def __init__(self,
parent,
startUrlCallback=None,
endUrlCallback=None,
enterLinkCallback=None,
leaveLinkCallback=None,
*args,
**kw):
self.startUrlCallback = startUrlCallback
self.endUrlCallback = endUrlCallback
self.enterLinkCallback = enterLinkCallback
self.leaveLinkCallback = leaveLinkCallback
self.initTags()
self.protocol = ''
self.location = ''
self.path = ''
self.dir = ''
formatter.NullWriter.__init__(self)
self.formatter = formatter.AbstractFormatter(self)
htmllib.HTMLParser.__init__(self, self.formatter)
ScrolledText.__init__(self, parent, *args, **kw)
self.text_area.config(font=(font_family, default_size))
self.bind('<Enter>', lambda event: self.focus())
self.bind('<KeyPress-Prior>', lambda event: self.pageChange(-1))
self.bind('<KeyPress-Next>', lambda event: self.pageChange(1))
class TextOutputPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'TextOutput.html')
def __init__(self, parent, title='Text output'):
BasePopup.__init__(self,
parent=parent,
title=title,
modal=False,
transient=False)
def body(self, master):
self.text = ScrolledText(master)
self.text.pack(side=Tkinter.TOP, expand=Tkinter.YES, fill=Tkinter.BOTH)
texts = ['Save text']
commands = [self.saveText]
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.pack()
def saveText(self):
fileSelectPopup = FileSelectPopup(
self,
file_types=[
FileType('Text', ['*.txt', '*.out', '*.text']),
FileType('All', ['*'])
],
title='Select text output save file')
fileName = fileSelectPopup.getFile()
if fileName:
writeFile = 1
if os.path.exists(fileName):
if not showYesNo('Overwrite file',
'Overwrite existing file %s?' % fileName):
writeFile = 0
if writeFile:
fout = open(fileName, 'w')
fout.write(self.text.text_area.getText())
fout.close()
def apply(self):
return True
def body(self, master):
self.text = ScrolledText(master)
self.text.pack(side=Tkinter.TOP, expand=Tkinter.YES, fill=Tkinter.BOTH)
texts = ['Save text']
commands = [self.saveText]
buttons = createHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.pack()
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):
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)
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
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 __init__(self,
parent,
project,
closeButton=False,
tempFiles=False,
*args,
**kw):
###########################################################################
# INIT VARIABLES
self.parent = parent
self.project = project
try:
self.nmrProject = (project.currentNmrProject or
project.newNmrProject(name='BLACKLEDGE_MODULE'))
except:
print '&&& Running MODULE popup from outside CCPN Analysis - debug only - no NmrCalc'
self.nmrProject = None
if self.nmrProject:
self.calcStore = project.findFirstNmrCalcStore(name=MODULE, nmrProject=self.nmrProject) or \
project.newNmrCalcStore(name=MODULE, nmrProject=self.nmrProject)
else:
self.calcStore = None
self.run = None
self.inputStructure = None
self.inputRdcConstraintList = None
self.inputDistanceConstraintList = [None]
self.inputUserDescriptionText = None
# path to the module executable
modPath = subprocess.Popen(
['which', 'module'],
stdout=subprocess.PIPE).communicate()[0].strip()
self.moduleExePath = modPath or ' NB. MODULE executable not found '
self.waiting = False
# for debug this could be False
if tempFiles:
self.useTempFiles = True
else:
self.useTempFiles = False
# create temp files for MODULE
if self.useTempFiles:
self.moduleTempDir = tempfile.mkdtemp(prefix='MODULE-')
else:
self.moduleTempDir = os.getcwd()
#djo35# self.calcStore = self.resetCalcStore(name='BLACKLEDGE_MODULE')
# END INIT OF VARIABLES
###########################################################################
###########################################################################
# START GUI CODE
Frame.__init__(self, parent, *args, **kw)
self.expandGrid(0, 0)
## Single Frame
# frame = Frame(self, grid=(0,0))
# or with Tabs?
options = ['Launch', 'Output', 'Runs']
tabbedFrame = TabbedFrame(self, options=options, grid=(0, 0))
frameA, frameB, frameC = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
frameA.expandGrid(14, 2)
row = 0
div = LabelDivider(frameA,
text='MODULE Setup',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
# allow the user to choose MODULE if either the one in PATH is incorrect or not found
button = Button(frameA, text='Select MODULE executable:',bd=1, \
command=self.selectExecutable, grid=(row,0), sticky="ew")
self.moduleExeEntry = Entry(frameA, text=self.moduleExePath, grid=(row,1), gridSpan=(1,3), \
width=32, sticky="ew", bd=1)
self.moduleExePath = self.moduleExeEntry.get()
# separator "MODULE input"
row += 1
div = LabelDivider(frameA,
text='MODULE input',
grid=(row, 0),
gridSpan=(1, 5))
row += 1
label = Label(frameA, text='Structure:', grid=(row, 1))
self.inputStructurePulldown = PulldownList(frameA, self.changeInputStructure, \
grid=(row,2))
# self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
label = Label(frameA, text='RDC constraints:', grid=(row, 1))
self.inputRdcConstraintsPulldown = PulldownList(frameA, self.changeInputRdcConstraintList, \
grid=(row,2))
#self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
label = Label(frameA, text='(Optional input)', grid=(row, 0))
label = Label(frameA, text='Distance constraints:', \
grid=(row,1))
self.inputDistanceConstraintsPulldown = PulldownList(frameA, self.changeInputDistanceConstraintList, \
grid=(row,2))
#self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
subFrameDepth = 4
subframe = LabelFrame(frameA, text='MODULE User Notes (store notes about how MODULE was run here)', \
grid=(row,0), gridSpan=(1,4))
subframe.expandGrid(subFrameDepth, 0)
self.moduleUserText = ScrolledText(subframe)
self.moduleUserText.grid(row=subFrameDepth,
column=0,
columnspan=4,
sticky='nsew')
# View Results
row += subFrameDepth
# row += 1
# div = LabelDivider(frameA, text='MODULE launch', grid=(row,0), gridSpan=(1,4))
row += 1
button = Button(frameA, text='Run MODULE', bd=1, command=self.executeModule, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_GREEN)
# grid=(row,0), gridSpan=(1,2), sticky="ew", bg=MODULE_GREEN)
###########################################################################
# Frame B (tab 2) Ouput
frameB.expandGrid(4, 1)
row = 0
subFrameDepth = 6
subframe = LabelFrame(frameB, text='MODULE Output', \
grid=(row,0), gridSpan=(1,5))
