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
class WriteDmsDialog(SaveModeless):
help = "UsersGuide/dms.html#writedms"
oneshot = True
def __init__(self):
SaveModeless.__init__(self,
clientPos='s',
clientSticky='ewns',
filters=[("DMS", "*.dms", ".dms")])
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 Apply(self):
path = self.getPaths()[0]
surf = self.surfList.getvalue()
if not surf:
replyobj.error("No surface chosen to save.\n")
return
from WriteDMS import writeDMS
replyobj.status("Writing DMS surface to %s\n" % path)
writeDMS(surf,
path,
writeNormals=self.saveNormalsVar.get(),
displayedOnly=self.displayedOnlyVar.get())
replyobj.status("Wrote DMS surface to %s\n" % path)
class WriteDmsDialog(SaveModeless):
help = "UsersGuide/dms.html#writedms"
oneshot = True
def __init__(self):
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("DMS", "*.dms", ".dms")])
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 Apply(self):
path = self.getPaths()[0]
surf = self.surfList.getvalue()
if not surf:
replyobj.error("No surface chosen to save.\n")
return
from WriteDMS import writeDMS
replyobj.status("Writing DMS surface to %s\n" % path)
writeDMS(surf, path, writeNormals=self.saveNormalsVar.get(),
displayedOnly=self.displayedOnlyVar.get())
replyobj.status("Wrote DMS surface to %s\n" % path)
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
class WriteMol2Dialog(SaveModeless):
keepShown = SaveModeless.default
name = "write Mol2"
help = "UsersGuide/savemodel.html#mol2"
def __init__(self):
self.prefs = preferences.addCategory("write Mol2 dialog",
preferences.HiddenCategory,
optDict={"multiSaveMol2": "multiple",
"hydrogen naming": "sybyl",
"residue numbers": True})
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Mol2", "*.mol2", ".mol2")])
openModels.addAddHandler(self._modelsChange, None)
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def configure(self, models=None, refreshList=True, selOnly=None):
if models is not None:
if len(models) > 1:
name = "Multiple Models "
elif models:
name = models[0].name + " "
else:
name = ""
self._toplevel.title("Save %sas Mol2 File" % name)
if refreshList:
self.modelList.setvalue(models)
if len(models) > 1:
self.multiSaveMenu.grid(row=self._msmRow,
column=0, sticky='w')
else:
self.multiSaveMenu.grid_forget()
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 Apply(self):
from chimera import dialogs
kw = {'status': replyobj.status}
paths = self.getPaths()
if not paths:
replyobj.error('No save location chosen.\n')
return
path = paths[0]
models = self.modelList.getvalue()
if not models:
replyobj.error("No models chosen to save.\n")
return
if float(self.modelList.size()) > 1.5:
if self.saveRelativeVar.get():
kw['relModel'] = self.relModelMenu.getvalue()
else:
if self.saveUntransformedVar.get():
kw['relModel'] = models[0]
if self.writeGaffVar.get():
kw['gaffType'] = True
from chimera import UserError
kw['gaffFailError'] = UserError
if self.rigidVar.get():
sel = selection.copyCurrent()
sel.addImplied()
selAtoms = sel.atoms()
selBonds = sel.bonds()
if selAtoms and selBonds:
kw['anchor'] = sel
sybylHydNaming = self.sybylHydNamesVar.get()
if sybylHydNaming:
self.prefs["hydrogen naming"] = "sybyl"
else:
self.prefs["hydrogen naming"] = "pdb"
kw['hydNamingStyle'] = self.prefs["hydrogen naming"]
kw['resNum'] = self.resNumsVar.get()
from WriteMol2 import writeMol2
if len(models) < 2:
replyobj.status("Writing %s to %s\n" %
(models[0].name, path))
writeMol2(models, path, **kw)
replyobj.status("Wrote %s to %s\n" %
(models[0].name, path))
return
saveOpt = self.multiSaveMenu.getvalue()
for key, value in self.labelMap.items():
if saveOpt == value:
break
self.prefs["multiSaveMol2"] = key
# write multiple models to multiple files
if key == "multiple":
if path.endswith(".mol2"):
start, end = path[:-4], ".mol2"
else:
start, end = path, ""
for m in models:
modelPath = start + m.oslIdent()[1:] + end
replyobj.status("Writing %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
writeMol2(m, modelPath, **kw)
replyobj.status("Wrote %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
return
kw["multimodelHandling"] = key
# write multiple models to single file
replyobj.status("Writing multiple models to %s\n" % path)
writeMol2(models, path, **kw)
replyobj.status("Wrote multiple models to %s\n" % path)
def _modelsChange(self, *args):
if len(openModels.listIds()) > 1:
self.untransformedButton.grid_forget()
self.relativeFrame.grid(row=self._rfRow,
column=0, sticky='w')
else:
self.relativeFrame.grid_forget()
self.untransformedButton.grid(row=self._rfRow,
column=0, sticky='w')
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()
class TrackXformDialog(ModelessDialog):
"""Class TrackXformDialog()
Dialog for tracking transforms in Chimera's camera coordinates.
