def __init__(self, box_changed_cb):
self.box_model = Box_Model()
self.box_changed_cb = box_changed_cb
self.ijk_in = None # Box coordinates
self.ijk_out = None
self.mode_name = 'volume subregion' # For mouse modes panel
self.bound_button = None
self.drag_mode = None
self.rotation_handler = None
callbacks = (self.mouse_down_cb, self.mouse_drag_cb, self.mouse_up_cb)
icon_file = 'selectregion.gif'
if icon_file:
import os.path
icon_path = os.path.join(os.path.dirname(__file__), icon_file)
from PIL import Image
image = Image.open(icon_path)
from chimera import chimage
from chimera import tkgui
icon = chimage.get(image, tkgui.app)
else:
icon = None
from chimera import mousemodes
mousemodes.addFunction(self.mode_name, callbacks, icon)
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)
def fillInUI(self, parent):
self.default_color = (0, 0, 0.8, 1)
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
mmf = Tkinter.Frame(parent)
mmf.grid(row=row, column=0, sticky='w')
row = row + 1
mb = Hybrid.Option_Menu(mmf, 'Use mouse ', 'button 1', 'button 2',
'button 3', 'ctrl button 1', 'ctrl button 2',
'ctrl button 3')
mb.variable.set('ctrl button 3')
mb.frame.grid(row=0, column=0, sticky='w')
mb.add_callback(self.bind_mouse_button_cb)
self.mouse_button = mb
mbl = Tkinter.Label(mmf, text=' to choose blobs')
mbl.grid(row=0, column=1, sticky='w')
crf = Tkinter.Frame(parent)
crf.grid(row=row, column=0, sticky='ew')
crf.columnconfigure(1, weight=1)
row = row + 1
cl = Tkinter.Label(crf, text='Color blob ')
cl.grid(row=0, column=0, sticky='w')
from CGLtk.color import ColorWell
sc = ColorWell.ColorWell(crf, color=self.default_color)
sc.grid(row=0, column=1, sticky='w')
self.blob_color = sc
msg = Tkinter.Label(parent, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
callbacks = (self.mouse_down_cb, self.mouse_drag_cb, self.mouse_up_cb)
icon = self.mouse_mode_icon('pickblob.gif')
from chimera import mousemodes
mousemodes.addFunction('pick blobs', callbacks, icon)
self.bind_mouse_button_cb()
def wrap_mouse_modes(self):
from chimera.mousemodes import addFunction, functionCallables
mt = {}
for mode in ('rotate', 'translate x,y', 'translate z'):
down_cb, drag_cb, up_cb = functionCallables(mode)
mt[mode] = {'down': down_cb, 'drag': drag_cb, 'up': up_cb}
m = self.mouse_cb
for mode in ('rotate', 'translate x,y', 'translate z'):
callbacks = (lambda v, e, mode=mode: m(v, e, mode, 'down'),
lambda v, e, mode=mode: m(v, e, mode, 'drag'),
lambda v, e, mode=mode: m(v, e, mode, 'up'))
addFunction(mode, callbacks)
return mt
def __init__(self):
self.bound_button = None
self.mode_name = 'group connected'
self.region = None
self.level = None
self.last_level = None # Last used grouping level.
self.last_y = 0
self.dragging = False
self.connected = set()
self.ungrouped_color = (0.8, 0.8, 0.8, 1.0)
self.background_show_all = True
from chimera import mousemodes
callbacks = (self.mouse_down_cb, self.mouse_drag_cb, self.mouse_up_cb)
icon = None
mousemodes.addFunction(self.mode_name, callbacks, icon)
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel,
None), icon=chimage.get(Image.open(os.path.join(myDir,
'ilabel.png')), tkgui.app))
addFunction('place key', (self._startOrGrabKey,
self._sizeOrMoveKey, None), icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
def register_mouse_modes(self):
# mode: (press, motion, release [, double press, double release])
rotate_funcs = (
self.start_rotation_cb,
self.rotation_cb,
self.stop_rotation_cb
)
rotate_icon = mouse_mode_icon('roticon.png')
from chimera import mousemodes
mousemodes.addFunction('constrained rotation', rotate_funcs,
rotate_icon)
translate_funcs = (
self.start_translation_cb,
self.translation_cb,
self.stop_translation_cb
)
translate_icon = mouse_mode_icon('transicon.png')
mousemodes.addFunction('constrained translation', translate_funcs,
translate_icon)
def __init__(self, seg_dialog):
"""__init__(seg_dialog) - initialize and add mouse callbacks.