#subframe.grid_columnconfigure(2, weight=1)
subframe.expandGrid(subFrameDepth, 0)
self.moduleOutputText = ScrolledText(subframe)
self.moduleOutputText.setState(state=Tkinter.DISABLED)
self.moduleOutputText.grid(row=subFrameDepth,
column=0,
columnspan=4,
sticky='nsew')
# separator "MODULE input"
row += 1
div = LabelDivider(frameB,
text='MODULE RDC Back Values',
grid=(row, 0),
gridSpan=(1, 5))
row += 1
button = Button(frameB, text='Import MODULE Back Values file', bd=1, command=self.importModuleBackValues, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_BLUE)
# grid=(row,0), gridSpan=(2,4), sticky="ew", bg=MODULE_BLUE)
row += 1
self.rdcOutputTable = None
frameB.grid_rowconfigure(row, weight=1)
headings = ('#', 'Resonances', 'Value', 'Back Value', 'Diff.', 'Error')
editWidgets = [None, None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None, None]
self.rdcOutputTable = ScrolledMatrix(frameB,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=4)
self.rdcOutputTable.grid(row=row,
column=0,
columnspan=4,
sticky='nsew')
row += 1
button = Button(frameB, text='Import MODULE Structure', bd=1, command=self.importModuleStructure, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_BLUE)
# grid=(row,0), gridSpan=(2,4), sticky="ew", bg=MODULE_BLUE)
###########################################################################
# Frame C (tab 3) NMR Calc display bits
frameC.expandGrid(4, 1)
row = 0
div = LabelDivider(frameC,
text='Stored MODULE Runs',
grid=(row, 0),
gridSpan=(1, 5))
# NmrCalc Run scrolled matrix
row += 1
self.runTable = None
frameC.grid_rowconfigure(row, weight=1)
headings = ('Run ID', 'notes', 'Status')
# self.editRunNotes = DataEntry.askString('Run Notes', 'Edit notes about Run', tipText='Notes about Run', parent=self)
# editWidgets = [None, self.editRunNotes, None]
editWidgets = [None, None, None]
editGetCallbacks = [None, None, None]
editSetCallbacks = [None, None, None]
self.runTable = ScrolledMatrix(frameC,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=4)
self.runTable.grid(row=row, column=0, columnspan=4, sticky='nsew')
row += 4
tipTexts = ['Load Selected Run', 'Delete Selected Run']
texts = ['Load Selected Run', 'Delete Selected']
commands = [self.loadRun, self.deleteRun]
colours = [MODULE_GREEN, MODULE_RED]
self.runButtons = ButtonList(frameC,
texts=texts,
tipTexts=tipTexts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 4))
self.runButtons.buttons[0].config(bg=MODULE_GREEN)
self.runButtons.buttons[1].config(bg=MODULE_RED)
###########################################################################
# Keep GUI up to date
self.updateAfter()
self.administerNotifiers(self.parent.registerNotify)
class BlackledgeModuleFrame(Frame):
""" Frame for handling MODULE calculation.
Note that the frame uses (or creates) an NmrCalcStore named 'BLACKLEDGE_MODULE'
and linked to the current NmrProject.
"""
def __init__(self,
parent,
project,
closeButton=False,
tempFiles=False,
*args,
**kw):
###########################################################################
# INIT VARIABLES
self.parent = parent
self.project = project
try:
self.nmrProject = (project.currentNmrProject or
project.newNmrProject(name='BLACKLEDGE_MODULE'))
except:
print '&&& Running MODULE popup from outside CCPN Analysis - debug only - no NmrCalc'
self.nmrProject = None
if self.nmrProject:
self.calcStore = project.findFirstNmrCalcStore(name=MODULE, nmrProject=self.nmrProject) or \
project.newNmrCalcStore(name=MODULE, nmrProject=self.nmrProject)
else:
self.calcStore = None
self.run = None
self.inputStructure = None
self.inputRdcConstraintList = None
self.inputDistanceConstraintList = [None]
self.inputUserDescriptionText = None
# path to the module executable
modPath = subprocess.Popen(
['which', 'module'],
stdout=subprocess.PIPE).communicate()[0].strip()
self.moduleExePath = modPath or ' NB. MODULE executable not found '
self.waiting = False
# for debug this could be False
if tempFiles:
self.useTempFiles = True
else:
self.useTempFiles = False
# create temp files for MODULE
if self.useTempFiles:
self.moduleTempDir = tempfile.mkdtemp(prefix='MODULE-')
else:
self.moduleTempDir = os.getcwd()
#djo35# self.calcStore = self.resetCalcStore(name='BLACKLEDGE_MODULE')
# END INIT OF VARIABLES
###########################################################################
###########################################################################
# START GUI CODE
Frame.__init__(self, parent, *args, **kw)
self.expandGrid(0, 0)
## Single Frame
# frame = Frame(self, grid=(0,0))
# or with Tabs?
options = ['Launch', 'Output', 'Runs']
tabbedFrame = TabbedFrame(self, options=options, grid=(0, 0))
frameA, frameB, frameC = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
frameA.expandGrid(14, 2)
row = 0
div = LabelDivider(frameA,
text='MODULE Setup',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
# allow the user to choose MODULE if either the one in PATH is incorrect or not found
button = Button(frameA, text='Select MODULE executable:',bd=1, \
command=self.selectExecutable, grid=(row,0), sticky="ew")
self.moduleExeEntry = Entry(frameA, text=self.moduleExePath, grid=(row,1), gridSpan=(1,3), \
width=32, sticky="ew", bd=1)
self.moduleExePath = self.moduleExeEntry.get()
# separator "MODULE input"
row += 1
div = LabelDivider(frameA,
text='MODULE input',
grid=(row, 0),
gridSpan=(1, 5))
row += 1
label = Label(frameA, text='Structure:', grid=(row, 1))
self.inputStructurePulldown = PulldownList(frameA, self.changeInputStructure, \
grid=(row,2))
# self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
label = Label(frameA, text='RDC constraints:', grid=(row, 1))
self.inputRdcConstraintsPulldown = PulldownList(frameA, self.changeInputRdcConstraintList, \
grid=(row,2))
#self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
label = Label(frameA, text='(Optional input)', grid=(row, 0))
label = Label(frameA, text='Distance constraints:', \
grid=(row,1))
self.inputDistanceConstraintsPulldown = PulldownList(frameA, self.changeInputDistanceConstraintList, \
grid=(row,2))
#self.constraintsFileEntry.bind('<Leave>', self.updateEntryParams)
row += 1
subFrameDepth = 4
subframe = LabelFrame(frameA, text='MODULE User Notes (store notes about how MODULE was run here)', \
grid=(row,0), gridSpan=(1,4))
subframe.expandGrid(subFrameDepth, 0)
self.moduleUserText = ScrolledText(subframe)