"""
title= 'Track Model Transfom'
name = 'track model transformation'
buttons = ('Close',)
# @ help = 'ContributedSoftware/SegmentTrack/trackxform.html'
dir_pkg = os.path.dirname(__file__)
help_path = os.path.join(dir_pkg, 'trackxform.html')
help_url = 'file://' + help_path
help = help_url
provideStatus = True
statusPosition = 'above'
statusResizing = False
statusWidth = 40
# ---------------------------------------------------------------------
# Fill in UI
# ---------------------------------------------------------------------
def fillInUI(self, parent):
"""fillInUI(parent)
"""
self.status('')
self.track_xform = None
# menu frame
row = 0
from chimera.widgets import ModelOptionMenu
self.menu = ModelOptionMenu(parent, command=self.menu_cb,
labelpos='w', label_text='Model:')
self.menu.grid(row=row, sticky='w', padx=8, pady=8)
# initial transform frame (itf)
row = row + 1
itf = Tkinter.Frame(parent,padx=8,pady=8)
itf.grid(row=row, column=0, sticky='nw')
# record initial
itfg = Hybrid.Button_Row(itf, 'Record transform ',
(('Record',self.record_initial_cb),))
itfg.frame.grid(row=0, column=0, columnspan=3, sticky='w')
# parameters
itfp = Tkinter.Frame(itf, padx=16)
itfp.grid(row=1, column=0, sticky='w')
self.init_trans, self.init_rot, self.init_ang = \
self._make_param_panel(itfp)
# current transform frame (ctf)
row = row + 1
ctf = Tkinter.Frame(parent, padx=8, pady=8)
ctf.grid(row=row, column=0, sticky='nw')
# get current
ctfg = Hybrid.Button_Row(ctf, 'Current transform ',
(('Get',self.record_current_cb),))
ctfg.frame.grid(row=0, column=0, sticky='w')
# parameters
ctfp = Tkinter.Frame(ctf, padx=16)
ctfp.grid(row=1, column=0, sticky='w')
self.curr_trans, self.curr_rot, self.curr_ang = \
self._make_param_panel(ctfp)
# listbox frame
row = row+1
from chimera.widgets import ModelScrolledListBox
self.listbox = ModelScrolledListBox(parent,
labelpos='w',
label_text='Model List:')
self.listbox.component('listbox')['selectmode'] = 'extended'
self.listbox.grid(row=row, sticky='w', padx=8, pady=8)
# apply frame (af)
row = row + 1
af = Tkinter.Frame(parent, padx=8, pady=8)
af.grid(row=row, column=0, sticky='nw')
# apply
afg = Hybrid.Button_Row(af, '',
(('Apply',self.apply_initial_cb),))
afg.frame.grid(row=0, column=0, sticky='w')
text = ' recorded transform to models\n'
text = text + ' selected in above model list '
afgL = Tkinter.Label(af, text = text)
afgL.grid(row=0, column=1, sticky='w')
# reset
afr = Hybrid.Button_Row(af, '',
(('Reset',self.reset_initial_cb),))
afr.frame.grid(row=1, column=0, sticky='w')
text = ' initial transform'
afrL = Tkinter.Label(af, text = text)
afrL.grid(row=1, column=1, sticky='w')
def Close(self):
"""Close() - close dialog.
