class NamingSystemPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'NamingSystem.html')
def __init__(self, parent, namingSysList=None, namingSysDict=None):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.namingSys = None
self.namingSysList = namingSysList
self.namingSysDict = namingSysDict
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(self,
parent=parent,
title='Choose namingSys',
modal=False,
transient=True)
def body(self, master):
#
# Popup gui
#
# First row
row = 0
label = Label(master, text="Choose a naming system:")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
label = Label(master, text="(% matches in brackets)")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.menu = PulldownMenu(master, entries=self.namingSysList)
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 = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0)
def apply(self):
self.namingSysName = self.namingSysDict[self.menu.getSelected()]
return True
class ItemSelectPopup(BasePopup):
def __init__(self,
parent,
entries,
label='',
message='',
select_text='Select',
*args,
**kw):
self.entries = entries
self.label = label
self.message = message
self.select_text = select_text
self.item = None
kw['title'] = 'Select item'
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def body(self, master):
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(1, weight=1)
row = 0
if (self.message):
label = Label(master, text=self.message)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row = row + 1
if (self.label):
label = Label(master, text=self.label)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.itemMenu = PulldownMenu(master, entries=self.entries)
self.itemMenu.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = [self.select_text]
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def apply(self):
self.item = self.itemMenu.getSelected()
return True
class BacusPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.project = parent.project
self.hNoesy = None
self.nNoesy = None
self.cNoesy = None
self.shiftList = None
BasePopup.__init__(self, parent, title="BACUS control module", **kw)
def body(self, guiParent):
guiParent.grid_columnconfigure(0, weight=1)
row = 0
guiParent.grid_rowconfigure(row, weight=1)
inputFrame = LabelFrame(guiParent, text='Inputs:')
inputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
label = Label(inputFrame, text='NOESY:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.hNoesyPulldown = PulldownMenu(inputFrame,callback=self.setHNoesy)
self.hNoesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='15N NOESY:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.nNoesyPulldown = PulldownMenu(inputFrame,callback=self.setNNoesy)
self.nNoesyPulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='13C NOESY:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.cNoesyPulldown = PulldownMenu(inputFrame,callback=self.setCNoesy)
self.cNoesyPulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='Shift List:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.shiftListPulldown = PulldownMenu(inputFrame,callback=self.setShiftList)
self.shiftListPulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='2d BACUS executable:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.executableEntry = Entry(inputFrame, text='/home/tjs23/clouds/justin/SpiBacusMidge/bacus/bacus_tjs.exe')
self.executableEntry.grid(row=4, column=1, sticky=Tkinter.NW)
self.executableButton = Button(inputFrame, text='Choose file', command=self.chooseExecutable)
self.executableButton.grid(row=5, column=1, sticky=Tkinter.EW)
row += 1
outputFrame = LabelFrame(guiParent, text='Output:')
outputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
row += 1
texts = ['Run BACUS 2d','Run BACUS 3d']
commands = [self.runBacus,self.runBacus3d]
self.bottomButtons = createDismissHelpButtonList(guiParent,texts=texts,commands=commands,expands=0,help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
def chooseExecutable(self):
fileTypes = [FileType('Table', ['*.exe']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types = fileTypes,
title = 'Choose 2d BACUS executable', dismiss_text = 'Cancel',
selected_file_must_exist = False)
fileName = fileSelectPopup.getFile()
if fileName:
self.executableEntry.set(fileName)
def update(self):
# set defaults via pulldown callbacks
names = [self.getPeakListlabel(x) for x in self.gethNoesys()]
if names:
self.hNoesyPulldown.setup(names,0)
else:
self.hNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getNNoesys()]
if names:
self.nNoesyPulldown.setup(names,0)
else:
self.nNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getCNoesys()]
if names:
self.cNoesyPulldown.setup(names,0)
else:
self.cNoesyPulldown.setup([],-1)
names = ['Shift List %d' % x.serial for x in self.getShiftLists()]
if names:
self.shiftListPulldown.setup(names,0)
else:
self.shiftListPulldown.setup([],-1)
self.updateButtons()
def updateButtons(self):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
self.bottomButtons.buttons[1].enable()
else:
self.bottomButtons.buttons[1].disable()
if self.hNoesy and self.executableEntry.get() and self.shiftList:
self.bottomButtons.buttons[0].enable()
else:
self.bottomButtons.buttons[0].disable()
def runBacus3d(self, fileRoot='CCPN1'):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
run3dBacus(fileRoot,self.shiftList,self.cNoesy,self.nNoesy)
def runBacus(self, fileRoot='CCPN1'):
executable = self.executableEntry.get()
if self.hNoesy and self.shiftList and executable:
run2dBacus(fileRoot, executable, self.hNoesy, self.shiftList)
def getPeakListlabel(self, peakList):
return '%s:%s:%d' % (peakList.dataSource.experiment.name, peakList.dataSource.name, peakList.serial)
def getShiftLists(self):
shiftLists = []
if self.project:
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
return list(shiftLists)
def setShiftList(self, index, name=None):
shiftLists = self.getShiftLists()
if shiftLists:
self.shiftList = shiftLists[index]
else:
self.shiftList = None
def gethNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
if isotopes == ['1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getNNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['15N', '1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getCNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['13C', '1H', '1H']:
for peakList in spectrum.peakLists:
if 'NOE' in experiment.name.upper():
peakLists.insert(0, peakList)
else:
peakLists.append(peakList)
return peakLists
def setHNoesy(self, index, name=None):
peakLists = self.gethNoesys()
if peakLists:
self.hNoesy = peakLists[index]
else:
self.hNoesy = None
def setNNoesy(self, index, name=None):
peakLists = self.getNNoesys()
if peakLists:
self.nNoesy = peakLists[index]
else:
self.nNoesy = None
def setCNoesy(self, index, name=None):
peakLists = self.getCNoesys()
if peakLists:
self.cNoesy = peakLists[index]
else:
self.cNoesy = None
def destroy(self):
BasePopup.destroy(self)
class 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
class PopupTemplate(BasePopup):
def __init__(self, parent, project=None, *args, **kw):
self.project = project
self.parent = parent
self.objects = self.getObjects()
self.object = None
BasePopup.__init__(self, parent=parent, title='Popup Template', **kw)
self.updateObjects()
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def floatEntryReturn(self, event):
value = self.floatEntry.get()
self.textWindow.setText('%s\n' % value)
def selectObject(self, object, row, col):
self.object = object
def getKeywords(self, object):
if object :
values = object.keywords
self.multiWidget.set(values)
def setKeywords(self, event):
values = self.multiWidget.get()
self.object.keywords = values
self.updateObjects()
def getNumber(self, object):
if object :
self.intEntry.set(object.quantity)
def setNumber(self, event):
value = self.intEntry.get()
self.object.quantity = value
self.updateObjects()
def toggleFrame1(self, isHidden):
if isHidden:
self.scrolledMatrix.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel2.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame2(self, isHidden):
if isHidden:
self.scrolledGraph.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame3(self, isHidden):
if isHidden:
self.scrolledCanvas.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel2.arrowOff()
def valueRampCallback(self, value):
self.textWindow.setText('%s\n' % value)
def checkRadioButtons(self, value):
self.textWindow.setText('%s\n' % value)
def selectPulldown(self, index, name):
self.textWindow.setText('%d, %s\n' % (index, name))
def toggleSelector(self, value):
self.textWindow.setText('%s\n' % value)
def changedCheckButtons(self, values):
self.textWindow.setText(','.join(values) + '\n')
def getObjects(self):
objects = []
objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) )
objects.append( Fruit('Orange', '#FF8000',4 ) )
objects.append( Fruit('Banana', '#FFF000',5 ) )
objects.append( Fruit('Pinapple','#FFD000',9 ) )
objects.append( Fruit('Kiwi', '#008000',12) )
objects.append( Fruit('Lime', '#00FF00',2 ) )
objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) )
objects.append( Fruit('Pear', '#408000',6 ) )
objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) )
objects.append( Fruit('Plumb', '#800080',7 ) )
return objects
def updateObjects(self, event=None):
textMatrix = []
objectList = []
colorMatrix = []
for object in self.objects:
datum = []
datum.append( object.name )
datum.append( None )
datum.append( object.quantity )
datum.append( ','.join(object.keywords) )
colors = [None, object.color, None, None]
textMatrix.append(datum)
objectList.append(object)
colorMatrix.append(colors)
if self.check.get():
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList)
else:
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix)
def selectFile(self):
fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = fileSelectPopup.getFile()
self.textWindow.setText('File Selected: %s\n' % fileName)
def showWarning(self, eventObject):
self.textWindow.setText('Text Entry Return Pressed\n')
showWarning('Warning Title','Warning Message')
return
def pressButton(self):
self.textWindow.setText('Button Pressed\n')
if showYesNo('Title','Prompt: Clear text window?'):
self.textWindow.clear()
return
def quit(self):
BasePopup.destroy(self)
class HelpFrame(Frame):
def __init__(self,
parent,
width=70,
height=20,
xscroll=False,
yscroll=True,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
row = 0
texts = ('back', 'forward', 'load')
commands = (self.prevUrl, self.nextUrl, self.loadUrl)
self.buttons = ButtonList(self, texts=texts, commands=commands)
self.buttons.grid(row=row, column=0)
self.url_entry = Entry(self, returnCallback=self.loadUrl)
self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.createFindFrame(frame)
row = row + 1
self.grid_rowconfigure(row, weight=1)
self.help_text = ScrolledHtml(self,
width=width,
height=height,
xscroll=xscroll,
yscroll=yscroll,
startUrlCallback=self.startOpenUrl,
endUrlCallback=self.endOpenUrl,
enterLinkCallback=self.setLinkLabel,
leaveLinkCallback=self.setLinkLabel)
self.help_text.grid(row=row,
column=0,
columnspan=3,
sticky=Tkinter.NSEW)
row = row + 1
self.link_label = Label(self)
self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
button = memops.gui.Util.createDismissButton(self,
dismiss_cmd=self.close)
button.grid(row=row, column=2)
self.urls = []
self.current = -1
self.updateUrlList = True
self.setButtonState()
def close(self):
if (self.popup):
if (self.popup.modal):
self.popup.do_grab()
popup = self.parent
while (not hasattr(popup, 'top')):
popup = popup.parent
popup.close()
def createFindFrame(self, master):
frame = Frame(master)
frame.grid(row=0, column=0, sticky=Tkinter.W)
arrow = ToggleArrow(frame, callback=self.toggleFindFrame)
arrow.grid(row=0, column=0)
button = Button(frame, text='find:', command=self.findPhrase)
button.grid(row=0, column=1)
self.find_entry = Entry(frame,
width=20,
returnCallback=self.findPhrase)
self.find_entry.grid(row=0, column=2)
self.find_frame = frame = Frame(master)
entries = ('search forwards', 'search backwards')
self.direction_buttons = PulldownMenu(frame, entries=entries)
self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5)
self.forwards_entries = entries = ('wrap search', 'stop at end')
self.backwards_entries = ('wrap search', 'stop at beginning')
self.wrap_buttons = PulldownMenu(frame, entries=entries)
self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5)
self.direction_buttons.callback = self.setWrapText
entries = ('case insensitive', 'case sensitive')
self.case_buttons = PulldownMenu(frame, entries=entries)
self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5)
entries = ('literal search', 'regex search')
self.pattern_buttons = PulldownMenu(frame, entries=entries)
self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5)
self.countVar = Tkinter.IntVar()
def setWrapText(self, entry_ind, entry):
if (entry_ind == 0):
entries = self.forwards_entries
else:
entries = self.backwards_entries
self.wrap_buttons.replace(
entries, selected_index=self.wrap_buttons.getSelectedIndex())
def findPhrase(self, *extra):
phrase = self.find_entry.get()
if (not phrase):
showError('No find phrase', 'Enter phrase in entry box.')
return
if (self.direction_buttons.getSelectedIndex() == 0):
forwards = 1
backwards = 0
else:
forwards = 0
backwards = 1
if (self.case_buttons.getSelectedIndex() == 0):
nocase = 1
else:
nocase = 0
if (self.pattern_buttons.getSelectedIndex() == 0):
exact = 1
regexp = 0
else:
exact = 0
regexp = 1
start = self.help_text.tag_nextrange(Tkinter.SEL, '1.0')
if (start):
start = start[0]
if (forwards):
start = '%s+1c' % start
else:
start = '%s-1c' % start
else:
start = Tkinter.CURRENT
if (self.wrap_buttons.getSelectedIndex() == 0):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp)
elif (forwards):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex=Tkinter.END)
else:
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex='1.0')
if (match):
self.help_text.see(match)
self.help_text.setSelection(
match, '%s+%dc' % (match, self.countVar.get()))
self.help_text.tag_config(Tkinter.SEL, background='gray70')
else:
showInfo('No match', 'No match found for phrase.')
def toggleFindFrame(self, isClosed):
if (isClosed):
self.find_frame.grid_forget()
else:
self.find_frame.grid(row=1, column=0, sticky=Tkinter.W)
def setButtonState(self):
n = len(self.urls)
if ((n >= 2) and (self.current > 0)):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[0].config(state=state)
if ((n >= 2) and (self.current < (n - 1))):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[1].config(state=state)
def setLinkLabel(self, url=''):
self.link_label.set(url)
def loadUrl(self, *extra):
url = self.url_entry.get()
if (url):
if (url.find(':') == -1):
if (url[:2] != '//'):
url = '//' + url
url = 'http:' + url
self.showUrl(url, forceLoad=True)
def newUrl(self, url):
self.current = self.current + 1
self.urls[self.current:] = [[url, 0.0]]
self.setButtonState()
#print 'newUrl', self.current, self.urls
def prevUrl(self):
if (self.current > 0): # True if called via button
(url, offset) = self.urls[self.current - 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current - 1
self.setButtonState()
#print 'prevUrl', self.current, self.urls
def nextUrl(self):
if (self.current < (len(self.urls) - 1)): # True if called via button
(url, offset) = self.urls[self.current + 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current + 1
self.setButtonState()
#print 'nextUrl', self.current, self.urls
def showText(self, message, popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.setState(Tkinter.NORMAL) # so that can add text
self.help_text.clear() # clear existing text
self.help_text.append(message)
self.help_text.setState(Tkinter.DISABLED) # make text read-only
self.open()
def startOpenUrl(self, yview):
if (self.urls):
self.urls[self.current][1] = yview[0]
def endOpenUrl(self, url):
#print 'endOpenUrl', url, self.updateUrlList
self.url_entry.set(url)
if (self.updateUrlList):
self.newUrl(url)
self.setLinkLabel()
self.open()
def showUrl(self,
url,
offset=None,
forceLoad=False,
allowModifyPath=True,
popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.openUrl(url,
forceLoad=forceLoad,
allowModifyPath=allowModifyPath)
if (offset is not None):
self.help_text.yview(Tkinter.MOVETO, str(offset))
class 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 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 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 LinkResonancesPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'LinkResonances.html')
def __init__(self,
parent,
formatNamesList,
formatNamesDict,
title='Link resonances setup'):
self.guiParent = parent
self.formatNamesList = formatNamesList
self.formatNamesDict = formatNamesDict
self.status = False
TemporaryBasePopup.__init__(self,
parent=parent,
title=title,
modal=False,
transient=False)
def body(self, master):
row = 0
label = Label(master, text='File format reference:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.menu = PulldownMenu(master, entries=self.formatNamesList)
self.menu.grid(row=row, column=1, sticky=Tkinter.E, ipadx=20)
row = row + 1
label = Label(master, text='Try to link unrecognized atom names')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.linkRes = CheckButton(master, selected=True)
self.linkRes.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Try IUPAC names (as backup)')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.iupacNames = CheckButton(master)
self.iupacNames.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Use ambiguous name information')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.useAmb = CheckButton(master)
self.useAmb.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Complete stereospecific assignment')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allStereo = CheckButton(master)
self.allStereo.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Force shift merges')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.shiftMerge = CheckButton(master)
self.shiftMerge.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master,
text='Status other atom for all single prochiral atoms')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allSingleProchiral = PulldownMenu(
master, entries=['Unknown', 'Same information', 'Always ignore'])
self.allSingleProchiral.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text='Status other atom for all possibly equivalent single atoms')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allSinglePossEquiv = PulldownMenu(
master, entries=['Unknown', 'Always equivalent', 'Always ignore'])
self.allSinglePossEquiv.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text=
'Automatically connect ambiguous resonances to stereospecific ones'
)
label.grid(row=row, column=0, sticky=Tkinter.E)
self.connStereo = CheckButton(master)
self.connStereo.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Use minimal number of popups')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.minimalPopups = CheckButton(master)
self.minimalPopups.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Verbose output')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.verbose = CheckButton(master, selected=True)
self.verbose.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text=
'Warning: it is recommended you save your project first,\nin case linkResonances is interrupted (this might corrupt the data).',
fg='red')
label.grid(row=row,
column=0,
columnspan=2,
ipady=15,
sticky=Tkinter.EW)
row = row + 1
texts = ['Link resonances to atoms']
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 apply(self):
self.assignFormat = self.formatNamesDict[self.menu.getSelected()]
self.globalStereoAssign = self.allStereo.isSelected()
self.useIupacMatching = self.iupacNames.isSelected()
self.useLinkResonancePopup = self.linkRes.isSelected()
self.minimalPrompts = self.minimalPopups.isSelected()
self.verbose = self.verbose.isSelected()
self.forceShiftMerge = self.shiftMerge.isSelected()
self.useAmbiguity = self.useAmb.isSelected()
self.autoConnectStereo = self.connStereo.isSelected()
self.setSingleProchiral = self.allSingleProchiral.getSelected()
self.setSinglePossEquiv = self.allSinglePossEquiv.getSelected()
self.status = True
return True
class GroupChemShiftsPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'GroupChemShifts.html')
def __init__(self, parent, project):
#
# Info for writing file...
#
self.groupText = {}
#
# Set up molSystem information
#
self.project = project
self.molSysList = list(project.sortedMolSystems())
self.molSystems = None
self.molSysLabelList = []
self.molSysLabelDict = {}
self.molSysRelationDict = {}
molSysLabel = 'All molSystems'
if self.setChainLabels(molSysLabel, self.molSysList):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = self.molSysList
for molSys in self.molSysList:
molSysLabel = '%s' % molSys.code
if self.setChainLabels(molSysLabel, [molSys]):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = [molSys]
if not self.molSysLabelList:
showWarning('Warning',
'No chemical shift lists available! Exiting...')