self.moduleUserText.grid(row=subFrameDepth,
column=0,
columnspan=4,
sticky='nsew')
# View Results
row += subFrameDepth
# row += 1
# div = LabelDivider(frameA, text='MODULE launch', grid=(row,0), gridSpan=(1,4))
row += 1
button = Button(frameA, text='Run MODULE', bd=1, command=self.executeModule, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_GREEN)
# grid=(row,0), gridSpan=(1,2), sticky="ew", bg=MODULE_GREEN)
###########################################################################
# Frame B (tab 2) Ouput
frameB.expandGrid(4, 1)
row = 0
subFrameDepth = 6
subframe = LabelFrame(frameB, text='MODULE Output', \
grid=(row,0), gridSpan=(1,5))
#subframe.grid_columnconfigure(2, weight=1)
subframe.expandGrid(subFrameDepth, 0)
self.moduleOutputText = ScrolledText(subframe)
self.moduleOutputText.setState(state=Tkinter.DISABLED)
self.moduleOutputText.grid(row=subFrameDepth,
column=0,
columnspan=4,
sticky='nsew')
# separator "MODULE input"
row += 1
div = LabelDivider(frameB,
text='MODULE RDC Back Values',
grid=(row, 0),
gridSpan=(1, 5))
row += 1
button = Button(frameB, text='Import MODULE Back Values file', bd=1, command=self.importModuleBackValues, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_BLUE)
# grid=(row,0), gridSpan=(2,4), sticky="ew", bg=MODULE_BLUE)
row += 1
self.rdcOutputTable = None
frameB.grid_rowconfigure(row, weight=1)
headings = ('#', 'Resonances', 'Value', 'Back Value', 'Diff.', 'Error')
editWidgets = [None, None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None, None]
self.rdcOutputTable = ScrolledMatrix(frameB,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=4)
self.rdcOutputTable.grid(row=row,
column=0,
columnspan=4,
sticky='nsew')
row += 1
button = Button(frameB, text='Import MODULE Structure', bd=1, command=self.importModuleStructure, \
grid=(row,0), gridSpan=(1,4), sticky="ew", bg=MODULE_BLUE)
# grid=(row,0), gridSpan=(2,4), sticky="ew", bg=MODULE_BLUE)
###########################################################################
# Frame C (tab 3) NMR Calc display bits
frameC.expandGrid(4, 1)
row = 0
div = LabelDivider(frameC,
text='Stored MODULE Runs',
grid=(row, 0),
gridSpan=(1, 5))
# NmrCalc Run scrolled matrix
row += 1
self.runTable = None
frameC.grid_rowconfigure(row, weight=1)
headings = ('Run ID', 'notes', 'Status')
# self.editRunNotes = DataEntry.askString('Run Notes', 'Edit notes about Run', tipText='Notes about Run', parent=self)
# editWidgets = [None, self.editRunNotes, None]
editWidgets = [None, None, None]
editGetCallbacks = [None, None, None]
editSetCallbacks = [None, None, None]
self.runTable = ScrolledMatrix(frameC,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=4)
self.runTable.grid(row=row, column=0, columnspan=4, sticky='nsew')
row += 4
tipTexts = ['Load Selected Run', 'Delete Selected Run']
texts = ['Load Selected Run', 'Delete Selected']
commands = [self.loadRun, self.deleteRun]
colours = [MODULE_GREEN, MODULE_RED]
self.runButtons = ButtonList(frameC,
texts=texts,
tipTexts=tipTexts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 4))
self.runButtons.buttons[0].config(bg=MODULE_GREEN)
self.runButtons.buttons[1].config(bg=MODULE_RED)
###########################################################################
# Keep GUI up to date
self.updateAfter()
self.administerNotifiers(self.parent.registerNotify)
# END GUI CODE
###########################################################################
###########################################################################
# FUNCTIONS CALLED FROM GUI
################
# OS interaction
def selectExecutable(self):
""" Choose the MODULE executable appropriate for your system. """
popup = FileSelectPopup(self, show_file=True)
executable = popup.getFile()
if executable:
self.moduleExeEntry.set(executable)
popup.destroy()
def executeModule(self):
""" Execute MODULE with all given parameters
Yeah it's a big function, bite me :-P
"""
# check that all params have been set
if not os.path.isfile(self.moduleExePath):
popup = showWarning('MODULE',
'Cannot find MODULE executable.',
parent=self)
return
if self.inputStructure is None:
popup = showWarning(
'MODULE',
'MODULE cannot run with out a structure for input.',
parent=self)
return
if self.inputRdcConstraintList is None:
popup = showWarning(
'MODULE',
'MODULE cannot run with out an RDC constraint list for input.',
parent=self)
return
# write temp PDB file
strucTempFile = tempfile.NamedTemporaryFile(mode='w',
suffix='.pdb',
dir=self.moduleTempDir,
delete=False)
strucTempFile.close()
makePdbFromStructure(strucTempFile.name,
self.inputStructure.structureEnsemble,
model=self.inputStructure)
# write temp RDC file
rdcTempFile = tempfile.NamedTemporaryFile(mode='w',
suffix='.tab',
dir=self.moduleTempDir,
delete=False)
moduleIo.writeConstraintList(rdcTempFile, self.inputRdcConstraintList)
rdcTempFile.close()
# command to be executed (to start MODULE)
moduleCommands = [
self.moduleExePath, strucTempFile.name, rdcTempFile.name
]
# if user has set Distance constraint list then fill add this (user optional)
if self.inputDistanceConstraintList:
distanceTempFile = tempfile.NamedTemporaryFile(
mode='w', suffix='.tab', dir=self.moduleTempDir, delete=False)
moduleIo.writeConstraintList(distanceTempFile,
self.inputDistanceConstraintList)
distanceTempFile.close()
moduleCommands.append(distanceTempFile.name)
# execute MODULE
moduleOutput = subprocess.Popen(
moduleCommands, stdout=subprocess.PIPE).communicate()[0]
# clean out the blank lines
for line in moduleOutput:
if line == '':
moduleOutput.pop(line)
# send the output to our screen
self.moduleOutputText.setState(state=Tkinter.NORMAL)
self.moduleOutputText.setText(text=moduleOutput)
self.moduleOutputText.setState(state=Tkinter.DISABLED)
# clean up temp files (delete has been set to False)
for tempFile in [strucTempFile.name, rdcTempFile.name]:
if os.path.isfile(tempFile):
os.unlink(tempFile)
if self.inputDistanceConstraintList:
if os.path.isfile(distanceTempFile.name):
os.unlink(distanceTempFile.name)
# create new run and store inputs
self.newRun()
self.updateRunInputs()
############################################################################
# Outputs:
############################
# Import MODULE PDB
def findModuleExportPdbFile(self):
""" Find the MODULE PDB export file, typically called temp%s.pdb
unless user has renamed it.
