class LabeledEntry(Frame):
def __init__(self,
parent,
label,
entry='',
separator=': ',
label_width=20,
entry_width=60,
label_anchor=Tkinter.E,
show='',
returnCallback=None,
tipText=None,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
self.separator = separator
text = label + separator
self.label = Label(self,
text=text,
width=label_width,
anchor=label_anchor)
self.label.grid(row=0, column=0, sticky=Tkinter.EW)
self.entry = Entry(self,
show=show,
width=entry_width,
returnCallback=returnCallback,
tipText=tipText)
self.entry.insert(0, entry)
self.entry.grid(row=0, column=1, sticky=Tkinter.EW)
def getLabel(self):
text = self.label.get()
n = text.find(self.separator)
if (n >= 0):
text = text[:n]
return text
def setLabel(self, text=''):
text = text + self.separator
self.label.set(text)
def getEntry(self):
return self.entry.get()
def setEntry(self, text=''):
self.entry.set(text)
class NewWindowPopup(BasePopup):
"""
**Create New Windows to Display Spectra**
This tool is used to make new windows for the graphical display of spectra,
which will usually be as contours. It is notable that some spectrum windows
will be made automatically when spectra are loaded if there is no existing
appropriate window to display a spectrum. However, making new spectrum windows
allows the user to specialise different windows for different tasks and gives
complete freedom as to which types of axis go in which direction. For example
the user may wish to make a new window so that a spectrum can be viewed from
an orthogonal, rotated aspect.
A new spectrum window is made by first considering whether it is similar to
any existing windows. If so, then the user selects the appropriate template
window to base the new one upon. The user then chooses a name for the window
via the "New window name" field, although the name may be changed after the
window is created. Usually the user does not need to consider the "Strips"
section, but if required the new window can be created with starting strips
and orthogonal sub-divisions (although these are not permanent). After setting
the required axes and spectrum visibility, as described below, the user clicks
on [Create Window!] to actually make the new spectrum display window.
**Axes**
The number and type of axes for the new window are chosen using the pulldown
menus in the "Axes" section. The idea is that the user chooses which NMR
isotopes should appear on the X, Y, & Z axes. Naturally, X and Y axes must
always be set to something, to represent the plane of the screen, but the Z
axes are optional. If not required, a Z axis may be set to "None" to indicate
that it will not be used. Up to four Z axes may be specified, labelled as
"z1", "z2" etc., and these represent extra dimensions orthogonal to the plane
of the screen, which are often conceptualised as depth axes.
It should be noted that the Y axis type may be set to "value", which refers to
a spectrum intensity axis, rather than an NMR isotope axis. Setting the Y axis
to "value" and only having the X axis set to an isotope is used to create
windows that can show 1D spectra. Such value axes can also be used for 2D and
higher dimensionality spectra, to show the data as an intensity graph (a
"slice") rather than as contours.
**Spectra**
The lower "Viewed Spectra" section lists all of the spectra within the project
that may be shown by a window with the selected axes. All spectra with
isotopes in their data dimensions that match the isotope types of the window
axes can potentially be displayed. This system also allows for displayed
spectra to have fewer dimensions than the axes has windows, as long as at
least the X and Y axes are present. For example a 2D H-N spectrum can be
shown in a 3D H-N-H window, but not a 3D H-H-N.
For spectra that have more than one data dimension of the same isotope, then
which data dimension goes with which window axis is not always known to
Analysis. Where there is ambiguity, this system will simply map the spectrum
data dimensions in order to the next matching window axis. If this mapping
turns out to be wrong, then it may be changed at any time via the main
_Windows settings; toggling the "Dim. Mapping" of the "Spectrum & Peak List
Mappings" tab.
For the spectra listed in the lower table, which may be placed in the new
window, the user has control over whether the spectra actually will appear.
Firstly the user can change the "Visible?" column, either via a double-click
or by using the appropriate lower buttons. By default spectra are set as not
being visible in new windows, and the user toggles the ones that should be
seen to "Yes". This basic spectrum visibility can readily be changed by the
toggle buttons that appear in the "toolbar" at the top of the spectrum
display, so the "Visible?" setting here is only about what initially appears.
The "In Toolbar?" setting of a spectrum is a way of allowing the user to state
that a spectrum should never appear in the window, and not even allow it to be
toggled on later via the toolbar at the top of the windows. This is a way of
reducing clutter, and allows certain windows to be used for particular subsets
of spectra. For example the user may wish to put the spectra for a temperature
series in one window, but not in other windows used for resonance assignment
where they would get in the way. The "In Toolbar" setting can be changed
after a window has been made, but only via the main Windows_ settings popup.
.. _Windows: EditWindowPopup.html
"""
def __init__(self, parent, *args, **kw):
self.visibleSpectra = parent.visibleSpectra
self.toolbarSpectra = parent.toolbarSpectra
self.waiting = False
self.window = None
BasePopup.__init__(self,
parent=parent,
title='Window : New Window',
**kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(2, weight=1)
row = 0
label = Label(guiFrame, text='Template window: ', grid=(row, 0))
tipText = 'Selects which window to use as the basis for making a new spectrum window; sets the axis types accordingly'
self.window_list = PulldownList(guiFrame,
grid=(row, 1),
callback=self.setAxisTypes,
tipText=tipText)
frame = LabelFrame(guiFrame,
text='Strips',
grid=(row, 2),
gridSpan=(2, 1))
buttons = UtilityButtonList(guiFrame,
doClone=False,
helpUrl=self.help_url,
grid=(row, 3))
row += 1
label = Label(guiFrame, text='New window name: ', grid=(row, 0))
tipText = 'A short name to identify the spectrum window, which will appear in the graphical interface'
self.nameEntry = Entry(guiFrame,
width=16,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(frame, text='Columns: ', grid=(0, 0))
tipText = 'The number of vertical strips/dividers to initially make in the spectrum window'
self.cols_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 1),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
label = Label(frame, text='Rows: ', grid=(0, 2))
tipText = 'The number of horizontal strips/dividers to initially make in the spectrum window'
self.rows_menu = PulldownList(frame,
objects=STRIP_NUMS,
grid=(0, 3),
texts=[str(x) for x in STRIP_NUMS],
tipText=tipText)
row += 1
div = LabelDivider(guiFrame,
text='Axes',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
self.axis_lists = {}
frame = Frame(guiFrame, grid=(row, 0), gridSpan=(1, 4))
col = 0
self.axisTypes = {}
self.axisTypesIncludeNone = {}
for label in AXIS_LABELS:
self.axisTypes[label] = None
w = Label(frame, text=' ' + label)
w.grid(row=0, column=col, sticky='w')
col += 1
if label in ('x', 'y'):
includeNone = False
tipText = 'Sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
else:
includeNone = True
tipText = 'Where required, sets the kind of measurement (typically ppm for a given isotope) that will be used along the window %s axis' % label
self.axisTypesIncludeNone[label] = includeNone
getAxisTypes = lambda label=label: self.getAxisTypes(label)
callback = lambda axisType, label=label: self.changedAxisType(
label, axisType)
self.axis_lists[label] = PulldownList(frame,
callback=callback,
tipText=tipText)
self.axis_lists[label].grid(row=0, column=col, sticky='w')
col += 1
frame.grid_columnconfigure(col, weight=1)
row += 1
div = LabelDivider(guiFrame,
text='Viewed Spectra',
grid=(row, 0),
gridSpan=(1, 4))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleVisible, self.toggleToolbar, None]
editSetCallbacks = [None, None, None, None]
tipTexts = [
'The "experiment:spectrum" name for the spectrum that may be viewed in the new window, given the axis selections',
'Sets whether the spectrum contours will be visible in the new window',
'Sets whether the spectrum appears at all in the window; if not in the toolbar it cannot be displayed',
'The number of peak lists the spectrum contains'
]
headingList = ['Spectrum', 'Visible?', 'In Toolbar?', 'Peak Lists']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
multiSelect=True,
grid=(row, 0),
gridSpan=(1, 4),
tipTexts=tipTexts)
row += 1
tipTexts = [
'Creates a new spectrum window with the specified parameters',
'Sets the contours of the selected spectra to be visible when the new window is made',
'Sets the contours of the selected spectra to not be displayed when the new window is made',
'Sets the selected spectra as absent from the window toolbar, and thus not displayable at all'
]
texts = [
'Create Window!', 'Selected\nVisible', 'Selected\nNot Visible',
'Selected\nNot In Toolbar'
]
commands = [
self.ok, self.setSelectedDisplay, self.setSelectedHide,
self.setSelectedAbsent
]
buttonList = ButtonList(guiFrame,
texts=texts,
grid=(row, 0),
commands=commands,
gridSpan=(1, 4),
tipTexts=tipTexts)
buttonList.buttons[0].config(bg='#B0FFB0')
self.updateAxisTypes()
self.updateWindow()
self.updateWindowName()
self.administerNotifiers(self.registerNotify)
self.updateAfter()
def administerNotifiers(self, notifyFunc):
self.registerNotify(self.updateWindowName,
'ccpnmr.Analysis.SpectrumWindow', '__init__')
for clazz in ('ccp.nmr.Nmr.Experiment', 'ccp.nmr.Nmr.DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAfter, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
for func in ('__init__', 'delete', 'setName', 'addSpectrumWindowGroup',
'removeSpectrumWindowGroup', 'setSpectrumWindowGroups'):
notifyFunc(self.updateWindow, 'ccpnmr.Analysis.SpectrumWindow',
func)
for func in ('addSpectrumWindow', 'removeSpectrumWindow',
'setSpectrumWindows'):
notifyFunc(self.updateWindow,
'ccpnmr.Analysis.SpectrumWindowGroup', func)
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAxisTypes, 'ccpnmr.Analysis.AxisType', func)
# Set visible contours, on commit, according to selection
# Get hold of spectrumWindowView ASAP
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def getSpectra(self):
spectrumIsotopes = {}
spectra = []
for experiment in self.nmrProject.sortedExperiments():
name = experiment.name
for spectrum in experiment.sortedDataSources():
spectrumIsotopes[spectrum] = []
spectra.append(['%s:%s' % (name, spectrum.name), spectrum])
for dataDim in spectrum.dataDims:
dimTypes = []
if dataDim.className != 'SampledDataDim':
for dataDimRef in dataDim.dataDimRefs:
expDimRef = dataDimRef.expDimRef
isotopes = set()
for isotopeCode in expDimRef.isotopeCodes:
isotopes.add(isotopeCode)
dimTypes.append(
(expDimRef.measurementType.lower(), isotopes))
else:
dimTypes.append('sampled')
spectrumIsotopes[spectrum].append(dimTypes)
axisIsotopes = {}
for label in AXIS_LABELS:
if label not in ('x', 'y'):
if self.axis_lists[label].getSelectedIndex() == 0:
continue
axisType = self.axis_lists[label].getObject()
axisIsotopes[label] = (axisType.measurementType.lower(),
set(axisType.isotopeCodes))
spectraSel = []
axes = axisIsotopes.keys()
axes.sort()
for name, spectrum in spectra:
dimIsotopes = spectrumIsotopes[spectrum]
for label in axes:
mType, selected = axisIsotopes[label]
if label == 'y' and mType == 'none':
continue # value axis
for i, dimTypes in enumerate(dimIsotopes):
for dimType in dimTypes:
if dimType == 'sampled':
if label != 'z1':
continue
axisType = self.axis_lists[label].getObject()
if axisType.name != 'sampled':
continue
dimIsotopes.pop(i)
break
else:
measurementType, isotopes = dimType
if (mType == measurementType) and (selected <=
isotopes):
dimIsotopes.pop(i)
break
else:
continue
break
else:
if label in ('x', 'y'):
break
else:
if not dimIsotopes:
spectraSel.append([name, spectrum])
return spectraSel
def setSelectedAbsent(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = False
self.toolbarSpectra[spectrum] = False
self.updateAfter()
def setSelectedDisplay(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = True
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def setSelectedHide(self):
for spectrum in self.scrolledMatrix.currentObjects:
self.visibleSpectra[spectrum] = False
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def toggleToolbar(self, spectrum):
boolean = not self.toolbarSpectra.get(spectrum, True)
self.toolbarSpectra[spectrum] = boolean
if boolean is False:
self.visibleSpectra[spectrum] = False
self.updateAfter()
def toggleVisible(self, spectrum):
boolean = not self.visibleSpectra.get(spectrum, False)
self.visibleSpectra[spectrum] = boolean
if boolean:
if not self.toolbarSpectra.get(spectrum, True):
self.toolbarSpectra[spectrum] = True
self.updateAfter()
def updateAfter(self, object=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self):
for spectrum in self.visibleSpectra.keys():
if spectrum.isDeleted:
del self.visibleSpectra[spectrum]
textMatrix = []
objectList = []
colorMatrix = []
for name, spectrum in self.getSpectra():
colours = [None, None, None, None]
if self.visibleSpectra.get(spectrum):
colours[0] = '#60F060'
isVisible = 'Yes'
self.visibleSpectra[
spectrum] = True # do not need this but play safe in case above if changed
else:
isVisible = 'No'
self.visibleSpectra[spectrum] = False
if self.toolbarSpectra.get(spectrum, True):
inToolbar = 'Yes'
self.toolbarSpectra[spectrum] = True
else:
colours[0] = '#600000'
inToolbar = 'No'
self.toolbarSpectra[spectrum] = False
datum = [
name, isVisible, inToolbar,
','.join(['%d' % pl.serial for pl in spectrum.peakLists])
]
textMatrix.append(datum)
objectList.append(spectrum)
colorMatrix.append(colours)
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
self.waiting = False
def updateAxisTypes(self, *extra):
for label in AXIS_LABELS:
names = []
objects = []
includeNone = self.axisTypesIncludeNone[label]
if includeNone:
names.append('None')
objects.append(None)
axisType = self.axisTypes[label]
axisTypes = self.getAxisTypes(label)
objects.extend(axisTypes)
if axisTypes:
if axisType not in objects:
axisType = objects[0]
index = objects.index(axisType)
names.extend([x.name for x in axisTypes])
else:
index = 0
self.axis_lists[label].setup(names, objects, index)
self.changedAxisType(label, axisType)
def changedAxisType(self, label, axisType):
if axisType is not self.axisTypes[label]:
self.axisTypes[label] = axisType
self.updateAfter()
def updateWindow(self, *extra):
window = self.window
windows = self.parent.getWindows()
if windows:
if window not in windows:
window = windows[0]
index = windows.index(window)
names = [x.name for x in windows]
else:
index = 0
names = []
self.window_list.setup(names, windows, index)
self.setAxisTypes(window)
def updateWindowName(self, *extra):
self.nameEntry.set(WindowBasic.defaultWindowName(self.project))
def getAxisTypes(self, label):
axisTypes = self.parent.getAxisTypes()
if label == 'z1':
axisTypes = [
axisType for axisType in axisTypes
if axisType.name == 'sampled' or not axisType.isSampled
]
else:
axisTypes = [
axisType for axisType in axisTypes if not axisType.isSampled
]
if label != 'y':
axisTypes = [
at for at in axisTypes
if at.name != WindowBasic.VALUE_AXIS_NAME
]
return axisTypes
def setAxisTypes(self, window):
project = self.project
if not project:
return
if window is self.window:
return
self.window = window
if window:
windowPanes = window.sortedSpectrumWindowPanes()
if windowPanes:
# might be empty because notifier called before windowPanes set up
windowPane = windowPanes[0]
for label in AXIS_LABELS:
axisPanel = windowPane.findFirstAxisPanel(label=label)
if axisPanel and axisPanel.panelType \
and axisPanel.panelType.axisType:
self.axis_lists[label].setSelected(
axisPanel.panelType.axisType)
elif label not in ('x', 'y'):
self.axis_lists[label].setIndex(0)
self.updateAfter()
def apply(self):
project = self.project
if not project:
return False
name = self.nameEntry.get().strip()
if not name:
showError('No name', 'Need to enter name', parent=self)
return False
names = [
window.name for window in self.analysisProject.spectrumWindows
]
if (name in names):
showError('Repeated name', 'Name already used', parent=self)
return False
axisTypes = []
for label in AXIS_LABELS:
if label not in ('x', 'y'):
if self.axis_lists[label].getSelectedIndex() == 0:
continue
axisType = self.axis_lists[label].getObject()
axisTypes.append(axisType)
ncols = self.cols_menu.getObject()
nrows = self.rows_menu.getObject()
window = WindowBasic.createSpectrumWindow(project,
name, [
axisTypes,
],
ncols=ncols,
nrows=nrows)
return True
class CreatePanelTypePopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.axisType = None
BasePopup.__init__(self,
parent=parent,
title='Create panel type',
modal=True,
**kw)
def body(self, master):
master.grid_columnconfigure(1, weight=1)
row = 0
label = Label(master, text='Panel name: ', grid=(row, 0))
tipText = 'Short text name for the new axis panel, e.g. "N2"'
self.name_entry = Entry(master,
width=15,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(master, text='Axis type:', grid=(row, 0))
tipText = 'The type of axis (isotope, time, sampled etc.) represented by panel type'
self.types_list = PulldownList(master, grid=(row, 1), tipText=tipText)
row += 1
tipTexts = [
'Create a new panel type object with the selected options & close the popup'
]
texts = ['Create']
commands = [self.ok]
buttons = UtilityButtonList(master,
texts=texts,
commands=commands,
doClone=False,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
master.grid_rowconfigure(row, weight=1)
self.administerNotifiers(self.registerNotify)
self.update()
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.update, 'ccpnmr.Analysis.AxisType', func)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def update(self, *extra):
axisType = self.axisType
axisTypes = self.parent.getAxisTypes()
names = [x.name for x in axisTypes]
if axisTypes:
if axisType not in axisTypes:
self.axisType = axisType = axisTypes[0]
index = axisTypes.index(axisType)
else:
index = 0
self.axisType = None
self.types_list.setup(names, axisTypes, index)
def apply(self):
name = self.name_entry.get()
if not name:
showError('No name', 'Need to enter name', parent=self)
return False
names = [
panelType.name for panelType in self.analysisProject.panelTypes
]
if name in names:
showError('Repeated name', 'Name already used', parent=self)
return False
axisType = self.types_list.getObject()
if not axisType:
showError('No axis type', 'Need to create axis type', parent=self)
return False
self.analysisProject.newPanelType(name=name, axisType=axisType)
return True
class 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 EditPeakPopup(BasePopup):
"""
**Edit Position, Intensity & Details for a Peak**
This popup window provides an means of editing peak information as an
alternative to editing values in the main peak tables. This popup is also used
to specify parameters for when a new peak is explicitly added to a peak list
using a tabular display.
The user can specify the position of the peak's dimensions in ppm, Hz or data
point units. Also, the user can adjust the height and volume peak intensity
values and a textual "Details" field, ,which can carry the user's comments
about the peak.
When editing an existing peak, no changes are made to the peak until the
[Update] button is pressed. Likewise for a new peak the [Add Peak] button
commits the changes. If the popup window is closed before the changes are
committed then the entire editing or peak addition operation is cancelled.
"""
def __init__(self, parent, peak=None, peakList=None, *args, **kw):
self.titleColor = '#000080'
self.numDims = 0
self.peak = peak
kw['borderwidth'] = 6
BasePopup.__init__(self, parent=parent, title='Edit Peak', **kw)
self.registerNotify(self.deletedPeak, 'ccp.nmr.Nmr.Peak', 'delete')
for func in ('setAnnotation', 'setDetails', 'setFigOfMerit'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.Peak', func)
for func in ('setAnnotation', 'setPosition', 'setNumAliasing'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakDim', func)
for func in ('__init__', 'delete', 'setValue'):
self.registerNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakIntensity',
func)
self.dimensionLabels = []
self.dimensionEntries = []
self.update(self.peak, peakList)
def body(self, guiParent):
self.geometry("+150+150")
guiParent.grid_columnconfigure(0, weight=1)
self.master_frame = guiParent
units = ('ppm', 'point', 'Hz')
self.unit = 'ppm'
self.specLabel = Label(guiParent,
fg=self.titleColor,
grid=(0, 0),
sticky='ew')
self.peakLabel = Label(guiParent, grid=(0, 1), sticky='ew')
self.unit_frame = frame = Frame(guiParent,
grid=(1, 1),
gridSpan=(1, 2))
self.unitLabel = Label(frame, text='Current units: ', grid=(0, 0))
tipText = 'Selects which unit of measurement to display peak dimension positions with'
self.unitSelect = PulldownList(frame,
callback=self.changeUnit,
texts=units,
grid=(0, 1),
tipText=tipText)
self.heightLabel = Label(guiParent,
text='Height',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak height; the value of the spectrum point intensity (albeit often interpolated)'
self.heightEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.volumeLabel = Label(guiParent,
text='Volume',
borderwidth=2,
relief='groove')
tipText = 'Sets the peak volume integral; normally a summation of data point values'
self.volumeEntry = FloatEntry(guiParent,
borderwidth=1,
tipText=tipText)
self.detailLabel = Label(guiParent,
text='Details',
borderwidth=2,
relief='groove')
tipText = 'A user-configurable textual comment for the peak, which appears an tables and occasionally on spectrum displays'
self.detailEntry = Entry(guiParent, borderwidth=1, tipText=tipText)
tipTexts = [
'Commits the specified values to update the peak and closes the popup',
]
texts = ['Update']
commands = [self.commit]
self.buttons = UtilityButtonList(guiParent,
texts=texts,
commands=commands,
doClone=False,
helpUrl=self.help_url,
tipTexts=tipTexts)
def open(self):
self.updatePeak()
BasePopup.open(self)
def updatePeak(self, object=None):
peak = None
if object:
if object.className == 'Peak':
peak = object
elif object.className == 'PeakDim':
peak = object.peak
elif object.className == 'PeakIntensity':
peak = object.peak
if (peak is None) or (peak is self.peak):
self.update(peak=self.peak)
def update(self, peak=None, peakList=None):
# first destroy old labels and entries (saves grid hassles)
for label in self.dimensionLabels:
label.destroy()
for entry in self.dimensionEntries:
entry.destroy()
# now setup required data
if peak:
title = 'Edit Peak'
self.buttons.buttons[0].config(text='Update')
else:
title = 'Add Peak'
self.buttons.buttons[0].config(text='Add Peak')
self.setTitle(title)
self.peak = peak
self.peakList = peakList
if not peakList:
if peak:
self.peakList = peak.peakList
else:
return
peakList = self.peakList
spectrum = peakList.dataSource.name
self.numDims = peakList.dataSource.numDim
self.posn = self.numDims * [0]
self.dataDims = peakList.dataSource.sortedDataDims()
if self.peak:
serial = self.peak.serial
dims = self.peak.sortedPeakDims()
details = self.peak.details
if not details:
details = ''
if self.peak.annotation:
annotn = '%0.16s' % self.peak.annotation
else:
annotn = ''
heightIntensity = self.peak.findFirstPeakIntensity(
intensityType='height')
volumeIntensity = self.peak.findFirstPeakIntensity(
intensityType='volume')
if heightIntensity:
height = heightIntensity.value
else:
height = 0.0
if volumeIntensity:
volume = volumeIntensity.value
else:
volume = 0.0
for i in range(self.numDims):
peakDim = dims[i]
dataDimRef = peakDim.dataDimRef
if dataDimRef:
self.posn[i] = peakDim.position + (
peakDim.numAliasing * dataDimRef.dataDim.numPointsOrig)
else:
self.posn[i] = peakDim.position
else:
dict = peakList.__dict__.get('serialDict')
if dict is None:
serial = 1
else:
serial = dict.get('peaks', 0) + 1
height = 0.0
volume = 0.0
details = ''
annotn = ''
self.specLabel.set(
text='Experiment: %s Spectrum: %s PeakList: %d' %
(peakList.dataSource.experiment.name, spectrum, peakList.serial))
self.peakLabel.set(text='Peak: %d' % serial)
self.dimensionLabels = self.numDims * ['']
self.dimensionEntries = self.numDims * ['']
for i in range(self.numDims):
pos = self.posn[i]
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
pos = unit_converter[('point', self.unit)](
pos, getPrimaryDataDimRef(dataDim))
self.dimensionLabels[i] = Label(self.master_frame,
text='F%d' % (i + 1),
borderwidth=2,
relief='groove')
tipText = 'The peak position in dimension %d, in the specified units' % (
i + 1)
self.dimensionEntries[i] = FloatEntry(self.master_frame,
borderwidth=1,
text='%8.4f' % pos,
tipText=tipText)
self.heightEntry.set(text='%f' % height)
self.volumeEntry.set(text='%f' % volume)
self.detailEntry.set(text=details)
row = 0
self.specLabel.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
self.peakLabel.grid(row=row, column=0, sticky='nsew')
self.unit_frame.grid(row=row, column=1, columnspan=2, sticky='nsew')
for i in range(self.numDims):
row = row + 1
self.dimensionLabels[i].grid(row=row, column=0, sticky='nsew')
self.dimensionEntries[i].grid(row=row,
column=1,
columnspan=3,
sticky='e')
row = row + 1
self.heightLabel.grid(row=row, column=0, sticky='nsew')
self.heightEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.volumeLabel.grid(row=row, column=0, sticky='nsew')
self.volumeEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.detailLabel.grid(row=row, column=0, sticky='nsew')
self.detailEntry.grid(row=row, column=1, columnspan=3, sticky='e')
row = row + 1
self.buttons.grid(row=row, column=0, columnspan=4, sticky='nsew')
def changeUnit(self, unit):
posDisp = self.numDims * [None]
for i in range(self.numDims):
posDisp[i] = float(self.dimensionEntries[i].get())
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
posDisp[i] = unit_converter[(self.unit, 'point')](
posDisp[i], getPrimaryDataDimRef(dataDim))
self.unit = unit
if self.unit != 'point':
for i in range(self.numDims):
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
posDisp[i] = unit_converter[('point', self.unit)](
posDisp[i], getPrimaryDataDimRef(dataDim))
for i in range(self.numDims):
value = posDisp[i]
if value is None:
self.dimensionEntries[i].set('None')
else:
self.dimensionEntries[i].set('%8.4f' % posDisp[i])
def commit(self):
posDisp = self.numDims * [0]
for i in range(self.numDims):
posDisp[i] = float(self.dimensionEntries[i].get())
if self.unit != 'point':
dataDim = self.dataDims[i]
if dataDim.className == 'FreqDataDim':
self.posn[i] = unit_converter[(self.unit, 'point')](
posDisp[i], getPrimaryDataDimRef(dataDim))
else:
self.posn[i] = posDisp[i]
if self.peak:
movePeak(self.peak, self.posn)
else:
self.peak = pickPeak(self.peakList, self.posn)
height = self.heightEntry.get()
volume = self.volumeEntry.get()
setManualPeakIntensity(self.peak, height, intensityType='height')
setManualPeakIntensity(self.peak, volume, intensityType='volume')
details = self.detailEntry.get() or None
self.peak.setDetails(details)
self.close()
def deletedPeak(self, peak):
if self.peak is peak:
self.close()
def destroy(self):
self.unregisterNotify(self.deletedPeak, 'ccp.nmr.Nmr.Peak', 'delete')
for func in ('setAnnotation', 'setDetails', 'setFigOfMerit'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.Peak', func)
for func in ('setAnnotation', 'setPosition', 'setNumAliasing'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakDim', func)
for func in ('__init__', 'delete', 'setValue'):
self.unregisterNotify(self.updatePeak, 'ccp.nmr.Nmr.PeakIntensity',
func)
BasePopup.destroy(self)
class OpenMacroPopup(BasePopup):
"""
**Locate Python Macro Scripts On Disk**
This popup is used to locate a Python file and function definition on disk
so that it can be loaded into Analysis as a "Macro". The top table
is a file browser that the user can navigate to the location of the Python
file (typically sending in ".py"). When a Python file is selected in the
upper table the system will look through the contents of the file to find
any macro functions that are defined within. Note that a macro function
is defined by the normal Python "def" keyword but must take "argSever"
as its first input argument.
Any macro functions in the selected file will be displayed in the
lower table. Clicking on the name of a function in this table
selects it for opening. The user may edit the name of the macro for
display purposes within Analysis. Finally clicking [Load Macro]
will add it to the CCPN project, stored in a user-specific way
inside the current Analysis profile. Once loaded into the
project the new macro will appear in the main macro table
(the "Macros" tab of `User Options`_)
.. _`User Options`: EditProfilesPopup.html
"""
def __init__(self, parent, **kw):
# TBD: properly
transient = True
BasePopup.__init__(self, parent=parent, title='Open macro', transient=transient, **kw)
def body(self, guiParent):
guiParent.grid_columnconfigure(1,weight=1)
row = 0
file_types = [ FileType('Python', ['*.py']), FileType('All', ['*']) ]
self.file_select = FileSelect(guiParent, file_types=file_types,
single_callback=self.chooseFile,
double_callback=self.chooseFile)
self.file_select.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
headingList=('Function',)
self.scrolledMatrix = ScrolledMatrix(guiParent, initialRows=4,
headingList=headingList, callback=self.selectFunction)
self.scrolledMatrix.grid(row=row, column=0, columnspan=2, sticky='nsew')
guiParent.grid_rowconfigure(row,weight=1)
row = row + 1
self.moduleLabel1 = Label(guiParent, text='Module: ')
self.moduleLabel1.grid(row=row, column=0, sticky='nw')
self.moduleLabel2 = Label(guiParent, text=' ')
self.moduleLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.functionLabel1 = Label(guiParent, text='Function: ')
self.functionLabel1.grid(row=row, column=0, sticky='nw')
self.functionLabel2 = Label(guiParent, text=' ')
self.functionLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.nameLabel = Label(guiParent, text='Name: ')
self.nameLabel.grid(row=row, column=0, sticky='nw')
self.nameEntry = Entry(guiParent, text=' ', width=40)
self.nameEntry.grid(row=row, column=1, sticky='nw')
row = row + 1
texts = [ 'Load Macro' ]
commands = [ self.loadMacro ]
buttons = UtilityButtonList(guiParent, texts=texts,
commands=commands, helpUrl=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.loadButton = buttons.buttons[0]
self.loadButton.disable()
self.path = None
self.module = None
self.function = None
def selectFunction(self, function, row, col):
if function:
self.loadButton.enable()
self.function = function
self.functionLabel2.set(function)
self.nameEntry.set(function)
def updateFunctions(self, file):
self.loadButton.disable()
functions = []
fileHandle = open(file, 'r')
line = fileHandle.readline()
textMatrix = []
while line :
match = re.match('\s*def\s+(\w+)\s*\(.*argServer',line)
if match:
function = match.group(1)
functions.append(function)
textMatrix.append( [function,] )
line = fileHandle.readline()
self.scrolledMatrix.update(objectList=functions,textMatrix=textMatrix)
def chooseFile(self, file):
fullPath =self.file_select.getFile()
if not os.path.isdir(fullPath) and file:
(self.path, module) = splitPath(fullPath)
module = re.sub('\..+?$','',module)
self.module = module
self.moduleLabel2.set(module)
self.updateFunctions(file)
def loadMacro(self):
if self.module and self.function and self.path:
name = self.nameEntry.get()
if not name:
name = self.function
analysisProfile = self.analysisProfile
m1 = analysisProfile.newMacro(name=name,path=self.path,
function=self.function,
module=self.module,ordering=1)
self.close()
class TableExportPopup(BasePopup):
def __init__(self,
parent,
headings,
entries,
title='',
file='',
*args,
**kw):
headings = [heading.replace('\n', ' ') for heading in headings]
if (headings[0].lower() == 'number'):
self.addNumber = False
else:
self.addNumber = True
headings.insert(0, 'Number')
if (not title):
title = 'Export data'
self.exportSelection = parent.tableExportSelection
self.headings = headings
self.entries = entries
self.file = file
kw['title'] = title
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def body(self, master):
master.grid_columnconfigure(2, weight=1)
row = 0
label = Label(master, text='Data to export:')
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.check_buttons = {}
i = 0
for heading in self.headings:
row = row + 1
isSelected = self.exportSelection.get(row, True)
self.check_buttons[i] = c = CheckButton(
master, selected=isSelected, callback=self.toggleCheckButton)
c.grid(row=row, column=1)
label = Label(master, text=heading)
label.grid(row=row, column=2, sticky=Tkinter.W)
i += 1
row = row + 1
button = Button(master, text='File:', command=self.findFile)
button.grid(row=row, column=0, sticky=Tkinter.W)
self.file_entry = Entry(master, text=self.file, width=30)
self.file_entry.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Format:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.format_menu = PulldownMenu(master, entries=exportFormats)
self.format_menu.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
master.grid_rowconfigure(row, weight=1)
texts = ['Save']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def toggleCheckButton(self, isSelected):
for i in self.check_buttons.keys():
self.exportSelection[i] = self.check_buttons[i].get()
def apply(self):
file = self.file_entry.get()
format = self.format_menu.getSelected()
join = exportJoin[format]
n = 0
headings = []
for heading in self.headings:
if self.check_buttons[n].get():
headings.append(n)
n += 1
if (not headings):
showError('Nothing selected',
'No data selected to export.',
parent=self)
return False
try:
fp = open(file, 'w')
except IOError, e:
showError('File error', str(e))
return False
for n in headings:
if (n != headings[0]):
fp.write(join)
fp.write(self.headings[n].encode('utf-8'))
fp.write('\n')
m = 0
for data in self.entries:
if data:
for n in headings:
if (n != headings[0]):
fp.write(join)
if (self.addNumber):
if (n == 0):
x = m + 1
else:
x = data[n - 1]
else:
x = data[n]
if (type(x) == type(float(1))):
if (x == 0):
t = '0'
elif ((abs(x) > 10000) or (abs(x) < 0.001)):
t = '%6.5e' % x
else:
t = '%6.5f' % x
else:
t = str(x)
fp.write(t)
fp.write('\n')
m = m + 1
fp.close()
return True
class NmrPipePseudoPopup(BasePopup):
pseudoEntries = ('Is Pseudo Expt', 'Is Not Pseudo Expt')
def __init__(self, parent, params, dim, fileName='', *args, **kw):
self.dim = dim
self.params = params
self.fileName = fileName
m = template_re.match(fileName)
if m:
n = len(m.groups(2))
ss = '%%0%dd' % n
template = re.sub(template_re, r'\1%s\3' % ss, fileName)
else:
template = fileName
self.template = template
BasePopup.__init__(self,
parent=parent,
title='NMRPipe Pseudo Data',
modal=True,
**kw)
def body(self, master):
fileName = self.fileName
directory = os.path.dirname(fileName)
if not directory:
directory = os.getcwd()
fileName = os.path.basename(fileName)
m = template_re.match(fileName)
if m:
n = len(m.groups(2))
ss = '%%0%dd' % n
template = re.sub(template_re, r'\1%s\3' % ss, fileName)
else:
template = fileName
master.rowconfigure(0, weight=1)
master.rowconfigure(1, weight=1)
master.columnconfigure(1, weight=1)
tipTexts = [
'The experiment is pseudo-N dimensional, with a sampled axis',
'The experiment is the regular kind with only NMR frequency axes'
]
self.pseudoButton = RadioButtons(
master,
entries=self.pseudoEntries,
select_callback=self.changedPseudoMode,
grid=(0, 0),
sticky='nw',
tipTexts=tipTexts)
frame = self.pseudoFrame = Frame(master)
self.pseudoFrame.grid(row=1, column=0, sticky='nsew')
row = 0
npts = self.params.npts[self.dim]
tipText = 'Number of data points (planes) along sampled axis'
label = Label(frame, text='Number of points: ')
label.grid(row=row, column=0, sticky='e')
self.nptsEntry = IntEntry(frame,
text=npts,
tipText=tipText,
width=8,
grid=(row, 1))
tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values'
Button(frame,
text='Load values from text file',
command=self.loadValues,
tipText=tipText,
grid=(row, 2),
sticky='ew')
row = row + 1
tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis'
label = Label(frame, text='Point values: ')
label.grid(row=row, column=0, sticky='e')
self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText)
self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'Fetch the Point values from the files given by the NMRPipe template'
button = Button(
frame,
text='Fetch values from file(s) specified by template below',
command=self.fetchValues,
tipText=tipText)
button.grid(row=row, column=1, columnspan=2, sticky='w')
row = row + 1
tipText = 'The directory where the data files reside'
button = Button(frame,
text='Data directory: ',
command=self.chooseDirectory)
button.grid(row=row, column=0, sticky='e')
self.directoryEntry = Entry(frame,
text=directory,
width=40,
tipText=tipText)
self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from'
button = Button(frame,
text='NMRPipe template: ',
command=self.chooseFile)
button.grid(row=row, column=0, sticky='e')
self.templateEntry = Entry(frame, text=template, tipText=tipText)
self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
for n in range(row):
frame.rowconfigure(n, weight=1)
frame.columnconfigure(1, weight=1)
buttons = UtilityButtonList(master,
closeText='Ok',
doClone=False,
closeCmd=self.updateParams,
helpUrl=self.help_url)
buttons.grid(row=2, column=0, sticky='ew')
def loadValues(self):
directory = self.parent.fileSelect.getDirectory()
fileSelectPopup = FileSelectPopup(self,
title='Select Sampled Data File',
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
directory=directory)
fileName = fileSelectPopup.file_select.getFile()
if not fileName:
return
fileObj = open(fileName, 'rU')
data = ''
line = fileObj.readline()
while line:
data += line
line = fileObj.readline()
fileObj.close()
data = re.sub(',\s+', ',', data)
data = re.sub('\s+', ',', data)
data = re.sub(',,', ',', data)
data = re.sub('[^0-9,.\-+eE]', '', data)
self.valueEntry.set(data)
def chooseDirectory(self):
directory = os.path.dirname(self.fileName)
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory, show_file=False)
directory = popup.getDirectory()
popup.destroy()
if directory:
self.directoryEntry.set(directory)
def chooseFile(self):
directory = self.directoryEntry.get()
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory)
file = popup.getFile()
popup.destroy()
if file:
template = os.path.basename(file)
self.templateEntry.set(template)
def updateParams(self):
params = self.params
if self.pseudoButton.get() == self.pseudoEntries[0]:
npts = self.nptsEntry.get()
params.npts[self.dim] = npts
values = self.valueEntry.get()
try:
params.setSampledDim(self.dim, values)
except ApiError, e:
showError('Set Sampled Dim', e.error_msg, parent=self)
return
params.fixNullDims(ignoreDim=self.dim)
else:
class IsotopeSchemeEditor(BasePopup):
"""
**Create and Edit Per-residue Reference Isotope Schemes**
This system allows the user to create schemes that describe particular
patterns of atomic isotope labelling in terms of combinations of isotopically
labelled forms of residues. Once constructed, these schemes may then be
applied to a molecule of known residue sequence to gauge the levels of
spin-active isotope incorporation in an NMR experiment. This information is
useful in several places withing Analysis, including giving more intelligent
assignment options and in the generation of distance restraints by matching
peak positions to chemical shifts. Although the schemes may be used directly
they are typically used as reference information for configuring the `Isotope
Labelling`_ system; where isotope labelling patterns are tied to particular
molecules and experiments.