"""
ModelessDialog.Close(self)
def menu_cb(self, val):
return
# ---------------------------------------------------------------------
# Paramaters panel
# ---------------------------------------------------------------------
def _make_param_panel(self, frame):
"""_make_param_panel(frame)
Input:
frame
Output:
translation translation text entry
rotation rotation text entry
angle angle text entry
Makes the parameters panel.
"""
row = 0
# translation
transL = Tkinter.Label(frame, text='Translation: ')
transL.grid(row=row, column=0, sticky='w')
trans = Tkinter.Label(frame, text='')
trans.grid(row=row, column=1, sticky='w')
# rotation axis
row = row + 1
rotL = Tkinter.Label(frame, text='Rotation Axes: ')
rotL.grid(row=row, column=0, sticky='w')
rot = Tkinter.Label(frame, text='')
rot.grid(row=row, column=1, sticky='w')
# rotation angle
row = row + 1
angL = Tkinter.Label(frame, text='Rotation Angle: ')
angL.grid(row=row, column=0, sticky='w')
ang = Tkinter.Label(frame, text='')
ang.grid(row=row, column=1, sticky='w')
return trans, rot, ang
# ---------------------------------------------------------------------
# Call back functions
# ---------------------------------------------------------------------
def record_initial_cb(self):
"""record_initial_cb() - callback func for record transform.
"""
model = self.menu.getvalue()
self.record_initial(model)
def record_current_cb(self):
"""record_current_cb() - callback func for current transform.
"""
model = self.menu.getvalue()
self.record_current(model)
def apply_initial_cb(self):
"""apply_initial_cb() - callback function for apply button.
"""
models = self.listbox.getvalue()
for model in models:
self.update_current(model)
model = self.menu.getvalue()
self.record_current(model)
def reset_initial_cb(self):
"""reset_initial_cb() - callback function for reset button.
"""
self.reset_initial()
# ---------------------------------------------------------------------
# Command line (for GUI) functions
# ---------------------------------------------------------------------
def set_model(self, model):
"""set_model(model) - set menu to model.
"""
self.menu.setvalue(model)
def record_initial(self, model):
"""record_initial(model) - record and display model transform.
"""
if not model:
msg = 'No initial model'
self.status(msg, color='blue', blankAfter=5)
self.track_xform = get_xform(model)
self._display_param_initial(self.track_xform)
def record_current(self, model):
"""record_current(model) - display current model transform.
"""
if not model:
msg = 'No current model'
self.status(msg, color='blue', blankAfter=5)
self._display_param_current(model)
def update_current(self, model):
"""update_current(model) - apply recorded transform to model.
"""
if not model:
msg = 'No current model'
self.status(msg, color='blue', blankAfter=5)
if not self.track_xform:
msg = 'No starting transform'
self.status(msg, color='blue', blankAfter=5)
update_xform(model, self.track_xform)
def reset_initial(self):
"""reset_initial() - reset all parameters
"""
self.track_xform = None
self._display_param_initial(None)
self._display_param_current(None)
# ---------------------------------------------------------------------
# GUI functions for parameters
# ---------------------------------------------------------------------
def _display_param_initial(self, xform):
"""_display_param_initial(xform) - display initial transform.
"""
vx, ax, an = self.get_param(xform=xform)
self.init_trans['text'] = vx
self.init_rot['text'] = ax
self.init_ang['text'] = an
def _display_param_current(self, model):
"""_display_param_current(model) - display current transform.
"""
vx, ax, an = self.get_param(model=model)
self.curr_trans['text'] = vx
self.curr_rot['text'] = ax
self.curr_ang['text'] = an
def get_param(self, xform=None, model=None):
"""get_param(xform=None, model=None) - transform parameters.
Input:
xform=None
model=None
Output:
translation
rotation vector
rotation angle
Get transform parameters as text strings, one each for
translation vector, rotation vector, and rotation angle.
Return empty text strings for no model and no xform.
"""
if not xform:
if model:
xform = model.openState.xform
else:
return '','',''
vx = xform.getTranslation()
ax, an = xform.getRotation()
vx_text = '(%7.3f, %7.3f, %7.3f)' % (vx.x, vx.y, vx.z)
ax_text = '(%8.4f, %8.4f, %8.4f)' % (ax.x, ax.y, ax.z)
an_text = '%7.3f' % (an)
return vx_text, ax_text, an_text
class Measure_Stick(ModelessDialog):
"""Class: Measure_Stick()
The main GUI dialog for measuring stick.