"""
modulePdbFileGood = False
def yes():
modulePdbFileGood = True
def cancel():
modulePdbFileGood = False
# MODULE writes pdb files to CWD no matter where you or it is
possibleFiles = glob.glob(os.path.join(os.getcwd(), 'temp*'))
# debug
# possibleFiles = glob.glob( os.path.join( os.getcwd(), 'module', 'temp*' ) )
if len(possibleFiles) == 1:
if os.path.isfile(possibleFiles[0]):
texts = ['Yes', 'No, choose another PDB file', 'Cancel']
objects = [yes, self.selectModulePdbExport, cancel]
func = showMulti('MODULE', 'Is this the PDB strcture you exported from MODULE?\n%s' % possibleFiles[0], \
texts=texts, objects=objects, parent=self)
func()
if modulePdbFileGood == True:
modulePdbFile = possibleFiles[0]
else:
return None
else:
modulePdbFile = self.selectModulePdbExport()
elif len(possibleFiles) > 1:
texts = ['%s' % fileName for fileName in possibleFiles]
objects = ['%s' % fileName for fileName in possibleFiles]
modulePdbFile = showMulti('MODULE', 'Multiple possible MODULE export\nfiles found, please select one:' % possibleFiles, \
texts=texts, objects=objects, parent=self)
if os.path.isfile(modulePdbFile):
modulePdbFile = modulePdbFile
else:
modulePdbFile = self.selectModulePdbExport()
return modulePdbFile
def selectModulePdbExport(self):
""" Choose the PDB file that was exported from MODULE. """
file_types = [
FileType("PDB structure files", ["*.pdb"]),
FileType("All files", ["*"])
]
popup = FileSelectPopup(self,
file_types,
dismiss_text='Cancel',
show_file=True)
chosenPdbFile = popup.getFile()
if os.path.isfile(chosenPdbFile):
modulePdbFile = chosenPdbFile
else:
warnPopup = showWarning('MODULE',
'File %s not found.' % chosenPdbFile,
parent=self)
return None
popup.destroy()
return modulePdbFile
def importModuleStructure(self):
""" Find MODULE structure file and import into Analysis (or attempt to, this will probably
barf as MODULE pdb files are not good)
"""
modulePdbFile = self.findModuleExportPdbFile()
if not modulePdbFile: return
# this stores the re-hacked MODULE pdb file and then removes it on close
tempPdb = tempfile.NamedTemporaryFile(mode='w',
suffix='.pdb',
dir=self.moduleTempDir,
delete=False)
tempPdb.close()
# if file found then add to project
if os.path.isfile(modulePdbFile):
moduleIo.BlackledgeToPdbConverter(modulePdbFile, tempPdb)
structure = getStructureFromFile(
self.inputStructure.parent.molSystem, tempPdb)
os.unlink(tempPdb)
############################
# Import MODULE Back Values
def findModuleExportBackValuesFile(self):
""" Find the Back Values file that the User hopefully exported from MODULE """
def yes():
moduleBvFileGood = True
def cancel():
moduleBvFileGood = False
# back value files are helpfully appended '*.back'
possibleFiles = glob.glob(os.path.join(os.getcwd(), '*.back'))
possibleFiles += glob.glob(os.path.join(self.moduleTempDir, '*.back'))
if len(possibleFiles) == 1:
if os.path.isfile(possibleFiles[0]):
texts = [
'Yes', 'No, choose another Back Values file', 'Cancel'
]
objects = [yes, self.selectModuleBvExport, cancel]
func = showMulti('MODULE', 'Is this the Back Values file that you exported from MODULE?\n%s' % possibleFiles[0], \
texts=texts, objects=objects, parent=self)
func()
if moduleBvFileGood == True:
moduleBackValueFile = possibleFiles[0]
else:
return None
else:
moduleBackValueFile = self.selectModuleBvExport()
elif len(possibleFiles) > 1:
texts = ['%s' % fileName for fileName in possibleFiles]
objects = ['%s' % fileName for fileName in possibleFiles]
chosenBvFile = showMulti('MODULE', 'Multiple possible MODULE Back Value\nfiles found, please select one:' % possibleFiles, \
texts=texts, objects=objects, parent=self)
if os.path.isfile(modulePdbFile):
moduleBackValueFile = chosenBvFile
else:
moduleBackValueFile = self.selectModuleBvExport()
return moduleBackValueFile
def selectModuleBvExport(self):
""" Choose the Back Value file that was exported from MODULE. """
file_types = [
FileType("Back Value files", ["*.back"]),
FileType("All files", ["*"])
]
popup = FileSelectPopup(self,
file_types,
dismiss_text='Cancel',
show_file=True)
chosenBvFile = popup.getFile()
if os.path.isfile(chosenBvFile):
moduleBackValueFile = chosenBvFile
else:
warnPopup = showWarning('MODULE',
'File %s not found.' % chosenBvFile,
parent=self)
return None
popup.destroy()
return moduleBackValueFile
def importModuleBackValues(self):
""" Attempt to find the Back Values file and then import it ... """
# find the Back Values file or ask user
backValFile = self.findModuleExportBackValuesFile()
if not backValFile: return
# create a new RDC list
if self.project:
nmrConstraintStore = self.project.newNmrConstraintStore(
nmrProject=self.project.findFirstNmrProject())
if self.inputStructure:
chain = self.inputStructure.parent.molSystem.findFirstChain()
else:
chain = None
if nmrConstraintStore and chain:
rdcList = moduleIo.getBackValuesListFromFile(
backValFile, chain, nmrConstraintStore)
# rdcRawData = moduleIo.getRawBackValuesFromFile( backValFile )
#
# for run in runs:
# runText.append( [run.getSerial(), run.getDetails(), run.getStatus()] )
self.rdcOutputTable.update(objectList=None, textMatrix=None)
# end OS interaction
####################
##################################
# get, set and update menu options
def changeInputRun(self, run):
self.run = run
def changeInputStructure(self, structure):
self.inputStructure = structure
def changeInputRdcConstraintList(self, constraintList):
self.inputRdcConstraintList = constraintList
def changeInputDistanceConstraintList(self, constraintList):
self.inputDistanceConstraintList = constraintList
def changeInputConstraintList(self, constraintList, className):
if className == 'RdcConstraintList':
self.changeInputRdcConstraintList(constraintList)
elif className == 'DistanceConstraintList':
self.changeInputDistanceConstraintList(constraintList)
def getInputConstraintList(self, className):
if className == 'RdcConstraintList':
return self.inputRdcConstraintList
elif className == 'DistanceConstraintList':
