def __init__(self,
parent,
label,
entry='',
separator=': ',
label_width=20,
entry_width=60,
label_anchor=Tkinter.E,
show='',
returnCallback=None,
tipText=None,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
self.separator = separator
text = label + separator
self.label = Label(self,
text=text,
width=label_width,
anchor=label_anchor)
self.label.grid(row=0, column=0, sticky=Tkinter.EW)
self.entry = Entry(self,
show=show,
width=entry_width,
returnCallback=returnCallback,
tipText=tipText)
self.entry.insert(0, entry)
self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
def body(self, master):
master.grid_columnconfigure(1, weight=1)
row = 0
label = Label(master, text='Axis unit name: ', grid=(row, 0))
tipText = 'Short textual name for the unit, e.g. "KPa" or "ms"'
self.nameEntry = Entry(master,
width=10,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(master, text='Unit is backwards: ', grid=(row, 0))
tipText = 'Whether the axis values decrease left to right & bottom to top. For example "ppm" does, but most units do not'
self.backwardsMenu = BooleanPulldownMenu(master,
grid=(row, 1),
tipText=tipText)
row += 1
tipTexts = [
'Make a new unit specification using the stated options and close this popup'
]
texts = ['Create']
commands = [self.ok]
buttons = UtilityButtonList(master,
texts=texts,
commands=commands,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
master.grid_rowconfigure(row, weight=1)
def body(self, master):
self.geometry('600x130')
master.grid_columnconfigure(1, weight=1)
for n in range(5):
master.grid_rowconfigure(n, weight=1)
row = 0
label = Label(master, text='Spectrum: ')
label.grid(row=row, column=0, sticky='e')
tipText = 'The spectrum for which the contour file is being added'
self.expt_spectrum = PulldownList(master,
callback=self.updateContourDir,
tipText=tipText)
self.expt_spectrum.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'The location of the directory where contour files are stored on disk'
label = Label(master, text='Contour dir: ')
label.grid(row=row, column=0, sticky='e')
self.dir_label = Label(master, text='', tipText=tipText)
self.dir_label.grid(row=row, column=1, sticky='w')
row = row + 1
label = Label(
master,
text=
'(file will be copied into Contour dir if it is not already in there)'
)
label.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'Browse for a file store contour data'
button = Button(master,
text='File name: ',
command=self.selectFile,
tipText=tipText)
button.grid(row=row, column=0, sticky='e')
tipText = 'Enter the name of the file to store contour data'
self.file_entry = Entry(master, tipText=tipText)
self.file_entry.grid(row=row, column=1, sticky='ew')
row = row + 1
texts = ['Add File']
commands = [self.addFile]
tipTexts = [
'Use the selected contour file in the current project, copying it to the contour directory if required',
]
self.buttons = UtilityButtonList(master,
texts=texts,
doClone=False,
tipTexts=tipTexts,
commands=commands,
helpUrl=self.help_url)
self.buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.curateNotifiers(self.registerNotify)
self.updateSpectrum()
def addLabelEntry(self,
n,
label='',
entry='',
show='',
frozen=False,
doGrid=True):
text = label + self.separator
l = Tkinter.Label(self,
text=text,
width=self.label_width,
anchor=self.label_anchor)
self.labels[n:n] = [l]
e = Entry(self,
text=entry,
show=show,
width=self.entry_width,
returnCallback=lambda n=n: self.returnCallback(n))
if (frozen):
e.config(bg='gray', state=Tkinter.DISABLED)
e.bind('<Button>', lambda event, e=e: e.focus())
else:
e.config(bg='white')
self.entries[n:n] = [e]
if (doGrid):
self.gridAll()
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 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 body(self, guiParent):
guiParent.grid_columnconfigure(1,weight=1)
row = 0
file_types = [ FileType('Python', ['*.py']), FileType('All', ['*']) ]
self.file_select = FileSelect(guiParent, file_types=file_types,
single_callback=self.chooseFile,
double_callback=self.chooseFile)
self.file_select.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
headingList=('Function',)
self.scrolledMatrix = ScrolledMatrix(guiParent, initialRows=4,
headingList=headingList, callback=self.selectFunction)
self.scrolledMatrix.grid(row=row, column=0, columnspan=2, sticky='nsew')
guiParent.grid_rowconfigure(row,weight=1)
row = row + 1
self.moduleLabel1 = Label(guiParent, text='Module: ')
self.moduleLabel1.grid(row=row, column=0, sticky='nw')
self.moduleLabel2 = Label(guiParent, text=' ')
self.moduleLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.functionLabel1 = Label(guiParent, text='Function: ')
self.functionLabel1.grid(row=row, column=0, sticky='nw')
self.functionLabel2 = Label(guiParent, text=' ')
self.functionLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.nameLabel = Label(guiParent, text='Name: ')
self.nameLabel.grid(row=row, column=0, sticky='nw')
self.nameEntry = Entry(guiParent, text=' ', width=40)
self.nameEntry.grid(row=row, column=1, sticky='nw')
row = row + 1
texts = [ 'Load Macro' ]
commands = [ self.loadMacro ]
buttons = UtilityButtonList(guiParent, texts=texts,
commands=commands, helpUrl=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.loadButton = buttons.buttons[0]
self.loadButton.disable()
self.path = None
self.module = None
self.function = None
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 __init__(self,
parent,
values,
initial_index=0,
orient=Tkinter.HORIZONTAL,
scale_length=200,
entry_width=5,
entry_format='%2.1f',
set_callback=None,
*args,
**kw):
assert len(values) > 0
self.entry_format = entry_format
self.values = tuple(values)
self.set_callback = set_callback
apply(Frame.__init__, (self, parent) + args, kw)
if (orient == Tkinter.HORIZONTAL):
self.grid_columnconfigure(1, weight=1)
sticky = Tkinter.EW
row = 0
col = 1
else:
self.grid_rowconfigure(1, weight=1)
sticky = Tkinter.NS
row = 1
col = 0
self.entry = Entry(self, width=entry_width)
self.entry.grid(row=0, column=0, sticky=sticky)
self.entry.bind('<KeyPress>', self.keyPress)
self.scale = Tkinter.Scale(self,
orient=orient,
length=scale_length,
from_=0,
to=len(values) - 1,
label='',
showvalue=0,
command=self.setCallback)
self.scale.grid(row=row, column=col, sticky=sticky)
self.set(initial_index)
def body(self, guiFrame):
self.geometry('600x250+600+250')
analysisProfile = self.analysisProfile
userName = analysisProfile.userName
userOrganisation = analysisProfile.userOrganisation
userEmail = analysisProfile.userEmail
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(1, weight=1)
explainText = 'To keep track of our users and which versions are being used\n' \
'we would like you to register your details with us.\n' \
'Collating the number of users is important for grant applications.\n' \
'Please do not use accents in any of the information\n' \
'because Python does not handle it gracefully.'
row = 0
label = Label(guiFrame,
text=explainText,
grid=(row, 0),
gridSpan=(1, 2),
sticky='ew')
row += 1
licenseAgreeText = 'I agree to abide by the rules of the CCPN licensing agreement.'
self.agreeButton = CheckButton(guiFrame,
licenseAgreeText,
tipText=licenseAgreeText)
self.agreeButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
self.entryWidgets = []
for (text, value) in (('Name', userName),
('Organisation', userOrganisation), ('Email',
userEmail)):
label = Label(guiFrame, text=text + ':', grid=(row, 0))
entry = Entry(guiFrame,
text=value or '',
grid=(row, 1),
sticky='ew',
tipText='Your ' + text)
self.entryWidgets.append(entry)
row += 1
texts = ['Register Now', 'Read License', 'Register Later']
tipTexts = ['Register now', 'Read License', 'Register later']
commands = [self.register, self.openLicense, self.close]
buttons = UtilityButtonList(guiFrame,
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
commands=commands,
texts=texts,
tipTexts=tipTexts)
self.buttons = buttons
def body(self, master):
#
# Popup window
#
self.widgets = []
row = 0
label = Label(master, text= "ChemComp formula '%s'" % self.formula)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= "Number of bonds: %d" % self.bondNumber)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
#
# Show relevant attributes...
#
for chemCompAttrInfo in self.chemCompInfo:
row = row + 1
attrName = chemCompAttrInfo[0]
label = Label(master, text = attrName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] == PulldownMenu:
self.widgets.append(PulldownMenu(master, entries = widgetInfo[1], selected_index = widgetInfo[1].index(chemCompAttrInfo[1])))
elif widgetInfo[0] == CheckButton:
self.widgets.append(CheckButton(master, selected = widgetInfo[1]))
else:
text = chemCompAttrInfo[1]
if not text:
text = ''
self.widgets.append(Entry(master, text = text))
self.widgets[-1].grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 2)
class LabeledEntry(Frame):
def __init__(self,
parent,
label,
entry='',
separator=': ',
label_width=20,
entry_width=60,
label_anchor=Tkinter.E,
show='',
returnCallback=None,
tipText=None,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
self.separator = separator
text = label + separator
self.label = Label(self,
text=text,
width=label_width,
anchor=label_anchor)
self.label.grid(row=0, column=0, sticky=Tkinter.EW)
self.entry = Entry(self,
show=show,
width=entry_width,
returnCallback=returnCallback,
tipText=tipText)
self.entry.insert(0, entry)
self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
def getLabel(self):
text = self.label.get()
n = text.find(self.separator)
if (n >= 0):
text = text[:n]
return text
def setLabel(self, text=''):
text = text + self.separator
self.label.set(text)
def getEntry(self):
return self.entry.get()
def setEntry(self, text=''):
self.entry.set(text)
def body(self, frame):
label = Label(frame, text=self.prompt)
if self.hide:
entry = Entry(frame, text=self.initVal, bg='white', show='*')
else:
entry = Entry(frame, text=self.initVal, bg='white')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry.grid(row=1, column=0, sticky=Tkinter.W)
entry.focus_set() # for the keypresses
return entry
def __init__(self, guiParent, dataText, dataObjects, dataValues, helpText,
selectionText, **kw):
Frame.__init__(self, guiParent, **kw)
label = Label(self, text=dataText + ':', grid=(0, 0))
self.selectionList = PulldownList(self,
objects=dataObjects,
texts=dataValues,
grid=(0, 1))
label = Label(self, text=helpText, grid=(1, 0), gridSpan=(1, 2))
label = Label(self, text=selectionText + ':', grid=(2, 0))
self.selectionEntry = Entry(self, grid=(2, 1))
def body(self, master):
#
# Popup window
#
row = 0
label = Label(master, text=self.topText)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
row = row + 1
self.valueWidgets = []
for i in range(0, len(self.valueList)):
value = self.valueList[i]
labelText = self.valueInfo[i]
label = Label(master, text=labelText)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.valueWidgets.append(Entry(master, text=str(value)))
self.valueWidgets[-1].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 body(self, master):
master.grid_columnconfigure(1, weight=1)
row = 0
label = Label(master, text='Panel name: ', grid=(row, 0))
tipText = 'Short text name for the new axis panel, e.g. "N2"'
self.name_entry = Entry(master,
width=15,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(master, text='Axis type:', grid=(row, 0))
tipText = 'The type of axis (isotope, time, sampled etc.) represented by panel type'
self.types_list = PulldownList(master, grid=(row, 1), tipText=tipText)
row += 1
tipTexts = [
'Create a new panel type object with the selected options & close the popup'
]
texts = ['Create']
commands = [self.ok]
buttons = UtilityButtonList(master,
texts=texts,
commands=commands,
doClone=False,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
master.grid_rowconfigure(row, weight=1)
self.administerNotifiers(self.registerNotify)
self.update()
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()
class CreatePanelTypePopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.axisType = None
BasePopup.__init__(self,
parent=parent,
title='Create panel type',
modal=True,
**kw)
def body(self, master):
master.grid_columnconfigure(1, weight=1)
row = 0
label = Label(master, text='Panel name: ', grid=(row, 0))
tipText = 'Short text name for the new axis panel, e.g. "N2"'
self.name_entry = Entry(master,
width=15,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(master, text='Axis type:', grid=(row, 0))
tipText = 'The type of axis (isotope, time, sampled etc.) represented by panel type'
self.types_list = PulldownList(master, grid=(row, 1), tipText=tipText)
row += 1
tipTexts = [
'Create a new panel type object with the selected options & close the popup'
]
texts = ['Create']
commands = [self.ok]
buttons = UtilityButtonList(master,
texts=texts,
commands=commands,
doClone=False,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
master.grid_rowconfigure(row, weight=1)
self.administerNotifiers(self.registerNotify)
self.update()
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.update, 'ccpnmr.Analysis.AxisType', func)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def update(self, *extra):
axisType = self.axisType
axisTypes = self.parent.getAxisTypes()
names = [x.name for x in axisTypes]
if axisTypes:
if axisType not in axisTypes:
self.axisType = axisType = axisTypes[0]
index = axisTypes.index(axisType)
else:
index = 0
self.axisType = None
self.types_list.setup(names, axisTypes, index)
def apply(self):
name = self.name_entry.get()
if not name:
showError('No name', 'Need to enter name', parent=self)
return False
names = [
panelType.name for panelType in self.analysisProject.panelTypes
]
if name in names:
showError('Repeated name', 'Name already used', parent=self)
return False
axisType = self.types_list.getObject()
if not axisType:
showError('No axis type', 'Need to create axis type', parent=self)
return False
self.analysisProject.newPanelType(name=name, axisType=axisType)
return True
class CingFrame(NmrSimRunFrame):
def __init__(self, parent, application, *args, **kw):
project = application.project
simStore = project.findFirstNmrSimStore(application=APP_NAME) or \
project.newNmrSimStore(application=APP_NAME, name=APP_NAME)
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.nmrProject = application.nmrProject
self.serverDone = False
NmrSimRunFrame.__init__(self, parent, project, simStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureFrame.grid_forget()
tab = self.tabbedFrame.frames[0]
frame = Frame(tab, grid=(1,0))
frame.expandGrid(2,1)
div = LabelDivider(frame, text='Structures', grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Ensemble: ', grid=(1,0))
self.structurePulldown = PulldownList(frame, callback=self.changeStructure, grid=(1,1))
headingList = ['Model','Use']
editWidgets = [None,None]
editGetCallbacks = [None,self.toggleModel]
editSetCallbacks = [None,None,]
self.modelTable = ScrolledMatrix(frame, grid=(2,0), gridSpan=(1,2),
callback=self.selectStructModel,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame, texts=texts, commands=commands, grid=(3,0), gridSpan=(1,2))
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1,0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0,0))
frame.expandGrid(None,2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
urls = [DEFAULT_URL,]
self.iCingBaseUrlPulldown = PulldownList(frame, texts=urls, objects=urls, index=0, grid=(srow,1))
srow +=1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
self.setZipFileName()
button = Button(frame, text='Choose File', bd=1, sticky='ew',
command=self.chooseZipFile, grid=(srow, 2))
srow +=1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
button = Button(frame, text='View Results HTML', bd=1, sticky='ew',
command=self.viewHtmlResults, grid=(srow, 2))
srow +=1
texts = ['Submit Project!', 'Check Run Status',
'Purge Server Result', 'Download Results']
commands = [self.runCingServer, self.checkStatus,
self.purgeCingServer, self.downloadResults]
self.buttonBar = ButtonList(frame, texts=texts, commands=commands,
grid=(srow, 0), gridSpan=(1,3))
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1,0))
frame.expandGrid(1,1)
label = Label(frame, text='Chain: ')
label.grid(row=0,column=0,sticky='w')
self.chainPulldown = PulldownList(frame, callback=self.changeChain)
self.chainPulldown.grid(row=0,column=1,sticky='w')
headingList = ['#','Residue','Linking','Decriptor','Use?']