Creates a box region selector for use in simple segmentation.
"""
self.box_model = Box_Model()
self.seg_dialog = seg_dialog
self.xyz_in = None
self.xyz_out = None
self.mode_name = 'seg box region'
self.bound_button = None
self.drag_button = None
callbacks = (self.mouse_down_cb, self.mouse_drag_cb,
self.mouse_up_cb)
icon_file = None
from chimera import mousemodes
mousemodes.addFunction(self.mode_name, callbacks, icon_file)
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel, None),
icon=chimage.get(
Image.open(os.path.join(myDir, 'ilabel.png')),
tkgui.app))
addFunction('place key',
(self._startOrGrabKey, self._sizeOrMoveKey, None),
icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
def fillInUI(self, parent):
self.distances = []
self.angleInfo = []
self.numMolecules = len(chimera.openModels.list(
modelTypes=[chimera.Molecule]))
chimera.triggers.addHandler('Molecule', self._molChange, None)
chimera.triggers.addHandler('PseudoBond', self._psbChange, None)
chimera.triggers.addHandler('Atom', self._atomChange, None)
chimera.triggers.addHandler('Model', self._modelChange, None)
distanceMonitor.updateCallbacks.append(self._distUpdateCB)
self.notebook = Pmw.NoteBook(parent,
raisecommand=self._nbRaiseCB,
lowercommand=self._nbLowerCB)
self.notebook.pack(fill='both', expand=1)
self.interfaces = {}
for pn in pageNames:
pageID = pn
## when more tabs shown, maybe do this...
#if '/' in pn:
# parts = pn.split('/')
# pn = "/ ".join(parts)
#if ' ' in pn:
# parts = pn.split(' ')
# pn = '\n'.join(parts)
self.notebook.add(pageID, tab_text=pn)
dp = self.notebook.page(DISTANCES)
from CGLtk.Table import SortableTable
self.distTable = SortableTable(dp)
self.distTable.grid(row=0, column=0, sticky='nsew', rowspan=7)
dp.columnconfigure(0, weight=1)
dp.rowconfigure(4, weight=1)
dp.rowconfigure(5, weight=1)
self.distTable.addColumn("ID", "id", format="%d")
self.distTable.addColumn("Atom 1",
lambda d, s=self: s.atomLabel(d.atoms[0]))
self.distTable.addColumn("Atom 2",
lambda d, s=self: s.atomLabel(d.atoms[1]))
self.distTable.addColumn("Distance", "distance", font="TkFixedFont")
self.distTable.setData(self.distances)
self.distTable.launch(browseCmd=self._distTableSelCB)
self.distButtons = Pmw.ButtonBox(dp, padx=0)
self.distButtons.add("Create", command=self._createDistance)
self.distButtons.add("Remove", command=self._removeDistance)
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.distButtons.numbuttons()):
self.distButtons.button(but).config(default='disabled')
self.distButtons.alignbuttons()
self.distButtons.grid(row=1, column=1)
self.distLabelChoice = Pmw.RadioSelect(dp, pady=0,
buttontype='radiobutton',
command=self._distLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.distLabelChoice.grid(row=2, column=1)
self.distLabelChoice.add("None", highlightthickness=0)
self.distLabelChoice.add("ID", highlightthickness=0)
self.distLabelChoice.add("Distance", highlightthickness=0)
self.distLabelChoice.invoke("Distance")
self.distPrecisionChoice = Pmw.Counter(dp, datatype={
'counter': self._distPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(precision()))
