def __init__(self, parent, analysis, orientation='horizontal', callback = None, *args, **kw):
self.analysis = analysis
self.callback = callback
apply(Frame.__init__, (self, parent) + args, kw)
label = Label(self, text='Experiment:')
label.grid(row=0, column=0, sticky='ne')
self.expt_list = ExperimentList(self, self.analysis.getExperiments,
callback=self.setSpectra)
self.expt_list.grid(row=0, column=1, sticky='nw')
if orientation in ['horizontal','h','H',Tkinter.HORIZONTAL]:
row = 0
col = 2
else:
row = 1
col = 0
label = Label(self, text='Spectrum:')
label.grid(row=row, column=col, sticky='ne')
self.spectrum_list = SpectrumList(self, self.getSpectra,
callback=self.setSpectrumProperties)
self.spectrum_list.grid(row=row, column=col+1, sticky='nw')
for func in notify_funcs:
Implementation.registerNotify(self.setExperiments, 'ccp.nmr.Nmr.Experiment', func)
Implementation.registerNotify(self.setSpectra, 'ccp.nmr.Nmr.DataSource', func)
def registerNotify(self,
notify,
classname,
funcname='',
application=None,
keyword=None,
modifyList=True):
if application is None:
application = self.application
if self.application:
self.application.registerNotify(notify, classname, funcname,
keyword)
elif application:
Application.registerNotify(notify, classname, funcname,
application, keyword)
else:
Implementation.registerNotify(notify, classname, funcname)
if modifyList:
cc = self.notifies.get(classname)
if cc is None:
cc = self.notifies[classname] = {}
if application is None:
key = funcname
else:
key = (funcname, application, keyword)
ff = cc.get(key)
if ff is None:
ff = cc[key] = []
ff.append(notify)
def __init__(self, parent, getAxisUnits):
self.getAxisUnits = getAxisUnits
ScrolledListbox.__init__(self, parent, xscroll=False, selectmode=Tkinter.MULTIPLE)
for func in notify_funcs:
Implementation.registerNotify(self.setAxisUnits, 'ccpnmr.Analysis.AxisUnit', func)
def __init__(self, parent, getAxisUnits, *args, **kw):
self.getAxisUnits = getAxisUnits
PulldownMenu.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(self.setAxisUnits, 'ccpnmr.Analysis.AxisUnit', func)
def __init__(self, parent, getSpectra, extra_label = '', *args, **kw):
self.getSpectra = getSpectra
self.extra_label = extra_label
PulldownMenu.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(self.setSpectra, 'ccp.nmr.Nmr.DataSource', func)
def doRegisters(self):
try:
Implementation.registerNotify(self.updateAfter, self.refClassName,
'delete')
except AttributeError:
# refClassName may be an abstract class,
# in which case registering will fail
return
def __init__(self, parent, getPeakLists, extra_label = '', *args, **kw):
self.getPeakLists = getPeakLists
self.extra_label = extra_label
PulldownMenu.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(self.setPeakLists, 'ccp.nmr.Nmr.PeakList', func)
def __init__(self, parent, getChains, extra_label='', *args, **kw):
self.getChains = getChains
self.extra_label = extra_label
PulldownMenu.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(self.setChains,
'ccp.molecule.MolSystem.Chain', func)
def __init__(self, parent, getColors, extra_label='', *args, **kw):
self.getColors = getColors
self.extra_label = extra_label
PulldownList.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(self.setColors,
'ccpnmr.Analysis.Color', func)
self.setColors()
def registerNotify(notify, classname, funcname, application = None, keyword = None):
if application is None or keyword is None:
assert application is None and keyword is None, 'application = %s, keyword = %s, both must be None' % (application, keyword)
return GenImp.registerNotify(notify, classname, funcname)
if funcname not in allowedNotifyFuncs:
raise GenImp.ApiError('illegal funcname "%s", must be in %s' % (funcname, allowedNotifyFuncs))
notifies = GenImp.getClassFromFullName(classname)._notifies
notifies = notifies.setdefault((funcname, application, keyword), [])
notifies.append(notify)
def __init__(self, parent, getSpectrumViews, extra_label='', *args, **kw):
self.getSpectrumViews = getSpectrumViews
self.extra_label = extra_label
PulldownMenu.__init__(self, parent, *args, **kw)
for func in notify_funcs:
Implementation.registerNotify(
self.setSpectrumViews, 'ccpnmr.Analysis.SpectrumWindowView',
func)
Implementation.registerNotify(self.setSpectrumViews,
'ccp.nmr.Nmr.Experiment', 'setName')
Implementation.registerNotify(self.setSpectrumViews,
'ccp.nmr.Nmr.DataSource', 'setName')
def __init__(self, parent, analysis, callback=None, *args, **kw):
self.analysis = analysis
self.callback = callback
apply(Frame.__init__, (self, parent) + args, kw)
label = Label(self, text='Experiment:')