return
#
# Some initializing...
#
self.chains = None
self.shiftList = None
self.shiftListLabel = None
self.results = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Group chemical shift values',
modal=False,
transient=True)
def setChainLabels(self, molSysLabel, molSysList):
#
# Set up chain information
#
chainLabelList = []
chainLabelDict = {}
chainLabelShiftListDict = {}
self.molSysRelationDict[molSysLabel] = [
chainLabelList, chainLabelDict, chainLabelShiftListDict
]
chains = []
for molSys in molSysList:
chains.extend(list(molSys.sortedChains()))
chainLabel = 'All chains'
if self.setShiftListLabels(chainLabel, chains,
self.molSysRelationDict[molSysLabel][2]):
self.molSysRelationDict[molSysLabel][0].append(chainLabel)
self.molSysRelationDict[molSysLabel][1][chainLabel] = chains
for chain in chains:
chainLabel = "'%s' (mol. '%s')" % (chain.code, chain.molecule.name)
if self.setShiftListLabels(
chainLabel, [chain],
self.molSysRelationDict[molSysLabel][2]):
self.molSysRelationDict[molSysLabel][0].append(chainLabel)
self.molSysRelationDict[molSysLabel][1][chainLabel] = [chain]
return self.molSysRelationDict[molSysLabel][0]
def setShiftListLabels(self, chainLabel, chains, chainLabelShiftListDict):
#
# Set up chemical shift list information (slooooww so done at start)
#
shiftLists = []
shiftListCount = {}
resonanceTracker = []
shiftListLabels = []
shiftListLabelsDict = {}
atomCount = 0
for chain in chains:
for residue in chain.residues:
for atom in residue.atoms:
atomCount += 1
if atom.atomSet:
for resonanceSet in atom.atomSet.resonanceSets:
for resonance in resonanceSet.resonances:
if resonance in resonanceTracker:
continue
resonanceTracker.append(resonance)
for shift in resonance.shifts:
if shift.parentList not in shiftLists:
shiftLists.append(shift.parentList)
shiftListCount[shift.parentList] = 0
shiftListCount[shift.parentList] += 1
for shiftList in shiftLists:
percentage = (shiftListCount[shift.parentList] * 100.0) / atomCount
shiftListLabel = "%d:%s (%.1f%%)" % (shiftList.serial,
shiftList.name, percentage)
shiftListLabels.append(shiftListLabel)
shiftListLabelsDict[shiftListLabel] = shiftList
chainLabelShiftListDict[chainLabel] = [
shiftListLabels, shiftListLabelsDict
]
return shiftListLabels
def body(self, master):
#
# Setup header
#
row = 0
self.columnSpan = 3
label = Label(
master,
text=
'Select molecular system, chains and chemical shift list to be analyzed:'
)
label.grid(row=row,
column=0,
columnspan=self.columnSpan,
sticky=Tkinter.EW)
row += 1
self.molSysSelect = PulldownMenu(master,
entries=self.molSysLabelList,
callback=self.setupChains)
self.molSysSelect.grid(row=row, column=0, sticky=Tkinter.W)
self.chainSelect = PulldownMenu(master,
entries=self.chainLabelList,
callback=self.setupShiftList)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftListLabels,
callback=self.setupPercentageFrame,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=2, sticky=Tkinter.W)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
master.grid_rowconfigure(row, weight=1)
for i in range(self.columnSpan):
master.grid_columnconfigure(i, weight=1)
self.percentageFrame = ScrolledFrame(master,
height=180,
doExtraConfig=False)
self.percentageFrame.grid(row=row,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
self.percentageFrameRow = row
self.percentageFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
master.grid_rowconfigure(row, weight=1)
self.resultsFrame = ScrolledFrame(master,
height=180,
doExtraConfig=False)
self.resultsFrame.grid(row=row,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
self.resultsFrameRow = row
self.resultsFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
row += 1
texts = ['Recalculate', 'Write to file']
commands = [
self.recalc, self.writeFile
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, columnspan=self.columnSpan, sticky=Tkinter.EW)
self.shiftListSelect.callback(0, self.shiftListLabels[0])
def setupChains(self, listIndex, molSysLabel):
molSystems = self.molSysLabelDict[molSysLabel]
if self.molSystems == molSystems:
return
self.molSystems = molSystems
self.chainLabelList = self.molSysRelationDict[molSysLabel][0]
self.chainLabelDict = self.molSysRelationDict[molSysLabel][1]
self.chainLabelShiftListDict = self.molSysRelationDict[molSysLabel][2]
if hasattr(self, 'chainSelect'):
self.chains = None
self.chainSelect.callback(0, self.chainLabelList[0])
def setupShiftList(self, listIndex, chainLabel):
chains = self.chainLabelDict[chainLabel]
if self.chains == chains:
return
self.chains = chains
#
# Reset the pulldown menu
#
if hasattr(self, 'chainSelect'):
self.chainSelect.replace(self.chainLabelList)
#
# Set up chemical shift lists
#
self.shiftListLabels = self.chainLabelShiftListDict[chainLabel][0]
self.shiftListLabelsDict = self.chainLabelShiftListDict[chainLabel][1]
if hasattr(self, 'percentageFrame'):
self.shiftList = None
self.shiftListLabel = None
self.setupPercentageFrame(0, self.shiftListLabels[0])
def setupPercentageFrame(self, listIndex, shiftListLabel):
if self.shiftListLabel == shiftListLabel:
return
self.shiftList = self.shiftListLabelsDict[shiftListLabel]
self.shiftListLabel = shiftListLabel
#
# Reset chemical shift groups...
#
self.shiftGroupsList = []
for i in range(1, 10):
shiftGroupLabel = 'Group_%s' % i
self.shiftGroupsList.append(shiftGroupLabel)
#
# Reset the pulldown menu
#
if hasattr(self, 'shiftListSelect'):
if hasattr(self.shiftListSelect,
'entries') and tuple(self.shiftListLabels) != tuple(
self.shiftListSelect.entries): # HACK
# otherwise can get infinite recursion but even with above could
# if no self.shiftListLabels because of "None" entry in PulldownMenu
self.shiftListSelect.replace(self.shiftListLabels)
self.shiftListSelect.setSelected(shiftListLabel)
#
# Reset frame...
#
self.percentageFrame.destroy()
self.percentageFrame = ScrolledFrame(self.percentageFrameMaster,
height=180,
doExtraConfig=False)
self.percentageFrame.grid(row=self.percentageFrameRow,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
#
# Recalculate results
#
self.results = makeChemShiftSelections(self.parent, self.chains,
self.shiftList)
resultKeys = self.results.keys()
resultKeys.sort()
#
# Set up the information
#
frameRow = 0
frame = self.percentageFrame.frame
self.shiftGroupObjects = {}
for resultKey in resultKeys:
allAtoms = self.results[resultKey][0]
shiftAtoms = self.results[resultKey][1]
percentage = shiftAtoms * 100.0 / allAtoms
label = Label(frame, text=resultKey)
label.grid(row=frameRow, column=0, sticky=Tkinter.W)
label = Label(frame, text="%.1f%%" % percentage)
label.grid(row=frameRow, column=1, sticky=Tkinter.W)
label = Label(frame, text="(%d/%d)" % (shiftAtoms, allAtoms))
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
self.shiftGroupObjects[resultKey] = PulldownMenu(
frame, entries=self.shiftGroupsList)
self.shiftGroupObjects[resultKey].grid(row=frameRow,
column=3,
sticky=Tkinter.E)
frameRow += 1
return True
def recalc(self):
groups = {}
groupsInfo = {}
for resultKey in self.shiftGroupObjects:
group = self.shiftGroupObjects[resultKey].getSelected()
if not groups.has_key(group):
groups[group] = []
groupsInfo[group] = [0, 0]
(allAtoms, shiftAtoms) = self.results[resultKey]
groupsInfo[group][0] += allAtoms
groupsInfo[group][1] += shiftAtoms
groups[group].append(resultKey)
#
# Reset frame...
#
self.resultsFrame.destroy()
self.resultsFrame = ScrolledFrame(self.resultsFrameMaster,
height=180,
doExtraConfig=False)
self.resultsFrame.grid(row=self.resultsFrameRow,
columnspan=self.columnSpan,
sticky=Tkinter.NSEW)
#
# Set info in lower frame
#
frameRow = 0
frame = self.resultsFrame.frame
groupKeys = groups.keys()
groupKeys.sort()
self.groupText = {}
for group in groupKeys:
percentage = groupsInfo[group][1] * 100.0 / groupsInfo[group][0]
label = Label(frame, text=group)
label.grid(row=frameRow, column=0, sticky=Tkinter.W)
label = Label(frame, text=groups[group][0])
label.grid(row=frameRow, column=1, sticky=Tkinter.W)
label = Label(frame, text="%.1f%%" % percentage)
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
label = Label(frame,
text="(%d/%d)" %
(groupsInfo[group][1], groupsInfo[group][0]))
label.grid(row=frameRow, column=3, sticky=Tkinter.W)
self.groupText[group] = "%-10s %-20s %8.1f%% (%d/%d)%s" % (
group, groups[group][0], percentage, groupsInfo[group][1],
groupsInfo[group][0], newline)
frameRow += 1
for otherResultKey in groups[group][1:]:
label = Label(frame, text=otherResultKey)
label.grid(row=frameRow, column=2, sticky=Tkinter.W)
self.groupText[group] += "%-10s %-20s%s" % ('', otherResultKey,
newline)
frameRow += 1
return True
def writeFile(self):
filePopup = FormatFilePopup(self, component='text')
if filePopup.fileSelected:
groupKeys = self.groupText.keys()
groupKeys.sort()
fout = open(filePopup.file, 'w')
fout.write("Project: %s" % self.project.name + newline)
fout.write("Molsystems: %s" % self.molSysSelect.getSelected() +
newline)
fout.write("Chains: %s" % self.chainSelect.getSelected() + newline)
fout.write("Shiftlist: %s" % self.shiftListSelect.getSelected() +
newline * 2)
for group in groupKeys:
fout.write(self.groupText[group])
print "Wrote file %s..." % filePopup.file
def apply(self):
return True
class TableExportPopup(BasePopup):
def __init__(self,
parent,
headings,
entries,
title='',
file='',
*args,
**kw):
headings = [heading.replace('\n', ' ') for heading in headings]
if (headings[0].lower() == 'number'):
self.addNumber = False
else:
self.addNumber = True
headings.insert(0, 'Number')
if (not title):
title = 'Export data'
self.exportSelection = parent.tableExportSelection
self.headings = headings
self.entries = entries
self.file = file
kw['title'] = title
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def body(self, master):
master.grid_columnconfigure(2, weight=1)
row = 0
label = Label(master, text='Data to export:')
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.check_buttons = {}
i = 0
for heading in self.headings:
row = row + 1
isSelected = self.exportSelection.get(row, True)
self.check_buttons[i] = c = CheckButton(
master, selected=isSelected, callback=self.toggleCheckButton)
c.grid(row=row, column=1)
label = Label(master, text=heading)
label.grid(row=row, column=2, sticky=Tkinter.W)
i += 1
row = row + 1
button = Button(master, text='File:', command=self.findFile)
button.grid(row=row, column=0, sticky=Tkinter.W)
self.file_entry = Entry(master, text=self.file, width=30)
self.file_entry.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Format:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.format_menu = PulldownMenu(master, entries=exportFormats)
self.format_menu.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
master.grid_rowconfigure(row, weight=1)
texts = ['Save']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def toggleCheckButton(self, isSelected):
for i in self.check_buttons.keys():
self.exportSelection[i] = self.check_buttons[i].get()
def apply(self):
file = self.file_entry.get()
format = self.format_menu.getSelected()
join = exportJoin[format]
n = 0
headings = []
for heading in self.headings:
if self.check_buttons[n].get():
headings.append(n)
n += 1
if (not headings):
showError('Nothing selected',
'No data selected to export.',
parent=self)
return False
try:
fp = open(file, 'w')
except IOError, e:
showError('File error', str(e))
return False
for n in headings:
if (n != headings[0]):
fp.write(join)
fp.write(self.headings[n].encode('utf-8'))
fp.write('\n')
m = 0
for data in self.entries:
if data:
for n in headings:
if (n != headings[0]):
fp.write(join)
if (self.addNumber):
if (n == 0):
x = m + 1
else:
x = data[n - 1]
else:
x = data[n]
if (type(x) == type(float(1))):
if (x == 0):
t = '0'
elif ((abs(x) > 10000) or (abs(x) < 0.001)):
t = '%6.5e' % x
else:
t = '%6.5f' % x
else:
t = str(x)
fp.write(t)
fp.write('\n')
m = m + 1
fp.close()
return True
class EditResStructuresPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.structure = None
self.constraintSet = None
self.cloud = None
self.cloudRmsdDict = {}
self.strucRmsdDict = {}
self.waiting = False
BasePopup.__init__(self,
parent=parent,
title="Resonance Cloud Structures",
**kw)
def body(self, guiFrame):
row = 0
guiFrame.grid_columnconfigure(1, weight=1)
guiFrame.grid_rowconfigure(0, weight=0)
guiFrame.grid_rowconfigure(1, weight=1)
self.generationLabel = Label(guiFrame, text='Structure Generation:')
constraintSets = []
constraintSetNames = []
index = -1
for constraintSet in self.project.nmrConstraintStores:
index += 1
constraintSets.append(constraintSet)
constraintSetNames.append(str(constraintSet.serial))
self.constraintSet = constraintSet
self.constrSetPulldown = PulldownMenu(guiFrame,
self.changeConstraintSet,
constraintSetNames,
selected_index=index,
do_initial_callback=False)
self.generationLabel.grid(row=row, column=0, columnspan=1, sticky='e')
self.constrSetPulldown.grid(row=row,
column=1,
columnspan=1,
sticky='w')
strucLabel = Label(guiFrame, text='Comparison structure')
strucLabel.grid(row=row, column=2, sticky='e')
self.strucPulldown = PulldownMenu(guiFrame,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=False)
self.strucPulldown.grid(row=row, column=3, sticky='w')
sdTolLabel = Label(guiFrame, text='Tolerance (SDs):')
sdTolLabel.grid(row=row, column=4, sticky='e')
self.sdToleranceEntry = FloatEntry(guiFrame, text=2.0, width=6)
self.sdToleranceEntry.grid(row=row, column=5, stick='w')
row += 1
colHeadings = ['#', 'File name', 'RMSD to mean', 'RMSD to structure']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
initialRows=10,
headingList=colHeadings,
callback=self.selectCell,
objectList=[],
textMatrix=[
[],
])
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=6,
sticky='nsew')
row += 1
texts = [
'Calc\nRMSD', 'Make Cloud\nfrom structure', 'Delete', 'Delete\nbad'
]
commands = [
self.calcRmsd, self.makeStrucCloud, self.deleteCloud,
self.filterClouds
]
self.bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
expands=False,
commands=commands,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, columnspan=6, sticky='nsew')
self.update()
for func in ('__init__', 'delete'):
self.registerNotify(self.updateStructureGen,
'ccp.nmr.Nmr.StructureGeneration', func)
def open(self):
self.updateAfter()
BasePopup.open(self)
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
structures.append(structure)
self.structure = structures[index - 1]
def filterClouds(self):
if self.constraintSet:
sdTolerance = self.sdToleranceEntry.get() or 2.0
keptClouds = []
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
meanGroupRmsds = []
for cloud in clouds:
rmsd = self.cloudRmsdDict.get(cloud)
if rmsd is not None:
meanGroupRmsds.append(rmsd)
meanRmsd = 0.0
N = 0
for rmsd in meanGroupRmsds:
meanRmsd += rmsd
N += 1
if N > 0:
meanRmsd /= float(N)
sd = 0.0
for rmsd in meanGroupRmsds:
sd += (rmsd - meanRmsd) * (rmsd - meanRmsd)
if N > 0:
sd /= float(N - 1)
sd = sqrt(sd)
print meanRmsd, '+/-', sd
n = 0
for cloud in clouds:
rmsd = self.cloudRmsdDict.get(cloud)
if rmsd is None:
keptClouds.append(cloud)
elif abs(rmsd - meanRmsd) > (sdTolerance * sd):
print 'Cloud %s is bad' % (cloud)
else:
keptClouds.append(cloud)
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=keptClouds)
self.updateAfter()
def makeStrucCloud(self):
if self.structure:
serials = self.guiParent.application.getValues(
self.constraintSet, 'cloudsResonances')
pdbFileName = 'CloudForStructure.pdb'
#from ccpnmr.clouds.AtomCoordList import AtomCoordList
from ccpnmr.c.AtomCoordList import AtomCoordList
atomCoordList = AtomCoordList()
resDict = {}
hmass = 25
print "L1", len(serials)
for resonance in self.nmrProject.resonances:
resDict[resonance.serial] = resonance
print "L2", len(resDict)
resonances = []
for serial in serials:
if resDict.get(serial) is not None:
resonances.append(resDict[serial])
print "L3", len(resonances)
C = 0
for resonance in resonances:
resonanceSet = resonance.resonanceSet
if resonanceSet:
i = resonanceSet.sortedResonances().index(resonance)
atomSet = resonance.resonanceSet.sortedAtomSets()[i]
coords = getAtomSetCoords(atomSet, self.structure)
coord = coords[0]
atomCoordList.add(hmass, coord.x, coord.y, coord.z)
C += 1
print "L4", len(atomCoordList)
from ccpnmr.clouds.FilterClouds import writeTypedPdbCloud
writeTypedPdbCloud(atomCoordList, pdbFileName, resonances)
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
clouds.append(pdbFileName)
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=clouds)
self.updateAfter()
def calcRmsd(self):
if self.constraintSet:
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
from ccpnmr.clouds.FilterClouds import filterClouds
rmsds = filterClouds(clouds)
n = len(clouds)
for i in range(n):
cloud = clouds[i]
rmsd = rmsds[i]
self.cloudRmsdDict[cloud] = rmsd
self.updateAfter()
def changeConstraintSet(self, i, name):
project = self.project
if project.nmrConstraintStores:
constraintSet = project.nmrConstraintStores[i]
else:
constraintSet = None
if constraintSet is not self.constraintSet:
self.constraintSet = constraintSet
self.cloud = None
self.updateAfter()
def deleteCloud(self):
if self.constraintSet and self.cloud and showOkCancel(
'Confirm', 'Really delete resonance cloud?', parent=self):
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
if clouds:
clouds.remove(self.cloud)
self.cloud = None
self.guiParent.application.setValues(self.constraintSet,
'clouds',
values=clouds)
self.updateAfter()
def selectCell(self, cloud, row, col):
self.cloud = cloud
self.bottomButtons.buttons[1].enable()
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def getConstraintSetNames(self):
names = []
constraintSets = self.project.nmrConstraintStores
for set in constraintSets:
names.append('%d' % set.serial)
return names
def updateStructureGen(self, *opt):
project = self.project
constraintSets = self.project.sortedNmrConstraintStores
if constraintSets:
constraintSetNames = self.getConstraintSetNames()
# set defaults
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
self.cloud = None
i = constraintSets.index(self.constraintSet)
self.constrSetPulldown.setup(constraintSetNames, i)
else:
self.constraintSet = None
self.cloud = None
self.constrSetPulldown.setup([], -1)
def destroy(self):
for func in ('__init__', 'delete'):
self.unregisterNotify(self.updateStructureGen,
'ccp.nmr.Nmr.StructureGeneration', func)
BasePopup.destroy(self)
def update(self):
objectList = []
textMatrix = []
if self.constraintSet:
clouds = self.guiParent.application.getValues(
self.constraintSet, 'clouds')
if clouds:
objectList = list(clouds)
i = 0
for cloud in objectList:
i += 1
datum = []
datum.append(i)
datum.append(cloud)
datum.append(self.cloudRmsdDict.get(cloud) or '-')
datum.append(self.strucRmsdDict.get(cloud) or '-')
textMatrix.append(datum)
if not self.cloud:
self.bottomButtons.buttons[1].disable()
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = False
class PredictKarplusPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.waiting = False
self.molSystem = None
self.residue = None
self.jCouplings = []
self.atomNames = []
self.measureJCouplingList = None
self.predictJCouplingList = None
self.coeffAtomNames = []
self.coefficients = {}
self.coefficient = None
for i in range(3):
self.coefficients[i] = {}
BasePopup.__init__(
self,
parent=parent,
title='Predict Karplus Coefficients from J Coupling',
**kw)
self.updateJCouplingLists()
self.updateMolSystems()
self.updateAfter()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1, minsize=500)
row = 0
frame = LabelFrame(guiFrame, text='General Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(1, weight=1)
label = Label(frame, text='Molecular System:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
self.changeMolSystem,
do_initial_callback=False)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Measured J coupling list:')
label.grid(row=0, column=2, sticky='w')
self.measureCouplingListPulldown = PulldownMenu(
frame, self.changeMeasureCouplingList)
self.measureCouplingListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Predicted J coupling list:')
label.grid(row=0, column=4, sticky='w')
self.predictCouplingListPulldown = PulldownMenu(
frame, self.changePredictCouplingList)
self.predictCouplingListPulldown.grid(row=0, column=5, sticky='w')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Angles & 3J Couplings')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Residue', 'Phi', 'Chi^2']
editWidgets = [None, None, None]
editGetCallbacks = [None, None, None]
editSetCallbacks = [None, None, None]
self.jCouplingEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setJCoupling())
i = 0
for names in couplingAtoms:
headingList.extend(
['Pred\nJ(%s,%s)' % names,
'Expt\nJ(%s,%s)' % names])
editWidgets.extend([None, self.jCouplingEntry])
editGetCallbacks.extend(
[None, lambda obj, i=i: self.getJCoupling(obj, i)])
editSetCallbacks.extend(
[None, lambda event, i=i: self.setJCoupling(i)])
i += 1
self.couplingMatrix = ScrolledMatrix(frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectJCoupling,
multiSelect=False)
self.couplingMatrix.grid(row=0, column=0, sticky='nsew')
self.couplingMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
row += 1
frame = LabelFrame(guiFrame, text='Karplus Coefficients')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = ['Phase']
editWidgets = [
None,
]
editGetCallbacks = [
None,
]
editSetCallbacks = [
None,
]
self.coefficientEntry = FloatEntry(
self, width=8, returnCallback=lambda event: self.setCoefficient())
for names in couplingAtoms:
headingList.append('J(%s,%s)' % names)
editWidgets.append(self.coefficientEntry)
editGetCallbacks.append(
lambda obj, n=names: self.getCoefficient(obj, n))
editSetCallbacks.append(
lambda event, n=names: self.setCoefficient(n))
headingList = [
'Phase', 'J(H,HA)', 'J(H,C)', 'J(H,CB)', 'J(C,HA)', 'J(C,C)',
'J(C,CB)'
]
self.coefficientMatrix = ScrolledMatrix(
frame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectCoefficient,
maxRows=3,
multiSelect=False)
self.coefficientMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = []
commands = []
self.bottomButtons = UtilityButtonList(guiFrame,
commands=commands,
texts=texts,
helpUrl=self.help_url)
self.bottomButtons.grid(row=row, column=0, sticky='ew')
for func in ('__init__', 'delete', 'setValue', 'setError'):
for clazz in ('ccp.nmr.Nmr.JCoupling', ):
self.registerNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.JCouplingList', ):
self.registerNotify(self.updateJCouplingLists, clazz, func)
def getJCouplingLists(self, isSimulated=False):
jCouplingLists = self.nmrProject.findAllMeasurementLists(
className='JCouplingList', isSimulated=isSimulated)
return jCouplingLists
def updateJCouplingLists(self, *obj):
jCouplingLists = self.getJCouplingLists(isSimulated=False)
names = [
'%d:%s' % (jcl.serial, jcl.name or '') for jcl in jCouplingLists
]
names.append('<New>')
index = -1
if jCouplingLists:
if self.measureJCouplingList in jCouplingLists:
index = jCouplingLists.index(self.measureJCouplingList)
else:
self.measureJCouplingList = jCouplingLists[0]
index = 0
else:
self.measureJCouplingList = None
self.measureCouplingListPulldown.setup(names, index)
jCouplingLists = self.getJCouplingLists(isSimulated=True)
names = ['%d:%s' % (jcl.serial, jcl.name) for jcl in jCouplingLists]
names.append('<New>')
index = -1
if jCouplingLists:
if self.predictJCouplingList in jCouplingLists:
index = jCouplingLists.index(self.predictJCouplingList)
else:
self.predictJCouplingList = jCouplingLists[0]
index = 0
else:
self.predictJCouplingList = None
self.predictCouplingListPulldown.setup(names, index)
def changeMeasureCouplingList(self, index, name):
if name == '<New>':
self.measureJCouplingList = None
else:
jCouplingLists = self.getJCouplingLists()
jCouplingList = jCouplingLists[index]
if jCouplingList is not self.measureJCouplingList:
self.measureJCouplingList = jCouplingList
if self.predictJCouplingList is self.measureJCouplingList:
for jCouplingList2 in jCouplingLists:
if self.measureJCouplingList is not jCouplingList2:
self.predictJCouplingList = jCouplingList2
break
else:
self.predictJCouplingList = None
self.updateAfter()
def changePredictCouplingList(self, index, name):
if name == '<New>':
self.predictJCouplingList = None
self.updateAfter()
else:
jCouplingLists = self.getJCouplingLists()
jCouplingList = jCouplingLists[index]
if jCouplingList is not self.predictJCouplingList:
self.predictJCouplingList = jCouplingList
if self.predictJCouplingList is self.measureJCouplingList:
for jCouplingList2 in jCouplingLists:
if self.predictJCouplingList is not jCouplingList2:
self.measureJCouplingList = jCouplingList2
break
else:
self.measureJCouplingList = None
self.updateAfter()
def doEditMarkExtraRules(self, obj, row, col):
i = (col - 3) / 2
if i > -1:
atoms = couplingAtoms[i]
residue = obj[0]
for atomName in atoms:
if not residue.findFirstAtom(name=atomName):
return False
return True
def open(self):
self.updateMolSystems()
BasePopup.open(self)
def selectJCoupling(self, object, row, col):
self.residue = object[0]
self.jCouplings = object[1:]
def selectCoefficient(self, object, row, col):
self.coefficient = object
def getCoefficient(self, object, atomNames):
self.coeffAtomNames = atomNames
coefficient = self.coefficients[object].get(atomNames)
self.coefficientEntry.set(coefficient)
def setCoefficient(self, atomNames=None):
if not atomNames:
atomNames = self.coeffAtomNames
value = self.coefficientEntry.get()
if atomNames and (self.coefficient is not None):
self.coefficients[self.coefficient][atomNames] = value
#print self.coefficient, atomNames, value
self.updateCoefficients()
def getJCoupling(self, object, index):
atomNames = couplingAtoms[index]
self.atomNames = atomNames
coupling = object[index + 1]
if not coupling:
residue = object[0]
coupling = self.getResidueJCoupling(self.measureJCouplingList,
residue, atomNames)
if coupling:
value = coupling.value
else:
value = None
self.jCouplingEntry.set(value)
def setJCoupling(self, index=None):
if not index:
atomNames = self.atomNames
index = couplingAtoms.index(atomNames)
else:
atomNames = couplingAtoms[index]
value = self.jCouplingEntry.get()
if self.residue and atomNames:
coupling = self.jCouplings[index]
if value is None:
if coupling:
if showOkCancel('Confirm',
'Really remove J coupling?',
parent=self):
coupling.delete()
else:
if not coupling:
self.setResidueJCoupling(self.measureJCouplingList,
self.residue,
atomNames,
value,
isSimulated=False)
else:
coupling.setValue(value)
def getResidueJCoupling(self, jCouplingList, residue, atomNames):
if jCouplingList:
return getResidueJCoupling(jCouplingList, residue, atomNames)
def setResidueJCoupling(self,
jCouplingList,
residue,
atomNames,
value,
isSimulated=False):
if jCouplingList is None:
jCouplingList = self.nmrProject.newJCouplingList(
isSimulated=isSimulated)
if isSimulated:
self.predictJCouplingList = jCouplingList
else:
self.measureJCouplingList = jCouplingList
setResidueJCoupling(jCouplingList, self.residue, atomNames, value)
def updateMolSystems(self, *obj):
index = -1
names = []
molSystems = self.project.sortedMolSystems()
if molSystems:
if self.molSystem not in molSystems:
self.molSystem = molSystems[0]
names = [ms.code for ms in molSystems]
index = molSystems.index(self.molSystem)
self.molSystemPulldown.setup(names, index)
def changeMolSystem(self, index, name):
molSystems = self.project.sortedMolSystems()
if molSystems:
molSystem = molSystems[index]
else:
molSystem = None
if molSystem is not self.molSystem:
self.molSystem = molSystem
self.updateAfter()
def updateAfter(self, object=None):
current = False
if object and (object.className == 'JCoupling'):
for resonance in object.resonances:
resonanceSet = resonance.resonanceSet
if resonanceSet:
molSystem = resonanceSet.findFirstAtomSet().findFirstAtom(
).topObject
if molSystem is self.molSystem:
current = True
break
else:
current = True
if self.waiting or (not current):
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self):
textMatrix = []
objectList = []
if self.molSystem:
chains = self.molSystem.sortedChains()
if len(chains) > 1:
doChains = False
else:
doChains = True
for chain in chains:
if doChains:
chainCode = chain.code
else:
chainCode = ''
for residue in chain.sortedResidues():
name = '%s%d%s' % (chainCode, residue.seqCode,
getResidueCode(residue))
phi = 0.0
chiSq = 0.0
datum = [name, phi, chiSq]
object = [
residue,
]
for atomNames in couplingAtoms:
couplingM = self.getResidueJCoupling(
self.measureJCouplingList, residue, atomNames)
couplingP = self.getResidueJCoupling(
self.predictJCouplingList, residue, atomNames)
pred = None
expt = None
if couplingM:
expt = couplingM.value
if couplingP:
pred = couplingP.value
datum.append(pred)
datum.append(expt)
object.append(couplingM)
objectList.append(object)
textMatrix.append(datum)
self.couplingMatrix.update(textMatrix=textMatrix,
objectList=objectList)
self.updateCoefficients()
self.waiting = False
def updateCoefficients(self):
textMatrix = []
objectList = []
for i in range(3):
name = 'C%d' % i
datum = [
name,
]
for atomNames in couplingAtoms:
datum.append(self.coefficients[i].get(atomNames))
textMatrix.append(datum)
objectList.append(i)
self.coefficientMatrix.update(textMatrix=textMatrix,
objectList=objectList)
def destroy(self):
for func in ('__init__', 'delete', 'setValue', 'setError'):
for clazz in ('ccp.nmr.Nmr.JCoupling', ):
self.unregisterNotify(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.JCouplingList', ):
self.unregisterNotify(self.updateJCouplingLists, clazz, func)
BasePopup.destroy(self)
class 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()
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)
def setupProchiralList(self, listIndex, chainLabel):
chain = self.resParentChainLabelDict[self.resParent][chainLabel]
self.chain = chain
self.prochiralListFrame.destroy()
self.prochiralListFrame = ScrolledFrame(self.prochiralListFrameMaster,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=self.prochiralListFrameRow,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
