def __init__(self,
parent,
label='',
command=None,
open_button=None,
show_on_open=False):
import Tkinter
f = Tkinter.Frame(parent)
self.frame = f
from chimera.widgets import ModelOptionMenu
m = ModelOptionMenu(f,
labelpos='w',
label_text=label,
listFunc=volume_models,
command=command)
m.grid(row=0, column=0, sticky='w')
self.menu = m
if open_button:
if not type(open_button) is str:
open_button = 'Browse...'
bb = Tkinter.Button(f,
text=open_button,
command=self.open_volume_cb)
bb.grid(row=0, column=1, sticky='w')
self.show_on_open = show_on_open
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
self.clientArea.columnconfigure(0, weight=1)
row = 0
from chimera.widgets import ModelOptionMenu
self.surfList = ModelOptionMenu(
self.clientArea,
labelpos='w',
label_text="Save surface:",
filtFunc=lambda m: isinstance(m, MSMSModel))
self.surfList.grid(row=row, column=0)
row += 1
self.saveNormalsVar = Tkinter.IntVar(self.clientArea)
self.saveNormalsVar.set(True)
Tkinter.Checkbutton(self.clientArea,
text="Save normals",
variable=self.saveNormalsVar).grid(row=row)
row += 1
self.displayedOnlyVar = Tkinter.IntVar(self.clientArea)
self.displayedOnlyVar.set(True)
Tkinter.Checkbutton(self.clientArea,
text="Limit output to"
" displayed surface sections",
variable=self.displayedOnlyVar).grid(row=row)
row += 1
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight = 1)
from CGLtk import Hybrid
import Pmw, Tkinter
from chimera.widgets import MoleculeOptionMenu
self.molMenu = MoleculeOptionMenu(parent, labelpos="w",
label_text="Select PDB:")
self.molMenu.grid(row = 1, column = 0, sticky = 'w')
from chimera.widgets import MoleculeChainOptionMenu
self.chainMenu = MoleculeChainOptionMenu(parent, labelpos="w",
label_text="Select Chain:")
self.chainMenu.grid(row = 2, column = 0, sticky = 'w')
from chimera.widgets import ModelOptionMenu
self.modelMenu = ModelOptionMenu(parent, labelpos="w",
label_text="Select MRC:")
self.modelMenu.grid(row = 3, column = 0, sticky = 'w')
import Pmw
self.radius = Pmw.EntryField(parent, labelpos="w",
label_text="Radius:")
self.radius.grid(row = 4, column = 0, sticky = 'w')
self.resolution = Pmw.EntryField(parent, labelpos="w",
label_text="Resolution:")
self.resolution.grid(row = 5, column = 0, sticky = 'w')
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(self.clientArea,
labelpos='w', label_text="Save models:",
listbox_selectmode='extended',
selectioncommand=lambda: self.configure(
self.modelList.getvalue(), refreshList=False))
self.modelList.grid(row=row, column=0, sticky='nsew')
self.clientArea.rowconfigure(row, weight=1)
self.clientArea.columnconfigure(0, weight=1)
row += 1
from chimera import dialogs
self.labelMap = {
"individual":
"a single file [individual @MOLECULE sections]",
"combined":
"a single file [combined @MOLECULE section]",
"multiple":
"multiple files [appending model number]"
}
preferred = self.labelMap[self.prefs["multiSaveMol2"]]
self.multiSaveMenu = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save multiple models in",
initialitem=preferred, items=self.labelMap.values())
# not always shown; remember row number
self._msmRow = row
row += 1
self.saveRelativeVar = Tkinter.IntVar(self.clientArea)
self.saveRelativeVar.set(False)
self.relativeFrame = f = Tkinter.Frame(self.clientArea)
Tkinter.Checkbutton(f, variable=self.saveRelativeVar,
text="Save relative to model:").grid(row=0,
column=0, sticky='e')
self.relModelMenu = ModelOptionMenu(f)
self.relModelMenu.grid(row=0, column=1, sticky='w')
self.saveUntransformedVar = Tkinter.IntVar(parent)
self.saveUntransformedVar.set(True)
self.untransformedButton = Tkinter.Checkbutton(self.clientArea,
variable=self.saveUntransformedVar,
text="Use untransformed coordinates")
self._rfRow = row
row += 1