label.grid(row=0, column=0, sticky='ne')
self.expt_list = ExperimentList(self,
self.analysis.getExperiments,
callback=self.setSpectra)
self.expt_list.grid(row=0, column=1, sticky='nw')
label = Label(self, text='Spectrum:')
label.grid(row=0, column=2, sticky='ne')
self.spectrum_list = SpectrumList(self,
self.getSpectra,
callback=self.setPeakLists)
self.spectrum_list.grid(row=0, column=3, sticky='nw')
label = Label(self, text='PeakList:')
label.grid(row=0, column=4, sticky='ne')
self.peak_list_list = PeakListList(self,
self.getPeakLists,
callback=self.doCallback)
self.peak_list_list.grid(row=0, column=5, sticky='nw')
for func in notify_funcs:
Implementation.registerNotify(self.setExperiments,
'ccp.nmr.Nmr.Experiment', func)
Implementation.registerNotify(self.setSpectra,
'ccp.nmr.Nmr.DataSource', func)
if func != 'setName':
Implementation.registerNotify(self.setPeakLists,
'ccp.nmr.Nmr.PeakList', func)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def doRegisters(self):
Implementation.registerNotify(self.updateAfter, self.refClassName, 'delete')
def body(self, guiFrame):
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
guiFrame.grid_rowconfigure(row, weight=1)
frame = LabelFrame(guiFrame, text='Input constraints')
frame.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame.grid_columnconfigure(2, weight=1)
srow = 0
label = Label(frame, text='Constraint set:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.constraintSetPulldown = PulldownMenu(
frame,
callback=self.changeConstraintSet,
selected_index=0,
do_initial_callback=0)
self.constraintSetPulldown.grid(row=srow, column=1, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 1:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance1Pulldown = PulldownMenu(
frame,
callback=self.changeDistance1ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance1Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr1Label = Label(frame, text='Constraints: 0')
self.numConstr1Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 2:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance2Pulldown = PulldownMenu(
frame,
callback=self.changeDistance2ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance2Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr2Label = Label(frame, text='Constraints: 0')
self.numConstr2Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 3:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance3Pulldown = PulldownMenu(
frame,
callback=self.changeDistance3ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance3Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr3Label = Label(frame, text='Constraints: 0')
self.numConstr3Label.grid(row=srow, column=2, sticky=Tkinter.W)
srow += 1
label = Label(frame, text='Dist constraint list 4:')
label.grid(row=srow, column=0, sticky=Tkinter.W)
self.distance4Pulldown = PulldownMenu(
frame,
callback=self.changeDistance4ConstraintList,
selected_index=0,
do_initial_callback=0)
self.distance4Pulldown.grid(row=srow, column=1, sticky=Tkinter.W)
self.numConstr4Label = Label(frame, text='Constraints: 0')
self.numConstr4Label.grid(row=srow, column=2, sticky=Tkinter.W)
row += 1
frame0 = LabelFrame(guiFrame, text='Cooling scheme')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
frame0.grid_rowconfigure(f0row, weight=1)
colHeadings = [
'Step', 'Initial\nTemp.', 'Final\nTemp.', 'Cooling\nSteps',
'MD Steps', 'MD Tau', 'Rep.\nScale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame0,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f0row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame0,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f0row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = LabelFrame(guiFrame, text='Dynamics control')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(1, weight=1)
f1row = 0
label20 = Label(frame1, text='Number of clouds:')
label20.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = IntEntry(frame1,
text=1,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f1row, column=1, sticky=Tkinter.NW)
label21 = Label(frame1, text='Cloud file prefix:')
label21.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame1,
text='t_intra_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame1,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
for func in ('__init__', 'delete', 'setName'):
for clazz in ('ccp.nmr.NmrConstraint.DistanceConstraintList', ):
Implementation.registerNotify(self.updateConstraintLists,
clazz, func)
for func in ('__init__', 'delete'):
Implementation.registerNotify(
self.updateConstraintSets,
'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