Because all of the different isotope labelled versions (isotopomers) of each
residue type are described independently, a scheme can be used to estimate the
specific amounts of incorporation present at multiple atom sites at the same
time. For example, although a residue type may have significant levels of 13C
at the CA and CB positions on average, there may be no form of the residue
where CA and CB are labelled at the same time, and thus CA-CB correlations
would not be observed in NMR.
This popup window is divided into three main tabs, the first describes the
overall schemes that are available; that would be applied to a molecule in a
given situation. The second tab details the residue isotopomer components
within the selected scheme, i.e. which labelled residue forms are present. The
last tab displays isotopomer labelling in a graphical, three-dimensional way.
If any isotope labelling schemes have been created or edited the user may
immediately save these to disk via the [Save Schemes] button to the right of
the tabs, although these will naturally be saved when the main CCPN project
is.
**Reference Schemes**
This table lists all of the reference isotope schemes that are available to
the project. A number of standard schemes are included by default, as part of
the main CCPN installation. However, the user is free to create new schemes,
either from a completely blank description or by copying and modifying one of
the existing schemes. By selecting on a isttope scheme row in the table the
scheme is selected to be active for the whole popup and the user can see the
contents of the scheme via the other two tabs.
It should be noted that the user cannot edit the standard schemes provided by
CCPN, given that these are stored with the software. Any new or copied schemes
that the user creates will be stored inside the current CCPN project. If a new
scheme should be made available to multiple projects, its XML file can be
copied into the main CCPN installation, if the user has appropriate write
access.
**Isotopomers**
The middle tab allows the user to view, and where appropriate edit, the
isotope labelling descriptions for the residues within the current scheme
(selected in the pulldown menu at the top). An isotope scheme is constructed
by specifying one or more isotopomers for each residue type. Each isotopomer
represents a different way of incorporating spin-active atom labels into a
given kind of residue. Often there will only be one labelled form of a
residue, and hence one isotopomer. However, with some kinds of isotope
enrichment, for example using glycerol 13C labelled at the C2 position,
connected labelled and unlabelled atom sites can be incorporated in
alternative ways, resulting in distinct forms of labelling patterns that are
not the result of a pure random mix. Knowing which labels are present at the
same time, in the same isotopomer form, can be very important for determining
which NMR correlations are possible.
In general use when looking through the default, immutable reference schemes
that come with CCPN the user can scroll through the isotopomer versions of
each residue in the upper table. By clicking on one of these rows the lower
table is filled with details of the amount of each kind of isotope (on
average) at each atom site. For the lower "Atom Labels" table only one kind of
chemical element is shown at a time, but the user may switch to a different
one via the "Chemical Element" pulldown.
**Editing Isotopomers**
When dealing with copied or new isotope schemes the user is allowed to
edit all aspects of the scheme. With a completely new scheme there will be no
isotopomer records to start with and it is common practice to fill in a
standard set of isotopomers, one for each residue type, made with a base level
of isotope incorporation. To set this base level the user can use [Set Default
Abundances] to manually specify values, although the default is to use natural
abundance levels, which is appropriate in most circumstances. With the base
levels set the [Add Default Abundance Set] will automatically fill-in a
starting set of isotopomers for the scheme. Extra isotopomers can be added for
a specific type of residue via the [Add New:] function and adjacent pulldown
menu or by copying existing ones; whichever is easier. Each isotopomer has an
editable weight to enable the user to indicate the relative abundance within a
given residue type.
Once a new isotopomer specification is created clicking on its row allows the
user to specify the isotope labelling pattern in the lower "Atom Labels"
table. Here the user selects which kind of chemical element to consider and
then double-clicks to edit the "Weighting" columns in the table. The
weightings represent the relative abundance of a given nuclear isotope at a
given atom site. The weightings could be set as ratios, fractions, or
percentages; it is only the relative proportion that is important. For example
if a carbon atom site was known to have 5% Carbon-12 and 95% Carbon-13
isotopes then the respective weights could be entered as 1 & 19 or 0.05 &
0.95; whatever is most convenient. For efficient setup of schemes the
[Propagate Abundances] function can be used to spread the same levels of
incorporation over several atom sites (from the last selected row).
**Isotopomer Structure**
The last tab is an alternative way of presenting the isotope patterns present
within the residues of the current scheme (selected in either of the first two
tabs). Here the user selects a residue type in the upper left pulldown menu
and then a numbered isotopomer, or an average of all isotopomers, in the right
hand pulldown menu. The structural display will show a moveable picture of the
residue (in a standard conformation) where unlabelled atom sites are
represented with grey spheres, labelled sites with yellow spheres and
intermediate incorporation with shades in between.
It should be noted that this kind of 3D display is only possible if there is
an idealised structure available for a residue type. This data will be
present for all of the regular biopolymer residues, but may be missing for
more unusual compounds; although a lack of coordinates does not impact upon
the isotopomer setup.
To move and rotate the three-dimensional residue display the following
keyboard controls may be used:
* Rotate: Arrow keys
* Zoom: Page Up & Page Down keys
* Translate: Arrow keys + Control key
Or alternatively the following mouse controls:
* Rotate: Middle button click & drag
* Zoom: Mouse wheel or middle button click + Shift key & drag up/down
* Translate: Middle button click & drag + Control key
Also an options menu appears when the right mouse button is clicked.
.. _`Isotope Labelling`: EditMolLabellingPopup.html
"""
def __init__(self, parent, project=None, *args, **kw):
if not project:
self.project = Implementation.MemopsRoot(
name='defaultUtilityProject')
else:
self.project = project
self.waiting = False
self.waitingAtom = False
self.molType = 'protein'
self.scheme = None
self.isotopomer = None
self.isotopomerV = False # Not None
self.ccpCodeV = None
self.element = 'C'
self.atomLabelTuple = None
self.isotopes = [x[0] for x in getSortedIsotopes(self.project, 'C')]
self.defaultAbun = {}
BasePopup.__init__(self,
parent=parent,
title='Molecule : Reference Isotope Schemes',
**kw)
def body(self, guiFrame):
self.geometry('700x600')
guiFrame.expandGrid(0, 0)
tipTexts = [
'A table of all of the reference isotope scheme definitions available to the project',
'A list of the residue isotopomers that comprise the selected isotope labelling scheme',
'A three-dimensional representation of residues and their isotopomer labelling'
]
options = ['Reference Schemes', 'Isotopomers', 'Isotopomer Structure']
tabbedFrame = TabbedFrame(guiFrame,
options=options,
grid=(0, 0),
tipTexts=tipTexts)
self.tabbedFrame = tabbedFrame
frameA, frameB, frameC = tabbedFrame.frames
#
# Schemes
#
frameA.expandGrid(0, 0)
tipTexts = [
'A short textual code that identifies the reference isotope scheme in graphical displays',
'The full name for the isotope scheme',
'A detailed description of the isotope scheme including user comments',
'The name of the CCPN data repository in which the isotope scheme is saved; "refData" is in the CCPn installation'
]
headingList = ['Code', 'Name', 'Description', 'Save Location']
self.schemeNameEntry = Entry(self,
text='',
returnCallback=self.setSchemeName,
width=20)
self.schemeDetailsEntry = Entry(self,
text='',
returnCallback=self.setSchemeDetails,
width=20)
editWidgets = [
None, self.schemeNameEntry, self.schemeDetailsEntry, None
]
editGetCallbacks = [
None, self.getSchemeName, self.getSchemeDetails, None
]
editSetCallbacks = [
None, self.setSchemeName, self.setSchemeDetails, None
]
self.schemeMatrix = ScrolledMatrix(frameA,
headingList=headingList,
callback=self.selectScheme,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
multiSelect=False,
grid=(0, 0),
tipTexts=tipTexts)
self.schemeMatrix.doEditMarkExtraRules = self.schemeEditRules
tipTexts = [
'Make a new reference isotope scheme definition based on a copy of the scheme currently selected',
'Delete the selected isotope scheme',
'Make a new, blank isotope scheme'
]
texts = ['Copy', 'Delete', 'New']
commands = [self.copyScheme, self.removeScheme, self.makeNewScheme]
self.schemeButtons = ButtonList(frameA,
texts=texts,
commands=commands,
grid=(1, 0),
tipTexts=tipTexts)
#
# Isotopomers
#
frameB.expandGrid(3, 0)
row = 0
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(0, 2)
tipText = 'Selects which of the available isotope schemes to view/edit'
label = Label(frame, text='Reference Scheme:', grid=(0, 0))
self.schemePulldown = PulldownList(frame,
callback=self.setLabellingScheme,
grid=(0, 1),
tipText=tipText)
row += 1
div = LabelDivider(frameB, text='Isotopomers', grid=(row, 0))
row += 1
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(1, 2)
self.isotopomerFrame = frame
self.abundanceWidget = MultiWidget(self,
FloatEntry,
relief='raised',
borderwidth=2,
callback=self.setDefaultAbundances,
useImages=False)
tipText = 'Opens a panel that allows you to set the basis/default abundances for C, H & N isotopes; used as the starting point for new isotopomer definitions'
self.abundanceButton = Button(frame,
text='Set Default\nAbundances',
borderwidth=1,
command=self.enterDefaultAbundances,
grid=(0, 0),
tipText=tipText)
tipText = 'Sets the basis/default abundances for C, H & N isotopes to their natural abundance proportions'
button = Button(frame,
text='Set Natural\nAbundance Default',
borderwidth=1,
command=self.resetDefaultAbundance,
grid=(0, 1),
sticky='ew',
tipText=tipText)
label = Label(frame, text='Molecule Type:', grid=(0, 2), sticky='e')
entries = standardResidueCcpCodes.keys()
entries.sort()
entries.reverse()
tipText = 'Selects which type of bio-polymer to define residue isotopomer labelling for'
self.molTypePulldown = PulldownList(frame,
callback=self.setMolType,
texts=entries,
grid=(0, 3),
tipText=tipText)
row += 1
tipTexts = [
'The CCPN code that identifies the kind of residue the isotopomer relates to',
'The number of the particular isotopomer (isotope pattern) within its residue type',
'The fraction of the total residues, of its kind, that the isotopomer make up'
]
headingList = ['Ccp Code', 'Variant', 'Weight']
self.isotopomerWeightEntry = FloatEntry(
self, text='', returnCallback=self.setIsotopomerWeight, width=6)
editWidgets = [None, None, self.isotopomerWeightEntry]
editGetCallbacks = [None, None, self.getIsotopomerWeight]
editSetCallbacks = [None, None, self.setIsotopomerWeight]
self.isotopomerMatrix = ScrolledMatrix(
frameB,
tipTexts=tipTexts,
headingList=headingList,
callback=self.selectIsotopomer,
editWidgets=editWidgets,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
multiSelect=True,
grid=(row, 0))
self.isotopomerMatrix.doEditMarkExtraRules = self.isotopomerEditRules
row += 1
frame = Frame(frameB, grid=(row, 0), sticky='ew')
frame.expandGrid(0, 0)
tipTexts = [
'Delete the selected residue isotopomers from the current isotope scheme',
'Make a new residue isotopomer definition by copying the details of the last selected isotopomer',
'Add a complete set of isotopomers to the isotope scheme, one for each residue type, based on the states default isotope abundances',
'For all residue isotopomers in the scheme, set the labelling of one kind of atom (the user is prompted) to its default isotopic incorporation ',
'Add a new residue isotopomer definition that uses the default isotopic incorporation'
]
texts = [
'Delete\nSelected', 'Copy\nSelected', 'Add Default\nAbundance Set',
'Set Atom Type\nTo Default', 'Add\nNew:'
]
commands = [
self.removeIsotopomers, self.duplicateResidues,
self.addDefaultIsotopomers, self.setAtomTypeDefault,
self.addNewIsotopomer
]
self.isotopomerButtons = ButtonList(frame,
texts=texts,
commands=commands,
grid=(0, 0),
tipTexts=tipTexts)
tipText = 'Selects which kind of residue isotopomer may be added to the current isotope scheme'
self.ccpCodePulldown = PulldownList(frame,
callback=None,
grid=(0, 1),
sticky='e',
tipText=tipText)
row += 1
div = LabelDivider(frameB, text='Atom Labels', grid=(row, 0))
row += 1
frame = Frame(frameB, grid=(row, 0))
frame.expandGrid(1, 3)
label = Label(frame, text='Chemical Element:', grid=(0, 0))
tipText = 'Selects which kind of atoms to select from the selected residue isotopomer; to display isotopic incorporation in the below table'
self.elementPulldown = PulldownList(frame,
callback=self.changeChemElement,
grid=(0, 1),
tipText=tipText)
self.updateChemElements()
label = Label(frame, text='Water Exchangeable Atoms:', grid=(0, 2))
tipText = 'Sets whether to show atoms considered as being "water exchangeable"; their isotopic labelling will rapidly equilibrate with aqueous solvent'
self.exchangeCheck = CheckButton(frame,
callback=self.updateAtomLabelsAfter,
grid=(0, 3),
selected=False,
tipText=tipText)
row += 1
# Tip texts set on update
headingList = [
'Atom\nName', 'Weighting\n13C'
'Weighting\n12C', '%12C', '%13C'
]
self.atomLabelTupleWeightEntry = FloatEntry(
self, text='', width=6, returnCallback=self.setAtomLabelWeight)
self.atomsMatrix = ScrolledMatrix(frameB,
headingList=headingList,
callback=self.selectAtomLabel,
multiSelect=True,
grid=(row, 0))
self.atomsMatrix.doEditMarkExtraRules = self.atomsEditRules
row += 1
tipTexts = [
'For the selected atom sites, in the current isotopomer, set their isotopic incorporation to the default values',
'Spread the isotopic incorporation values from the last selected atom site to all selected atoms sites'
]
texts = ['Reset Selected to Default Abundance', 'Propagate Abundances']
commands = [self.setAtomLabelsDefault, self.propagateAbundances]
self.atomButtons = ButtonList(frameB,
texts=texts,
commands=commands,
grid=(row, 0),
tipTexts=tipTexts)
#
# View Frame
#
frameC.expandGrid(1, 0)
row = 0
frame = Frame(frameC, grid=(row, 0), sticky='ew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Residue Type:', grid=(0, 0))
tipText = 'Selects which kind of residue, within the current isotope scheme, to show isotopomer structures for'
self.viewCcpCodePulldown = PulldownList(
frame,
callback=self.selectViewCcpcode,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text='Isotopomer:', grid=(0, 2))
tipText = 'Selects which kind of isotopomer (labelling pattern) to display, from the selected residue type.'
self.viewIsotopomerPulldown = PulldownList(
frame,
callback=self.selectViewIsotopomer,
grid=(0, 3),
tipText=tipText)
row += 1
self.viewIsotopomerFrame = ViewIsotopomerFrame(frameC,
None,
grid=(row, 0))
#
# Main
#
tipTexts = [
'Save all changes to the reference isotope scheme to disk; the saves ALL changes to the CCPN installation for all projects to use',
]
texts = ['Save Schemes']
commands = [self.saveSchemes]
self.bottomButtons = UtilityButtonList(tabbedFrame.sideFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
grid=(0, 0),
sticky='e',
tipTexts=tipTexts)
self.updateChemElements()
self.updateCcpCodes()
self.updateSchemes()
self.administerNotifiers(self.registerNotify)
def atomsEditRules(self, atomLabel, row, col):
if self.scheme:
return isSchemeEditable(self.scheme)
else:
return False
def isotopomerEditRules(self, isotopomer, row, col):
if self.scheme:
return isSchemeEditable(self.scheme)
else:
return False
def schemeEditRules(self, scheme, row, col):
return isSchemeEditable(scheme)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setLongName', 'setDetails'):
for clazz in ('ccp.molecule.ChemCompLabel.LabelingScheme', ):
notifyFunc(self.updateSchemes, clazz, func)
for func in ('__init__', 'delete', 'setWeight'):
notifyFunc(self.updateIsotopomersAfter,
'ccp.molecule.ChemCompLabel.Isotopomer', func)
notifyFunc(self.updateAtomLabelsAfter,
'ccp.molecule.ChemCompLabel.AtomLabel', func)
def getCcpCodeIsotopomers(self, ccpCode):
chemCompLabel = self.scheme.findFirstChemCompLabel(
molType=self.molType, ccpCode=ccpCode)
if chemCompLabel:
isotopomers = list(chemCompLabel.isotopomers)
else:
isotopomers = []
return isotopomers
def selectViewCcpcode(self, ccpCode):
if ccpCode != self.ccpCodeV:
self.ccpCodeV = ccpCode
self.isotopomerV = False
self.updateViewIsotopomerPulldown()
def selectViewIsotopomer(self, isotopomer):
self.isotopomerV = isotopomer
if isotopomer is None:
isotopomers = self.getCcpCodeIsotopomers(self.ccpCodeV)
else:
isotopomers = [
isotopomer,
]
self.viewIsotopomerFrame.setIsotopomers(isotopomers)
def updateViewCcpCodePulldown(self):
if self.scheme:
codes = self.getCcpCodes(self.molType)
if self.ccpCodeV not in codes:
self.ccpCodeV = codes[0]
self.isotopomerV = False # Not None
self.updateViewIsotopomerPulldown()
index = codes.index(self.ccpCodeV)
else:
codes = []
index = 0
self.viewCcpCodePulldown.setup(codes, codes, index)
def updateViewIsotopomerPulldown(self):
index = 0
isotopomers = []
names = []
if self.scheme:
isotopomers = self.getCcpCodeIsotopomers(self.ccpCodeV)
names = ['%d' % i.serial for i in isotopomers]
isotopomers.insert(0, None)
names.insert(0, '<All>')
if self.isotopomerV not in isotopomers:
self.isotopomerV = None
isotopomers = self.getCcpCodeIsotopomers(self.ccpCodeV)
self.viewIsotopomerFrame.setIsotopomers(isotopomers)
self.viewIsotopomerPulldown.setup(names, isotopomers, index)
def updateButtons(self):
buttonsA = self.schemeButtons.buttons
buttonsB = self.isotopomerButtons.buttons
buttonsC = self.atomButtons.buttons
if self.scheme:
buttonsA[0].enable()
isEditable = isSchemeEditable(self.scheme)
if isEditable:
buttonsA[1].enable()
else:
buttonsA[1].disable()
buttonsB[2].enable()
buttonsB[3].enable()
self.bottomButtons.buttons[0].enable()
if isEditable:
if self.isotopomer:
for button in buttonsB:
button.enable()
for button in buttonsC:
button.enable()
else:
buttonsB[0].disable()
buttonsB[1].disable()
buttonsB[3].disable()
buttonsC[0].disable()
buttonsC[1].disable()
buttonsB[2].enable()
buttonsB[4].enable()
else:
for button in buttonsB:
button.disable()
for button in buttonsC:
button.disable()
else:
buttonsA[0].disable()
buttonsA[1].disable()
for button in buttonsB:
button.disable()
for button in buttonsC:
button.disable()
self.bottomButtons.buttons[0].disable()
def resetDefaultAbundance(self):
self.defaultAbun = {}
def setDefaultAbundances(self, values):
self.abundanceWidget.place_forget()
if values is not None:
i = 0
for element in elementSymbols: # TBD getAllIsotopes
for code, isotope in getSortedIsotopes(self.project, element):
self.defaultAbun[isotope] = values[i]
i += 1
def enterDefaultAbundances(self):
x = self.isotopomerFrame.winfo_x()
y = self.isotopomerFrame.winfo_y()
x0 = self.abundanceButton.winfo_x()
y0 = self.abundanceButton.winfo_y()
values = []
options = []
for element in elementSymbols: # TBD getAllIsotopes
for code, isotope in getSortedIsotopes(self.project, element):
options.append(code + ':')
values.append(
self.defaultAbun.get(isotope, 100.0 * isotope.abundance))
N = len(values)
self.abundanceWidget.maxRows = N
self.abundanceWidget.minRows = N
self.abundanceWidget.set(values=values, options=options)
self.abundanceWidget.place(x=x + x0, y=y + y0)
def selectAtomLabel(self, obj, row, col):
self.atomLabelTuple = (obj, col)
def setMolType(self, molType):
if molType != self.molType:
self.molType = molType
self.isotopomer = None
self.updateCcpCodes()
self.updateIsotopomers()
def getCcpCodes(self, molType):
codes = []
for code in standardResidueCcpCodes[molType]:
codes.append(code)
codes.sort()
return codes
def updateCcpCodes(self):
codes = self.getCcpCodes(self.molType)
if self.isotopomer:
index = codes.index(self.isotopomer.ccpCode)
else:
index = 0
self.ccpCodePulldown.setup(codes, codes, index)
def setIsotopomerWeight(self, event):
value = self.isotopomerWeightEntry.get()
if value is not None:
self.isotopomer.setWeight(abs(value))
def getIsotopomerWeight(self, isotopomer):
if isotopomer:
self.isotopomerWeightEntry.set(isotopomer.weight)
def setSchemeName(self, event):
text = self.schemeNameEntry.get()
if text:
text = text.strip() or None
else:
text = None
self.scheme.setLongName(text)
def getSchemeName(self, scheme):
if scheme:
self.schemeNameEntry.set(scheme.longName)
def getSchemeDetails(self, scheme):
if scheme:
self.schemeDetailsEntry.set(scheme.details)
def setSchemeDetails(self, event):
text = self.schemeDetailsEntry.get()
if text:
text = text.strip() or None
else:
text = None
self.scheme.setDetails(text)
def updateSchemes(self, obj=None):
textMatrix = []
objectList = []
for labelingScheme in self.project.sortedLabelingSchemes():
repository = labelingScheme.findFirstActiveRepository()
if repository:
saveLocation = repository.name
else:
saveLocation = None
line = [
labelingScheme.name, labelingScheme.longName,
labelingScheme.details, saveLocation
]
textMatrix.append(line)
objectList.append(labelingScheme)
self.schemeMatrix.update(textMatrix=textMatrix, objectList=objectList)
self.updateSchemePulldown()
self.updateIsotopomers()
def updateSchemePulldown(self):
scheme = self.scheme
schemes = self.project.sortedLabelingSchemes()
names = [ls.longName or ls.name for ls in schemes]
if names:
if scheme not in schemes:
scheme = schemes[0]
index = schemes.index(scheme)
else:
index = 0
scheme = None
self.setLabellingScheme(scheme)
self.schemePulldown.setup(names, schemes, index)
def copyScheme(self):
if self.scheme:
name = askString('Input text', 'New Scheme Code:', '', parent=self)
scheme = self.project.findFirstLabelingScheme(name=name)
if scheme:
showWarning('Failure', 'Scheme name already in use')
return
if name:
newScheme = copySubTree(self.scheme,
self.project,
topObjectParameters={'name': name})
else:
showWarning('Failure', 'No name specified')
else:
showWarning('Failure', 'No scheme selected to copy')
def removeScheme(self):
if self.scheme and isSchemeEditable(self.scheme):
self.scheme.delete()
self.scheme = None
def makeNewScheme(self):
name = askString('Input text', 'New Scheme Code:', '', parent=self)
if name:
scheme = self.project.findFirstLabelingScheme(name=name)
if scheme:
showWarning('Failure', 'Scheme name already in use')
else:
scheme = self.project.newLabelingScheme(name=name)
self.scheme = scheme
else:
showWarning('Failure', 'No name specified')
def setLabellingScheme(self, scheme):
if scheme is not self.scheme:
self.scheme = scheme
self.isotopomerV = False
self.isotopomer = None
self.updateIsotopomers()
def selectScheme(self, object, row, col):
self.setLabellingScheme(object)
self.updateSchemePulldown()
def open(self):
BasePopup.open(self)
self.updateSchemes()
def saveSchemes(self):
schemes = [x for x in self.project.labelingSchemes if x.isModified]
if schemes:
for scheme in schemes:
scheme.save()
showInfo('Notice', 'Successfully saved %d schemes' % len(schemes))
self.updateSchemes()
else:
showWarning('Notice', 'No modified schemes to save')
def addNewIsotopomer(self):
if self.scheme:
ccpCode = self.ccpCodePulldown.getObject()
chemCompLabel = self.getChemCompLabel(self.molType, ccpCode)
self.makeIsotopomer(chemCompLabel)
def makeIsotopomer(self, chemCompLabel, weight=1.0):
isotopomer = chemCompLabel.newIsotopomer(weight=weight)
chemComp = chemCompLabel.chemComp
for chemAtom in chemComp.chemAtoms:
if chemAtom.elementSymbol:
chemElement = chemAtom.chemElement
for isotope in chemElement.isotopes:
code = '%d%s' % (isotope.massNumber,
chemAtom.elementSymbol)
weight = self.defaultAbun.get(isotope,
100.0 * isotope.abundance)
isotopomer.newAtomLabel(name=chemAtom.name,
subType=chemAtom.subType,
isotopeCode=code,
weight=weight)
return isotopomer
def getChemCompLabel(self, molType, ccpCode):
chemCompLabel = None
if self.scheme:
chemCompLabel = self.scheme.findFirstChemCompLabel(molType=molType,
ccpCode=ccpCode)
if not chemCompLabel:
chemCompLabel = self.scheme.newChemCompLabel(molType=molType,
ccpCode=ccpCode)
return chemCompLabel
def selectIsotopomer(self, obj, row, col):
self.isotopomer = obj
self.updateChemElements()
self.updateAtomLabels()
def updateIsotopomersAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateIsotopomers)
def updateIsotopomers(self):
self.updateViewCcpCodePulldown()
self.updateViewIsotopomerPulldown()
textMatrix = []
objectList = []
if self.scheme:
chemCompLabels = [(label.ccpCode, label)
for label in self.scheme.chemCompLabels]
chemCompLabels.sort()
for key, chemCompLabel in chemCompLabels:
if chemCompLabel.molType == self.molType:
for isotopomer in chemCompLabel.sortedIsotopomers():
line = [
chemCompLabel.ccpCode, isotopomer.serial,
isotopomer.weight
]
textMatrix.append(line)
objectList.append(isotopomer)
self.isotopomerMatrix.update(textMatrix=textMatrix,
objectList=objectList)
self.updateAtomLabelsAfter()
self.waiting = False
def setAtomTypeDefault(self):
if self.scheme:
atomName = askString(
'Query',
'Specify atom name to set\ndefault abundance for',
'H',
parent=self)
if not atomName:
return
atomLabels = []
for chemCompLabel in self.scheme.chemCompLabels:
if chemCompLabel.molType == self.molType:
for isotopomer in chemCompLabel.isotopomers:
# Multiple because of isotopes and subTypes
atomLabels += isotopomer.findAllAtomLabels(
name=atomName)
if atomLabels:
for atomLabel in atomLabels:
isotope = atomLabel.isotope
weight = self.defaultAbun.get(isotope,
100.0 * isotope.abundance)
atomLabel.weight = weight
else:
data = (atomName, self.scheme.name)
msg = 'Atom name %s does not match any atoms in %s scheme isotopomers' % data
showWarning('Failure', msg)
def addDefaultIsotopomers(self):
if self.scheme:
codes = self.getCcpCodes(self.molType)
for ccpCode in codes:
chemCompLabel = self.getChemCompLabel(self.molType, ccpCode)
if not chemCompLabel.isotopomers:
self.makeIsotopomer(chemCompLabel)
def removeIsotopomers(self):
isotopomers = self.isotopomerMatrix.currentObjects
if isotopomers:
for isotopomer in isotopomers:
isotopomer.delete()
self.isotopomer = None
def duplicateResidues(self):
isotopomers = self.isotopomerMatrix.currentObjects
for isotopomer in isotopomers:
chemCompLabel = isotopomer.chemCompLabel
new = copySubTree(isotopomer, chemCompLabel)
def updateChemElements(self):
if self.isotopomer:
chemCompLabel = self.isotopomer.chemCompLabel
elementDict = {}
for chemAtom in chemCompLabel.chemComp.chemAtoms:
symbol = chemAtom.elementSymbol
if symbol:
elementDict[symbol] = True
names = elementDict.keys()
names.sort()
else:
names = ['C', 'N', 'H']
if self.element not in names:
index = 0
else:
index = names.index(self.element)
self.elementPulldown.setup(names, names, index)
def updateAtomLabelsAfter(self, obj=None):
if self.waitingAtom:
return
else:
self.waitingAtom = True
self.after_idle(self.updateAtomLabels)
def updateAtomLabels(self):
element = self.elementPulldown.getText()
textMatrix = []
objectList = []
headingList = [
'Atom Name',
]
tipTexts = [
'The name of the atom within its residue, for which to set isotopic abundances, within the selected isotopomer',
]
isotopeCodes = [x[0] for x in getSortedIsotopes(self.project, element)]
headingList.extend(['Weighting\n%s' % x for x in isotopeCodes])
tip = 'The amount of %s isotope incorporation; can be a ratio, percentage or fraction (the value used is relative to the sum of all weights)'
tipTexts.extend([tip % x for x in isotopeCodes])
tip = 'The percentage %s isotope incorporation, calculated using stated weights'
headingList.extend(['%%%s' % x for x in isotopeCodes])
tipTexts.extend([tip % x for x in isotopeCodes])
editWidgets = [
None,
]
editGetCallbacks = [
None,
]
editSetCallbacks = [
None,
]
editWidgets.extend(
[self.atomLabelTupleWeightEntry for x in isotopeCodes])
editGetCallbacks.extend(
[self.getAtomLabelWeight for x in isotopeCodes])
editSetCallbacks.extend(
[self.setAtomLabelWeight for x in isotopeCodes])
editWidgets.extend([None for x in isotopeCodes])
editGetCallbacks.extend([None for x in isotopeCodes])
editSetCallbacks.extend([None for x in isotopeCodes])
doExchangeable = self.exchangeCheck.get()
if self.isotopomer:
atomDict = {}
for atomLabel in self.isotopomer.sortedAtomLabels():
if atomLabel.chemAtom.elementSymbol == element:
if (not doExchangeable) and (
atomLabel.chemAtom.waterExchangeable):
continue
name = atomLabel.name
subType = atomLabel.subType
atomDict[(name, subType)] = True
atomNames = atomDict.keys()
atomNames = greekSortAtomNames(atomNames)
for atomName, subType in atomNames:
if subType == 1:
name = atomName
else:
name = '%s:%d' % (atomName, subType)
line = [
name,
]
atomLabels = []
sumWeights = 0.0
for isotope in isotopeCodes:
atomLabel = self.isotopomer.findFirstAtomLabel(
name=atomName, subType=subType, isotopeCode=isotope)
atomLabels.append(atomLabel)
if atomLabel:
weight = atomLabel.weight
sumWeights += weight
line.append(weight)
else:
line.append(0.0)
if sumWeights:
for atomLabel in atomLabels:
line.append(100.0 * atomLabel.weight / sumWeights)
else:
for atomLabel in atomLabels:
line.append(None)
textMatrix.append(line)
objectList.append(atomLabels)
self.atomsMatrix.update(textMatrix=textMatrix,
objectList=objectList,
headingList=headingList,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.waitingAtom = False
self.updateButtons()
def setAtomLabelWeight(self, event):
value = self.atomLabelTupleWeightEntry.get()
if value is not None:
atomLabels, col = self.atomLabelTuple
chemAtom = None
for label in atomLabels:
if label:
chemAtom = label.chemAtom
break
atomLabel = atomLabels[col - 1]
if chemAtom and (atomLabel is None):
isotopeCode, isotope = getSortedIsotopes(
self.project, chemAtom.elementSymbol)[col - 1]
atomLabel = self.isotopomer.newAtomLabel(
name=chemAtom.name,
subType=chemAtom.subType,
isotopeCode=isotopeCode,
weight=value)
atomLabel.setWeight(value)
def setAtomLabelsDefault(self):
atomLabelTuples = self.atomsMatrix.currentObjects
for atomLabels in atomLabelTuples:
for atomLabel in atomLabels:
isotope = atomLabel.isotope
weight = self.defaultAbun.get(isotope,
100.0 * isotope.abundance)
atomLabel.weight = weight
def propagateAbundances(self):
atomLabels, col = self.atomLabelTuple
atomLabelTuples = self.atomsMatrix.currentObjects
weightDict = {}
for atomLabel in atomLabels:
weightDict[atomLabel.isotope] = atomLabel.weight
for atomLabels0 in atomLabelTuples:
if atomLabels0 != atomLabels:
for atomLabel in atomLabels0:
atomLabel.weight = weightDict[atomLabel.isotope]
def getAtomLabelWeight(self, null):
atomLabels, col = self.atomLabelTuple
if atomLabels and (col > 0):
atomLabel = atomLabels[col - 1]
if atomLabel is None:
weight = 0.0
else:
weight = atomLabel.weight
self.atomLabelTupleWeightEntry.set(weight)
def changeChemElement(self, name):
self.element = name
self.isotopes = [x[0] for x in getSortedIsotopes(self.project, name)]
self.updateAtomLabels()
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
class EditMeasurementListsPopup(BasePopup):
"""
**The NMR Derived Measurements and Their Lists**
The purpose of this popup window is to display lists of measurements within
the current CCPN project. A "Measurement" in this regard is a value that is
derived from NMR data and connects to one or more resonances (which may be
assigned to atoms). The most commonly encountered kind of measurement is the
chemical shift, which is usually derived from recording the positions of peaks
in spectra. In this instance the chemical shift measurement of a resonance is
made when it is assigned to the dimension of a peak. Because CCPN allows
multiple shift lists (technically a type of measurement list) a resonance may
have a several chemical shift measurements; useful studying different
conditions.
There are several different kinds of measurement and hence measurement list that
may be included within a CCPN project, for example J-coupling, hydrogen
exchange rate, chemical shift anisotropy, T1 relaxation and chemical shift.
All types will be displayed by this popup if they are available within the
current project, although Analysis does not necessarily have tools to record
all of these different kinds of measurement.
The layout of this popup consists of two tabs, one for the organising lists
that contain the measurements and another to display the individual
measurements within a single list. With the exception of blank
lists for chemical shifts, measurement lists are not made using this popup,
instead they are made at the point where an analysis is performed, e.g. T1
lists are made with data from the `Follow Intensity Changes`_
tool.
The second tab, containing the "Measurements" table displays the details of
the individual measured values within a selected list. What the values mean
and which units they are in, if any, naturally depends on the kind of list
being viewed. If measurements are made within CCPN software (as opposed to
being imported) then the individual measurements usually record the spectrum
peaks that were used in the calculation of the measured value, e.g. the peaks
for which positions record chemical shift or intensities record T1.
**Caveats & Tips**
If there is no chemical shift list within a project a new one will be made
automatically to record the shifts of any assignments.
The shift list with which an experiment is associate may be changed via the "Shift
List" column of the main `Experiments`_ table.