editWidgets = [None,None,None,None,None]
editGetCallbacks = [None,None,None,None,self.toggleResidue]
editSetCallbacks = [None,None,None,None,None,]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky = 'nsew')
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame, texts=texts, commands=commands,)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(simStore)
self.administerNotifiers(application.registerNotify)
def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query',msg, parent=self):
self.purgeCingServer()
def getServerUrl(self, baseUrl):
iCingUrl = os.path.join(baseUrl, 'icing/serv/iCingServlet')
return iCingUrl
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structure = self.structure
if not structure:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
ensembleText = getModelsString(run)
if not ensembleText:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueText = getResiduesString(structure)
if not residueText:
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID, self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY, self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials, self.getServerUrl(url))
if results:
showInfo('Info','iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info','Purge failed')
self.update()
def chooseZipFile(self):
fileTypes = [ FileType('Zip', ['*.zip']), ]
popup = FileSelectPopup(self, file_types=fileTypes, file=self.resultFileEntry.get(),
title='Results zip file location', dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def setZipFileName(self):
zipFile = '%s_CING_report.zip' % self.project.name
self.resultFileEntry.set(zipFile)
def selectStructModel(self, model, row, col):
self.model = model
def selectResidue(self, residue, row, col):
self.residue = residue
def deactivateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = False
self.updateResidues()
def activateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = True
self.updateResidues()
def activateModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model not in self.run.inputStructures:
self.run.addInputStructure(model)
self.updateModels()
def disableModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model in self.run.inputStructures:
self.run.removeInputStructure(model)
self.updateModels()
def toggleModel(self, *opt):
if self.model and self.run:
if self.model in self.run.inputStructures:
self.run.removeInputStructure(self.model)
else:
self.run.addInputStructure(self.model)
self.updateModels()
def toggleResidue(self, *opt):
if self.residue:
self.residue.useInCing = not self.residue.useInCing
self.updateResidues()
def updateResidues(self):
if self.residue and (self.residue.topObject is not self.structure):
self.residue = None
textMatrix = []
objectList = []
colorMatrix = []
if self.chain:
chainCode = self.chain.code
for residue in self.chain.sortedResidues():
msResidue = residue.residue
if not hasattr(residue, 'useInCing'):
residue.useInCing = True
if residue.useInCing:
colors = [None, None, None, None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None, None, None, None]
use = 'No'
datum = [residue.seqCode,
msResidue.ccpCode,
msResidue.linking,
msResidue.descriptor,
use,]
textMatrix.append(datum)
objectList.append(residue)
colorMatrix.append(colors)
self.residueMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def updateChains(self):
index = 0
names = []
chains = []
chain = self.chain
if self.structure:
chains = self.structure.sortedCoordChains()
names = [chain.code for chain in chains]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
self.changeChain(chain)
self.chainPulldown.setup(names, chains, index)
def updateStructures(self):
index = 0
names = []
structures = []
structure = self.structure
if self.run:
model = self.run.findFirstInputStructure()
if model:
structure = model.structureEnsemble
structures0 = [(s.ensembleId, s) for s in self.project.structureEnsembles]
structures0.sort()
for eId, structure in structures0:
name = '%s:%s' % (structure.molSystem.code, eId)
structures.append(structure)
names.append(name)
if structures:
if structure not in structures:
structure = structures[-1]
index = structures.index(structure)
self.changeStructure(structure)
self.structurePulldown.setup(names, structures, index)
def updateModels(self):
textMatrix = []
objectList = []
colorMatrix = []
if self.structure and self.run:
used = self.run.inputStructures
for model in self.structure.sortedModels():
if model in used:
colors = [None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None]
use = 'No'
datum = [model.serial,use]
textMatrix.append(datum)
objectList.append(model)
colorMatrix.append(colors)
self.modelTable.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def changeStructure(self, structure):
if self.project and (self.structure is not structure):
self.project.currentEstructureEnsemble = structure
self.structure = structure
if self.run:
self.run.inputStructures = structure.sortedModels()
self.updateModels()
self.updateChains()
def changeChain(self, chain):
if self.project and (self.chain is not chain):
self.chain = chain
self.updateResidues()
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('Python', ['*.py']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title='Python file', dismiss_text='Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
simStore = project.findFirstNmrSimStore(application='CING') or \
project.newNmrSimStore(application='CING', name='CING')
else:
simStore = None
if not self.project:
return
self.setZipFileName()
if not self.project.currentNmrProject:
name = self.project.name
self.nmrProject = self.project.newNmrProject(name=name)
else:
self.nmrProject = self.project.currentNmrProject
self.update(simStore)
def update(self, simStore=None):
NmrSimRunFrame.update(self, simStore)
run = self.run
urls = [DEFAULT_URL,]
index = 0
if run:
userId = getRunParameter(run, iCingRobot.FORM_USER_ID)
accessKey = getRunParameter(run, iCingRobot.FORM_ACCESS_KEY)
if userId and accessKey:
self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId),
(iCingRobot.FORM_ACCESS_KEY, accessKey)]
url = getRunParameter(run, ICING_BASE_URL)
if url:
htmlUrl = getRunParameter(run, HTML_RESULTS_URL)
self.iCingBaseUrl = url
self.resultsUrl = htmlUrl # May be None
self.resultUrlEntry.set(self.resultsUrl)
if self.iCingBaseUrl and self.iCingBaseUrl not in urls:
index = len(urls)
urls.append(self.iCingBaseUrl)
self.iCingBaseUrlPulldown.setup(urls, urls, index)
self.updateButtons()
self.updateStructures()
self.updateModels()
self.updateChains()
def updateButtons(self, event=None):
buttons = self.buttonBar.buttons
if self.project and self.run:
buttons[0].enable()
if self.resultsUrl and self.serverCredentials:
buttons[1].enable()
buttons[2].enable()
buttons[3].enable()
else:
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
else:
buttons[0].disable()
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
class NewWindowPopup(BasePopup):
"""
**Create New Windows to Display Spectra**
This tool is used to make new windows for the graphical display of spectra,
which will usually be as contours. It is notable that some spectrum windows
will be made automatically when spectra are loaded if there is no existing
appropriate window to display a spectrum. However, making new spectrum windows
allows the user to specialise different windows for different tasks and gives
complete freedom as to which types of axis go in which direction. For example
the user may wish to make a new window so that a spectrum can be viewed from
an orthogonal, rotated aspect.
A new spectrum window is made by first considering whether it is similar to
any existing windows. If so, then the user selects the appropriate template
window to base the new one upon. The user then chooses a name for the window
via the "New window name" field, although the name may be changed after the
window is created. Usually the user does not need to consider the "Strips"
section, but if required the new window can be created with starting strips
and orthogonal sub-divisions (although these are not permanent). After setting
the required axes and spectrum visibility, as described below, the user clicks
on [Create Window!] to actually make the new spectrum display window.
**Axes**
The number and type of axes for the new window are chosen using the pulldown
menus in the "Axes" section. The idea is that the user chooses which NMR
isotopes should appear on the X, Y, & Z axes. Naturally, X and Y axes must
always be set to something, to represent the plane of the screen, but the Z
axes are optional. If not required, a Z axis may be set to "None" to indicate
that it will not be used. Up to four Z axes may be specified, labelled as
"z1", "z2" etc., and these represent extra dimensions orthogonal to the plane
of the screen, which are often conceptualised as depth axes.
It should be noted that the Y axis type may be set to "value", which refers to
a spectrum intensity axis, rather than an NMR isotope axis. Setting the Y axis
to "value" and only having the X axis set to an isotope is used to create
windows that can show 1D spectra. Such value axes can also be used for 2D and
higher dimensionality spectra, to show the data as an intensity graph (a
"slice") rather than as contours.
**Spectra**
The lower "Viewed Spectra" section lists all of the spectra within the project
that may be shown by a window with the selected axes. All spectra with
isotopes in their data dimensions that match the isotope types of the window
axes can potentially be displayed. This system also allows for displayed
spectra to have fewer dimensions than the axes has windows, as long as at
least the X and Y axes are present. For example a 2D H-N spectrum can be
shown in a 3D H-N-H window, but not a 3D H-H-N.
For spectra that have more than one data dimension of the same isotope, then
which data dimension goes with which window axis is not always known to
Analysis. Where there is ambiguity, this system will simply map the spectrum
data dimensions in order to the next matching window axis. If this mapping
turns out to be wrong, then it may be changed at any time via the main
_Windows settings; toggling the "Dim. Mapping" of the "Spectrum & Peak List
Mappings" tab.
For the spectra listed in the lower table, which may be placed in the new
window, the user has control over whether the spectra actually will appear.
Firstly the user can change the "Visible?" column, either via a double-click
or by using the appropriate lower buttons. By default spectra are set as not
being visible in new windows, and the user toggles the ones that should be
seen to "Yes". This basic spectrum visibility can readily be changed by the
toggle buttons that appear in the "toolbar" at the top of the spectrum
display, so the "Visible?" setting here is only about what initially appears.
The "In Toolbar?" setting of a spectrum is a way of allowing the user to state
that a spectrum should never appear in the window, and not even allow it to be
toggled on later via the toolbar at the top of the windows. This is a way of
reducing clutter, and allows certain windows to be used for particular subsets
of spectra. For example the user may wish to put the spectra for a temperature
series in one window, but not in other windows used for resonance assignment
where they would get in the way. The "In Toolbar" setting can be changed
after a window has been made, but only via the main Windows_ settings popup.
