def body(self, master):
self.geometry('600x400')
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
self.result = ''
self.file_select = FileSelect(master,
file_types=self.file_types,
directory=self.directory,
prompt=self.prompt,
show_file=self.show_file,
file=self.initial_file,
multiSelect=self.multiSelect,
default_dir=self.default_dir)
self.file_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
texts = ['Ok']
commands = [self.ok]
if (self.extra_dismiss_text):
texts.append(self.extra_dismiss_text)
commands.append(self.extra)
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text=self.dismiss_text)
buttons.grid(row=1, column=0, sticky=Tkinter.EW)
def body(self, master):
#
# Popup window
#
row = 0
label = Label(master, text= self.text)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
self.multiSelect = ScrolledListbox(master,
width = 50,
height = 5,
selectmode = Tkinter.MULTIPLE,
initial_list = self.selectionList)
self.multiSelect.grid(row=row, column=0, sticky=Tkinter.E, ipadx = 20)
master.grid_columnconfigure(0, weight=1)
master.grid_rowconfigure(row, weight=1)
if self.selectedItems:
self.multiSelect.setSelectedItems(self.selectedItems)
if self.endText:
row = row + 1
label = Label(master, text= self.endText)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text = self.dismissText, help_url=self.help_url)
buttons.grid(row=row, column=0)
def body(self, master):
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(1, weight=1)
row = 0
if (self.message):
label = Label(master, text=self.message)
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row = row + 1
if (self.label):
label = Label(master, text=self.label)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.itemMenu = PulldownMenu(master, entries=self.entries)
self.itemMenu.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
texts = [self.select_text]
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def body(self, master):
row = 0
label = Label(master, text= "CcpNmr resonance -> atom mapping file writer.")
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.W)
row += 1
label = Label(master, text= "File formats:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.formatListBox = ScrolledListbox(master, width = 50, height = 5, selectmode = Tkinter.MULTIPLE,
initial_list = self.formats)
self.formatListBox.grid(row=row, column=1, sticky=Tkinter.EW)
# Default is all formats selected...
self.formatListBox.setSelectedItems(self.formatListBox.getItems())
row += 1
label = Label(master, text= "Mapping output file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master, text = self.defaultText, command = self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = [ 'Write mapping' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, columnspan = 2, column=0)
def body(self, master):
#
# Popup gui
#
# First row
row = 0
label = Label(master, text="Choose a naming system:")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
label = Label(master, text="(% matches in brackets)")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.menu = PulldownMenu(master, entries=self.namingSysList)
self.menu.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Exit',
help_url=self.help_url)
buttons.grid(row=row, column=0)
def body(self, guiParent):
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
buttons = createDismissHelpButtonList(frame,
dismiss_text='Quit',
dismiss_cmd=self.quit,
help_url=self.help_url,
expands=1)
buttons.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.helpButton = buttons.buttons[-1]
self.helpButtonCommand = self.helpButton.buttonCommand # the command with no project
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.otherMenu = self.makeOtherMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def body(self, master):
self.geometry('600x500')
master.grid_rowconfigure(1, weight=1)
master.grid_columnconfigure(0, weight=1)
label = Label(master, text='Select Project Directory')
label.grid(row=0, column=0, sticky=Tkinter.W)
file_types = [FileType('Project', ['*.xml']), FileType('All', ['*'])]
self.file_select = FileSelect(master,
file_types=file_types,
show_file=False,
double_callback=self.ok,
getRowColor=self.getEntryColor,
getExtraCell=self.getProjectFileText,
extraHeadings=('Status', ),
extraJustifies=('left', ))
self.file_select.grid(row=1, column=0, sticky=Tkinter.NSEW)
texts = ['Open']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=2, column=0, sticky=Tkinter.EW)
self.ok_button = buttons.buttons[0]
def body(self, master):
#
# Popup window
#
row = 0
if self.topText:
label = Label(master, text= self.topText)
label.grid(row=row, column=0, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= self.text)
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menu = PulldownMenu(master, entries = self.selectionList, selected_index = self.selectedIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.E, ipadx = 20)
row = row + 1
texts = [ 'OK' ]
commands = [ self.ok ] # This calls 'ok' in BasePopup, this then calls 'apply' in here
if self.dismissButton:
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text = self.dismissText, help_url=self.help_url)
else:
buttons = createHelpButtonList(master, texts=texts, commands=commands, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 3)
def body(self, master):
#
# Popup window
#
row = 0
if self.headerLines:
for headerLine in self.headerLines:
label = Label(master, text= headerLine)
label.grid(row=row, column=0, columnspan = 3, sticky=Tkinter.EW)
row += 1
label = Label(master, text= "Residue type '%s'" % self.ccpCode)