return self.inputDistanceConstraintList
# end get and set
##################################
####################
# NMR Calc runs etc.
def loadRun(self):
pass
def deleteRun(self):
pass
def changeRun(self):
pass
def newRun(self):
if self.calcStore:
self.run = self.calcStore.newRun(status='provisional')
def updateRunInputs(self, event=None):
self.inputUserDescriptionText = self.moduleUserText.getText() or None
# store input parameters in run
if self.run:
# set the path to the MODULE executable used
setRunTextParameter(self.run, MODULE_EXE, self.moduleExePath)
# set the input structure sent to MODULE
sEnsemble = self.inputStructure.StructureEnsemble
self.run.newStructureEnsembleData(sEnsemble.ensembleId,
sEnsemble.molSystem.code,
name=STRUCTURE_DATA,
ioRole=INPUT)
# set the input RDC constraint list
rdcConst = self.inputRdcConstraintList
self.run.newConstraintStoreData(rdcConst.nmrConstraintStore.serial,
name=RDC_CONSTRAINT_DATA,
ioRole=INPUT)
# set the input RDC constraint list (optional)
distConst = self.inputDistanceConstraintList
if distConst:
self.run.newConstraintStoreData(
distConst.nmrConstraintStore.serial,
name=DIST_CONSTRAINT_DATA,
ioRole=INPUT)
# set the input user data (if any)
setRunTextParameter(self.run, USER_DESCRIPTION_DATA,
self.inputUserDescriptionText)
def editRunNotes(self):
pass
# end NMR calc stuff
####################
######################
# update and noitfiers
def administerNotifiers(self, notifyFunc):
for func in ['__init__', 'delete']:
for clazz in ['RdcConstraintList', 'DistanceConstraintList']:
notifyFunc(self.updateAfter, 'ccp.nmr.NmrConstraint.' + clazz,
func)
notifyFunc(self.updateAfter, 'ccp.nmr.NmrCalc.Run', func)
def destroy(self):
self.administerNotifiers(self.parent.unregisterNotify)
Frame.destroy(self)
def updateAll(self):
# tab A
self.updateModuleExecutablePath()
self.updateInputStructure()
self.updateInputRdcConstraintList()
self.updateInputDistanceConstraintList()
# tab C
self.updateInputRuns()
self.waiting = False
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateAll)
def updateInputRuns(self):
if self.calcStore:
runs = [
r for r in self.calcStore.sortedRuns()
if r.status == PROVISIONAL
]
if not runs:
self.newRun()
runs = [self.run]
runText = []
for run in runs:
runText.append(
[run.getSerial(),
run.getDetails(),
run.getStatus()])
self.runTable.update(objectList=runs, textMatrix=runText)
def updateModuleExecutablePath(self):
self.moduleExePath = self.moduleExeEntry.get()
def updateInputStructure(self):
index = None
# names = ['<None>']
# structures = [None]
names = []
structures = []
for molSystem in self.project.sortedMolSystems():
for ensemble in molSystem.sortedStructureEnsembles():
for structure in ensemble.sortedModels():
structures.append(structure)
if structures:
for i, model in enumerate(structures):
if model is None: continue
ee = model.structureEnsemble
name = '%s:%d:%d' % (ee.molSystem.code, ee.ensembleId,
model.serial)
names.append(name)
if self.inputStructure not in structures:
self.changeInputStructure(structures[0])
index = structures.index(self.inputStructure)
else:
self.inputStructure = None
self.inputStructurePulldown.setup(names, structures, index or -1)
def updateInputConstraintList(self, className, obj=None):
index = None
# if DistanceConstraintList then None must be an option
# names = ['<None>']
# constraintLists = [None]
if className == 'DistanceConstraintList':
names = ['<None>']
constraintLists = [None]
else:
names = []
constraintLists = []
for nmrConstraintStore in self.parent.project.sortedNmrConstraintStores(
):
for constraintList in nmrConstraintStore.sortedConstraintLists():
if not className or constraintList.className == className:
constraintLists.append(constraintList)
if constraintLists:
for constList in constraintLists:
if constList is None: continue
store = constList.nmrConstraintStore
name = '%d:%d' % (store.serial, constList.serial)
names.append(name)
if self.getInputConstraintList(className) not in constraintLists:
self.changeInputConstraintList(constraintLists[0], className)
index = constraintLists.index(
self.getInputConstraintList(className))
else:
self.changeInputConstraintList(None, className)
if className == 'RdcConstraintList':
self.inputRdcConstraintsPulldown.setup(names, constraintLists,
index or -1)
elif className == 'DistanceConstraintList':
self.inputDistanceConstraintsPulldown.setup(
names, constraintLists, index or -1)
def updateInputRdcConstraintList(self):
self.updateInputConstraintList('RdcConstraintList')
def updateInputDistanceConstraintList(self):
self.updateInputConstraintList('DistanceConstraintList')
def __init__(self, parent, project, closeButton=False, *args, **kw):
self.parent = parent
self.project = project
self.nmrProject = (project.currentNmrProject
or project.newNmrProject(name='PALES'))
self.calcStore = None
self.run = None
self.inpStructure = None
self.inpConstraintList = None
self.workingDir = None
self.waiting = False
self.palesMode = None
self.resetCalcStore()
Frame.__init__(self, parent, *args, **kw)
self.expandGrid(0, 0)
options = ['Input Data', 'Extra Input', 'View Results']
tabbedFrame = TabbedFrame(self, options=options, grid=(0, 0))
frameA, frameX, frameB = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
label = Label(tabbedFrame.sideFrame,
text='Run Number:',
grid=(0, 0),
sticky='e')
tipText = 'Selects which calculation job or "run" is currently being viewed or edited'
self.runPulldown = PulldownList(tabbedFrame.sideFrame,
callback=self.changeRun,
grid=(0, 1),
sticky='e',
tipText=tipText)
tipTexts = ['Delete the current calculation run settings']
texts = ['Delete Run']
commands = [self.deleteRun]
if closeButton:
ButtonListClass = UtilityButtonList
else:
ButtonListClass = ButtonList
runButtons = ButtonListClass(tabbedFrame.sideFrame,
texts=texts,
tipTexts=tipTexts,
commands=commands,
sticky='e',
grid=(0, 2))
# Input data
frameA.expandGrid(2, 1)
row = 0
label = Label(frameA, text='Pales mode:', grid=(row, 0), sticky='w')
self.palesModePulldown = PulldownList(frameA,
callback=self.changePalesMode,
grid=(row, 1))
tipTexts = [
'Make a setup for a new calculation run',
'Make a new calculation run by copying the current one',
]
texts = ['New Run', 'Copy Run']
commands = [self.newRun, self.copyRun]
if closeButton:
ButtonListClass = UtilityButtonList
else:
ButtonListClass = ButtonList
runButtons = ButtonList(frameA,
texts=texts,
tipTexts=tipTexts,
commands=commands,
sticky='e',
grid=(row, 2))
runButtons.buttons[0].config(bg='#B0FFB0')
row += 1
subframe1 = LabelFrame(frameA,
text='Description',
grid=(row, 0),
gridSpan=(1, 3))
subframe1.expandGrid(0, 1)
self.modeDescription = Label(subframe1, grid=(row, 0), sticky='w')
row += 1
# setup generic table headings, justification and widget getters/setters
self.inputMatrix = GenericDataMatrix(frameA, progParameters)
self.inputMatrix.grid(row=row, column=0, columnspan=3, sticky='nsew')
row += 1
label = Label(frameA, text='Comments:', grid=(row, 0))
self.detailsEntryIn = Entry(frameA,
grid=(row, 1),
gridSpan=(1, 2),
sticky="ew")
self.detailsEntryIn.bind('<Leave>', self.changeDetailsIn)
row += 1
button = Button(frameA,
text='Select working dir:',
bd=1,
command=self.selectWorkingDir,
grid=(row, 0),
sticky="ew")
self.workingDirEntry = Entry(frameA,
text='.',
grid=(row, 1),
gridSpan=(1, 2),
width=48,
sticky="ew",
bd=1)
row += 1
button = Button(frameA,
text='Execute Pales:',
bd=1,
command=self.executePales,
grid=(row, 0),
gridSpan=(1, 3),
sticky="new")
# Extra input
# setup generic table headings, justification and widget getters/setters
frameX.expandGrid(0, 0)
self.extraInputMatrix = GenericDataMatrix(frameX, progParameters)
self.extraInputMatrix.grid(row=0, column=0, sticky='nsew')
# View Results
frameB.expandGrid(7, 1)
row = 0
subframe1 = LabelFrame(frameB,
text='Command Options:',
grid=(row, 0),
gridSpan=(1, 4))
# gridSpan=(1,2))
subframe1.expandGrid(0, 1)
self.palesOptionsLabel = Label(subframe1, grid=(row, 0), sticky='w')
row += 1
div = LabelDivider(frameB, text='Data', grid=(row, 0), gridSpan=(1, 4))
row += 1
self.outputMatrix = GenericDataMatrix(frameB,
progParameters,
initialRows=4)
self.outputMatrix.grid(row=0, column=0, sticky='nsew')
self.outputMatrix.grid(row=row,
column=0,
columnspan=(4),
sticky='nsew')
row += 1
button = Button(frameB,
text='View Selected',
bd=1,
command=self.viewPalesData,
grid=(row, 0),
gridSpan=(1, 4),
sticky="ew")
row += 1
label = Label(frameB, text='Comments:', grid=(row, 0), sticky="w")
self.detailsEntry = Entry(frameB,
grid=(row, 1),
gridSpan=(1, 3),
sticky="ew")
self.detailsEntry.bind('<Leave>', self.changeDetails)
row += 1
subframe2 = LabelFrame(frameB,
text='Calculated Order Matrix:',
grid=(row, 0),
gridSpan=(1, 4))
#subframe2.grid_columnconfigure(5, weight=1)
subframe2.expandGrid(1, 5)
label = Label(subframe2, text='Daxial', grid=(0, 0), sticky='ew')
label = Label(subframe2, text='Drhombic', grid=(0, 1), sticky='ew')
label = Label(subframe2, text='Psi', grid=(0, 2), sticky='ew')
label = Label(subframe2, text='Phi', grid=(0, 3), sticky='ew')
label = Label(subframe2, text='Theta', grid=(0, 4), sticky='ew')
self.outputTensorLabels = ll = []
for ii in range(5):
label = Label(subframe2, text='<None>', grid=(1, ii), sticky='ew')
ll.append(label)
row += 1
div = LabelDivider(frameB,
text='Program Output',
grid=(row, 0),
gridSpan=(1, 4),
sticky='sew')
#textFrame1 = LabelFrame(frameB, text='Pales Output File', grid=(5,0),
# gridSpan=(1,6), sticky='nsew')
#textFrame1.expandGrid(0,0)
row += 1
self.palesOutputText = ScrolledText(frameB, xscroll=False)
self.palesOutputText.grid(row=row,
column=0,
columnspan=4,
sticky='nsew')
self.updateAfter()
self.administerNotifiers(self.parent.registerNotify)
class PalesFrame(Frame):
""" Frame for handling PALES calculation.
Note that the frame uses (or creates) an NmrCalcStore named 'PALES'
and linked to the current NmrProject.
"""
def __init__(self, parent, project, closeButton=False, *args, **kw):
self.parent = parent
self.project = project
self.nmrProject = (project.currentNmrProject
or project.newNmrProject(name='PALES'))
self.calcStore = None
self.run = None
self.inpStructure = None
self.inpConstraintList = None
self.workingDir = None
self.waiting = False
self.palesMode = None
self.resetCalcStore()
Frame.__init__(self, parent, *args, **kw)
self.expandGrid(0, 0)
options = ['Input Data', 'Extra Input', 'View Results']
tabbedFrame = TabbedFrame(self, options=options, grid=(0, 0))
frameA, frameX, frameB = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
label = Label(tabbedFrame.sideFrame,
text='Run Number:',
grid=(0, 0),
sticky='e')
tipText = 'Selects which calculation job or "run" is currently being viewed or edited'
self.runPulldown = PulldownList(tabbedFrame.sideFrame,
callback=self.changeRun,
grid=(0, 1),
sticky='e',
tipText=tipText)
tipTexts = ['Delete the current calculation run settings']
texts = ['Delete Run']
commands = [self.deleteRun]
if closeButton:
ButtonListClass = UtilityButtonList
else:
ButtonListClass = ButtonList
runButtons = ButtonListClass(tabbedFrame.sideFrame,
texts=texts,
tipTexts=tipTexts,
commands=commands,
sticky='e',
grid=(0, 2))
# Input data
frameA.expandGrid(2, 1)
row = 0
label = Label(frameA, text='Pales mode:', grid=(row, 0), sticky='w')
self.palesModePulldown = PulldownList(frameA,
callback=self.changePalesMode,
grid=(row, 1))