.. _Windows: EditWindowPopup.html
"""
def __init__(self, parent, *args, **kw):
self.visibleSpectra = parent.visibleSpectra
self.toolbarSpectra = parent.toolbarSpectra
self.waiting = False
self.window = None
BasePopup.__init__(self,
parent=parent,
title='Window : New Window',
**kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(2, weight=1)
row = 0
label = Label(guiFrame, text='Template window: ', grid=(row, 0))
tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly'
self.window_list = PulldownList(guiFrame,
grid=(row, 1),
callback=self.setAxisTypes,
tipText=tipText)
frame = LabelFrame(guiFrame,
text='Strips',
grid=(row, 2),
gridSpan=(2, 1))
buttons = UtilityButtonList(guiFrame,
doClone=False,
helpUrl=self.help_url,
grid=(row, 3))
row += 1
label = Label(guiFrame, text='New window name: ', grid=(row, 0))
tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface'
self.nameEntry = Entry(guiFrame,
width=16,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(frame, text='Columns: ', grid=(0, 0))
tipText = 'The number of vertical strips/dividers to initially make in the spectrum window'
self.cols_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 1),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
label = Label(frame, text='Rows: ', grid=(0, 2))
tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window'
self.rows_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 3),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
row += 1
div = LabelDivider(guiFrame,
text='Axes',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
self.axis_lists = {}
frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4))
col = 0
self.axisTypes = {}
self.axisTypesIncludeNone = {}
for label in AXIS_LABELS:
self.axisTypes[label] = None
w = Label(frame, text=' ' + label)
w.grid(row=0, column=col, sticky='w')
col += 1
if label in ('x', 'y'):
includeNone = False
tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
else:
includeNone = True
tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
self.axisTypesIncludeNone[label] = includeNone
getAxisTypes = lambda label=label: self.getAxisTypes(label)
callback = lambda axisType, label=label: self.changedAxisType(
label, axisType)
self.axis_lists[label] = PulldownList(frame,
callback=callback,
tipText=tipText)
self.axis_lists[label].grid(row=0, column=col, sticky='w')
col += 1
frame.grid_columnconfigure(col, weight=1)
row += 1
div = LabelDivider(guiFrame,
text='Viewed Spectra',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None]
editSetCallbacks = [None, None, None, None]
tipTexts = [
'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections',
'Sets whether the spectrum contours will be visible in the new window',
'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed',
'The number of peak lists the spectrum contains'
]
headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
multiSelect=True,
grid=(row, 0),
gridSpan=(1, 4),
tipTexts=tipTexts)
row += 1
tipTexts = [
'Creates a new spectrum window with the specified parameters',
'Sets the contours of the selected spectra to be visible when the new window is made',
'Sets the contours of the selected spectra to not be displayed when the new window is made',
'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all'
]
texts = [
'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible',
'Selected\nNot In Toolbar'
]
commands = [
self.ok, self.setSelectedDisplay, self.setSelectedHide,
self.setSelectedAbsent
]
buttonList = ButtonList(guiFrame,
texts=texts,
grid=(row, 0),
commands=commands,
gridSpan=(1, 4),
tipTexts=tipTexts)
buttonList.buttons[0].config(bg='#B0FFB0')
self.updateAxisTypes()
self.updateWindow()
self.updateWindowName()
self.administerNotifiers(self.registerNotify)
self.updateAfter()
def administerNotifiers(self, notifyFunc):
self.registerNotify(self.updateWindowName,
'ccpnmr.Analysis.SpectrumWindow', '__init__')
for clazz in ('ccp.nmr.Nmr.Experiment', 'ccp.nmr.Nmr.DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
for func in ('__init__', 'delete', 'setName', 'addSpectrumWindowGroup',
'removeSpectrumWindowGroup', 'setSpectrumWindowGroups'):
notifyFunc(self.updateWindow, 'ccpnmr.Analysis.SpectrumWindow',
func)
for func in ('addSpectrumWindow', 'removeSpectrumWindow',
'setSpectrumWindows'):
notifyFunc(self.updateWindow,
'ccpnmr.Analysis.SpectrumWindowGroup', func)
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAxisTypes, 'ccpnmr.Analysis.AxisType', func)
# Set visible contours, on commit, according to selection
# Get hold of spectrumWindowView ASAP
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def getSpectra(self):
spectrumIsotopes = {}
spectra = []
for experiment in self.nmrProject.sortedExperiments():
name = experiment.name
for spectrum in experiment.sortedDataSources():
spectrumIsotopes[spectrum] = []
spectra.append(['%s:%s' % (name, spectrum.name), spectrum])
for dataDim in spectrum.dataDims:
dimTypes = []
if dataDim.className != 'SampledDataDim':
for dataDimRef in dataDim.dataDimRefs:
expDimRef = dataDimRef.expDimRef
isotopes = set()
for isotopeCode in expDimRef.isotopeCodes:
isotopes.add(isotopeCode)
dimTypes.append(
(expDimRef.measurementType.lower(), isotopes))
else:
dimTypes.append('sampled')
spectrumIsotopes[spectrum].append(dimTypes)
axisIsotopes = {}
for label in AXIS_LABELS:
if label not in ('x', 'y'):
if self.axis_lists[label].getSelectedIndex() == 0:
continue
axisType = self.axis_lists[label].getObject()
axisIsotopes[label] = (axisType.measurementType.lower(),
set(axisType.isotopeCodes))
spectraSel = []
axes = axisIsotopes.keys()
axes.sort()
for name, spectrum in spectra:
dimIsotopes = spectrumIsotopes[spectrum]
for label in axes:
mType, selected = axisIsotopes[label]
if label == 'y' and mType == 'none':
continue # value axis
for i, dimTypes in enumerate(dimIsotopes):
for dimType in dimTypes:
if dimType == 'sampled':
if label != 'z1':
continue
axisType = self.axis_lists[label].getObject()
if axisType.name != 'sampled':
continue
dimIsotopes.pop(i)
break
else:
measurementType, isotopes = dimType
if (mType == measurementType) and (selected <=
isotopes):
dimIsotopes.pop(i)
break
else:
continue
break
else:
if label in ('x', 'y'):
break
else:
if not dimIsotopes:
spectraSel.append([name, spectrum])
return spectraSel
def setSelectedAbsent(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = False
self.toolbarSpectra[spectrum] = False
self.updateAfter()
def setSelectedDisplay(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = True
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def setSelectedHide(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = False
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def toggleToolbar(self, spectrum):
boolean = not self.toolbarSpectra.get(spectrum, True)
self.toolbarSpectra[spectrum] = boolean
if boolean is False:
self.visibleSpectra[spectrum] = False
self.updateAfter()
def toggleVisible(self, spectrum):
boolean = not self.visibleSpectra.get(spectrum, False)
self.visibleSpectra[spectrum] = boolean
if boolean:
if not self.toolbarSpectra.get(spectrum, True):
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def updateAfter(self, object=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self):
for spectrum in self.visibleSpectra.keys():
if spectrum.isDeleted:
del self.visibleSpectra[spectrum]
textMatrix = []
objectList = []
colorMatrix = []
for name, spectrum in self.getSpectra():
colours = [None, None, None, None]
if self.visibleSpectra.get(spectrum):
colours[0] = '#60F060'
isVisible = 'Yes'
self.visibleSpectra[
spectrum] = True # do not need this but play safe in case above if changed
else:
isVisible = 'No'
self.visibleSpectra[spectrum] = False
if self.toolbarSpectra.get(spectrum, True):
inToolbar = 'Yes'
self.toolbarSpectra[spectrum] = True
else:
colours[0] = '#600000'
inToolbar = 'No'
self.toolbarSpectra[spectrum] = False
datum = [
name, isVisible, inToolbar,
','.join(['%d' % pl.serial for pl in spectrum.peakLists])
]
textMatrix.append(datum)
objectList.append(spectrum)
colorMatrix.append(colours)
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
self.waiting = False
def updateAxisTypes(self, *extra):
for label in AXIS_LABELS:
names = []
objects = []
includeNone = self.axisTypesIncludeNone[label]
if includeNone:
names.append('None')
objects.append(None)
axisType = self.axisTypes[label]
axisTypes = self.getAxisTypes(label)
objects.extend(axisTypes)
if axisTypes:
if axisType not in objects:
axisType = objects[0]
index = objects.index(axisType)
names.extend([x.name for x in axisTypes])
else:
index = 0
self.axis_lists[label].setup(names, objects, index)
self.changedAxisType(label, axisType)
def changedAxisType(self, label, axisType):
if axisType is not self.axisTypes[label]:
self.axisTypes[label] = axisType
self.updateAfter()
def updateWindow(self, *extra):
window = self.window
windows = self.parent.getWindows()
if windows:
if window not in windows:
window = windows[0]
index = windows.index(window)
names = [x.name for x in windows]
else:
index = 0
names = []
self.window_list.setup(names, windows, index)
self.setAxisTypes(window)
def updateWindowName(self, *extra):
self.nameEntry.set(WindowBasic.defaultWindowName(self.project))
def getAxisTypes(self, label):
axisTypes = self.parent.getAxisTypes()
if label == 'z1':
axisTypes = [
axisType for axisType in axisTypes
if axisType.name == 'sampled' or not axisType.isSampled
]
else:
axisTypes = [
axisType for axisType in axisTypes if not axisType.isSampled
]
if label != 'y':
axisTypes = [
at for at in axisTypes
if at.name != WindowBasic.VALUE_AXIS_NAME
]
return axisTypes
def setAxisTypes(self, window):
project = self.project
if not project:
return
if window is self.window:
return
self.window = window
if window:
windowPanes = window.sortedSpectrumWindowPanes()
if windowPanes:
# might be empty because notifier called before windowPanes set up
windowPane = windowPanes[0]
for label in AXIS_LABELS:
axisPanel = windowPane.findFirstAxisPanel(label=label)
if axisPanel and axisPanel.panelType \
and axisPanel.panelType.axisType:
self.axis_lists[label].setSelected(
axisPanel.panelType.axisType)
elif label not in ('x', 'y'):
self.axis_lists[label].setIndex(0)
self.updateAfter()
def apply(self):
project = self.project
if not project:
return False
name = self.nameEntry.get().strip()
if not name:
showError('No name', 'Need to enter name', parent=self)
return False
names = [
window.name for window in self.analysisProject.spectrumWindows
]
if (name in names):
showError('Repeated name', 'Name already used', parent=self)
return False
axisTypes = []
for label in AXIS_LABELS:
if label not in ('x', 'y'):
if self.axis_lists[label].getSelectedIndex() == 0:
continue
axisType = self.axis_lists[label].getObject()
axisTypes.append(axisType)
ncols = self.cols_menu.getObject()
nrows = self.rows_menu.getObject()
window = WindowBasic.createSpectrumWindow(project,
name, [
axisTypes,
],
ncols=ncols,
nrows=nrows)
return True
def setupAtomFrame(self,resetFrame = False, resetStatus = True):
frameRow = 0
self.atomWidgets = []
if resetFrame:
self.atomFrame = ScrolledFrame(self.atomFrameMaster, width = self.frameWidth, height = 300, doExtraConfig = False)
self.atomFrame.grid(row=self.atomFrameRow, column=0, columnspan = self.columnspan, sticky=Tkinter.NSEW)
frame = self.atomFrame.frame
#
# Make fake info at top for col length...
#
colNum = 0
for chemCompAtomInfo in self.chemCompAtoms[0]:
attrName = chemCompAtomInfo[0]
label = Label(frame, text = '', width = len(attrName) + 2)
label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW)
colNum += 1
#
# Now atom info...
#
for chemCompAtom in self.chemCompAtoms:
frameRow += 1
colNum = 0
self.atomWidgets.append([])
for chemCompAtomInfo in chemCompAtom:
attrName = chemCompAtomInfo[0]
if attrName == 'bondedAtoms':
bondedAtomText = ""
for otherAtom in chemCompAtomInfo[1]:
bondedAtomText += otherAtom[0][1] + ','
label = Label(frame, text = bondedAtomText[:-1])
label.grid(row=frameRow, column=colNum, sticky=Tkinter.EW)
else:
if attrName in self.nonEntryAttributes:
widgetInfo = self.nonEntryAttributes[attrName]
if widgetInfo[0] == PulldownMenu:
self.atomWidgets[-1].append(PulldownMenu(frame, entries = widgetInfo[1], selected_index = widgetInfo[1].index(chemCompAtomInfo[1])))
elif widgetInfo[0] == CheckButton:
self.atomWidgets[-1].append(CheckButton(frame, selected = chemCompAtomInfo[1]))
else:
text = chemCompAtomInfo[1]
if not text:
text = ''
self.atomWidgets[-1].append(Entry(frame, text = text, width = 5))
self.atomWidgets[-1][-1].grid(row=frameRow, column=colNum)
colNum += 1
class AnnealingSettingsTab(object):
'''This class describes the tab in the GUI where the user
can change setting that govern the monte carlo / annleaing
procedure. This also includes which information from the ccpn
analysis project is used and which information is
ignored. This includes:
* present sequential assignments
* tentative assignments
* amino acid type information
* whether to include untyped spin systems
* assignments to peak dimensions
ALso the chain can be selected here.
Furthermore the user can set the temperature
regime of the annealing, the amount of times the procedure
is repeated to obtain statistics. The fraction of peaks
that is left out in each run to diversify the results,
the treshhold score for amino acid typing and the treshhold
collabelling for a peak to be expected.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.minIsoFrac = 0.1
self.leavePeaksOutFraction = 0.0
self.minTypeScore = 1.0
self.chain = None
self.amountOfRepeats = 10
self.amountOfSteps = 10000
self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022,
0.033, 0.050, 0.075, 0.113,
0.170, 0.256, 0.384, 0.576,
0.864, 1.297, 1.946, 2.919,
4.378, 6.568, 9.852, 14.77,
22.16, 33.25]
self.energyDataSets = [[]]
self.residues = []
self.body()
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def runCalculations(self):
'''Run all calculations. Also triggers the disabling of
some buttons and fields.
'''
self.startButton.disable()
self.disableIllegalButtonsAfterPrecalculations()
self.guiParent.connector.runAllCalculations()
self.startButton.configure(text='More runs')
self.startButton.enable()
def disableIllegalButtonsAfterPrecalculations(self):
'''Disable buttons and field the user can not alter
any longer after the model is set up and the
'pre-calculations' have finished.
This is done because this part of the calculation
should only be run once. All settings that would
be changed after this point will not have any influence.
'''
illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry,
self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck,
self.useTypeCheck, self.useDimensionalAssignmentsCheck,
self.useTentativeCheck]
for illegalButton in illegalButtons:
illegalButton.configure(state='disabled')
self.molPulldown.disable()
def getChainName(self, chain):
'''Get the name for a chain.
args: chain: ccpn analysis
chain object
returns: chain name
'''
return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType)
def getChains(self):
'''Get all chains present in the project.
returns: list of ccpn analysis chain objects
'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateChains(self, *opt):
'''Updates the list of chains if a new one is added
to or deleted from the project. Updates the
pull down list where a chain can be selected.
'''
index = 0
texts = []
chains = self.getChains()
chain = self.chain
if chains:
if chain not in chains:
chain = chains[0]
texts = [self.getChainName(c) for c in chains]
index = chains.index(chain)
else:
chain = None
self.molPulldown.setup(texts, chains, index)
if chain is not self.chain:
self.chain = chain
def changeMolecule(self, chain):
'''Select a molecular chain.'''
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges(fromChain=True)
def updateStepEntry(self, event=None):
'''Update the value and entry that sets the amount of
steps per temperature point.
'''
value = self.NAStepEntry.get()
if value == self.amountOfSteps:
return
if value < 1:
self.NAStepEntry.set(1)
self.amountOfSteps = 1
else:
self.amountOfSteps = value
self.NAStepEntry.set(value)
def updateRepeatEntry(self, event=None):
'''Update the value and entry of that sets
the amount of times the whole annealing
procedure is repeated in order
to obtain statistics.
