self.nitrogenLabel,
maxIter=self.maxIter)
#constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList and self.noesyPeakList:
constraintHead = self.distanceConstraintList.nmrConstraintStore
if self.adcAtomTypes:
adcDict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
allowedAtomTypes = adcDict[self.adcAtomTypes]
print "Making ADCs"
self.antiDistConstraintList = makeNoeAdcs(
resonances[:],
self.noesyPeakList.dataSource,
constraintHead,
allowedAtomTypes=allowedAtomTypes)
print "Done ADCs"
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
item = constraint.findFirstItem()
resonances = list(item.resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setOrigData(distance)
self.update()
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def getNoesys3d(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
if spectrum.numDim != 3:
continue
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict3d[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def getNoesys(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
if name == '<None>':
self.noesyPeakList = None
else:
self.noesyPeakList = self.peakListDict[name]
self.getPeaks()
self.getResonances()
self.update()
def setNoesy1(self, index, name=None):
if not name:
name = self.tmix1Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList1 = self.peakListDict[name]
else:
self.noesyPeakList1 = None
self.update()
def setNoesy2(self, index, name=None):
if not name:
name = self.tmix2Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList2 = self.peakListDict[name]
else:
self.noesyPeakList2 = None
self.update()
def setNoesy3(self, index, name=None):
if not name:
name = self.tmix3Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList3 = self.peakListDict[name]
else:
self.noesyPeakList3 = None
self.update()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
if name != '<None>':
self.noesyPeakList3d = self.peakListDict3d[name]
self.noesyPeaks = self.noesyPeakList3d.sortedPeaks()
else:
self.noesyPeakList3d = None
self.noesyPeaks = []
self.getResonances()
self.update()
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
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 body(self, master):
# Master is the owner widget (not self.parent) - parent of the widget here
#
# Popup window
#
self.entries = []
self.labels = []
value = 0
row = 0
label = Label(master, text="Window function:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menuRow = row
self.menu = PulldownMenu(master,
entries=self.windowFuncList,
selected_index=self.winFuncIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.W, ipadx=20)
self.menulabel = Label(
master,
text="(" +
self.windowFunctions[self.format][self.winFuncIndex][1] + ")")
self.menulabel.grid(row=row, column=2, sticky=Tkinter.E)
#
# Setup arguments - make room for four
#
for argIndex in range(0, self.maxArgs):
row = row + 1
try:
argRef = self.windowFunctions[self.format][
self.winFuncIndex][2][argIndex]
argName = argRef[0]
argValue = argRef[1]
except:
argName = None
argValue = None
self.labels.append(Label(master, text="%s" % argName))
self.labels[-1].grid(row=row, column=0, sticky=Tkinter.EW)
self.entries.append(Entry(master, text=str(argValue)))
self.entries[-1].grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
if not argName:
self.labels[-1].grid_forget()
self.entries[-1].grid_forget()
#
# Add callback to menu after setup
#
self.menu.callback = self.updateWindow
row = row + 1
texts = ['OK']
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, column=0, columnspan=3)
def getSelected(self):
selected_index = PulldownMenu.getSelectedIndex(self)
return self.indexToBoolean[selected_index]
class WindowFunctionSelect(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'WindowFunctionSelect.html')
def __init__(self, parent, format, dim, getValue):
#
# General setup
#
self.maxArgs = 4
self.nmrPipe = 'nmrPipe'
self.azara = 'azara'
self.format = format
self.freqDataDim = parent.freqDataDims[format][dim]
self.expDimRef = parent.expDimRefs[dim]