label.grid(row=row, column=0, columnspan = 3, sticky=Tkinter.EW)
row = row + 1
matchNameString = "[%s]" % self.matchName
if self.matchInfoPopup:
label = Label(master, text= "%s:" % self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
button = Tkinter.Button(master, text= matchNameString, command = lambda : self.matchInfoPopup(self,self.matchName), fg = 'blue')
button.grid(row=row, column=1, columnspan = 2)
else:
label = Label(master, text= "%s:" %self.matchType)
label.grid(row=row, column=0, sticky=Tkinter.E)
label = Label(master, text= matchNameString, fg = 'blue')
label.grid(row=row, column=1, columnspan = 2)
if self.shifts:
row = row + 1
label = Label(master, text= "(shifts: %s ppm)" % self.shifts)
label.grid(row=row, column=1, columnspan = 2, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text= "Pick atom:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.menu = PulldownMenu(master, entries = self.chemAtomList)
self.menu.grid(row=row, column=1, columnspan = 2, ipadx = 20)
row = row + 1
label = Label(master, text= "Propagate\nmapping to:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.propagateMenu = PulldownMenu(master, entries = self.propagateList, selected_index = self.selectedIndex)
self.propagateMenu.grid(row=row, column=1, columnspan = 2)
row = row + 1
texts = [ 'OK' , 'Show all atoms']
commands = [ self.ok, self.showAllAtoms] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, dismiss_text = 'Do not link', dismiss_cmd = self.doNotLink, help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan = 3)
def 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, 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):
row = 0
label = Label(master,
text="BMRB chemical shift deposition file writer.")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Shift lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master,
entries=self.shiftLists,
callback=self.setChainList,
do_initial_callback=False)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Chains (only one per file):")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainListSelect = PulldownMenu(master, entries=self.chainList)
self.chainListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
self.setChainList(0, self.shiftLists[0])
row += 1
label = Label(master, text="Chemical shift deposition file:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileButton = Tkinter.Button(master,
text=self.defaultText,
command=self.selectFile)
self.fileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
texts = ['Write file']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def body(self, master):
self.geometry('600x500')
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
self.dataLocationFrame = DataLocationFrame(master, self.project)
self.dataLocationFrame.grid(row=0, column=0, sticky='nsew')
buttons = createDismissHelpButtonList(master,
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=1, column=0, sticky='ew')
self.dataLocationFrame.administerNotifiers(self.registerNotify)
def body(self, master):
self.frame = ChemCompFrame(master, self.project, **self.keywds)
self.frame.pack(side=Tkinter.TOP,
expand=Tkinter.YES,
fill=Tkinter.BOTH)
texts = ['OK']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_url=self.help_url)
buttons.pack()
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 body(self, master):
master.grid_columnconfigure(0, weight=1)
for i in range(6):
master.grid_rowconfigure(i, weight=1)
self.geometry('600x400')
#
# Popup window
#
row = 0
label = Label(master, text="Residue type '%s'" % self.code3Letter)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Resonance '%s'" % self.resName)
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text="Pick resonance(s):")
label.grid(row=row, column=0, sticky=Tkinter.W)
row = row + 1
self.list = ScrolledListbox(master,
width=50,
height=5,
selectmode=self.selectmode,
initial_list=self.resonanceList)
self.list.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text=self.helpText, fg='blue')
label.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands)
buttons.grid(row=row, column=0)
def body(self, master):
self.alarm_id = None
self.root_widget = getRoot(self)
row = 0
label = Label(master, text='Widget count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.count_label = Label(master,
text='',
tipText='Number of Tkinter widget objects')
self.count_label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
ind = 1
label = Label(master, text='Auto count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.on_off_buttons = RadioButtons(master,
entries=self.on_off_entries,
select_callback=self.applyAuto,
selected_index=ind)
self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Auto frequency:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.freq_entry = IntEntry(master,
text=60,
returnCallback=self.applyAuto)
self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text='seconds')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
texts = ['Do Immediate Count']
commands = [self.applyManual]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
self.doCount()
def body(self, master):
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
row = 0
self.printFrame = PrintFrame(master,
project=self.project,
appKey=self.appKey)
self.printFrame.grid(row=row, column=0, sticky=Tkinter.EW)
row = row + 1
texts = ['Save']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, sticky=Tkinter.EW)
def body(self, master):
self.geometry('600x400')
#
# Quick check
#
if not self.chains:
showError("No chains",
"No chains available - cannot use export/import cycle.")