'''
value = self.repeatEntry.get()
if value == self.amountOfRepeats:
return
if value < 1:
self.repeatEntry.set(1)
self.amountOfRepeats = 1
else:
self.amountOfRepeats = value
self.repeatEntry.set(value)
def updateMinTypeScoreEntry(self, event=None):
'''Updates the value and the entry for the
treshhold value for amino acid typing.
'''
value = self.minTypeScoreEntry.get()
if value == self.minTypeScore:
return
if value < 0:
self.minTypeScoreEntry.set(0.0)
self.minTypeScore = 0.0
elif value > 100:
self.minTypeScoreEntry.set(100.0)
self.minTypeScore = 100.0
else:
self.minTypeScoreEntry.set(value)
self.minTypeScore = value
def updateMinLabelEntry(self, event=None):
'''Updates the minimum colabelling fraction
for which a peak is expected to be present
in the spectra.
'''
value = self.minLabelEntry.get()
if value == self.minIsoFrac:
return
if value < 0:
self.minIsoFrac = 0.0
self.minLabelEntry.set(0.0)
elif value > 1:
self.minIsoFrac = 1.0
self.minLabelEntry.set(1.0)
else:
self.minIsoFrac = value
self.minLabelEntry.set(value)
def updateLeavePeaksOutEntry(self, event=None):
'''Updates the value and entry of the fraction
of peaks that should be left out in each
run in order to diversify the results.
'''
value = self.leaveOutPeaksEntry.get()
if value == self.leavePeaksOutFraction:
return
if value < 0:
self.leavePeaksOutFraction = 0.0
self.leaveOutPeaksEntry.set(0.0)
elif value > 1:
self.leavePeaksOutFraction = 1.0
self.leaveOutPeaksEntry.set(1.0)
else:
self.leavePeaksOutFraction = value
self.leaveOutPeaksEntry.set(value)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def addEnergyPoint(self, energy, time):
'''Adds a point to the graph that shows the progress
of the annealling procedure.
args: energy: the y-value
time: the x-value
'''
point = (time, energy * -1)
# This means one run has finished
if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1):
self.energyDataSets.append([point])
else:
self.energyDataSets[-1].append(point)
colors = colorSeries
Ncolors = len(colors)
NdataSets = len(self.energyDataSets)
colorList = (NdataSets / Ncolors) * colors + \
colors[:NdataSets % Ncolors]
self.energyPlot.update(dataSets=self.energyDataSets,
dataColors=colorList)
# Forcing the graph to draw, eventhough calculations
# are still running. Only do this with high numbers of
# steps, otherwise drawing takes longer than annealling.
if self.amountOfSteps >= 100000:
self.energyPlot.draw()
def body(self, guiFrame):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
def 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 body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def __init__(self, parent, application, *args, **kw):
project = application.project
simStore = project.findFirstNmrSimStore(application=APP_NAME) or \
project.newNmrSimStore(application=APP_NAME, name=APP_NAME)
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.nmrProject = application.nmrProject
self.serverDone = False
NmrSimRunFrame.__init__(self, parent, project, simStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureFrame.grid_forget()
tab = self.tabbedFrame.frames[0]
frame = Frame(tab, grid=(1,0))
frame.expandGrid(2,1)
div = LabelDivider(frame, text='Structures', grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Ensemble: ', grid=(1,0))
self.structurePulldown = PulldownList(frame, callback=self.changeStructure, grid=(1,1))
headingList = ['Model','Use']
editWidgets = [None,None]
editGetCallbacks = [None,self.toggleModel]
editSetCallbacks = [None,None,]
self.modelTable = ScrolledMatrix(frame, grid=(2,0), gridSpan=(1,2),
callback=self.selectStructModel,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame, texts=texts, commands=commands, grid=(3,0), gridSpan=(1,2))
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1,0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0,0))
frame.expandGrid(None,2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
urls = [DEFAULT_URL,]
self.iCingBaseUrlPulldown = PulldownList(frame, texts=urls, objects=urls, index=0, grid=(srow,1))
srow +=1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
self.setZipFileName()
button = Button(frame, text='Choose File', bd=1, sticky='ew',
command=self.chooseZipFile, grid=(srow, 2))
srow +=1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
button = Button(frame, text='View Results HTML', bd=1, sticky='ew',
command=self.viewHtmlResults, grid=(srow, 2))
srow +=1
texts = ['Submit Project!', 'Check Run Status',
'Purge Server Result', 'Download Results']
commands = [self.runCingServer, self.checkStatus,
self.purgeCingServer, self.downloadResults]
self.buttonBar = ButtonList(frame, texts=texts, commands=commands,
grid=(srow, 0), gridSpan=(1,3))
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1,0))
frame.expandGrid(1,1)
label = Label(frame, text='Chain: ')
label.grid(row=0,column=0,sticky='w')
self.chainPulldown = PulldownList(frame, callback=self.changeChain)
self.chainPulldown.grid(row=0,column=1,sticky='w')
headingList = ['#','Residue','Linking','Decriptor','Use?']
editWidgets = [None,None,None,None,None]
editGetCallbacks = [None,None,None,None,self.toggleResidue]
editSetCallbacks = [None,None,None,None,None,]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky = 'nsew')
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame, texts=texts, commands=commands,)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(simStore)
self.administerNotifiers(application.registerNotify)
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 CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index-2
format = ['PDB','CCPN','CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get()
if not file:
showWarning('Failure','No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append( ('script',script) )
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [ FileType('CING', ['project.xml']),
FileType('All', ['*'])
]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Select CING project file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy,name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'PDB file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir,name,dummy = nTpath( fileName )
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CCPN project XML file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir,name,dummy = nTpath( fileName )
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CYANA fproject file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self ):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self ):
fName = self.projEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open( name=fName, status='old', verbose=False )
#end def
def initPdb(self ):
fName = self.pdbEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open( self.nameEntry.get(), status='new' )
self.project.initPDB( pdbFile=fName, convention = 'PDB' )
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:',geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:',geometry
sys.exit(0) # remove later
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(2, weight=1)
row = 0
label = Label(guiFrame, text='Template window: ', grid=(row, 0))
tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly'
self.window_list = PulldownList(guiFrame,
grid=(row, 1),
callback=self.setAxisTypes,
tipText=tipText)
frame = LabelFrame(guiFrame,
text='Strips',
grid=(row, 2),
gridSpan=(2, 1))
buttons = UtilityButtonList(guiFrame,
doClone=False,
helpUrl=self.help_url,
grid=(row, 3))
row += 1
label = Label(guiFrame, text='New window name: ', grid=(row, 0))
tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface'
self.nameEntry = Entry(guiFrame,
width=16,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(frame, text='Columns: ', grid=(0, 0))
tipText = 'The number of vertical strips/dividers to initially make in the spectrum window'
self.cols_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 1),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
label = Label(frame, text='Rows: ', grid=(0, 2))
tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window'
self.rows_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 3),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
row += 1
div = LabelDivider(guiFrame,
text='Axes',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
self.axis_lists = {}
frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4))
col = 0
self.axisTypes = {}
self.axisTypesIncludeNone = {}
for label in AXIS_LABELS:
self.axisTypes[label] = None
w = Label(frame, text=' ' + label)
w.grid(row=0, column=col, sticky='w')
col += 1
if label in ('x', 'y'):
includeNone = False
tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
else:
includeNone = True
tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
self.axisTypesIncludeNone[label] = includeNone
getAxisTypes = lambda label=label: self.getAxisTypes(label)
callback = lambda axisType, label=label: self.changedAxisType(
label, axisType)
self.axis_lists[label] = PulldownList(frame,
callback=callback,
tipText=tipText)
self.axis_lists[label].grid(row=0, column=col, sticky='w')
col += 1
frame.grid_columnconfigure(col, weight=1)
row += 1
div = LabelDivider(guiFrame,
text='Viewed Spectra',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None]
editSetCallbacks = [None, None, None, None]
tipTexts = [
'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections',
'Sets whether the spectrum contours will be visible in the new window',
'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed',
'The number of peak lists the spectrum contains'
]
headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
multiSelect=True,
grid=(row, 0),
gridSpan=(1, 4),
tipTexts=tipTexts)
row += 1
tipTexts = [
'Creates a new spectrum window with the specified parameters',
'Sets the contours of the selected spectra to be visible when the new window is made',
'Sets the contours of the selected spectra to not be displayed when the new window is made',
'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all'
]
texts = [
'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible',
'Selected\nNot In Toolbar'
]
commands = [
self.ok, self.setSelectedDisplay, self.setSelectedHide,
self.setSelectedAbsent
]
buttonList = ButtonList(guiFrame,
texts=texts,
grid=(row, 0),
commands=commands,
gridSpan=(1, 4),
tipTexts=tipTexts)
buttonList.buttons[0].config(bg='#B0FFB0')
self.updateAxisTypes()
self.updateWindow()
self.updateWindowName()
self.administerNotifiers(self.registerNotify)
self.updateAfter()
class MeccanoPopup(BasePopup):
def __init__(self, parent, project, *args, **kw):
self.alignMedium = None
self.chain = None
self.constraint = None
self.constraintSet = None
self.molSystem = None
self.project = project
self.run = None
self.shiftList = None
self.tensor = None
BasePopup.__init__(self, parent=parent, title='MECCANO', *args, **kw)
self.curateNotifiers(self.registerNotify)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
options = ['Parameters','Restraints','Alignment Media & Tensors','About Meccano']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
frameA, frameB, frameC, frameD = tabbedFrame.frames
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_rowconfigure(13, weight=1)
frameB.grid_columnconfigure(1, weight=1)
frameB.grid_rowconfigure(1, weight=1)
frameC.grid_columnconfigure(0, weight=1)
frameC.grid_rowconfigure(1, weight=1)
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(0, weight=1)
texts = ['Run MECCANO!']
commands = [self.runMeccano]
bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts,
commands=commands, expands=True)
bottomButtons.grid(row=1, column=0, sticky='ew')
if not Meccano:
bottomButtons.buttons[0].disable()
# Parameters
row = 0
label = Label(frameA, text='Calculation Run:')
label.grid(row=row,column=0,sticky='w')
self.runPulldown = PulldownList(frameA, callback=self.selectRun)
self.runPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Shift List (for CO):')
label.grid(row=row,column=0,sticky='w')
self.shiftListPulldown = PulldownList(frameA, callback=self.selectShiftList)
self.shiftListPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Keep Copy of Used Shifts:')
label.grid(row=row,column=0,sticky='w')
self.toggleCopyShifts = CheckButton(frameA)
self.toggleCopyShifts.grid(row=row,column=1,sticky='w')
self.toggleCopyShifts.set(True)
row += 1
label = Label(frameA, text='Molecular System:')
label.grid(row=row,column=0,sticky='w')
self.molSystemPulldown = PulldownList(frameA, callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Chain:')
label.grid(row=row,column=0,sticky='w')
self.chainPulldown = PulldownList(frameA, callback=self.selectChain)
self.chainPulldown.grid(row=row,column=1,sticky='w')
self.chainPulldown.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='First Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.firstResEntry = IntEntry(frameA, text=None, width=8)
self.firstResEntry.grid(row=row,column=1,sticky='w')
self.firstResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Last Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.lastResEntry = IntEntry(frameA, text=None, width=8)
self.lastResEntry.grid(row=row,column=1,sticky='w')
self.lastResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Max Num Optimisation Steps:')
label.grid(row=row,column=0,sticky='w')
self.maxOptStepEntry = IntEntry(frameA, text=500, width=8)
self.maxOptStepEntry.grid(row=row,column=1,sticky='w')
self.maxOptStepEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Num Optimisation Peptide Planes:')
label.grid(row=row,column=0,sticky='w')
self.numOptPlaneEntry = IntEntry(frameA, text=2, width=8)
self.numOptPlaneEntry.grid(row=row,column=1,sticky='w')
self.numOptPlaneEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Min Num Optimisation Hits:')
label.grid(row=row,column=0,sticky='w')
self.numOptHitsEntry = IntEntry(frameA, text=5, width=8)
self.numOptHitsEntry.grid(row=row,column=1,sticky='w')
self.numOptHitsEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='File Name Prefix:')
label.grid(row=row,column=0,sticky='w')
self.pdbFileEntry = Entry(frameA, text='Meccano', width=8)
self.pdbFileEntry.grid(row=row,column=1,sticky='w')
self.pdbFileEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write Output File (.out):')
label.grid(row=row,column=0,sticky='w')
self.toggleWriteOutFile = CheckButton(frameA)
self.toggleWriteOutFile.grid(row=row,column=1,sticky='w')
self.toggleWriteOutFile.set(False)
self.toggleWriteOutFile.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write PDB File (.pdb):')
label.grid(row=row,column=0,sticky='w')
self.toggleWritePdbFile = CheckButton(frameA)
self.toggleWritePdbFile.grid(row=row,column=1,sticky='w')
self.toggleWritePdbFile.set(True)
self.toggleWritePdbFile.bind('<Leave>', self.updateRunParams)
if not Meccano:
row += 1
label = Label(frameA, text='The Meccano executable is not available (it needs to be compiled)', fg='red')
label.grid(row=row,column=0,columnspan=2,sticky='w')
# Restraints
label = Label(frameB, text='Constraint Set:')
label.grid(row=0,column=0,sticky='w')
self.constraintSetPulldown = PulldownList(frameB, callback=self.selectConstraintSet)
self.constraintSetPulldown.grid(row=0,column=1,sticky='w')
self.alignMediumPulldown= PulldownList(self, callback=self.setAlignMedium)
headingList = ['#','List Type','Use?','Alignment\nMedium','Num\nRestraints']
editWidgets = [None,None,None,self.alignMediumPulldown,None]
editGetCallbacks = [None,None,self.toggleUseRestraints,self.getAlignMedium,None]
editSetCallbacks = [None,None,None,self.setAlignMedium,None]
self.restraintMatrix = ScrolledMatrix(frameB,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=None,
multiSelect=True)
self.restraintMatrix.grid(row=1,column=0,columnspan=2,sticky='nsew')
# Alignment Media
div = LabelDivider(frameC,text='Alignment Media')
div.grid(row=0,column=0,sticky='ew')
self.mediumNameEntry = Entry(self, returnCallback=self.setMediumName)
self.mediumDetailsEntry = Entry(self, returnCallback=self.setMediumDetails)
headingList = ['#','Name','Details','Static Tensor','Dynamic Tensor']
editWidgets = [None, self.mediumNameEntry, self.mediumDetailsEntry, None, None]
editGetCallbacks = [None, self.getMediumName, self.getMediumDetails, None, None]
editSetCallbacks = [None, self.setMediumName, self.setMediumDetails, None, None]
self.mediaMatrix = ScrolledMatrix(frameC,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAlignMedium,
multiSelect=True)
self.mediaMatrix.grid(row=1,column=0,sticky='nsew')
texts = ['Add Alignment medium','Remove Alignment Medium']
commands = [self.addAlignMedium,self.removeAlignMedium]
buttonList = ButtonList(frameC, texts=texts, commands=commands, expands=True)
buttonList.grid(row=2,column=0,sticky='nsew')
self.editAxialEntry = FloatEntry(self, returnCallback=self.setAxial)
self.editRhombicEntry = FloatEntry(self, returnCallback=self.setRhombic)
self.editAlphaEulerEntry = FloatEntry(self, returnCallback=self.setEulerAlpha)
self.editBetaEulerEntry = FloatEntry(self, returnCallback=self.setEulerBeta)
self.editGammaEulerEntry = FloatEntry(self, returnCallback=self.setEulerGamma)
div = LabelDivider(frameC,text='Alignment Tensors')
div.grid(row=3,column=0,sticky='ew')
headingList = ['Type', u'Axial (\u03B6)',u'Rhombic (\u03B7)',
u'Euler \u03B1',u'Euler \u03B2',u'Euler \u03B3']
editWidgets = [None,self.editAxialEntry,
self.editRhombicEntry,self.editAlphaEulerEntry,
self.editBetaEulerEntry,self.editGammaEulerEntry]
editSetCallbacks = [None,self.setAxial,self.setRhombic,
self.setEulerAlpha,self.setEulerBeta,self.setEulerGamma]
editGetCallbacks = [None,self.getAxial,self.getRhombic,
self.getEulerAlpha,self.getEulerBeta,self.getEulerGamma]
self.tensorMatrix = ScrolledMatrix(frameC, maxRows=2,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectTensor,
multiSelect=True)
self.tensorMatrix.grid(row=4,column=0,sticky='nsew')
texts = ['Add Static Tensor','Add Dynamic Tensor','Remove Tensor']
commands = [self.addStaticTensor,self.addDynamicTensor,self.removeTensor]
buttonList = ButtonList(frameC,texts=texts, commands=commands, expands=True)
buttonList.grid(row=5,column=0,sticky='ew')
# About
label = Label(frameD, text='About Meccano...')