#
# TODO: also handle case one resonance, two atomSets!?!?
#
frameRow = 0
x = y = 0
frame = self.prochiralListFrame.frame
self.resonanceObjects = {}
self.resonanceLabelDict = {}
#
# Reuse previous settings...
#
if len(self.chainResonancesDict[self.resParent][chain]) == len(
self.chainAtomSetsDict[self.resParent][chain]):
usePreviousSettings = True
else:
usePreviousSettings = False
for i in range(0, len(self.chainAtomSetsDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
isStereo = False
hasResonances = False
isValidCase = False
resonances = []
if usePreviousSettings and self.chainResonancesDict[
self.resParent][chain][i]:
resonances = self.chainResonancesDict[
self.resParent][chain][i][3]
isStereo = self.chainResonancesDict[
self.resParent][chain][i][0]
hasResonances = True
isValidCase = True
else:
for atomSet in atomSetGroup:
resonanceSets = atomSet.sortedResonanceSets()
if resonanceSets:
hasResonances = True
for resonanceSet in resonanceSets:
for resonance in resonanceSet.sortedResonances():
if resonance not in resonances:
resonances.append(resonance)
if len(resonanceSets) == 1:
isValidCase = True
if len(resonanceSet.atomSets) == 1:
isStereo = True
else:
# Case only one resonance but stereo assigned
resonances.append(0)
if len(resonances) == 1:
# Case only one resonance, not stereo assigned
resonances.append(None)
#
# Set up only for valid cases
#
if hasResonances and isValidCase:
if not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(
[isStereo, False, False, resonances])
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
rowspan = 2
checkButton = CheckButton(
frame,
selected=isStereo,
callback=lambda status=isStereo, fr=frameRow, item=i, setup
=False: self.toggleResonances(status, fr, item, setup))
checkButton.grid(row=frameRow,
rowspan=rowspan,
column=0,
sticky=Tkinter.EW)
label = Label(frame, text=ccpCode, width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=1,
sticky=Tkinter.E)
label = Label(frame, text=str(seqCode), width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=2,
sticky=Tkinter.W)
#
# Set up the atom names
#
for j in range(0, len(atomSetGroup)):
atomSet = atomSetGroup[j]
label = Label(frame, text=atomSet.name)
label.grid(row=frameRow + j,
column=3,
sticky=Tkinter.E,
ipadx=4)
#
# Set up the resonances
#
self.resonanceObjects[frameRow] = {
True: [[], []],
False: [[], []]
}
resonanceLabelList = []
for resonance in resonances:
if not resonance:
resonanceLabel = 'unknown'
else:
if hasattr(resonance, 'shifts') and resonance.shifts:
shiftLabel = " (shifts: "
for shift in resonance.sortedShifts():
shiftLabel += "%.2f, " % shift.value
shiftLabel = shiftLabel[:-2] + ")"
else:
shiftLabel = ""
resonanceLabel = "'%d.%s'%s" % (
seqCode, resonance.name, shiftLabel)
self.resonanceLabelDict[resonanceLabel] = resonance
resonanceLabelList.append(resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow, column=4, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(separator)
separator = CrossLine(frame,
height=20,
width=30,
canvas_bg=frame['bg'],
color='dimgray')
self.resonanceObjects[frameRow][False][0].append(separator)
resonanceList = PulldownMenu(
frame,
entries=resonanceLabelList,
callback=lambda selInd=x, selItem=y, fr=frameRow, item=i:
self.setProchiralLabels(selInd, selItem, fr, item),
do_initial_callback=False,
label_color='red')
resonanceList.grid(row=frameRow, column=5, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(resonanceList)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[0],
fg='dimgray')
self.resonanceObjects[frameRow][False][0].append(
resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + 1, column=4)
self.resonanceObjects[frameRow][True][1].append(separator)
self.resonanceObjects[frameRow][False][1].append(None)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='red')
resonanceLabel.grid(row=frameRow + 1,
column=5,
sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][1].append(resonanceLabel)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='dimgray')
self.resonanceObjects[frameRow][False][1].append(
resonanceLabel)
if not isStereo:
checkButton.callback(isStereo, setup=True)
separator = Separator(frame, height=1)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + rowspan,
columnspan=6,
sticky=Tkinter.EW)
frameRow += rowspan + 1
elif not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(None)
return True
class CloudHomologueAssignPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.molSystem = None
self.chain = None
self.assignment = None
self.scores = []
BasePopup.__init__(self, parent, title="Cloud Threader", **kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def update(self):
if self.assignment and self.scores:
self.assignButton.enable()
else:
self.assignButton.disable()
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def assignSpinSystems(self):
if self.assignment and self.scores:
if showWarning('Query','Are you sure?'):
threshold = self.thresholdEntry.get() or -4.0
i = 0
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=None)
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
i += 1
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=residue)
showWarning('Done','%d residues assigned' % i)
def getMolSystems(self):
names = []
for molSystem in self.project.molSystems:
if molSystem.chains:
names.append( '%s' % (molSystem.code) )
return names
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
def updateMolSystems(self, *opt):
names = self.getMolSystems()
if names:
if not self.molSystem:
self.molSystem = self.project.findFirstMolSystem(code=names[0])
self.molSysPulldown.setup(names, names.index(self.molSystem.code))
def getChains(self):
chains = []
if self.molSystem:
for chain in self.molSystem.chains:
chains.append( [chain.code, chain] )
return chains
def changeChain(self, i, name=None):
if not name:
i = self.chainPulldown.selected_index
chains = self.getChains()
if chains:
self.chain = chains[i][1]
def updateChains(self, *chain):
chains = self.getChains()
if chains:
names = [x[0] for x in chains]
if (not self.chain) or (self.chain.code not in names):
self.chain = chains[0][1]
self.chainPulldown.setup(names, names.index(self.chain.code) )
self.update()
def destroy(self):
for func in ('__init__','delete'):
Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
BasePopup.destroy(self)
class ProchiralStatusPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'ProchiralStatus.html')
def __init__(self, parent, chainList, chainAtomSetsDict):
self.chainList = chainList
self.chainAtomSetsDict = chainAtomSetsDict
self.resParentDict = {}
self.resParentList = []
self.resParentChainLabelDict = {}
self.resParentChainLabelList = {}
self.chainResonancesDict = {}
for resParent in self.chainAtomSetsDict.keys():
if isinstance(resParent, NmrConstraint.NmrConstraintStore):
strucGens = resParent.structureGenerations
strucGenSerials = [str(sg.serial) for sg in strucGens]
strucGenLabel = string.join(strucGenSerials, ',')
resParentLabel = "Constraint set %d (strucGens %s)" % (
resParent.serial, strucGenSerials)
else:
resParentLabel = "Nmr project %s" % resParent.name
self.resParentDict[resParentLabel] = resParent
self.resParentList.append(resParentLabel)
self.chainResonancesDict[resParent] = {}
self.resParentChainLabelDict[resParent] = {}
self.resParentChainLabelList[resParent] = []
for chain in self.chainList:
self.project = chain.root
if self.chainAtomSetsDict[resParent].has_key(
chain) and self.chainAtomSetsDict[resParent][chain]:
chainLabel = "Molecular system '%s':Chain '%s' (molecule '%s')" % (
chain.molSystem.code, chain.code, chain.molecule.name)
self.resParentChainLabelList[resParent].append(chainLabel)
self.resParentChainLabelDict[resParent][chainLabel] = chain
self.chainResonancesDict[resParent][chain] = []
# modal = true means that it won't continue unless this one returns value
TemporaryBasePopup.__init__(
self,
parent=parent,
title="Project '%s': " % self.project.name +
'Set status prochiral atoms/resonances',
modal=False,
transient=True)
def body(self, master):
#
# Setup header
#
row = 0
label = Label(master, text='Select the resonance list:')
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text='Select the chain:')
label.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
self.resParentSelect = PulldownMenu(master,
entries=self.resParentList,
callback=self.setupResParentList,
do_initial_callback=False)
self.resParentSelect.grid(row=row, column=0, sticky=Tkinter.EW)
self.chainSelect = PulldownMenu(master,
entries=[],
callback=self.setupProchiralList,
do_initial_callback=False)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=2, sticky=Tkinter.EW)
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row, weight=1)
for i in range(2):
master.grid_columnconfigure(i, weight=1)
self.prochiralListFrame = ScrolledFrame(master,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
self.prochiralListFrameRow = row
self.prochiralListFrameMaster = master
row = row + 1
texts = ['Set all', 'Set chain']
commands = [
self.ok, self.setStereo
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
self.resParentSelect.callback(0, self.resParentList[0])
def setupResParentList(self, listIndex, resParentLabel):
resParent = self.resParentDict[resParentLabel]
self.resParent = resParent
self.chainSelect.setup(self.resParentChainLabelList[self.resParent], 0)
self.chainSelect.callback(
0, self.resParentChainLabelList[self.resParent][0])
def setupProchiralList(self, listIndex, chainLabel):
chain = self.resParentChainLabelDict[self.resParent][chainLabel]
self.chain = chain
self.prochiralListFrame.destroy()
self.prochiralListFrame = ScrolledFrame(self.prochiralListFrameMaster,
width=200,
doExtraConfig=False)
self.prochiralListFrame.grid(row=self.prochiralListFrameRow,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
#
# TODO: also handle case one resonance, two atomSets!?!?
#
frameRow = 0
x = y = 0
frame = self.prochiralListFrame.frame
self.resonanceObjects = {}
self.resonanceLabelDict = {}
#
# Reuse previous settings...
#
if len(self.chainResonancesDict[self.resParent][chain]) == len(
self.chainAtomSetsDict[self.resParent][chain]):
usePreviousSettings = True
else:
usePreviousSettings = False
for i in range(0, len(self.chainAtomSetsDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
isStereo = False
hasResonances = False
isValidCase = False
resonances = []
if usePreviousSettings and self.chainResonancesDict[
self.resParent][chain][i]:
resonances = self.chainResonancesDict[
self.resParent][chain][i][3]
isStereo = self.chainResonancesDict[
self.resParent][chain][i][0]
hasResonances = True
isValidCase = True
else:
for atomSet in atomSetGroup:
resonanceSets = atomSet.sortedResonanceSets()
if resonanceSets:
hasResonances = True
for resonanceSet in resonanceSets:
for resonance in resonanceSet.sortedResonances():
if resonance not in resonances:
resonances.append(resonance)
if len(resonanceSets) == 1:
isValidCase = True
if len(resonanceSet.atomSets) == 1:
isStereo = True
else:
# Case only one resonance but stereo assigned
resonances.append(0)
if len(resonances) == 1:
# Case only one resonance, not stereo assigned
resonances.append(None)
#
# Set up only for valid cases
#
if hasResonances and isValidCase:
if not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(
[isStereo, False, False, resonances])
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
rowspan = 2
checkButton = CheckButton(
frame,
selected=isStereo,
callback=lambda status=isStereo, fr=frameRow, item=i, setup
=False: self.toggleResonances(status, fr, item, setup))
checkButton.grid(row=frameRow,
rowspan=rowspan,
column=0,
sticky=Tkinter.EW)
label = Label(frame, text=ccpCode, width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=1,
sticky=Tkinter.E)
label = Label(frame, text=str(seqCode), width=5)
label.grid(row=frameRow,
rowspan=rowspan,
column=2,
sticky=Tkinter.W)
#
# Set up the atom names
#
for j in range(0, len(atomSetGroup)):
atomSet = atomSetGroup[j]
label = Label(frame, text=atomSet.name)
label.grid(row=frameRow + j,
column=3,
sticky=Tkinter.E,
ipadx=4)
#
# Set up the resonances
#
self.resonanceObjects[frameRow] = {
True: [[], []],
False: [[], []]
}
resonanceLabelList = []
for resonance in resonances:
if not resonance:
resonanceLabel = 'unknown'
else:
if hasattr(resonance, 'shifts') and resonance.shifts:
shiftLabel = " (shifts: "
for shift in resonance.sortedShifts():
shiftLabel += "%.2f, " % shift.value
shiftLabel = shiftLabel[:-2] + ")"
else:
shiftLabel = ""
resonanceLabel = "'%d.%s'%s" % (
seqCode, resonance.name, shiftLabel)
self.resonanceLabelDict[resonanceLabel] = resonance
resonanceLabelList.append(resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow, column=4, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(separator)
separator = CrossLine(frame,
height=20,
width=30,
canvas_bg=frame['bg'],
color='dimgray')
self.resonanceObjects[frameRow][False][0].append(separator)
resonanceList = PulldownMenu(
frame,
entries=resonanceLabelList,
callback=lambda selInd=x, selItem=y, fr=frameRow, item=i:
self.setProchiralLabels(selInd, selItem, fr, item),
do_initial_callback=False,
label_color='red')
resonanceList.grid(row=frameRow, column=5, sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][0].append(resonanceList)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[0],
fg='dimgray')
self.resonanceObjects[frameRow][False][0].append(
resonanceLabel)
separator = Separator(frame, height=1, width=30)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + 1, column=4)
self.resonanceObjects[frameRow][True][1].append(separator)
self.resonanceObjects[frameRow][False][1].append(None)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='red')
resonanceLabel.grid(row=frameRow + 1,
column=5,
sticky=Tkinter.EW)
self.resonanceObjects[frameRow][True][1].append(resonanceLabel)
resonanceLabel = Label(frame,
text="%s" % resonanceLabelList[1],
fg='dimgray')
self.resonanceObjects[frameRow][False][1].append(
resonanceLabel)
if not isStereo:
checkButton.callback(isStereo, setup=True)
separator = Separator(frame, height=1)
separator.setColor('black', bgColor='black')
separator.grid(row=frameRow + rowspan,
columnspan=6,
sticky=Tkinter.EW)
frameRow += rowspan + 1
elif not usePreviousSettings:
self.chainResonancesDict[self.resParent][chain].append(None)
return True
def setProchiralLabels(self, selInd, selItem, fr, item):
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][False][0][1].set(resonanceLabel)
selInd = not selInd
resonanceLabel = self.resonanceObjects[fr][True][0][1].entries[selInd]
self.resonanceObjects[fr][True][1][1].set(resonanceLabel)
self.resonanceObjects[fr][False][1][1].set(resonanceLabel)
self.chainResonancesDict[self.resParent][
self.chain][item][2] = not self.chainResonancesDict[
self.resParent][self.chain][item][2]
self.chainResonancesDict[self.resParent][self.chain][item][3].reverse()
def toggleResonances(self, status, frameRow, item, setup):
if not setup:
self.chainResonancesDict[self.resParent][
self.chain][item][0] = status
self.chainResonancesDict[self.resParent][
self.chain][item][1] = not self.chainResonancesDict[
self.resParent][self.chain][item][1]
for i in range(0, len(self.resonanceObjects[frameRow])):
#
# Remove other widgets from grid
#
rpds = self.resonanceObjects[frameRow][not status][i]
for rpd in rpds:
if rpd:
rpd.grid_forget()
#
# Set current widgets
#
rpds = self.resonanceObjects[frameRow][status][i]
for j in range(0, len(rpds)):
rpd = rpds[j]
if rpd:
keywds = {}
if j == 1:
keywds['sticky'] = Tkinter.W
if j == 0:
if not status:
keywds['rowspan'] = 2
rpd.grid(row=frameRow + i, column=4 + j, **keywds)
def setStereo(self, chain=None):
if not chain:
chain = self.chain
if self.chainResonancesDict[self.resParent][chain]:
for i in range(
0, len(self.chainResonancesDict[self.resParent][chain])):
atomSetGroup = self.chainAtomSetsDict[self.resParent][chain][i]
(stereoStatus, stereoStatusChanged, resChanged, resonances
) = self.chainResonancesDict[self.resParent][chain][i]
if stereoStatusChanged or (stereoStatus and resChanged):
residue = atomSetGroup[0].findFirstAtom().residue
ccpCode = residue.molResidue.ccpCode
seqCode = residue.seqCode
atomText = "%s/%s" % (atomSetGroup[0].name,
atomSetGroup[1].name)
if stereoStatusChanged:
if stereoStatus:
stereoText = "non-stereospecific to stereospecific."
else:
stereoText = "stereospecific to non-stereospecific."