self.destroy()
#
# Set it all up
#
columnspan = 2
row = 0
label = Label(master, text="AutoAssign export/import cycle.")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
row += 1
label = Label(
master,
fg='red',
text=
"Popup to export %s data from the CCPN data model,\nrun %s, then re-import the output."
% (self.format, self.format))
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Set up export file info
#
row += 1
label = Label(master,
text="Export menu (using date/time label '%s')" %
self.dateTimeFlag)
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
(chainList, self.chainDict) = createSelection(self.chains)
label = Label(master, text="Select chain to export:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainSelect = PulldownMenu(master, entries=chainList)
self.chainSelect.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(master, text="Export %s project file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectExportFileButton = Tkinter.Button(
master,
text='Select export file',
command=(lambda: self.selectExportProjectFile()))
self.selectExportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.exportButton = Tkinter.Button(master,
text='Export',
command=(lambda: self.doExport()))
self.exportButton.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Set up import file info
#
row += 1
label = Label(master, text="Re-import menu")
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row += 1
#
# Select the right chain with the right date/time flag...
#
label = Label(master, text="Select chain with correct date/time flag:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.chainDateTimeSelect = PulldownMenu(
master, entries=self.chainDateTimeStamps)
self.chainDateTimeSelect.grid(row=row, column=1, sticky=Tkinter.W)
# TODO UPDATE THIS WHEN EXPORT BUTTON PRESSED AND GETTING OK FROM EXPORT ITSELF!
# Probably also need just a message if no importDateTimeStamp available...
row += 1
label = Label(master, text="Import %s output file:" % self.format)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.selectImportFileButton = Tkinter.Button(
master,
text='Select import file',
command=(lambda: self.selectImportShiftFile()))
self.selectImportFileButton.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
self.importButton = Tkinter.Button(master,
text='Import',
command=(lambda: self.doImport()))
self.importButton.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
#
# Make a break...
#
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
row += 1
buttons = createDismissHelpButtonList(master,
texts=[],
commands=[],
help_url=self.help_url)
buttons.grid(row=row, columnspan=columnspan, column=0)
def body(self, master):
master.grid_columnconfigure(0, weight=1)
master.grid_rowconfigure(0, weight=1)
master.grid_rowconfigure(1, weight=1)
self.geometry('500x500')
fileNames = []
# All files have to be in same directory!
if self.files and self.files[0].find(dirsep) > -1:
(path, fileName) = splitPath(self.files[0])
directory = path
fileNames.append(fileName)
for file in self.files[1:]:
(path, fileName) = splitPath(file)
fileNames.append(fileName)
else:
path = None
directory = normalisePath(os.path.abspath(os.curdir))
fileNames = []
#print directory
#print fileName
file_types = []
if fileTypeDict.has_key(self.component):
if self.format and fileTypeDict[self.component].has_key(
self.format):
file_types.extend([
FileType(self.format,
fileTypeDict[self.component][self.format])
])
if fileTypeDict[self.component].has_key('generic'):
file_types.extend([
FileType('generic',
fileTypeDict[self.component]['generic'])
])
file_types.extend([FileType('All', ['*'])])
self.file_select = FileSelect(master,
file_types=file_types,
directory=directory,
double_callback=self.ok,
multiSelect=self.multiSelect)
if self.multiSelect:
self.file_select.setFiles(fileNames)
else:
if fileNames:
fileName = fileNames[0]
else:
fileName = ''
self.file_select.setFile(fileName)
self.file_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
texts = [self.selectionText]
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands)
buttons.grid(row=1, column=0, sticky=Tkinter.EW)
def body(self, guiFrame):
row = 0
guiFrame.grid_columnconfigure(3, weight=1)
label = Label(guiFrame, text='Cloud file names:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileNameEntry = Entry(guiFrame,
text='testHistone\d+.pdb',
returnCallback=self.loadClouds)
self.fileNameEntry.grid(row=row, column=1, sticky=Tkinter.W)
strucLabel = Label(guiFrame, text='Comparison structure')
strucLabel.grid(row=row, column=2, sticky=Tkinter.W)