#
# Window function settings (different per program)
#
self.windowFunctions = {}
specWidth = self.freqDataDim.spectralWidthOrig
# TODO: these for azara still have to change a bit...
self.windowFunctions[self.azara] = [
['sine', 'sinebell', [['Angle (deg)', 0, 'deg']]],
['sine^2', 'sinebell2', [['Angle (deg)', 0, 'deg']]],
['exponential (fixed)', 'decay', [['End value', 0.5, 'end']]],
[
'exponential', 'decay_sw',
[['Line broadening (Hz)', 10, 'lb'],
['Spectral width (Hz)', specWidth, 'sw']]
],
[
'gaussian (fixed)', 'gaussian',
[['Total points fraction for max', 0.25, 'frac'],
['End value', 1, 'end']]
],
[
'gaussian', 'gaussian_sw',
[['Line broadening (Hz)', 10, 'lb'],
['Sharpening factor', 0.7, 'shrp'],
['Spectral width (Hz)', specWidth, 'sw']]
],
[
'inverse cosine', 'inv_cosine',
[['Frequency (Hz)', 0, 'freq'],
['Spectral width (Hz)', specWidth, 'sw']]
]
]
self.windowFunctions[self.nmrPipe] = [
[
'sine', 'SP',
[['Start sine at (pi)', 0, 'off'],
['End sine at (pi)', 1, 'end'], ['Sine to power', 1, 'pow']]
], ['exponential', 'EM', [['Line broadening (Hz)', 10, 'lb']]],
[
'lorentz-gauss', 'GM',
[['Inverse exp width (Hz)', 0, 'g1'],
['Gaussian width (Hz)', 0, 'g2'], ['Center (0-1)', 0, 'g3']]
],
[
'gaussian', 'GMB',
[['Exponential term', 0, 'lb'], ['Gaussian term', 0, 'gb']]
],
[
'trapezoid', 'TM',
[['Ramp length left', 0, 't1'], ['Ramp length right', 0, 't2']]
],
[
'triangle', 'TRI',
[['Point loc of apex', 0,
'loc'], ['Left edge height', 0, 'lHi'],
['Right edge height', 0, 'rHi']]
]
]
#
# Make list of names for pulldown menu
#
self.windowFuncList = []
for (winFunc, winFuncAppl,
winFuncArgs) in self.windowFunctions[format]:
self.windowFuncList.append(winFunc)
#
# Get the right window function from appldata (if there)
#
self.windowFunctionKeyword = 'windowFunction'
self.winFuncIndex = self.getWindowFunctionIndex()
#
# Set defaults depending on nucleus type if no window function set
#
if self.winFuncIndex == -1:
if format == self.nmrPipe:
self.winFuncIndex = 0
if self.expDimRef.isotopeCodes[0] == '1H':
# use SP '-off 0.3333 -pow 2.0'
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][0][1] = 0.3333
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][2][1] = 2.0
else:
# for non-H, use SP '-off 0.5 -pow 2.0'
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][0][1] = 0.5
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][2][1] = 2.0
elif format == self.azara:
self.winFuncIndex = 1
if self.expDimRef.isotopeCodes[0] == '1H':
# use sinebell2 60
self.windowFunctions[self.azara][
self.winFuncIndex][2][0][1] = 60
else:
# for non-H, use sinebell2 90
self.windowFunctions[self.azara][
self.winFuncIndex][2][0][1] = 90
# Get actual values for arguments from appldata if they exists!
self.updateWindowFunctions()
# Also using this to return the current window function 'string value'
if not getValue:
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(
self,
parent=parent,
title='Select window function',
modal=False,
transient=True,
)
def body(self, master):
# Master is the owner widget (not self.parent) - parent of the widget here
#
# Popup window
#
self.entries = []
self.labels = []
value = 0
row = 0
label = Label(master, text="Window function:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menuRow = row
self.menu = PulldownMenu(master,
entries=self.windowFuncList,
selected_index=self.winFuncIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.W, ipadx=20)
self.menulabel = Label(
master,
text="(" +
self.windowFunctions[self.format][self.winFuncIndex][1] + ")")
self.menulabel.grid(row=row, column=2, sticky=Tkinter.E)
#
# Setup arguments - make room for four
#
for argIndex in range(0, self.maxArgs):
row = row + 1
try:
argRef = self.windowFunctions[self.format][
self.winFuncIndex][2][argIndex]
argName = argRef[0]
argValue = argRef[1]
except:
argName = None
argValue = None
self.labels.append(Label(master, text="%s" % argName))
self.labels[-1].grid(row=row, column=0, sticky=Tkinter.EW)
self.entries.append(Entry(master, text=str(argValue)))
self.entries[-1].grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
if not argName:
self.labels[-1].grid_forget()
self.entries[-1].grid_forget()
#
# Add callback to menu after setup
#
self.menu.callback = self.updateWindow
row = row + 1
texts = ['OK']
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, column=0, columnspan=3)
def getApplDataAndReturnString(self):
keyword = self.windowFunctionKeyword
returnString = self.windowFunctions[self.format][self.winFuncIndex][0]
winFuncName = self.windowFunctions[self.format][self.winFuncIndex][1]
for (argName, argValue, argShort
) in self.windowFunctions[self.format][self.winFuncIndex][2]:
applData = self.freqDataDim.findFirstApplicationData(
application=self.format,
keyword=keyword + winFuncName + argShort)
returnString += ' ' + argShort
if not applData:
returnString += ' ' + str(argValue)
else:
returnString += ' ' + str(applData.value)
return returnString
def updateWindowFunctions(self):
keyword = self.windowFunctionKeyword
winFuncName = self.windowFunctions[self.format][self.winFuncIndex][1]
#
# Update windowfunction parameters
#
for i in range(
0,
len(self.windowFunctions[self.format][self.winFuncIndex][2])):
(argName, argValue, argShort
) = self.windowFunctions[self.format][self.winFuncIndex][2][i]
applData = self.freqDataDim.findFirstApplicationData(
application=self.format,
keyword=keyword + winFuncName + argShort)
if applData:
self.windowFunctions[self.format][
self.winFuncIndex][2][i][1] = str(applData.value)
def setApplData(self):
keyword = self.windowFunctionKeyword
winFuncName = self.windowFunctions[self.format][self.winFuncIndex][1]
#
# Set windowfunction
#
applData = self.freqDataDim.findFirstApplicationData(
application=self.format, keyword=keyword)
if not applData:
applData = createAppData(self.freqDataDim,
application=self.format,
keyword=keyword,
value=winFuncName)
else:
applData.value = winFuncName
#
# Set windowfunction parameters
#
for (argName, argValue, argShort
) in self.windowFunctions[self.format][self.winFuncIndex][2]:
applData = self.freqDataDim.findFirstApplicationData(
application=self.format,
keyword=keyword + winFuncName + argShort)
if not applData:
applData = createAppData(self.freqDataDim,
application=self.format,
keyword=keyword + winFuncName +
argShort,
value=str(argValue))
else:
applData.value = str(argValue)
def getWindowFunctionIndex(self):
keyword = self.windowFunctionKeyword
applData = self.freqDataDim.findFirstApplicationData(
application=self.format, keyword=keyword)
if applData:
origWinFuncAppl = applData.value
for i in range(0, len(self.windowFunctions[self.format])):
(winFunc, winFuncAppl,
winFuncArgs) = self.windowFunctions[self.format][i]
if winFuncAppl == origWinFuncAppl:
return i
return -1
def updateWindow(self, *args):
#
# First do a value update of the current stuff?
#
#
# Reset arguments
#
row = self.menuRow
self.winFuncIndex = self.menu.getSelectedIndex()
self.menulabel.set(
"(" + self.windowFunctions[self.format][self.winFuncIndex][1] +
")")
for argIndex in range(0, self.maxArgs):
row = row + 1
try:
argRef = self.windowFunctions[self.format][
self.winFuncIndex][2][argIndex]
argName = argRef[0]
argValue = argRef[1]
except:
argName = None
argValue = None
self.labels[argIndex].set(argName)
self.labels[argIndex].grid(row=row, column=0, sticky=Tkinter.W)
self.entries[argIndex].set(str(argValue))
self.entries[argIndex].grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
if not argName:
self.entries[argIndex].grid_forget()
self.labels[argIndex].grid_forget()
def setWindowFunctionsValues(self):
self.winFuncIndex
for argIndex in range(
0,
len(self.windowFunctions[self.format][self.winFuncIndex][2])):
argValue = returnFloat(self.entries[argIndex].get())
self.windowFunctions[self.format][
self.winFuncIndex][2][argIndex][1] = argValue
def apply(self):
self.winFuncIndex = self.menu.getSelectedIndex()
self.setWindowFunctionsValues()
self.setApplData()
return True
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 AutoAssignIOCyclePopup(BasePopup):
help_url = joinPath(getHelpUrlDir(),'AutoAssignIOCycle.html')
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.autoAssignFormat = AutoAssignFormat(project, guiParent = parent)
self.format = 'autoAssign'
self.chainStampSep = '-'
self.dateTimeFlag = time.strftime("%Y%m%d.%H:%M")
self.getPreviousDateTimeStamps()
self.getChainsAndChainStamps()
self.importFileName = self.exportFileName = None
BasePopup.__init__(self, parent=parent, title="Project '%s': " % project.name + 'AutoAssign export/import cycle.', modal=True, transient=True)
def getPreviousDateTimeStamps(self):
self.dateTimeStamps = []
appData = self.project.findAllApplicationData(application = self.format, keyword = dateTimeStamp_kw)
for appDatum in appData:
self.dateTimeStamps.append(appDatum.value)
def getChainsAndChainStamps(self):
self.chains = []
self.chainDateTimeStamps = []
self.chainDateTimeStampDict = {}
for molSys in self.project.sortedMolSystems():
for chain in molSys.sortedChains():
self.chains.append(chain)
appData = chain.findFirstApplicationData(application = self.format, keyword = dateTimeStamp_kw)
if appData and appData.value in self.dateTimeStamps:
(tlist,tdict) = createSelection([chain])
cdtsTag = "%s%s%s" % (tlist[0],self.chainStampSep,appData.value)
self.chainDateTimeStamps.append(cdtsTag)
self.chainDateTimeStampDict[cdtsTag] = chain
def body(self, master):
self.geometry('600x400')
#
# Quick check
#
if not self.chains:
showError("No chains","No chains available - cannot use export/import cycle.")
self.destroy()
#
# Set it all up
#
columnspan = 2
row = 0
label = Label(master, text= "AutoAssign export/import cycle.")