print " Warning: Changed '%s.%d' prochiral resonances for atoms %s from %s" % (
ccpCode, seqCode, atomText, stereoText)
self.chainResonancesDict[
self.resParent][chain][i][1] = False
self.chainResonancesDict[
self.resParent][chain][i][2] = False
if stereoStatus:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[0]:
resonanceSet.removeAtomSet(atomSetGroup[1])
if resonances[1]:
if not resonances[0]:
# Remove right atom set if only one resonance...
resonanceSet.removeAtomSet(atomSetGroup[0])
else:
# Only create a new resonance set if two resonances present!
resonanceSet.removeResonance(resonances[1])
if isinstance(
self.resParent,
NmrConstraint.NmrConstraintStore):
newResonanceSet = self.resParent.newFixedResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
newResonanceSet = self.resParent.newResonanceSet(
resonances=[resonances[1]],
atomSets=[atomSetGroup[1]])
else:
if resonances[0]:
resonanceSet = atomSetGroup[
0].findFirstResonanceSet()
if resonances[1]:
atomSetGroup[1].findFirstResonanceSet(
).delete()
resonanceSet.addResonance(resonances[1])
resonanceSet.addAtomSet(atomSetGroup[1])
elif resonances[1]:
resonanceSet = atomSetGroup[1].resonanceSets[0]
resonanceSet.addAtomSet(atomSetGroup[0])
elif stereoStatus and resChanged:
print " Warning: Changed resonance assignment for '%s.%d' stereospecifically assigned atoms %s." % (
ccpCode, seqCode, atomText)
self.chainResonancesDict[
self.resParent][chain][i][2] = False
resonanceSets = []
for i in range(0, 2):
if atomSetGroup[i].resonanceSets:
resonanceSets.append(
atomSetGroup[i].findFirstResonanceSet())
else:
resonanceSets.append(None)
for i in range(0, 2):
resonanceSet = resonanceSets[i]
if resonanceSet:
resonanceSet.addAtomSet(atomSetGroup[not i])
resonanceSet.removeAtomSet(atomSetGroup[i])
def apply(self):
for chain in self.chainList:
self.setStereo(chain=chain)
return True
class 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
class SetupStructureCalcFrame(Frame):
def __init__(self, parent, application, *args, **kw):
self.parent = parent
self.molSystem = None
self.constraintSet = None
self.application = application
self.project = application.project
self.waiting = False
self.tableObj = None
Frame.__init__(self, parent=parent, **kw)
self.grid_columnconfigure(3, weight=1)
label = Label(self, text='Molecular system: ')
label.grid(row=0, column=0, sticky='nw')
self.molSysPulldown = PulldownMenu(
self,
self.changeMolSystem,
tipText='Select which molecular system to use in the calculation')
self.molSysPulldown.grid(row=0, column=1, sticky='nw')
label = Label(self, text='Constraint Set: ')
label.grid(row=0, column=2, sticky='nw')
self.constraintSetPulldown = PulldownMenu(
self,
self.changeConstraintSet,
tipText='Select which set of restraints to use in the calculation')
self.constraintSetPulldown.grid(row=0, column=3, sticky='nw')
self.shiftListPulldown = PulldownMenu(
parent,
callback=self.setShiftList,
do_initial_callback=False,
tipText='select the shift list to use in the calculation')
tipTexts = [
'The type of ccp object used in the calculation',
'The identifier for the input data',
'A toggle whether to use the data',
'Whether to filter violated restraints',
'Whether to keep CCPN assignments (otherwise new restraint assignments will be used)',
'Whether the restraints are overly anbiguous and need refining',
'The shift list to use for shift-peak matching'
]
headingList = [
'Input Class', 'Id', 'Use?', 'Filter\nViolated',
'Keep\nAssignments?', 'Ambiguous\nProtocol', 'Shift List'
]
editWidgets = [
None, None, None, None, None, None, self.shiftListPulldown
]
editGetCallbacks = [
None, None, self.toggleUse, self.toggleFilterViol,
self.toggleKeepAssign, self.toggleAmbig, self.getShiftList
]
editSetCallbacks = [
None, None, None, None, None, None, self.setShiftList
]
self.grid_rowconfigure(1, weight=1)
self.scrolledMatrix = ScrolledMatrix(self,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True,
tipTexts=tipTexts,
callback=self.selectCell)
self.scrolledMatrix.grid(row=1, column=0, columnspan=4, sticky='nsew')
self.scrolledMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
#texts = ['','','']
#commands = [None,None,None]
#self.bottomButtons = ButtonList(self, texts=texts, expands=True, commands=commands)
#self.bottomButtons.grid(row=2, column=0, columnspan=4, sticky='ew')
self.updateMolSystems()
self.updateConstraintSets()
notify = self.application.registerNotify
for func in ('__init__', 'delete'):
notify(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notify(self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem',
func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete', 'setName'):
notify(self.updateAfter, 'ccp.nmr.Nmr.Experiment', func)
notify(self.updateAfter, 'ccp.nmr.Nmr.DataSource', func)
def doEditMarkExtraRules(self, obj, row, col):
className = obj.className
if className == 'PeakList':
if col == 5:
return False
elif className == 'DistanceConstraintList':
if col in (4, 6):
return False
else:
if col in (4, 5, 6):
return False
return True
def toggleUse(self, obj):
bool = not obj.setupStructureCalcFrameDict['use']
obj.setupStructureCalcFrameDict['use'] = bool
self.updateAfter()
def toggleFilterViol(self, obj):
bool = not obj.setupStructureCalcFrameDict['filter']
obj.setupStructureCalcFrameDict['filter'] = bool
self.updateAfter()
def toggleKeepAssign(self, obj):
bool = not obj.setupStructureCalcFrameDict['preserve']
obj.setupStructureCalcFrameDict['preserve'] = bool
self.updateAfter()
def toggleAmbig(self, obj):
bool = not obj.setupStructureCalcFrameDict['ambig']
obj.setupStructureCalcFrameDict['ambig'] = bool
self.updateAfter()
def selectCell(self, obj, row, col):
self.tableObj = obj
def getShiftList(self, peakList):
names = []
index = -1
shiftLists = getShiftLists(self.project.currentNmrProject)
if shiftLists:
shiftList = peakList.dataSource.experiment.shiftList
if shiftList not in shiftLists:
shiftList = shiftLists[0]
names = [sl.name or str(sl.serial) for sl in shiftLists]
index = shiftLists.index(shiftList)
print "getShiftList", names, index
self.shiftListPulldown.setup(names, index)
def setShiftList(self, index, name=None):
print "setShiftList", index, name
if not name:
index = self.shiftListPulldown.getSelectedIndex()
shiftList = getShiftLists(self.project.currentNmrProject)[index]
self.tableObj.setupStructureCalcFrameDict['shiftList'] = shiftList
self.updateAfter()
def updateMolSystems(self, *opt):
names = []
index = -1
molSystems = self.getMolSystems()
if molSystems:
names = [ms.code for ms in molSystems]
if self.molSystem not in molSystems:
self.molSystem = molSystems[0]
index = molSystems.index(self.molSystem)
self.molSysPulldown.setup(names, index)
def getMolSystems(self):
molSystems = []
if self.project:
for molSystem in self.project.molSystems:
if molSystem.chains:
molSystems.append(molSystem)
return molSystems
def getTableObjects(self):
objs = []
if self.project:
objs = getThroughSpacePeakLists(self.project)
if self.constraintSet:
objs.extend(list(self.constraintSet.constraintLists))
return objs
def updateConstraintSets(self, obj=None):
names = []
index = -1
if self.project and self.project.currentNmrProject:
constraintSets = self.project.currentNmrProject.sortedNmrConstraintStores(
)
if constraintSets:
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
names = [str(cs.serial) for cs in constraintSets]
index = constraintSets.index(self.constraintSet)
names.append('<None>')
self.constraintSetPulldown.setup(names, index)
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
self.updateAfter()
def changeConstraintSet(self, i, name):
if name == '<None>':
self.constraintSet = None
else:
self.constraintSet = self.project.currentNmrProject.sortedNmrConstraintStores(
)[i]
self.updateAfter()
def update(self):
textMatrix = []
objectList = []
#headingList = ['Input Class','Use?','Filter\nViolated',
# 'Keep\nAssignments?','Ambigous\nProtocol','Shift List']
for obj in self.getTableObjects():
if not hasattr(obj, 'setupStructureCalcFrameDict'):
obj.setupStructureCalcFrameDict = dict = {}
dict['use'] = True
dict['filter'] = True
dict['preserve'] = False
dict['ambig'] = False
dict['shiftList'] = None
new = True
else:
dict = obj.setupStructureCalcFrameDict
new = False
className = obj.className
if className == 'PeakList':
spectrum = obj.dataSource
experiment = spectrum.experiment
shiftList = dict['shiftList'] or experiment.shiftList
if shiftList:
shiftListName = shiftList.name
else:
shiftListName = '<None>'
if new and (self.molSystem not in experiment.molSystems):
dict['use'] = False
ident = '%s:%s:%d' % (experiment.name, spectrum.name,
obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = dict['filter'] and 'Yes' or 'No'
preserved = dict['preserve'] and 'Yes' or 'No'
ambig = None
elif className == 'DistanceConstraintList':
shiftListName = None
if new:
dict['filter'] = True
dict['ambig'] = False
ident = '%s:%d' % (obj.name or '', obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = dict['filter'] and 'Yes' or 'No'
preserved = None
ambig = dict['ambig'] and 'Yes' or 'No'
else:
shiftListName = None
if new:
dict['filter'] = False
dict['ambig'] = False
ident = '%s:%d' % (obj.name or '', obj.serial)
used = dict['use'] and 'Yes' or 'No'
filtered = None
preserved = None
ambig = None
datum = [
className, ident, used, filtered, preserved, ambig,
shiftListName
]
textMatrix.append(datum)
objectList.append(obj)
self.waiting = False
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList)
def getAriaData(self):
if not self.project:
showWarning('Failure', 'No active project', parent=self)
return
if not self.molSystem:
showWarning('Failure', 'No molecular system selected', parent=self)
return
if len(self.molSystem.chains) > 1:
code = self.molSystem.findFirstChain().code
code = askString('Multiple chains',
'Enter chain code:',
code,
parent=self)
chain = self.molSystem.findFirstChain(code=code)
else:
chain = self.molSystem.findFirstChain()
peakData = []
dihedrals = []
ambigs = []
unambigs = []
jCouplings = []
for obj in self.scrolledMatrix.objectList:
opts = obj.setupStructureCalcFrameDict
if not opts['use']:
continue
className = obj.className
key = getObjectKeyString(obj)
if className == 'PeakList':
shiftList = opts['shiftList']
if not shiftList:
continue
datum = {
'shifts': {
KEY_ID: getObjectKeyString(shiftList)
},
'peaks': {
KEY_ID: key
},
'use_assignments': opts['preserve'],
'trust_assigned_peaks': opts['filter']
}
peakData.append(datum)
elif className == 'DistanceConstraintList':
if opts['ambig']:
ambigs.append({
KEY_ID: key,
'filter_contributions': opts['filter']
})
else:
unambigs.append({
KEY_ID: key,
'filter_contributions': opts['filter']
})
elif className == 'JCouplingConstraintList':
jCouplings.append({KEY_ID: key})
elif className == 'DihedralConstraintList':
dihedrals.append({KEY_ID: key})
projFileName = os.path.join(self.project.url.path, self.project.path)
dict = {
KEY_GENERAL: {
'project_name': self.project.name
},
KEY_CCPN: {
'filename': projFileName
},
KEY_MOLECULAR_SYSTEM: {
KEY_ID: getObjectKeyString(chain)
},
KEY_NOES: peakData,
KEY_DIHEDRALS: dihedrals,
KEY_DISTANCES_AMBIG: ambigs,
KEY_DISTANCES_UNAMBIG: unambigs,
KEY_JCOUPLINGS: jCouplings
}
return dict
def updateAll(self):
self.project = self.application.project
self.updateMolSystems()
self.updateConstraintSets()
self.updateAfter()
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def destroy(self):
notify = self.application.unregisterNotify
for func in ('__init__', 'delete'):
notify(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notify(self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem',
func)
notify(self.updateMolSystems, 'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete', 'setName'):
notify(self.updateAfter, 'ccp.nmr.Nmr.Experiment', func)
notify(self.updateAfter, 'ccp.nmr.Nmr.DataSource', func)
Frame.destroy(self)
class CloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 50
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.peakListDict = {}
self.noesyPeakList = None
self.tocsyPeakList = None
self.noesy3dPeakList = None
self.hsqcPeakList = None
self.maxIntens = 37000000
self.resonances = None
self.origResonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.numClouds = 100
self.filePrefix = 'cloud_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
self.structure = None
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Resonance Clouds Analysis",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
self.adcAtomTypes = name
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
resonances = []
for constraint in self.distanceConstraintList.constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
startMdProcess(self.numClouds, self.distanceConstraintList,
resonances, self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def showPeaks(self):
self.guiParent.viewPeaks(peaks=self.noesyPeaks)
def showResonances(self):
pass
#self.guiParent.viewResonances(resonances=self.resonances)
def setupResonances(self):
if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList:
disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList,
self.tocsyPeakList, self.hsqcPeakList)
(self.origResonances, self.noesyPeaks,
null) = getCloudsResonanceList(self.guiParent.argumentServer,
hsqcPeakList=self.hsqcPeakList,
tocsy3dPeakList=self.tocsyPeakList,
noesy2dPeakList=self.noesyPeakList)
self.setButtonStates()
def setButtonStates(self):
if self.origResonances:
self.label03a.set('Resonances found: %d' %
(len(self.origResonances)))
if self.noesyPeaks:
self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks)))
if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList:
self.setupButtons.buttons[0].enable()
else:
self.setupButtons.buttons[0].disable()
if self.noesyPeaks:
self.setupButtons.buttons[1].enable()
else:
self.setupButtons.buttons[1].disable()
if self.origResonances:
self.setupButtons.buttons[2].enable()
else:
self.setupButtons.buttons[2].disable()
if self.noesyPeaks and self.origResonances:
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.midgeButtons.buttons[1].enable()
self.distConstrLabel.set(
'Distance constraints: %d' %
len(self.distanceConstraintList.constraints))
else:
self.distConstrLabel.set('Distance constraints:')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
'Anti-distance constraints: %d' %
len(self.antiDistConstraintList.constraints))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('Anti-distance constraints:')
self.midgeButtons.buttons[2].disable()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
def getNoesys(self):
names = []
spectra = getSpectraByType(self.project, '2dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
self.noesyPeakList = self.peakListDict[name]
self.setButtonStates()
def getTocsys(self):
names = []
spectra = getSpectraByType(self.project, '3dTOCSY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.tocsyPeakList:
self.tocsyPeakList = peakList
return names
def getNoesy3ds(self):
names = []
spectra = getSpectraByType(self.project, '3dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesy3dPeakList:
self.noesy3dPeakList = peakList
return names
def setTocsy(self, index, name=None):
if not name:
name = self.tocsyPulldown.getSelected()
self.tocsyPeakList = self.peakListDict[name]
self.setButtonStates()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
self.noesy3dPeakList = self.peakListDict[name]
self.setButtonStates()
def getHsqcs(self):
names = []
spectra = getSpectraByType(self.project, 'HSQC')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.hsqcPeakList:
self.hsqcPeakList = peakList
return names
def setHsqc(self, index, name=None):
if not name:
name = self.hsqcPulldown.getSelected()
self.hsqcPeakList = self.peakListDict[name]
self.setButtonStates()
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def getMaxIntens(self, obj):
self.maxIntensEntry.set(self.maxIntens)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def setMaxIntens(self, event):
value = self.maxIntensEntry.get()
if value is not None:
self.maxIntens = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
class EditSymmetryPopup(BasePopup):
def __init__(self, parent, project):
self.parent = parent
self.project = project
self.singleMolecule = True
self.molSystem = None
self.molecules = []
self.symmetrySet = None
self.symmetryOp = None
self.waiting = False
BasePopup.__init__(self, parent=parent, title='Symmetry Operations')
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=0, column=0, sticky='ew')