tipTexts = [
'Make a setup for a new calculation run',
'Make a new calculation run by copying the current one',
]
texts = ['New Run', 'Copy Run']
commands = [self.newRun, self.copyRun]
if closeButton:
ButtonListClass = UtilityButtonList
else:
ButtonListClass = ButtonList
runButtons = ButtonList(frameA,
texts=texts,
tipTexts=tipTexts,
commands=commands,
sticky='e',
grid=(row, 2))
runButtons.buttons[0].config(bg='#B0FFB0')
row += 1
subframe1 = LabelFrame(frameA,
text='Description',
grid=(row, 0),
gridSpan=(1, 3))
subframe1.expandGrid(0, 1)
self.modeDescription = Label(subframe1, grid=(row, 0), sticky='w')
row += 1
# setup generic table headings, justification and widget getters/setters
self.inputMatrix = GenericDataMatrix(frameA, progParameters)
self.inputMatrix.grid(row=row, column=0, columnspan=3, sticky='nsew')
row += 1
label = Label(frameA, text='Comments:', grid=(row, 0))
self.detailsEntryIn = Entry(frameA,
grid=(row, 1),
gridSpan=(1, 2),
sticky="ew")
self.detailsEntryIn.bind('<Leave>', self.changeDetailsIn)
row += 1
button = Button(frameA,
text='Select working dir:',
bd=1,
command=self.selectWorkingDir,
grid=(row, 0),
sticky="ew")
self.workingDirEntry = Entry(frameA,
text='.',
grid=(row, 1),
gridSpan=(1, 2),
width=48,
sticky="ew",
bd=1)
row += 1
button = Button(frameA,
text='Execute Pales:',
bd=1,
command=self.executePales,
grid=(row, 0),
gridSpan=(1, 3),
sticky="new")
# Extra input
# setup generic table headings, justification and widget getters/setters
frameX.expandGrid(0, 0)
self.extraInputMatrix = GenericDataMatrix(frameX, progParameters)
self.extraInputMatrix.grid(row=0, column=0, sticky='nsew')
# View Results
frameB.expandGrid(7, 1)
row = 0
subframe1 = LabelFrame(frameB,
text='Command Options:',
grid=(row, 0),
gridSpan=(1, 4))
# gridSpan=(1,2))
subframe1.expandGrid(0, 1)
self.palesOptionsLabel = Label(subframe1, grid=(row, 0), sticky='w')
row += 1
div = LabelDivider(frameB, text='Data', grid=(row, 0), gridSpan=(1, 4))
row += 1
self.outputMatrix = GenericDataMatrix(frameB,
progParameters,
initialRows=4)
self.outputMatrix.grid(row=0, column=0, sticky='nsew')
self.outputMatrix.grid(row=row,
column=0,
columnspan=(4),
sticky='nsew')
row += 1
button = Button(frameB,
text='View Selected',
bd=1,
command=self.viewPalesData,
grid=(row, 0),
gridSpan=(1, 4),
sticky="ew")
row += 1
label = Label(frameB, text='Comments:', grid=(row, 0), sticky="w")
self.detailsEntry = Entry(frameB,
grid=(row, 1),
gridSpan=(1, 3),
sticky="ew")
self.detailsEntry.bind('<Leave>', self.changeDetails)
row += 1
subframe2 = LabelFrame(frameB,
text='Calculated Order Matrix:',
grid=(row, 0),
gridSpan=(1, 4))
#subframe2.grid_columnconfigure(5, weight=1)
subframe2.expandGrid(1, 5)
label = Label(subframe2, text='Daxial', grid=(0, 0), sticky='ew')
label = Label(subframe2, text='Drhombic', grid=(0, 1), sticky='ew')
label = Label(subframe2, text='Psi', grid=(0, 2), sticky='ew')
label = Label(subframe2, text='Phi', grid=(0, 3), sticky='ew')
label = Label(subframe2, text='Theta', grid=(0, 4), sticky='ew')
self.outputTensorLabels = ll = []
for ii in range(5):
label = Label(subframe2, text='<None>', grid=(1, ii), sticky='ew')
ll.append(label)
row += 1
div = LabelDivider(frameB,
text='Program Output',
grid=(row, 0),
gridSpan=(1, 4),
sticky='sew')
#textFrame1 = LabelFrame(frameB, text='Pales Output File', grid=(5,0),
# gridSpan=(1,6), sticky='nsew')
#textFrame1.expandGrid(0,0)
row += 1
self.palesOutputText = ScrolledText(frameB, xscroll=False)
self.palesOutputText.grid(row=row,
column=0,
columnspan=4,
sticky='nsew')
self.updateAfter()
self.administerNotifiers(self.parent.registerNotify)
def updatePalesOptions(self):
palesMode = self.palesMode
dd = palesModes.get(palesMode)
# NBNB TBD
def resetCalcStore(self, calcStore=None):
""" Reset self.calcStore if missing or deleted
"""
if calcStore is None or calcStore is self.calcStore:
nmrProject = self.nmrProject
calcStore = self.project.findFirstNmrCalcStore(
nmrProject=nmrProject, name='PALES')
if calcStore is None:
calcStore = self.project.newNmrCalcStore(
nmrProject=self.nmrProject, name='PALES')
if self.calcStore is not calcStore:
self.calcStore = calcStore
if self.run is not None:
self.run = None
self.updateAfter()
def selectWorkingDir(self):
popup = FileSelectPopup(self, show_file=False)
directory = popup.getDirectory()
if directory:
self.workingDirEntry.set(directory)
popup.destroy()
self.updateAfter()
def changeDetails(self, event):
if self.run:
value = self.detailsEntry.get().strip() or None
if value != self.run.details:
self.run.details = value
def changeDetailsIn(self, event):
if self.run:
value = self.detailsEntryIn.get().strip() or None
if value != self.run.details:
self.run.details = value
def updateDetails(self):
if self.run:
text = self.run.details
else:
text = ''
self.detailsEntry.set(text)
self.detailsEntryIn.set(text)
def changePalesMode(self, mode):
if mode and (mode is not self.palesMode):
run = self.run
if runIsEditable(run):
palesModeObj = run.findFirstRunParameter(name='Pales Mode')
if palesModeObj is None:
palesModeObj = run.newRunParameter(name='Pales Mode',
ioRole='input')
palesModeObj.textValue = mode
self.palesMode = mode
self.initialiseRun()
self.updateAfter()
def updatePalesModes(self, obj=None):
names = []
index = 0
modes = []
for tag in palesModeList:
modeInfo = palesModes[tag]
names.append(modeInfo['text'])
modes.append(tag)
if obj is not None:
mode = obj
else:
mode = self.palesMode
try:
index = modes.index(mode)
except ValueError:
index = 0
self.palesMode = modes[index]
self.palesModePulldown.setup(names, modes, index)
tag = modes[index]
self.modeDescription.set(palesModes[tag].get('info'))
def copyRun(self):