self.strucPulldown = PulldownMenu(guiFrame,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.strucPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
sdTolLabel = Label(guiFrame, text='Tolerance (SDs):')
sdTolLabel.grid(row=row, column=0, sticky=Tkinter.W)
self.sdToleranceEntry = FloatEntry(guiFrame, text=2.0, width=6)
self.sdToleranceEntry.grid(row=row, column=1, stick=Tkinter.W)
atomTypes = ['All', 'H', 'H HA', 'H HA HB']
label = Label(guiFrame, text='RMSD Atom Types:')
label.grid(row=row, column=2, sticky=Tkinter.W)
self.atomsPulldown = PulldownMenu(guiFrame,
entries=atomTypes,
callback=self.setAtomTypes,
selected_index=0,
do_initial_callback=0)
self.atomsPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = ['#', 'File name', 'RMSD to mean']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
initialRows=10,
headingList=colHeadings,
callback=self.selectCell,
objectList=[],
textMatrix=[
[],
],
multiSelect=1)
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
texts = [
'Load\nClouds', 'Align\nClouds', 'Calc\nRMSD',
'Make Cloud\nfrom structure', 'Remove', 'Remove\nbad'
]
commands = [
self.loadClouds, self.alignClouds, self.calcRmsd,
self.makeStrucCloud, self.deleteClouds, self.filterClouds
]
self.bottomButtons = createDismissHelpButtonList(
guiFrame,
texts=texts,
expands=1,
commands=commands,
help_url=self.help_url)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.update()
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def body(self, guiFrame):
self.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, master):
#
# Peaklist setup
#
self.peakListDict = {}
for experiment in self.project.currentNmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
for peakList in dataSource.sortedPeakLists():
peakListLabel = "%s:%s:%d:%s" % (
experiment.name, dataSource.name, peakList.serial,
peakList.name)
self.peakListDict[peakListLabel] = peakList
peakListLabels = self.peakListDict.keys()
peakListLabels.sort()
#
# chemical shift list setup
#
self.shiftListDict = {}
self.shiftListDict['None'] = None
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
shiftListLabel = "%d:%s" % (shiftList.serial, shiftList.name)
self.shiftListDict[shiftListLabel] = shiftList
shiftListLabels = self.shiftListDict.keys()
shiftListLabels.sort()
row = 0
label = Label(master, text="Generation of chemical shift list")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Peak lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.peakListBox = ScrolledListbox(master,
width=50,
height=5,
selectmode=Tkinter.MULTIPLE,
initial_list=peakListLabels)
self.peakListBox.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use existing shift list:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master, entries=shiftListLabels)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use multiple assignments:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.useAllContribs = CheckButton(master)
self.useAllContribs.grid(row=row, column=1, sticky=Tkinter.W)
#
# Setup the default shift error per nucleus
#
self.defaultShiftError = {}
for (nucl, text, defValue) in [('1H', 'proton', '0.002'),
('13C', 'carbon', '0.1'),
('15N', 'nitrogen', '0.1')]:
row += 1
label = Label(master, text="Default %s shift error:" % text)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.defaultShiftError[nucl] = Entry(master, text=defValue)
self.defaultShiftError[nucl].grid(row=row,
column=1,
sticky=Tkinter.W)
row += 1
texts = ['Create shift list']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def body(self, guiParent):
now = datetime.date.today().strftime('%y%m%d')
filePrefix = '%s_%s' % (self.project.name, now)
projDir = getUserDataPath(self.project)
directory = os.path.dirname(projDir)
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Archive File:')
label.grid(row=row, column=0, sticky=Tkinter.E)
tipText = 'File name (excluding .tgz ending) for archive'
self.fileEntry = Entry(guiParent, text=filePrefix, tipText=tipText)
self.fileEntry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(guiParent, text='.tgz (automatically appended)')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
self.backupCheck = CheckButton(
guiParent,
text='Include *.xml.bak files',
tipText='If checked include *.xml.bak files')
self.backupCheck.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
self.dataCheck = CheckButton(
guiParent,
text='Include data files which are in project directory',
tipText=
'If checked include data files if they are located in project directory'
)
self.dataCheck.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W)