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='MolSystem:')
label.grid(row=0, column=0, sticky='w')
self.molSystemPulldown = PulldownMenu(frame,
callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=0, column=1, sticky='w')
self.molLabel = Label(frame, text='Molecule:')
self.molLabel.grid(row=0, column=2, sticky='w')
self.moleculePulldown = PulldownMenu(frame,
callback=self.selectMolecule)
self.moleculePulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Same Molecule Symmetry:')
label.grid(row=0, column=4, sticky='w')
self.molSelect = CheckButton(frame, callback=self.toggleSingleMolecule)
self.molSelect.grid(row=0, column=5, sticky='w')
self.molSelect.set(self.singleMolecule)
frame = LabelFrame(guiFrame, text='Symmetry Operations')
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
self.symmCodePulldown = PulldownMenu(self,
callback=self.setSymmCode,
do_initial_callback=False)
self.segLengthEntry = IntEntry(self,
returnCallback=self.setSegLength,
width=6)
self.setChainMulti = MultiWidget(self,
CheckButton,
callback=self.setChains,
minRows=0,
useImages=False)
self.setSegmentMulti = MultiWidget(self,
IntEntry,
callback=self.setSegments,
minRows=0,
useImages=False)
editWidgets = [
None, self.symmCodePulldown, self.segLengthEntry,
self.setChainMulti, self.setSegmentMulti
]
editGetCallbacks = [
None, self.getSymmCode, self.getSegLength, self.getChains,
self.getSegments
]
editSetCallbacks = [
None, self.setSymmCode, self.setSegLength, self.setChains,
self.setSegments
]
headings = [
'#', 'Symmetry\nType', 'Segment\nLength', 'Chains',
'Segment\nPositions'
]
self.symmetryMatrix = ScrolledMatrix(frame,
headingList=headings,
callback=self.selectSymmetry,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.symmetryMatrix.grid(row=0, column=0, sticky='nsew')
texts = ['Add Symmetry Op', 'Remove Symmetrey Op']
commands = [self.addSymmOp, self.removeSymmOp]
buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
buttonList.grid(row=2, column=0, sticky='ew')
self.updateMolSystems()
self.updateMolecules()
self.updateSymmetriesAfter()
self.notify(self.registerNotify)
def open(self):
self.updateMolSystems()
self.updateMolecules()
self.updateSymmetriesAfter()
BasePopup.open(self)
def notify(self, notifyFunc):
for func in ('__init__', 'delete', 'setSymmetryCode',
'setSegmentLength'):
notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Symmetry',
func)
for func in ('__init__', 'delete', 'setfirstSeqId'):
notifyFunc(self.updateSymmetriesAfter, 'molsim.Symmetry.Segment',
func)
def getSymmCode(self, symmetryOp):
"""Get allowed symmetry operators from the model"""
symmetryOpCodes = symmetryOp.parent.metaclass.container.getElement(
'SymmetryOpCode').enumeration
index = 0
if symmetryOp.symmetryCode in symmetryOpCodes:
index = symmetryOpCodes.index(symmetryOp.symmetryCode)
self.symmCodePulldown.setup(symmetryOpCodes, index)
def getSegLength(self, symmetryOp):
if symmetryOp and symmetryOp.segmentLength:
self.segLengthEntry.set(symmetryOp.segmentLength)
def getChains(self, symmetryOp):
chains = []
for chain in self.molSystem.chains:
if chain.residues:
if chain.molecule in self.molecules: chains.append(chain.code)
chains.sort()
values = []
for chain in chains:
if symmetryOp.findFirstSegment(chainCode=chain):
values.append(True)
else:
values.append(False)
self.setChainMulti.set(values=values, options=chains)
def getSegments(self, symmetryOp):
values = []
names = []
if symmetryOp:
for segment in symmetryOp.sortedSegments():
names.append(segment.chainCode)
values.append(segment.firstSeqId)
n = len(values)
self.setSegmentMulti.maxRows = n
self.setSegmentMulti.minRows = n
self.setSegmentMulti.set(values=values, options=names)
def setSymmCode(self, index, name=None):
"""Set the symmetry code as NCS,C2,C3,C4,C5,C6"""
if self.symmetryOp:
symmCode = self.symmCodePulldown.getSelected()
self.symmetryOp.symmetryCode = symmCode
def setSegLength(self, event):
value = self.segLengthEntry.get() or 1
self.symmetryOp.segmentLength = value
def setChains(self, obj):
if self.symmetryOp and obj:
codes = self.setChainMulti.options
segment = self.symmetryOp.findFirstSegment()
values = self.setChainMulti.get()
if segment: seqId0 = segment.firstSeqId
else: seqId0 = 1
for i in range(len(values)):
segment = self.symmetryOp.findFirstSegment(chainCode=codes[i])
if segment and not values[i]: segment.delete()
elif values[i] and not segment:
chain = self.molSystem.findFirstChain(code=codes[i])
residue = chain.findFirstResidue(seqid=seqId0)
if residue: seqId = seqId0
else:
residue = chain.sortedResidues()[0]
seqId = residue.seqId
residue2 = chain.findFirstResidue(
seqid=seqId + self.symmetryOp.segmentLength)
if not residue2:
residue2 = chain.sortedResidues()[-1]
self.symmetryOp.segmentLength = (residue2.seqId -
seqId) + 1
segment = self.symmetryOp.newSegment(chainCode=codes[i],
firstSeqId=seqId)
self.symmetryMatrix.keyPressEscape()
def setSegments(self, obj):
if self.symmetryOp and obj:
segments = self.symmetryOp.sortedSegments()
values = self.setSegmentMulti.get()
for i in range(len(values)):
seqCode = values[i]
chain = self.molSystem.findFirstChain(
code=segments[i].chainCode)
residue = chain.findFirstResidue(seqCode=seqCode)
if residue: seqId = residue.seqId
if segments[i].firstSeqId != seqId:
segments[i].delete()
segments[i] = self.symmetryOp.newSegment(
chainCode=chain.code, firstSeqId=seqId)
self.symmetryMatrix.keyPressEscape()
def selectSymmetry(self, obj, row, col):
self.symmetryOp = obj
def addSymmOp(self):
if self.molSystem:
if not self.symmetrySet:
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet(
)
if not self.symmetrySet:
objGen = self.project.newMolSystemSymmetrySet
self.symmetrySet = objGen(symmetrySetId=1,
molSystem=self.molSystem)
segLen = len(self.molSystem.findFirstChain().residues)
symmetry = self.symmetrySet.newSymmetry(segmentLength=segLen)
def removeSymmOp(self):
if self.symmetryOp: self.symmetryOp.delete()
def toggleSingleMolecule(self, boolean):
self.singleMolecule = not boolean
self.updateMolSystems()
self.updateMolecules()
def setMolecules(self, molecules):
self.molecules = molecules
if self.symmetrySet:
for symmetryOp in self.symmetrySet.symmetries:
for segment in symmetryOp.segments:
chain = self.molSystem.findFirstChain(
code=segment.chainCode)
if chain and (chain.molecule not in molecules):
segment.delete()
def selectMolecule(self, index, name):
self.setMolecules(self.getMolecules()[index])
self.updateSymmetries()
def getMolecules(self):
counts = {}
moleculesList = []
for chain in self.molSystem.chains:
molecule = chain.molecule
counts[molecule] = counts.get(molecule, 0) + 1
molecules = counts.keys()
if self.singleMolecule:
for molecule in counts:
if counts[molecule] > 1: moleculesList.append([
molecule,
])
elif molecules:
molecules = counts.keys()
n = len(molecules)
moleculesList.append([
molecules[0],
])
if n > 1:
moleculesList.append([
molecules[1],
])
moleculesList.append([molecules[0], molecules[1]])
if n > 2:
moleculesList.append([
molecules[2],
])
moleculesList.append([molecules[1], molecules[2]])
moleculesList.append(
[molecules[0], molecules[1], molecules[2]])
if n > 3:
moleculesList.append([
molecules[3],
])
moleculesList.append([molecules[0], molecules[3]])
moleculesList.append([molecules[1], molecules[3]])
moleculesList.append([molecules[2], molecules[3]])
moleculesList.append(
[molecules[0], molecules[1], molecules[3]])
moleculesList.append(
[molecules[0], molecules[2], molecules[3]])
moleculesList.append(
[molecules[1], molecules[2], molecules[3]])
moleculesList.append(
[molecules[0], molecules[1], molecules[2], molecules[3]])
return moleculesList
def updateMolecules(self):
names = []
index = -1
moleculesList = self.getMolecules()
if moleculesList:
if self.molecules not in moleculesList:
self.setMolecules(moleculesList[0])
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet(
)
index = moleculesList.index(self.molecules)
names = []
for molecules in moleculesList:
names.append(','.join([mol.name for mol in molecules]))
else:
self.molecules = []
self.moleculePulldown.setup(names, index)
def selectMolSystem(self, index, name):
self.molSystem = self.getMolSystems()[index]
self.symmetrySet = self.molSystem.findFirstMolSystemSymmetrySet()
self.updateSymmetries()
def getMolSystems(self):
molSystems = []
for molSystem in self.project.sortedMolSystems():
n = len(molSystem.chains)
if self.singleMolecule and (n > 1): molSystems.append(molSystem)
elif n > 0: molSystems.append(molSystem)
return molSystems
def updateMolSystems(self):
names = []
index = -1
molSystems = self.getMolSystems()
if molSystems:
if self.molSystem not in molSystems: self.molSystem = molSystems[0]
index = molSystems.index(self.molSystem)
names = [ms.code for ms in molSystems]
else:
self.molSystem = None
self.molSystemPulldown.setup(names, index)
def updateSymmetriesAfter(self, obj=None):
if self.waiting: return
else:
self.waiting = True
self.after_idle(self.updateSymmetries)
def updateSymmetries(self):
textMatrix = []
objectList = []
if self.symmetrySet:
for symmetryOp in self.symmetrySet.symmetries:
chains = []
segments = []
length = symmetryOp.segmentLength
for segment in symmetryOp.sortedSegments():
code = segment.chainCode
chain = self.molSystem.findFirstChain(code=code)
if chain:
chains.append(code)
seqId = segment.firstSeqId
residue1 = chain.findFirstResidue(seqId=seqId)
residue2 = chain.findFirstResidue(seqId=seqId +
length - 1)
segments.append(
'%s:%d-%d' %
(code, residue1.seqCode, residue2.seqCode))
datum = [
symmetryOp.serial, symmetryOp.symmetryCode, length,
'\n'.join(chains), '\n'.join(segments)
]
objectList.append(symmetryOp)
textMatrix.append(datum)
self.symmetryMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = False
def destroy(self):
self.notify(self.unregisterNotify)
BasePopup.destroy(self)
class FilterCloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.structure = None
self.name = None
self.clouds = []
self.rmsds = []
self.names = []
self.atomTypes = None
self.waiting = 0
BasePopup.__init__(self, parent=parent, title="Filter Clouds", **kw)
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()
def alignClouds(self):
pattern = self.fileNameEntry.get()
self.names = getFileNamesFromPattern(pattern, '.')
self.clouds = getCloudsFromFile(self.names, self.guiParent.project)
alignClouds(self.clouds, self.names)
def loadClouds(self):
pattern = self.fileNameEntry.get()
self.names = getFileNamesFromPattern(pattern, '.')
self.clouds = getCloudsFromFile(self.names, self.guiParent.project)
self.name = None
self.rmsds = [None for x in range(len(self.clouds))]
self.updateAfter()
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.structures:
structures.append(structure)
self.structure = structures[index - 1]
self.updateButtons()
def setAtomTypes(self, index, name=None):
self.atomTypes = atomTypeList[index]
def filterClouds(self):
if self.clouds:
sdTolerance = self.sdToleranceEntry.get() or 2.0
keptClouds = []
meanRmsd = 0.0
N = 0
for rmsd in self.rmsds:
meanRmsd += rmsd or 0.0
N += 1
if N > 0:
meanRmsd /= float(N)
sd = 0.0
for r in self.rmsds:
rmsd = r or 0.0
sd += (rmsd - meanRmsd) * (rmsd - meanRmsd)
if N > 0:
sd /= float(N - 1)
sd = sqrt(sd)
print meanRmsd, '+/-', sd
for i in range(len(self.clouds), 0, -1):
rmsd = self.rmsds[i]
if abs(rmsd - meanRmsd) > (sdTolerance * sd):
self.rmsds.pop(i)
self.names.pop(i)
self.clouds.pop(i)
#print 'Cloud %s is bad' % (cloud)
self.updateAfter()
def makeStrucCloud(self):
if self.structure and self.clouds:
pdbFileName = 'CloudForStructure.pdb'
atomCoordList = []
atomCoordList0 = []
resDict = {}
hmass = 25
resonances = self.clouds[0].keys()
resonances2 = []
C = 0
for resonance in resonances:
if resonance == 'rmsd':
continue
resonanceSet = resonance.resonanceSet
if resonanceSet:
i = list(resonanceSet.resonances).index(resonance)
atomSet = list(resonance.resonanceSet.atomSets)[i]
coords = getAtomSetCoords(atomSet, self.structure)
coord = coords[0]
atomCoordList.append([coord.x, coord.y, coord.z])
atomCoordList0.append([coord.x, coord.y, coord.z])
resonances2.append(resonance)
C += 1
print len(atomCoordList)
print len(resonances), len(resonances2)
print "Generating Mean"
cloudsList = []
for cloud in self.clouds:
orderCloud = []
for resonance in resonances2:
x, y, z = cloud.get(resonance) or (0.0, 0.0, 0.0)
orderCloud.append([-x, -y, -z])
cloudsList.append(orderCloud)
(meanCloud, cloudsList) = alignToMeanCloud(cloudsList)
weights = [1.0 for x in atomCoordList]
centerCoords(atomCoordList)
print "init cen", getMeanCoords(atomCoordList)
print "mean cen", getMeanCoords(meanCloud)
print "Print aligning struct clouds to mean", len(meanCloud), len(
atomCoordList), len(weights)
atomCoordsList, error, rotMat = alignCoordinates(
meanCloud, atomCoordList, weights)
print " Rotation", rotMat
writeTypedPdbCloud(atomCoordList, pdbFileName, resonances2)
print "Getting centres"
oldCentre = getMeanCoords(atomCoordList0)
newCentre = getMeanCoords(atomCoordList)
delta = [
newCentre[i] - oldCentre[i] for i in range(len(oldCentre))
]
print " New centre", newCentre
print " Old centre", oldCentre
print " Delta", delta
#inverseRot = inverseMatrix(rotMat)
model = self.structure.findFirstModel()
coordinates = model.coordinates
offset = 0
iis = (0, 1, 2)
for atom in self.structure.orderedAtoms:
next = offset + 3
coords = [coordinates[offset + ii] + delta[ii] for ii in iis]
coords = matrixVecMultiply(rotMat, coords)
coordinates[offset:next] = coords
offset = next
model.setSubmatrixData('coordinates', coordinates)
clouds = getCloudsFromFile([
pdbFileName,
], self.structure.root)
self.clouds.append(clouds[0])
self.rmsds.append(None)
self.names.append(pdbFileName)
self.updateAfter()
def calcRmsd(self):
if self.clouds:
if len(self.scrolledMatrix.currentObjects) < 2:
clouds = self.clouds
else:
clouds = []
for name in self.scrolledMatrix.currentObjects:
clouds.append(self.clouds[self.names.index(name)])
self.rmsds = filterClouds(clouds, atomTypes=self.atomTypes)
self.updateAfter()
def deleteClouds(self):
if self.names and self.name and showOkCancel(
'Confirm', 'Really remove selected clouds?'):
indices = []
for name in self.scrolledMatrix.currentObjects:
i = self.names.index(name)
indices.append(i)
indices.sort()
indices.reverse()
for i in indices:
self.clouds.pop(i)
self.rmsds.pop(i)
self.names.pop(i)
self.name = None
self.updateAfter()
def selectCell(self, name, row, col):
self.name = name
self.updateButtons()
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = 1
self.after_idle(self.update)
def destroy(self):
BasePopup.destroy(self)
def updateButtons(self):
if self.names:
self.bottomButtons.buttons[1].enable()
self.bottomButtons.buttons[2].enable()
self.bottomButtons.buttons[5].enable()
else:
self.bottomButtons.buttons[1].disable()
self.bottomButtons.buttons[2].enable()
self.bottomButtons.buttons[5].disable()
if self.name:
self.bottomButtons.buttons[4].enable()
else:
self.bottomButtons.buttons[4].disable()
if self.structure and self.clouds:
self.bottomButtons.buttons[3].enable()
else:
self.bottomButtons.buttons[3].disable()
def update(self):
textMatrix = []
objectList = self.names
self.updateButtons()
i = 0
for name in objectList:
datum = []
datum.append(i + 1)
datum.append(name)
datum.append(self.rmsds[i])
textMatrix.append(datum)
i += 1
if not objectList:
textMatrix = [
[],
]
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = 0
class ConfirmSeqSpinSystemsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.spinSystems = []
self.spectrum = None
self.spectra = []
self.waiting = 0
self.shiftList = None
self.spinSystem = None
self.link = '-1'
BasePopup.__init__(self,
parent=parent,
title="Confirm Sequential Spin System",
**kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame)
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Shift List:')
label.grid(row=0, column=0, sticky='w')
self.shiftListPulldown = PulldownMenu(frame,
callback=self.setShiftList)
self.shiftListPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Sequential Link Type:')
label.grid(row=0, column=2, sticky='w')
entries = ['-1', '-1,+1', '+1']
self.linkPulldown = PulldownMenu(frame,
callback=self.setLink,
entries=entries,
do_initial_callback=False,
selected_index=entries.index(
self.link))
self.linkPulldown.grid(row=0, column=3, sticky='w')
row += 1
frame = LabelFrame(guiFrame, text='Link Atoms:')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
labels = ['C', 'CA', 'CB', 'CG', 'CD', 'H', 'HA', 'HB', 'HG', 'HD']
selected = ['CA', 'CB']