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
label = Label(master, fg = 'red', text= "Popup to export %s data from the CCPN data model,\nrun %s, then re-import the output." % (self.format,self.format))
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Set up export file info
#
row += 1
label = Label(master, text= "Export menu (using date/time label '%s')" % self.dateTimeFlag)
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
(chainList,self.chainDict) = createSelection(self.chains)
label = Label(master, text= "Select chain to export:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainSelect = PulldownMenu(master,entries = chainList)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(master, text= "Export %s project file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectExportFileButton = Tkinter.Button(master, text = 'Select export file', command = (lambda : self.selectExportProjectFile()))
self.selectExportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.exportButton = Tkinter.Button(master, text = 'Export', command = (lambda : self.doExport()))
self.exportButton.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Set up import file info
#
row += 1
label = Label(master, text= "Re-import menu")
label.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
#
# Select the right chain with the right date/time flag...
#
label = Label(master, text= "Select chain with correct date/time flag:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainDateTimeSelect = PulldownMenu(master,entries = self.chainDateTimeStamps)
self.chainDateTimeSelect.grid(row=row, column=1, sticky=Tkinter.W)
# TODO UPDATE THIS WHEN EXPORT BUTTON PRESSED AND GETTING OK FROM EXPORT ITSELF!
# Probably also need just a message if no importDateTimeStamp available...
row += 1
label = Label(master, text= "Import %s output file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectImportFileButton = Tkinter.Button(master, text = 'Select import file', command = (lambda : self.selectImportShiftFile()))
self.selectImportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.importButton = Tkinter.Button(master, text = 'Import', command = (lambda : self.doImport()))
self.importButton.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master,height = 3)
separator.setColor('black', bgColor = 'black')
separator.grid(row=row, column=0, columnspan = columnspan, sticky=Tkinter.EW)
row += 1
buttons = createDismissHelpButtonList(master, texts=[], commands=[], help_url=self.help_url)
buttons.grid(row=row, columnspan = columnspan, column=0)
def selectExportProjectFile(self):
if self.exportFileName:
fileName = self.exportFileName
else:
fileName = 'table.aat'
popup = FormatFilePopup(self, file = fileName, component = 'project', format = self.format, title = 'Select name for %s project file to export.' % self.format)
if popup.fileSelected:
self.selectExportFileButton.config(text = popup.file)
self.exportFileName = popup.file
def selectImportShiftFile(self):
if self.exportFileName:
fileName = self.exportFileName
else:
fileName = 'autoAssign.out'
popup = FormatFilePopup(self, file = fileName, component = 'shifts', format = self.format, title = 'Select name for %s output file to re-import.' % self.format)
if popup.fileSelected:
self.selectImportFileButton.config(text = popup.file)
self.importFileName = popup.file
def doExport(self):
if self.exportFileName:
chain = self.chainDict[self.chainSelect.getSelected()]
returnValue = self.autoAssignFormat.writeProject(self.exportFileName, chain = chain, setTag = self.dateTimeFlag)
if not returnValue:
showError("No export file written","There were problems while exporting the %s project file." % self.format)
else:
showInfo("File written","File written successfully")
cdtsTag = "%s-%s" % (self.chainSelect.getSelected(),self.dateTimeFlag)
if not cdtsTag in self.chainDateTimeSelect.entries:
if "<None>" in self.chainDateTimeSelect.entries:
self.chainDateTimeSelect.entries.pop(self.chainDateTimeSelect.entries.index("<None>"))
self.chainDateTimeSelect.replace([cdtsTag] + self.chainDateTimeSelect.entries)
self.chainDateTimeStampDict[cdtsTag] = chain
else:
showError("No export file defined","Please define a name for the %s project file to export to." % self.format)
def doImport(self):
if self.importFileName:
cdtsTag = self.chainDateTimeSelect.getSelected()
if not self.chainDateTimeStampDict.has_key(cdtsTag):
showError("No import tag defined","No chain with date/time stamp defined - cannot re-import.")