Measurements other than chemical shift, like T1 and T2 relaxation times will only
appear within this system if a measurement list entity is formally made. Simply
measuring values from spectra, for example using the `Follow Intensity Changes`_
tool
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Experiments`: EditExperimentPopup.html
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.experiment = None
self.measurementList = None
self.measurementListB = None
self.measurement = None
self.waitingList = False
self.waitingMeasurement = False
BasePopup.__init__(self,
parent,
title="Resonance : Measurement Lists",
**kw)
def body(self, guiFrame):
self.geometry('600x600')
guiFrame.expandGrid(0, 0)
tipTexts = [
'A table of all the NMR measurement lists in the project, including shift lists, T1 lists, J-coupling lists etc.',
'A table listing all of the individual measurements within an NMR measurement list'
]
options = ['Measurement Lists', 'Measurements Table']
tabbedFrame = TabbedFrame(guiFrame,
options=options,
grid=(0, 0),
tipTexts=tipTexts)
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
# Measurement Lists
frameA.expandGrid(1, 0)
self.detailsEntry = Entry(self,
text='',
returnCallback=self.setDetails,
width=12)
self.nameEntry = Entry(self,
text='',
returnCallback=self.setName,
width=12)
row = 0
frame0 = Frame(frameA, grid=(row, 0), gridSpan=(1, 2))
frame0.grid_columnconfigure(2, weight=1)
label = Label(frame0, text='Experiment:', grid=(0, 0), sticky='e')
tipText = 'Selects an experiment, if required, to restrict the measurement list table display; showing only lists which were derived using the experiment'
self.experimentPulldown = PulldownList(frame0,
callback=self.setExperiment,
grid=(0, 1),
tipText=tipText)
row += 1
tipTexts = [
'The serial number of measurement list',
'The type of measurement list, e.g. shift list, T1 list, J coupling list',
'A short identifying name for the list, for graphical displays',
'The number of measurements contained within the list',
'The unit of measurement used for the values in the list',
'The names of the experiments which were used to derive the measurements',
'A user-specified textual comment for the measurement list'
]
justifyList = [
'center', 'center', 'center', 'center', 'center', 'left'
]
#colHeadings = ['List Type','Name','Size','Unit','Experiments','Other Info','Details']
colHeadings = [
'#', 'List Type', 'Name', 'Size', 'Unit', 'Experiments', 'Details'
]
editWidgets = [
None, None, self.nameEntry, None, None, None, None,
self.detailsEntry
]
editGetCallbacks = [
None, None, self.getName, None, None, None, None, self.getDetails
]
editSetCallbacks = [
None, None, self.setName, None, None, None, None, self.setDetails
]
self.listsMatrix = ScrolledMatrix(
frameA,
grid=(row, 0),
gridSpan=(1, 2),
justifyList=justifyList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=colHeadings,
callback=self.selectListCell,
deleteFunc=self.deleteMeasurementList,
tipTexts=tipTexts)
row += 1
tipTexts = [
'Show a table of the individual measurements within the selected measurement list',
'Make a new, blank chemical shift list within the project',
'Make a synthetic chemical shift list using random coil values, adjusting protein backbone values for sequence where approprate',
'Delete the selected measurement list'
]
texts = [
'Show Measurements', 'New Shift List',
'Make Random Coil Shift List', 'Delete'
]
commands = [
self.showMeasurements, self.addShiftList,
self.makeRandomCoilShiftList, self.deleteMeasurementList
]
self.listButtons = ButtonList(frameA,
texts=texts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
# Measurements
self.measurementDetailsEntry = Entry(
self, text='', returnCallback=self.setMeasurementDetails, width=12)
self.measurementMeritEntry = FloatEntry(
self, returnCallback=self.setMeasurementMerit, width=6)
row = 0
frame0 = Frame(frameB, grid=(row, 0))
frame0.grid_columnconfigure(2, weight=1)
label = Label(frame0,
text='Measurement List:',
grid=(0, 0),
sticky='e')
tipText = 'Selects the measurement list to display measurements for'
self.listPulldown = PulldownList(frame0,
callback=self.setMeasurementList,
grid=(0, 1),
tipText=tipText)
row += 1
frameB.expandGrid(row, 0)
tipTexts = [
'The serial number of the measurement within its containing list',
'The number or assignment of the NMR resonance(s) to which the measurement applies',
'The numeric value of the NMR measurement on the specified resonance(s), and the unit of measurement',
'The standard deviation error in the measured value',
'The molecular chain, if any, to which the measurement relates by virtue of atom assigned resonances',
'The isotope type(s) of the measures resonance(s)',
'A figure-of-merit value for the measurement indicating its quality or reliability',
'The number of peaks in the CCPN project used to take the measurement',
'A user-defined textual comment for the measurement'
]
justifyList = [
'center', 'center', 'center', 'center', 'center', 'center',
'center', 'center', 'center', 'left'
]
colHeadings = [
'#', 'Resonance', 'Value', 'SD', 'Chain', 'Isotope',
'Fig of\nMerit', 'Peaks', 'Details'
]
editWidgets = [
None, None, None, None, None, None, self.measurementMeritEntry,
None, self.measurementDetailsEntry
]
editGetCallbacks = [
None, None, None, None, None, None, self.getMeasurementMerit,
self.showPeaks, self.getMeasurementDetails
]
editSetCallbacks = [
None, None, None, None, None, None, self.setMeasurementMerit, None,
self.setMeasurementDetails
]
self.measurementsMatrix = ScrolledMatrix(
frameB,
grid=(row, 0),
multiSelect=True,
tipTexts=tipTexts,
justifyList=justifyList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=colHeadings,
callback=self.selectMeasurementCell)
row += 1
tipTexts = [
'Show a table containing peaks that were used to derive the selected measurements',
'For some measurement lists (currently only shift lists) manually trigger a recalculation of values',
'Show a table containing the resonances that relate to the selected measurements',
'Delete the selected measurement records; cannot be done for chemical shift values still ties to peaks via assignment'
]
texts = ['Show Peaks', 'Recalculate', 'Show Resonances', 'Delete']
commands = [
self.showPeaks, self.recalculateMeasurements, self.showResonances,
self.deleteMeasurements
]
self.measurementButtons = ButtonList(frameB,
texts=texts,
grid=(row, 0),
commands=commands,
tipTexts=tipTexts)
# Main Frame
self.bottomButtons = UtilityButtonList(tabbedFrame.sideFrame,
helpUrl=self.help_url,
grid=(0, 0),
gridSpan=(1, 2),
sticky='e')
self.updateMeasurementListAfter()
self.updateMeasurementsAfter()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName', 'setDipolarRelaxList',
'setHExchProtectionList', 'setHExchRateList',
'setNoeList', 'setJCouplingList', 'setRdcList',
'setShiftAnisotropyList', 'setShiftDifferenceList',
'setShiftList', 'setT1List', 'setT1RhoList', 'setT2List'):
for clazz in ('ccp.nmr.Nmr.Experiment', ):
notifyFunc(self.updateExperiments, clazz, func)
for func in ('__init__', 'delete', 'setDetails', 'setName',
'addExperiment', 'removeExperiment', 'setExperiments'):
for clazz in ('ccp.nmr.Nmr.DipolarRelaxList',
'ccp.nmr.Nmr.HExchProtectionList',
'ccp.nmr.Nmr.HExchRateList', 'ccp.nmr.Nmr.NoeList',
'ccp.nmr.Nmr.JCouplingList', 'ccp.nmr.Nmr.RdcList',
'ccp.nmr.Nmr.ShiftAnisotropyList',
'ccp.nmr.Nmr.ShiftDifferenceList',
'ccp.nmr.Nmr.ShiftList', 'ccp.nmr.Nmr.T1List',
'ccp.nmr.Nmr.T1RhoList', 'ccp.nmr.Nmr.T2List'):
notifyFunc(self.updateMeasurementListAfter, clazz, func)
# Measurements
for func in ('__init__', 'delete'):
for clazz in ('ccp.nmr.Nmr.DipolarRelaxation',
'ccp.nmr.Nmr.HExchProtection',
'ccp.nmr.Nmr.HExchRate', 'ccp.nmr.Nmr.Noe',
'ccp.nmr.Nmr.JCoupling', 'ccp.nmr.Nmr.Rdc',
'ccp.nmr.Nmr.Shift', 'ccp.nmr.Nmr.ShiftAnisotropy',
'ccp.nmr.Nmr.ShiftDifference', 'ccp.nmr.Nmr.T1',
'ccp.nmr.Nmr.T1Rho', 'ccp.nmr.Nmr.T2'):
notifyFunc(self.updateMeasurementAfter, clazz, func)
for func in ('__init__', 'delete', 'setDetails', 'setError',
'setFigOfMerit', 'setValue', 'setPeaks', 'addPeak',
'removePeak'):
for clazz in ('ccp.nmr.Nmr.DipolarRelaxation',
'ccp.nmr.Nmr.HExchProtection',
'ccp.nmr.Nmr.HExchRate', 'ccp.nmr.Nmr.Noe',
'ccp.nmr.Nmr.JCoupling', 'ccp.nmr.Nmr.Rdc',
'ccp.nmr.Nmr.Shift', 'ccp.nmr.Nmr.ShiftAnisotropy',
'ccp.nmr.Nmr.ShiftDifference', 'ccp.nmr.Nmr.T1',
'ccp.nmr.Nmr.T1Rho', 'ccp.nmr.Nmr.T2'):
self.registerNotify(self.updateMeasurementAfter, clazz, func)
def open(self):
self.updateMeasurementListAfter()
self.updateMeasurementsAfter()
BasePopup.open(self)
def makeRandomCoilShiftList(self):
molSystems = self.project.molSystems
shiftList = makeRandomCoilShiftList(molSystems)
def addShiftList(self):
shiftList = newShiftList(self.project)
self.setExperiment(None)
def getName(self, measurementList):
if measurementList:
self.nameEntry.set(measurementList.name)
def setName(self, event):
text = self.nameEntry.get()
if text and text != ' ':
self.measurementList.setName(text)
def getDetails(self, measurementList):
if measurementList and measurementList.details:
self.detailsEntry.set(measurementList.details)
def setDetails(self, event):
text = self.detailsEntry.get()
if text and text != ' ':
self.measurementList.setDetails(text)
def setExperiment(self, experiment):
if experiment is not self.experiment:
self.experiment = experiment
self.measurementList = None
self.updateMeasurementListAfter()
def deleteMeasurementList(self, *event):
if self.measurementList:
if (len(self.measurementList.experiments) >
0) and (self.measurementList.className == 'ShiftList'):
showWarning(
'Warning',
'Deletion of shift lists with associated experiments prohibited',
parent=self)
return
elif len(self.measurementList.measurements) > 0:
if showOkCancel('Confirm',
'List is not empty. Really delete?',
parent=self):
self.measurementList.delete()
self.measurementList = None
else:
return
else:
self.measurementList.delete()
self.measurementList = None
def showMeasurements(self):
self.updateMeasurements(self.measurementList)
self.tabbedFrame.select(1)
def selectListCell(self, object, row, col):
self.measurementList = object
if self.measurementList:
self.listButtons.buttons[0].enable()
self.listButtons.buttons[3].enable()
self.setMeasurementList(self.measurementList)
def updateMeasurementAfter(self, measurement):
if (self.experiment is None) or (
self.experiment in measurement.parentList.experiments):
self.updateMeasurementListAfter()
if measurement.parentList is self.measurementListB:
self.updateMeasurementsAfter()
def updateMeasurementListAfter(self, measurementList=None):
self.updateListPulldown()
if self.waitingList:
return
if (measurementList is None) \
or (self.experiment is None) \
or (self.experiment in measurementList.experiments):
self.waitingList = True
self.after_idle(self.updateListsTable)
def updateExperiments(self, null=None):
index = 0
experiments = [
None,
] + self.nmrProject.sortedExperiments()
names = [
'<Any>',
] + [e.name for e in experiments[1:]]
experiment = self.experiment
if experiments:
if experiment not in experiments:
experiment = experiments[0]
index = experiments.index(experiment)
else:
experiment = None
if self.experiment is not experiment:
self.experiment = experiment
self.updateMeasurementListAfter()
self.experimentPulldown.setup(names, experiments, index)
def updateListsTable(self, experiment=None):
if experiment is None:
experiment = self.experiment
else:
self.experiment = experiment
if self.experiment is None:
self.measureList = None
self.updateExperiments()
if self.measurementList:
self.listButtons.buttons[0].enable()
self.listButtons.buttons[3].enable()
else:
self.listButtons.buttons[0].disable()
self.listButtons.buttons[3].disable()
if self.experiment == None:
measurementLists = self.nmrProject.sortedMeasurementLists()
else:
measurementLists = []
lists = self.nmrProject.sortedMeasurementLists()
for measurementList in lists:
if self.experiment in measurementList.experiments:
measurementLists.append(measurementList)
objectList = []
textMatrix = []
for measurementList in measurementLists:
objectList.append(measurementList)
names = ['%s' % (e.name) for e in measurementList.experiments]
if len(names) > 6:
names.insert(int(len(names) / 2), '\n')
experimentText = ' '.join(names)
"""otherInfoText = ''
for attribute in measurementList.metaclass.getAllAttributes():
name = attribute.name
otherInfoText += '%s:%s ' % (name,getattr(measurementList, name))
for role in measurementList.metaclass.getAllRoles():
name = role.name
otherInfoText += '%s:%s ' % (name,getattr(measurementList, name))"""
datum = [
measurementList.serial,
measurementList.className,
measurementList.name,
len(measurementList.measurements),
measurementList.unit,
experimentText,
#otherInfoText,
measurementList.details
]
textMatrix.append(datum)
if not objectList:
textMatrix.append([])
self.listsMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.waitingList = False
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
# Measurement functions
def deleteMeasurements(self):
measurements = self.measurementsMatrix.currentObjects
if measurements:
className = self.measurementListB.className
if className == 'ShiftList':
msg = 'Really delete %s chemical shifts?' % len(measurements)
if not showOkCancel('Confirm', msg, parent=self):
return
untouched = set()
for shift in measurements:
for peakDim in shift.peakDims:
shiftList = peakDim.peak.peakList.dataSource.experiment.shiftList
if shiftList is self.measurementListB:
untouched.add(shift)
break
else:
shift.delete()
if untouched:
if len(untouched) > 1:
msg = 'Could not delete %d shifts because they are still assigned to peaks' % len(
untouched)
else:
msg = 'Could not delete shift because it is still assigned to peaks'
showWarning('Warning', msg, parent=self)
else:
msg = 'Really delete %d %s measurements?' % (len(measurements),
className[:-4])
if not showOkCancel('Confirm', msg, parent=self):
return
for measurement in measurements:
measurement.delete()
def recalculateMeasurements(self):
measurements = self.measurementsMatrix.currentObjects
if measurements and (self.measurementListB.className == 'ShiftList'):
for shift in measurements:
averageShiftValue(shift)
def showPeaks(self, *event):
measurements = self.measurementsMatrix.currentObjects
if measurements:
peaksDict = {}
for measurement in measurements:
for peak in measurement.peaks:
peaksDict[peak] = 1
peaks = peaksDict.keys()
if len(peaks) > 0:
self.guiParent.viewPeaks(peaks)
def showResonances(self, *event):
measurements = self.measurementsMatrix.currentObjects
if measurements:
resonances = set()
for measurement in measurements:
if hasattr(measurement, 'resonances'):
resonances.update(measurement.resonances)
else:
resonances.add(measurement.resonance)
if resonances:
self.guiParent.viewSelectedResonances(resonances)
def setMeasurementList(self, measurementList):
if measurementList is not self.measurementListB:
self.measurementListB = measurementList
self.updateMeasurementsAfter()
def getMeasurementMerit(self, measurement):
if measurement:
self.measurementMeritEntry.set(measurement.figOfMerit)
def setMeasurementMerit(self, event):
value = self.measurementMeritEntry.get()
if value is not None:
self.measurement.setFigOfMerit(max(0.0, min(1.0, float(value))))
def getMeasurementDetails(self, measurement):
if measurement and measurement.details:
self.measurementDetailsEntry.set(measurement.details)
def setMeasurementDetails(self, event):
text = self.measurementDetailsEntry.get()
if text and text != ' ':
self.measurement.setDetails(text)
def selectMeasurementCell(self, object, row, col):
self.measurement = object
if self.measurement:
self.measurementButtons.buttons[0].enable()
self.measurementButtons.buttons[2].enable()
if self.measurementListB.className == 'ShiftList':
self.measurementButtons.buttons[1].enable()
else:
self.measurementButtons.buttons[1].disable()
def getMeasurementListName(self, measurementList):
name = measurementList.name or \
'%d:%s' % (measurementList.serial,measurementList.className)
return name
def updateListPulldown(self, null=None):
index = 0
measurementLists = self.nmrProject.sortedMeasurementLists()
nameFunc = self.getMeasurementListName
names = [nameFunc(ml) for ml in measurementLists]
measurementList = self.measurementListB
if measurementLists:
if measurementList not in measurementLists:
measurementList = measurementLists[0]
index = measurementLists.index(measurementList)
else:
measurementList = None
if self.measurementListB is not measurementList:
self.measurementListB = measurementList
self.updateMeasurementsAfter()
self.listPulldown.setup(names, measurementLists, index)
def updateMeasurementsAfter(self, *opt):
if self.waitingMeasurement:
return
else:
self.waitingMeasurement = True
self.after_idle(self.updateMeasurements)
def updateMeasurements(self, measurementList=None):
headingList = [
'#', 'Resonance', 'Value', 'SD', 'Chain', 'Isotope',
'Fig of\nMerit', 'Peaks', 'Details'
]
if measurementList is not None:
self.measurementListB = measurementList
self.updateListPulldown()
if self.measurementListB is None:
self.measurement = None
measurements = []
else:
if self.measurementListB.unit:
headingList[2] = 'Value\n(%s)' % (self.measurementListB.unit)
measurements = self.measurementListB.sortedMeasurements()
if measurements and hasattr(measurements[0], 'resonances'):
headingList[1] = 'Resonances'
headingList[5] = 'Isotopes'
if self.measurement:
self.measurementButtons.buttons[0].enable()
self.measurementButtons.buttons[2].enable()
if self.measurementListB.className == 'ShiftList':
self.measurementButtons.buttons[1].enable()
else:
self.measurementButtons.buttons[1].disable()
else:
self.measurementButtons.buttons[0].disable()
self.measurementButtons.buttons[1].disable()
self.measurementButtons.buttons[2].disable()
objectList = []
textMatrix = []
i = 0
for measurement in measurements:
i += 1
resonanceText = ''
isotopeText = ''
chainText = ''
if hasattr(measurement, 'resonances'):
resonanceText = ' '.join(
[makeResonanceGuiName(r) for r in measurement.resonances])
isotopeText = ' '.join(
[r.isotopeCode for r in measurement.resonances])
residueDict = {}
for resonance in measurement.resonances:
if resonance.resonanceSet:
residue = resonance.resonanceSet.findFirstAtomSet(
).findFirstAtom().residue
residueDict[residue] = None
keys = residueDict.keys()
if len(keys) == 1:
residue = keys[0]
residueNum = residue.seqCode
chainText = '%s:%s' % (residue.chain.molSystem.code,
residue.chain.code)
elif hasattr(measurement, 'resonance'):
resonance = measurement.resonance
resonanceText = makeResonanceGuiName(resonance)
isotopeText = measurement.resonance.isotopeCode
if resonance.resonanceSet:
residue = resonance.resonanceSet.findFirstAtomSet(
).findFirstAtom().residue
chainText = '%s:%s' % (residue.chain.molSystem.code,
residue.chain.code)
datum = [
i, resonanceText, measurement.value, measurement.error,
chainText, isotopeText, measurement.figOfMerit,
len(measurement.peaks), measurement.details or ' '
]
objectList.append(measurement)
textMatrix.append(datum)
if not objectList:
textMatrix.append([])
tipTexts = self.measurementsMatrix.tipTexts # unchanged, despite variable headings
self.measurementsMatrix.update(headingList=headingList,
objectList=objectList,
textMatrix=textMatrix,
tipTexts=tipTexts)
self.waitingMeasurement = False
class OpenSpectrumPopup(BasePopup):
r"""
**Locate Spectrum Data for Use in CCPN Project**
This popup window enables the user to locate spectrum data within a file
system and associate the files (typically binary) with an experiment and
spectrum name so that it may be visualised and accessed within the current
CCPN project. Spectra of many different origins and file formats may be
loaded, which currently includes Bruker, Varian, Felix, NMRPipe, NmrView,
SPARKY/UCSF, Azara and the factorised shape format "USF3". Depending upon the
file format of the spectrum, data loaded the user may be required to either
select a parameter file which then refers to the actual spectrum intensity
data; this is true for Bruker "procs" and AZARA ".par" files, or alternatively
a spectrum data file itself that contains referencing information; this is
the case for SPARKY/UCSF, NmrView and NMRPipe spectra.
The layout of the popup involved two sections; the upper of which is for
navigating to and selecting the spectrum or parameter files within the
file-system, and the lower is for specifying how each spectrum is loaded into
the CCPN project. It should be noted that when spectrum parameters are read
the first time, the relevant information is copied into the CCPN project,
where it may be adjusted independently of the original file information. No
copies of the spectrum intensity data are made, the CCPN project merely refers
to the spectrum data on disk, although the data file for a loaded spectrum may
subsequently be moved or replaced.
In normal operation the user first selects the kind of spectrum file format
that will be loaded via the upper "File format" pulldown menu and then checks
that the "File type" pulldown (toward the bottom of the file browser) is set
to detect the appropriate kinds of filename; if a helpful file name filter is
not available the user can add one via the "Manual Select" field, taking care
to add any wild-card symbols, like the asterisk in "\*.ft3". Next the spectrum
data or parameter files, appropriate to the selected format, are located by
navigating within the file-system browser. When the required spectrum files are
visible the user selects one *or more* to load. Multiple file selections may
be made using left-click with <Ctrl> (toggle selection) or <Shift> (select
range). It should be noted that when selecting Bruker files, when using the
standard Bruker directory structure, the user only needs to navigate to the
numbered spectrum directory; by default the "procs" file two levels down is
searched for, e.g. "123/pdata/1/procs" is shown in the directory containing
the "123" directory.
When spectrum or parameter files are selected in the file table, the lower
"Spectra To Open" table is filled to reflect the selection. The user should
then be mindful of the settings within this table and may choose to edit
various things by double-clicking on the appropriate cell. Typically the user
just adjusts the name of the independent "Experiment" and "Spectrum" records.
These names are usually concatenated like "expName:specName" in CCPN graphical
displays so there is no need to repeat a name in both fields; this only takes
up more space. The Experiment, which is a record of *what was done
experimentally*, commonly has a short name like "HNCA" or "HSQC_298K" so the
user readily knows how to interpret the experimental data. The Spectrum, which
is a record of *the data that was collected*, commonly has a short name to
identify the spectrum number or file name. An Experiment record may contain
several Spectrum records, so the spectrum's name need minimally only identify
it amongst others from the same experiment. The Shift List value may be
changed if the user knows that the experiment represents a distinct set of
conditions, with different spectrum peak/resonance positions, to existing or
other experiments being entered. Each shift list will be curated separately,
to give separate chemical shift values for assignments made under different
conditions (even when relating to the same atoms). The shift list that an
experiment uses may also be changed at any time after loading.
When all spectra and options are specified the [Open Spectrum] button will
load the relevant data into the CCPN project. If the "Skip verification
dialogs" option is set it is assumed that all of the spectrum point to
frequency referencing information, and any data file references, are correct.
Otherwise, the user will be prompted to confirm the file details and
referencing information for each spectrum in turn. Finally, after loading the
user is asked to set the type of NMR experiment, in terms of general
magnetisation transfer pathway, that was performed.
**Caveats & Tips**
If the name of an Experiment that is *already within the CCPN project* is
used, then the loaded spectrum will (assuming it is compatible) be entered
under that existing experiment record; no new experiment entity will be
defined. The user may legitimately use this feature to load several spectra
that relate to the same experiment; typically where spectra are different
projections. To facilitate this the "Use shared experiment" option can be
selected.
Although experiments and spectra may be renamed after loading, a spectrum
record may not be placed under a different experiment once created; deletion
and re-loading is the only mans of achieving this, and care must be taken in
transferring any assignments.
"""
def __init__(self, parent, *args, **kw):
self.experiment = None
self.currentObject = None
#self.currentObjects = [] # looks obsolete
BasePopup.__init__(self,
parent=parent,
title='Experiment : Open Spectra',
**kw)
def open(self):
self.message()
BasePopup.open(self)
def body(self, guiFrame):
self.fileSelect = None
names, objects = self.getShiftLists()
self.shiftListPulldown = PulldownList(self,
callback=self.setShiftList,
texts=names,
objects=objects)
self.windowPulldown = PulldownList(self,
texts=WINDOW_OPTS,
callback=self.setWindow)
self.experimentEntry = Entry(self,
width=16,
returnCallback=self.setExperiment)
self.spectrumEntry = Entry(self,
width=16,
returnCallback=self.setSpectrum)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
leftFrame = LabelFrame(guiFrame, text='File Selection')
leftFrame.grid(row=0, column=0, sticky='nsew')
leftFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(leftFrame, text='File format:')
label.grid(row=row, column=0, sticky='w')
tipText = 'Selects which kind of spectrum file is being loaded; what its data matrix format is'
self.formatPulldown = PulldownList(leftFrame,
callback=self.chooseFormat,
texts=file_formats,
tipText=tipText,
grid=(row, 1))
self.detailsLabel = Label(leftFrame, text='Show details:')
tipText = 'Whether to show an annotation that describes the spectrum in the file selection; currently only uses comment fields from Bruker spectra'
self.detailsSelect = CheckButton(leftFrame,
selected=False,
callback=self.showDetails,
tipText=tipText)
self.titleRow = row
self.detailsSelected = False
row = row + 1
leftFrame.grid_rowconfigure(row, weight=1)
file_types = [FileType('All', ['*'])]
self.fileSelect = FileSelect(leftFrame,
multiSelect=True,
file_types=file_types,
single_callback=self.chooseFiles,
extraHeadings=('Details', ),
extraJustifies=('left', ),
displayExtra=False,
getExtraCell=self.getDetails,
manualFileFilter=True)
self.fileSelect.grid(row=row, column=0, columnspan=6, sticky='nsew')
rightFrame = LabelFrame(guiFrame, text='Spectra To Open')
rightFrame.grid(row=1, column=0, sticky='nsew')
rightFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(rightFrame,
text='Skip verification dialogs:',
grid=(row, 0))
tipText = 'Whether to allow the user to check file interpretation and referencing information before the spectrum is loaded'
self.verifySelect = CheckButton(rightFrame,
selected=False,
grid=(row, 1),
tipText=tipText)
label = Label(rightFrame, text='Use shared experiment:', grid=(row, 2))
tipText = 'When selecting multiple spectrum files, whether the loaded spectra will all belong to (derive from) the same experiment; useful for projection spectra etc.'
self.sharedExpSelect = CheckButton(rightFrame,
selected=False,
tipText=tipText,
callback=self.useShared,
grid=(row, 3))
row = row + 1
rightFrame.grid_rowconfigure(row, weight=1)
tipTexts = [
'A short textual name for the experiment record that the loaded spectrum will belong to; may be a new experiment or the name of an existing one',
'A short textual name to identify the spectrum within its experiment; typically a few characters or spectrum number, rather than a repeat of the experiment name',
'The location of the file, relative to the current directory, that the spectrum data will be loaded from',
'Sets which window or windows the spectrum will initially appear within once loaded',
'Sets which shift list the experiment (and hence loaded spectrum) will use to curate chemical shift information; can be changed after load time'
]
headingList = [
'Experiment', 'Spectrum', 'File', 'Windows', 'Shift List'
]
editWidgets = [
self.experimentEntry, self.spectrumEntry, None,
self.windowPulldown, self.shiftListPulldown
]
editGetCallbacks = [
self.getExperiment, self.getSpectrum, None, self.getWindow,
self.getShiftList
]
editSetCallbacks = [
self.setExperiment, self.setSpectrum, None, self.setWindow,
self.setShiftList
]
self.scrolledMatrix = ScrolledMatrix(rightFrame,
headingList=headingList,
callback=self.selectCell,
editWidgets=editWidgets,
multiSelect=True,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts,
grid=(row, 0),
gridSpan=(1, 4))
row = row + 1
tipTexts = [
'Load spectrum or spectra into the CCPN project using the selected file(s)',
]
texts = ['Open Spectrum']
commands = [self.openSpectra]
bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
tipTexts=tipTexts,
doClone=False,
commands=commands,
helpUrl=self.help_url)
bottomButtons.grid(row=row, column=0, columnspan=1, sticky='ew')
self.openButton = bottomButtons.buttons[0]
self.chooseFormat('Azara')
self.message()
def message(self):
if not self.project or len(self.nmrProject.experiments) < 1:
pass
#self.parent.ticker.setMessage('Choose spectrum files to open.... ')
def showDetails(self, isSelected):
self.detailsSelected = isSelected
self.fileSelect.updateDisplayExtra(isSelected)
# below is so that when Details column is toggled on it will actually
# be seen without having to use the scrollbar
self.fileSelect.fileList.refreshSize()
def useShared(self, isSelected):
self.chooseFiles(forceUpdate=True)
#if isSelected:
#objects = self.scrolledMatrix.objectList
#if len(objects) > 1:
# self.currentObject = objects[0]
# text = objects[0][0]
# self.chooseFiles()
# for oo in objects[1:]:
# oo[0] = text
# if self.project:
# self.experiment = self.nmrProject.findFirstExperiment(name=text)
#self.update()
def gridDetails(self, bool):
if bool:
self.detailsLabel.grid(row=self.titleRow, column=2, sticky='w')
self.detailsSelect.grid(row=self.titleRow, column=3, sticky='w')
self.fileSelect.updateDisplayExtra(self.detailsSelected)
else:
self.detailsLabel.grid_forget()
self.detailsSelect.grid_forget()
self.fileSelect.updateDisplayExtra(False)
def openSpectra(self):
noVerify = self.verifySelect.getSelected()
# tracks if 'add to existing experiment' has already ben OK'ed
self.okExpSet = set()
directory = self.fileSelect.getDirectory()
spectra = []
specIndex = 0
for obj in self.scrolledMatrix.objectList:
fileName = uniIo.joinPath(directory, obj.fileName)
spectrum = self.openSpectrum(obj.exptName, obj.specName, fileName,
obj.window, obj.shiftListName)
specIndex += 1
if (spectrum):
# check endianness if we are not verifying
spectra.append(spectrum)
if noVerify:
isBigEndian = isSpectrumBigEndian(
spectrum) # according to data in file
if isBigEndian is not None:
isBigEndianCurr = getIsSpectrumBigEndian(
spectrum) # according to data model
setIsSpectrumBigEndian(spectrum, isBigEndian)
if isBigEndian != isBigEndianCurr:
if isBigEndian:
s = 'big'
else:
s = 'little'
print 'WARNING: swapped endianess of spectrum to %s endian' % s
#
del self.okExpSet
if noVerify and len(spectra) > 1 and self.sharedExpSelect.getSelected(
):
# if we are using a shared experiment and not verifying,
# set referencing to match first spectrum for all
# get reference spectrum and set up data structure
# use most recent pre-existing spectrum, otherwise first new one
refSpec = spectra[0]
for spec in spectra[0].experiment.sortedDataSources():
if spec in spectra:
break
else:
refSpec = spec
ddrLists = {}
refDdrs = []
for dataDim in refSpec.sortedDataDims():
for ddr in dataDim.dataDimRefs:
ddrLists[ddr.expDimRef] = []
refDdrs.append(ddr)
# get dataDimRefs, store by ExpDimRef,
# checking that all spectra have data dim refs for same set of xdr
nTotal = len(ddrLists)
for spec in spectra:
nFound = 0
for dataDim in spec.sortedDataDims():
for ddr in dataDim.dataDimRefs:
xdr = ddr.expDimRef
ll = ddrLists.get(xdr)
if ll is None:
# something did not match - do nothing
break
else:
ll.append(ddr)
nFound += 1
else:
if nFound == nTotal:
# we are OK. Do next spectrum
continue
# something did not match - do nothing
break
else:
# all spectra matched. Now reset O1 references to match reference
if refSpec is spectra[0]:
startAt = 1
else:
startAt = 0
for refDdr in refDdrs:
dataDim = refDdr.dataDim
centrePoint = dataDim.numPointsOrig / 2 - dataDim.pointOffset + 1
refValue = refDdr.pointToValue(centrePoint)
xdr = refDdr.expDimRef
for ddr in ddrLists[xdr][startAt:]:
dataDim = ddr.dataDim
centrePoint = dataDim.numPointsOrig / 2 - dataDim.pointOffset + 1
ddr.refPoint = centrePoint
ddr.refValue = refValue
# set refExperiment if there is only one possibility
experiments = []
ignoreSet = set()
showPopup = False
for spectrum in spectra:
experiment = spectrum.experiment
if experiment not in ignoreSet:
ignoreSet.add(experiment)
if not experiment.refExperiment:
experiments.append(spectrum.experiment)
if noVerify:
resetCategory = False
if not hasattr(experiment, 'category'):
if (hasattr(experiment, 'pulProgName')
and hasattr(experiment, 'pulProgType')):
# this is first time we get here, and we have external name and source
# use external source to set fullType
experiment.category = 'use external'
resetCategory = True
refExperiments = getRefExperiments(experiment)
if resetCategory and not refExperiments:
# no refExperiments match external source.
# unset 'use external' category
del experiment.category
if len(refExperiments) == 1:
# only one possibility, just set it
setRefExperiment(experiment, refExperiments[0])
# wb104: 20 Oct 2014: do not popup Experiment types dialog if noVerify
#else:
# showPopup = True
# Pop up refExperiment verification
if experiments and (showPopup or not noVerify):
self.parent.initRefExperiments(experiments)
# set up internal Analysis data
for spectrum in spectra:
self.parent.finishInitSpectrum(spectrum)
print 'finished opening spectrum', spectrum.experiment.name, spectrum.name
def chooseFiles(self, forceUpdate=False, *file):
directory = self.fileSelect.getDirectory()
fileNames = self.fileSelect.fileList.currentObjects
fullFileNames1 = [uniIo.joinPath(directory, x) for x in fileNames]
fullFileNames2 = [x.fileName for x in self.scrolledMatrix.objectList]
fullFileNames2 = [uniIo.joinPath(directory, x) for x in fullFileNames2]
if fullFileNames1 == fullFileNames2 and not forceUpdate:
return
objectList = []
textMatrix = []
format = self.formatPulldown.getText()
shiftListName = self.getShiftLists()[0][0]
windowOpt = WINDOW_OPTS[1]
oneUp = os.path.dirname
if format == 'Bruker':
if self.sharedExpSelect.getSelected():
nameTemplate = 'Bruker_%d'
next = self.getNextExpNum(nfiles=len(fileNames),
nameTemplate=nameTemplate)
exptName = nameTemplate % (next)
for i, fileName in enumerate(fileNames):
fullFileName = fullFileNames1[i]
specName = os.path.basename(
oneUp(oneUp(oneUp(fullFileName))))
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
for i, fileName in enumerate(fileNames):
fullFileName = fullFileNames1[i]
try: # below should not fail
ss1 = oneUp(fullFileName)
specName = os.path.basename(ss1)
ss2 = os.path.basename(oneUp(oneUp(ss1)))
exptName = 'Bruker_' + ss2
except: # just put in something
ss = os.path.basename(fullFileName)
exptName = 'Bruker_' + ss
specName = ss
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
next = self.getNextExpNum(nfiles=len(fileNames))
if self.sharedExpSelect.getSelected():
exptName = 'Expt_%d' % (next)
for i, fileName in enumerate(fileNames):
specName = re.sub('\.\w+$', '', fileName)
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
for i, fileName in enumerate(fileNames):
exptName = 'Expt_%d' % (next + i)
specName = re.sub('\.\w+$', '', fileName)
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
if len(fileNames) > 1:
self.openButton.config(text='Open Spectra')
else:
self.openButton.config(text='Open Spectrum')
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def getNextExpNum(self, nfiles=0, nameTemplate='Expt_%d'):
""" get suitable free integer to use for exp names
"""
next = 1
if self.project:
nmrProject = self.nmrProject
ii = len(nmrProject.experiments)
# find first exp number that is not taken
# NBNB TBD could consider expname = specname, specname = proc dir
next = ii + 1
if nfiles:
while ii < next + nfiles:
ii += 1
if nmrProject.findFirstExperiment(name=nameTemplate % ii):
next = ii + 1
#
return next
def getDetails(self, fullfile):
details = ''
if os.path.isfile(fullfile):
format = self.formatPulldown.getText()
detailsDir = os.path.dirname(fullfile)
detailsFile = uniIo.joinPath(detailsDir, details_file_dict[format])
if os.path.exists(detailsFile):
fp = open(detailsFile)
details = fp.read().strip().replace('\n',
' ').replace('\r', ' ')
fp.close()
return (details, )
def update(self):
objectList = self.scrolledMatrix.objectList
textMatrix = [(obj.exptName, obj.specName, obj.fileName, obj.window,
obj.shiftListName) for obj in objectList]
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def selectCell(self, obj, row, col):
self.currentObject = obj
if self.project:
self.experiment = self.nmrProject.findFirstExperiment(
name=obj.exptName)
else:
self.experiment = None
def getWindow(self, obj):
if obj:
self.windowPulldown.set(obj.window)
def setWindow(self, opt):
if isinstance(opt, RowObject):
self.currentObject.window = opt.window
else:
self.currentObject.window = opt
self.update()
def setShiftList(self, obj=None):
if self.project:
project = self.project
shiftList = self.shiftListPulldown.getObject()
if shiftList is None:
shiftList = newShiftList(project, unit='ppm')
if self.experiment and shiftList and (
shiftList is not self.experiment.shiftList):
setExperimentShiftList(self.experiment, shiftList)
self.currentObject.shiftListName = shiftList.name
self.update()
def getShiftList(self, object):
names, shiftLists = self.getShiftLists()
if names:
self.shiftListPulldown.setup(names, shiftLists, 0)
if self.experiment and self.experiment.shiftList:
name = self.experiment.shiftList.name
else:
name = object.shiftListName
if name is not None:
self.shiftListPulldown.set(name)
def getShiftLists(self):
if self.project:
names = []
objects = getShiftLists(self.nmrProject)
for shiftList in objects:
if not shiftList.name:
shiftList.name = 'ShiftList %d' % shiftList.serial
names.append(shiftList.name)
objects.append(None)
names.append('<New>')
else:
objects = [
None,
]
names = [
'ShiftList 1',
]
return names, objects
def chooseFormat(self, format):
if format in ('Bruker', 'Varian'):
self.gridDetails(True)
else:
self.gridDetails(False)
file_types = []
file_type = file_type_dict.get(format)
if (file_type):
file_types.extend([file_type])
file_types.append(FileType('All', ['*']))
file_types.append(self.fileSelect.manualFilter)
self.fileSelect.setFileTypes(file_types)
def getSpectrum(self, obj):
if obj:
self.spectrumEntry.set(obj.specName)
def setSpectrum(self, *event):
if self.currentObject:
text = self.spectrumEntry.get()
if text and text != ' ':
for data in self.scrolledMatrix.objectList:
if data is self.currentObject:
continue
if (data.specName
== text) and (data.exptName
== self.currentObject.exptName):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
elif (self.experiment) and (
self.experiment.findFirstDataSource(name=text)):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
self.currentObject.specName = text
self.update()
def getExperiment(self, obj):
if obj:
self.experimentEntry.set(obj.exptName)
def setExperiment(self, *event):
if self.currentObject:
text = self.experimentEntry.get()
if text and text != ' ':
if self.sharedExpSelect.getSelected():
# share one experiment for all rows
for oo in self.scrolledMatrix.objectList:
oo.exptName = text
else:
#separate experiments
self.currentObject.exptName = text
if self.project:
self.experiment = self.nmrProject.findFirstExperiment(
name=text)
self.update()
def updateShiftLists(self):
if self.project:
name = self.expt_entry.get()
e = self.nmrProject.findFirstExperiment(name=name)
else:
e = None
names, objects = self.getShiftLists()
if e and e.shiftList:
index = objects.index(e.shiftList)
else:
index = 0
self.shiftListPulldown.setup(names, objects, index)
def openSpectrum(self,
exptName,
specName,
file,
windowOpt=WINDOW_OPTS[2],
shiftListName='<New>',
extraData=None):
# input checks
if not file:
showError('No file', 'Need to enter file', parent=self)
return None
if not exptName:
showError('Experiment',
'Need to enter experiment name',
parent=self)
return None
if not specName:
showError('Spectrum', 'Need to enter spectrum name', parent=self)
return None
# get or set up project
project = self.project
if not project:
self.project = project = defaultProject()
self.parent.initProject(project)
self.nmrProject = self.parent.nmrProject
self.analysisProject = self.parent.analysisProject
#Default ShiftList with name 'ShiftList 1' created
# set up shift list
if shiftListName == '<New>':
shiftList = None
else:
shiftList = self.nmrProject.findFirstMeasurementList(
className='ShiftList', name=shiftListName)
# read params
format = self.formatPulldown.getText()
clazz = params_class_dict[format]
try:
params = clazz(file, extraData=extraData)
except Implementation.ApiError, e:
showError('Reading params file',
'Fatal error: ' + e.error_msg,
parent=self)
return None
dim = params.pseudoDataDim()
if dim is not None:
if format == 'NMRPipe':
popup = NmrPipePseudoPopup(self, params, dim, file)
popup.destroy()
elif format == 'Bruker':
popup = BrukerPseudoPopup(self, params, dim)
popup.destroy()
# get or set up experiment
experiment = self.nmrProject.findFirstExperiment(name=exptName)
if experiment:
expIsNew = False
if experiment.findFirstDataSource(name=specName):
showError('Duplicate name',
'Duplicate spectrum name "%s" in experiment %s' %
(specName, experiment.name),
parent=self)
return None
elif (experiment.dataSources and experiment not in self.okExpSet):
if showOkCancel('Multiple Spectra Warning',
'Really put multiple '
'spectra into existing experiment %s?' %
experiment.name,
parent=self):
self.okExpSet.add(experiment)
else:
return
else:
expIsNew = True
try:
# Will also work for shiftList == None
experiment = Nmr.Experiment(self.nmrProject,
name=exptName,
numDim=params.ndim,
shiftList=shiftList)
except Implementation.ApiError, experiment:
showError('Experiment', experiment.error_msg, parent=self)
return None
class CingFrame(NmrCalcRunFrame):
def __init__(self, parent, application, *args, **kw):
project = application.project
self.nmrProject = nmrProject = application.nmrProject
if project:
calcStore = project.findFirstNmrCalcStore(name=APP_NAME, nmrProject=nmrProject) or \
project.newNmrCalcStore(name=APP_NAME, nmrProject=nmrProject)
else:
calcStore = None
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.serverDone = False
NmrCalcRunFrame.__init__(self, parent, project, calcStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureTable.grid_forget()
self.structureButtons.grid_forget()
self.ensemblePulldown.grid_forget()
self.modelButtons.grid_forget()
self.modelPulldown.grid_forget()
frame = self.inputTabs.frames[0]
frame.grid_rowconfigure(0, weight=0)
frame.grid_rowconfigure(1, weight=1)
label = Label(frame, text='Ensemble: ', grid=(0, 0))
self.structurePulldown = PulldownList(
frame,
callback=self.changeStructure,
grid=(0, 1),
tipText='The structure ensemble coordinates to submit')
tipTexts = [
'Conformational model number', 'Whether analyse this model'
]
headingList = ['Model', 'Use']
editWidgets = [None, None]
editGetCallbacks = [None, self.toggleModel]
editSetCallbacks = [
None,
None,
]
self.modelTable = ScrolledMatrix(frame,
grid=(1, 0),
gridSpan=(1, 2),
callback=self.selectStructModel,
multiSelect=True,
tipTexts=tipTexts,
editWidgets=editWidgets,
initialRows=2,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
tipTexts = [
'Activate the selected models so that they will be consedered in the analysis',
'Deactivate the selected models so that they will not be considered in the analysis'
]
texts = ['Activate Selected', 'Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame,
texts=texts,
commands=commands,
grid=(2, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1, 0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0, 0))
frame.expandGrid(None, 2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
self.iCingBaseUrlPulldown = PulldownList(
frame,
texts=URLS,
objects=URLS,
index=0,
grid=(srow, 1),
tipText='Web location of iCING server to use')
srow += 1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(
frame,
bd=1,
text='',
grid=(srow, 1),
width=50,
tipText='Name of file to store compressed CING results in')
self.setZipFileName()
button = Button(frame,
text='Choose File',
bd=1,
sticky='ew',
command=self.chooseZipFile,
grid=(srow, 2),
tipText='Select file to overwrite with CING results')
srow += 1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(
frame,
bd=1,
text='',
grid=(srow, 1),
width=50,
tipText='Web location where CING results will be posted')
button = Button(frame,
text='View Results HTML',
bd=1,
sticky='ew',
command=self.viewHtmlResults,
grid=(srow, 2),
tipText='Open the HTML CING results in a web browser')
srow += 1
tipTexts = [
'Submit the CCPN project to the CING server',
'Determin whether the iCING job is complete, pending or has failed',
'Remove all trace of the last submissionfrom the iCING server',
'Download the compressed CING results, including HTML'
]
texts = [
'Submit Project!', 'Check Run Status', 'Purge Server Result',
'Download Results'
]
commands = [
self.runCingServer, self.checkStatus, self.purgeCingServer,
self.downloadResults
]
self.buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
grid=(srow, 0),
gridSpan=(1, 3),
tipTexts=tipTexts)
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1, 0))
frame.expandGrid(1, 1)
label = Label(frame, text='Chain: ')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Select the molecular system chain to consider')
self.chainPulldown.grid(row=0, column=1, sticky='w')
headingList = ['#', 'Residue', 'Linking', 'Decriptor', 'Use?']
tipTexts = [
'Sequence number', 'Residue type code',
'In-chain connectivity of residue',
'Protonation and steriochemical state',
'Whether to consider the residue in the analysis'
]
editWidgets = [None, None, None, None, None]
editGetCallbacks = [None, None, None, None, self.toggleResidue]
editSetCallbacks = [
None,
None,
None,
None,
None,
]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew')
tipTexts = [
'Use the selected residues in the analysis',
'Do not use the selected residues in the analysis'
]
texts = ['Activate Selected', 'Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame,
texts=texts,
commands=commands,
tipTexts=tipTexts)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(calcStore)
self.administerNotifiers(application.registerNotify)
def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query', msg, parent=self):
self.purgeCingServer()
def getServerUrl(self, baseUrl):
iCingUrl = os.path.join(baseUrl, 'icing/icing/serv/iCingServlet')
return iCingUrl
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structureData = self.getStructureData()
if not structureData:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
if not structureData.models:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueData = self.getResidueData()
if not (residueData and residueData.residues):
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.run.status = 'pending'
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(
self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.run.status = 'failed'
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(
iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(
credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID,
self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY,
self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
#run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials,
self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
self.run.status = 'failed'
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
self.run.status = 'completed'
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials,
self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials,
self.getServerUrl(url))
if results:
showInfo('Info', 'iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info', 'Purge failed')
self.update()
def chooseZipFile(self):
fileTypes = [
FileType('Zip', ['*.zip']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
file=self.resultFileEntry.get(),
title='Results zip file location',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def setZipFileName(self):
if self.project:
zipFile = '%s_CING_report.zip' % self.project.name
self.resultFileEntry.set(zipFile)
else:
self.resultFileEntry.set('CING_report.zip')
def selectStructModel(self, model, row, col):
self.model = model
def selectResidue(self, residue, row, col):
self.residue = residue
def getResidueData(self):
chain = self.chain.chain
chainCode = chain.code
msCode = chain.molSystem.code
dataObj = self.run.findFirstData(className=RESIDUE_DATA,
ioRole='input',
molSystemCode=msCode,
chainCode=chainCode,
name=APP_NAME)
if not dataObj:
dataObj = self.run.newMolResidueData(molSystemCode=msCode,
chainCode=chainCode,
ioRole='input',
name=APP_NAME)
# if not dataObj.residueSeqIds:
seqIds = [r.seqId for r in self.chain.sortedResidues()]
dataObj.residueSeqIds = seqIds
return dataObj
def getStructureData(self):
eId = self.structure.ensembleId
msCode = self.structure.molSystem.code
dataObj = self.run.findFirstData(className=STRUCTURE_DATA,
molSystemCode=msCode,
ensembleId=eId,
ioRole='input',
name=APP_NAME)
if not dataObj:
dataObj = self.run.newStructureEnsembleData(ioRole='input',
molSystemCode=msCode,
ensembleId=eId,
name=APP_NAME)
# if not dataObj.modelSerials:
serials = [m.serial for m in self.structure.sortedModels()]
dataObj.modelSerials = serials
for dataObjB in self.run.findAllData(className=STRUCTURE_DATA,
name=APP_NAME,
ioRole='input'):
if dataObjB is not dataObj:
dataObjB.delete()
return dataObj
def deactivateResidues(self):
if self.run and self.chain:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
for residue in self.residueMatrix.currentObjects:
seqId = residue.seqId
if seqId in seqIds:
seqIds.remove(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def activateResidues(self):
if self.run and self.chain:
for residue in self.residueMatrix.currentObjects:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
for residue in self.residueMatrix.currentObjects:
seqId = residue.seqId
if seqId not in seqIds:
seqIds.add(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def activateModels(self):
if self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
for model in self.modelTable.currentObjects:
serial = model.serial
if serial not in serials:
serials.add(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def disableModels(self):
if self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
for model in self.modelTable.currentObjects:
serial = model.serial
if serial in serials:
serials.remove(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def toggleModel(self, *opt):
if self.model and self.run and self.structure:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
serial = self.model.serial
if serial in serials:
serials.remove(serial)
else:
serials.add(serial)
serials = list(serials)
serials.sort()
dataObj.modelSerials = serials
self.updateModels()
def toggleResidue(self, *opt):
if self.residue and self.run:
dataObj = self.getResidueData()
seqIds = set(dataObj.residueSeqIds)
seqId = self.residue.seqId
if seqId in seqIds:
seqIds.remove(seqId)
else:
seqIds.add(seqId)
seqIds = list(seqIds)
seqIds.sort()
dataObj.residueSeqIds = seqIds
self.updateResidues()
def updateResidues(self):
if self.residue and (self.residue.topObject is not self.structure):
self.residue = None
textMatrix = []
objectList = []
colorMatrix = []
if self.chain:
resDataObj = self.getResidueData()
selectedRes = set(resDataObj.residues)
chainCode = self.chain.code
for residue in self.chain.sortedResidues():
msResidue = residue.residue
if msResidue in selectedRes:
colors = [None, None, None, None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None, None, None, None]
use = 'No'
datum = [
residue.seqCode,
msResidue.ccpCode,
msResidue.linking,
msResidue.descriptor,
use,
]
textMatrix.append(datum)
objectList.append(residue)
colorMatrix.append(colors)
self.residueMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def updateChains(self):
index = 0
names = []
chains = []
chain = self.chain
if self.structure:
chains = self.structure.sortedCoordChains()
names = [chain.code for chain in chains]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
self.changeChain(chain)
self.chainPulldown.setup(names, chains, index)
def updateStructures(self):
index = 0
names = []
structures = []
structure = self.structure
if self.run:
structures0 = [(s.ensembleId, s)
for s in self.project.structureEnsembles]
structures0.sort()
for eId, structure0 in structures0:
name = '%s:%s' % (structure0.molSystem.code, eId)
structures.append(structure0)
names.append(name)
if structures:
if structure not in structures:
structure = structures[-1]
index = structures.index(structure)
if self.structure is not structure:
self.changeStructure(structure)
self.structurePulldown.setup(names, structures, index)
def updateModels(self, obj=None):
textMatrix = []
objectList = []
colorMatrix = []
if self.structure and self.run:
strucDataObj = self.getStructureData()
selectedSerials = set(strucDataObj.modelSerials)
for model in self.structure.sortedModels():
if model.serial in selectedSerials:
colors = [None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None]
use = 'No'
datum = [model.serial, use]
textMatrix.append(datum)
objectList.append(model)
colorMatrix.append(colors)
self.modelTable.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def changeStructure(self, structure):
if self.project and (self.structure is not structure):
self.project.currentEstructureEnsemble = structure
self.structure = structure
if self.run:
dataObj = self.getStructureData()
serials = set(dataObj.modelSerials)
serials2 = set([m.serial for m in structure.models])
serials = list(serials & serials2)
serials.sort()
dataObj.modelSerials = serials
dataObj.ensembleId = structure.ensembleId
dataObj.molSystemCode = structure.molSystem.code
# Could clean up residue data if required
# prob OK to have haning around in case structure
# changes back
#for dataObj in self.run.findAllData(className=RESIDUE_DATA,
# ioRole='input',
# molSystemCode=msCode,
# name=APP_NAME)
# dataObj.delete()
self.updateModels()
self.updateChains()
def changeChain(self, chain):
if self.project and (self.chain is not chain):
self.chain = chain
self.updateResidues()
#def chooseValidScript(self):
#
# # Prepend default Cyana file extension below
# fileTypes = [ FileType('Python', ['*.py']), ]
# popup = FileSelectPopup(self, file_types = fileTypes,
# title='Python file', dismiss_text='Cancel',
# selected_file_must_exist = True)
# fileName = popup.getFile()
# self.validScriptEntry.set(fileName)
# popup.destroy()
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = nmrProject = project.currentNmrProject
calcStore = project.findFirstNmrCalcStore(name='CING', nmrProject=nmrProject) or \
project.newNmrCalcStore(name='CING', nmrProject=nmrProject)
else:
calcStore = None
if not self.project:
return
self.setZipFileName()
if not self.project.currentNmrProject:
name = self.project.name
self.nmrProject = self.project.newNmrProject(name=name)
else:
self.nmrProject = self.project.currentNmrProject
self.update(calcStore)
def update(self, calcStore=None):
NmrCalcRunFrame.update(self, calcStore)
run = self.run
urls = URLS
index = 0
if run:
userId = getRunTextParameter(run, iCingRobot.FORM_USER_ID)
accessKey = getRunTextParameter(run, iCingRobot.FORM_ACCESS_KEY)
if userId and accessKey:
self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId),
(iCingRobot.FORM_ACCESS_KEY,
accessKey)]
url = getRunTextParameter(run, ICING_BASE_URL)
if url:
htmlUrl = getRunTextParameter(run, HTML_RESULTS_URL)
self.iCingBaseUrl = url
self.resultsUrl = htmlUrl # May be None
self.resultUrlEntry.set(self.resultsUrl)
if self.iCingBaseUrl and self.iCingBaseUrl not in urls:
index = len(urls)
urls.append(self.iCingBaseUrl)
self.iCingBaseUrlPulldown.setup(urls, urls, index)
self.updateButtons()
self.updateStructures()
self.updateModels()
self.updateChains()
def updateButtons(self, event=None):
buttons = self.buttonBar.buttons
if self.project and self.run:
buttons[0].enable()
if self.resultsUrl and self.serverCredentials:
buttons[1].enable()
buttons[2].enable()
buttons[3].enable()
else:
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
else:
buttons[0].disable()
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
class AnnealingSettingsTab(object):
'''This class describes the tab in the GUI where the user
can change setting that govern the monte carlo / annleaing
procedure. This also includes which information from the ccpn
analysis project is used and which information is
ignored. This includes:
* present sequential assignments
* tentative assignments
* amino acid type information
* whether to include untyped spin systems
* assignments to peak dimensions
ALso the chain can be selected here.
Furthermore the user can set the temperature
regime of the annealing, the amount of times the procedure
is repeated to obtain statistics. The fraction of peaks
that is left out in each run to diversify the results,
the treshhold score for amino acid typing and the treshhold
collabelling for a peak to be expected.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.minIsoFrac = 0.1
self.leavePeaksOutFraction = 0.0
self.minTypeScore = 1.0
self.chain = None
self.amountOfRepeats = 10
self.amountOfSteps = 10000
self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022,
0.033, 0.050, 0.075, 0.113,
0.170, 0.256, 0.384, 0.576,
0.864, 1.297, 1.946, 2.919,
4.378, 6.568, 9.852, 14.77,
22.16, 33.25]
self.energyDataSets = [[]]
self.residues = []
self.body()
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def runCalculations(self):
'''Run all calculations. Also triggers the disabling of
some buttons and fields.
'''
self.startButton.disable()
self.disableIllegalButtonsAfterPrecalculations()
self.guiParent.connector.runAllCalculations()
self.startButton.configure(text='More runs')
self.startButton.enable()
def disableIllegalButtonsAfterPrecalculations(self):
'''Disable buttons and field the user can not alter
any longer after the model is set up and the
'pre-calculations' have finished.
This is done because this part of the calculation
should only be run once. All settings that would
be changed after this point will not have any influence.
'''
illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry,
self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck,
self.useTypeCheck, self.useDimensionalAssignmentsCheck,
self.useTentativeCheck]
for illegalButton in illegalButtons:
illegalButton.configure(state='disabled')
self.molPulldown.disable()
def getChainName(self, chain):
'''Get the name for a chain.
args: chain: ccpn analysis
chain object
returns: chain name
'''
return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType)
def getChains(self):
'''Get all chains present in the project.
returns: list of ccpn analysis chain objects
'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateChains(self, *opt):
'''Updates the list of chains if a new one is added
to or deleted from the project. Updates the
pull down list where a chain can be selected.
'''
index = 0
texts = []
chains = self.getChains()
chain = self.chain
if chains:
if chain not in chains:
chain = chains[0]
texts = [self.getChainName(c) for c in chains]
index = chains.index(chain)
else:
chain = None
self.molPulldown.setup(texts, chains, index)
if chain is not self.chain:
self.chain = chain
def changeMolecule(self, chain):
'''Select a molecular chain.'''
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges(fromChain=True)
def updateStepEntry(self, event=None):
'''Update the value and entry that sets the amount of
steps per temperature point.
'''
value = self.NAStepEntry.get()
if value == self.amountOfSteps:
return
if value < 1:
self.NAStepEntry.set(1)
self.amountOfSteps = 1
else:
self.amountOfSteps = value
self.NAStepEntry.set(value)
def updateRepeatEntry(self, event=None):
'''Update the value and entry of that sets
the amount of times the whole annealing
procedure is repeated in order
to obtain statistics.
'''
value = self.repeatEntry.get()
if value == self.amountOfRepeats:
return
if value < 1:
self.repeatEntry.set(1)
self.amountOfRepeats = 1
else:
self.amountOfRepeats = value
self.repeatEntry.set(value)
def updateMinTypeScoreEntry(self, event=None):
'''Updates the value and the entry for the
treshhold value for amino acid typing.
'''
value = self.minTypeScoreEntry.get()
if value == self.minTypeScore:
return
if value < 0:
self.minTypeScoreEntry.set(0.0)
self.minTypeScore = 0.0
elif value > 100:
self.minTypeScoreEntry.set(100.0)
self.minTypeScore = 100.0
else:
self.minTypeScoreEntry.set(value)
self.minTypeScore = value
def updateMinLabelEntry(self, event=None):
'''Updates the minimum colabelling fraction
for which a peak is expected to be present
in the spectra.
'''
value = self.minLabelEntry.get()
if value == self.minIsoFrac:
return
if value < 0:
self.minIsoFrac = 0.0
self.minLabelEntry.set(0.0)
elif value > 1:
self.minIsoFrac = 1.0
self.minLabelEntry.set(1.0)
else:
self.minIsoFrac = value
self.minLabelEntry.set(value)
def updateLeavePeaksOutEntry(self, event=None):
'''Updates the value and entry of the fraction
of peaks that should be left out in each
run in order to diversify the results.
'''
value = self.leaveOutPeaksEntry.get()
if value == self.leavePeaksOutFraction:
return
if value < 0:
self.leavePeaksOutFraction = 0.0
self.leaveOutPeaksEntry.set(0.0)
elif value > 1:
self.leavePeaksOutFraction = 1.0
self.leaveOutPeaksEntry.set(1.0)
else:
self.leavePeaksOutFraction = value
self.leaveOutPeaksEntry.set(value)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def addEnergyPoint(self, energy, time):
'''Adds a point to the graph that shows the progress
of the annealling procedure.
args: energy: the y-value
time: the x-value
'''
point = (time, energy * -1)
# This means one run has finished
if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1):
self.energyDataSets.append([point])
else:
self.energyDataSets[-1].append(point)
colors = colorSeries
Ncolors = len(colors)
NdataSets = len(self.energyDataSets)
colorList = (NdataSets / Ncolors) * colors + \
colors[:NdataSets % Ncolors]
self.energyPlot.update(dataSets=self.energyDataSets,
dataColors=colorList)
# Forcing the graph to draw, eventhough calculations
# are still running. Only do this with high numbers of
# steps, otherwise drawing takes longer than annealling.
if self.amountOfSteps >= 100000:
self.energyPlot.draw()
class EntryScale(Frame):
def __init__(self,
parent,
values,
initial_index=0,
orient=Tkinter.HORIZONTAL,
scale_length=200,
entry_width=5,
entry_format='%2.1f',
set_callback=None,
*args,
**kw):
assert len(values) > 0
self.entry_format = entry_format
self.values = tuple(values)
self.set_callback = set_callback
apply(Frame.__init__, (self, parent) + args, kw)
if (orient == Tkinter.HORIZONTAL):
self.grid_columnconfigure(1, weight=1)
sticky = Tkinter.EW
row = 0
col = 1
else:
self.grid_rowconfigure(1, weight=1)
sticky = Tkinter.NS
row = 1
col = 0
self.entry = Entry(self, width=entry_width)
self.entry.grid(row=0, column=0, sticky=sticky)
self.entry.bind('<KeyPress>', self.keyPress)
self.scale = Tkinter.Scale(self,
orient=orient,
length=scale_length,
from_=0,
to=len(values) - 1,
label='',
showvalue=0,
command=self.setCallback)
self.scale.grid(row=row, column=col, sticky=sticky)
self.set(initial_index)
def get(self):
return self.scale.get()
def getValue(self):
return self.values[self.get()]
def set(self, index):
assert index >= 0 and index < len(
self.values), 'index = %s, len(self.values) = %s' % (
index, len(self.values))
self.scale.set(index)
self.setEntry()
def setEntry(self):
index = self.get()
text = self.entry_format % self.values[index]
self.entry.set(text)
def setCallback(self, ignore):
self.setEntry()
if (self.set_callback):
self.set_callback(self.get())
def keyPress(self, event):
if (event.keysym == 'Return'):
text = self.entry.get()
try:
value = text.atof()
except:
return
min_index = 0
min_diff = abs(self.values[0] - value)
for i in range(1, len(self.values)):
diff = abs(self.values[i] - value)
if (diff < min_diff):
min_index = i
min_diff = diff
self.set(min_index)
class AriaRunFrame(NmrCalcRunFrame):
def __init__(self, parent, project, calcStore, *args, **kw):
NmrCalcRunFrame.__init__(self, parent, project, calcStore,
inputTypes=(PEAK_DATA, CONSTRAINT_DATA),
chainSelection=True, *args, **kw)
self.calcStore = calcStore
self.optPeakList = None
self.optConstraintList = None
frame = self.tabbedFrame.frames[1]
headingList = ['PeakList','Filter\nViolated?',
'Keep\nAssignments?','Shift List']
editWidgets = [None, None, None, None]
editGetCallbacks = [None, self.toggleFilterViol,
self.toggleKeepAssign, None]
editSetCallbacks = [None, None, None, None]
row = 0
subFrame = Frame(frame, grid=(row,0))
subFrame.expandGrid(0,1)
label = Label(subFrame, text='File Name Prefix:', grid=(0,0))
self.filePrefixEntry = Entry(subFrame, text='aria', grid=(0,1), sticky="ew")
self.filePrefixEntry.bind('<Leave>', self.updateEntryParams)
label = Label(subFrame, text='CNS Executable:', grid=(1,0))
self.cnsExeEntry = Entry(subFrame, text='', grid=(1,1), sticky="ew")
self.cnsExeEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectCnsExe, grid=(1,2))
label = Label(subFrame, text='Working Directory:', grid=(2,0))
self.workingDirEntry = Entry(subFrame, text='', grid=(2,1), sticky="ew")
self.workingDirEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectWorkingDir, grid=(2,2))
label = Label(subFrame, text='Temporary Directory:', grid=(3,0))
self.tempDirEntry = Entry(subFrame, text='', grid=(3,1), sticky="ew")
self.tempDirEntry.bind('<Leave>', self.updateEntryParams)
button = Button(subFrame, text='Select File',bd=1,bg='#C0E0FF',
command=self.selectTempDir, grid=(3,2))
row += 1
frame.expandGrid(row,0)
self.grid_rowconfigure(row, weight=1)
self.optPeakListMatrix = ScrolledMatrix(frame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True, grid=(row,0),
callback=self.selectOptPeakList)
row += 1
frame.expandGrid(row,0)
headingList = ['Constraint List',
'Name',
'Filter\nViolated?',
'Ambiguous\nProtocol?',]
editWidgets = [None, None, None, None]
editGetCallbacks = [None, None, self.toggleFilterViol, self.toggleAmbig]
editSetCallbacks = [None, None, None, None]
self.optConstraintMatrix = ScrolledMatrix(frame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
multiSelect=True, grid=(row,0),
callback=self.selectConstraintList)
self.optConstraintMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
self.update(calcStore)
def update(self, calcStore=None):
NmrCalcRunFrame.update(self, calcStore)
self.updateSettings()
# Need to run NmrCalcRunFrame.update before
# this to get new self.run, self.project
if self.run:
repository = self.project.findFirstRepository(name='userData')
defaultDir = repository.url.path
filePrefix = getRunTextParameter(self.run, FILE_PREFIX) or self.project.name
cnsExe = getRunTextParameter(self.run, CNS_EXE) or '/usr/bin/cns'
workingDir = getRunTextParameter(self.run, WORKING_DIR) or defaultDir
tempDir = getRunTextParameter(self.run, TEMP_DIR) or defaultDir
self.filePrefixEntry.set(filePrefix)
self.cnsExeEntry.set(cnsExe)
self.workingDirEntry.set(workingDir)
self.tempDirEntry.set(tempDir)
self.updateEntryParams()
def updateEntryParams(self, event=None):
if self.run:
repository = self.project.findFirstRepository(name='userData')
defaultDir = repository.url.path
filePrefix = self.filePrefixEntry.get() or self.project.name
cnsExe = self.cnsExeEntry.get() or '/usr/bin/cns'
workingDir = self.workingDirEntry.get() or defaultDir
tempDir = self.tempDirEntry.get() or defaultDir
setRunParameter(self.run, FILE_PREFIX, filePrefix)
setRunParameter(self.run, CNS_EXE, cnsExe)
setRunParameter(self.run, WORKING_DIR, workingDir)
setRunParameter(self.run, TEMP_DIR, tempDir)
def selectCnsExe(self):
fileTypes = [ FileType("All", ["*"]), FileType("EXE", ["*.exe"]) ]
popup = FileSelectPopup(self, fileTypes)
file = popup.getFile()
if file:
self.cnsExeEntry.set( file )
popup.destroy()
self.updateEntryParams()
def selectWorkingDir(self):
popup = FileSelectPopup(self, show_file=False)
directory = popup.getDirectory()
if directory:
self.workingDirEntry.set( directory )
popup.destroy()
self.updateEntryParams()
def selectTempDir(self):
popup = FileSelectPopup(self, show_file=False)
directory = popup.getDirectory()
if directory:
self.tempDirEntry.set( directory )
popup.destroy()
self.updateEntryParams()
def getPeakLists(self):
# overwrites superclass
return getThroughSpacePeakLists(self.project)
def administerNotifiers(self, notifyFunc):
NmrCalcRunFrame.administerNotifiers(self, notifyFunc)
for func in ('__init__','delete','setName'):
#notifyFunc(self.updateSettings, 'ccp.nmr.NmrConstraint.AbstractConstraintList', func)
notifyFunc(self.updateSettings, 'ccp.nmr.NmrConstraint.DistanceConstraintList', func)
notifyFunc(self.updateSettings, 'ccp.nmr.NmrConstraint.DihedralConstraintList', func)
notifyFunc(self.updateSettings, 'ccp.nmr.NmrConstraint.HBondConstraintList', func)
def selectOptPeakList(self, obj, row, col):
self.optPeakList = obj
def selectConstraintList(self, obj, row, col):
self.optConstraintList = obj
def doEditMarkExtraRules(self, obj, row, col):
if col in (2,3):
cSet = obj.nmrConstraintStore
if cSet:
for cList in obj.constraintLists:
if cList.className[:-14] != 'Distance':
# i.e. ambig protocols and viol filtering
# is only for dist constraints, not dihedral etc
return False
return True
def toggleUseInCalc(self, dataObj):
toggleObjBooleanParameter(dataObj, USE_IN_CALC)
self.updateSettings()
def toggleFilterViol(self, dataObj):
toggleObjBooleanParameter(dataObj, FILTER_VIOL)
self.updateSettings()
def toggleKeepAssign(self, dataObj):
toggleObjBooleanParameter(dataObj, KEEP_ASSIGN)
self.updateSettings()
def toggleAmbig(self, dataObj):
toggleObjBooleanParameter(dataObj, AMBIG_PROTOCOL)
self.updateSettings()
def updateSettings(self, obj=None):
textMatrix = []
objectList = []
run = self.run
if run:
peakListsData = []
constraintData = []
molSystemData = None
for dataObj in run.sortedInputs():
className = dataObj.className
if className == 'PeakListData':
peakList = dataObj.peakList
if peakList:
peakListsData.append((dataObj, peakList))
elif className == 'MolSystemData':
molSystem = dataObj.molSystem
if molSystem:
molSystemData = (dataObj, molSystem)
elif className == 'ConstraintStoreData':
nmrConstraintStore = dataObj.nmrConstraintStore
if nmrConstraintStore:
constraintLists = dataObj.constraintLists or \
nmrConstraintStore.sortedConstraintLists()
# Chould be only one
for constraintList in constraintLists:
if constraintList is None:
# Prob happens when serial no longer exists
continue
constraintData.append((dataObj, constraintList))
for dataObj, peakList in peakListsData:
spectrum = peakList.dataSource
experiment = spectrum.experiment
filterViol = getObjBooleanParameter(dataObj, FILTER_VIOL)
keepAssign = getObjBooleanParameter(dataObj, KEEP_ASSIGN)
shiftList = peakList.dataSource.experiment.shiftList
if shiftList:
shiftListName = '%d:%s' % (shiftList.serial,shiftList.name)
else:
shiftListName = None
ident = '%s:%s:%d' % (experiment.name,spectrum.name,peakList.serial)
textMatrix.append([ident,
filterViol and 'Yes' or 'No',
keepAssign and 'Yes' or 'No',
shiftListName])
objectList.append(dataObj)
self.optPeakListMatrix.update(textMatrix=textMatrix,objectList=objectList)
textMatrix = []
objectList = []
for dataObj, constraintList in constraintData:
#useInCalc = getObjBooleanParameter(dataObj, USE_IN_CALC)
cSet = dataObj.constraintStoreSerial
cType = constraintList.className[:-14]
if cType == 'Distance':
filterViol = getObjBooleanParameter(dataObj, FILTER_VIOL)
ambigProtocol = getObjBooleanParameter(dataObj, AMBIG_PROTOCOL)
ambigProtocol = ambigProtocol and 'Yes' or 'No'
filterViol = filterViol and 'Yes' or 'No'
else:
ambigProtocol = None
filterViol = None
ident = '%s - %d:%d' % (cType, cSet, constraintList.serial)
textMatrix.append([ident,
constraintList.name,
filterViol,
ambigProtocol])
objectList.append(dataObj)
self.optConstraintMatrix.update(textMatrix=textMatrix,
objectList=objectList)
class CingFrame(NmrSimRunFrame):
def __init__(self, parent, application, *args, **kw):
project = application.project
simStore = project.findFirstNmrSimStore(application=APP_NAME) or \
project.newNmrSimStore(application=APP_NAME, name=APP_NAME)
self.application = application
self.residue = None
self.structure = None
self.serverCredentials = None
self.iCingBaseUrl = DEFAULT_URL
self.resultsUrl = None
self.chain = None
self.nmrProject = application.nmrProject
self.serverDone = False
NmrSimRunFrame.__init__(self, parent, project, simStore, *args, **kw)
# # # # # # New Structure Frame # # # # #
self.structureFrame.grid_forget()
tab = self.tabbedFrame.frames[0]
frame = Frame(tab, grid=(1,0))
frame.expandGrid(2,1)
div = LabelDivider(frame, text='Structures', grid=(0,0), gridSpan=(1,2))
label = Label(frame, text='Ensemble: ', grid=(1,0))
self.structurePulldown = PulldownList(frame, callback=self.changeStructure, grid=(1,1))
headingList = ['Model','Use']
editWidgets = [None,None]
editGetCallbacks = [None,self.toggleModel]
editSetCallbacks = [None,None,]
self.modelTable = ScrolledMatrix(frame, grid=(2,0), gridSpan=(1,2),
callback=self.selectStructModel,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
headingList=headingList)
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateModels, self.disableModels]
buttons = ButtonList(frame, texts=texts, commands=commands, grid=(3,0), gridSpan=(1,2))
# # # # # # Submission frame # # # # # #
tab = self.tabbedFrame.frames[1]
tab.expandGrid(1,0)
frame = LabelFrame(tab, text='Server Job Submission', grid=(0,0))
frame.expandGrid(None,2)
srow = 0
label = Label(frame, text='iCing URL:', grid=(srow, 0))
urls = [DEFAULT_URL,]
self.iCingBaseUrlPulldown = PulldownList(frame, texts=urls, objects=urls, index=0, grid=(srow,1))
srow +=1
label = Label(frame, text='Results File:', grid=(srow, 0))
self.resultFileEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
self.setZipFileName()
button = Button(frame, text='Choose File', bd=1, sticky='ew',
command=self.chooseZipFile, grid=(srow, 2))
srow +=1
label = Label(frame, text='Results URL:', grid=(srow, 0))
self.resultUrlEntry = Entry(frame, bd=1, text='', grid=(srow,1), width=50)
button = Button(frame, text='View Results HTML', bd=1, sticky='ew',
command=self.viewHtmlResults, grid=(srow, 2))
srow +=1
texts = ['Submit Project!', 'Check Run Status',
'Purge Server Result', 'Download Results']
commands = [self.runCingServer, self.checkStatus,
self.purgeCingServer, self.downloadResults]
self.buttonBar = ButtonList(frame, texts=texts, commands=commands,
grid=(srow, 0), gridSpan=(1,3))
for button in self.buttonBar.buttons[:1]:
button.config(bg=CING_BLUE)
# # # # # # Residue frame # # # # # #
frame = LabelFrame(tab, text='Residue Options', grid=(1,0))
frame.expandGrid(1,1)
label = Label(frame, text='Chain: ')
label.grid(row=0,column=0,sticky='w')
self.chainPulldown = PulldownList(frame, callback=self.changeChain)
self.chainPulldown.grid(row=0,column=1,sticky='w')
headingList = ['#','Residue','Linking','Decriptor','Use?']
editWidgets = [None,None,None,None,None]
editGetCallbacks = [None,None,None,None,self.toggleResidue]
editSetCallbacks = [None,None,None,None,None,]
self.residueMatrix = ScrolledMatrix(frame,
headingList=headingList,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
callback=self.selectResidue)
self.residueMatrix.grid(row=1, column=0, columnspan=2, sticky = 'nsew')
texts = ['Activate Selected','Inactivate Selected']
commands = [self.activateResidues, self.deactivateResidues]
self.resButtons = ButtonList(frame, texts=texts, commands=commands,)
self.resButtons.grid(row=2, column=0, columnspan=2, sticky='ew')
"""
# # # # # # Validate frame # # # # # #
frame = LabelFrame(tab, text='Validation Options', grid=(2,0))
frame.expandGrid(None,2)
srow = 0
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=0,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='Assignments and shifts')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=0,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='Restraints')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckQueen = CheckButton(frame)
self.selectCheckQueen.grid(row=srow, column=0,sticky='nw' )
self.selectCheckQueen.set(False)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=1,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=0,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='User Python script\n(overriding option)')
label.grid(row=srow,column=1,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,sticky='ew')
scriptButton = Button(frame, bd=1,
command=self.chooseValidScript,
text='Browse')
scriptButton.grid(row=srow,column=3,sticky='ew')
"""
# # # # # # # # # #
self.update(simStore)
self.administerNotifiers(application.registerNotify)
def downloadResults(self):
if not self.run:
msg = 'No current iCing run'
showWarning('Failure', msg, parent=self)
return
credentials = self.serverCredentials
if not credentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
fileName = self.resultFileEntry.get()
if not fileName:
msg = 'No save file specified'
showWarning('Failure', msg, parent=self)
return
if os.path.exists(fileName):
msg = 'File %s already exists. Overwite?' % fileName
if not showOkCancel('Query', msg, parent=self):
return
url = self.iCingBaseUrl
iCingUrl = self.getServerUrl(url)
logText = iCingRobot.iCingFetch(credentials, url, iCingUrl, fileName)
print logText
msg = 'Results saved to file %s\n' % fileName
msg += 'Purge results from iCing server?'