self.sybylHydNamesVar = Tkinter.IntVar(self.clientArea)
self.sybylHydNamesVar.set(
self.prefs["hydrogen naming"] == "sybyl")
Tkinter.Checkbutton(self.clientArea,
variable=self.sybylHydNamesVar,
text="Use Sybyl-style hydrogen naming (e.g. HE12"
" rather than 2HE1)").grid(row=row, column=0,
sticky="w")
row += 1
self.resNumsVar = Tkinter.IntVar(self.clientArea)
self.resNumsVar.set(self.prefs["residue numbers"])
Tkinter.Checkbutton(self.clientArea, variable=self.resNumsVar,
text="Include residue sequence numbers in substructure"
" names").grid(row=row, column=0, sticky='w')
row += 1
self.writeGaffVar = Tkinter.IntVar(self.clientArea)
self.resNumsVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.writeGaffVar,
text="Write Amber/GAFF atom types instead of Sybyl atom types"
).grid(row=row, column=0, sticky='w')
row += 1
self.rigidVar = Tkinter.IntVar(self.clientArea)
self.rigidVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.rigidVar,
text="Write current selection to @SETS section of file"
).grid(row=row, column=0, sticky="w")
row += 1
def fillInUI(self, parent):
self.requested_halt = False
self.xform_handler = None
self.last_relative_xform = None
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from VolumeViewer import Volume_Menu
ff = Tkinter.Frame(parent)
ff.grid(row=row, column=0, sticky='w')
row = row + 1
from chimera.widgets import ModelOptionMenu
om = ModelOptionMenu(ff,
labelpos='w',
label_text='Fit ',
listFunc=fit_object_models,
sortFunc=compare_fit_objects,
command=self.object_chosen_cb)
om.grid(row=0, column=0, sticky='w')
self.object_menu = om
fm = Volume_Menu(ff, ' in map ')
fm.frame.grid(row=0, column=1, sticky='w')
self.map_menu = fm
gf = Tkinter.Frame(parent)
gf.grid(row=row, column=0, sticky='w')
row += 1
cl = Tkinter.Label(gf, text='Correlation')
cl.grid(row=0, column=0, sticky='w')
cv = Tkinter.Label(gf,
width=6,
anchor='w',
relief=Tkinter.SUNKEN,
borderwidth=2)
cv.grid(row=0, column=1, padx=5, sticky='w')
self.corr_label = cv
al = Tkinter.Label(gf, text='Average map value')
al.grid(row=0, column=2, sticky='w')
av = Tkinter.Label(gf,
width=6,
anchor='w',
relief=Tkinter.SUNKEN,
borderwidth=2)
av.grid(row=0, column=3, padx=5, sticky='w')
self.ave_label = av
ub = Tkinter.Button(gf, text='Update', command=self.update_metric_cb)
ub.grid(row=0, column=4, sticky='w')
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
ru = Hybrid.Checkbutton(opf, 'Real-time correlation / average update',
False)
ru.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.realtime_update = ru.variable
ru.callback(self.realtime_cb)
sm = Hybrid.Checkbutton_Entries(
opf, False, 'Use map simulated from atoms, resolution ', (4, ''))
sm.frame.grid(row=orow, column=0, sticky='nw')
orow += 1
self.simulate_map, self.map_resolution = sm.variables
self.simulate_map.add_callback(self.simulate_map_cb)
sm.entries[0].bind('<KeyPress-Return>', self.simulate_resolution_cb)
dt = Hybrid.Checkbutton(
opf, 'Use only data above contour level from first map', True)
dt.button.grid(row=orow, column=0, sticky='w')
orow += 1
dt.button['state'] = 'disabled'
self.limit_data = dt
self.above_threshold = dt.variable
opt = Hybrid.Radiobutton_Row(opf, 'Optimize ',
('overlap', 'correlation'))
opt.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.optimize = opt.variable
self.opt_widget = opt
cam = Hybrid.Checkbutton(
opf, 'Correlation calculated about mean data value', False)
cam.button.grid(row=orow, column=0, sticky='w')
orow += 1
cam.button['state'] = 'disabled'
self.cam_widget = cam
self.corr_about_mean = cam.variable
al = Hybrid.Checkbutton_Row(opf, 'Allow ', ('rotation', 'shift'))
al.frame.grid(row=orow, column=0, sticky='w')
orow += 1
ar, ash = [c.variable for c in al.checkbuttons]
ar.set(True)
ash.set(True)
self.allow_rotation = ar