label.grid(row=0,column=0,sticky='w')
#
self.geometry('500x400')
self.updateShiftLists()
self.updateMolSystems()
self.updateResidueRanges()
self.updateConstraintSets()
self.updateAlignMedia()
self.updateRuns()
def close(self):
self.updateRunParams()
BasePopup.close(self)
def destroy(self):
self.updateRunParams()
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateConstraintSetsAfter, 'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
for func in ('__init__', 'delete','setName','setConditionState'):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraintList',
'ccp.nmr.NmrConstraint.DihedralConstraintList',
'ccp.nmr.NmrConstraint.DistanceConstraintList',
'ccp.nmr.NmrConstraint.HBondConstraintList',
'ccp.nmr.NmrConstraint.JCouplingConstraintList',
'ccp.nmr.NmrConstraint.RdcConstraintList'):
notifyFunc(self.updateConstraintListsAfter, clazz, func)
for func in ('__init__', 'delete',):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraint',
'ccp.nmr.NmrConstraint.DihedralConstraint',
'ccp.nmr.NmrConstraint.DistanceConstraint',
'ccp.nmr.NmrConstraint.HBondConstraint',
'ccp.nmr.NmrConstraint.JCouplingConstraint',
'ccp.nmr.NmrConstraint.RdcConstraint'):
notifyFunc(self.updateConstraintsAfter, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateShiftListsAfter,'ccp.nmr.Nmr.ShiftList', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateMolSystemsAfter,'ccp.molecule.MolSystem.MolSystem', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateChainsAfter,'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete','setDynamicAlignment',
'setStaticAlignment','setName','setDetails'):
notifyFunc(self.updateAlignMediaAfter,'ccp.nmr.NmrConstraint.ConditionState', func)
def updateAlignMediaAfter(self, alignMedium):
if alignMedium.nmrConstraintStore is self.constraintSet:
self.after_idle(self.updateAlignMedia)
if alignMedium is self.alignMedium:
self.after_idle(self.updateTensors)
def updateConstraintSetsAfter(self, constraintSet):
self.after_idle(self.updateConstraintSets)
def updateShiftListsAfter(self, shiftList):
self.after_idle(self.updateShiftLists)
def updateMolSystemsAfter(self, molSystem):
self.after_idle(self.updateMolSystems)
def updateChainsAfter(self, chain):
self.after_idle(self.updateChains)
def updateConstraintsAfter(self, constraint):
if constraint.parent.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def updateConstraintListsAfter(self, constraintList):
if constraintList.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def runMeccano(self):
#
#
# Input checks first
#
#
warning = ''
if not self.molSystem:
warning += 'No molecular system selected\n'
if not self.chain:
warning += 'No chain selected\n'
if not self.constraintSet:
warning += 'No selected constraint set\n'
else:
constraintLists = [cl for cl in self.constraintSet.constraintLists if cl.useForMeccano]
if not constraintLists:
warning += 'No constraint lists selected for use\n'
first, last = self.updateResidueRanges()
if (last-first) < 2:
warning += 'Too few peptide planes selected\n'
if warning:
showWarning('Cannot run MECCANO','Encountered the following problems:\n' + warning)
return
if not self.run:
self.run = self.makeSimRun()
self.updateRunParams()
if self.toggleCopyShifts.get() and self.shiftList:
shiftList = self.run.findFirstOutputMeasurementList(className='ShiftList')
if not shiftList:
shiftList = self.project.currentNmrProject.newShiftList(name='Meccano Input')
self.run.setOutputMeasurementLists([shiftList,])
shiftDict = {}
for shift in shiftList.shifts:
shiftDict[shift.resonance] = shift
for shift in self.shiftList.shifts:
resonance = shift.resonance
resonanceSet = resonance.resonanceSet
if resonanceSet:
atom = resonanceSet.findFirstAtomSet().findFirstAtom()
if (atom.name == 'C') and (atom.residue.molResidue.molType == 'protein'):
shift2 = shiftDict.get(resonance)
if shift2:
shift2.value = shift.value
shift2.error = shift.error
else:
shiftList.newShift(resonance=resonance, value=shift.value, error=shift.error)
#
#
# Accumulate data from CCPN data model & GUI
#
#
# Sequence
residues = self.chain.sortedResidues()
residueDict = {}
seqData = []
for residue in residues:
molResidue = residue.molResidue
code1Letter = molResidue.chemComp.code1Letter
if not code1Letter:
msg = 'Encountered non-standard residue type: %s'
showWarning('Cannot run MECCANO', msg % residue.ccpCode)
return
seqCode = residue.seqCode
seqData.append((seqCode, code1Letter))
residueDict[seqCode] = residue.chemCompVar.chemComp.code3Letter
# Media, RDCs & Dihedrals
rdcLists = []
dihedralLists = []
for constraintList in constraintLists:
if constraintList.className == 'RdcConsraintList':
if constraintList.conditionState:
rdcLists.append(constraintList)
elif constraintList.className == 'DihedralConstraintList':
dihedralLists.append(dihedralLists)
f = PI_OVER_180
mediaData = []
for constraintList in rdcLists:
medium = constraintList.conditionState
dynamicTensor = medium.dynamicAlignment
staticTensor = medium.staticAlignment
if not (dynamicTensor or staticTensor):
continue
if dynamicTensor:
dynamicTensorData = ['Dynamic', dynamicTensor.aAxial, dynamicTensor.aRhombic,
f*dynamicTensor.alpha, f*dynamicTensor.beta, f*dynamicTensor.gamma]
if staticTensor:
staticTensorData = ['Static', staticTensor.aAxial, staticTensor.aRhombic,
f*staticTensor.alpha, f*staticTensor.beta, f*staticTensor.gamma]
if not dynamicTensor:
dynamicTensorData = staticTensorData
elif not staticTensor:
staticTensorData = dynamicTensorData
rdcData = []
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
resonanceA, resonanceB = [fr.resonance for fr in items[0].resonances]
resonanceSetA = resonanceA.resonanceSet
if not resonanceSetA:
continue
resonanceSetB = resonanceB.resonanceSet
if not resonanceSetB:
continue
resNameA = getResonanceName(resonanceA)
resNameB = getResonanceName(resonanceB)
residueA = resonanceSetA.findFirstAtomSet().findFirstAtom().residue
residueB = resonanceSetB.findFirstAtomSet().findFirstAtom().residue
seqA = residueA.seqCode
seqB = residueB.seqCode
value = restraint.targetValue
error = restraint.error
if error is None:
key = [resNameA,resNameB]
key.sort()
sigma = DEFAULT_ERRORS.get(tuple(key), 1.0)
rdcData.append([seqA, resNameA, seqB, resNameB, value, error])
mediaData.append((dynamicTensorData,staticTensorData,rdcData))
oneTurn = 360.0
dihedralDict = {}
for constraintList in dihedralLists:
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
item = items[0]
resonances = [fr.resonance for fr in item.resonances]
resonanceSets = [r.resonanceSet for r in resonances]
if None in resonanceSets:
continue
atoms = [rs.findFirstAtomSet().findFirstAtom() for rs in resonanceSets]
atomNames = [a.name for a in atoms]
if atomNames == PHI_ATOM_NAMES:
isPhi = True
elif atomNames == PSI_ATOM_NAMES:
isPhi = False
else:
continue
residue = atoms[2].residue
if residue.chain is not self.chain:
continue
if isPhi:
residuePrev = getLinkedResidue(residue, linkCode='prev')
if not residuePrev:
continue
atomC0 = residuePrev.findFirstAtom(name='C')
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atoms2 = [atomC0, atomN, atomCa, atomC]
else:
residueNext = getLinkedResidue(residue, linkCode='next')
if not residueNext:
continue
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atomN2 = residueNext.findFirstAtom(name='N')
atoms2 = [atomN, atomCa, atomC, atomN2]
if atoms != atoms2:
continue
value = item.targetValue
error = item.error
if error is None:
upper = item.upperLimit
lower = item.lowerLimit
if (upper is not None) and (lower is not None):
dUpper = angleDifference(value, lower, oneTurn)
dLower = angleDifference(upper, value, oneTurn)
error = max(dUpper, dLower)
elif lower is not None:
error = angleDifference(value, lower, oneTurn)
elif upper is not None:
error = angleDifference(upper, value, oneTurn)
else:
error = 30.0 # Arbitrary, but sensible for TALOS, DANGLE
seqCode = residue.seqCode
if not dihedralDict.has_key(seqCode):
dihedralDict[seqCode] = [None, None, None, None] # Phi, Psi, PhiErr, PsiErr
if isPhi:
dihedralDict[seqCode][0] = value
dihedralDict[seqCode][2] = error
else:
dihedralDict[seqCode][1] = value
dihedralDict[seqCode][3] = error
phipsiData = []
seqCodes = dihedralDict.keys()
seqCodes.sort()
for seqCode in seqCodes:
data = dihedralDict[seqCode]
if None not in data:
phi, psi, phiErr, psiErr = data
phipsiData.append((seqCode, phi, psi, phiErr, psiErr))
# User options
firstPPlaneFrag = self.firstResEntry.get() or 1
lastPPlaneFrag = self.lastResEntry.get() or 1
ppNbMin = self.numOptPlaneEntry.get() or 1
minValueBest = self.numOptHitsEntry.get() or 2
maxValueBest = self.maxOptStepEntry.get() or 5
strucData = Meccano.runFwd(firstPPlaneFrag, lastPPlaneFrag, ppNbMin,
minValueBest, maxValueBest, RAMACHANDRAN_DATABASE,
seqData, mediaData, phipsiData)
if strucData:
fileName = 'CcpnMeccanoPdb%f.pdb' % time.time()
fileObj = open(fileName, 'w')
ch = self.chain.pdbOneLetterCode.strip()
if not ch:
ch = self.chain.code[0].upper()
i = 1
for atomType, resNb, x, y, z in strucData:
resType = residueDict.get(resNb, '???')