if showYesNo('Query',msg, parent=self):
self.purgeCingServer()
def getServerUrl(self, baseUrl):
iCingUrl = os.path.join(baseUrl, 'icing/serv/iCingServlet')
return iCingUrl
def viewHtmlResults(self):
resultsUrl = self.resultsUrl
if not resultsUrl:
msg = 'No current iCing results URL'
showWarning('Failure', msg, parent=self)
return
webBrowser = WebBrowser(self.application, popup=self.application)
webBrowser.open(self.resultsUrl)
def runCingServer(self):
if not self.project:
return
run = self.run
if not run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
structure = self.structure
if not structure:
msg = 'No structure ensemble selected'
showWarning('Failure', msg, parent=self)
return
ensembleText = getModelsString(run)
if not ensembleText:
msg = 'No structural models selected from ensemble'
showWarning('Failure', msg, parent=self)
return
residueText = getResiduesString(structure)
if not residueText:
msg = 'No active residues selected in structure'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrlPulldown.getObject()
url.strip()
if not url:
msg = 'No iCing server URL specified'
showWarning('Failure', msg, parent=self)
self.iCingBaseUrl = None
return
msg = 'Submit job now? You will be informed when the job is done.'
if not showOkCancel('Confirm', msg, parent=self):
return
self.iCingBaseUrl = url
iCingUrl = self.getServerUrl(url)
self.serverCredentials, results, tarFileName = iCingRobot.iCingSetup(self.project, userId='ccpnAp', url=iCingUrl)
if not results:
# Message already issued on failure
self.serverCredentials = None
self.resultsUrl = None
self.update()
return
else:
credentials = self.serverCredentials
os.unlink(tarFileName)
entryId = iCingRobot.iCingProjectName(credentials, iCingUrl).get(iCingRobot.RESPONSE_RESULT)
baseUrl, htmlUrl, logUrl, zipUrl = iCingRobot.getResultUrls(credentials, entryId, url)
self.resultsUrl = htmlUrl
# Save server data in this run for persistence
setRunParameter(run, iCingRobot.FORM_USER_ID, self.serverCredentials[0][1])
setRunParameter(run, iCingRobot.FORM_ACCESS_KEY, self.serverCredentials[1][1])
setRunParameter(run, ICING_BASE_URL, url)
setRunParameter(run, HTML_RESULTS_URL, htmlUrl)
self.update()
run.inputStructures = structure.sortedModels()
# select residues from the structure's chain
#iCingRobot.iCingResidueSelection(credentials, iCingUrl, residueText)
# Select models from ensemble
#iCingRobot.iCingEnsembleSelection(credentials, iCingUrl, ensembleText)
# Start the actual run
self.serverDone = False
iCingRobot.iCingRun(credentials, iCingUrl)
# Fetch server progress occasionally, report when done
# this function will call itself again and again
self.after(CHECK_INTERVAL, self.timedCheckStatus)
self.update()
def timedCheckStatus(self):
if not self.serverCredentials:
return
if self.serverDone:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
self.serverDone = True
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
return
self.after(CHECK_INTERVAL, self.timedCheckStatus)
def checkStatus(self):
if not self.serverCredentials:
return
status = iCingRobot.iCingStatus(self.serverCredentials, self.getServerUrl(self.iCingBaseUrl))
if not status:
#something broke, already warned
return
result = status.get(iCingRobot.RESPONSE_RESULT)
if result == iCingRobot.RESPONSE_DONE:
msg = 'CING run is complete!'
showInfo('Completion', msg, parent=self)
self.serverDone = True
return
else:
msg = 'CING job is not done.'
showInfo('Processing', msg, parent=self)
self.serverDone = False
return
def purgeCingServer(self):
if not self.project:
return
if not self.run:
msg = 'No CING run setup'
showWarning('Failure', msg, parent=self)
return
if not self.serverCredentials:
msg = 'No current iCing server job'
showWarning('Failure', msg, parent=self)
return
url = self.iCingBaseUrl
results = iCingRobot.iCingPurge(self.serverCredentials, self.getServerUrl(url))
if results:
showInfo('Info','iCing server results cleared')
self.serverCredentials = None
self.iCingBaseUrl = None
self.serverDone = False
deleteRunParameter(self.run, iCingRobot.FORM_USER_ID)
deleteRunParameter(self.run, iCingRobot.FORM_ACCESS_KEY)
deleteRunParameter(self.run, HTML_RESULTS_URL)
else:
showInfo('Info','Purge failed')
self.update()
def chooseZipFile(self):
fileTypes = [ FileType('Zip', ['*.zip']), ]
popup = FileSelectPopup(self, file_types=fileTypes, file=self.resultFileEntry.get(),
title='Results zip file location', dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def setZipFileName(self):
zipFile = '%s_CING_report.zip' % self.project.name
self.resultFileEntry.set(zipFile)
def selectStructModel(self, model, row, col):
self.model = model
def selectResidue(self, residue, row, col):
self.residue = residue
def deactivateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = False
self.updateResidues()
def activateResidues(self):
for residue in self.residueMatrix.currentObjects:
residue.useInCing = True
self.updateResidues()
def activateModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model not in self.run.inputStructures:
self.run.addInputStructure(model)
self.updateModels()
def disableModels(self):
if self.run:
for model in self.modelTable.currentObjects:
if model in self.run.inputStructures:
self.run.removeInputStructure(model)
self.updateModels()
def toggleModel(self, *opt):
if self.model and self.run:
if self.model in self.run.inputStructures:
self.run.removeInputStructure(self.model)
else:
self.run.addInputStructure(self.model)
self.updateModels()
def toggleResidue(self, *opt):
if self.residue:
self.residue.useInCing = not self.residue.useInCing
self.updateResidues()
def updateResidues(self):
if self.residue and (self.residue.topObject is not self.structure):
self.residue = None
textMatrix = []
objectList = []
colorMatrix = []
if self.chain:
chainCode = self.chain.code
for residue in self.chain.sortedResidues():
msResidue = residue.residue
if not hasattr(residue, 'useInCing'):
residue.useInCing = True
if residue.useInCing:
colors = [None, None, None, None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None, None, None, None]
use = 'No'
datum = [residue.seqCode,
msResidue.ccpCode,
msResidue.linking,
msResidue.descriptor,
use,]
textMatrix.append(datum)
objectList.append(residue)
colorMatrix.append(colors)
self.residueMatrix.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def updateChains(self):
index = 0
names = []
chains = []
chain = self.chain
if self.structure:
chains = self.structure.sortedCoordChains()
names = [chain.code for chain in chains]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
self.changeChain(chain)
self.chainPulldown.setup(names, chains, index)
def updateStructures(self):
index = 0
names = []
structures = []
structure = self.structure
if self.run:
model = self.run.findFirstInputStructure()
if model:
structure = model.structureEnsemble
structures0 = [(s.ensembleId, s) for s in self.project.structureEnsembles]
structures0.sort()
for eId, structure in structures0:
name = '%s:%s' % (structure.molSystem.code, eId)
structures.append(structure)
names.append(name)
if structures:
if structure not in structures:
structure = structures[-1]
index = structures.index(structure)
self.changeStructure(structure)
self.structurePulldown.setup(names, structures, index)
def updateModels(self):
textMatrix = []
objectList = []
colorMatrix = []
if self.structure and self.run:
used = self.run.inputStructures
for model in self.structure.sortedModels():
if model in used:
colors = [None, CING_BLUE]
use = 'Yes'
else:
colors = [None, None]
use = 'No'
datum = [model.serial,use]
textMatrix.append(datum)
objectList.append(model)
colorMatrix.append(colors)
self.modelTable.update(objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix)
def changeStructure(self, structure):
if self.project and (self.structure is not structure):
self.project.currentEstructureEnsemble = structure
self.structure = structure
if self.run:
self.run.inputStructures = structure.sortedModels()
self.updateModels()
self.updateChains()
def changeChain(self, chain):
if self.project and (self.chain is not chain):
self.chain = chain
self.updateResidues()
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('Python', ['*.py']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title='Python file', dismiss_text='Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
def updateAll(self, project=None):
if project:
self.project = project
self.nmrProject = project.currentNmrProject
simStore = project.findFirstNmrSimStore(application='CING') or \
project.newNmrSimStore(application='CING', name='CING')
else:
simStore = None
if not self.project:
return
self.setZipFileName()
if not self.project.currentNmrProject:
name = self.project.name
self.nmrProject = self.project.newNmrProject(name=name)
else:
self.nmrProject = self.project.currentNmrProject
self.update(simStore)
def update(self, simStore=None):
NmrSimRunFrame.update(self, simStore)
run = self.run
urls = [DEFAULT_URL,]
index = 0
if run:
userId = getRunParameter(run, iCingRobot.FORM_USER_ID)
accessKey = getRunParameter(run, iCingRobot.FORM_ACCESS_KEY)
if userId and accessKey:
self.serverCredentials = [(iCingRobot.FORM_USER_ID, userId),
(iCingRobot.FORM_ACCESS_KEY, accessKey)]
url = getRunParameter(run, ICING_BASE_URL)
if url:
htmlUrl = getRunParameter(run, HTML_RESULTS_URL)
self.iCingBaseUrl = url
self.resultsUrl = htmlUrl # May be None
self.resultUrlEntry.set(self.resultsUrl)
if self.iCingBaseUrl and self.iCingBaseUrl not in urls:
index = len(urls)
urls.append(self.iCingBaseUrl)
self.iCingBaseUrlPulldown.setup(urls, urls, index)
self.updateButtons()
self.updateStructures()
self.updateModels()
self.updateChains()
def updateButtons(self, event=None):
buttons = self.buttonBar.buttons
if self.project and self.run:
buttons[0].enable()
if self.resultsUrl and self.serverCredentials:
buttons[1].enable()
buttons[2].enable()
buttons[3].enable()
else:
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
else:
buttons[0].disable()
buttons[1].disable()
buttons[2].disable()
buttons[3].disable()
class BackupProjectPopup(BasePopup):
"""
**Create Automatic Project Backup**
The purpose of this dialog is to allow the user to create backups
of their project automatically. The XML files for the backup go
into a separate directory from the project itself. If the project
directory is called PROJECTDIR then the default for the backup
directory is PROJECTDIR_backup, although that can be changed to
something else in this dialog.
Other than the backup directory, the user can specify the frequency
of the backup, in minutes.
The "Apply Auto Settings" does not have to be applied if the user
has changed the on/off setting or if the user has changed the
Auto-backup frequency and entered a carriage return.
The "Do Immediate Backup" is in case the user wants to do a backup
then and there.
There is no backup for the backup.
"""
on_off_entries = ['on', 'off']
def __init__(self, parent, help_msg='', help_url='', *args, **kw):
self.help_msg = help_msg
self.help_url = help_url
BasePopup.__init__(self, parent=parent, title='Project : Backup', **kw)
def body(self, guiFrame):
self.geometry('500x130')
guiFrame.grid_columnconfigure(2, weight=1)
guiFrame.grid_rowconfigure(3, weight=1)
self.alarm_id = None
row = 0
tipText = 'Browse for the directory into which project backups will be made'
button = Button(guiFrame,
text='Directory:',
command=self.selectDir,
grid=(row, 0),
tipText=tipText,
sticky='ew')
repository = self.project.findFirstRepository(name='backup')
if repository:
text = repository.url.path
else: # this is trouble, but should not happen
text = ''
tipText = 'Enter the name of the directory into which project backups will be made'
self.dir_entry = Entry(guiFrame,
text=text,
tipText=tipText,
width=40,
returnCallback=self.applyAuto,
grid=(row, 1),
gridSpan=(1, 2),
sticky='ew')
row += 1
label = Label(guiFrame, text='Auto-backup:', grid=(row, 0))
if self.analysisProject.doAutoBackup:
ind = 0
else:
ind = 1
tipTexts = [
'Toggle the timed automatic backup on',
'Toggle the timed automatic backup off'
]
self.on_off_buttons = RadioButtons(guiFrame,
entries=self.on_off_entries,
tipTexts=tipTexts,
select_callback=self.applyAuto,
selected_index=ind,
grid=(row, 1))
row += 1
tipText = 'The number of minutes to wait before automatic project backups'
label = Label(guiFrame, text='Auto-backup frequency:', grid=(row, 0))
self.freq_entry = IntEntry(guiFrame,
text=self.analysisProject.autoBackupFreq,
returnCallback=self.applyAuto,
tipText=tipText)
self.freq_entry.grid(row=row, column=1)
label = Label(guiFrame, text=' (minutes)', grid=(row, 2))
row = row + 1
# Blank for expansion
row = row + 1
texts = ['Apply Auto Settings', 'Do Immediate Backup']
commands = [self.applyAuto, self.applyManual]
tipTexts = [
'Commit the specified settings and commence automated CCPN project backup',
'Backup the CCPN project now, into the specified backup directory'
]
buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
doClone=False,
helpMsg=self.help_msg,
helpUrl=self.help_url,
tipTexts=tipTexts,
grid=(row, 0),
gridSpan=(1, 3),
sticky='nsew')
def selectDir(self):
popup = FileSelectPopup(self, show_file=False)
dir = popup.getDirectory()
popup.destroy()
if (dir):
self.dir_entry.set(dir)
self.setDir()
def setDir(self):
directory = self.dir_entry.get()
if not directory:
showWarning('No directory',
'No directory specified, not setting backup directory',
parent=self)
return
if not os.path.abspath(directory):
directory = joinPath(os.getcwd(), directory)
if os.path.exists(directory):
if not os.path.isdir(directory):
showWarning('Path not directory',
'Path "%s" exists but is not a directory' %
directory,
parent=self)
return
else:
if showYesNo(
'Directory does not exist',
'Directory "%s" does not exist, should it be created?' %
directory,
parent=self):
os.mkdir(directory)
else:
showWarning(
'Directory not created',
'Directory "%s" not created so not setting backup directory'
% directory,
parent=self)
return
repository = self.project.findFirstRepository(name='backup')
if not repository:
showWarning(
'No backup repository',
'No backup repository found (something wrong somewhere)',
parent=self)
return
url = repository.url
if url.path != directory:
repository.url = Url(path=normalisePath(directory))
def setFreq(self):
freq = self.freq_entry.get()
if (freq is None):
freq = 0
self.analysisProject.autoBackupFreq = freq
def setInfo(self):
self.setFreq()
self.setDir()
on_off = (self.on_off_buttons.get() == 'on')
self.analysisProject.doAutoBackup = on_off
def applyAuto(self, *event):
self.setInfo()
on_off = self.on_off_buttons.get()
if on_off == 'on':
self.parent.setBackupOn()
else:
self.parent.setBackupOff()
def applyManual(self):
self.setDir()
self.parent.doBackup()
class CreateContourFilePopup(BasePopup):
"""
**Create Contour Files for Project**
The purpose of this dialog is to allow the user to create new contour
files for the project. Not only the spectrum has to be specified, but
also the two dimensions (X, Y) that are going to be contoured. The
table specifies the conditions that specify the region being contoured,
in terms of what is included and excluded.
For now, only one condition (which is an "include" condition) is allowed.
This also means that the "Add Condition" and "Delete Condition" buttons
are disabled.
The contour directory is specified by the program, using the project
directory but the file name can be specified by the user.
The contour levels used are the ones that are current for the spectrum,
as set in the `Contour Levels dialog`_.
See also: `Spectrum Contour Files`_, `Add Existing Contour Files`_.
.. _`Contour Levels dialog`: EditContourLevelsPopup.html
.. _`Spectrum Contour Files`: EditContourFilesPopup.html
.. _`Add Existing Contour Files`: AddContourFilePopup.html
"""
def __init__(self, parent, *args, **kw):
self.spectrumConditions = []
self.col = None
self.spectrum = None
BasePopup.__init__(self, parent=parent, title='New Contour File', **kw)
def body(self, master):
self.geometry('650x200')
master.grid_columnconfigure(1, weight=1)
row = 0
frame = Frame(master, grid=(row, 0), gridSpan=(1,2))
label = Label(frame, text='Spectrum: ', grid=(row, 0))
tipText = 'Selects the experiment and spectrum for which to make a contour file'
self.expt_spectrum = PulldownList(frame, grid=(row, 1),
tipText=tipText, callback=self.update)
label = Label(frame, text=' (X-dim, Y-dim): ', grid=(row, 2))
tipText = 'Selects which dimensions (projection) of the spectrum form the X and Y axes of the contour file'
self.dim_menu = PulldownList(frame, grid=(row, 3), tipText=tipText,
callback=self.updateFile)
row = row + 1
master.grid_rowconfigure(row, weight=1)
#### for now not editable because only allow one include region
###self.conditionMenu = PulldownMenu(self, entries=('include', 'exclude'),
### callback=self.selectedCondition, do_initial_callback=False)
self.regionEntry = FloatEntry(self, text='', returnCallback=self.setRegion, width=10)
tipTexts = ['Whether to include or exclude the region in the contour file',
'',
'',
'']
headingList = ['Condition','','','','']
editSetCallbacks = [None]
editGetCallbacks = [None]
###editWidgets = [self.conditionMenu]
editWidgets = [None]
self.conditionTable = ScrolledMatrix(master, initialRows=6,
grid=(row, 0), gridSpan=(1,2),
tipTexts=tipTexts,
headingList=headingList,
callback=self.selectCell,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
# TBD: make directory editable
row = row + 1
label = Label(master, text='Contour dir: ', grid=(row, 0), sticky='e')
tipText = 'The directory location on disk into which contour files are saved'
self.dir_label = Label(master, text='', grid=(row, 1), tipText=tipText)
row = row + 1
label = Label(master, text='File name: ', grid=(row, 0), sticky='e')
tipText = 'Sets the name of the contour file to save to disk'
self.file_entry = Entry(master, grid=(row, 1), tipText=tipText)
##row = row + 1
##label = Label(master, text='Contour levels: ')
##label.grid(row=row, column=0, sticky='e')
##self.levels_entry = FloatEntry(master, isArray=True, returnCallback=self.saveLevels)
##self.levels_entry.grid(row=row, column=1, sticky='ew')
row = row + 1
tipTexts = ['Add a new contour region for including in or excluding from the contour file ',
'Remove the selected contour region from the table',
'Make the specified contour file using the input settings & regions']
texts = [ 'Add Condition', 'Delete Condition', 'Contour and Save' ]
commands = [ self.addCondition, self.deleteCondition, self.contourAndSaveSpectrum ]
self.buttons = UtilityButtonList(master, texts=texts, commands=commands,
doClone=False, helpUrl=self.help_url,
grid=(row, 0), gridSpan=(1,2), tipTexts=tipTexts)
### TBD disabled for now
for n in range(2):
self.buttons.buttons[n].config(state='disabled')
self.curateNotifiers(self.registerNotify)
self.updateSpectrum()
self.updateDimMenu()
def destroy(self):
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
for clazz in ('Experiment', 'DataSource'):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateNotifier, 'ccp.nmr.Nmr.%s' % clazz, func)
def update(self, spectrum):
if spectrum is self.spectrum:
return
self.spectrum = spectrum
self.updateDimMenu()
self.updateConditionTable()
self.updateFile()
##self.updateLevels()
def updateSpectrum(self, spectrum=None):
if not spectrum:
spectrum = self.spectrum
spectra = self.parent.getSpectra()
if spectra:
if spectrum not in spectra:
spectrum = spectra[0]
index = spectra.index(spectrum)
names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra]
else:
index = 0
names = []
self.expt_spectrum.setup(names, spectra, index)
self.update(spectrum)
def updateNotifier(self, *extra):
self.updateSpectrum()
def updateFile(self, *extra):
spectrum = self.spectrum
if not spectrum:
return
analysisSpectrum = spectrum.analysisSpectrum
if not analysisSpectrum:
return
dims = self.dim_menu.getText()
dims = [int(dim) for dim in dims.split(', ')]
(xdim, ydim) = dims
storedContour = analysisSpectrum.findFirstStoredContour(dims=dims)
if not storedContour:
storedContour = analysisSpectrum.findFirstStoredContour()
if storedContour:
fileName = storedContour.path
else:
fileName = '%s_%s_%d_%d.cnt' % (spectrum.experiment.name, spectrum.name, xdim, ydim)
path = self.getContourDir()
self.dir_label.set(path)
self.file_entry.set(fileName)
def getContourDir(self):
spectrum = self.spectrum
if not spectrum:
return ''
analysisSpectrum = spectrum.analysisSpectrum
if not analysisSpectrum:
return ''
url = analysisSpectrum.contourDir
if url: # should be the case since set in Analysis.py
path = url.dataLocation
else:
path = ''
return path
"""
def saveFile(self, *extra):
spectrum = self.spectrum
if not spectrum:
return
analysisSpectrum = spectrum.analysisSpectrum
if not analysisSpectrum:
return
fileName = self.file_entry.get()
if fileName:
application = self.project.application
application.setValue(spectrum, keyword='contourFileName', value=fileName)
"""
def updateDimMenu(self):
entries = []
spectrum = self.spectrum
if spectrum:
ndim = spectrum.numDim
for xdim in range(1, ndim):
dataDim = spectrum.findFirstDataDim(dim=xdim)
if dataDim.className != 'SampledDataDim':
for ydim in range(xdim+1, ndim+1):
dataDim = spectrum.findFirstDataDim(dim=ydim)
if dataDim.className != 'SampledDataDim':
entries.append('%d, %d' % (xdim, ydim))
self.dim_menu.setup(entries, objects=None, index=0)
def updateConditionTable(self, *extra):
spectrum = self.spectrum
if spectrum:
ndim = spectrum.numDim
else:
ndim = 0
tipTexts = ['Whether to include or exclude the region in the contour file',]
headingList = ['Condition']
###editWidgets = [self.conditionMenu] + 2*ndim*[self.regionEntry]
###editGetCallbacks = [self.getCondition]
###editSetCallbacks = [self.setCondition]
editWidgets = [None] + 2*ndim*[self.regionEntry]
editGetCallbacks = [None]
editSetCallbacks = [None]
for i in range(ndim):
dim = i + 1
headingList.extend(['Dim %d Min' % dim, 'Dim %d Max' % dim])
editGetCallbacks.append(lambda obj, i=i: self.getRegionMin(obj, i))
editGetCallbacks.append(lambda obj, i=i: self.getRegionMax(obj, i))
editSetCallbacks.append(lambda obj, i=i: self.setRegionMin(obj, i))
editSetCallbacks.append(lambda obj, i=i: self.setRegionMax(obj, i))
tipTexts.append('Lower bound of dimension %d region to include or exclude' % dim)
tipTexts.append('Upper bound of dimension %d region to include or exclude' % dim)
objectList = []
textMatrix = []
self.spectrumConditions = self.getSpectrumConditions()
for spectrumCondition in self.spectrumConditions:
(condition, region) = spectrumCondition
objectList.append(spectrumCondition)
textRow = [condition]
for i in range(ndim):
r = region[i]
if r:
rMin = r[0]
rMax = r[1]
else:
rMin = rMax = None
textRow.append(rMin)
textRow.append(rMax)
textMatrix.append(textRow)
self.conditionTable.update(objectList=objectList, textMatrix=textMatrix,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets)
"""
def updateLevels(self):
spectrum = self.getSpectrum()
if spectrum:
analysisSpectrum = spectrum.analysisSpectrum
levels = analysisSpectrum.posLevels + analysisSpectrum.negLevels
scale = spectrum.scale / self.analysisProject.globalContourScale
levels = [ level/scale for level in levels ]
else:
levels = []
self.levels_entry.set(levels)
def saveLevels(self):
spectrum = self.spectrum
if not spectrum:
return
"""
def getRegionMin(self, spectrumCondition, dim):
#print 'getRegionMin'
(condition, region) = spectrumCondition
self.regionEntry.set(region[dim][0])
def setRegionMin(self, spectrumCondition, dim):
#print 'setRegionMin'
(condition, region) = spectrumCondition
(r0, r1) = region[dim]
r = self.regionEntry.get()
region[dim] = (r, r1)
self.setSpectrumConditions()
self.updateConditionTable()
def getRegionMax(self, spectrumCondition, dim):
#print 'getRegionMax'
(condition, region) = spectrumCondition
self.regionEntry.set(region[dim][1])
def setRegionMax(self, spectrumCondition, dim):
#print 'setRegionMax'
(condition, region) = spectrumCondition
(r0, r1) = region[dim]
r = self.regionEntry.get()
region[dim] = (r0, r)
self.setSpectrumConditions()
self.updateConditionTable()
def setRegion(self, *extra):
spectrumCondition = self.getCurrentObject()
if spectrumCondition and self.col is not None:
col = self.col - 1 # -1 because of condition
dim = col / 2
if col % 2: # max
self.setRegionMax(spectrumCondition, dim)
else: # min
self.setRegionMin(spectrumCondition, dim)
""" not needed for now
def getCondition(self, spectrumCondition):
#print 'getCondition'
(condition, region) = spectrumCondition
self.conditionMenu.set(condition)
def setCondition(self, spectrumCondition):
#print 'setCondition'
spectrumCondition[0] = self.conditionMenu.get()
self.setSpectrumConditions()
def selectedCondition(self, ind, condition):
spectrumCondition = self.getCurrentObject()
if spectrumCondition is not None:
self.setCondition(spectrumCondition)
"""
def getSpectrumConditions(self):
spectrum = self.spectrum
if not spectrum:
return []
application = self.project.application
spectrumConditions = application.getValue(spectrum, keyword='contourFileConditions')
if spectrumConditions:
spectrumConditions = eval(spectrumConditions)
else:
region = []
for i in range(spectrum.numDim):
dim = i + 1
region.append(self.getWholeRegion(spectrum, dim))
spectrumCondition = ['include', region]
spectrumConditions = [spectrumCondition]
self.setSpectrumConditions(spectrumConditions)
return spectrumConditions
def setSpectrumConditions(self, spectrumConditions = None):
spectrum = self.spectrum
if spectrum:
if not spectrumConditions:
spectrumConditions = self.spectrumConditions
application = self.project.application
application.setValue(spectrum, keyword='contourFileConditions', value=str(spectrumConditions))
def getDimMin(self, spectrum, dim):
dataDim = spectrum.findFirstDataDim(dim=dim)
if dataDim.className == 'SampledDataDim':
r = 1.0
else:
converter = UnitConverter.pnt2ppm
dataDimRef = ExperimentBasic.getPrimaryDataDimRef(dataDim)
r = converter(float(dataDim.numPoints), dataDimRef)
return r
def getDimMax(self, spectrum, dim):
dataDim = spectrum.findFirstDataDim(dim=dim)
if dataDim.className == 'SampledDataDim':
r = float(dataDim.numPoints)
else:
converter = UnitConverter.pnt2ppm
dataDimRef = ExperimentBasic.getPrimaryDataDimRef(dataDim)
r = converter(1.0, dataDimRef)
return r
def getWholeRegion(self, spectrum, dim):
rMin = self.getDimMin(spectrum, dim)
rMax = self.getDimMax(spectrum, dim)
return (rMin, rMax)
def getCurrentObject(self):
# sometimes row highlighting stops so obj passed into selectCell might no longer be current
# so instead use direct interrogation of scrolledMatrix
obj = self.conditionTable.currentObject
return obj
def selectCell(self, obj, row, col):
# see note about obj in getCurrentObject()
self.col = col
def addCondition(self):
spectrum = self.spectrum
if spectrum:
ndim = spectrum.numDim
spectrumCondition = ['exclude', ndim*[(None,None)]]
self.spectrumConditions.append(spectrumCondition)
self.setSpectrumConditions()
self.updateConditionTable()
def deleteCondition(self):
spectrumCondition = self.getCurrentObject()
if spectrumCondition:
self.spectrumConditions.remove(spectrumCondition)
self.setSpectrumConditions()
self.updateConditionTable()
def continueIfFileNameUsed(self, fileName):
result = True
storedContoursToDelete = []
for analysisSpectrum in self.analysisProject.analysisSpectra:
for storedContour in analysisSpectrum.storedContours:
if storedContour.fullPath == fileName:
storedContoursToDelete.append(storedContour)
if storedContoursToDelete:
if len(storedContoursToDelete) == 1:
s = ''
t = 's'
else:
s = 's'
t = ''
result = showYesNo('File used', 'Stored contour%s already use%s this fileName, and will be deleted: continue?' % (s, t), parent=self)
if result:
for storedContour in storedContoursToDelete:
try:
storedContour.delete()
except:
pass
return result
def contourAndSaveSpectrum(self):
spectrum = self.spectrum
if not spectrum:
return
if not self.spectrumConditions:
return
###self.saveFile()
fileName = self.file_entry.get()
if not fileName:
showError('No filename', 'No filename given', parent=self)
return
contourDir = self.getContourDir()
fullPath = joinPath(contourDir, fileName)
if not self.continueIfFileNameUsed(fullPath):
return
directory = os.path.dirname(fullPath)
if not os.path.exists(directory):
os.makedirs(directory)
dims = self.dim_menu.getText()
(xdim, ydim) = [int(dim) for dim in dims.split(', ')]
##self.saveLevels()
##levels = self.levels_entry.get()
##if not levels:
## showError('No levels', 'No contour levels given', parent=self)
## return
analysisSpectrum = spectrum.analysisSpectrum
levels = analysisSpectrum.posLevels + analysisSpectrum.negLevels
scale = spectrum.scale / self.analysisProject.globalContourScale
levels = [ level/scale for level in levels ]
spectrumCondition = self.spectrumConditions[0]
(condition, region) = spectrumCondition
ndim = spectrum.numDim
firstInt = ndim * [0]
lastInt = ndim * [0]
for i in range(ndim):
try:
(firstInt[i], lastInt[i]) = self.convertToPoints(spectrum, i, region[i])
except Exception, e:
showError('Invalid region', str(e), parent=self)
try:
#print 'about to saveSpectrumContours', fullPath, xdim, ydim, levels, firstInt, lastInt
saveSpectrumContours(spectrum, fullPath, xdim, ydim, levels, firstInt, lastInt,
mem_cache=self.parent.mem_cache)
except Exception, e:
showError('Save error', str(e), parent=self)
return
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')
class CloudHomologueAssignPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.molSystem = None
self.chain = None
self.assignment = None
self.scores = []
BasePopup.__init__(self, parent, title="Cloud Threader", **kw)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(guiFrame, text='Molecular system: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.molSysPulldown = PulldownMenu(guiFrame, self.changeMolSystem, selected_index=-1, do_initial_callback=0)
self.molSysPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Clouds files: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.filenameEntry = Entry(guiFrame,text='perfect00.pdb')
self.filenameEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Chain: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=-1, do_initial_callback=0)
self.chainPulldown.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Thread steps: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.numStepsEntry = IntEntry(guiFrame,text=3000)
self.numStepsEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Homologue PDB file: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.pdbEntry = Entry(guiFrame,text='')
self.pdbEntry.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Dist. Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.distEntry = FloatEntry(guiFrame,text=3.0)
self.distEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
label = Label(guiFrame, text='Global score: ')
label.grid(row=row, column=0, sticky=Tkinter.NW)
self.globalScoreLabel = Label(guiFrame, text='')
self.globalScoreLabel.grid(row=row, column=1, sticky=Tkinter.NW)
label = Label(guiFrame, text='Assignment Threshold: ')
label.grid(row=row, column=2, sticky=Tkinter.NW)
self.thresholdEntry = FloatEntry(guiFrame,text=-4.5)
self.thresholdEntry.grid(row=row, column=3, sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.graph = ScrolledGraph(guiFrame, width=300, height=200)
self.graph.grid(row=row, column=0, columnspan=4, sticky = Tkinter.NSEW)
row += 1
texts = ['Run','Assign!']
commands = [self.run, self.assignSpinSystems]
bottomButtons = createDismissHelpButtonList(guiFrame,texts=texts,commands=commands,expands=0,help_url=None)
bottomButtons.grid(row=row, column=0, columnspan=4, sticky=Tkinter.EW)
self.assignButton = bottomButtons.buttons[1]
for func in ('__init__','delete'):
Implementation.registerNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.registerNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
self.updateMolSystems()
self.updateChains()
def update(self):
if self.assignment and self.scores:
self.assignButton.enable()
else:
self.assignButton.disable()
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def assignSpinSystems(self):
if self.assignment and self.scores:
if showWarning('Query','Are you sure?'):
threshold = self.thresholdEntry.get() or -4.0
i = 0
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=None)
for residue in self.assignment.keys():
if self.scores[residue] > threshold:
i += 1
spinSystem = self.assignment[residue]
assignSpinSystemResidue(spinSystem,residue=residue)
showWarning('Done','%d residues assigned' % i)
def getMolSystems(self):
names = []
for molSystem in self.project.molSystems:
if molSystem.chains:
names.append( '%s' % (molSystem.code) )
return names
def changeMolSystem(self, i, name):
self.molSystem = self.project.findFirstMolSystem(code=name)
def updateMolSystems(self, *opt):
names = self.getMolSystems()
if names:
if not self.molSystem:
self.molSystem = self.project.findFirstMolSystem(code=names[0])
self.molSysPulldown.setup(names, names.index(self.molSystem.code))
def getChains(self):
chains = []
if self.molSystem:
for chain in self.molSystem.chains:
chains.append( [chain.code, chain] )
return chains
def changeChain(self, i, name=None):
if not name:
i = self.chainPulldown.selected_index
chains = self.getChains()
if chains:
self.chain = chains[i][1]
def updateChains(self, *chain):
chains = self.getChains()
if chains:
names = [x[0] for x in chains]
if (not self.chain) or (self.chain.code not in names):
self.chain = chains[0][1]
self.chainPulldown.setup(names, names.index(self.chain.code) )
self.update()
def destroy(self):
for func in ('__init__','delete'):
Implementation.unregisterNotify(self.updateMolSystems, 'ccp.molecule.MolSystem.MolSystem', func)
Implementation.unregisterNotify(self.updateChains, 'ccp.molecule.MolSystem.Chain', func)
BasePopup.destroy(self)
class SaveProjectFrame(Frame):
def __init__(self,
guiParent,
project,
callback=None,
help_msg='',
help_url='',
dismiss_text='',
modal=False,
*args,
**kw):
self.project = project
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
self.modal = modal
self.did_save = False
Frame.__init__(self, guiParent, *args, **kw)
projDir = Io.getUserDataPath(self.project)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Project Name:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.proj_name_entry = Entry(
guiParent,
text=self.project.name,
returnCallback=self.updateInfo,
leaveCallback=self.updateInfo,
tipText='The name used for the project save directory')
self.proj_name_entry.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(guiParent, text='Project Directory:')
label.grid(row=row, column=0, sticky=Tkinter.E)
label = self.proj_dir_label = Label(guiParent, text=projDir)
label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
guiParent,
text='Note: Project Directory = Save Location + Project Name')
label.grid(row=row, column=1, sticky=Tkinter.W)
text = 'Save binary data with project'
tipText = 'Copy data files (e.g. for spectra) into new project directory if not already in current project directory: careful, this can take some time'
row = row + 1
self.dataCheckButton = CheckButton(guiParent,
text=text,
tipText=tipText)
self.dataCheckButton.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
guiParent.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiParent, text='Save Location')
labelFrame.grid(row=row, column=0, columnspan=2, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
directory = os.path.dirname(projDir)
self.proj_dir_select = FileSelect(
labelFrame,
directory=directory,
select_dir_callback=self.selectDir,
change_dir_callback=self.updateInfo,
should_change_dir_callback=self.shouldChangeDir,
getRowColor=self.getEntryColor,
show_file=False)
self.proj_dir_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = ['Save']
tipTexts = ['Save project with specified name in specified directory']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
except IOError, e:
showError('Save project', str(e))
class ArchiveProjectPopup(BasePopup):
"""
**Archive the Project**
This popup window enables the user to archive the CCPN Project into a gzipped
tar file. By default it only includes the *.xml files which reside in the
project directory. If the "Include *.xml.bak files" check button is checked
then it will also include the *.xml.bak files which reside in the project
directory. If the "Include data files which are in the project directory"
check button is checked then it will also include the binary data files
which reside in the project directory.
**Caveats & Tips**
The archive excludes the reference data *.xml files (quite sensibly).