self.distPrecisionChoice.grid(row=3, column=1)
self.showUnitsVar = Tkinter.IntVar(dp)
self.showUnitsVar.set(showUnits())
Tkinter.Checkbutton(dp, text="Show Angstrom symbol",
variable=self.showUnitsVar,
command=self._showUnitsChangeCB).grid(row=4, column=1)
self.distSelectsAtomsVar = Tkinter.IntVar(dp)
self.distSelectsAtomsVar.set(False)
Tkinter.Checkbutton(dp, variable=self.distSelectsAtomsVar,
text="Choosing in table\nselects atoms\n(and pseudobond)"
).grid(row=5, column=1)
from chimera.pbgPanel import attributesCmd
Tkinter.Button(dp, text="Display options...", command=
lambda dm=distanceMonitor: attributesCmd([dm])
).grid(row=6, column=1)
for d in distanceMonitor.pseudoBonds:
self.newDistance(d)
atp = self.notebook.page(ANGLES)
from CGLtk.Table import SortableTable
self.angleTable = SortableTable(atp)
self.angleTable.grid(row=0, column=0, sticky='nsew', rowspan=4)
atp.columnconfigure(0, weight=1)
atp.rowconfigure(2, weight=1)
for i in range(4):
self.angleTable.addColumn("Atom %d" % (i+1), lambda atoms, s=self,
i=i: i >= len(atoms) and "N/A" or s.atomLabel(atoms[i]))
self.angleTable.addColumn("Angle/Torsion",
lambda atoms, s=self: s._angleLabel(atoms), font="TkFixedFont")
self.angleTable.setData(self.angleInfo)
self.angleTable.launch(browseCmd=self._angleTableSelCB)
self._osHandler = None
self.angleButtons = Pmw.ButtonBox(atp, padx=0)
self.angleButtons.add("Create", command=self._createAngle)
self.angleButtons.add("Remove", command=self._removeAngle,
state='disabled')
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.angleButtons.numbuttons()):
self.angleButtons.button(but).config(default='disabled')
self.angleButtons.alignbuttons()
self.angleButtons.grid(row=0, column=1)
self.anglePrecisionChoice = Pmw.Counter(atp, datatype={
'counter': self._anglePrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[ANGLE_PRECISION]))
self.anglePrecisionChoice.grid(row=1, column=1)
self.angleSelectsComponentsVar = Tkinter.IntVar(atp)
self.angleSelectsComponentsVar.set(True)
Tkinter.Checkbutton(atp, variable=self.angleSelectsComponentsVar,
text="Choosing in table selects\ncomponent atoms/bonds"
).grid(row=3, column=1)
brp = self.notebook.page(BONDROTS)
self.rotations = []
self.rotInfo = {}
labeledButton = Pmw.LabeledWidget(brp, labelpos="e",
label_text="selected bond as torsion")
labeledButton.grid(row=0, column=0, columnspan=2)
self.createRotButton = Tkinter.Button(labeledButton.interior(),
text="Activate", command=self._createRotation, pady=0)
self.createRotButton.grid()
tableFrame = Tkinter.Frame(brp, pady="0.1i")
tableFrame.grid(row=1, column=0, columnspan=2, sticky='ns')
from CGLtk.Table import ScrolledTable
self.rotTable = ScrolledTable(tableFrame, hscrollmode='none')
self.rotTable.setColumnTitle(0, "ID")
self.rotTable.setColumnTitle(1, "Near")
self.rotTable.setColumnTitle(2, "Bond")
self.rotTable.setColumnTitle(3, "Far")
self.angleTitle = Tkinter.StringVar(parent)
self.angleTitle.set("Torsion")
self.rotTable.setColumnTitle(4, self.angleTitle,
pyclass=Tkinter.Button, pady=0,