line = PDB_FORMAT % ('ATOM',i,'%-3s' % atomType,'',resType,ch,resNb,'',x,y,z,1.0,1.0)
i += 1
fileObj.close()
ensemble = getStructureFromFile(self.molSystem, fileName)
if not self.toggleWritePdbFile.get():
os.unlink(fileName)
self.run.outputEnsemble = ensemble
self.run = None
self.updateRuns()
def getMediumName(self, alignMedium):
self.mediumNameEntry.set(alignMedium.name)
def getMediumDetails(self, alignMedium):
self.mediumDetailsEntry.set(alignMedium.details)
def setMediumName(self, event):
value = self.mediumNameEntry.get()
self.alignMedium.name = value or None
def setMediumDetails(self, event):
value = self.mediumDetailsEntry.get()
self.alignMedium.details = value or None
def setAlignMedium(self, alignMedium):
if self.constraintSet:
self.constraintSet.conditionState = alignMedium
def getAlignMedium(self, constraintList):
media = self.getAlignmentMedia()
names = [am.name for am in media]
if constraintList.conditionState in media:
index = media.index(constraintList.conditionState)
else:
index = 0
self.alignMediumPulldown.setup(names, media, index)
def toggleUseRestraints(self, constraintList):
bool = constraintList.useForMeccano
bool = not bool
if bool and (not constraintList.conditionState) \
and (constraintList.className == 'RdcConsraintList'):
msg = 'Cannot use RDC restraint list for Meccano '
msg += 'unless it is first associated with an amigment medium'
showWarning('Warning', msg, parent=self)
else:
constraintList.useForMeccano = bool
self.updateConstraintLists()
def addStaticTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.staticAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def addDynamicTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.dynamicAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def removeTensor(self):
if self.alignMedium and self.tensor:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = None
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = None
self.updateAlignMediaAfter(self.alignMedium)
def addAlignMedium(self):
if self.constraintSet:
medium = self.constraintSet.newConditionState()
medium.name = 'Align Medium %d' % medium.serial
def removeAlignMedium(self):
if self.alignMedium:
self.alignMedium.delete()
def updateTensor(self, aAxial=None, aRhombic=None, alpha=None, beta=None, gamma=None):
aAxial = aAxial or self.tensor.aAxial
aRhombic = aRhombic or self.tensor.aRhombic
alpha = alpha or self.tensor.alpha
beta = beta or self.tensor.beta
gamma = gamma or self.tensor.gamma
tensor = Implementation.SymmTracelessMatrix(aAxial=aAxial,
aRhombic=aRhombic,
alpha=alpha,beta=beta,
gamma=gamma)
if self.alignMedium:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = tensor
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = tensor
self.tensor = tensor
def setAxial(self, event):
value = self.editAxialEntry.get()
self.updateTensor(aAxial=value)
self.updateTensors()
def setRhombic(self, event):
value = self.editRhombicEntry.get()
self.updateTensor(aRhombic=value)
self.updateTensors()
def setEulerAlpha(self, event):
value = self.editAlphaEulerEntry.get()
self.updateTensor(alpha=value)
self.updateTensors()
def setEulerBeta(self, event):
value = self.editBetaEulerEntry.get()
self.updateTensor(beta=value)
self.updateTensors()
def setEulerGamma(self, event):
value = self.editGammaEulerEntry.get()
self.updateTensor(gamma=value)
self.updateTensors()
def getAxial(self, tensor):
value = tensor.aAxial
self.editAxialEntry.set(value)
def getRhombic(self, tensor):
value = tensor.aRhombic
self.editRhombicEntry.set(value)
def getEulerAlpha(self, tensor):
value = tensor.alpha
self.editAlphaEulerEntry.set(value)
def getEulerBeta(self, tensor):
value = tensor.beta
self.editBetaEulerEntry.set(value)
def getEulerGamma(self, tensor):
value = tensor.gamma
self.editGammaEulerEntry.set(value)
def selectTensor(self, tensor, row, col):
self.tensor = tensor
def selectAlignMedium(self, alignMedium, row, col):
self.alignMedium = alignMedium
self.updateTensors()
def getAlignmentMedia(self):
if self.constraintSet:
return self.constraintSet.sortedConditionStates()
else:
return []
def updateAlignMedia(self):
textMatrix = []
objectList = []
if self.constraintSet:
objectList = self.getAlignmentMedia()
for conditionState in objectList:
staticTensor = None
dyamicTensor = None
tensor = conditionState.dynamicAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
dyamicTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
tensor = conditionState.staticAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
staticTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
datum = [conditionState.serial,
conditionState.name,
conditionState.details,
dyamicTensor,
staticTensor]
textMatrix.append(datum)
if dyamicTensor or staticTensor:
if not self.alignMedium:
self.alignMedium = conditionState
self.mediaMatrix.update(textMatrix=textMatrix, objectList=objectList)
if self.alignMedium:
self.mediaMatrix.selectObject(self.alignMedium)
def updateTensors(self):
textMatrix = []
objectList = []
conditionState = self.alignMedium
if conditionState:
tensor = conditionState.dynamicAlignment
if tensor:
datum = ['Dynamic', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
tensor = conditionState.staticAlignment
if tensor:
datum = ['Static', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
self.tensorMatrix.update(textMatrix=textMatrix, objectList=objectList)
def getMolSystems(self):
molSystems = []
for molSystem in self.project.sortedMolSystems():
if molSystem.chains:
molSystems.append(molSystem)
return molSystems
def updateMolSystems(self, *notifyObj):
index = 0
names = []
molSystems = self.getMolSystems()
molSystem = self.molSystem
if molSystems:
if molSystem not in molSystems:
molSystem = molSystems[0]
index = molSystems.index(molSystem)
names = [ms.code for ms in molSystems]
else:
self.molSystem = None
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
self.molSystemPulldown.setup(texts=names, objects=molSystems, index=index)
def selectMolSystem(self, molSystem):
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
def updateChains(self, *notifyObj):
index = 0
names = []
chains = []
chain = self.chain
if self.molSystem:
chains = [c for c in self.molSystem.sortedChains() if c.residues]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
names = [c.code for c in chains]
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
self.chainPulldown.setup(texts=names, objects=chains, index=index)
def selectChain(self, chain):
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
def updateResidueRanges(self):
first = self.firstResEntry.get()
last = self.lastResEntry.get()
if self.chain:
residues = self.chain.sortedResidues()
firstSeq = residues[0].seqCode
lastSeq = residues[-2].seqCode
if first < firstSeq:
first = firstSeq
if last == first:
last = lastSeq
elif last > lastSeq:
last = lastSeq
if first > last:
last, first = first, last
self.firstResEntry.set(first)
self.lastResEntry.set(last)
return first, last
def getConstraintSets(self):
constraintSets = []
nmrProject = self.project.currentNmrProject
for constraintSet in nmrProject.sortedNmrConstraintStores():
for constraintList in constraintSet.constraintLists:
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintSets.append(constraintSet)
break
return constraintSets
def updateConstraintSets(self, *notifyObj):
index = 0
names = []
constraintSets = self.getConstraintSets()
constraintSet = self.constraintSet
if constraintSets:
if constraintSet not in constraintSets:
constraintSet = constraintSets[0]
index = constraintSets.index(constraintSet)
names = ['%d' % cs.serial for cs in constraintSets]
if constraintSet is not self.constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
self.constraintSetPulldown.setup(texts=names, objects=constraintSets, index=index)
def selectConstraintSet(self, constraintSet):
if self.constraintSet is not constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
def getConstraintLists(self):
constraintLists = []
if self.constraintSet:
for constraintList in self.constraintSet.sortedConstraintLists():
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintLists.append(constraintList)
return constraintLists
def updateConstraintLists(self, *notifyObj):
textMatrix = []
objectList = self.getConstraintLists()
for constraintList in objectList:
if not hasattr(constraintList, 'useForMeccano'):
if constraintList.conditionState \
or (constraintList.className != 'RdcConstraintList'):
bool = True
else:
bool = False
constraintList.useForMeccano = bool
if constraintList.conditionState:
alignMedium = constraintList.conditionState.name
else:
alignMedium = None
datum = [constraintList.serial,
constraintList.className[:-14],
constraintList.useForMeccano and 'Yes' or 'No',
alignMedium,
len(constraintList.constraints)]
textMatrix.append(datum)
self.restraintMatrix.update(textMatrix=textMatrix, objectList=objectList)
def selectConstraint(self, obj, row, column):
if self.constraint is not obj:
self.constraint = obj
def getSimStore(self):
simStore = self.project.findFirstNmrSimStore(name='meccano')
if not simStore:
simStore = self.project.newNmrSimStore(name='meccano')
return simStore
def getRuns(self):
runs = [None, ]
if self.molSystem and self.constraintSet:
simStore = self.getSimStore()
runs += simStore.sortedRuns()
return runs
def updateRuns(self, *notifyObj):
index = 0
names = ['<New>']
runs = self.getRuns()
run = self.run
if runs:
if run not in runs:
run = runs[0]
index = runs.index(run)
names += [r.serial for r in runs if r]
if run is not self.run:
self.updateConstraintSets()
self.updateMolSystems()
self.updateShiftLists()
self.runPulldown.setup(names, runs, index)
def updateRunParams(self, event=None):
if self.run and self.molSystem and self.constraintSet:
simRun = self.run
simRun.inputConstraintStore = self.constraintSet
simRun.molSystem = self.molSystem
if self.shiftList:
simRun.setInputMeasurementLists([self.shiftList,])
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
def makeSimRun(self, template=None):
simStore = self.getSimStore()
if template:
molSystem = template.molSystem
constraintSet = template.inputConstraintStore
shiftList = template.findFirstInputMeasurementList(className='ShiftList')
protocol = template.annealProtocol
else:
molSystem = self.molSystem
constraintSet = self.constraintSet
shiftList = self.shiftList
protocol = self.annealProtocol
simRun = simStore.newRun(annealProtocol=protocol,
molSystem=molSystem,
inputConstraintStore=protocol)
if shiftList:
simRun.addInputMeasurementList(shiftList)
if template:
for param in template.runParameters:
simRun.newRunParameter(code=param.code,
id=param.id,
booleanValue=param.booleanValue,
floatValue=param.floatValue,
intValue=param.intValue,
textValue=param.textValue)
else:
if self.chain:
chainCode = self.chain.code
else:
chaincode = 'A'
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
simRun.newRunParameter(code='ChainCode', id=1,
textValue=chainCode)
return simRun
def selectRun(self, simRun):
if self.run is not simRun:
if simRun:
if simRun.outputEnsemble:
msg = 'Selected run has already been used to generate a structure.'
msg += 'A new run will be setup based on the selection.'
showWarning('Warning',msg)
simRun = self.makeSimRun(template=simRun)
molSystem = simRun.molSystem
constraintSet = simRun.inputConstraintStore
shiftList = simRun.findFirstInputMeasurementList(className='ShiftList')
if molSystem and (self.molSystem is not molSystem):
self.molSystem = molSystem
self.updateMolSystems()
if constraintSet and (self.constraintSet is not constraintSet):
self.constraintSet = constraintSet
self.updateConstraintSets()
if shiftList and (self.shiftList is not shiftList):
self.shiftList = shiftList
self.updateShiftLists()
firstPepPlane = simRun.findFirstrunParameter(code='FirstPepPlane')
lastPepPlane = simRun.findFirstrunParameter(code='LastPepPlane')
maxOptSteps = simRun.findFirstrunParameter(code='MaxOptSteps')
numOptPlanes = simRun.findFirstrunParameter(code='NumOptPlanes')
minOptHits = simRun.findFirstrunParameter(code='MinOptHits')
chainCode = simRun.findFirstrunParameter(code='ChainCode')
if firstPepPlane is not None:
self.firstResEntry.set(firstPepPlane.intValue or 0)
if lastPepPlane is not None:
self.lastResEntry.set(lastPepPlane.intValue or 0)
if maxOptSteps is not None:
self.maxOptStepEntry.set(maxOptSteps.intValue or 0)
if numOptPlanes is not None:
self.numOptPlaneEntry.set(numOptPlanes.intValue or 0)
if minOptHits is not None:
self.numOptHitsEntry.set(minOptHits.intValue or 0)
if chainCode is not None:
chainCode = chainCode.textValue or 'A'
if self.molSystem:
chain = self.molSystem.findFirsChain(code=chainCode)
if chain:
self.selectChain(chain)
self.run = simRun
def updateShiftLists(self, *notifyObj):
index = 0
names = []
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
shiftLists = [(sl.serial, sl) for sl in shiftLists]
shiftLists.sort()
shiftLists = [x[1] for x in shiftLists]
shiftList = self.shiftList
if shiftLists:
if shiftList not in shiftLists:
shiftList = shiftLists[0]
index = shiftLists.index(shiftList)
names = ['%d'% sl.serial for sl in shiftLists]
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftListPulldown.setup(texts=names, objects=shiftLists, index=index)
def selectShiftList(self, shiftList):
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftList = shiftList
class CloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 50
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.peakListDict = {}
self.noesyPeakList = None
self.tocsyPeakList = None
self.noesy3dPeakList = None
self.hsqcPeakList = None
self.maxIntens = 37000000
self.resonances = None
self.origResonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.numClouds = 100
self.filePrefix = 'cloud_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
self.structure = None
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Resonance Clouds Analysis",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
self.adcAtomTypes = name
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
resonances = []
for constraint in self.distanceConstraintList.constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
startMdProcess(self.numClouds, self.distanceConstraintList,
resonances, self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def showPeaks(self):
self.guiParent.viewPeaks(peaks=self.noesyPeaks)
def showResonances(self):
pass
#self.guiParent.viewResonances(resonances=self.resonances)
def setupResonances(self):
if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList:
disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList,
self.tocsyPeakList, self.hsqcPeakList)
(self.origResonances, self.noesyPeaks,
null) = getCloudsResonanceList(self.guiParent.argumentServer,
hsqcPeakList=self.hsqcPeakList,
tocsy3dPeakList=self.tocsyPeakList,
noesy2dPeakList=self.noesyPeakList)
self.setButtonStates()
def setButtonStates(self):
if self.origResonances:
self.label03a.set('Resonances found: %d' %
(len(self.origResonances)))
if self.noesyPeaks:
self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks)))
if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList:
self.setupButtons.buttons[0].enable()
else:
self.setupButtons.buttons[0].disable()
if self.noesyPeaks:
self.setupButtons.buttons[1].enable()
else:
self.setupButtons.buttons[1].disable()
if self.origResonances:
self.setupButtons.buttons[2].enable()
else:
self.setupButtons.buttons[2].disable()
if self.noesyPeaks and self.origResonances:
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.midgeButtons.buttons[1].enable()
self.distConstrLabel.set(
'Distance constraints: %d' %
len(self.distanceConstraintList.constraints))
else:
self.distConstrLabel.set('Distance constraints:')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
'Anti-distance constraints: %d' %
len(self.antiDistConstraintList.constraints))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('Anti-distance constraints:')
self.midgeButtons.buttons[2].disable()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
def getNoesys(self):
names = []
spectra = getSpectraByType(self.project, '2dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
self.noesyPeakList = self.peakListDict[name]
self.setButtonStates()
def getTocsys(self):
names = []
spectra = getSpectraByType(self.project, '3dTOCSY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.tocsyPeakList:
self.tocsyPeakList = peakList
return names
def getNoesy3ds(self):
names = []
spectra = getSpectraByType(self.project, '3dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesy3dPeakList:
self.noesy3dPeakList = peakList
return names
def setTocsy(self, index, name=None):
if not name:
name = self.tocsyPulldown.getSelected()
self.tocsyPeakList = self.peakListDict[name]
self.setButtonStates()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
self.noesy3dPeakList = self.peakListDict[name]
self.setButtonStates()
def getHsqcs(self):
names = []
spectra = getSpectraByType(self.project, 'HSQC')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.hsqcPeakList:
self.hsqcPeakList = peakList
return names
def setHsqc(self, index, name=None):
if not name:
name = self.hsqcPulldown.getSelected()
self.hsqcPeakList = self.peakListDict[name]
self.setButtonStates()
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def getMaxIntens(self, obj):
self.maxIntensEntry.set(self.maxIntens)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def setMaxIntens(self, event):
value = self.maxIntensEntry.get()
if value is not None:
self.maxIntens = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
options = ['Parameters','Restraints','Alignment Media & Tensors','About Meccano']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
frameA, frameB, frameC, frameD = tabbedFrame.frames
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_rowconfigure(13, weight=1)
frameB.grid_columnconfigure(1, weight=1)
frameB.grid_rowconfigure(1, weight=1)
frameC.grid_columnconfigure(0, weight=1)
frameC.grid_rowconfigure(1, weight=1)
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(0, weight=1)
texts = ['Run MECCANO!']