self.atomSelector = PartitionedSelector(frame,
objects=labels,
labels=labels,
selected=selected,
toggledBg='#808080',
callback=self.changeAtoms,
maxRowObjects=10)
self.atomSelector.grid(row=0, column=0, sticky='ew')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Predicted Residue Assignments')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
headingList = [
'#', 'Predicted\nResidue', 'Prob.', 'Links', 'CA', 'CA -1', 'CB',
'CB -1'
]
self.spinSystemMatrix = ScrolledMatrix(frame,
headingList=headingList,
callback=self.selectSpinSystem,
multiSelect=1)
self.spinSystemMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
texts = ['Link Selected', 'Link All', 'Commit Assignment']
commands = [
self.linkSelectedSpinSystems, self.linkAllSpinSystems,
self.commitAssignments
]
buttonList = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url)
buttonList.grid(row=row, column=0, sticky='ew')
self.buttons = buttonList.buttons
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.ShiftList', ):
self.registerNotify(self.updateShiftLists, clazz, func)
for func in ('__init__', 'delete', 'setNmrChains', 'setResidue',
'setResonances', 'addResonance', 'removeResonance'):
self.registerNotify(self.updateSpinSystemsAfter,
'ccp.nmr.Nmr.ResonanceGroup', func)
self.updateShiftLists()
def setLink(self, index, name):
self.link = name
self.updateSpinSystemsAfter()
def updateButtons(self):
if len(self.spinSystemMatrix.currentObjects) > 1:
self.buttons[0].enable()
else:
self.buttons[0].disable()
if self.spinSystemMatrix.objectList:
self.buttons[1].enable()
else:
self.buttons[1].disable()
if self.spinSystem:
self.buttons[2].enable()
else:
self.buttons[2].disable()
def changeAtoms(self, *opt):
self.updateSpinSystemsAfter()
def getShiftListNames(self, shiftLists):
shiftListNames = []
for shiftList in shiftLists:
if not hasattr(shiftList, 'name'):
shiftList.name = "ShiftList " + str(shiftList.serial)
elif not shiftList.name:
shiftList.name = "ShiftList " + str(shiftList.serial)
shiftListNames.append(shiftList.name)
return shiftListNames
def updateShiftLists(self, *opt):
shiftLists = list(
self.nmrProject.findAllMeasurementLists(className='ShiftList'))
shiftListNames = self.getShiftListNames(shiftLists)
shiftList = None
index = -1
if shiftListNames:
if self.shiftList in shiftLists:
shiftList = self.shiftList
else:
shiftList = shiftLists[0]
index = shiftLists.index(shiftList)
self.shiftList = shiftList
self.shiftListPulldown.setup(shiftListNames, index)
def setShiftList(self, index, name=None):
shiftLists = list(
self.nmrProject.findAllMeasurementLists(className='ShiftList'))
if shiftLists:
self.shiftList = shiftLists[index]
else:
self.shiftList = None
self.updateSpinSystemsAfter()
def linkSelectedSpinSystems(self):
spinSystems = self.spinSystemMatrix.currentObjects
self.linkSpinSystems(spinSystems)
def linkAllSpinSystems(self):
spinSystems = self.spinSystemMatrix.objectList
self.linkSpinSystems(spinSystems)
def linkSpinSystems(self, spinSystems):
data = []
for spinSystem in spinSystems:
residue, p = self.getProbableResidue(spinSystem)
key = '%s%s%4.4d' % (residue.chain.molSystem.code,
residue.chain.code, residue.seqCode)
data.append([key, residue.seqCode, residue, spinSystem])
data.sort()
seqCodes = [x[1] for x in data]
residues = [x[2] for x in data]
spinSystems = [x[3] for x in data]
N = len(data)
for i in range(N):
if i > 0:
delta = seqCodes[i] - seqCodes[i - 1]
if delta == 1 and (residues[i].chain is residues[i - 1].chain):
ss = findConnectedSpinSystem(spinSystems[i], delta=-1)
if ss:
mergeSpinSystems(
ss,
spinSystems[i -
1]) # copy resonances across & delete
makeSeqSpinSystemLink(spinSystems[i - 1],
spinSystems[i],
delta=1)
if i < N - 1:
delta = seqCodes[i + 1] - seqCodes[i]
if delta == 1 and (residues[i].chain is residues[i + 1].chain):
ss = findConnectedSpinSystem(spinSystems[i], delta=1)
if ss:
mergeSpinSystems(
ss,
spinSystems[i +
1]) # copy resonances across & delete
makeSeqSpinSystemLink(spinSystems[i],
spinSystems[i + 1],
delta=1)
self.updateSpinSystemsAfter()
def commitAssignments(self):
merge = showYesNo('Query', 'Merge with any existing spin systems?',
self)
for spinSystem in self.spinSystemMatrix.currentObjects:
if not spinSystem.residue:
residue, p = self.getProbableResidue(spinSystem)
assignSpinSystemResidue(spinSystem, residue, warnMerge=merge)
def getProbableResidue(self, spinSystem):
residue = None
probability = 0.0
if spinSystem.residue:
return spinSystem.residue, 1.0
data = []
for residueProb in spinSystem.residueProbs:
data.append((residueProb.weight, residueProb.possibility))
data.sort()
if data:
residue, probability = data[-1]
return residue, probability
def getTentativeSpinSystems(self):
spinSystemsList = []
if self.project:
for spinSystem in self.nmrProject.sortedResonanceGroups():
if spinSystem.residueProbs and not spinSystem.residue:
#if spinSystem.residue:
residue, p = self.getProbableResidue(spinSystem)
key = '%s%s%4.4d' % (residue.chain.molSystem.code,
residue.chain.code, residue.seqCode)
spinSystemsList.append((key, spinSystem))
spinSystemsList.sort()
return [x[1] for x in spinSystemsList]
def updateSpinSystemsAfter(self, spinSystem=None):
if self.waiting:
return
else:
if spinSystem:
if not spinSystem.residueProbs:
return
if spinSystem.residue:
return
self.waiting = True
self.after_idle(self.updateSpinSystems)
def getHeadings(self):
headingList = ['#', 'Predicted\nResidue', 'Prob.', 'Links']
atoms = self.atomSelector.getSelected()
for atom in atoms:
headingList.append(atom)
if self.link == '-1':
headingList.append('%s -1' % atom)
headingList.append('D %s -1' % atom)
elif self.link == '+1':
headingList.append('%s +1' % atom)
headingList.append('D %s +1' % atom)
else:
headingList.append('%s -1' % atom)
headingList.append('D %s -1' % atom)
headingList.append('%s +1' % atom)
headingList.append('D %s +1' % atom)
return headingList
def addShiftData(self, spinSystem, datum):
prevSS, nextSS = self.getConnectedSpinSystems(spinSystem)
atoms = self.atomSelector.getSelected()
dict = {}
residue, p = self.getProbableResidue(spinSystem)
prevRes = residue.chain.findFirstResidue(seqCode=residue.seqCode - 1)
nextRes = residue.chain.findFirstResidue(seqCode=residue.seqCode + 1)
prevSS0 = None
nextSS0 = None
for ss in self.getTentativeSpinSystems():
if self.getProbableResidue(ss)[0] is prevRes:
prevSS0 = ss
if self.getProbableResidue(ss)[0] is nextRes:
nextSS0 = ss
if nextSS0 and prevSS0:
break
for atom in atoms:
resonances = []
resonancesPrev = []
resonancesNext = []
resonancesPrev0 = []
resonancesNext0 = []
for resonance0 in spinSystem.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonances.append(resonance0)
break
text = ''
if resonances:
text = self.getResonanceText(resonances)
datum.append(text)
if prevSS and ('-1' in self.link):
for resonance0 in prevSS.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonancesPrev.append(resonance0)
break
deltasPrev = []
if prevSS0 and resonancesPrev:
for resonance1 in prevSS0.sortedResonances():
for name1 in resonance1.assignNames:
if name1[:2] == atom:
shift1 = resonance1.findFirstShift(
parentList=self.shiftList)
deltas = []
for resonance2 in resonancesPrev:
shift2 = resonance2.findFirstShift(
parentList=self.shiftList)
if shift1 and shift2:
deltas.append(
abs(shift1.value - shift2.value))
if deltas:
deltas.sort()
deltasPrev.append('%.2f' % deltas[0])
break
if nextSS and ('+1' in self.link):
for resonance0 in nextSS.sortedResonances():
for name in resonance0.assignNames:
if name[:2] == atom:
resonancesNext.append(resonance0)
break
deltasNext = []
if nextSS0 and resonancesNext:
for resonance1 in nextSS0.sortedResonances():
for name1 in resonance1.assignNames:
if name1[:2] == atom:
shift1 = resonance1.findFirstShift(
parentList=self.shiftList)
deltas = []
for resonance2 in resonancesNext:
shift2 = resonance2.findFirstShift(
parentList=self.shiftList)
if shift1 and shift2:
deltas.append(
abs(shift1.value - shift2.value))
if deltas:
deltas.sort()
deltasNext.append('%.2f' % deltas[0])
break
if self.link == '-1':
ppms = ''
diff = ''
if resonancesPrev:
ppms = self.getResonanceText(resonancesPrev)
diff = ','.join(deltasPrev)
datum.append(ppms)
datum.append(diff)
elif self.link == '+1':
ppms = ''
diff = ''
if resonancesNext:
ppms = self.getResonanceText(resonancesNext)
diff = ','.join(deltasNext)
datum.append(ppms)
datum.append(diff)
else:
ppms = ''
diff = ''
if resonancesPrev:
ppms = self.getResonanceText(resonancesPrev)
diff = ','.join(deltasPrev)
datum.append(ppms)
datum.append(diff)
ppms = ''
diff = ''
if resonancesNext:
ppms = self.getResonanceText(resonancesNext)
diff = ','.join(deltasNext)
datum.append(ppms)
datum.append(diff)
def updateSpinSystems(self):
textMatrix = []
objectList = []
colorMatrix = []
headingList = self.getHeadings()
for spinSystem in self.getTentativeSpinSystems():
residueText = None
residue, probability = self.getProbableResidue(spinSystem)
if residue:
residueText = '%d%s' % (residue.seqCode,
getResidueCode(residue))
links = []
color = '#D04040'
if findConnectedSpinSystem(spinSystem, delta=-1):
links.append('-1')
if findConnectedSpinSystem(spinSystem, delta=1):
links.append('+1')
if len(links) == 2:
color = '#40B040'
elif len(links) == 1:
color = '#B0B040'
datum = []
datum.append(spinSystem.serial)
datum.append(residueText)
datum.append(probability)
datum.append(' '.join(links))
self.addShiftData(spinSystem, datum)
colors = [None] * len(headingList)
colors[3] = color
objectList.append(spinSystem)
textMatrix.append(datum)
colorMatrix.append(colors)
if self.spinSystem not in objectList:
self.spinSystem = None
self.spinSystemMatrix.update(headingList=headingList,
objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
self.updateButtons()
self.waiting = False
def getResonanceText(self, resonances):
shifts = []
for resonance in resonances:
shift = resonance.findFirstShift(parentList=self.shiftList)
if shift:
shifts.append('%.2f' % shift.value)
return ','.join(shifts)
def getConnectedSpinSystems(self, spinSystem):
if self.link == '-1':
prevSS = findConnectedSpinSystem(spinSystem, delta=-1)
nextSS = None
elif self.link == '+1':
prevSS = None
nextSS = findConnectedSpinSystem(spinSystem, delta=1)
else:
prevSS = findConnectedSpinSystem(spinSystem, delta=-1)
nextSS = findConnectedSpinSystem(spinSystem, delta=1)
return prevSS, nextSS
def selectSpinSystem(self, object, row, col):
self.spinSystem = object
self.updateButtons()
def destroy(self):
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.ShiftList', ):
self.unregisterNotify(self.updateShiftLists, clazz, func)
for func in ('__init__', 'delete', 'setNmrChains', 'setResidue',
'setResonances', 'addResonance', 'removeResonance'):
self.unregisterNotify(self.updateSpinSystemsAfter,
'ccp.nmr.Nmr.ResonanceGroup', func)
BasePopup.destroy(self)
class 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
class MidgePopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 15
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.ratioHD = 0.9
self.peakListDict = {}
self.peakListDict3d = {}
self.noesyPeakList = None
self.noesy3dPeakList = None
self.carbonLabel = 0
self.nitrogenLabel = 1
self.noesyPeakList1 = None
self.noesyPeakList2 = None
self.noesyPeakList3 = None
self.noesyPeakList3d = None
self.resonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.adcAtomTypes = None
self.structure = None
BasePopup.__init__(self,
parent,
title="Relaxation Matrix Optimisation",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
def setCarbonLabel(self, boolean):
self.carbonLabel = boolean
def setNitrogenLabel(self, boolean):
self.nitrogenLabel = boolean
def update(self):
if self.resonances and (
(self.noesyPeaks and self.noesyPeakList1 and self.noesyPeakList2
and self.noesyPeakList3) or self.noesyPeakList3d):
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.distConstrLabel.set(
str(len(self.distanceConstraintList.constraints)))
self.midgeButtons.buttons[1].enable()
else:
self.distConstrLabel.set('')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
str(len(self.antiDistConstraintList.constraints)))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('')
self.midgeButtons.buttons[2].disable()
if self.resonances:
self.numResonancesLabel.set(str(len(self.resonances)))
else:
self.numResonancesLabel.set('')
if self.noesyPeaks:
self.numPeaksLabel.set(str(len(self.noesyPeaks)))
else:
self.numPeaksLabel.set('')
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['<None>', 'HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
if name == '<None>':
name = None
self.adcAtomTypes = name
def getResonances(self):
resonanceDict = {}
if self.noesyPeaks:
for peak in self.noesyPeaks:
for peakDim in peak.peakDims:
for contrib in peakDim.peakDimContribs:
resonanceDict[contrib.resonance] = 1
# TBD: Set resonance.name for typing
self.resonances = resonanceDict.keys()
def getPeaks(self):
if self.noesyPeakList:
self.noesyPeaks = self.noesyPeakList.sortedPeaks()
def calculateDistances(self):
resonances = list(self.resonances)
resDict = {}
for resonance in resonances:
resDict[resonance.serial] = resonance
ratioHD = self.ratioHDEntry.get() or self.ratioHD
tmix1 = self.tmix1Entry.get() or 60
tmix2 = self.tmix2Entry.get() or 120
tmix3 = self.tmix3Entry.get() or 200
data = [(tmix1, self.noesyPeakList1), (tmix2, self.noesyPeakList2),
(tmix3, self.noesyPeakList3)]
data.sort()
mixingTimes = [x[0] for x in data]
peakLists = [x[1] for x in data]
# get a clean, symmetric and normalised NOE matrix
noeMatrix = getNoeMatrixFromPeaks(self.noesyPeaks,
resonances,
peakLists,
mixingTimes,
ratioHD=ratioHD,
analysis=self.guiParent)
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList, resonances = optimiseRelaxation(
resonances,
noeMatrix,
self.mixTime,
self.specFreq,
self.corrTime,
self.leakRate,
self.carbonLabel,
self.nitrogenLabel,
maxIter=self.maxIter)
#constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList and self.noesyPeakList:
constraintHead = self.distanceConstraintList.nmrConstraintStore
if self.adcAtomTypes:
adcDict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
allowedAtomTypes = adcDict[self.adcAtomTypes]
print "Making ADCs"
self.antiDistConstraintList = makeNoeAdcs(
resonances[:],
self.noesyPeakList.dataSource,
constraintHead,
allowedAtomTypes=allowedAtomTypes)
print "Done ADCs"
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
item = constraint.findFirstItem()
resonances = list(item.resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setOrigData(distance)
self.update()
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def getNoesys3d(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
if spectrum.numDim != 3:
continue
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict3d[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def getNoesys(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
if name == '<None>':
self.noesyPeakList = None
else:
self.noesyPeakList = self.peakListDict[name]
self.getPeaks()
self.getResonances()
self.update()
def setNoesy1(self, index, name=None):
if not name:
name = self.tmix1Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList1 = self.peakListDict[name]
else:
self.noesyPeakList1 = None
self.update()
def setNoesy2(self, index, name=None):
if not name:
name = self.tmix2Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList2 = self.peakListDict[name]
else:
self.noesyPeakList2 = None
self.update()
def setNoesy3(self, index, name=None):
if not name:
name = self.tmix3Pulldown.getSelected()
if name != '<None>':
self.noesyPeakList3 = self.peakListDict[name]
else:
self.noesyPeakList3 = None
self.update()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
if name != '<None>':
self.noesyPeakList3d = self.peakListDict3d[name]
self.noesyPeaks = self.noesyPeakList3d.sortedPeaks()
else:
self.noesyPeakList3d = None
self.noesyPeaks = []
self.getResonances()
self.update()
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
class WriteBmrbChemShiftDepPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'WriteBmrbChemShiftDep.html')
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.selectedFormats = []
self.defaultText = 'Select file'
self.chainDict = {}
self.chainList = []
self.shiftListDict = {}
self.shiftLists = []
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
if shiftList.measurements != ():
label = str(shiftList.serial) + ':' + str(shiftList.name)
self.shiftListDict[label] = shiftList
self.shiftLists.append(label)
if not self.shiftLists:
showError('Error', 'No shift lists available!')