command=self._toggleAngleType)
brp.rowconfigure(1, weight=1)
brp.columnconfigure(0, weight=1)
brp.columnconfigure(1, weight=1)
tableFrame.rowconfigure(0, weight=1)
tableFrame.columnconfigure(0, weight=1)
self.rotTable.columnconfigure(4, weight=1)
self.rotTable.grid(row=0, column=0, sticky='news')
self.dialSizeLabels = ["small", "medium", "large"]
Pmw.OptionMenu(tableFrame,
items=self.dialSizeLabels, labelpos='w',
initialitem=self.dialSizeLabels[prefs[ROT_DIAL_SIZE]],
label_text="Dial size:", command=self._dialSizeChangeCB,
).grid(row=1, column=0, sticky='e')
f = Tkinter.Frame(brp)
f.grid(row=2, column=0, columnspan=2)
self.mouseModeVar = Tkinter.IntVar(f)
self.mouseModeVar.set(False)
self.needTorWidgets = []
self.needTorWidgets.append(Tkinter.Checkbutton(f, text="Rotate",
variable=self.mouseModeVar, command=self._mouseModeCB))
self.needTorWidgets[-1].grid(row=0, column=0)
self.rotModeTorsMenu = Pmw.OptionMenu(f)
self.rotModeTorsMenu.grid(row=0, column=1)
self.needTorWidgets.append(self.rotModeTorsMenu)
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._modeButton = self.buttonLabels[0]
self.rotModeButMenu = Pmw.OptionMenu(f, labelpos='w',
command=self._modeButtonCB,
label_text="using", items=self.buttonLabels)
self.rotModeButMenu.grid(row=0, column=2)
self.needTorWidgets.append(self.rotModeButMenu)
self.rotLabelChoice = Pmw.RadioSelect(brp, pady=0,
buttontype='radiobutton', hull_pady=".1i",
command=self._rotLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.rotLabelChoice.grid(row=3, rowspan=2, column=0)
self.rotLabelChoice.add("None", highlightthickness=0)
self.rotLabelChoice.add("ID", highlightthickness=0)
self.rotLabelChoice.add("Name", highlightthickness=0)
self.rotLabelChoice.add("Angle", highlightthickness=0)
self.rotLabelChoice.invoke(prefs[ROT_LABEL])
self.torsionPrecisionChoice = Pmw.Counter(brp, datatype={
'counter': self._torsionPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[TORSION_PRECISION]))
self.torsionPrecisionChoice.grid(row=3, column=1)
self.showDegreeSymbolVar = Tkinter.IntVar(brp)
self.showDegreeSymbolVar.set(prefs[SHOW_DEGREE_SYMBOL])
Tkinter.Checkbutton(brp, text="Show degree symbol",
variable=self.showDegreeSymbolVar,
command=self._showDegreeSymbolChangeCB).grid(
row=4, column=1)
self.setTorWidgetsState("disabled")
mousemodes.addFunction("rotate bond", (lambda v, e:
v.recordPosition(e.time, e.x, e.y, "rotate"),
self._mouseSphere,
lambda v, e: v.setCursor(None)))
if GEOMETRIES in pageNames:
gp = self.notebook.page(GEOMETRIES)
from Geometry import GeometryInterface
self.interfaces[GEOMETRIES] = GeometryInterface(gp, self.status)
if METALS in pageNames:
mp = self.notebook.page(METALS)
from Metals import MetalsInterface
self.interfaces[METALS] = MetalsInterface(mp,
self.status)
self.notebook.setnaturalsize()
def register_resize_mouse_mode(self):
from chimera.mousemodes import addFunction
callbacks = (self.mouse_down_cb, self.mouse_drag_cb, self.mouse_up_cb)
addFunction('resize surfaces', callbacks)
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)