commands = [self.runMeccano]
bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts,
commands=commands, expands=True)
bottomButtons.grid(row=1, column=0, sticky='ew')
if not Meccano:
bottomButtons.buttons[0].disable()
# Parameters
row = 0
label = Label(frameA, text='Calculation Run:')
label.grid(row=row,column=0,sticky='w')
self.runPulldown = PulldownList(frameA, callback=self.selectRun)
self.runPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Shift List (for CO):')
label.grid(row=row,column=0,sticky='w')
self.shiftListPulldown = PulldownList(frameA, callback=self.selectShiftList)
self.shiftListPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Keep Copy of Used Shifts:')
label.grid(row=row,column=0,sticky='w')
self.toggleCopyShifts = CheckButton(frameA)
self.toggleCopyShifts.grid(row=row,column=1,sticky='w')
self.toggleCopyShifts.set(True)
row += 1
label = Label(frameA, text='Molecular System:')
label.grid(row=row,column=0,sticky='w')
self.molSystemPulldown = PulldownList(frameA, callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Chain:')
label.grid(row=row,column=0,sticky='w')
self.chainPulldown = PulldownList(frameA, callback=self.selectChain)
self.chainPulldown.grid(row=row,column=1,sticky='w')
self.chainPulldown.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='First Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.firstResEntry = IntEntry(frameA, text=None, width=8)
self.firstResEntry.grid(row=row,column=1,sticky='w')
self.firstResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Last Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.lastResEntry = IntEntry(frameA, text=None, width=8)
self.lastResEntry.grid(row=row,column=1,sticky='w')
self.lastResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Max Num Optimisation Steps:')
label.grid(row=row,column=0,sticky='w')
self.maxOptStepEntry = IntEntry(frameA, text=500, width=8)
self.maxOptStepEntry.grid(row=row,column=1,sticky='w')
self.maxOptStepEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Num Optimisation Peptide Planes:')
label.grid(row=row,column=0,sticky='w')
self.numOptPlaneEntry = IntEntry(frameA, text=2, width=8)
self.numOptPlaneEntry.grid(row=row,column=1,sticky='w')
self.numOptPlaneEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Min Num Optimisation Hits:')
label.grid(row=row,column=0,sticky='w')
self.numOptHitsEntry = IntEntry(frameA, text=5, width=8)
self.numOptHitsEntry.grid(row=row,column=1,sticky='w')
self.numOptHitsEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='File Name Prefix:')
label.grid(row=row,column=0,sticky='w')
self.pdbFileEntry = Entry(frameA, text='Meccano', width=8)
self.pdbFileEntry.grid(row=row,column=1,sticky='w')
self.pdbFileEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write Output File (.out):')
label.grid(row=row,column=0,sticky='w')
self.toggleWriteOutFile = CheckButton(frameA)
self.toggleWriteOutFile.grid(row=row,column=1,sticky='w')
self.toggleWriteOutFile.set(False)
self.toggleWriteOutFile.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write PDB File (.pdb):')
label.grid(row=row,column=0,sticky='w')
self.toggleWritePdbFile = CheckButton(frameA)
self.toggleWritePdbFile.grid(row=row,column=1,sticky='w')
self.toggleWritePdbFile.set(True)
self.toggleWritePdbFile.bind('<Leave>', self.updateRunParams)
if not Meccano:
row += 1
label = Label(frameA, text='The Meccano executable is not available (it needs to be compiled)', fg='red')
label.grid(row=row,column=0,columnspan=2,sticky='w')
# Restraints
label = Label(frameB, text='Constraint Set:')
label.grid(row=0,column=0,sticky='w')
self.constraintSetPulldown = PulldownList(frameB, callback=self.selectConstraintSet)
self.constraintSetPulldown.grid(row=0,column=1,sticky='w')
self.alignMediumPulldown= PulldownList(self, callback=self.setAlignMedium)
headingList = ['#','List Type','Use?','Alignment\nMedium','Num\nRestraints']
editWidgets = [None,None,None,self.alignMediumPulldown,None]
editGetCallbacks = [None,None,self.toggleUseRestraints,self.getAlignMedium,None]
editSetCallbacks = [None,None,None,self.setAlignMedium,None]
self.restraintMatrix = ScrolledMatrix(frameB,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=None,
multiSelect=True)
self.restraintMatrix.grid(row=1,column=0,columnspan=2,sticky='nsew')
# Alignment Media
div = LabelDivider(frameC,text='Alignment Media')
div.grid(row=0,column=0,sticky='ew')
self.mediumNameEntry = Entry(self, returnCallback=self.setMediumName)
self.mediumDetailsEntry = Entry(self, returnCallback=self.setMediumDetails)
headingList = ['#','Name','Details','Static Tensor','Dynamic Tensor']
editWidgets = [None, self.mediumNameEntry, self.mediumDetailsEntry, None, None]
editGetCallbacks = [None, self.getMediumName, self.getMediumDetails, None, None]
editSetCallbacks = [None, self.setMediumName, self.setMediumDetails, None, None]
self.mediaMatrix = ScrolledMatrix(frameC,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAlignMedium,
multiSelect=True)
self.mediaMatrix.grid(row=1,column=0,sticky='nsew')
texts = ['Add Alignment medium','Remove Alignment Medium']
commands = [self.addAlignMedium,self.removeAlignMedium]
buttonList = ButtonList(frameC, texts=texts, commands=commands, expands=True)
buttonList.grid(row=2,column=0,sticky='nsew')
self.editAxialEntry = FloatEntry(self, returnCallback=self.setAxial)
self.editRhombicEntry = FloatEntry(self, returnCallback=self.setRhombic)
self.editAlphaEulerEntry = FloatEntry(self, returnCallback=self.setEulerAlpha)
self.editBetaEulerEntry = FloatEntry(self, returnCallback=self.setEulerBeta)
self.editGammaEulerEntry = FloatEntry(self, returnCallback=self.setEulerGamma)
div = LabelDivider(frameC,text='Alignment Tensors')
div.grid(row=3,column=0,sticky='ew')
headingList = ['Type', u'Axial (\u03B6)',u'Rhombic (\u03B7)',
u'Euler \u03B1',u'Euler \u03B2',u'Euler \u03B3']
editWidgets = [None,self.editAxialEntry,
self.editRhombicEntry,self.editAlphaEulerEntry,
self.editBetaEulerEntry,self.editGammaEulerEntry]
editSetCallbacks = [None,self.setAxial,self.setRhombic,
self.setEulerAlpha,self.setEulerBeta,self.setEulerGamma]
editGetCallbacks = [None,self.getAxial,self.getRhombic,
self.getEulerAlpha,self.getEulerBeta,self.getEulerGamma]
self.tensorMatrix = ScrolledMatrix(frameC, maxRows=2,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectTensor,
multiSelect=True)
self.tensorMatrix.grid(row=4,column=0,sticky='nsew')
texts = ['Add Static Tensor','Add Dynamic Tensor','Remove Tensor']
commands = [self.addStaticTensor,self.addDynamicTensor,self.removeTensor]
buttonList = ButtonList(frameC,texts=texts, commands=commands, expands=True)
buttonList.grid(row=5,column=0,sticky='ew')
# About
label = Label(frameD, text='About Meccano...')
label.grid(row=0,column=0,sticky='w')
#
self.geometry('500x400')
self.updateShiftLists()
self.updateMolSystems()
self.updateResidueRanges()
self.updateConstraintSets()
self.updateAlignMedia()
self.updateRuns()
class EditExperimentSeriesPopup(BasePopup):
"""
**Setup Experiment Series for Chemical Shift and Intensity Changes**
The purpose of this popup is to setup ordered groups of experiments that are
related by the variation in some condition or parameter, but otherwise the
kind of experiment being run is the same. For example the user could setup
experiments for a temperature series, ligand binding titration or relaxation
rate measurement.
The layout is divided into two tables. The upper table shows all of the series
that are known to the current project and the lower table shows all of the
experiments or planes that comprise the selected series. These series relate
to both groups of separate experiments (and hence spectra) and also single
experiment where one dimension is not for NMR frequency but rather a "sampled"
dimension and thus effectively combines many experiments (e.g. for different
T1 values) as different planes. A stack of effectively 2D experiments combined
in this manner is typically referred to as pseudo-3D. - The experiment is 3D
but there are only two NMR dimensions.
Series which are stacks of planes in a single experiment entity are
automatically detected and entered into the table once they are loaded. Series
that are constructed from multiple, separate experiments however must be setup
by the user. To setup a new series of this kind [Add Series] makes a new,
empty NMR series. Next the user should change the "Parameter varied" column to
specify what type of thing is varied between the different experiments. The
user then adds experiments into this series with the [Add Series Point]
function at the bottom. Once the points have been added to the series the name
of the experiment for each point may be changed. Initially, arbitrary
experiments appear for the series points, so these almost always have to be
adjusted.
Once a stacked-plane experiment or series of experiments is setup, the user
next sets (or checks) the value of the parameter associated with each point in
the lower table. When loading stacked-plane experiments these values may come
though automatically, if they are present in the spectrum header or parameter
file. Given a completed NMR series specification the user may then extract the
relevant data from the series using one of the analysis tools like `Follow
Intensity Changes`_ or `Follow Shift Changes`_.
**Caveats & Tips**
Make sure the "Parameter Varied" for a given NMR series is appropriate to the
type of analysis being performed. Many tools that extract T1 or Kd
measurements for example look for specific types of series.
The "Set/Unset Ref Plane" function is only used in certain kinds of series
such as those that use trains of CPMG pulses.