else:
chain = self.chainDateTimeStampDict[cdtsTag]
(chainText,curDateTimeStamp) = cdtsTag.split(self.chainStampSep)
#
# Get relevant info from data model (not immediately necessary but as example)
#
# Note that could in principle use the normal peakNum tag, but dangerous in case
# multiple exports were done... this is more laborious though.
#
peakLists = []
rootPeakListTag = str((curDateTimeStamp,'isRoot'))
rootPeakNumToPeak = {}
for nmrExp in self.project.currentNmrProject.sortedExperiments():
for ds in nmrExp.sortedDataSources():
for peakList in ds.sortedPeakLists():
appData = peakList.findAllApplicationData(application = self.format, keyword = dateTimeStamp_kw)
for appDatum in appData:
if appDatum and appDatum.value == curDateTimeStamp:
peakLists.append(peakList)
if peakList.findFirstApplicationData(application = self.format, keyword = ioCycleTag_kw, value = rootPeakListTag):
for peak in peakList.sortedPeaks():
appData = peak.findFirstApplicationData(application = self.format, keyword = ioCycleTag_kw)
if appData:
(curTag,peakNum) = eval(appData.value)
if curTag == curDateTimeStamp:
rootPeakNumToPeak[peakNum] = peak
#
# Now get the actual chemical shift info from the AutoAssign output file
#
autoAssignChemShiftFile = AutoAssignChemShiftFile(self.importFileName)
autoAssignChemShiftFile.read()
#
# Set the mapping between the chain residues and the seqCode in the chem shift file
#
residues = list(chain.sortedResidues())
seqCodeToResidue = {}
for i in range(0,len(residues)):
residue = residues[i]
(seqCode,code1Letter) = autoAssignChemShiftFile.seqCodes[i]
seqCode = returnInt(seqCode)
seqCodeToResidue[seqCode] = residue
for rawChemShift in autoAssignChemShiftFile.chemShifts:
peak = None
residue = None
prevResidue = None
seqCode = rawChemShift.seqCode
atomName = rawChemShift.atomName
#allValues = rawChemShift.allValues
#rawChemShift.spinSystemId
if seqCodeToResidue.has_key(seqCode):
residue = seqCodeToResidue[seqCode]
else:
# THIS SHOULD NEVER HAPPEN!
print " Error: no match for seqCode %d while re-importing project." % seqCode
continue
#
# Set info on residue/atom level
#
atom = self.findMatchingAtom(residue,atomName)
self.autoAssignFormat.setSeqAssignTag(atom,rawChemShift.value,AppDataClass = Implementation.AppDataFloat)
#
# Set info on peak level
#
if rawChemShift.peakId:
(peakNum,rootName) = rawChemShift.peakId.split('.') # TODO set this somewhere?
peakNum = returnInt(peakNum)
if rootPeakNumToPeak.has_key(peakNum):
peak = rootPeakNumToPeak[peakNum]
self.autoAssignFormat.setSeqAssignTag(peak,str((chain.code,residue.seqId)))
else:
showError("No import file defined","Please define a name for the %s shift output file to import." % self.format)
def findMatchingAtom(self,residue,atomName):
atom = residue.findFirstAtom(name = atomName)
if not atom:
# Rough search but should be OK for bb atoms
namingSystem = residue.chemCompVar.chemComp.findFirstNamingSystem(name = 'XPLOR')
chemAtomSysName = findChemAtomSysName(namingSystem,{'sysName': atomName})
atom = residue.findFirstAtom(name = chemAtomSysName.atomName)
return atom
def apply(self):
if not 0:
showError("No root spectrum","Can't continue: need a root spectrum...")
return False
return True
def setupSequenceFrame(self, resetFrame=False, resetStatus=True):
frameRow = 0
x = y = 0
if resetFrame:
self.sequenceFrame = ScrolledFrame(self.sequenceFrameMaster,
width=70,
height=300,
doExtraConfig=False)
self.sequenceFrame.grid(row=self.sequenceFrameRow,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
frame = self.sequenceFrame.frame
#
# Just use the first one as reference!
#
sequences = self.localCreateMoleculeDict[self.molName][1]
(self.origSequence, self.origSequenceList) = sequences[0]
if len(sequences) > 1:
multipleSequences = True
else:
multipleSequences = False
#
# Set info...
#
label = Label(frame, text='', width=10)
label.grid(row=frameRow, column=0, sticky=Tkinter.EW)
label = Label(frame, text='', width=35)
label.grid(row=frameRow, column=1, sticky=Tkinter.EW)
label = Label(frame, text='', width=20)
label.grid(row=frameRow, column=2, sticky=Tkinter.EW)
frameRow += 1
self.ccvButtons = []
if resetStatus or resetFrame:
self.statusList = []
self.moveStatus = {}
#
# Set up a list of status entries
#
statusEntries = [self.okText, self.deleteText]
for newMolName in self.newMoleculeList:
for appendCode in [self.startText, self.endText]:
statusEntries.append('%s of %s' % (appendCode, newMolName))
self.moveStatus[statusEntries[-1]] = (newMolName,
appendCode)