"""
def __init__(self,
parent,
project,
title='Project : Archive',
callback=None,
help_msg='',
help_url='',
dismiss_text='',
*args,
**kw):
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
BasePopup.__init__(self,
parent=parent,
project=project,
title=title,
*args,
**kw)
def body(self, guiParent):
now = datetime.date.today().strftime('%y%m%d')
filePrefix = '%s_%s' % (self.project.name, now)
projDir = getUserDataPath(self.project)
directory = os.path.dirname(projDir)
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Archive File:')
label.grid(row=row, column=0, sticky=Tkinter.E)
tipText = 'File name (excluding .tgz ending) for archive'
self.fileEntry = Entry(guiParent, text=filePrefix, tipText=tipText)
self.fileEntry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(guiParent, text='.tgz (automatically appended)')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
self.backupCheck = CheckButton(
guiParent,
text='Include *.xml.bak files',
tipText='If checked include *.xml.bak files')
self.backupCheck.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
self.dataCheck = CheckButton(
guiParent,
text='Include data files which are in project directory',
tipText=
'If checked include data files if they are located in project directory'
)
self.dataCheck.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W)
row = row + 1
labelFrame = LabelFrame(guiParent, text='Archive Location')
labelFrame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
self.dirSelect = FileSelect(labelFrame,
directory=directory,
show_file=False)
self.dirSelect.grid(row=0, column=0, sticky=Tkinter.NSEW)
guiParent.grid_rowconfigure(row, weight=1)
row = row + 1
texts = ['Save']
tipTexts = ['Create archive file']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def save(self):
filePrefix = self.fileEntry.get()
directory = self.dirSelect.getDirectory()
filePrefix = joinPath(directory, filePrefix)
fileName = filePrefix + '.tgz'
if os.path.exists(fileName):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % fileName,
parent=self):
return
includeBackups = self.backupCheck.isSelected()
includeData = self.dataCheck.isSelected()
packageProject(self.project, filePrefix, includeBackups, includeData)
class FilterCloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.structure = None
self.name = None
self.clouds = []
self.rmsds = []
self.names = []
self.atomTypes = None
self.waiting = 0
BasePopup.__init__(self, parent=parent, title="Filter Clouds", **kw)
def body(self, guiFrame):
row = 0
guiFrame.grid_columnconfigure(3, weight=1)
label = Label(guiFrame, text='Cloud file names:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.fileNameEntry = Entry(guiFrame,
text='testHistone\d+.pdb',
returnCallback=self.loadClouds)
self.fileNameEntry.grid(row=row, column=1, sticky=Tkinter.W)
strucLabel = Label(guiFrame, text='Comparison structure')
strucLabel.grid(row=row, column=2, sticky=Tkinter.W)
self.strucPulldown = PulldownMenu(guiFrame,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.strucPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
sdTolLabel = Label(guiFrame, text='Tolerance (SDs):')
sdTolLabel.grid(row=row, column=0, sticky=Tkinter.W)
self.sdToleranceEntry = FloatEntry(guiFrame, text=2.0, width=6)
self.sdToleranceEntry.grid(row=row, column=1, stick=Tkinter.W)
atomTypes = ['All', 'H', 'H HA', 'H HA HB']
label = Label(guiFrame, text='RMSD Atom Types:')
label.grid(row=row, column=2, sticky=Tkinter.W)
self.atomsPulldown = PulldownMenu(guiFrame,
entries=atomTypes,
callback=self.setAtomTypes,
selected_index=0,
do_initial_callback=0)
self.atomsPulldown.grid(row=row, column=3, sticky=Tkinter.W)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
colHeadings = ['#', 'File name', 'RMSD to mean']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
initialRows=10,
headingList=colHeadings,
callback=self.selectCell,
objectList=[],
textMatrix=[
[],
],
multiSelect=1)
self.scrolledMatrix.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
texts = [
'Load\nClouds', 'Align\nClouds', 'Calc\nRMSD',
'Make Cloud\nfrom structure', 'Remove', 'Remove\nbad'
]
commands = [
self.loadClouds, self.alignClouds, self.calcRmsd,
self.makeStrucCloud, self.deleteClouds, self.filterClouds
]
self.bottomButtons = createDismissHelpButtonList(
guiFrame,
texts=texts,
expands=1,
commands=commands,
help_url=self.help_url)
self.bottomButtons.grid(row=row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.update()
def alignClouds(self):
pattern = self.fileNameEntry.get()
self.names = getFileNamesFromPattern(pattern, '.')
self.clouds = getCloudsFromFile(self.names, self.guiParent.project)
alignClouds(self.clouds, self.names)
def loadClouds(self):
pattern = self.fileNameEntry.get()
self.names = getFileNamesFromPattern(pattern, '.')
self.clouds = getCloudsFromFile(self.names, self.guiParent.project)
self.name = None
self.rmsds = [None for x in range(len(self.clouds))]
self.updateAfter()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structures:
structures.append(structure)
self.structure = structures[index - 1]
self.updateButtons()
def setAtomTypes(self, index, name=None):
self.atomTypes = atomTypeList[index]
def filterClouds(self):
if self.clouds:
sdTolerance = self.sdToleranceEntry.get() or 2.0
keptClouds = []
meanRmsd = 0.0
N = 0
for rmsd in self.rmsds:
meanRmsd += rmsd or 0.0
N += 1
if N > 0:
meanRmsd /= float(N)
sd = 0.0
for r in self.rmsds:
rmsd = r or 0.0
sd += (rmsd - meanRmsd) * (rmsd - meanRmsd)
if N > 0:
sd /= float(N - 1)
sd = sqrt(sd)
print meanRmsd, '+/-', sd
for i in range(len(self.clouds), 0, -1):
rmsd = self.rmsds[i]
if abs(rmsd - meanRmsd) > (sdTolerance * sd):
self.rmsds.pop(i)
self.names.pop(i)
self.clouds.pop(i)
#print 'Cloud %s is bad' % (cloud)
self.updateAfter()
def makeStrucCloud(self):
if self.structure and self.clouds:
pdbFileName = 'CloudForStructure.pdb'
atomCoordList = []
atomCoordList0 = []
resDict = {}
hmass = 25
resonances = self.clouds[0].keys()
resonances2 = []
C = 0
for resonance in resonances:
if resonance == 'rmsd':
continue
resonanceSet = resonance.resonanceSet
if resonanceSet:
i = list(resonanceSet.resonances).index(resonance)
atomSet = list(resonance.resonanceSet.atomSets)[i]
coords = getAtomSetCoords(atomSet, self.structure)
coord = coords[0]
atomCoordList.append([coord.x, coord.y, coord.z])
atomCoordList0.append([coord.x, coord.y, coord.z])
resonances2.append(resonance)
C += 1
print len(atomCoordList)
print len(resonances), len(resonances2)
print "Generating Mean"
cloudsList = []
for cloud in self.clouds:
orderCloud = []
for resonance in resonances2:
x, y, z = cloud.get(resonance) or (0.0, 0.0, 0.0)
orderCloud.append([-x, -y, -z])
cloudsList.append(orderCloud)
(meanCloud, cloudsList) = alignToMeanCloud(cloudsList)
weights = [1.0 for x in atomCoordList]
centerCoords(atomCoordList)
print "init cen", getMeanCoords(atomCoordList)
print "mean cen", getMeanCoords(meanCloud)
print "Print aligning struct clouds to mean", len(meanCloud), len(
atomCoordList), len(weights)
atomCoordsList, error, rotMat = alignCoordinates(
meanCloud, atomCoordList, weights)
print " Rotation", rotMat
writeTypedPdbCloud(atomCoordList, pdbFileName, resonances2)
print "Getting centres"
oldCentre = getMeanCoords(atomCoordList0)
newCentre = getMeanCoords(atomCoordList)
delta = [
newCentre[i] - oldCentre[i] for i in range(len(oldCentre))
]
print " New centre", newCentre
print " Old centre", oldCentre
print " Delta", delta
#inverseRot = inverseMatrix(rotMat)
model = self.structure.findFirstModel()
coordinates = model.coordinates
offset = 0
iis = (0, 1, 2)
for atom in self.structure.orderedAtoms:
next = offset + 3
coords = [coordinates[offset + ii] + delta[ii] for ii in iis]
coords = matrixVecMultiply(rotMat, coords)
coordinates[offset:next] = coords
offset = next
model.setSubmatrixData('coordinates', coordinates)
clouds = getCloudsFromFile([
pdbFileName,
], self.structure.root)
self.clouds.append(clouds[0])
self.rmsds.append(None)
self.names.append(pdbFileName)
self.updateAfter()
def calcRmsd(self):
if self.clouds:
if len(self.scrolledMatrix.currentObjects) < 2:
clouds = self.clouds
else:
clouds = []
for name in self.scrolledMatrix.currentObjects:
clouds.append(self.clouds[self.names.index(name)])
self.rmsds = filterClouds(clouds, atomTypes=self.atomTypes)
self.updateAfter()
def deleteClouds(self):
if self.names and self.name and showOkCancel(
'Confirm', 'Really remove selected clouds?'):
indices = []
for name in self.scrolledMatrix.currentObjects:
i = self.names.index(name)
indices.append(i)
indices.sort()
indices.reverse()
for i in indices:
self.clouds.pop(i)
self.rmsds.pop(i)
self.names.pop(i)
self.name = None
self.updateAfter()
def selectCell(self, name, row, col):
self.name = name
self.updateButtons()
def updateAfter(self, *opt):
if self.waiting:
return
else:
self.waiting = 1
self.after_idle(self.update)
def destroy(self):
BasePopup.destroy(self)
def updateButtons(self):
if self.names:
self.bottomButtons.buttons[1].enable()
self.bottomButtons.buttons[2].enable()
self.bottomButtons.buttons[5].enable()
else:
self.bottomButtons.buttons[1].disable()
self.bottomButtons.buttons[2].enable()
self.bottomButtons.buttons[5].disable()
if self.name:
self.bottomButtons.buttons[4].enable()
else:
self.bottomButtons.buttons[4].disable()
if self.structure and self.clouds:
self.bottomButtons.buttons[3].enable()
else:
self.bottomButtons.buttons[3].disable()
def update(self):
textMatrix = []
objectList = self.names
self.updateButtons()
i = 0
for name in objectList:
datum = []
datum.append(i + 1)
datum.append(name)
datum.append(self.rmsds[i])
textMatrix.append(datum)
i += 1
if not objectList:
textMatrix = [
[],
]
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
self.waiting = 0
class CloudsPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.project = parent.getProject()
self.waiting = 0
self.specFreq = 800.13
self.maxIter = 50
self.mixTime = 60
self.corrTime = 11.5
self.leakRate = 2.0
self.peakListDict = {}
self.noesyPeakList = None
self.tocsyPeakList = None
self.noesy3dPeakList = None
self.hsqcPeakList = None
self.maxIntens = 37000000
self.resonances = None
self.origResonances = None
self.noesyPeaks = None
self.distanceConstraintList = None
self.antiDistConstraintList = None
self.numClouds = 100
self.filePrefix = 'cloud_'
self.cloudsFiles = []
self.adcAtomTypes = 'HN'
self.structure = None
# step num, initial temp, final temp, cooling steps, MD steps, MD tau, rep scale
self.coolingScheme = []
self.coolingScheme.append([1, 1, 1, 3, 500, 0.001, 0])
self.coolingScheme.append([2, 80000, 4000, 19, 1000, 0.001, 0])
self.coolingScheme.append([3, 4000, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([4, 15000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([5, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([6, 8000, 1, 3, 1000, 0.001, 0])
self.coolingScheme.append([7, 1, 1, 5, 500, 0.001, 0])
self.coolingScheme.append([8, 3000, 25, 60, 2500, 0.001, 1])
self.coolingScheme.append([9, 25, 25, 1, 7500, 0.001, 1])
self.coolingScheme.append([10, 10, 10, 1, 7500, 0.001, 1])
self.coolingScheme.append([11, 0.01, 0.01, 1, 7500, 0.0005, 1])
self.coolingStep = None
BasePopup.__init__(self,
parent,
title="Resonance Clouds Analysis",
**kw)
def body(self, guiFrame):
self.specFreqEntry = IntEntry(self,
text=self.specFreq,
width=8,
returnCallback=self.setSpecFreq)
self.maxIterEntry = IntEntry(self,
text=self.maxIter,
width=8,
returnCallback=self.setMaxIter)
self.mixTimeEntry = FloatEntry(self,
text=self.mixTime,
width=8,
returnCallback=self.setMixTime)
self.corrTimeEntry = FloatEntry(self,
text=self.corrTime,
width=8,
returnCallback=self.setCorrTime)
self.leakRateEntry = FloatEntry(self,
text=self.leakRate,
width=8,
returnCallback=self.setLeakRate)
self.maxIntensEntry = IntEntry(self,
text=self.maxIntens,
width=8,
returnCallback=self.setMaxIntens)
self.mdInitTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdInitTemp)
self.mdFinTempEntry = FloatEntry(self,
text='',
returnCallback=self.setMdFinTemp)
self.mdCoolStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdCoolSteps)
self.mdSimStepsEntry = IntEntry(self,
text='',
returnCallback=self.setMdSimSteps)
self.mdTauEntry = FloatEntry(self,
text='',
returnCallback=self.setMdTau)
self.mdRepScaleEntry = FloatEntry(self,
text='',
returnCallback=self.setMdRepScale)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame0 = LabelFrame(guiFrame, text='Setup peak lists')
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame0.grid_columnconfigure(1, weight=1)
f0row = 0
label00 = Label(frame0, text='1H-1H NOESY spectrum')
label00.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesyPulldown = PulldownMenu(frame0,
entries=self.getNoesys(),
callback=self.setNoesy,
selected_index=0,
do_initial_callback=0)
self.noesyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label01 = Label(frame0, text='15N HSQC spectrum')
label01.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.hsqcPulldown = PulldownMenu(frame0,
entries=self.getHsqcs(),
callback=self.setHsqc,
selected_index=0,
do_initial_callback=0)
self.hsqcPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC TOCSY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.tocsyPulldown = PulldownMenu(frame0,
entries=self.getTocsys(),
callback=self.setTocsy,
selected_index=0,
do_initial_callback=0)
self.tocsyPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
label02 = Label(frame0, text='15N HSQC NOESY spectrum')
label02.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.noesy3dPulldown = PulldownMenu(frame0,
entries=self.getNoesy3ds(),
callback=self.setNoesy3d,
selected_index=0,
do_initial_callback=0)
self.noesy3dPulldown.grid(row=f0row, column=1, sticky=Tkinter.NW)
f0row += 1
texts = ['Setup resonances & peaks', 'Show Peaks', 'Show resonances']
commands = [self.setupResonances, self.showPeaks, self.showResonances]
self.setupButtons = ButtonList(frame0,
expands=1,
texts=texts,
commands=commands)
self.setupButtons.grid(row=f0row,
column=0,
columnspan=2,
sticky=Tkinter.NSEW)
f0row += 1
self.label03a = Label(frame0, text='Resonances found: 0')
self.label03a.grid(row=f0row, column=0, sticky=Tkinter.NW)
self.label03b = Label(frame0, text='NOESY peaks found: 0')
self.label03b.grid(row=f0row, column=1, sticky=Tkinter.NW)
row += 1
frame1 = LabelFrame(guiFrame, text='Calculate distance constraints')
frame1.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame1.grid_columnconfigure(3, weight=1)
f1row = 0
frame1.grid_rowconfigure(f1row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
colHeadings = [
'Spectrometer\nfrequency', 'Max\niterations', 'Mixing\ntime (ms)',
'Correl.\ntime (ns)', 'Leak\nrate', 'Max\nintensity'
]
editWidgets = [
self.specFreqEntry,
self.maxIterEntry,
self.mixTimeEntry,
self.corrTimeEntry,
self.leakRateEntry,
self.maxIntensEntry,
]
editGetCallbacks = [
self.getSpecFreq,
self.getMaxIter,
self.getMixTime,
self.getCorrTime,
self.getLeakRate,
self.getMaxIntens,
]
editSetCallbacks = [
self.setSpecFreq,
self.setMaxIter,
self.setMixTime,
self.setCorrTime,
self.setLeakRate,
self.setMaxIntens,
]
self.midgeParamsMatrix = ScrolledMatrix(
frame1,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=1,
initialCols=5,
headingList=colHeadings,
callback=None,
objectList=[
'None',
],
textMatrix=[
data,
])
self.midgeParamsMatrix.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
label10 = Label(frame1, text='Benchmark structure')
label10.grid(row=f1row, column=0, sticky=Tkinter.NW)
self.structurePulldown = PulldownMenu(frame1,
entries=self.getStructures(),
callback=self.setStructure,
selected_index=0,
do_initial_callback=0)
self.structurePulldown.grid(row=f1row, column=1, sticky=Tkinter.NW)
label11 = Label(frame1, text='ADC atom types:')
label11.grid(row=f1row, column=2, sticky=Tkinter.NW)
self.adcAtomsPulldown = PulldownMenu(frame1,
entries=self.getAdcAtomTypes(),
callback=self.setAdcAtomTypes,
selected_index=0,
do_initial_callback=0)
self.adcAtomsPulldown.grid(row=f1row, column=3, sticky=Tkinter.NW)
f1row += 1
texts = [
'Calculate distances', 'Show distance\nconstraints',
'Show anti-distance\nconstraints'
]
commands = [
self.calculateDistances, self.showConstraints,
self.showAntiConstraints
]
self.midgeButtons = ButtonList(frame1,
expands=1,
texts=texts,
commands=commands)
self.midgeButtons.grid(row=f1row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f1row += 1
self.distConstrLabel = Label(frame1, text='Distance constraints:')
self.distConstrLabel.grid(row=f1row,
column=0,
columnspan=2,
sticky=Tkinter.NW)
self.antiConstrLabel = Label(frame1, text='Anti-distance constraints:')
self.antiConstrLabel.grid(row=f1row,
column=2,
columnspan=2,
sticky=Tkinter.NW)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame2 = LabelFrame(guiFrame, text='Proton cloud molecular dynamics')
frame2.grid(row=row, column=0, sticky=Tkinter.NSEW)
frame2.grid_columnconfigure(1, weight=1)
f2row = 0
frame2.grid_rowconfigure(f2row, weight=1)
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate
]
colHeadings = [
'Step', 'Initial temp.', 'Final temp.', 'Cooling steps',
'MD steps', 'MD tau', 'Rep. scale'
]
editWidgets = [
None, self.mdInitTempEntry, self.mdFinTempEntry,
self.mdCoolStepsEntry, self.mdSimStepsEntry, self.mdTauEntry,
self.mdRepScaleEntry
]
editGetCallbacks = [
None, self.getMdInitTemp, self.getMdFinTemp, self.getMdCoolSteps,
self.getMdSimSteps, self.getMdTau, self.getMdRepScale
]
editSetCallbacks = [
None, self.setMdInitTemp, self.setMdFinTemp, self.setMdCoolSteps,
self.setMdSimSteps, self.setMdTau, self.setMdRepScale
]
self.coolingSchemeMatrix = ScrolledMatrix(
frame2,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
maxRows=9,
initialRows=12,
headingList=colHeadings,
callback=self.selectCoolingStep,
objectList=self.coolingScheme,
textMatrix=self.coolingScheme)
self.coolingSchemeMatrix.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
f2row += 1
texts = ['Move earlier', 'Move later', 'Add step', 'Remove step']
commands = [
self.moveStepEarlier, self.moveStepLater, self.addCoolingStep,
self.removeCoolingStep
]
self.coolingSchemeButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.coolingSchemeButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.EW)
f2row += 1
label20 = Label(frame2, text='Number of clouds:')
label20.grid(row=f2row, column=0, sticky=Tkinter.NW)
self.numCloudsEntry = FloatEntry(frame2,
text=100,
returnCallback=self.setNumClouds,
width=10)
self.numCloudsEntry.grid(row=f2row, column=1, sticky=Tkinter.NW)
label21 = Label(frame2, text='Cloud file prefix:')
label21.grid(row=f2row, column=2, sticky=Tkinter.NW)
self.filePrefixEntry = Entry(frame2,
text='cloud_',
returnCallback=self.setFilePrefix,
width=10)
self.filePrefixEntry.grid(row=f2row, column=3, sticky=Tkinter.NW)
f2row += 1
texts = ['Start molecular dynamics', 'Show dynamics progress']
commands = [self.startMd, self.showMdProgress]
self.mdButtons = ButtonList(frame2,
expands=1,
commands=commands,
texts=texts)
self.mdButtons.grid(row=f2row,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
row += 1
self.bottomButtons = createDismissHelpButtonList(guiFrame,
expands=0,
help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.setButtonStates()
def getStructures(self):
names = [
'<None>',
]
for molSystem in self.project.sortedMolSystems():
for structure in molSystem.sortedStructureEnsembles():
names.append('%s:%d' % (molSystem.name, structure.ensembleId))
return names
def setStructure(self, index, name=None):
if index < 1:
self.structure = None
else:
structures = []
for molSystem in self.project.molSystems:
for structure in molSystem.structureEnsembles:
structures.append(structure)
self.structure = structures[index - 1]
def getAdcAtomTypes(self):
return ['HN', 'HN HA', 'HN HA HB']
def setAdcAtomTypes(self, index, name=None):
if name is None:
name = self.adcAtomsPulldown.getSelected()
self.adcAtomTypes = name
def startMd(self):
self.setNumClouds()
self.setFilePrefix()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
resDict = {}
for resonance in self.guiParent.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
resonances = []
for constraint in self.distanceConstraintList.constraints:
for item in constraint.items:
for fixedResonance in item.resonances:
if resDict.get(
fixedResonance.resonanceSerial) is not None:
resonances.append(
resDict[fixedResonance.resonanceSerial])
resDict[fixedResonance.resonanceSerial] = None
startMdProcess(self.numClouds, self.distanceConstraintList,
resonances, self.coolingScheme, self.filePrefix)
#structGen = self.distanceConstraintList.structureGeneration
serials = []
for resonance in resonances:
serials.append(resonance.serial)
clouds = []
for i in range(self.numClouds):
clouds.append('%s%3.3d.pdb' % (self.filePrefix, i))
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'clouds',
values=clouds)
self.guiParent.application.setValues(
self.distanceConstraintList.nmrConstraintStore,
'cloudsResonances',
values=serials)
# do better than this check for creation
def showMdProgress(self):
n = 0
m = self.numClouds
for i in range(m):
pdbFileName = '%s%3.3d.pdb' % (self.filePrefix, i)
if os.path.exists(pdbFileName):
n += 1
p = n * 100 / float(m)
text = 'Done %d of %d clouds (%1.2f)%%' % (n, m, p)
showInfo('MD Progress', text)
def setFilePrefix(self, text=None):
if not text:
text = self.filePrefixEntry.get()
if text:
self.filePrefix = text
def setNumClouds(self, n=None, *event):
if not n:
n = self.numCloudsEntry.get()
if n:
self.numClouds = int(n)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def showConstraints(self):
if self.distanceConstraintList:
self.guiParent.browseConstraints(
constraintList=self.distanceConstraintList)
def showAntiConstraints(self):
if self.antiDistConstraintList:
self.guiParent.browseConstraints(
constraintList=self.antiDistConstraintList)
def showPeaks(self):
self.guiParent.viewPeaks(peaks=self.noesyPeaks)
def showResonances(self):
pass
#self.guiParent.viewResonances(resonances=self.resonances)
def setupResonances(self):
if self.noesyPeakList and self.noesy3dPeakList and self.tocsyPeakList and self.hsqcPeakList:
disambiguateNoesyPeaks(self.noesyPeakList, self.noesy3dPeakList,
self.tocsyPeakList, self.hsqcPeakList)
(self.origResonances, self.noesyPeaks,
null) = getCloudsResonanceList(self.guiParent.argumentServer,
hsqcPeakList=self.hsqcPeakList,
tocsy3dPeakList=self.tocsyPeakList,
noesy2dPeakList=self.noesyPeakList)
self.setButtonStates()
def setButtonStates(self):
if self.origResonances:
self.label03a.set('Resonances found: %d' %
(len(self.origResonances)))
if self.noesyPeaks:
self.label03b.set('NOESY peaks found: %d' % (len(self.noesyPeaks)))
if self.noesyPeakList and self.tocsyPeakList and self.hsqcPeakList:
self.setupButtons.buttons[0].enable()
else:
self.setupButtons.buttons[0].disable()
if self.noesyPeaks:
self.setupButtons.buttons[1].enable()
else:
self.setupButtons.buttons[1].disable()
if self.origResonances:
self.setupButtons.buttons[2].enable()
else:
self.setupButtons.buttons[2].disable()
if self.noesyPeaks and self.origResonances:
self.midgeButtons.buttons[0].enable()
else:
self.midgeButtons.buttons[0].disable()
if self.distanceConstraintList:
self.midgeButtons.buttons[1].enable()
self.distConstrLabel.set(
'Distance constraints: %d' %
len(self.distanceConstraintList.constraints))
else:
self.distConstrLabel.set('Distance constraints:')
self.midgeButtons.buttons[1].disable()
if self.antiDistConstraintList:
self.antiConstrLabel.set(
'Anti-distance constraints: %d' %
len(self.antiDistConstraintList.constraints))
self.midgeButtons.buttons[2].enable()
else:
self.antiConstrLabel.set('Anti-distance constraints:')
self.midgeButtons.buttons[2].disable()
if (self.distanceConstraintList and self.antiDistConstraintList
and (self.numClouds > 0) and self.filePrefix):
self.mdButtons.buttons[0].enable()
self.mdButtons.buttons[1].enable()
else:
self.mdButtons.buttons[0].disable()
self.mdButtons.buttons[1].disable()
def getNoesys(self):
names = []
spectra = getSpectraByType(self.project, '2dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def setNoesy(self, index, name=None):
if not name:
name = self.noesyPulldown.getSelected()
self.noesyPeakList = self.peakListDict[name]
self.setButtonStates()
def getTocsys(self):
names = []
spectra = getSpectraByType(self.project, '3dTOCSY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.tocsyPeakList:
self.tocsyPeakList = peakList
return names
def getNoesy3ds(self):
names = []
spectra = getSpectraByType(self.project, '3dNOESY')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesy3dPeakList:
self.noesy3dPeakList = peakList
return names
def setTocsy(self, index, name=None):
if not name:
name = self.tocsyPulldown.getSelected()
self.tocsyPeakList = self.peakListDict[name]
self.setButtonStates()
def setNoesy3d(self, index, name=None):
if not name:
name = self.noesy3dPulldown.getSelected()
self.noesy3dPeakList = self.peakListDict[name]
self.setButtonStates()
def getHsqcs(self):
names = []
spectra = getSpectraByType(self.project, 'HSQC')
for spectrum in spectra:
for peakList in spectrum.peakLists:
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.hsqcPeakList:
self.hsqcPeakList = peakList
return names
def setHsqc(self, index, name=None):
if not name:
name = self.hsqcPulldown.getSelected()
self.hsqcPeakList = self.peakListDict[name]
self.setButtonStates()
def getMdInitTemp(self, coolingStep):
self.mdInitTempEntry.set(coolingStep[1])
def getMdFinTemp(self, coolingStep):
self.mdFinTempEntry.set(coolingStep[2])
def getMdCoolSteps(self, coolingStep):
self.mdCoolStepsEntry.set(coolingStep[3])
def getMdSimSteps(self, coolingStep):
self.mdSimStepsEntry.set(coolingStep[4])
def getMdTau(self, coolingStep):
self.mdTauEntry.set(coolingStep[5])
def getMdRepScale(self, coolingStep):
self.mdRepScaleEntry.set(coolingStep[6])
def setMdInitTemp(self, event):
value = self.mdInitTempEntry.get()
if value is not None:
self.coolingStep[1] = value
self.updateCoolingScheme()
def setMdFinTemp(self, event):
value = self.mdFinTempEntry.get()
if value is not None:
self.coolingStep[2] = value
self.updateCoolingScheme()
def setMdCoolSteps(self, event):
value = self.mdCoolStepsEntry.get()
if value is not None:
self.coolingStep[3] = value
self.updateCoolingScheme()
def setMdSimSteps(self, event):
value = self.mdSimStepsEntry.get()
if value is not None:
self.coolingStep[4] = value
self.updateCoolingScheme()
def setMdTau(self, event):
value = self.mdTauEntry.get()
if value is not None:
self.coolingStep[5] = value
self.updateCoolingScheme()
def setMdRepScale(self, event):
value = self.mdRepScaleEntry.get()
if value is not None:
self.coolingStep[6] = value
self.updateCoolingScheme()
def selectCoolingStep(self, object, row, col):
self.coolingStep = object
def moveStepEarlier(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i > 0:
coolingStep = self.coolingScheme[i - 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i
self.coolingScheme[i - 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def moveStepLater(self):
if self.coolingStep:
i = self.coolingStep[0] - 1
if i < len(self.coolingScheme) - 1:
coolingStep = self.coolingScheme[i + 1]
coolingStep[0] = i + 1
self.coolingStep[0] = i + 2
self.coolingScheme[i + 1] = self.coolingStep
self.coolingScheme[i] = coolingStep
self.updateCoolingScheme()
self.coolingSchemeMatrix.hilightObject(self.coolingStep)
def addCoolingStep(self):
i = len(self.coolingScheme) + 1
datum = [i, 3000, 100, 10, 2500, 0.001, 1]
self.coolingScheme.append(datum)
self.updateCoolingScheme()
def removeCoolingStep(self):
if self.coolingStep:
coolingScheme = []
i = 0
for coolingStep in self.coolingScheme:
if coolingStep is not self.coolingStep:
i += 1
coolingStep[0] = i
coolingScheme.append(coolingStep)
self.coolingScheme = coolingScheme
self.updateCoolingScheme()
def updateCoolingScheme(self):
objectList = self.coolingScheme
textMatrix = self.coolingScheme
self.coolingSchemeMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def updateMidgeParams(self):
data = [
self.specFreq, self.maxIter, self.mixTime, self.corrTime,
self.leakRate, self.maxIntens
]
self.midgeParamsMatrix.update(textMatrix=[
data,
])
def getSpecFreq(self, obj):
self.specFreqEntry.set(self.specFreq)
def getMaxIter(self, obj):
self.maxIterEntry.set(self.maxIter)
def getMixTime(self, obj):
self.mixTimeEntry.set(self.mixTime)
def getCorrTime(self, obj):
self.corrTimeEntry.set(self.corrTime)
def getLeakRate(self, obj):
self.leakRateEntry.set(self.leakRate)
def getMaxIntens(self, obj):
self.maxIntensEntry.set(self.maxIntens)
def setSpecFreq(self, event):
value = self.specFreqEntry.get()
if value is not None:
self.specFreq = value
self.updateMidgeParams()
def setMaxIter(self, event):
value = self.maxIterEntry.get()
if value is not None:
self.maxIter = value
self.updateMidgeParams()
def setMixTime(self, event):
value = self.mixTimeEntry.get()
if value is not None:
self.mixTime = value
self.updateMidgeParams()
def setCorrTime(self, event):
value = self.corrTimeEntry.get()
if value is not None:
self.corrTime = value
self.updateMidgeParams()
def setLeakRate(self, event):
value = self.leakRateEntry.get()
if value is not None:
self.leakRate = value
self.updateMidgeParams()
def setMaxIntens(self, event):
value = self.maxIntensEntry.get()
if value is not None:
self.maxIntens = value
self.updateMidgeParams()
def destroy(self):
BasePopup.destroy(self)
class PCSPopup(BasePopup):
def __init__(self, parent, *args, **kw):
BasePopup.__init__(self, parent, *args, **kw)
def body(self, guiFrame):
spectraFrame = LabelFrame(guiFrame, text='Spectra', grid=(0, 0))
Label(spectraFrame, text='Diamagnetic Spectrum:', grid=(0, 0))
self.diaSpecPulldown = PulldownList(spectraFrame,
callback=self.changeDiaSpec,
grid=(0, 1))
Label(spectraFrame, text='Paramagnetic Spectrum:', grid=(1, 0))
self.paraSpecPulldown = PulldownList(spectraFrame,
callback=self.changeParaSpec,
grid=(1, 1))
pcsIOFrame = LabelFrame(guiFrame, text='PCS', grid=(1, 0))
Label(pcsIOFrame, text='Write Experimental PCS:', grid=(0, 0))
self.expPCSEntry = Entry(pcsIOFrame,
text='pcsexp.npc',
width=32,
grid=(0, 1))
Button(pcsIOFrame,
command=self.writePCSFileChange,
grid=(0, 2),
text='Choose File')
Label(pcsIOFrame, text='Read Calculated PCS:', grid=(1, 0))
self.calPCSEntry = Entry(pcsIOFrame,
text='pcscal.npc',
width=32,
grid=(1, 1))
Button(pcsIOFrame,
command=self.readPCSFileChange,
grid=(1, 2),
text='Choose File')
scriptFrame = LabelFrame(guiFrame,
text='Paramagpy Script',
grid=(2, 0))
Label(scriptFrame, text='PCS fitting script:', grid=(0, 0))
self.scriptEntry = Entry(scriptFrame,
text='paramagpy_fit_pcs.py',
width=32,
grid=(0, 1))
Button(scriptFrame,
command=self.writeScriptFileChange,
grid=(0, 2),
text='Choose File')
commandFrame = LabelFrame(guiFrame, text='Commands', grid=(3, 0))
Button(commandFrame,
command=self.writePCS,
grid=(0, 0),
text='Write PCS')
Button(commandFrame,
command=self.fitTensor,
grid=(0, 1),
text='Fit Tensor')
Button(commandFrame,
command=self.readPCS,
grid=(0, 2),
text='Read PCS')
self.updateSpecPulldown()
def updateSpecPulldown(self):
spectra = ExperimentBasic.getSpectra(self.project)
names = []
for spectrum in spectra:
names.append("{}:{}".format(spectrum.experiment.name,
spectrum.name))
self.diaSpecPulldown.setup(names, spectra, 0)
self.paraSpecPulldown.setup(names, spectra, 0)
if len(spectra) > 1:
self.diaSpec = spectra[0]
self.paraSpec = spectra[1]
def changeDiaSpec(self, spectrum):
self.diaSpec = spectrum
def changeParaSpec(self, spectrum):
self.paraSpec = spectrum
def writePCSFileChange(self):
fileTypes = [FileType('PCS', ['*.npc']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(
self,
file=os.path.basename(self.expPCSEntry.get()),
directory=os.path.dirname(self.expPCSEntry.get()),
file_types=fileTypes,
title='Save PCS values to file',
dismiss_text='Cancel',
selected_file_must_exist=False,
multiSelect=False,
)
self.expPCSEntry.set(fileSelectPopup.getFile())
def readPCSFileChange(self):
fileTypes = [FileType('PCS', ['*.npc']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(
self,
file=os.path.basename(self.calPCSEntry.get()),
directory=os.path.dirname(self.calPCSEntry.get()),
file_types=fileTypes,
title='Save PCS values to file',
dismiss_text='Cancel',
selected_file_must_exist=False,
multiSelect=False,
)
self.calPCSEntry.set(fileSelectPopup.getFile())
def writeScriptFileChange(self):
fileTypes = [FileType('python', ['*.py']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(
self,
file=os.path.basename(self.scriptEntry.get()),
directory=os.path.dirname(self.scriptEntry.get()),
file_types=fileTypes,
title='Paramagpy script',
dismiss_text='Cancel',
selected_file_must_exist=False,
multiSelect=False,
)
self.scriptEntry.set(fileSelectPopup.getFile())
def writePCS(self):
diaPeaks = self.diaSpec.getActivePeakList()
paraPeaks = self.paraSpec.getActivePeakList()
deltaPeaks = self.subtract_peak_lists(diaPeaks, paraPeaks)
self.write_npc(deltaPeaks)
def readPCS(self):
print(self.diaSpec.experiment.name)
print(self.paraSpec.experiment.name)
calPCSName = os.path.abspath(self.calPCSEntry.get())
if not os.path.isfile(calPCSName):
showWarning(
"PCS file not found",
"Cound not find backcalculated PCS values. Please ensure the following file exists:\n{}"
.format(calPCSName))
return
pcs_values = {}
with open(calPCSName) as o:
for line in o:
try:
sequence, atomName, pcsValue, error = line.split()
key = int(sequence), atomName
pcs_values[key] = float(pcsValue)
except ValueError:
print("Line ignored in calculated PCS file:\n{}".format(
line))
peakListDia = self.diaSpec.getActivePeakList()
newPeakList = self.paraSpec.newPeakList(isSimulated=True)
newPeakList.analysisPeakList.setSymbolColor("#FF0000")
newPeakList.setDetails("Back-calculated PCS")
for diaPeak in peakListDia.sortedPeaks():
paraPeak = newPeakList.newPeak()
paraPeak.setAnnotation(diaPeak.getAnnotation())
for ddim, pdim in zip(diaPeak.sortedPeakDims(),
paraPeak.sortedPeakDims()):
pdim.setAnnotation(ddim.getAnnotation())
if not ddim.dataDimRef:
paraPeak.delete()
break
contrib = ddim.findFirstPeakDimContrib()
if not contrib:
paraPeak.delete()
break
resonance = contrib.getResonance()
if not resonance:
paraPeak.delete()
break
if not resonance.resonanceSet:
paraPeak.delete()
break
residue = getResonanceResidue(resonance)
sequence = residue.seqCode
atomName = resonance.getAssignNames()[0]
key = sequence, atomName
if key in pcs_values:
newShift = ddim.getValue() + pcs_values[key]
if self.within_axis(pdim, newShift):
pdim.setValue(newShift)
else:
paraPeak.delete()
break
else:
paraPeak.delete()
break
def fitTensor(self):
scriptName = os.path.abspath(self.scriptEntry.get())
expPCSName = os.path.abspath(self.expPCSEntry.get())
if not os.path.isfile(scriptName):
showWarning(
"Script not found",
"Could not find paramagpy script. Please ensure the following script exists:\n{}"
.format(scriptName))
return
if not os.access(scriptName, os.X_OK):
showWarning(
"Invalid permissions",
"The paramagpy script does not have executable permissions. Please run in the terminal:\nchmod +x {}"
.format(scriptName))
return
if not os.path.isfile(expPCSName):
showWarning(
"PCS file not found",
"Cound not find experimental PCS file.\nEnsure the following file exists:{}"
.format(expPCSName))
return
subprocess.call([scriptName, expPCSName])
def write_npc(self, pcsValues):
fileName = os.path.abspath(self.expPCSEntry.get())
with open(fileName, 'w') as o:
for key in sorted(pcsValues):
seq, atom = key
value = pcsValues[key]
line = "{0:<4d}{1:<2}{2:15.8f} 0.0\n".format(seq, atom, value)
o.write(line)
o.close()
showInfo("Wrote PCS", "Wrote experimental PCS to: {}".format(fileName))
@staticmethod
def extract_peaks(peakList):
out = []
for peak in peakList.sortedPeaks():
tmp = {}
for peakDim in peak.sortedPeakDims():
if not peakDim.dataDimRef:
continue
contrib = peakDim.findFirstPeakDimContrib()
if not contrib:
continue
resonance = contrib.getResonance()
if not resonance:
continue
if not resonance.resonanceSet:
continue
residue = getResonanceResidue(resonance)
sequence = residue.seqCode
atomName = resonance.getAssignNames()[0]
tmp[(sequence, atomName)] = peakDim
out.append((peak, tmp))
return out
@staticmethod
def within_axis(peakDim, value):
dataDim = peakDim.getDataDim()
dr = dataDim.findFirstDataDimRef()
diff = dr.spectralWidthOrig - dr.spectralWidth
low = dr.refValue - dr.spectralWidth + dr.spectralWidthOrig / 2.