self.allow_shift = ash
mm = Hybrid.Checkbutton(opf, 'Move whole molecules', True)
mm.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.move_whole_molecules = mm.variable
self.mwm_button = mm.button
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=40, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
self.halt_button = self.buttonWidgets['Halt']
self.allow_halt(False)
self.update_gray_out()
self.activate_undo_redo()
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(self.clientArea,
labelpos='w', label_text="Save models:",
listbox_selectmode='extended',
selectioncommand=lambda: self.configure(
self.modelList.getvalue(), refreshList=False))
self.modelList.grid(row=row, column=0, sticky='nsew')
self.clientArea.rowconfigure(row, weight=1)
self.clientArea.columnconfigure(0, weight=1)
row += 1
import Tkinter, Pmw
self.dispOnlyVar = Tkinter.IntVar(parent)
self.dispOnlyVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.dispOnlyVar,
text="Save displayed atoms only").grid(row=row,
column=0, sticky='w')
row += 1
self.selOnlyVar = Tkinter.IntVar(parent)
self.selOnlyVar.set(False)
Tkinter.Checkbutton(self.clientArea, variable=self.selOnlyVar,
text="Save selected atoms only").grid(row=row,
column=0, sticky='w')
row += 1
self.saveRelativeVar = Tkinter.IntVar(parent)
self.saveRelativeVar.set(False)
self.relativeFrame = f = Tkinter.Frame(self.clientArea)
Tkinter.Checkbutton(f, variable=self.saveRelativeVar,
text="Save relative to model:"
).grid(row=0, column=0, sticky='e')
self.relModelMenu = ModelOptionMenu(f)
self.relModelMenu.grid(row=0, column=1, sticky='w')
self.saveUntransformedVar = Tkinter.IntVar(parent)
self.saveUntransformedVar.set(True)
self.untransformedButton = Tkinter.Checkbutton(self.clientArea,
variable=self.saveUntransformedVar,
text="Use untransformed coordinates")
self._rfRow = row
row += 1
self.frameSave = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save",
initialitem="current frame",
items=["current frame", "all frames"])
# not always shown; remember row number
self._fsRow = row
row += 1
from chimera import dialogs
self.labelMap = {
"single": "a single file",
"multiple":
"multiple files [appending model number]"
}
preferred = self.labelMap[self.prefs["multiSavePDB"]]
self.multiSaveMenu = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Save multiple models in",
initialitem=preferred, items=self.labelMap.values())
# not always shown; remember row number
self._msmRow = row
row += 1
def __init__(self, clipDialog, model):
from chimera.widgets import ModelOptionMenu
self.clipDialog = clipDialog
self.model = model
self.clipDependentWidgets = []
Tkinter.Frame.__init__(self, clipDialog.uiMaster())
interior = self # used to be a Pmw.Group instead of a Frame!
self.clipVar = Tkinter.IntVar(interior)
self.clipVar.set(self.model.useClipPlane)
Tkinter.Checkbutton(interior,
command=self._toggleClip,
text="Enable clipping",
variable=self.clipVar).grid(row=0, sticky='w')
slabFrame = Tkinter.Frame(interior)
slabFrame.grid(row=1, sticky='w')
self.slabVar = Tkinter.IntVar(interior)
self.slabVar.set(self.model.useClipThickness)
cbutton = Tkinter.Checkbutton(slabFrame,
command=self._changeSlab,
text="Use slab mode with thickness",
variable=self.slabVar)
cbutton.grid(row=0, column=0, sticky='w')
self.clipDependentWidgets.append(cbutton)
self.slabThicknessVar = Tkinter.DoubleVar(slabFrame)
self.slabThicknessVar.set(self.model.clipThickness)
entry = Tkinter.Entry(slabFrame,
width=4,
textvariable=self.slabThicknessVar)
entry.grid(row=0, column=1, sticky='w')
entry.bind('<KeyPress-Return>', self._changeSlab)
self.clipDependentWidgets.append(entry)
butFrame = Tkinter.Frame(interior)
butFrame.grid(row=2, sticky='w')
button = Tkinter.Button(
butFrame,
pady=0,