#
# Start creating all the objects...
#
for seqIndex in range(0, len(self.origSequenceList)):
(seqEl, ccHead, ccVar) = self.origSequenceList[seqIndex]
#
# Set the original sequence code info...
#
seqCode = seqEl.seqCode
if hasattr(seqEl, 'code3Letter') and seqEl.code3Letter:
seqText = seqEl.code3Letter
else:
seqText = seqEl.code1Letter
label = Label(frame, text="%s-%d" % (seqText, seqCode))
label.grid(row=frameRow, column=0, sticky=Tkinter.EW)
#
# Set the chemCompVar info
#
keywds = {}
if ccHead:
textCode = "%s (%s)" % (ccHead.ccpCode, ccHead.molType)
if ccVar:
textCode += ": %s,%s" % (ccVar.linking, ccVar.descriptor)
else:
textCode = 'Select chemCompVar for %s' % textCode
keywds['fg'] = 'red'
else:
textCode = 'Select chemCompVar'
keywds['fg'] = 'red'
self.ccvButtons.append(
Tkinter.Button(frame,
text=textCode,
command=lambda seqIndex=seqIndex: self.
selectChemCompVar(seqIndex),
**keywds))
self.ccvButtons[-1].grid(row=frameRow, column=1, sticky=Tkinter.EW)
#
# Set the selector...
#
if resetStatus or resetFrame:
self.statusList.append(
PulldownMenu(frame,
entries=statusEntries,
label_color='red'))
self.statusList[-1].grid(row=frameRow,
column=2,
sticky=Tkinter.EW)
frameRow += 1
return True
class CreateShiftListPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'CreateShiftList.html')
def __init__(self, parent, project):
self.project = project
self.peakLists = []
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Create shift list from peak lists',
modal=False,
transient=True)
def body(self, master):
#
# Peaklist setup
#
self.peakListDict = {}
for experiment in self.project.currentNmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
for peakList in dataSource.sortedPeakLists():
peakListLabel = "%s:%s:%d:%s" % (
experiment.name, dataSource.name, peakList.serial,
peakList.name)
self.peakListDict[peakListLabel] = peakList
peakListLabels = self.peakListDict.keys()
peakListLabels.sort()
#
# chemical shift list setup
#
self.shiftListDict = {}
self.shiftListDict['None'] = None
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
shiftListLabel = "%d:%s" % (shiftList.serial, shiftList.name)
self.shiftListDict[shiftListLabel] = shiftList
shiftListLabels = self.shiftListDict.keys()
shiftListLabels.sort()
row = 0
label = Label(master, text="Generation of chemical shift list")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Peak lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.peakListBox = ScrolledListbox(master,
width=50,
height=5,
selectmode=Tkinter.MULTIPLE,
initial_list=peakListLabels)
self.peakListBox.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use existing shift list:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master, entries=shiftListLabels)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use multiple assignments:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.useAllContribs = CheckButton(master)
self.useAllContribs.grid(row=row, column=1, sticky=Tkinter.W)
#
# Setup the default shift error per nucleus
#
self.defaultShiftError = {}
for (nucl, text, defValue) in [('1H', 'proton', '0.002'),
('13C', 'carbon', '0.1'),
('15N', 'nitrogen', '0.1')]:
row += 1
label = Label(master, text="Default %s shift error:" % text)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.defaultShiftError[nucl] = Entry(master, text=defValue)
self.defaultShiftError[nucl].grid(row=row,
column=1,
sticky=Tkinter.W)
row += 1
texts = ['Create shift list']
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 apply(self):
selectedPeakLists = self.peakListBox.getSelectedItems()
for peakListLabel in selectedPeakLists:
self.peakLists.append(self.peakListDict[peakListLabel])
chemShiftList = self.shiftListDict[self.shiftListSelect.getSelected()]
if not chemShiftList:
chemShiftListName = askString("Enter chemical shift list name",
"New chemical shift list name", '',
self)
else:
chemShiftListName = chemShiftList.name
useAllContribs = self.useAllContribs.isSelected()
defaultShiftError = {}
for nucl in self.defaultShiftError.keys():
defaultShiftError[nucl] = returnFloat(
self.defaultShiftError[nucl].get())
listCreated = createChemShifts(self.peakLists,
guiParent=self.parent,
multiDialog=self.parent.multiDialog,
shiftList=chemShiftList,
useAllContribs=useAllContribs,
defaultShiftError=defaultShiftError,
shiftListName=chemShiftListName)
if listCreated:
showInfo(
"Success",
"Succesfully created a chemical shift list from peaklist(s)")
return True
class SingleResonanceStatusPopup(BasePopup):
def __init__(self,
parent,
message,
nmrRes,
optionList,
title,
urlFile=None):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.singleResonanceStatus = None
self.message = message
self.optionList = optionList
self.nmrRes = nmrRes
if urlFile:
self.help_url = joinPath(getHelpUrlDir(), urlFile + '.html')
else:
self.help_url = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def body(self, master):
master.grid_columnconfigure(0, weight=1)
for i in range(3):
master.grid_rowconfigure(i, weight=1)
self.geometry('600x400')
# Master is the owner widget (not self.parent) - parent of the widget here
row = 0