# TBD: Inputs only?
if self.run:
self.configure(cursor="watch")
run = copySubTree(self.run, self.calcStore)
run.status = 'provisional'
# remove output
for data in run.findAllData(ioRole='output'):
data.delete()
for parObj in run.findAllRunParameters(ioRole='output'):
parObj.delete()
self.run = run
self.updateAfter()
self.after_idle(lambda: self.configure(cursor=""))
def newRun(self):
if self.calcStore:
self.run = self.calcStore.newRun(status='provisional')
self.initialiseRun()
self.updateAfter()
def initialiseRun(self):
""" Create objects for known parameters
"""
print '### initialiseRun', self.run and runIsEditable(self.run)
run = self.run
if run is None or not runIsEditable(run):
return
# set up
tag = self.palesMode
modeData = palesModes[tag]
currentTags = set(modeData['fixedpar'] + modeData['mandatories'] +
modeData['optionals'])
# set palesMode if missing
self.updatePalesModes()
# remove parameters no longer needed
for obj in run.runParameters:
if obj.name not in currentTags:
obj.delete()
for obj in run.data:
if obj.name not in currentTags:
obj.delete()
self.inputMatrix.updateGeneric(run=run,
paramList=(modeData['fixedpar'] +
modeData['mandatories']))
self.extraInputMatrix.updateGeneric(run=run,
paramList=modeData['optionals'])
for ii, name in enumerate(modeData['fixedpar']):
value = modeData['fixedvalues'][ii]
code, parType, default, info = progParameters[name]
self.inputMatrix.setupRunObject(run,
name,
code,
parType,
default,
info,
value=value)
def getPalesOptions(self):
run = self.run
if run is None:
return
palesMode = self.palesMode
return 'NBNB TBD'
def changeRun(self, run):
print '### changeRun', self.run, run
if run and (run is not self.run):
self.run = run
self.updateAfter()
def deleteRun(self):
if self.run:
msg = 'Really delete calculation run %d?' % self.run.serial
if showOkCancel('Query', msg, parent=self):
self.run.delete()
self.run = None
self.updateAfter()
def updateRunsAfter(self, obj=None):
print '### updateRunsAfter', obj, self.waiting
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateRuns)
def updateRunDataAfter(self, obj=None):
print '### updateRunDataAfter', obj
if obj is None:
run = None
else:
run = obj.run
self.updateRunAfter(run=run)
def updateRunAfter(self, run=None):
""" update all if run is curent run, otherwise update run pulldown only
"""
print '### updateRunAfter', run, self.waiting
if self.waiting:
return
elif run is None:
return
elif run is self.run:
self.waiting = True
self.after_idle(self.update)
else:
self.waiting = True
self.after_idle(self.updateRuns)
def updateAfter(self, obj=None):
if self.waiting:
return
self.waiting = True
self.configure(cursor="watch")
self.after_idle(self.update)
def updateRuns(self, run=None):
""" Update run pulldown only
"""
print '### updateRuns', run
names = []
index = 0
runs = []
run = self.run
if self.calcStore is None or self.calcStore.isDeleted:
self.resetCalcStore()
runs = self.calcStore.sortedRuns()
if runs:
if run not in runs:
run = runs[-1]
index = runs.index(run)
names = []
for r in runs:
if runIsEditable(r):
names.append('%d' % r.serial)
else:
names.append('%d (uneditable)' % r.serial)
else:
run = None
if run is not self.run:
self.changeRun(run)
print '###', names, runs, index
self.runPulldown.setup(names, runs, index)
self.waiting = False
def update(self, obj=None):
print '### update', self.run
self.updateRuns(obj)
run = self.run
if run is None:
palesMode = self.palesMode = None
self.palesOptionsLabel.set('')
for label in self.outputTensorLabels:
label.set('<None>')
self.palesOutputText.setText()
else:
# Pales command NBNB TBD
#valueObj = run.findFirstRunParameter(code='command')
#if valueObj is None:
# self.palesCommandLabel.set('')
#else:
# self.palesCommandLabel.set(valueObj.textValue)
palesModeObj = run.findFirstRunParameter(ioRole='input',
name='Pales Mode')
if palesModeObj is None:
palesMode = None
else:
palesMode = palesModeObj.textValue
# Output orientation matrix
keywords = ('dAxialOut', 'dRhombicOut', 'psiOut', 'phiOut',
'thetaOut')
for ii, label in enumerate(self.outputTensorLabels):
keyword = keywords[ii]
valueObj = run.findFirstRunParameter(code=keyword,
ioRole='output')
if valueObj is None:
label.set('<None>')
else:
label.set(valueObj.floatValue)
# Pales output text
valueObj = run.findFirstRunParameter(ioRole='output',
name='Output Text')
if valueObj:
self.palesOutputText.setText(valueObj.textValue)
else:
self.palesOutputText.setText()
self.updatePalesModes(palesMode)
self.palesOptionsLabel.set(self.getPalesOptions())
#self.updateInputMatrix()
#self.updateExtraInputMatrix()
#self.updateOutputMatrix()
self.inputMatrix.updateGeneric()
self.extraInputMatrix.updateGeneric()
self.outputMatrix.updateGeneric()
self.updateDetails()
self.after_idle(lambda: self.configure(cursor=""))
self.waiting = False
def administerNotifiers(self, notifyFunc):
notifyFunc(self.updateRunsAfter, 'ccp.nmr.NmrCalc.NmrCalcStore',
'delete')
notifyFunc(self.updateRunsAfter, 'ccp.nmr.NmrCalc.Run', '__init__')
notifyFunc(self.updateRunAfter, 'ccp.nmr.NmrCalc.Run', 'delete')
notifyFunc(self.updateRunAfter, 'ccp.nmr.NmrCalc.Run', 'setDetails')
NC = 'ccp.nmr.NmrCalc.'
nmrCalcClasses = [
'RunParameter',
'EnergyTerm',
'ConstraintStoreData',
'ViolationListData',
'MolSystemData',
'MolResidueData',
'SpectrumData',
'PeakListData',
'SpinSystemData',
'StructureEnsembleData',
'ExternalData',
'FloatMatrixData',
'TensorData',
'MeasurementListData',
'DerivedListData',
]
for clazz in nmrCalcClasses:
notifyFunc(self.updateRunDataAfter, NC + clazz, '')
def destroy(self):
self.administerNotifiers(self.parent.unregisterNotify)
Frame.destroy(self)
def executePales(self):
# NBNB TBD
pass
def viewPalesData(self):
# NBNB TBD
valueObj = self.outputMatrix
if isinstance(valueObj, NmrCalc.ExternalData):
dataStore = valueObj.dataStore
if dataStore is not None:
wb = WebBrowser(self, name='PalesData')
wb.open(dataStore.fullPath)
elif isinstance(valueObj, NmrCalc.MeasurementListData):
mm = valueObj.measurementList
if mm is not None:
popup = self.parent.editMeasurementLists()
popup.tabbedFrame.select(1)
popup.setMeasurementList(mm)
elif isinstance(valueObj, NmrCalc.StructureEnsembleData):
models = valueObj.models
if len(models) == 1:
popup = self.parent.editStructures()
popup.tabbedFrame.select(3)
popup.changeModel(models[0])
popup.changeTab(3)
elif isinstance(valueObj, NmrCalc.ConstraintStoreData):
constraintLists = valueObj.constraintLists
if len(constraintLists) == 1:
popup = self.parent.browseConstraints()
popup.tabbedFrame.select(2)
popup.changeRestraintList(constraintLists[0])