"""
title= 'Measure Stick'
name = 'measure stick'
buttons = ('Compute...','Close')
help = ''
# @ help = 'ContributedSoftware/MeasureStick/init.html'
dir_pkg = os.path.dirname(__file__)
help_path = os.path.join(dir_pkg, 'init.html')
help_url = 'file://' + help_path
help = help_url
provideStatus = True
statusPosition = 'above'
statusResizing = False
statusWidth = 40
# ---------------------------------------------------------------------
# Fill in UI
# ---------------------------------------------------------------------
def fillInUI(self, parent):
"""fillInUI(parent)
"""
self.status('')
self.volume_path_dialog = None
parent.columnconfigure(0, weight=1)
self.toplevel_widget = parent.winfo_toplevel() # @ whatisthis
# parameters frame (pf)
row = 0
pf = Tkinter.Frame(parent)
pf.grid(row = row, column = 0, sticky = 'w',padx=8,pady=8)
self._make_parameters_panel(pf)
# checkbox to show relative coord
row = row + 1
relative_text = ' Show coord relative to open model '
rm = Hybrid.Checkbutton(parent, relative_text, 0)
rm.button.grid(row=row, column=0, sticky='w',padx=8)
self.relative_xyz = rm.variable
# menu frame
row = row + 1
from chimera.widgets import ModelOptionMenu
self.menu = ModelOptionMenu(parent, command=self.menu_cb,
labelpos='w', label_text='Model:')
self.menu.grid(row=row, sticky='w', padx=8, pady=2)
# ---------------------------------------------------------------------
# Panels
# ---------------------------------------------------------------------
def _make_parameters_panel(self, frame):
"""_make_parameters_panel(frame)
Make a panel in the GUI for parmeters
(distance and atom location).
"""
row = 0
# distance
dfL = Tkinter.Label(frame, text=' Distance ')
dfL.grid(row=row, column=0, sticky='w')
dfE = Hybrid.Entry(frame, ' ', 7, '0.0')
dfE.frame.grid(row=row, column=1, columnspan=3, sticky='w')
dfE.entry['state'] = 'readonly'
self.distance_value = dfE.variable
# atom 1 location
row = row + 1
self.marker1_xyz = []
a1L = Tkinter.Label(frame, text=' XYZ 1 ')
a1L.grid(row=row, column=0, sticky='w',pady=2)
for a in range(3):
a1E = Hybrid.Entry(frame, ' ', 7, '0.0')
a1E.frame.grid(row=row, column=a+1, sticky='w')
a1E.entry['state'] = 'readonly'
self.marker1_xyz.append(a1E.variable)
# atom 2 location
row = row + 1
self.marker2_xyz = []
a2L = Tkinter.Label(frame, text=' XYZ 2 ')
a2L.grid(row=row, column=0, sticky='w',pady=2)
for a in range(3):
a2E = Hybrid.Entry(frame, ' ', 7, '0.0')
a2E.frame.grid(row=row, column=a+1, sticky='w')
a2E.entry['state'] = 'readonly'
self.marker2_xyz.append(a2E.variable)
return
def menu_cb(self, val):
return
# ---------------------------------------------------------------------
# Distance and Location functions
# ---------------------------------------------------------------------
def get_parameters_value(self):
"""get_parameters_value():
Output:
dist distance
marker1d marker 1 location
marker2d marker 2 location
Get parameters - distance and location of markers.
"""
if self.volume_path_dialog == None:
msg = 'No marker set present!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
return None,None,None
linked_list = self.volume_path_dialog.selected_links()
if len(linked_list) == 0:
msg = 'No links present/selected!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
return None, None, None
link = linked_list[0]
dist = self.find_link_distance(link)
marker1d, marker2d = self.find_marker_location(link)
return dist, marker1d, marker2d
def find_link_distance(self, link):
"""find_link_distance(link)
Input:
link markerset link
Output:
dist distance or None if link is None
Find distance of link.
"""
if link == None:
return None
from VolumePath import markerset
distance = markerset.distance
dist = distance(link.marker1.xyz(), link.marker2.xyz())
return dist
def find_marker_location(self, link):
"""find_marker_location(link)
Input:
link markerset link
Output:
marker1d marker 1 location
marker2d marker 2 location
Find marker location.