row = row + 1
labelFrame = LabelFrame(guiParent, text='Archive Location')
labelFrame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
self.dirSelect = FileSelect(labelFrame,
directory=directory,
show_file=False)
self.dirSelect.grid(row=0, column=0, sticky=Tkinter.NSEW)
guiParent.grid_rowconfigure(row, weight=1)
row = row + 1
texts = ['Save']
tipTexts = ['Create archive file']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
row = 0
labelFrame0 = LabelFrame(guiFrame, text='Input data')
labelFrame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame0.grid_columnconfigure(3, weight=1)
label = Label(labelFrame0, text='Assigned NOESY spectrum')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='H/D ratio: ')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.ratioHDEntry = FloatEntry(labelFrame0, text=self.ratioHD, width=6)
self.ratioHDEntry.grid(row=0, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 1:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.tmix1Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy1,
selected_index=-0,
do_initial_callback=0)
self.tmix1Pulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=1, column=2, sticky=Tkinter.NW)
self.tmix1Entry = FloatEntry(labelFrame0, text=60, width=6)
self.tmix1Entry.grid(row=1, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 2:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.tmix2Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy2,
selected_index=0,
do_initial_callback=0)
self.tmix2Pulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=2, column=2, sticky=Tkinter.NW)
self.tmix2Entry = FloatEntry(labelFrame0, text=120, width=6)
self.tmix2Entry.grid(row=2, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='NOESY spectrum 3:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.tmix3Pulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys(),
callback=self.setNoesy3,
selected_index=0,
do_initial_callback=0)
self.tmix3Pulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(labelFrame0, text='Tmix (ms): ')
label.grid(row=3, column=2, sticky=Tkinter.NW)
self.tmix3Entry = FloatEntry(labelFrame0, text=200, width=6)
self.tmix3Entry.grid(row=3, column=3, sticky=Tkinter.NW)
label = Label(labelFrame0, text='3D NOESY:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(labelFrame0,
entries=self.getNoesys3d(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=4, column=1, sticky=Tkinter.NW)
label10 = Label(labelFrame0, text='Num peaks:')
label10.grid(row=5, column=0, sticky=Tkinter.NW)
self.numPeaksLabel = Label(labelFrame0, text='0')
self.numPeaksLabel.grid(row=5, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame0, text='Num resonances:')
label11.grid(row=5, column=2, sticky=Tkinter.NW)
self.numResonancesLabel = Label(labelFrame0, text='0')
self.numResonancesLabel.grid(row=5, column=3, sticky=Tkinter.NW)
row += 1
labelFrame1 = LabelFrame(guiFrame, text='Parameters')
labelFrame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame1.grid_columnconfigure(3, weight=1)
label = Label(labelFrame1, text='15N labelled sample:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.nitrogenSelect = CheckButton(labelFrame1,
callback=self.setNitrogenLabel)
self.nitrogenSelect.grid(row=0, column=1, sticky=Tkinter.W)
self.nitrogenSelect.set(1)
label = Label(labelFrame1, text='13C labelled sample:')
label.grid(row=0, column=2, sticky=Tkinter.NW)
self.carbonSelect = CheckButton(labelFrame1,
callback=self.setCarbonLabel)
self.carbonSelect.grid(row=0, column=3, sticky=Tkinter.W)
self.carbonSelect.set(0)
labelFrame1.grid_rowconfigure(1, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
]
self.midgeParamsMatrix = ScrolledMatrix(
labelFrame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
label10 = Label(labelFrame1, text='Benchmark structure')
label10.grid(row=2, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(labelFrame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label11 = Label(labelFrame1, text='ADC atom types:')
label11.grid(row=2, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(labelFrame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=2, column=3, sticky=Tkinter.NW)
row += 1
labelFrame2 = LabelFrame(guiFrame, text='Output')
labelFrame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
labelFrame2.grid_columnconfigure(3, weight=1)
label20 = Label(labelFrame2, text='Distance constraints:')
label20.grid(row=0, column=0, sticky=Tkinter.NW)
self.distConstrLabel = Label(labelFrame2, text='0')
self.distConstrLabel.grid(row=0, column=1, sticky=Tkinter.NW)