command=lambda: chimera.tkgui.normalizeClipFacing(self.model),
text="Orient plane")
button.grid(row=0, column=0, sticky='e')
self.clipDependentWidgets.append(button)
label = Tkinter.Label(butFrame, text="perpendicular to line of sight")
label.grid(row=0, column=1, sticky='w')
self.clipDependentWidgets.append(label)
label = Tkinter.Label(butFrame,
text="with center of rotation at center of view")
label.grid(row=1, column=0, columnspan=2)
self.clipDependentWidgets.append(label)
butFrame = Tkinter.Frame(interior)
butFrame.grid(row=3, sticky='w')
button = Tkinter.Button(butFrame,
pady=0,
command=clipDialog._flipPlane,
text="Flip plane")
button.grid(row=0, column=0, sticky='e')
self.clipDependentWidgets.append(button)
label = Tkinter.Label(butFrame, text="180 degrees")
label.grid(row=0, column=1, sticky='w')
self.clipDependentWidgets.append(label)
butFrame = Tkinter.Frame(interior)
butFrame.grid(row=4, sticky='w')
button = Tkinter.Button(
butFrame,
pady=0,
command=lambda: self.clipDialog._align(self.menu.getvalue()),
text="Align plane")
button.grid(row=0, column=0, sticky='e')
self.clipDependentWidgets.append(button)
self.menu = ModelOptionMenu(butFrame, labelpos='w', label_text="with")
def kludge(self=self.menu, **kw):
newKw = {}
for k, v in kw.items():
newKw["menubutton_" + k] = v
newKw["label_" + k] = v
self.configure(**newKw)
self.menu.config = kludge
self.menu.grid(row=0, column=1, sticky='w')
self.clipDependentWidgets.append(self.menu)
label = Tkinter.Label(butFrame, text="clip plane")
label.grid(row=0, column=2, sticky='w')
self.clipDependentWidgets.append(label)
self.mouseVar = Tkinter.IntVar(interior)
self.mouseVar.set(getClipModel() == model)
self.mouseActiveButton = Tkinter.Checkbutton(
interior,
command=self._toggleMouse,
variable=self.mouseVar,
text="Adjust clipping with mouse as below")
self.mouseActiveButton.grid(row=5, sticky='w')
self.clipDependentWidgets.append(self.mouseActiveButton)
if not self.clipVar.get():
for w in self.clipDependentWidgets:
w.config(state='disabled')
def fillInUI(self, parent):
import Pmw
from chimera.widgets import ModelOptionMenu
self.menu = ModelOptionMenu(parent,
command=self._menuCB,
labelpos='w',
label_text="Model:")
self.menu.grid(row=0, sticky='w')
self.infoArea = None
self.normMouse = None
self.clipMouse = [None, None]
if self.menu.getvalue() is not None:
self.menu.invoke() # cause callback
group = Pmw.Group(parent, tag_text="Clip Motion Assignments")
group.grid(row=2, sticky="nsew")
self.buttonLabels = []
self.labelValues = {}
for mod in ("", ) + mousemodes.usedMods:
for but in mousemodes.usedButtons:
if mod:
self.buttonLabels.append(mod.lower() + " button " + but)
self.labelValues[self.buttonLabels[-1]]\
= (but, (mod,))
else:
self.buttonLabels.append("button " + but)
self.labelValues[self.buttonLabels[-1]]\
= (but, ())
self.transMenu = Pmw.OptionMenu(
group.interior(),
command=lambda bname: self._assignmentChange(0, bname),
initialitem="button 2",
items=self.buttonLabels,
labelpos='n',
label_text="Translation")
self.transMenu.grid(row=0, column=0)
self.pivotMenu = Pmw.OptionMenu(
group.interior(),
command=lambda bname: self._assignmentChange(1, bname),
initialitem="button 3",
items=self.buttonLabels,
labelpos='n',
label_text="Rotation")
self.pivotMenu.grid(row=0, column=1)
mousemodes.addFunction("plane rotate",
(lambda v, e: self._planeStart(v, e, "rotate"),
self._planeRot, self._planeStop))
mousemodes.addFunction(
"plane translate",
(lambda v, e: self._planeStart(v, e, "translate z"),
self._planeTrans, self._planeStop))
def showCapDialog():
from SurfaceCap.gui import Capper_Dialog
from chimera import dialogs
d = dialogs.display(Capper_Dialog.name)
d.show_caps.set(True)
Tkinter.Button(parent,
text="Cap clipped surfaces...",
pady=0,
command=showCapDialog).grid(row=3)