"""
if link == None:
return None,None
from VolumePath import markerset
distance = markerset.distance
dist = distance(link.marker1.xyz(), link.marker2.xyz())
marker1d = link.marker1.xyz()
marker2d = link.marker2.xyz()
if self.relative_xyz.get():
marker1d, marker2d = self.find_marker_relative(link)
# show labels for marker 1 and 2
if not link.marker1.note():
link.marker1.set_note('1')
link.marker1.show_note(1)
if not link.marker2.note():
link.marker2.set_note('2')
link.marker2.show_note(1)
return marker1d, marker2d
def find_marker_relative(self, link):
"""find_marker_relative(link)
Input:
link markerset link
Output:
marker1d marker 1 location relative to model
marker2d marker 2 location relative to model
Find marker location relative to model.
"""
from VolumeViewer import slice
# open model and marker set
om = self.menu.getvalue()
ms = link.marker1.marker_set
# xform of open model and marker set
xf_om = om.openState.xform
xf_ms = ms.transform()
# get marker object coordinates
m1_xyz = link.marker1.xyz()
m2_xyz = link.marker2.xyz()
# get object coordinates relative to model
marker1d = self.transform_coord(m1_xyz, xf_ms, xf_om)
marker2d = self.transform_coord(m2_xyz, xf_ms, xf_om)
return marker1d, marker2d
def transform_coord(self, from_xyz, from_xform, to_xform):
"""transform_coord(from_xyz, from_xform, to_xform)
Input:
from_xyz from object coordinates
from_xform from object's transform
to_xform to objcet's transform
Output:
to_xyz to object coordinates
Convert coordinates from 'from object' to 'to object'
"""
import VolumePath
to_xyz = VolumePath.transform_coordinates(from_xyz,
from_xform,to_xform)
return to_xyz
def update_parameters_value(self):
"""update_parameters_value()
"""
dist, marker1d, marker2d = self.get_parameters_value()
if (dist != None and marker1d != None and marker2d != None):
msg = 'Measured in Angstrom units\n'
self.status(msg, color='blue', blankAfter=10)
replyobj.info(msg)
if dist == None: dist = 0.0
if marker1d == None: marker1d = 0.0,0.0,0.0
if marker2d == None: marker2d = 0.0,0.0,0.0
self.distance_value.set('%6.3f' % dist)
for a in range(3):
self.marker1_xyz[a].set('%6.3f' % marker1d[a])
self.marker2_xyz[a].set('%6.3f' % marker2d[a])
return
def Compute(self):
"""Compute parameters
"""
if self.volume_path_dialog == None:
import VolumePath
self.volume_path_dialog = VolumePath.volume_path_dialog()
self.update_parameters_value()
class WritePDBdialog(SaveModeless):
keepShown = SaveModeless.default
help = "UsersGuide/savemodel.html"
name = "write PDB"
def __init__(self):
self.prefs = preferences.addCategory("write PDB dialog",
preferences.HiddenCategory,
optDict={"multiSavePDB": "multiple"})
self.haveTraj = False
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("PDB", "*.pdb", ".pdb")])
openModels.addAddHandler(self._modelsChange, None),
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def configure(self, models=None, refreshList=True, selOnly=None):
if models is not None:
if len(models) > 1:
name = "Multiple Models "
elif models:
name = models[0].name + " "
else:
name = ""
self._toplevel.title("Save %sas PDB File" % name)
if refreshList:
self.modelList.setvalue(models)
self._trajCheck()
if len(models) > 1:
self.multiSaveMenu.grid(row=self._msmRow,
column=0, sticky='w')
else:
self.multiSaveMenu.grid_forget()
if selOnly is not None:
self.selOnlyVar.set(selOnly)
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 map(self, *args):
self.handler = triggers.addHandler("CoordSet",
self._trajCheck, None)
self._trajCheck()
def unmap(self, *args):
triggers.deleteHandler("CoordSet", self.handler)
self.handler = None
def Apply(self):
from chimera import dialogs
selOnly = self.selOnlyVar.get()
paths = self.getPaths()
if not paths:
replyobj.error('No save location chosen.\n')
return
path = paths[0]
models = self.modelList.getvalue()