return
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Write BMRB chemical shift deposition file',
modal=False,
transient=True)
def body(self, master):
row = 0
label = Label(master,
text="BMRB chemical shift deposition file writer.")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Shift lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftLists,
callback=self.setChainList,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Chains (only one per file):")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainListSelect = PulldownMenu(master, entries=self.chainList)
self.chainListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
self.setChainList(0, self.shiftLists[0])
row += 1
label = Label(master, text="Chemical shift deposition file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master,
text=self.defaultText,
command=self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = ['Write file']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def setChainList(self, shiftListIndex, shiftListLabel):
#
# Has to be done... very slow this.
#
shiftList = self.shiftListDict[shiftListLabel]
self.chainDict = {}
self.chainList = []
for shift in shiftList.measurements:
if shift.resonance:
rs = shift.resonance.resonanceSet
if rs:
atom = rs.findFirstAtomSet().findFirstAtom()
chain = atom.residue.chain
if chain not in self.chainDict.values():
label = chain.molSystem.code + ":'" + chain.code + "'"
self.chainDict[label] = chain
self.chainList.append(label)
self.chainListSelect.clearMenuItems()
if self.chainList:
self.chainListSelect.setup(self.chainList, 0)
def selectFile(self):
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
fileName = 'bmrb.csdep'
popup = FormatFilePopup(self,
file=fileName,
component='csdep',
format='bmrb')
if popup.fileSelected:
self.fileButton.config(text=popup.file)
popup.destroy()
def apply(self):
shiftListLabel = self.shiftListSelect.getSelected()
shiftList = self.shiftListDict[shiftListLabel]
try:
chainLabel = self.chainListSelect.getSelected()
chain = self.chainDict[chainLabel]
except:
showError(
"No chains",
"No chains were present or selected. Try running linkResonances first."
)
return False
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeBmrbChemShiftDeposition(self.guiParent, chain,
shiftList, fileName)
if fileCreated:
showInfo("Success",
"Succesfully wrote chemical shift deposition file")
else:
showError("Not written",
"Error writing file %s. File not written" % fileName)
return False
return True
class HcloudsMdPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.constraintSet = None
self.constrLists = [None] * 4
self.numClouds = 100
self.filePrefix = 't_intra_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Hydrogen Cloud Molecular Dynamics",
**kw)
def body(self, guiFrame):
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Input constraints')
frame.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame.grid_columnconfigure(2, weight=1)
srow = 0
label = Label(frame, text='Constraint set:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.constraintSetPulldown = PulldownMenu(
frame,
callback=self.changeConstraintSet,
selected_index=0,
do_initial_callback=0)
self.constraintSetPulldown.grid(row=srow, column=1, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 1:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance1Pulldown = PulldownMenu(
frame,
callback=self.changeDistance1ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance1Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr1Label = Label(frame, text='Constraints: 0')
self.numConstr1Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 2:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance2Pulldown = PulldownMenu(
frame,
callback=self.changeDistance2ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance2Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr2Label = Label(frame, text='Constraints: 0')
self.numConstr2Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 3:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance3Pulldown = PulldownMenu(
frame,
callback=self.changeDistance3ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance3Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr3Label = Label(frame, text='Constraints: 0')
self.numConstr3Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 4:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance4Pulldown = PulldownMenu(
frame,
callback=self.changeDistance4ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance4Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr4Label = Label(frame, text='Constraints: 0')
self.numConstr4Label.grid(row=srow, column=2, sticky=Tkinter.W)
row += 1
frame0 = LabelFrame(guiFrame, text='Cooling scheme')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
frame0.grid_rowconfigure(f0row, weight=1)
colHeadings = [
'Step', 'Initial\nTemp.', 'Final\nTemp.', 'Cooling\nSteps',
'MD Steps', 'MD Tau', 'Rep.\nScale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame0,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f0row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame0,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = LabelFrame(guiFrame, text='Dynamics control')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(1, weight=1)
f1row = 0
label20 = Label(frame1, text='Number of clouds:')
label20.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = IntEntry(frame1,
text=1,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f1row, column=1, sticky=Tkinter.NW)
label21 = Label(frame1, text='Cloud file prefix:')
label21.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame1,
text='t_intra_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame1,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.registerNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.registerNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
def getContraintSetNames(self):
names = []
constraintSets = self.project.currentNmrProject.nmrConstraintStores
for set in constraintSets:
names.append('%d' % set.serial)
return names
def changeConstraintSet(self, i, name):
project = self.project
if project.currentNmrProject.nmrConstraintStores:
constraintSet = project.currentNmrProject.sortedNmrConstraintStores(
)[i]
else:
constraintSet = None
if constraintSet is not self.constraintSet:
self.constraintSet = constraintSet
self.updateConstraintLists()
self.update()
def updateConstraintLists(self, *opt):
constrListData = self.getConstraintLists()
constrListNames = [x[0] for x in constrListData]
constraintLists = [x[1] for x in constrListData]
# copes with self.constraintSet being None
if constrListNames:
i = 0
for constraintList in self.constrLists:
if constraintList not in constraintLists:
if i == 0:
self.constrLists[i] = constraintLists[0]
else:
self.constrLists[i] = None
i += 1
constraintLists.append(None)
constrListNames.append('<None>')
self.distance1Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[0]))
self.distance2Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[1]))
self.distance3Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[2]))
self.distance4Pulldown.setup(
constrListNames, constraintLists.index(self.constrLists[3]))
else:
self.constrLists = [None] * 4
self.distance1Pulldown.setup([], -1)
self.distance2Pulldown.setup([], -1)
self.distance3Pulldown.setup([], -1)
self.distance4Pulldown.setup([], -1)
def updateConstraintSets(self, *opt):
project = self.project
constraintSets = list(project.currentNmrProject.nmrConstraintStores)
if constraintSets:
constraintSetNames = self.getContraintSetNames()
# set defaults
if self.constraintSet not in constraintSets:
self.constraintSet = constraintSets[0]
if self.constraintSet:
j = 0
for constraintList in self.constrLists:
if constraintList and (constraintList.nmrConstraintStore
is not self.constraintSet):
if self.constraintSet.constraintLists and j == 0:
self.constrLists[
j] = self.constraintSet.constraintLists[0]
else:
self.constrLists[j] = None
j += 1
else:
self.constrLists = [None] * 4
i = constraintSets.index(self.constraintSet)
self.constraintSetPulldown.setup(constraintSetNames, i)
else:
self.constraintSet = None
self.constrLists = [None] * 4
self.constraintSetPulldown.setup([], -1)
def getConstraintListName(self, constraintList):
if constraintList.name:
listName = ':%s' % (constraintList.name)
else:
listName = ''
name = '%d:%d:%s%s' % (constraintList.nmrConstraintStore.serial,
constraintList.serial,
constraintList.className[:-14], listName)
return name
def getConstraintLists(self):
constraintLists = []
if self.constraintSet:
for constraintList in self.constraintSet.constraintLists:
if constraintList.className == 'DistanceConstraintList':
name = self.getConstraintListName(constraintList)
constraintLists.append([name, constraintList])
return constraintLists
def changeDistance1ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 0)
def changeDistance2ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 1)
def changeDistance3ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 2)
def changeDistance4ConstraintList(self, i, name):
self.changeDistanceConstraintList(i, name, 3)
def changeDistanceConstraintList(self, i, name, listNum):
project = self.project
constraintLists = self.getConstraintLists()
if constraintLists and (i < 4):
self.constrLists[listNum] = constraintLists[i][1]
else:
self.constrLists[listNum] = None
self.update()
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if ((self.constrLists != [None] * 4) and (self.numClouds > 0)
and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
constraints = []
constraintStore = None
for dcl in self.constrLists:
if dcl:
constraintStore = dcl.nmrConstraintStore
constraints.extend(list(dcl.constraints))
resonances = []
for constraint in constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if fixedResonance.resonanceSerial is None:
resonance = newResonance(
self.guiParent.project,
isotopeCode=fixedResonance.isotopeCode)
resonance.setName(fixedResonance.name)
fixedResonance.setResonanceSerial(resonance.serial)
resDict[resonance.serial] = resonance
if fixedResonance.resonanceSet:
atomSets = list(
fixedResonance.resonanceSet.atomSets)
assignAtomsToRes(atomSets, resonance)
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
resonances, intraConstraintList = self.makeIntraConstraints(
resonances, constraintStore)
constraints.extend(list(intraConstraintList.constraints))
resonances, interConstraintList = self.makeInterConstraints(
resonances, constraintStore)
constraints.extend(list(interConstraintList.constraints))
startMdProcess(self.numClouds, constraints, resonances,
self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(constraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(constraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def makeInterConstraints(self, resonances, constraintSet):
from ccpnmr.analysis.core.ConstraintBasic import getFixedResonance
from ccpnmr.analysis.core.AssignmentBasic import findConnectedSpinSystem
project = constraintSet.root
constraintList = constraintSet.newDistanceConstraintList()
constraintList.name = 'Seq connections'
resDict = {}
spinSystemDict = {}
for resonance in resonances:
resDict[resonance] = True
spinSystem = resonance.resonanceGroup
if spinSystem:
spinSystemDict[spinSystem] = None
spinSystems = spinSystemDict.keys()
for spinSystem in spinSystems:
nextSpinSystem = findConnectedSpinSystem(spinSystem, delta=1)
if nextSpinSystem:
ca = spinSystem.newAtoms.get('CA')
c = spinSystem.newAtoms.get('C')
n = nextSpinSystem.newAtoms.get('N')
if ca and c and n:
if resDict.get(ca) is None:
resonances.append(ca)
if resDict.get(c) is None:
resonances.append(c)
if resDict.get(n) is None:
resonances.append(n)
c_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.32,
upperLimit=1.35,
lowerLimit=1.29,
error=0.06)
# below based on angle constraints
ca_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=2.415,
upperLimit=2.513,
lowerLimit=2.316,
error=0.197)
frCa = getFixedResonance(constraintSet, ca)
frC = getFixedResonance(constraintSet, c)
frN = getFixedResonance(constraintSet, n)
item = ca_n.newDistanceConstraintItem(
resonances=[frCa, frN])
item = c_n.newDistanceConstraintItem(resonances=[frC, frN])
return resonances, constraintList
def makeIntraConstraints(self, resonances, constraintSet):
from ccpnmr.analysis.core.ConstraintBasic import getFixedResonance
project = constraintSet.root
constraintList = constraintSet.newDistanceConstraintList()
constraintList.name = 'Backbone intra'
dict = {}
for resonance in resonances:
if resonance.resonanceGroup and resonance.assignNames:
dict[resonance] = 1
resonance.resonanceGroup.newAtoms = {}
for resonance in dict.keys():
ss = resonance.resonanceGroup
if resonance.assignNames[0] == 'H':
for resonance2 in ss.resonances:
if dict.get(resonance2
) and resonance2.assignNames[0][:2] == 'HA':
ca = ss.newAtoms.get('CA')
if ca is None:
ca = project.newResonance(isotopeCode='13C',
assignNames=[
'CA',
])
resonances.append(ca)
c = ss.newAtoms.get('C')
if c is None:
c = project.newResonance(isotopeCode='13C',
assignNames=[
'C',
])
resonances.append(c)
n = ss.newAtoms.get('N')
if n is None:
n = project.newResonance(isotopeCode='15N',
assignNames=[
'N',
])
resonances.append(n)
ss.newAtoms['C'] = c
ss.newAtoms['CA'] = ca
ss.newAtoms['N'] = n
frCa = getFixedResonance(constraintSet, ca)
frC = getFixedResonance(constraintSet, c)
frN = getFixedResonance(constraintSet, n)
frH = getFixedResonance(constraintSet, resonance)
frha = getFixedResonance(constraintSet, resonance2)
h_n = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.01,
upperLimit=1.1,
lowerLimit=0.9,
error=0.2)
n_ca = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.465,
upperLimit=1.50,
lowerLimit=1.43,
error=0.07)
ca_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.525,
upperLimit=1.55,
lowerLimit=1.50,
error=0.05)
# below based on angle constraints
n_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=2.464,
upperLimit=2.572,
lowerLimit=2.356,
error=0.216)
item = h_n.newDistanceConstraintItem(
resonances=[frH, frN])
item = n_ca.newDistanceConstraintItem(
resonances=[frN, frCa])
item = ca_c.newDistanceConstraintItem(
resonances=[frCa, frC])
item = n_c.newDistanceConstraintItem(
resonances=[frN, frC])
if ss.newAtoms.get('CAHA') is None:
ca_ha = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
item = ca_ha.newDistanceConstraintItem(
resonances=[frC, frha])
ss.newAtoms['CAHA'] = 1
if resonance.assignNames[0][:2] == 'HA':
for resonance2 in ss.resonances:
if dict.get(resonance2
) and resonance2.assignNames[0][:2] == 'HB':
ca = ss.newAtoms.get('CA')
if ca is None:
ca = project.newResonance(isotopeCode='13C',
assignNames=[
'CA',
])
resonances.append(ca)
cb = ss.newAtoms.get('CB')
if cb is None:
cb = project.newResonance(isotopeCode='13C',
assignNames=[
'CB',
])
resonances.append(cb)
ss.newAtoms['CA'] = cb
ss.newAtoms['CB'] = ca
ss.newAtoms['CAHA'] = 1
frCA = getFixedResonance(constraintSet, ca)
frCB = getFixedResonance(constraintSet, cb)
frHA = getFixedResonance(constraintSet, resonance)
frHB = getFixedResonance(constraintSet, resonance2)
c_b = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
c_c = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.53,
upperLimit=1.56,
lowerLimit=1.51,
error=0.05)
item = c_b.newDistanceConstraintItem(
resonances=[frCB, frHB])
item = c_c.newDistanceConstraintItem(
resonances=[frCA, frCB])
if ss.newAtoms.get('CAHA') is None:
c_a = constraintList.newDistanceConstraint(
weight=1.0,
origData=1.0,
targetValue=1.09,
upperLimit=1.19,
lowerLimit=0.99,
error=0.2)
item = c_a.newDistanceConstraintItem(
resonances=[frCA, frHA])
ss.newAtoms['CAHA'] = 1
return resonances, constraintList
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def update(self):
self.updateConstraintSets()
self.updateConstraintLists()
if (self.constrLists != [None] * 4) and self.coolingScheme:
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
if self.constrLists[0]:
self.numConstr1Label.set('Constraints: ' +
str(len(self.constrLists[0].constraints)))
else:
self.numConstr1Label.set('Constraints: 0')
if self.constrLists[1]:
self.numConstr2Label.set('Constraints: ' +
str(len(self.constrLists[1].constraints)))
else:
self.numConstr2Label.set('Constraints: 0')
if self.constrLists[2]:
self.numConstr3Label.set('Constraints: ' +
str(len(self.constrLists[2].constraints)))
else:
self.numConstr3Label.set('Constraints: 0')
if self.constrLists[3]:
self.numConstr4Label.set('Constraints: ' +
str(len(self.constrLists[3].constraints)))
else:
self.numConstr4Label.set('Constraints: 0')
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def destroy(self):
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.unregisterNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.unregisterNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
BasePopup.destroy(self)