high = dr.refValue + dr.spectralWidthOrig / 2.
return low < value < high
def subtract_peak_lists(self, diamagPeaks, paramagPeaks):
dpeaks = self.extract_peaks(diamagPeaks)
ppeaks = self.extract_peaks(paramagPeaks)
dvals = {}
pvals = {}
for peak, dic in dpeaks:
dvals.update(dic)
for peak, dic in ppeaks:
pvals.update(dic)
out = {}
for key in set(dvals) & set(pvals):
out[key] = pvals[key].value - dvals[key].value
return out
class MeccanoPopup(BasePopup):
def __init__(self, parent, project, *args, **kw):
self.alignMedium = None
self.chain = None
self.constraint = None
self.constraintSet = None
self.molSystem = None
self.project = project
self.run = None
self.shiftList = None
self.tensor = None
BasePopup.__init__(self, parent=parent, title='MECCANO', *args, **kw)
self.curateNotifiers(self.registerNotify)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
options = ['Parameters','Restraints','Alignment Media & Tensors','About Meccano']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
frameA, frameB, frameC, frameD = tabbedFrame.frames
frameA.grid_columnconfigure(1, weight=1)
frameA.grid_rowconfigure(13, weight=1)
frameB.grid_columnconfigure(1, weight=1)
frameB.grid_rowconfigure(1, weight=1)
frameC.grid_columnconfigure(0, weight=1)
frameC.grid_rowconfigure(1, weight=1)
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(0, weight=1)
texts = ['Run MECCANO!']
commands = [self.runMeccano]
bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts,
commands=commands, expands=True)
bottomButtons.grid(row=1, column=0, sticky='ew')
if not Meccano:
bottomButtons.buttons[0].disable()
# Parameters
row = 0
label = Label(frameA, text='Calculation Run:')
label.grid(row=row,column=0,sticky='w')
self.runPulldown = PulldownList(frameA, callback=self.selectRun)
self.runPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Shift List (for CO):')
label.grid(row=row,column=0,sticky='w')
self.shiftListPulldown = PulldownList(frameA, callback=self.selectShiftList)
self.shiftListPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Keep Copy of Used Shifts:')
label.grid(row=row,column=0,sticky='w')
self.toggleCopyShifts = CheckButton(frameA)
self.toggleCopyShifts.grid(row=row,column=1,sticky='w')
self.toggleCopyShifts.set(True)
row += 1
label = Label(frameA, text='Molecular System:')
label.grid(row=row,column=0,sticky='w')
self.molSystemPulldown = PulldownList(frameA, callback=self.selectMolSystem)
self.molSystemPulldown.grid(row=row,column=1,sticky='w')
row += 1
label = Label(frameA, text='Chain:')
label.grid(row=row,column=0,sticky='w')
self.chainPulldown = PulldownList(frameA, callback=self.selectChain)
self.chainPulldown.grid(row=row,column=1,sticky='w')
self.chainPulldown.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='First Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.firstResEntry = IntEntry(frameA, text=None, width=8)
self.firstResEntry.grid(row=row,column=1,sticky='w')
self.firstResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Last Peptide Plane:')
label.grid(row=row,column=0,sticky='w')
self.lastResEntry = IntEntry(frameA, text=None, width=8)
self.lastResEntry.grid(row=row,column=1,sticky='w')
self.lastResEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Max Num Optimisation Steps:')
label.grid(row=row,column=0,sticky='w')
self.maxOptStepEntry = IntEntry(frameA, text=500, width=8)
self.maxOptStepEntry.grid(row=row,column=1,sticky='w')
self.maxOptStepEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Num Optimisation Peptide Planes:')
label.grid(row=row,column=0,sticky='w')
self.numOptPlaneEntry = IntEntry(frameA, text=2, width=8)
self.numOptPlaneEntry.grid(row=row,column=1,sticky='w')
self.numOptPlaneEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Min Num Optimisation Hits:')
label.grid(row=row,column=0,sticky='w')
self.numOptHitsEntry = IntEntry(frameA, text=5, width=8)
self.numOptHitsEntry.grid(row=row,column=1,sticky='w')
self.numOptHitsEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='File Name Prefix:')
label.grid(row=row,column=0,sticky='w')
self.pdbFileEntry = Entry(frameA, text='Meccano', width=8)
self.pdbFileEntry.grid(row=row,column=1,sticky='w')
self.pdbFileEntry.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write Output File (.out):')
label.grid(row=row,column=0,sticky='w')
self.toggleWriteOutFile = CheckButton(frameA)
self.toggleWriteOutFile.grid(row=row,column=1,sticky='w')
self.toggleWriteOutFile.set(False)
self.toggleWriteOutFile.bind('<Leave>', self.updateRunParams)
row += 1
label = Label(frameA, text='Write PDB File (.pdb):')
label.grid(row=row,column=0,sticky='w')
self.toggleWritePdbFile = CheckButton(frameA)
self.toggleWritePdbFile.grid(row=row,column=1,sticky='w')
self.toggleWritePdbFile.set(True)
self.toggleWritePdbFile.bind('<Leave>', self.updateRunParams)
if not Meccano:
row += 1
label = Label(frameA, text='The Meccano executable is not available (it needs to be compiled)', fg='red')
label.grid(row=row,column=0,columnspan=2,sticky='w')
# Restraints
label = Label(frameB, text='Constraint Set:')
label.grid(row=0,column=0,sticky='w')
self.constraintSetPulldown = PulldownList(frameB, callback=self.selectConstraintSet)
self.constraintSetPulldown.grid(row=0,column=1,sticky='w')
self.alignMediumPulldown= PulldownList(self, callback=self.setAlignMedium)
headingList = ['#','List Type','Use?','Alignment\nMedium','Num\nRestraints']
editWidgets = [None,None,None,self.alignMediumPulldown,None]
editGetCallbacks = [None,None,self.toggleUseRestraints,self.getAlignMedium,None]
editSetCallbacks = [None,None,None,self.setAlignMedium,None]
self.restraintMatrix = ScrolledMatrix(frameB,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=None,
multiSelect=True)
self.restraintMatrix.grid(row=1,column=0,columnspan=2,sticky='nsew')
# Alignment Media
div = LabelDivider(frameC,text='Alignment Media')
div.grid(row=0,column=0,sticky='ew')
self.mediumNameEntry = Entry(self, returnCallback=self.setMediumName)
self.mediumDetailsEntry = Entry(self, returnCallback=self.setMediumDetails)
headingList = ['#','Name','Details','Static Tensor','Dynamic Tensor']
editWidgets = [None, self.mediumNameEntry, self.mediumDetailsEntry, None, None]
editGetCallbacks = [None, self.getMediumName, self.getMediumDetails, None, None]
editSetCallbacks = [None, self.setMediumName, self.setMediumDetails, None, None]
self.mediaMatrix = ScrolledMatrix(frameC,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectAlignMedium,
multiSelect=True)
self.mediaMatrix.grid(row=1,column=0,sticky='nsew')
texts = ['Add Alignment medium','Remove Alignment Medium']
commands = [self.addAlignMedium,self.removeAlignMedium]
buttonList = ButtonList(frameC, texts=texts, commands=commands, expands=True)
buttonList.grid(row=2,column=0,sticky='nsew')
self.editAxialEntry = FloatEntry(self, returnCallback=self.setAxial)
self.editRhombicEntry = FloatEntry(self, returnCallback=self.setRhombic)
self.editAlphaEulerEntry = FloatEntry(self, returnCallback=self.setEulerAlpha)
self.editBetaEulerEntry = FloatEntry(self, returnCallback=self.setEulerBeta)
self.editGammaEulerEntry = FloatEntry(self, returnCallback=self.setEulerGamma)
div = LabelDivider(frameC,text='Alignment Tensors')
div.grid(row=3,column=0,sticky='ew')
headingList = ['Type', u'Axial (\u03B6)',u'Rhombic (\u03B7)',
u'Euler \u03B1',u'Euler \u03B2',u'Euler \u03B3']
editWidgets = [None,self.editAxialEntry,
self.editRhombicEntry,self.editAlphaEulerEntry,
self.editBetaEulerEntry,self.editGammaEulerEntry]
editSetCallbacks = [None,self.setAxial,self.setRhombic,
self.setEulerAlpha,self.setEulerBeta,self.setEulerGamma]
editGetCallbacks = [None,self.getAxial,self.getRhombic,
self.getEulerAlpha,self.getEulerBeta,self.getEulerGamma]
self.tensorMatrix = ScrolledMatrix(frameC, maxRows=2,
headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectTensor,
multiSelect=True)
self.tensorMatrix.grid(row=4,column=0,sticky='nsew')
texts = ['Add Static Tensor','Add Dynamic Tensor','Remove Tensor']
commands = [self.addStaticTensor,self.addDynamicTensor,self.removeTensor]
buttonList = ButtonList(frameC,texts=texts, commands=commands, expands=True)
buttonList.grid(row=5,column=0,sticky='ew')
# About
label = Label(frameD, text='About Meccano...')
label.grid(row=0,column=0,sticky='w')
#
self.geometry('500x400')
self.updateShiftLists()
self.updateMolSystems()
self.updateResidueRanges()
self.updateConstraintSets()
self.updateAlignMedia()
self.updateRuns()
def close(self):
self.updateRunParams()
BasePopup.close(self)
def destroy(self):
self.updateRunParams()
self.curateNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def curateNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateConstraintSetsAfter, 'ccp.nmr.NmrConstraint.NmrConstraintStore', func)
for func in ('__init__', 'delete','setName','setConditionState'):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraintList',
'ccp.nmr.NmrConstraint.DihedralConstraintList',
'ccp.nmr.NmrConstraint.DistanceConstraintList',
'ccp.nmr.NmrConstraint.HBondConstraintList',
'ccp.nmr.NmrConstraint.JCouplingConstraintList',
'ccp.nmr.NmrConstraint.RdcConstraintList'):
notifyFunc(self.updateConstraintListsAfter, clazz, func)
for func in ('__init__', 'delete',):
for clazz in ('ccp.nmr.NmrConstraint.CsaConstraint',
'ccp.nmr.NmrConstraint.DihedralConstraint',
'ccp.nmr.NmrConstraint.DistanceConstraint',
'ccp.nmr.NmrConstraint.HBondConstraint',
'ccp.nmr.NmrConstraint.JCouplingConstraint',
'ccp.nmr.NmrConstraint.RdcConstraint'):
notifyFunc(self.updateConstraintsAfter, clazz, func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateShiftListsAfter,'ccp.nmr.Nmr.ShiftList', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateMolSystemsAfter,'ccp.molecule.MolSystem.MolSystem', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateChainsAfter,'ccp.molecule.MolSystem.Chain', func)
for func in ('__init__', 'delete','setDynamicAlignment',
'setStaticAlignment','setName','setDetails'):
notifyFunc(self.updateAlignMediaAfter,'ccp.nmr.NmrConstraint.ConditionState', func)
def updateAlignMediaAfter(self, alignMedium):
if alignMedium.nmrConstraintStore is self.constraintSet:
self.after_idle(self.updateAlignMedia)
if alignMedium is self.alignMedium:
self.after_idle(self.updateTensors)
def updateConstraintSetsAfter(self, constraintSet):
self.after_idle(self.updateConstraintSets)
def updateShiftListsAfter(self, shiftList):
self.after_idle(self.updateShiftLists)
def updateMolSystemsAfter(self, molSystem):
self.after_idle(self.updateMolSystems)
def updateChainsAfter(self, chain):
self.after_idle(self.updateChains)
def updateConstraintsAfter(self, constraint):
if constraint.parent.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def updateConstraintListsAfter(self, constraintList):
if constraintList.parent is self.constraintSet:
self.after_idle(self.updateConstraintLists)
def runMeccano(self):
#
#
# Input checks first
#
#
warning = ''
if not self.molSystem:
warning += 'No molecular system selected\n'
if not self.chain:
warning += 'No chain selected\n'
if not self.constraintSet:
warning += 'No selected constraint set\n'
else:
constraintLists = [cl for cl in self.constraintSet.constraintLists if cl.useForMeccano]
if not constraintLists:
warning += 'No constraint lists selected for use\n'
first, last = self.updateResidueRanges()
if (last-first) < 2:
warning += 'Too few peptide planes selected\n'
if warning:
showWarning('Cannot run MECCANO','Encountered the following problems:\n' + warning)
return
if not self.run:
self.run = self.makeSimRun()
self.updateRunParams()
if self.toggleCopyShifts.get() and self.shiftList:
shiftList = self.run.findFirstOutputMeasurementList(className='ShiftList')
if not shiftList:
shiftList = self.project.currentNmrProject.newShiftList(name='Meccano Input')
self.run.setOutputMeasurementLists([shiftList,])
shiftDict = {}
for shift in shiftList.shifts:
shiftDict[shift.resonance] = shift
for shift in self.shiftList.shifts:
resonance = shift.resonance
resonanceSet = resonance.resonanceSet
if resonanceSet:
atom = resonanceSet.findFirstAtomSet().findFirstAtom()
if (atom.name == 'C') and (atom.residue.molResidue.molType == 'protein'):
shift2 = shiftDict.get(resonance)
if shift2:
shift2.value = shift.value
shift2.error = shift.error
else:
shiftList.newShift(resonance=resonance, value=shift.value, error=shift.error)
#
#
# Accumulate data from CCPN data model & GUI
#
#
# Sequence
residues = self.chain.sortedResidues()
residueDict = {}
seqData = []
for residue in residues:
molResidue = residue.molResidue
code1Letter = molResidue.chemComp.code1Letter
if not code1Letter:
msg = 'Encountered non-standard residue type: %s'
showWarning('Cannot run MECCANO', msg % residue.ccpCode)
return
seqCode = residue.seqCode
seqData.append((seqCode, code1Letter))
residueDict[seqCode] = residue.chemCompVar.chemComp.code3Letter
# Media, RDCs & Dihedrals
rdcLists = []
dihedralLists = []
for constraintList in constraintLists:
if constraintList.className == 'RdcConsraintList':
if constraintList.conditionState:
rdcLists.append(constraintList)
elif constraintList.className == 'DihedralConstraintList':
dihedralLists.append(dihedralLists)
f = PI_OVER_180
mediaData = []
for constraintList in rdcLists:
medium = constraintList.conditionState
dynamicTensor = medium.dynamicAlignment
staticTensor = medium.staticAlignment
if not (dynamicTensor or staticTensor):
continue
if dynamicTensor:
dynamicTensorData = ['Dynamic', dynamicTensor.aAxial, dynamicTensor.aRhombic,
f*dynamicTensor.alpha, f*dynamicTensor.beta, f*dynamicTensor.gamma]
if staticTensor:
staticTensorData = ['Static', staticTensor.aAxial, staticTensor.aRhombic,
f*staticTensor.alpha, f*staticTensor.beta, f*staticTensor.gamma]
if not dynamicTensor:
dynamicTensorData = staticTensorData
elif not staticTensor:
staticTensorData = dynamicTensorData
rdcData = []
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
resonanceA, resonanceB = [fr.resonance for fr in items[0].resonances]
resonanceSetA = resonanceA.resonanceSet
if not resonanceSetA:
continue
resonanceSetB = resonanceB.resonanceSet
if not resonanceSetB:
continue
resNameA = getResonanceName(resonanceA)
resNameB = getResonanceName(resonanceB)
residueA = resonanceSetA.findFirstAtomSet().findFirstAtom().residue
residueB = resonanceSetB.findFirstAtomSet().findFirstAtom().residue
seqA = residueA.seqCode
seqB = residueB.seqCode
value = restraint.targetValue
error = restraint.error
if error is None:
key = [resNameA,resNameB]
key.sort()
sigma = DEFAULT_ERRORS.get(tuple(key), 1.0)
rdcData.append([seqA, resNameA, seqB, resNameB, value, error])
mediaData.append((dynamicTensorData,staticTensorData,rdcData))
oneTurn = 360.0
dihedralDict = {}
for constraintList in dihedralLists:
for restraint in constraintList.constraints:
items = list(restraint.items)
if len(items) != 1:
continue
item = items[0]
resonances = [fr.resonance for fr in item.resonances]
resonanceSets = [r.resonanceSet for r in resonances]
if None in resonanceSets:
continue
atoms = [rs.findFirstAtomSet().findFirstAtom() for rs in resonanceSets]
atomNames = [a.name for a in atoms]
if atomNames == PHI_ATOM_NAMES:
isPhi = True
elif atomNames == PSI_ATOM_NAMES:
isPhi = False
else:
continue
residue = atoms[2].residue
if residue.chain is not self.chain:
continue
if isPhi:
residuePrev = getLinkedResidue(residue, linkCode='prev')
if not residuePrev:
continue
atomC0 = residuePrev.findFirstAtom(name='C')
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atoms2 = [atomC0, atomN, atomCa, atomC]
else:
residueNext = getLinkedResidue(residue, linkCode='next')
if not residueNext:
continue
atomN = residue.findFirstAtom(name='N')
atomCa = residue.findFirstAtom(name='CA')
atomC = residue.findFirstAtom(name='C')
atomN2 = residueNext.findFirstAtom(name='N')
atoms2 = [atomN, atomCa, atomC, atomN2]
if atoms != atoms2:
continue
value = item.targetValue
error = item.error
if error is None:
upper = item.upperLimit
lower = item.lowerLimit
if (upper is not None) and (lower is not None):
dUpper = angleDifference(value, lower, oneTurn)
dLower = angleDifference(upper, value, oneTurn)
error = max(dUpper, dLower)
elif lower is not None:
error = angleDifference(value, lower, oneTurn)
elif upper is not None:
error = angleDifference(upper, value, oneTurn)
else:
error = 30.0 # Arbitrary, but sensible for TALOS, DANGLE
seqCode = residue.seqCode
if not dihedralDict.has_key(seqCode):
dihedralDict[seqCode] = [None, None, None, None] # Phi, Psi, PhiErr, PsiErr
if isPhi:
dihedralDict[seqCode][0] = value
dihedralDict[seqCode][2] = error
else:
dihedralDict[seqCode][1] = value
dihedralDict[seqCode][3] = error
phipsiData = []
seqCodes = dihedralDict.keys()
seqCodes.sort()
for seqCode in seqCodes:
data = dihedralDict[seqCode]
if None not in data:
phi, psi, phiErr, psiErr = data
phipsiData.append((seqCode, phi, psi, phiErr, psiErr))
# User options
firstPPlaneFrag = self.firstResEntry.get() or 1
lastPPlaneFrag = self.lastResEntry.get() or 1
ppNbMin = self.numOptPlaneEntry.get() or 1
minValueBest = self.numOptHitsEntry.get() or 2
maxValueBest = self.maxOptStepEntry.get() or 5
strucData = Meccano.runFwd(firstPPlaneFrag, lastPPlaneFrag, ppNbMin,
minValueBest, maxValueBest, RAMACHANDRAN_DATABASE,
seqData, mediaData, phipsiData)
if strucData:
fileName = 'CcpnMeccanoPdb%f.pdb' % time.time()
fileObj = open(fileName, 'w')
ch = self.chain.pdbOneLetterCode.strip()
if not ch:
ch = self.chain.code[0].upper()
i = 1
for atomType, resNb, x, y, z in strucData:
resType = residueDict.get(resNb, '???')
line = PDB_FORMAT % ('ATOM',i,'%-3s' % atomType,'',resType,ch,resNb,'',x,y,z,1.0,1.0)
i += 1
fileObj.close()
ensemble = getStructureFromFile(self.molSystem, fileName)
if not self.toggleWritePdbFile.get():
os.unlink(fileName)
self.run.outputEnsemble = ensemble
self.run = None
self.updateRuns()
def getMediumName(self, alignMedium):
self.mediumNameEntry.set(alignMedium.name)
def getMediumDetails(self, alignMedium):
self.mediumDetailsEntry.set(alignMedium.details)
def setMediumName(self, event):
value = self.mediumNameEntry.get()
self.alignMedium.name = value or None
def setMediumDetails(self, event):
value = self.mediumDetailsEntry.get()
self.alignMedium.details = value or None
def setAlignMedium(self, alignMedium):
if self.constraintSet:
self.constraintSet.conditionState = alignMedium
def getAlignMedium(self, constraintList):
media = self.getAlignmentMedia()
names = [am.name for am in media]
if constraintList.conditionState in media:
index = media.index(constraintList.conditionState)
else:
index = 0
self.alignMediumPulldown.setup(names, media, index)
def toggleUseRestraints(self, constraintList):
bool = constraintList.useForMeccano
bool = not bool
if bool and (not constraintList.conditionState) \
and (constraintList.className == 'RdcConsraintList'):
msg = 'Cannot use RDC restraint list for Meccano '
msg += 'unless it is first associated with an amigment medium'
showWarning('Warning', msg, parent=self)
else:
constraintList.useForMeccano = bool
self.updateConstraintLists()
def addStaticTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.staticAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def addDynamicTensor(self):
if self.alignMedium:
tensor = Implementation.SymmTracelessMatrix(aAxial=0.0,aRhombic=0.0,
alpha=0.0,beta=0.0,
gamma=0.0)
self.alignMedium.dynamicAlignment = tensor
self.updateAlignMediaAfter(self.alignMedium)
def removeTensor(self):
if self.alignMedium and self.tensor:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = None
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = None
self.updateAlignMediaAfter(self.alignMedium)
def addAlignMedium(self):
if self.constraintSet:
medium = self.constraintSet.newConditionState()
medium.name = 'Align Medium %d' % medium.serial
def removeAlignMedium(self):
if self.alignMedium:
self.alignMedium.delete()
def updateTensor(self, aAxial=None, aRhombic=None, alpha=None, beta=None, gamma=None):
aAxial = aAxial or self.tensor.aAxial
aRhombic = aRhombic or self.tensor.aRhombic
alpha = alpha or self.tensor.alpha
beta = beta or self.tensor.beta
gamma = gamma or self.tensor.gamma
tensor = Implementation.SymmTracelessMatrix(aAxial=aAxial,
aRhombic=aRhombic,
alpha=alpha,beta=beta,
gamma=gamma)
if self.alignMedium:
if self.tensor is self.alignMedium.dynamicAlignment:
self.alignMedium.dynamicAlignment = tensor
elif self.tensor is self.alignMedium.staticAlignment:
self.alignMedium.staticAlignment = tensor
self.tensor = tensor
def setAxial(self, event):
value = self.editAxialEntry.get()
self.updateTensor(aAxial=value)
self.updateTensors()
def setRhombic(self, event):
value = self.editRhombicEntry.get()
self.updateTensor(aRhombic=value)
self.updateTensors()
def setEulerAlpha(self, event):
value = self.editAlphaEulerEntry.get()
self.updateTensor(alpha=value)
self.updateTensors()
def setEulerBeta(self, event):
value = self.editBetaEulerEntry.get()
self.updateTensor(beta=value)
self.updateTensors()
def setEulerGamma(self, event):
value = self.editGammaEulerEntry.get()
self.updateTensor(gamma=value)
self.updateTensors()
def getAxial(self, tensor):
value = tensor.aAxial
self.editAxialEntry.set(value)
def getRhombic(self, tensor):
value = tensor.aRhombic
self.editRhombicEntry.set(value)
def getEulerAlpha(self, tensor):
value = tensor.alpha
self.editAlphaEulerEntry.set(value)
def getEulerBeta(self, tensor):
value = tensor.beta
self.editBetaEulerEntry.set(value)
def getEulerGamma(self, tensor):
value = tensor.gamma
self.editGammaEulerEntry.set(value)
def selectTensor(self, tensor, row, col):
self.tensor = tensor
def selectAlignMedium(self, alignMedium, row, col):
self.alignMedium = alignMedium
self.updateTensors()
def getAlignmentMedia(self):
if self.constraintSet:
return self.constraintSet.sortedConditionStates()
else:
return []
def updateAlignMedia(self):
textMatrix = []
objectList = []
if self.constraintSet:
objectList = self.getAlignmentMedia()
for conditionState in objectList:
staticTensor = None
dyamicTensor = None
tensor = conditionState.dynamicAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
dyamicTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
tensor = conditionState.staticAlignment
if tensor:
vals = (tensor.aAxial, tensor.aRhombic, tensor.alpha, tensor.beta, tensor.gamma)
staticTensor = u'\u03B6:%.3f \u03B7:%.3f \u03B1:%.3f \u03B2:%.3f \u03B3:%.3f ' % vals
datum = [conditionState.serial,
conditionState.name,
conditionState.details,
dyamicTensor,
staticTensor]
textMatrix.append(datum)
if dyamicTensor or staticTensor:
if not self.alignMedium:
self.alignMedium = conditionState
self.mediaMatrix.update(textMatrix=textMatrix, objectList=objectList)
if self.alignMedium:
self.mediaMatrix.selectObject(self.alignMedium)
def updateTensors(self):
textMatrix = []
objectList = []
conditionState = self.alignMedium
if conditionState:
tensor = conditionState.dynamicAlignment
if tensor:
datum = ['Dynamic', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
tensor = conditionState.staticAlignment
if tensor:
datum = ['Static', tensor.aAxial, tensor.aRhombic,
tensor.alpha, tensor.beta, tensor.gamma]
textMatrix.append(datum)
objectList.append(tensor)
self.tensorMatrix.update(textMatrix=textMatrix, objectList=objectList)
def getMolSystems(self):
molSystems = []
for molSystem in self.project.sortedMolSystems():
if molSystem.chains:
molSystems.append(molSystem)
return molSystems
def updateMolSystems(self, *notifyObj):
index = 0
names = []
molSystems = self.getMolSystems()
molSystem = self.molSystem
if molSystems:
if molSystem not in molSystems:
molSystem = molSystems[0]
index = molSystems.index(molSystem)
names = [ms.code for ms in molSystems]
else:
self.molSystem = None
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
self.molSystemPulldown.setup(texts=names, objects=molSystems, index=index)
def selectMolSystem(self, molSystem):
if self.molSystem is not molSystem:
if self.run:
self.run.molSystem = molSystem
self.molSystem = molSystem
self.updateChains()
def updateChains(self, *notifyObj):
index = 0
names = []
chains = []
chain = self.chain
if self.molSystem:
chains = [c for c in self.molSystem.sortedChains() if c.residues]
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
names = [c.code for c in chains]
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
self.chainPulldown.setup(texts=names, objects=chains, index=index)
def selectChain(self, chain):
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges()
def updateResidueRanges(self):
first = self.firstResEntry.get()
last = self.lastResEntry.get()
if self.chain:
residues = self.chain.sortedResidues()
firstSeq = residues[0].seqCode
lastSeq = residues[-2].seqCode
if first < firstSeq:
first = firstSeq
if last == first:
last = lastSeq
elif last > lastSeq:
last = lastSeq
if first > last:
last, first = first, last
self.firstResEntry.set(first)
self.lastResEntry.set(last)
return first, last
def getConstraintSets(self):
constraintSets = []
nmrProject = self.project.currentNmrProject
for constraintSet in nmrProject.sortedNmrConstraintStores():
for constraintList in constraintSet.constraintLists:
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintSets.append(constraintSet)
break
return constraintSets
def updateConstraintSets(self, *notifyObj):
index = 0
names = []
constraintSets = self.getConstraintSets()
constraintSet = self.constraintSet
if constraintSets:
if constraintSet not in constraintSets:
constraintSet = constraintSets[0]
index = constraintSets.index(constraintSet)
names = ['%d' % cs.serial for cs in constraintSets]
if constraintSet is not self.constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
self.constraintSetPulldown.setup(texts=names, objects=constraintSets, index=index)
def selectConstraintSet(self, constraintSet):
if self.constraintSet is not constraintSet:
if self.run:
self.run.inputConstraintStore = constraintSet
self.constraintSet = constraintSet
self.updateConstraintLists()
def getConstraintLists(self):
constraintLists = []
if self.constraintSet:
for constraintList in self.constraintSet.sortedConstraintLists():
if constraintList.className not in ('ChemShiftConstraintList','somethingElse'):
constraintLists.append(constraintList)
return constraintLists
def updateConstraintLists(self, *notifyObj):
textMatrix = []
objectList = self.getConstraintLists()
for constraintList in objectList:
if not hasattr(constraintList, 'useForMeccano'):
if constraintList.conditionState \
or (constraintList.className != 'RdcConstraintList'):
bool = True
else:
bool = False
constraintList.useForMeccano = bool
if constraintList.conditionState:
alignMedium = constraintList.conditionState.name
else:
alignMedium = None
datum = [constraintList.serial,
constraintList.className[:-14],
constraintList.useForMeccano and 'Yes' or 'No',
alignMedium,
len(constraintList.constraints)]
textMatrix.append(datum)
self.restraintMatrix.update(textMatrix=textMatrix, objectList=objectList)
def selectConstraint(self, obj, row, column):
if self.constraint is not obj:
self.constraint = obj
def getSimStore(self):
simStore = self.project.findFirstNmrSimStore(name='meccano')
if not simStore:
simStore = self.project.newNmrSimStore(name='meccano')
return simStore
def getRuns(self):
runs = [None, ]
if self.molSystem and self.constraintSet:
simStore = self.getSimStore()
runs += simStore.sortedRuns()
return runs
def updateRuns(self, *notifyObj):
index = 0
names = ['<New>']
runs = self.getRuns()
run = self.run
if runs:
if run not in runs:
run = runs[0]
index = runs.index(run)
names += [r.serial for r in runs if r]
if run is not self.run:
self.updateConstraintSets()
self.updateMolSystems()
self.updateShiftLists()
self.runPulldown.setup(names, runs, index)
def updateRunParams(self, event=None):
if self.run and self.molSystem and self.constraintSet:
simRun = self.run
simRun.inputConstraintStore = self.constraintSet
simRun.molSystem = self.molSystem
if self.shiftList:
simRun.setInputMeasurementLists([self.shiftList,])
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
def makeSimRun(self, template=None):
simStore = self.getSimStore()
if template:
molSystem = template.molSystem
constraintSet = template.inputConstraintStore
shiftList = template.findFirstInputMeasurementList(className='ShiftList')
protocol = template.annealProtocol
else:
molSystem = self.molSystem
constraintSet = self.constraintSet
shiftList = self.shiftList
protocol = self.annealProtocol
simRun = simStore.newRun(annealProtocol=protocol,
molSystem=molSystem,
inputConstraintStore=protocol)
if shiftList:
simRun.addInputMeasurementList(shiftList)
if template:
for param in template.runParameters:
simRun.newRunParameter(code=param.code,
id=param.id,
booleanValue=param.booleanValue,
floatValue=param.floatValue,
intValue=param.intValue,
textValue=param.textValue)
else:
if self.chain:
chainCode = self.chain.code
else:
chaincode = 'A'
simRun.newRunParameter(code='FirstPepPlane',id=1,
intValue=self.firstResEntry.get() or 0)
simRun.newRunParameter(code='LastPepPlane' ,id=1,
intValue=self.lastResEntry.get() or 0)
simRun.newRunParameter(code='MaxOptSteps', id=1,
intValue=self.maxOptStepEntry.get() or 0)
simRun.newRunParameter(code='NumOptPlanes', id=1,
intValue=self.numOptPlaneEntry.get() or 0)
simRun.newRunParameter(code='MinOptHits', id=1,
intValue=self.numOptHitsEntry.get() or 0)
simRun.newRunParameter(code='ChainCode', id=1,
textValue=chainCode)
return simRun
def selectRun(self, simRun):
if self.run is not simRun:
if simRun:
if simRun.outputEnsemble:
msg = 'Selected run has already been used to generate a structure.'
msg += 'A new run will be setup based on the selection.'
showWarning('Warning',msg)
simRun = self.makeSimRun(template=simRun)
molSystem = simRun.molSystem
constraintSet = simRun.inputConstraintStore
shiftList = simRun.findFirstInputMeasurementList(className='ShiftList')
if molSystem and (self.molSystem is not molSystem):
self.molSystem = molSystem
self.updateMolSystems()
if constraintSet and (self.constraintSet is not constraintSet):
self.constraintSet = constraintSet
self.updateConstraintSets()
if shiftList and (self.shiftList is not shiftList):
self.shiftList = shiftList
self.updateShiftLists()
firstPepPlane = simRun.findFirstrunParameter(code='FirstPepPlane')
lastPepPlane = simRun.findFirstrunParameter(code='LastPepPlane')
maxOptSteps = simRun.findFirstrunParameter(code='MaxOptSteps')
numOptPlanes = simRun.findFirstrunParameter(code='NumOptPlanes')
minOptHits = simRun.findFirstrunParameter(code='MinOptHits')
chainCode = simRun.findFirstrunParameter(code='ChainCode')
if firstPepPlane is not None:
self.firstResEntry.set(firstPepPlane.intValue or 0)
if lastPepPlane is not None:
self.lastResEntry.set(lastPepPlane.intValue or 0)
if maxOptSteps is not None:
self.maxOptStepEntry.set(maxOptSteps.intValue or 0)
if numOptPlanes is not None:
self.numOptPlaneEntry.set(numOptPlanes.intValue or 0)
if minOptHits is not None:
self.numOptHitsEntry.set(minOptHits.intValue or 0)
if chainCode is not None:
chainCode = chainCode.textValue or 'A'
if self.molSystem:
chain = self.molSystem.findFirsChain(code=chainCode)
if chain:
self.selectChain(chain)
self.run = simRun
def updateShiftLists(self, *notifyObj):
index = 0
names = []
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
shiftLists = [(sl.serial, sl) for sl in shiftLists]
shiftLists.sort()
shiftLists = [x[1] for x in shiftLists]
shiftList = self.shiftList
if shiftLists:
if shiftList not in shiftLists:
shiftList = shiftLists[0]
index = shiftLists.index(shiftList)
names = ['%d'% sl.serial for sl in shiftLists]
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftListPulldown.setup(texts=names, objects=shiftLists, index=index)
def selectShiftList(self, shiftList):
if shiftList is not self.shiftList:
if self.run:
self.run.setInputMeasurementLists([shiftList])
self.shiftList = shiftList
class 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 HelpFrame(Frame):
def __init__(self,
parent,
width=70,
height=20,
xscroll=False,
yscroll=True,
*args,
**kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_columnconfigure(1, weight=1)
row = 0
texts = ('back', 'forward', 'load')
commands = (self.prevUrl, self.nextUrl, self.loadUrl)
self.buttons = ButtonList(self, texts=texts, commands=commands)
self.buttons.grid(row=row, column=0)
self.url_entry = Entry(self, returnCallback=self.loadUrl)
self.url_entry.grid(row=row, column=1, columnspan=2, sticky=Tkinter.EW)
row = row + 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.createFindFrame(frame)
row = row + 1
self.grid_rowconfigure(row, weight=1)
self.help_text = ScrolledHtml(self,
width=width,
height=height,
xscroll=xscroll,
yscroll=yscroll,
startUrlCallback=self.startOpenUrl,
endUrlCallback=self.endOpenUrl,
enterLinkCallback=self.setLinkLabel,
leaveLinkCallback=self.setLinkLabel)
self.help_text.grid(row=row,
column=0,
columnspan=3,
sticky=Tkinter.NSEW)
row = row + 1
self.link_label = Label(self)
self.link_label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
button = memops.gui.Util.createDismissButton(self,
dismiss_cmd=self.close)
button.grid(row=row, column=2)
self.urls = []
self.current = -1
self.updateUrlList = True
self.setButtonState()
def close(self):
if (self.popup):
if (self.popup.modal):
self.popup.do_grab()
popup = self.parent
while (not hasattr(popup, 'top')):
popup = popup.parent
popup.close()
def createFindFrame(self, master):
frame = Frame(master)
frame.grid(row=0, column=0, sticky=Tkinter.W)
arrow = ToggleArrow(frame, callback=self.toggleFindFrame)
arrow.grid(row=0, column=0)
button = Button(frame, text='find:', command=self.findPhrase)
button.grid(row=0, column=1)
self.find_entry = Entry(frame,
width=20,
returnCallback=self.findPhrase)
self.find_entry.grid(row=0, column=2)
self.find_frame = frame = Frame(master)
entries = ('search forwards', 'search backwards')
self.direction_buttons = PulldownMenu(frame, entries=entries)
self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5)
self.forwards_entries = entries = ('wrap search', 'stop at end')
self.backwards_entries = ('wrap search', 'stop at beginning')
self.wrap_buttons = PulldownMenu(frame, entries=entries)
self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5)
self.direction_buttons.callback = self.setWrapText
entries = ('case insensitive', 'case sensitive')
self.case_buttons = PulldownMenu(frame, entries=entries)
self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5)
entries = ('literal search', 'regex search')
self.pattern_buttons = PulldownMenu(frame, entries=entries)
self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5)
self.countVar = Tkinter.IntVar()
def setWrapText(self, entry_ind, entry):
if (entry_ind == 0):
entries = self.forwards_entries
else:
entries = self.backwards_entries
self.wrap_buttons.replace(
entries, selected_index=self.wrap_buttons.getSelectedIndex())
def findPhrase(self, *extra):
phrase = self.find_entry.get()
if (not phrase):
showError('No find phrase', 'Enter phrase in entry box.')