label21 = Label(labelFrame2, text='Anti-distance constraints:')
label21.grid(row=0, column=2, sticky=Tkinter.NW)
self.antiConstrLabel = Label(labelFrame2, text='0')
self.antiConstrLabel.grid(row=0, column=3, sticky=Tkinter.NW)
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(labelFrame2,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=1,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
self.getPeaks()
self.getResonances()
self.update()
self.geometry('600x400')
def body(self, parent):
row = 0
columnspan = 3
if self.numDim != None:
columnspan += 1
if self.topText:
label = Label(parent, text=self.topText)
label.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.EW)
row = row + 1
if self.expName:
expNameText = " for experiment '%s'" % self.expName
else:
expNameText = ''
label = Label(
parent,
text=
'Select a reference experiment%s from the list below, then press Create'
% expNameText)
label.grid(row=row, column=0, columnspan=columnspan, sticky=Tkinter.EW)
row = row + 1
colHeadings = self.getHeadings()
parent.grid_rowconfigure(row, weight=1, minsize=300)
parent.grid_columnconfigure(0, weight=1, minsize=100)
self.table = ScrolledMatrix(parent,
headingList=colHeadings,
callback=None)
self.table.grid(row=row,
column=0,
columnspan=columnspan,
sticky=Tkinter.NSEW)
row = row + 1
texts = ['Create']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
if self.numDim != None:
texts.append('Show all experiments')
commands.append(self.showAll)
buttons = createDismissHelpButtonList(parent,
texts=texts,
commands=commands,
dismiss_text='Skip',
help_url=self.help_url)
buttons.grid(row=row, column=0)
self.update()
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)
def body(self, master):
# Master is the owner widget (not self.parent) - parent of the widget here
#
# Popup window
#
self.entries = []
self.labels = []
value = 0
row = 0
label = Label(master, text="Window function:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
self.menuRow = row
self.menu = PulldownMenu(master,
entries=self.windowFuncList,
selected_index=self.winFuncIndex)
self.menu.grid(row=row, column=1, sticky=Tkinter.W, ipadx=20)
self.menulabel = Label(
master,
text="(" +
self.windowFunctions[self.format][self.winFuncIndex][1] + ")")
self.menulabel.grid(row=row, column=2, sticky=Tkinter.E)
#
# Setup arguments - make room for four
#
for argIndex in range(0, self.maxArgs):
row = row + 1
try:
argRef = self.windowFunctions[self.format][
self.winFuncIndex][2][argIndex]
argName = argRef[0]
argValue = argRef[1]
except:
argName = None
argValue = None
self.labels.append(Label(master, text="%s" % argName))
self.labels[-1].grid(row=row, column=0, sticky=Tkinter.EW)
self.entries.append(Entry(master, text=str(argValue)))
self.entries[-1].grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
if not argName:
self.labels[-1].grid_forget()
self.entries[-1].grid_forget()
#
# Add callback to menu after setup
#
self.menu.callback = self.updateWindow
row = row + 1
texts = ['OK']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def body(self, master):
self.geometry('700x500')
#
# Setup header
#
row = 0
label = Label(master, text='Original', width=10)
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master, text='Modify ChemCompVar', width=35)
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text='Status', width=20)
label.grid(row=row, column=2, sticky=Tkinter.EW)
label = Label(master, text='', width=5)
label.grid(row=row, column=3, sticky=Tkinter.EW)
row += 1
label = Label(master, text='code', width=10)
label.grid(row=row, column=0, sticky=Tkinter.EW)
label = Label(master,
text='ccpCode (molType): linking, descriptor',
width=35)
label.grid(row=row, column=1, sticky=Tkinter.EW)
label = Tkinter.Button(master,
text='Add new molecule',
command=self.addNewMolecule)
label.grid(row=row, column=2)
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=3, sticky=Tkinter.EW)
row += 1
# THIS BIT TELLS MASTER TO CONFIGURE WINDOW ON INSIDE WIDGET!!
master.grid_rowconfigure(row, weight=1)
for i in range(4):
master.grid_columnconfigure(i, weight=1)
self.sequenceFrame = ScrolledFrame(master,
width=70,
height=300,
doExtraConfig=False)
self.sequenceFrame.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.sequenceFrameRow = row
self.sequenceFrameMaster = master
row += 1
separator = Separator(master, height=3)
separator.setColor('black', bgColor='black')
separator.grid(row=row, columnspan=3, sticky=Tkinter.EW)
row += 1
texts = ['Change', 'Change and quit']
commands = [
self.updateMolDict, self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
self.setupSequenceFrame()