label = Label(master,
text="Residue %s-%d" %
(self.nmrRes.molResidue.ccpCode, self.nmrRes.seqCode))
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
label = Label(master, text=self.message)
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.menu = PulldownMenu(master, entries=self.optionList)
self.menu.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0)
def apply(self):
self.singleResonanceStatus = self.optionList.index(
self.menu.getSelected())
return True
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
class SelectionListPopup(TemporaryBasePopup):
def __init__(self, parent, selectionList, title = 'Select', text = 'Select', topText = None, dismissText = None, selected = None, selectionDict = None, urlFile = None, dismissButton = True, modal = False):
self.selectionList = selectionList
self.selectionDict = selectionDict
self.text = text
self.dismissButton = dismissButton
if dismissButton:
if dismissText:
self.dismissText = dismissText
else:
self.dismissText = 'dismiss'
self.topText = topText
self.isSelected = None
if not selected:
self.selectedIndex = 0
else:
self.selectedIndex = self.selectionList.index(selected)
if urlFile:
self.help_url = joinPath(getHelpUrlDir(),urlFile + '.html')
else:
self.help_url = None
TemporaryBasePopup.__init__(self,parent = parent, title = title, modal = modal, transient=True)
def body(self, master):
#
# Popup window
#
row = 0
if self.topText:
label = Label(master, text= self.topText)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= self.text)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menu = PulldownMenu(master, entries = self.selectionList, selected_index = self.selectedIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.E, ipadx = 20)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
if self.dismissButton:
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text = self.dismissText, help_url=self.help_url)
else:
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 3)
def apply(self):
self.isSelected = self.menu.getSelected()
if self.selectionDict:
self.selection = self.selectionDict[self.isSelected]
else:
self.selection = self.isSelected
return True
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 CloudHomologueAssignPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.molSystem = None
self.chain = None
self.assignment = None
self.scores = []
BasePopup.__init__(self, parent, title="Cloud Threader", **kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def update(self):
if self.assignment and self.scores:
self.assignButton.enable()
else:
self.assignButton.disable()
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def assignSpinSystems(self):
if self.assignment and self.scores:
if showWarning('Query','Are you sure?'):
threshold = self.thresholdEntry.get() or -4.0
i = 0
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=None)
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
i += 1
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=residue)
showWarning('Done','%d residues assigned' % i)
def getMolSystems(self):
names = []
for molSystem in self.project.molSystems:
if molSystem.chains:
names.append( '%s' % (molSystem.code) )
return names
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
def updateMolSystems(self, *opt):
names = self.getMolSystems()
if names:
if not self.molSystem:
self.molSystem = self.project.findFirstMolSystem(code=names[0])
self.molSysPulldown.setup(names, names.index(self.molSystem.code))
def getChains(self):
chains = []
if self.molSystem:
for chain in self.molSystem.chains:
chains.append( [chain.code, chain] )
return chains
def changeChain(self, i, name=None):
if not name:
i = self.chainPulldown.selected_index
chains = self.getChains()
if chains:
self.chain = chains[i][1]
def updateChains(self, *chain):
chains = self.getChains()
if chains:
names = [x[0] for x in chains]
if (not self.chain) or (self.chain.code not in names):
self.chain = chains[0][1]
self.chainPulldown.setup(names, names.index(self.chain.code) )
self.update()
def destroy(self):
for func in ('__init__','delete'):
Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
BasePopup.destroy(self)
def body(self, master):
#
# Initialize
#
#
# Get chem shift range
#
peakChemShiftRange = []
if not self.peaks:
return
elif hasattr(self.peaks[0], 'ppm'):
peakUnit = 'ppm'
elif hasattr(self.peaks[0], 'point'):
peakUnit = 'point'
else:
return
for peak in self.peaks:
peakInfo = getattr(peak, peakUnit)
for dim in range(0, len(peakInfo)):
if len(peakChemShiftRange) < dim + 1:
peakChemShiftRange.append([999999, -999999])
if peakChemShiftRange[dim][0] > peakInfo[dim]:
peakChemShiftRange[dim][0] = peakInfo[dim]
if peakChemShiftRange[dim][1] < peakInfo[dim]:
peakChemShiftRange[dim][1] = peakInfo[dim]
#
# Make datadimref lists
#
dataDimRefList = []
self.dataDimRefDict = {}
dataDimRefSelection = []
for i in self.order:
dataDim = self.dataSource.sortedDataDims()[i]
if dataDim.dim == 1:
addInfo = " (acqu)"
else:
addInfo = ""
for dataDimRef in dataDim.dataDimRefs:
# Note: key for dataDimRef is expDimRef!
isotopeString = string.join(dataDimRef.expDimRef.isotopeCodes,
dirsep)
selectionString = "Dim %d, nucl %s, refValue %s%s" % (
dataDim.dim, isotopeString, dataDimRef.refValue, addInfo)
# In principle this could go wrong if one expDim has two expDimRefs with same isotopelist
# (but what would be the use? Is this a good constraint?)
dataDimRefList.append(selectionString)
self.dataDimRefDict[selectionString] = dataDimRef
dataDimRefSelection.append(dataDimRefList[-1])
#
# Add on a None dimension if necessary
#
if self.numDim < len(peakChemShiftRange):
dataDimRefSelection.append('None')
dataDimRefList.append('None')
self.dataDimRefDict['None'] = None
#
# Popup info
#
#
# Header labels
#
row = 0
label = Label(master, text="Peak dim")
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text="Chem. shift range")
label.grid(row=row, column=1, sticky=Tkinter.EW)
# TODO: add in peak dim column headers if known (for nmrView for example)
label = Label(master, text="DataDimRef selection")
label.grid(row=row, column=2, sticky=Tkinter.EW)
#
# Selection per peakDim
#
self.dataDimRefMenu = []
for peakDim in range(0, len(peakChemShiftRange)):
row = row + 1
label = Label(master, text=str(peakDim))
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text="%.3f - %.3f %s" %
(peakChemShiftRange[peakDim][0],
peakChemShiftRange[peakDim][1], peakUnit))
label.grid(row=row, column=1, sticky=Tkinter.EW)
if peakDim < len(dataDimRefList):
selectedIndex = dataDimRefList.index(
dataDimRefSelection[peakDim])
else:
selectedIndex = len(dataDimRefList) - 1
self.dataDimRefMenu.append(
PulldownMenu(master,
entries=dataDimRefList,
selected_index=selectedIndex))
self.dataDimRefMenu[-1].grid(row=row,
column=2,
sticky=Tkinter.E,
ipadx=20)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def body(self, guiFrame):
row = 0
guiFrame.grid_columnconfigure(3, weight=1)
label = Label(guiFrame, text='Cloud file names:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileNameEntry = Entry(guiFrame,
text='testHistone\d+.pdb',
returnCallback=self.loadClouds)
self.fileNameEntry.grid(row=row, column=1, sticky=Tkinter.W)
strucLabel = Label(guiFrame, text='Comparison structure')
strucLabel.grid(row=row, column=2, sticky=Tkinter.W)
self.strucPulldown = PulldownMenu(guiFrame,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.strucPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
sdTolLabel = Label(guiFrame, text='Tolerance (SDs):')
sdTolLabel.grid(row=row, column=0, sticky=Tkinter.W)
self.sdToleranceEntry = FloatEntry(guiFrame, text=2.0, width=6)
self.sdToleranceEntry.grid(row=row, column=1, stick=Tkinter.W)
atomTypes = ['All', 'H', 'H HA', 'H HA HB']
label = Label(guiFrame, text='RMSD Atom Types:')
label.grid(row=row, column=2, sticky=Tkinter.W)
self.atomsPulldown = PulldownMenu(guiFrame,
entries=atomTypes,
callback=self.setAtomTypes,
selected_index=0,
do_initial_callback=0)
self.atomsPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = ['#', 'File name', 'RMSD to mean']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
initialRows=10,
headingList=colHeadings,
callback=self.selectCell,
objectList=[],
textMatrix=[
[],
],
multiSelect=1)
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
texts = [
'Load\nClouds', 'Align\nClouds', 'Calc\nRMSD',
'Make Cloud\nfrom structure', 'Remove', 'Remove\nbad'
]
commands = [
self.loadClouds, self.alignClouds, self.calcRmsd,
self.makeStrucCloud, self.deleteClouds, self.filterClouds
]
self.bottomButtons = createDismissHelpButtonList(
guiFrame,
texts=texts,
expands=1,
commands=commands,
help_url=self.help_url)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.update()