if not models:
replyobj.error("No models chosen to save.\n")
return
if len(openModels.listIds()) > 1:
if self.saveRelativeVar.get():
relModel = self.relModelMenu.getvalue()
else:
relModel = None
else:
if self.saveUntransformedVar.get():
relModel = models[0]
else:
relModel = None
if self.haveTraj and self.frameSave.getvalue() == "all frames":
allFrames=True
else:
allFrames=False
import Midas
if len(models) < 2:
replyobj.status("Writing %s to %s\n" %
(models[0].name, path))
Midas.write(models, relModel, path,
allFrames=allFrames,
dispOnly=self.dispOnlyVar.get(),
selOnly=selOnly)
replyobj.status("Wrote %s to %s\n" %
(models[0].name, path))
return
saveOpt = self.multiSaveMenu.getvalue()
for key, value in self.labelMap.items():
if saveOpt == value:
break
self.prefs["multiSavePDB"] = key
# write multiple models to multiple files
if key == "multiple":
if path.endswith(".pdb"):
start, end = path[:-4], ".pdb"
else:
start, end = path, ""
for m in models:
modelPath = start + m.oslIdent()[1:] + end
replyobj.status("Writing %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
Midas.write(m, relModel, modelPath,
allFrames=allFrames,
dispOnly=self.dispOnlyVar.get(),
selOnly=selOnly)
replyobj.status("Wrote %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
return
# write multiple models to single file
replyobj.status("Writing multiple models to %s\n" % path)
Midas.write(models, relModel, path, allFrames=allFrames,
dispOnly=self.dispOnlyVar.get(),
selOnly=selOnly)
replyobj.status("Wrote multiple models to %s\n" % path)
def _modelsChange(self, *args):
# can't query listbox, since it hangs off of same trigger
if len(openModels.listIds()) > 1:
self.untransformedButton.grid_forget()
self.relativeFrame.grid(row=self._rfRow,
column=0, sticky='w')
else:
self.relativeFrame.grid_forget()
self.untransformedButton.grid(row=self._rfRow,
column=0, sticky='w')
def _trajCheck(self, *args):
haveTraj = False
for m in self.modelList.getvalue():
if len(m.coordSets) > 1:
haveTraj = True
break
if haveTraj == self.haveTraj:
return
self.haveTraj = haveTraj
if self.haveTraj:
self.frameSave.grid(row=self._fsRow, column=0,
sticky='w')
else:
self.frameSave.grid_forget()
class ClipFrame(Tkinter.Frame):
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 destroy(self):
delattr(self, 'model')
if self.mouseVar.get():
self.clipDialog.stopMouseClip()
Tkinter.Frame.destroy(self)
def _toggleClip(self):
if self.clipVar.get():
try:
initClip(self.model)
except ValueError:
replyobj.error("Model cannot currently be"
" clipped [no valid bounding box]\n")
self.clipVar.set(False)
return
self.slabThicknessVar.set(self.model.clipThickness)
for w in self.clipDependentWidgets:
w.config(state='normal')
else:
self.model.useClipPlane = False
if getClipModel() == self.model:
self.clipDialog.stopMouseClip()
self.mouseVar.set(False)
for w in self.clipDependentWidgets:
w.config(state='disabled')
def _toggleMouse(self):
if self.mouseVar.get():
self.clipDialog.startMouseClip(self.model)
else:
self.clipDialog.stopMouseClip()
def _changeSlab(self, event=None):
self.model.useClipThickness = self.slabVar.get()
try:
thick = float(self.slabThicknessVar.get())
except ValueError:
replyobj.error("Invalid slab thickness.\n")
return
self.model.clipThickness = thick
class ClipDialog(ModelessDialog):
name = "per-model clipping"
title = "Per-Model Clipping"
buttons = ("Close", )
help = 'ContributedSoftware/per-model/per-model.html'
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 Close(self):
if self.infoArea and self.infoArea.mouseVar.get():
self.infoArea.mouseVar.set(False)
self.stopMouseClip()
ModelessDialog.Close(self)
def setModel(self, model):
self.menu.setvalue(model)
def startMouseClip(self, model):
setClipModel(model)
if self.normMouse is not None: # clipping already ongoing
return
transVal = self.transMenu.getvalue()