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.expSeries = None
self.conditionPoint = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Experiment : NMR Series", **kw)
def body(self, guiFrame):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
#for func in ('__init__', 'delete','setName'):
for func in ('__init__', 'delete','setName','setConditionNames',
'addConditionName','removeConditionName'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.NmrExpSeries', func)
for func in ('__init__', 'delete','setName'):
notifyFunc(self.updateExperiments,'ccp.nmr.Nmr.Experiment', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateDataDim,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete','setCondition','setUnit','setValue','setError'):
notifyFunc(self.updateConditionsAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('__init__', 'delete','setCondition'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('setConditionVaried', 'setPointErrors',
'addPointError', 'removePointError',
'setPointValues','addPointValue',
'removePointValue','setUnit'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateColorSchemes,'ccpnmr.AnalysisProfile.ColorScheme', func)
def open(self):
self.updateAfter()
BasePopup.open(self)
def updateColorSchemes(self, scheme=None):
index = 0
prevScheme = self.colorSchemePulldown.getObject()
schemes = getHueSortedColorSchemes(self.analysisProfile)
schemes = [s for s in schemes if len(s.colors) > 1]
colors = [list(s.colors) for s in schemes]
if schemes:
names = [s.name for s in schemes]
if prevScheme in schemes:
index = schemes.index(prevScheme)
else:
names = []
self.colorSchemePulldown.setup(names, schemes, index, colors)
def autoColorSpectra(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
scheme = self.colorSchemePulldown.getObject()
if scheme:
colors = scheme.colors
else:
colors = ['#FF0000','#00FF00','#0000FF']
cdict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionName = list(self.expSeries.conditionNames)[0]
expList = []
for sampleCondition in cdict.get(conditionName, []):
expList.append( (sampleCondition.value, sampleCondition.parent.experiments) )
expList.sort()
m = len(expList)-1.0
c = len(colors)-1
for i, (value, experiments) in enumerate(expList):
p = c*i/m
j = int(p)
r1, g1, b1 = Color.hexToRgb(colors[j])
r2, g2, b2 = Color.hexToRgb(colors[min(c,j+1)])
f2 = p-j
f1 = 1.0-f2
r = (r1*f1)+(r2*f2)
g = (g1*f1)+(g2*f2)
b = (b1*f1)+(b2*f2)
hexColor = Color.hexRepr(r,g,b)
for experiment in experiments:
for spectrum in experiment.dataSources:
if spectrum.dataType == 'processed':
analysisSpec = getAnalysisSpectrum(spectrum)
if analysisSpec.posColors:
analysisSpec.posColors = [hexColor,]
elif analysisSpec.negColors:
analysisSpec.negColors = [hexColor,]
def getUnusedExperiments(self):
sampleExperiments = getSampledDimExperiments(self.nmrProject)
experiments = []
for experiment in self.nmrProject.sortedExperiments():
if experiment in sampleExperiments:
continue
if self.expSeries and (self.expSeries.className != 'Experiment'):
if experiment in self.expSeries.experiments:
continue
experiments.append(experiment)
return experiments
def conditionTableShow(self, object, row, col):
if type(object) is type(()):
dataDim, index = object
refPlane = dataDim.analysisDataDim.refSamplePlane
if refPlane == index:
return False
if col == 1:
return False
return True
def setSampledReferencePlane(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
if self.conditionPoint:
dataDim, point = self.conditionPoint
analysisDataDim = dataDim.analysisDataDim
refPoint = analysisDataDim.refSamplePlane
if refPoint == point:
analysisDataDim.refSamplePlane = None
else:
analysisDataDim.refSamplePlane = point
self.updateAfter()
def checkAddSampleCondition(self, experiment):
conditionSet = getExperimentConditionSet(experiment)
conditionName = self.expSeries.conditionNames[0]
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
sampleConditions = condDict.get(conditionName, [])
units = [sc.unit for sc in sampleConditions if sc.unit]
if units:
sortList = list(set(units))
sortList.sort(key = lambda u:units.count(u))
unit = sortList[-1]
else:
unit = CONDITION_UNITS_DICT[conditionName][0]
condition = conditionSet.findFirstSampleCondition(condition=conditionName)
if not condition:
condition = conditionSet.newSampleCondition(condition=conditionName,
unit=unit, value=0.0, error=0.0)
def addConditionPoint(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
experiments = self.getUnusedExperiments()
if not experiments:
showWarning('Warning','No experiments available', parent=self)
return
experiment = experiments[0]
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
self.checkAddSampleCondition(experiment)
self.updateAfter()
def deleteConditionPoint(self, *event):
if self.conditionPoint and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series point?', parent=self):
conditionSet = self.conditionPoint.sampleConditionSet
experiments = [e for e in conditionSet.experiments if e in self.expSeries.experiments]
for experiment in experiments:
self.expSeries.removeExperiment(experiment)
for experiment in experiments:
for expSeries in experiment.nmrExpSeries:
if self.conditionPoint.condition in self.expSeries.conditionNames:
break
else:
continue
break
else:
self.conditionPoint.delete()
self.conditionPoint = None
def selectConditionPoint(self, object, row, col):
if object:
self.conditionPoint = object
self.updateButtons()
def selectExpSeries(self, object, row, col):
if object:
self.expSeries = object
self.checkExperimentConditionsConsistent()
self.updateConditions()
def checkExperimentConditionsConsistent(self):
if self.expSeries.className != 'Experiment':
for experiment in self.expSeries.experiments:
self.checkAddSampleCondition(experiment)
def getUnits(self):
units = []
if self.expSeries:
if self.expSeries.className == 'Experiment':
conditionName = getExperimentSampledDim(self.expSeries).conditionVaried
else:
conditionName = self.expSeries.conditionNames[0]
units = CONDITION_UNITS_DICT.get(conditionName)
if not units:
units = ['?',]
return units
def getUnit(self, sampleCondition):
index = -1
units = self.getUnits()
if units:
if sampleCondition:
if type(sampleCondition) is type(()):
dataDim, index = sampleCondition
unit = dataDim.unit
else:
unit = sampleCondition.unit
if unit not in units:
unit = units[0]
index = units.index(unit)
self.unitPulldown.setup(units,units,index)
def setUnit(self, obj):
name = self.unitPulldown.getObject()
if self.conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
dataDim.setUnit(name)
else:
self.conditionPoint.setUnit(name)
def getConditionNames(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
names = ['delay time','mixing time','num delays','pulsing frequency','gradient strength']
else:
names = CONDITION_UNITS_DICT.keys()
names.sort()
return names
def setConditionName(self, obj):
name = self.conditionNamesPulldown.getObject()
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
dataDim.conditionVaried = name
else:
self.expSeries.setConditionNames([name,])
def getConditionName(self, expSeries):
index = 0
names = self.getConditionNames()
if names:
if expSeries:
if expSeries.className == 'Experiment':
name = getExperimentSampledDim(expSeries).conditionVaried
else:
name = expSeries.conditionNames[0]
if name:
index = names.index(name)
else:
index = 0
self.conditionNamesPulldown.setup(names,names,index)
def getName(self, expSeries):
if expSeries :
self.nameEntry.set(expSeries.name)
def setName(self, event):
text = self.nameEntry.get()
if text and text != ' ':
self.expSeries.setName( text )
def getValue(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
value = dataDim.pointValues[index]
else:
value = conditionPoint.value
self.valueEntry.set(value)
def setValue(self, event):
value = self.valueEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
values = list(dataDim.pointValues)
values[index] = value
dataDim.setPointValues(values)
else:
self.conditionPoint.setValue( value )
def getError(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
if index < len(dataDim.pointErrors):
error = dataDim.pointValues[index]
else:
error = 0.0
else:
error = conditionPoint.error
self.errorEntry.set(error)
def setError(self, event):
value = self.errorEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
pointErrors = dataDim.pointErrors
if pointErrors:
values = list(pointErrors)
else:
values = [0.0] * dataDim.numPoints
values[index] = value
dataDim.setPointErrors(values)
else:
self.conditionPoint.setError( value )
def getDetails(self, expSeries):
if expSeries :
self.detailsEntry.set(expSeries.details)
def setDetails(self, event):
text = self.detailsEntry.get()
if text and text != ' ':
self.expSeries.setDetails( text )
def addExpSeries(self):
expSeries = self.nmrProject.newNmrExpSeries(conditionNames=['delay time',])
def deleteExpSeries(self, *event):
if self.expSeries and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series?', parent=self):
self.expSeries.delete()
self.expSeries = None
self.conditionPoint = None
def getExperiments(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
return [self.expSeries,]
else:
return self.nmrProject.sortedExperiments()
def getExperiment(self, sampleCondition):
index = 0
names = []
if self.conditionPoint and (type(self.conditionPoint) != type(())):
index = 0
experiment = self.conditionPoint.parent.findFirstExperiment()
experiments = self.getUnusedExperiments()
name = experiment.name
names = [name] + [e.name for e in experiments]
experiments = [experiment,] + experiments
self.experimentPulldown.setup(names,experiments,index)
def setExperiment(self, obj):
experiment = self.experimentPulldown.getObject()
if self.conditionPoint and (type(self.conditionPoint) != type(())):
conditionSet = getExperimentConditionSet(experiment)
if conditionSet is not self.conditionPoint.parent:
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
unit = self.conditionPoint.unit
if not unit:
unit = CONDITION_UNITS_DICT[self.expSeries.conditionNames[0]]
condition = self.conditionPoint.condition
experiments = set(self.expSeries.experiments)
for experiment0 in self.conditionPoint.parent.experiments:
if experiment0 in experiments:
experiments.remove(experiment0)
self.expSeries.experiments = experiments
value = self.conditionPoint.value
error = self.conditionPoint.error
self.conditionPoint.delete()
self.conditionPoint = conditionSet.findFirstSampleCondition(condition=condition)
if self.conditionPoint:
self.conditionPoint.unit = unit
self.updateAfter()
else:
self.conditionPoint = conditionSet.newSampleCondition(condition=condition,unit=unit,
value=value,error=error)
def updateDataDim(self, sampledDataDim):
experiment = sampledDataDim.dataSource.experiment
self.updateExperiments(experiment)
def updateExperiments(self, experiment):
experiments = self.getExperiments()
names = [e.name for e in experiments]
self.experimentPulldown.setup(names, experiments,0)
if getExperimentSampledDim(experiment):
self.updateAfter()
elif self.expSeries:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.updateConditionsAfter()
elif experiment in self.expSeries.experiments:
self.updateConditionsAfter()
def updateConditionsAfter(self, sampleCondition=None):
if self.waitingConditions:
return
if sampleCondition:
experiments = sampleCondition.sampleConditionSet.experiments
for experiment in experiments:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
elif experiment in self.expSeries.experiments:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
else:
self.waitingConditions = True
self.after_idle(self.updateConditions)
def updateConditions(self):
self.updateButtons()
objectList = []
textMatrix = []
colorMatrix = []
nCols = len(self.conditionPointsMatrix.headingList)
defaultColors = [None] * nCols
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
analysisDataDim = getAnalysisDataDim(dataDim)
conditionVaried = dataDim.conditionVaried
expName = self.expSeries.name
unit = dataDim.unit
pointValues = dataDim.pointValues
pointErrors = dataDim.pointErrors
refPlane = analysisDataDim.refSamplePlane
for i in range(dataDim.numPoints):
if i < len(pointErrors):
error = pointErrors[i]
else:
error = None
pointText = ':%3d' % (i+1)
if i == refPlane:
datum = ['* Ref Plane *',
expName+pointText,
None,
None,
None]
colorMatrix.append(['#f08080'] * nCols)
else:
datum = [conditionVaried ,
expName+pointText,
pointValues[i],
error,
unit]
colorMatrix.append(defaultColors)
textMatrix.append(datum)
objectList.append((dataDim, i))
else:
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionNames = self.expSeries.conditionNames
for conditionName in conditionNames:
for sampleCondition in condDict.get(conditionName, []):
datum = [sampleCondition.condition,
' '.join([e.name for e in sampleCondition.parent.experiments]),
sampleCondition.value,
sampleCondition.error,
sampleCondition.unit]
textMatrix.append(datum)
objectList.append(sampleCondition)
colorMatrix.append(defaultColors)
self.conditionPointsMatrix.update(objectList=objectList,
colorMatrix=colorMatrix,
textMatrix=textMatrix)
self.waitingConditions = 0
def updateAfter(self, object=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def updateButtons(self):
if self.expSeries is None:
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].disable()
elif self.expSeries.className == 'Experiment':
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].enable()
else:
self.seriesButtons.buttons[1].enable()
self.seriesButtons.buttons[2].enable()
self.conditionPointsButtons.buttons[0].enable()
self.conditionPointsButtons.buttons[2].disable()
if self.conditionPoint is None:
self.conditionPointsButtons.buttons[1].disable()
else:
self.conditionPointsButtons.buttons[1].enable()
def update(self):
self.updateButtons()
objectList = []
textMatrix = []
for experiment in getSampledDimExperiments(self.nmrProject):
getExperimentConditionSet(experiment)
sampledDim = getExperimentSampledDim(experiment)
datum = [None,
experiment.name,
1,
sampledDim.conditionVaried,
sampledDim.numPoints]
textMatrix.append(datum)
objectList.append(experiment)
for expSeries in self.nmrProject.sortedNmrExpSeries():
experiments = expSeries.experiments
conditionSets = len([e.sampleConditionSet for e in experiments if e.sampleConditionSet])
datum = [expSeries.serial,
expSeries.name or ' ',
len(experiments),
','.join(expSeries.conditionNames),
conditionSets]
textMatrix.append(datum)
objectList.append(expSeries)
self.seriesMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.updateConditions()
self.waiting = False
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def body(self, master):
self.geometry('600x400')
columnspan = 5
row = 0
label = Label(master, text="AutoAssign project file setup window.")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.W)
#
# Set up the spectra
#
row += 1
label = Label(master, text="Spectrum type")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
label = Label(master, text="CCPN peak list")
label.grid(row=row, column=2, columnspan=2, sticky=Tkinter.W)
label = Label(master, text="Phase") # TODO What's this?
label.grid(row=row, column=4, sticky=Tkinter.W)
self.spectrumSelectWidget = {}
self.spectrumPhaseWidget = {}
for i in range(len(self.autoAssignProjectFile.defaultSpectra)):
row += 1
specType = self.autoAssignProjectFile.defaultSpectra[i][0]
if i == 0:
labelText = "%s (root)" % specType
else:
labelText = "%s" % specType
label = Label(master, text=labelText)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
self.spectrumSelectWidget[specType] = PulldownMenu(
master, entries=self.peakNameList)
self.spectrumSelectWidget[specType].grid(row=row,
column=2,
columnspan=2,
sticky=Tkinter.W)
self.spectrumPhaseWidget[specType] = Entry(master,
text="",
width=4)
self.spectrumPhaseWidget[specType].grid(row=row,
column=4,
sticky=Tkinter.W)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Set up the tolerances
#
row += 1
label = Label(master, text="Atom tolerances")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
toleranceAtoms = self.autoAssignProjectFile.toleranceAtoms
toleranceDefault = self.autoAssignProjectFile.toleranceDefault
self.toleranceWidget = {}
for i in range(0, len(toleranceAtoms), 2):
row += 1
for j in range(2):
curPos = i + j
if curPos == len(toleranceAtoms):
break
toleranceAtom = toleranceAtoms[curPos]
label = Label(master, text=toleranceAtom)
label.grid(row=row, column=2 * j, sticky=Tkinter.E)
self.toleranceWidget[toleranceAtom] = Entry(
master, text=str(toleranceDefault[curPos]), width=6)
self.toleranceWidget[toleranceAtom].grid(row=row,
column=1 + 2 * j,
sticky=Tkinter.W)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
row += 1
label = Label(
master,
text="Will save the peak files in the project file directory.",
fg='red')
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=columnspan, column=0)