return
if (self.direction_buttons.getSelectedIndex() == 0):
forwards = 1
backwards = 0
else:
forwards = 0
backwards = 1
if (self.case_buttons.getSelectedIndex() == 0):
nocase = 1
else:
nocase = 0
if (self.pattern_buttons.getSelectedIndex() == 0):
exact = 1
regexp = 0
else:
exact = 0
regexp = 1
start = self.help_text.tag_nextrange(Tkinter.SEL, '1.0')
if (start):
start = start[0]
if (forwards):
start = '%s+1c' % start
else:
start = '%s-1c' % start
else:
start = Tkinter.CURRENT
if (self.wrap_buttons.getSelectedIndex() == 0):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp)
elif (forwards):
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex=Tkinter.END)
else:
match = self.help_text.search(phrase,
start,
count=self.countVar,
forwards=forwards,
backwards=backwards,
nocase=nocase,
exact=exact,
regexp=regexp,
stopindex='1.0')
if (match):
self.help_text.see(match)
self.help_text.setSelection(
match, '%s+%dc' % (match, self.countVar.get()))
self.help_text.tag_config(Tkinter.SEL, background='gray70')
else:
showInfo('No match', 'No match found for phrase.')
def toggleFindFrame(self, isClosed):
if (isClosed):
self.find_frame.grid_forget()
else:
self.find_frame.grid(row=1, column=0, sticky=Tkinter.W)
def setButtonState(self):
n = len(self.urls)
if ((n >= 2) and (self.current > 0)):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[0].config(state=state)
if ((n >= 2) and (self.current < (n - 1))):
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
self.buttons.buttons[1].config(state=state)
def setLinkLabel(self, url=''):
self.link_label.set(url)
def loadUrl(self, *extra):
url = self.url_entry.get()
if (url):
if (url.find(':') == -1):
if (url[:2] != '//'):
url = '//' + url
url = 'http:' + url
self.showUrl(url, forceLoad=True)
def newUrl(self, url):
self.current = self.current + 1
self.urls[self.current:] = [[url, 0.0]]
self.setButtonState()
#print 'newUrl', self.current, self.urls
def prevUrl(self):
if (self.current > 0): # True if called via button
(url, offset) = self.urls[self.current - 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current - 1
self.setButtonState()
#print 'prevUrl', self.current, self.urls
def nextUrl(self):
if (self.current < (len(self.urls) - 1)): # True if called via button
(url, offset) = self.urls[self.current + 1]
self.updateUrlList = False
self.showUrl(url, offset=offset, allowModifyPath=False)
self.updateUrlList = True
self.current = self.current + 1
self.setButtonState()
#print 'nextUrl', self.current, self.urls
def showText(self, message, popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.setState(Tkinter.NORMAL) # so that can add text
self.help_text.clear() # clear existing text
self.help_text.append(message)
self.help_text.setState(Tkinter.DISABLED) # make text read-only
self.open()
def startOpenUrl(self, yview):
if (self.urls):
self.urls[self.current][1] = yview[0]
def endOpenUrl(self, url):
#print 'endOpenUrl', url, self.updateUrlList
self.url_entry.set(url)
if (self.updateUrlList):
self.newUrl(url)
self.setLinkLabel()
self.open()
def showUrl(self,
url,
offset=None,
forceLoad=False,
allowModifyPath=True,
popup=None):
self.popup = popup
if (popup):
self.parent.modal = popup.modal
self.help_text.openUrl(url,
forceLoad=forceLoad,
allowModifyPath=allowModifyPath)
if (offset is not None):
self.help_text.yview(Tkinter.MOVETO, str(offset))
class CreateAxisUnitPopup(BasePopup):
def __init__(self, parent, *args, **kw):
BasePopup.__init__(self,
parent=parent,
title='Create axis unit',
modal=True,
**kw)
def body(self, master):
master.grid_columnconfigure(1, weight=1)
row = 0
label = Label(master, text='Axis unit name: ', grid=(row, 0))
tipText = 'Short textual name for the unit, e.g. "KPa" or "ms"'
self.nameEntry = Entry(master,
width=10,
grid=(row, 1),
tipText=tipText)
row += 1
label = Label(master, text='Unit is backwards: ', grid=(row, 0))
tipText = 'Whether the axis values decrease left to right & bottom to top. For example "ppm" does, but most units do not'
self.backwardsMenu = BooleanPulldownMenu(master,
grid=(row, 1),
tipText=tipText)
row += 1
tipTexts = [
'Make a new unit specification using the stated options and close this popup'
]
texts = ['Create']
commands = [self.ok]
buttons = UtilityButtonList(master,
texts=texts,
commands=commands,
closeText='Cancel',
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
master.grid_rowconfigure(row, weight=1)
def apply(self):
unit = self.nameEntry.get()
if (not unit):
showError('No unit', 'Need to enter unit')
return False
units = [axisUnit.unit for axisUnit in self.analysisProject.axisUnits]
if (unit in units):
showError('Repeated unit', 'Unit already used')
return False
isBackwards = self.backwardsMenu.getSelected()
self.analysisProject.newAxisUnit(unit=unit, isBackwards=isBackwards)
return True
class EditExperimentSeriesPopup(BasePopup):
"""
**Setup Experiment Series for Chemical Shift and Intensity Changes**
The purpose of this popup is to setup ordered groups of experiments that are
related by the variation in some condition or parameter, but otherwise the
kind of experiment being run is the same. For example the user could setup
experiments for a temperature series, ligand binding titration or relaxation
rate measurement.
The layout is divided into two tables. The upper table shows all of the series
that are known to the current project and the lower table shows all of the
experiments or planes that comprise the selected series. These series relate
to both groups of separate experiments (and hence spectra) and also single
experiment where one dimension is not for NMR frequency but rather a "sampled"
dimension and thus effectively combines many experiments (e.g. for different
T1 values) as different planes. A stack of effectively 2D experiments combined
in this manner is typically referred to as pseudo-3D. - The experiment is 3D
but there are only two NMR dimensions.
Series which are stacks of planes in a single experiment entity are
automatically detected and entered into the table once they are loaded. Series
that are constructed from multiple, separate experiments however must be setup
by the user. To setup a new series of this kind [Add Series] makes a new,
empty NMR series. Next the user should change the "Parameter varied" column to
specify what type of thing is varied between the different experiments. The
user then adds experiments into this series with the [Add Series Point]
function at the bottom. Once the points have been added to the series the name
of the experiment for each point may be changed. Initially, arbitrary
experiments appear for the series points, so these almost always have to be
adjusted.
Once a stacked-plane experiment or series of experiments is setup, the user
next sets (or checks) the value of the parameter associated with each point in
the lower table. When loading stacked-plane experiments these values may come
though automatically, if they are present in the spectrum header or parameter
file. Given a completed NMR series specification the user may then extract the
relevant data from the series using one of the analysis tools like `Follow
Intensity Changes`_ or `Follow Shift Changes`_.
**Caveats & Tips**
Make sure the "Parameter Varied" for a given NMR series is appropriate to the
type of analysis being performed. Many tools that extract T1 or Kd
measurements for example look for specific types of series.
The "Set/Unset Ref Plane" function is only used in certain kinds of series
such as those that use trains of CPMG pulses.
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
"""
def __init__(self, parent, *args, **kw):
self.guiParent = parent
self.expSeries = None
self.conditionPoint = None
self.waiting = 0
BasePopup.__init__(self, parent, title="Experiment : NMR Series", **kw)
def body(self, guiFrame):
self.geometry("500x500")
self.nameEntry = Entry(self, text='', returnCallback=self.setName, width=12)
self.detailsEntry = Entry(self, text='', returnCallback=self.setDetails, width=16)
self.valueEntry = FloatEntry(self, text='', returnCallback=self.setValue, width=10)
self.errorEntry = FloatEntry(self, text='', returnCallback=self.setError, width=8)
self.conditionNamesPulldown = PulldownList(self, callback=self.setConditionName,
texts=self.getConditionNames())
self.unitPulldown = PulldownList(self, callback=self.setUnit,
texts=self.getUnits())
self.experimentPulldown = PulldownList(self, callback=self.setExperiment)
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
frame = Frame(guiFrame, grid=(row, 0))
frame.expandGrid(None,0)
div = LabelDivider(frame, text='Current Series', grid=(0, 0))
utilButtons = UtilityButtonList(frame, helpUrl=self.help_url, grid=(0,1))
row += 1
frame0 = Frame(guiFrame, grid=(row, 0))
frame0.expandGrid(0,0)
tipTexts = ['The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)',
'The name of the experiment series, which may be a single pseudo-nD experiment',
'The number of separate experiments (and hence spectra) present in the series',
'The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc.',
'The number of separate points, each with a separate experiment/plane and parameter value, in the series']
headingList = ['#','Name','Experiments','Parameter\nVaried','Num\nPoints']
editWidgets = [None, self.nameEntry, None, self.conditionNamesPulldown, None]
editGetCallbacks = [None, self.getName, None, self.getConditionName, None]
editSetCallbacks = [None, self.setName, None, self.setConditionName, None]
self.seriesMatrix = ScrolledMatrix(frame0, tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectExpSeries,
deleteFunc=self.deleteExpSeries,
grid=(0,0), gridSpan=(None, 3))
tipTexts = ['Make a new, blank NMR series specification in the CCPN project',
'Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead',
'Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme']
texts = ['Add Series','Delete Series',
'Auto Colour Spectra']
commands = [self.addExpSeries,self.deleteExpSeries,
self.autoColorSpectra]
self.seriesButtons = ButtonList(frame0, texts=texts, commands=commands,
grid=(1,0), tipTexts=tipTexts)
label = Label(frame0, text='Scheme:', grid=(1,1))
tipText = 'Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series'
self.colorSchemePulldown = PulldownList(frame0, grid=(1,2), tipText=tipText)
row += 1
div = LabelDivider(guiFrame, text='Experimental Parameters & Conditions', grid=(row, 0))
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
frame1 = Frame(guiFrame, grid=(row, 0))
frame1.expandGrid(0,0)
tipTexts = ['The kind of experimental parameter that is being used to define the NMR series',
'The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment',
'The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series',
'The estimated error in value of the condition',
'The measurement unit in which the value of the condition is represented']
headingList = ['Parameter','Experiment','Value','Error','Unit']
editWidgets = [None,self.experimentPulldown,self.valueEntry,self.errorEntry, self.unitPulldown]
editGetCallbacks = [None,self.getExperiment, self.getValue, self.getError, self.getUnit]
editSetCallbacks = [None,self.setExperiment, self.setValue, self.setError, self.setUnit]
self.conditionPointsMatrix = ScrolledMatrix(frame1, grid=(0,0), tipTexts=tipTexts,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectConditionPoint,
deleteFunc=self.deleteConditionPoint)
self.conditionPointsMatrix.doEditMarkExtraRules = self.conditionTableShow
tipTexts = ['Add a new point to the NMR series with an associated parameter value and experiment',
'Remove the selected point from the series, including any associated parameter value',
'For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference']
texts = ['Add Series Point','Delete Series Point','Set/Unset Ref Plane']
commands = [self.addConditionPoint,self.deleteConditionPoint,self.setSampledReferencePlane]
self.conditionPointsButtons = ButtonList(frame1, texts=texts, commands=commands,
tipTexts=tipTexts, grid=(1,0))
self.updateAfter()
self.updateColorSchemes()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
#for func in ('__init__', 'delete','setName'):
for func in ('__init__', 'delete','setName','setConditionNames',
'addConditionName','removeConditionName'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.NmrExpSeries', func)
for func in ('__init__', 'delete','setName'):
notifyFunc(self.updateExperiments,'ccp.nmr.Nmr.Experiment', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateDataDim,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete','setCondition','setUnit','setValue','setError'):
notifyFunc(self.updateConditionsAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('__init__', 'delete','setCondition'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampleCondition', func)
for func in ('setConditionVaried', 'setPointErrors',
'addPointError', 'removePointError',
'setPointValues','addPointValue',
'removePointValue','setUnit'):
notifyFunc(self.updateAfter,'ccp.nmr.Nmr.SampledDataDim', func)
for func in ('__init__', 'delete'):
notifyFunc(self.updateColorSchemes,'ccpnmr.AnalysisProfile.ColorScheme', func)
def open(self):
self.updateAfter()
BasePopup.open(self)
def updateColorSchemes(self, scheme=None):
index = 0
prevScheme = self.colorSchemePulldown.getObject()
schemes = getHueSortedColorSchemes(self.analysisProfile)
schemes = [s for s in schemes if len(s.colors) > 1]
colors = [list(s.colors) for s in schemes]
if schemes:
names = [s.name for s in schemes]
if prevScheme in schemes:
index = schemes.index(prevScheme)
else:
names = []
self.colorSchemePulldown.setup(names, schemes, index, colors)
def autoColorSpectra(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
scheme = self.colorSchemePulldown.getObject()
if scheme:
colors = scheme.colors
else:
colors = ['#FF0000','#00FF00','#0000FF']
cdict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionName = list(self.expSeries.conditionNames)[0]
expList = []
for sampleCondition in cdict.get(conditionName, []):
expList.append( (sampleCondition.value, sampleCondition.parent.experiments) )
expList.sort()
m = len(expList)-1.0
c = len(colors)-1
for i, (value, experiments) in enumerate(expList):
p = c*i/m
j = int(p)
r1, g1, b1 = Color.hexToRgb(colors[j])
r2, g2, b2 = Color.hexToRgb(colors[min(c,j+1)])
f2 = p-j
f1 = 1.0-f2
r = (r1*f1)+(r2*f2)
g = (g1*f1)+(g2*f2)
b = (b1*f1)+(b2*f2)
hexColor = Color.hexRepr(r,g,b)
for experiment in experiments:
for spectrum in experiment.dataSources:
if spectrum.dataType == 'processed':
analysisSpec = getAnalysisSpectrum(spectrum)
if analysisSpec.posColors:
analysisSpec.posColors = [hexColor,]
elif analysisSpec.negColors:
analysisSpec.negColors = [hexColor,]
def getUnusedExperiments(self):
sampleExperiments = getSampledDimExperiments(self.nmrProject)
experiments = []
for experiment in self.nmrProject.sortedExperiments():
if experiment in sampleExperiments:
continue
if self.expSeries and (self.expSeries.className != 'Experiment'):
if experiment in self.expSeries.experiments:
continue
experiments.append(experiment)
return experiments
def conditionTableShow(self, object, row, col):
if type(object) is type(()):
dataDim, index = object
refPlane = dataDim.analysisDataDim.refSamplePlane
if refPlane == index:
return False
if col == 1:
return False
return True
def setSampledReferencePlane(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
if self.conditionPoint:
dataDim, point = self.conditionPoint
analysisDataDim = dataDim.analysisDataDim
refPoint = analysisDataDim.refSamplePlane
if refPoint == point:
analysisDataDim.refSamplePlane = None
else:
analysisDataDim.refSamplePlane = point
self.updateAfter()
def checkAddSampleCondition(self, experiment):
conditionSet = getExperimentConditionSet(experiment)
conditionName = self.expSeries.conditionNames[0]
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
sampleConditions = condDict.get(conditionName, [])
units = [sc.unit for sc in sampleConditions if sc.unit]
if units:
sortList = list(set(units))
sortList.sort(key = lambda u:units.count(u))
unit = sortList[-1]
else:
unit = CONDITION_UNITS_DICT[conditionName][0]
condition = conditionSet.findFirstSampleCondition(condition=conditionName)
if not condition:
condition = conditionSet.newSampleCondition(condition=conditionName,
unit=unit, value=0.0, error=0.0)
def addConditionPoint(self):
if self.expSeries and (self.expSeries.className != 'Experiment'):
experiments = self.getUnusedExperiments()
if not experiments:
showWarning('Warning','No experiments available', parent=self)
return
experiment = experiments[0]
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
self.checkAddSampleCondition(experiment)
self.updateAfter()
def deleteConditionPoint(self, *event):
if self.conditionPoint and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series point?', parent=self):
conditionSet = self.conditionPoint.sampleConditionSet
experiments = [e for e in conditionSet.experiments if e in self.expSeries.experiments]
for experiment in experiments:
self.expSeries.removeExperiment(experiment)
for experiment in experiments:
for expSeries in experiment.nmrExpSeries:
if self.conditionPoint.condition in self.expSeries.conditionNames:
break
else:
continue
break
else:
self.conditionPoint.delete()
self.conditionPoint = None
def selectConditionPoint(self, object, row, col):
if object:
self.conditionPoint = object
self.updateButtons()
def selectExpSeries(self, object, row, col):
if object:
self.expSeries = object
self.checkExperimentConditionsConsistent()
self.updateConditions()
def checkExperimentConditionsConsistent(self):
if self.expSeries.className != 'Experiment':
for experiment in self.expSeries.experiments:
self.checkAddSampleCondition(experiment)
def getUnits(self):
units = []
if self.expSeries:
if self.expSeries.className == 'Experiment':
conditionName = getExperimentSampledDim(self.expSeries).conditionVaried
else:
conditionName = self.expSeries.conditionNames[0]
units = CONDITION_UNITS_DICT.get(conditionName)
if not units:
units = ['?',]
return units
def getUnit(self, sampleCondition):
index = -1
units = self.getUnits()
if units:
if sampleCondition:
if type(sampleCondition) is type(()):
dataDim, index = sampleCondition
unit = dataDim.unit
else:
unit = sampleCondition.unit
if unit not in units:
unit = units[0]
index = units.index(unit)
self.unitPulldown.setup(units,units,index)
def setUnit(self, obj):
name = self.unitPulldown.getObject()
if self.conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
dataDim.setUnit(name)
else:
self.conditionPoint.setUnit(name)
def getConditionNames(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
names = ['delay time','mixing time','num delays','pulsing frequency','gradient strength']
else:
names = CONDITION_UNITS_DICT.keys()
names.sort()
return names
def setConditionName(self, obj):
name = self.conditionNamesPulldown.getObject()
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
dataDim.conditionVaried = name
else:
self.expSeries.setConditionNames([name,])
def getConditionName(self, expSeries):
index = 0
names = self.getConditionNames()
if names:
if expSeries:
if expSeries.className == 'Experiment':
name = getExperimentSampledDim(expSeries).conditionVaried
else:
name = expSeries.conditionNames[0]
if name:
index = names.index(name)
else:
index = 0
self.conditionNamesPulldown.setup(names,names,index)
def getName(self, expSeries):
if expSeries :
self.nameEntry.set(expSeries.name)
def setName(self, event):
text = self.nameEntry.get()
if text and text != ' ':
self.expSeries.setName( text )
def getValue(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
value = dataDim.pointValues[index]
else:
value = conditionPoint.value
self.valueEntry.set(value)
def setValue(self, event):
value = self.valueEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
values = list(dataDim.pointValues)
values[index] = value
dataDim.setPointValues(values)
else:
self.conditionPoint.setValue( value )
def getError(self, conditionPoint):
if conditionPoint:
if type(self.conditionPoint) is type(()):
dataDim, index = conditionPoint
if index < len(dataDim.pointErrors):
error = dataDim.pointValues[index]
else:
error = 0.0
else:
error = conditionPoint.error
self.errorEntry.set(error)
def setError(self, event):
value = self.errorEntry.get()
if value is not None:
if type(self.conditionPoint) is type(()):
dataDim, index = self.conditionPoint
pointErrors = dataDim.pointErrors
if pointErrors:
values = list(pointErrors)
else:
values = [0.0] * dataDim.numPoints
values[index] = value
dataDim.setPointErrors(values)
else:
self.conditionPoint.setError( value )
def getDetails(self, expSeries):
if expSeries :
self.detailsEntry.set(expSeries.details)
def setDetails(self, event):
text = self.detailsEntry.get()
if text and text != ' ':
self.expSeries.setDetails( text )
def addExpSeries(self):
expSeries = self.nmrProject.newNmrExpSeries(conditionNames=['delay time',])
def deleteExpSeries(self, *event):
if self.expSeries and (self.expSeries.className != 'Experiment'):
if showOkCancel('Confirm','Really delete series?', parent=self):
self.expSeries.delete()
self.expSeries = None
self.conditionPoint = None
def getExperiments(self):
if self.expSeries and (self.expSeries.className == 'Experiment'):
return [self.expSeries,]
else:
return self.nmrProject.sortedExperiments()
def getExperiment(self, sampleCondition):
index = 0
names = []
if self.conditionPoint and (type(self.conditionPoint) != type(())):
index = 0
experiment = self.conditionPoint.parent.findFirstExperiment()
experiments = self.getUnusedExperiments()
name = experiment.name
names = [name] + [e.name for e in experiments]
experiments = [experiment,] + experiments
self.experimentPulldown.setup(names,experiments,index)
def setExperiment(self, obj):
experiment = self.experimentPulldown.getObject()
if self.conditionPoint and (type(self.conditionPoint) != type(())):
conditionSet = getExperimentConditionSet(experiment)
if conditionSet is not self.conditionPoint.parent:
if experiment not in self.expSeries.experiments:
self.expSeries.addExperiment(experiment)
unit = self.conditionPoint.unit
if not unit:
unit = CONDITION_UNITS_DICT[self.expSeries.conditionNames[0]]
condition = self.conditionPoint.condition
experiments = set(self.expSeries.experiments)
for experiment0 in self.conditionPoint.parent.experiments:
if experiment0 in experiments:
experiments.remove(experiment0)
self.expSeries.experiments = experiments
value = self.conditionPoint.value
error = self.conditionPoint.error
self.conditionPoint.delete()
self.conditionPoint = conditionSet.findFirstSampleCondition(condition=condition)
if self.conditionPoint:
self.conditionPoint.unit = unit
self.updateAfter()
else:
self.conditionPoint = conditionSet.newSampleCondition(condition=condition,unit=unit,
value=value,error=error)
def updateDataDim(self, sampledDataDim):
experiment = sampledDataDim.dataSource.experiment
self.updateExperiments(experiment)
def updateExperiments(self, experiment):
experiments = self.getExperiments()
names = [e.name for e in experiments]
self.experimentPulldown.setup(names, experiments,0)
if getExperimentSampledDim(experiment):
self.updateAfter()
elif self.expSeries:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.updateConditionsAfter()
elif experiment in self.expSeries.experiments:
self.updateConditionsAfter()
def updateConditionsAfter(self, sampleCondition=None):
if self.waitingConditions:
return
if sampleCondition:
experiments = sampleCondition.sampleConditionSet.experiments
for experiment in experiments:
if self.expSeries.className == 'Experiment':
if experiment is self.expSeries:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
elif experiment in self.expSeries.experiments:
self.waitingConditions = True
self.after_idle(self.updateConditions)
break
else:
self.waitingConditions = True
self.after_idle(self.updateConditions)
def updateConditions(self):
self.updateButtons()
objectList = []
textMatrix = []
colorMatrix = []
nCols = len(self.conditionPointsMatrix.headingList)
defaultColors = [None] * nCols
if self.expSeries:
if self.expSeries.className == 'Experiment':
dataDim = getExperimentSampledDim(self.expSeries)
analysisDataDim = getAnalysisDataDim(dataDim)
conditionVaried = dataDim.conditionVaried
expName = self.expSeries.name
unit = dataDim.unit
pointValues = dataDim.pointValues
pointErrors = dataDim.pointErrors
refPlane = analysisDataDim.refSamplePlane
for i in range(dataDim.numPoints):
if i < len(pointErrors):
error = pointErrors[i]
else:
error = None
pointText = ':%3d' % (i+1)
if i == refPlane:
datum = ['* Ref Plane *',
expName+pointText,
None,
None,
None]
colorMatrix.append(['#f08080'] * nCols)
else:
datum = [conditionVaried ,
expName+pointText,
pointValues[i],
error,
unit]
colorMatrix.append(defaultColors)
textMatrix.append(datum)
objectList.append((dataDim, i))
else:
condDict = getNmrExpSeriesSampleConditions(self.expSeries)
conditionNames = self.expSeries.conditionNames
for conditionName in conditionNames:
for sampleCondition in condDict.get(conditionName, []):
datum = [sampleCondition.condition,
' '.join([e.name for e in sampleCondition.parent.experiments]),
sampleCondition.value,
sampleCondition.error,
sampleCondition.unit]
textMatrix.append(datum)
objectList.append(sampleCondition)
colorMatrix.append(defaultColors)
self.conditionPointsMatrix.update(objectList=objectList,
colorMatrix=colorMatrix,
textMatrix=textMatrix)
self.waitingConditions = 0
def updateAfter(self, object=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def updateButtons(self):
if self.expSeries is None:
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].disable()
elif self.expSeries.className == 'Experiment':
self.seriesButtons.buttons[1].disable()
self.seriesButtons.buttons[2].disable()
self.conditionPointsButtons.buttons[0].disable()
self.conditionPointsButtons.buttons[1].disable()
self.conditionPointsButtons.buttons[2].enable()
else:
self.seriesButtons.buttons[1].enable()
self.seriesButtons.buttons[2].enable()
self.conditionPointsButtons.buttons[0].enable()
self.conditionPointsButtons.buttons[2].disable()
if self.conditionPoint is None:
self.conditionPointsButtons.buttons[1].disable()
else:
self.conditionPointsButtons.buttons[1].enable()
def update(self):
self.updateButtons()
objectList = []
textMatrix = []
for experiment in getSampledDimExperiments(self.nmrProject):
getExperimentConditionSet(experiment)
sampledDim = getExperimentSampledDim(experiment)
datum = [None,
experiment.name,
1,
sampledDim.conditionVaried,
sampledDim.numPoints]
textMatrix.append(datum)
objectList.append(experiment)
for expSeries in self.nmrProject.sortedNmrExpSeries():
experiments = expSeries.experiments
conditionSets = len([e.sampleConditionSet for e in experiments if e.sampleConditionSet])
datum = [expSeries.serial,
expSeries.name or ' ',
len(experiments),
','.join(expSeries.conditionNames),
conditionSets]
textMatrix.append(datum)
objectList.append(expSeries)
self.seriesMatrix.update(objectList=objectList, textMatrix=textMatrix)
self.updateConditions()
self.waiting = False
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
class PrintFrame(LabelFrame):
def __init__(self,
parent,
getOption=None,
setOption=None,
text='Print Options',
haveTicks=False,
doOutlineBox=True,
*args,
**kw):
self.getOption = getOption
self.setOption = setOption
self.haveTicks = haveTicks
self.doOutlineBox = doOutlineBox
LabelFrame.__init__(self, parent=parent, text=text, *args, **kw)
self.file_select_popup = None
self.getOptionValues()
try:
size_index = self.paper_types.index(self.paper_type)
except:
size_index = 0
try:
other_unit_index = self.paper_units.index(self.other_unit)
except:
other_unit_index = 0
try:
orientation_index = self.paper_orientations.index(self.orientation)
except:
orientation_index = 0
try:
style_index = self.style_choices.index(self.output_style)
except:
style_index = 0
try:
format_index = self.format_choices.index(self.output_format)
except:
format_index = 0
if haveTicks:
try:
tick_location_index = self.tick_locations.index(
self.tick_location)
except:
tick_location_index = 0
self.grid_columnconfigure(2, weight=1)
row = 0
label = Label(self, text='File:')
label.grid(row=row, column=0, sticky='e')
self.file_entry = Entry(self, width=40, text=self.file_name)
self.file_entry.grid(row=row, column=1, columnspan=2, sticky='ew')
button = Button(self, text='Choose File', command=self.findFile)
button.grid(row=row, column=3, rowspan=2, sticky='nsew')
row += 1
label = Label(self, text='Title:')
label.grid(row=row, column=0, sticky='e')
self.title_entry = Entry(self, width=40, text=self.title)
self.title_entry.grid(row=row, column=1, columnspan=2, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(4, weight=1)
label = Label(frame, text='Paper size:')
label.grid(row=0, column=0, sticky='e')
entries = []
for t in paper_types:
if t == Output.other_paper_type:
entry = t
else:
(w, h, u) = paper_sizes[t]
entry = t + ' (%2.1f %s x %2.1f %s)' % (w, u, h, u)
entries.append(entry)
self.size_menu = PulldownList(frame,
callback=self.changedSize,
texts=entries,
index=size_index)
self.size_menu.grid(row=0, column=1, sticky='w')
self.other_frame = Frame(frame)
self.other_frame.grid_columnconfigure(0, weight=1)
self.other_entry = FloatEntry(self.other_frame,
text=self.other_size,
isArray=True)
self.other_entry.grid(row=0, column=0, sticky='ew')
self.other_unit_menu = PulldownList(self.other_frame,
texts=paper_units,
index=other_unit_index)
self.other_unit_menu.grid(row=0, column=1, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='Orientation:')
label.grid(row=0, column=0, sticky='e')
self.orientation_menu = PulldownList(frame,
texts=paper_orientations,
index=orientation_index)
self.orientation_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Style:')
label.grid(row=0, column=2, sticky='e')
self.style_menu = PulldownList(frame,
texts=style_choices,
index=style_index)
self.style_menu.grid(row=0, column=3, sticky='w')
label = Label(frame, text=' Format:')
label.grid(row=0, column=4, sticky='e')
self.format_menu = PulldownList(frame,
callback=self.changedFormat,
texts=format_choices,
index=format_index)
self.format_menu.grid(row=0, column=5, sticky='w')
if haveTicks:
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Tick Location:')
label.grid(row=0, column=0, sticky='e')
self.tick_menu = PulldownList(frame,
texts=tick_locations,
index=tick_location_index)
self.tick_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Tick Placement:')
label.grid(row=0, column=2, sticky='e')
self.tick_buttons = CheckButtons(frame,
entries=tick_placements,
selected=self.tick_placement)
self.tick_buttons.grid(row=0, column=3, sticky='w')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Include:')
label.grid(row=0, column=0, sticky='e')
self.border_buttons = CheckButtons(frame,
entries=border_decorations,
selected=self.border_decoration)
self.border_buttons.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Scaling:')
label.grid(row=0, column=2, sticky='e')
self.scaling_scale = Scale(frame,
orient=Tkinter.HORIZONTAL,
value=self.scaling)
self.scaling_scale.grid(row=0, column=3, sticky='ew')
def destroy(self):
self.setOptionValues()
if self.file_select_popup:
self.file_select_popup.destroy()
Frame.destroy(self)
def getOptionValues(self):
getOption = self.getOption
if getOption:
file_name = getOption('FileName', defaultValue='')
title = getOption('Title', defaultValue='')
paper_type = getOption('PaperSize', defaultValue=paper_types[0])
paper_type = paper_type_dict.get(paper_type, paper_types[0])
other_height = getOption('OtherHeight', defaultValue=10)
other_width = getOption('OtherWidth', defaultValue=10)
other_size = [other_height, other_width]
other_unit = getOption('OtherUnit', defaultValue=paper_units[0])
orientation = getOption('Orientation',
defaultValue=paper_orientations[0])
in_color = getOption('InColor', defaultValue=True)
if in_color:
output_style = style_choices[0]
else:
output_style = style_choices[1]
format_option = getOption('OutputFormat',
defaultValue=format_options[0])
output_format = format_choices[format_options.index(format_option)]
if self.haveTicks:
tick_outside = getOption('TickOutside',
defaultValue=tick_locations[0])
if tick_outside:
tick_location = tick_locations.index(PrintTicks.Outside)
else:
tick_location = tick_locations.index(PrintTicks.Inside)
tick_placement = getTickPlacement1(
getOption('TickPlacement', defaultValue='nsew'))
dateTime = getOption('ShowsDateTime', defaultValue=True)
fileName = getOption('ShowsFileName', defaultValue=True)
border_decoration = []
if dateTime:
border_decoration.append(border_decorations[0])
if fileName:
border_decoration.append(border_decorations[1])
scaling = getOption('Scaling', defaultValue=0.9)
scaling = int(round(100.0 * scaling))
else:
file_name = ''
title = ''
paper_type = paper_types[0]
other_unit = paper_units[0]
other_size = ''
orientation = paper_orientations[0]
output_style = style_choices[0]
output_format = format_choices[0]
if self.haveTicks:
tick_location = tick_locations[0]
tick_placement = tick_placements
border_decoration = border_decorations
scaling = 90
if not self.haveTicks:
tick_location = None
tick_placement = None
self.file_name = file_name
self.title = title
self.paper_type = paper_type
self.other_unit = other_unit
self.other_size = other_size
self.orientation = orientation
self.output_style = output_style
self.output_format = output_format
self.tick_location = tick_location
self.tick_placement = tick_placement
self.border_decoration = border_decoration
self.scaling = scaling
def setOptionValues(self):
self.file_name = file_name = self.file_entry.get()
self.title = title = self.title_entry.get()
n = self.size_menu.getSelectedIndex()
self.paper_type = paper_type = paper_types[n]
if paper_type == Output.other_paper_type:
other_size = self.other_entry.get()
other_unit = self.other_unit_menu.getText()
else:
other_size = None
other_unit = None
self.other_size = other_size
self.other_unit = other_unit
self.paper_orientation = paper_orientation = self.orientation_menu.getText(
)
self.output_style = output_style = self.style_menu.getText()
self.output_format = output_format = self.format_menu.getText()
if self.haveTicks:
tick_location = self.tick_menu.getText()
tick_placement = self.tick_buttons.getSelected()
else:
tick_location = tick_placement = None
self.tick_location = tick_location
self.tick_placement = tick_placement
self.border_decoration = border_decoration = self.border_buttons.getSelected(
)
scaling = self.scaling_scale.get()
self.scaling = scaling = int(round(scaling))
setOption = self.setOption
if setOption:
setOption('FileName', value=file_name)
setOption('Title', value=title)
if paper_type == Output.other_paper_type:
setOption('OtherHeight', value=other_size[0])
setOption('OtherWidth', value=other_size[1])
setOption('OtherUnit', value=other_unit)
else:
paper_type = paper_type_inverse_dict[paper_type]
setOption('PaperSize', value=paper_type)
setOption('Orientation', value=paper_orientation)
in_color = (output_style == style_choices[0])
setOption('InColor', value=in_color)
output_format = format_options[format_choices.index(output_format)]
setOption('OutputFormat', value=output_format)
if self.haveTicks:
tick_outside = (tick_location == PrintTicks.Outside)
setOption('TickOutside', value=tick_outside)
tick_placement = getTickPlacement2(tick_placement)
setOption('TickPlacement', value=tick_placement)
dateTime = (border_decorations[0] in border_decoration)
fileName = (border_decorations[1] in border_decoration)
setOption('ShowsDateTime', value=dateTime)
setOption('ShowsFileName', value=fileName)
setOption('Scaling', value=0.01 * scaling)
def findFile(self):
if self.file_select_popup:
self.file_select_popup.open()
else:
file_types = [
FileType('All', ['*']),
FileType('PostScript', ['*.ps', '*.eps']),
FileType('PDF', ['*.pdf', '*.ai'])
]
self.file_select_popup = FileSelectPopup(self,
file_types=file_types)
file = self.file_select_popup.getFile()
if file:
self.file_entry.set(file)
def changedSize(self, entry):
if entry == Output.other_paper_type:
self.other_frame.grid(row=0, column=2, columnspan=2, sticky='w')
else:
self.other_frame.grid_forget()
def changedFormat(self, entry):
file_suffix = file_suffixes.get(entry)
if not file_suffix:
return
file_name = self.file_entry.get()
if not file_name:
return
for suffix in format_suffixes:
if file_name.endswith(suffix):
if suffix != file_suffix:
n = len(suffix)
file_name = file_name[:-n] + file_suffix
self.file_entry.set(file_name)
break
else:
file_name = file_name + file_suffix
self.file_entry.set(file_name)
# width and height are of plot, in pixels
def getOutputHandler(self, width, height, fonts=None):
if not fonts:
fonts = []
else:
fonts = list(fonts)
for n in range(len(fonts)):
if fonts[n] == 'Times':
fonts[n] = 'Times-Roman'
self.setOptionValues()
if not self.file_name:
showError('No file', 'No file specified', parent=self)
return None
if os.path.exists(self.file_name):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % self.file_name,
parent=self):
return None
if (self.paper_type == Output.other_paper_type):
paper_size = self.other_size + [self.other_unit]
else:
paper_size = paper_sizes[self.paper_type]
output_scaling = self.scaling / 100.0
font = 'Times-Roman'
border_text = {}
for decoration in self.border_decoration:
if (decoration == 'Time & date'):
location = 'se'
text = time.ctime(time.time())
elif (decoration == 'File name'):
location = 'sw'
text = self.file_name
else:
continue # should not be here
border_text[location] = (text, font, 12)
if (self.title):
location = 'n'
border_text[location] = (self.title, font, 18)
if font not in fonts:
fonts.append(font)
outputHandler = PrintHandler.getOutputHandler(
self.file_name,
width,
height,
output_scaling=output_scaling,
paper_size=paper_size,
paper_orientation=self.paper_orientation,
output_style=self.output_style,
output_format=self.output_format,
border_text=border_text,
fonts=fonts,
do_outline_box=self.doOutlineBox)
return outputHandler
def getAspectRatio(self):
self.setOptionValues()
if self.paper_type == Output.other_paper_type:
paper_size = self.other_size
else:
paper_size = paper_sizes[self.paper_type]
r = paper_size[1] / paper_size[0]
if self.paper_orientation == 'Landscape':
r = 1.0 / r
return r