pivotVal = self.pivotMenu.getvalue()
if transVal == pivotVal:
replyobj.error("Cannot assign both clip functions to"
" same button\n")
return
self.normMouse = [
mousemodes.getFuncName(*self.labelValues[transVal]),
mousemodes.getFuncName(*self.labelValues[pivotVal])
]
self._activateMouse(0, transVal)
self._activateMouse(1, pivotVal)
def stopMouseClip(self):
if self.normMouse is None: # already stopped
return
setClipModel(None)
self._restoreButton(0)
self._restoreButton(1)
self.normMouse = None
def _activateMouse(self, but, butName):
self.clipMouse[but] = butName
args = self.labelValues[butName] + (
["plane translate", "plane rotate"][but], )
mousemodes.setButtonFunction(*args)
def _align(self, refModel):
if not refModel.useClipPlane:
from chimera import LimitationError
raise LimitationError("Cannot align clip planes:"
" both models must have clipping on")
matchModel = self.menu.getvalue()
refMat = refModel.openState.xform
matchMat = matchModel.openState.xform
if refMat == matchMat:
matchModel.clipPlane = refModel.clipPlane
return
xf = matchMat.inverse()
xf.multiply(refMat)
refClip = refModel.clipPlane
matchModel.clipPlane = chimera.Plane(xf.apply(refClip.origin),
xf.apply(refClip.normal))
def _assignmentChange(self, pos, val):
if self.normMouse is None: # no ongoing clip
return
if val == self.clipMouse[1 - pos]:
replyobj.error("Cannot assign both clip functions to"
" same button\n")
[self.transMenu, self.pivotMenu][pos].setvalue(self.clipMouse[pos])
return
# restore former function to button
self._restoreButton(pos)
# remember normal function of new button
self._rememberButton(pos, val)
# assign clip function to new button
self._activateMouse(pos, val)
def _flipPlane(self):
model = self.menu.getvalue()
p = model.clipPlane
normal = p.normal
normal.negate()
p.normal = normal
model.clipPlane = p
def _menuCB(self, model):
if self.infoArea:
self.infoArea.grid_forget()
if isinstance(self.infoArea, ClipFrame):
self.infoArea.destroy()
if model:
self.infoArea = ClipFrame(self, model)
self.infoArea.grid(row=1, sticky='nsew')
else:
self.infoArea = None
def _rememberButton(self, but, butName):
self.normMouse[but] = mousemodes.getFuncName(
*self.labelValues[butName])
def _restoreButton(self, but):
# restore former function of translation (but == 0) or
# pivot button (but == 1)
restoreFunc = self.normMouse[but]
restoreArgs = self.labelValues[self.clipMouse[but]] + (restoreFunc, )
mousemodes.setButtonFunction(*restoreArgs)
def _planeRot(self, viewer, event):
xf = viewer.vsphere(event.time, event.x, event.y, event.state % 2 == 1)
if xf.isIdentity():
return
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
axis, angle = clipModel.openState.xform.getRotation()
mxf = chimera.Xform.rotation(axis, angle)
mxfinv = chimera.Xform.rotation(axis, -angle)
mxfinv.multiply(xf)
mxfinv.multiply(mxf)
p.xformNormal(mxfinv)
clipModel.clipPlane = p
def _doPlaneAutospin(self, trigger, xform, frameNumber):
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
p.xformNormal(xform)
clipModel.clipPlane = p
def _planeStart(self, viewer, event, cursor):
viewer.recordPosition(event.time, event.x, event.y, cursor),
clipModel = getClipModel()
if not clipModel:
return
viewer.showPlaneModel = clipModel, .5
def _planeStop(self, viewer, event):
viewer.setCursor(None)
viewer.showPlaneModel = None, 0
def _planeTrans(self, viewer, event):
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
dx, dy = viewer.delta(event.x, event.y, event.state % 2 == 1)
axis, angle = clipModel.openState.xform.getRotation()
mxf = chimera.Xform.rotation(axis, angle)
n = mxf.apply(p.normal)
# figure out major axis of normal in lab space
if abs(n.x) >= abs(n.y):
axis = (0, 1)
else:
axis = (1, 0)
# reassign normal so there are no zeros
# in mouse adjustment calculation
def fuzzySign(x):
if x < -1e-6:
return -1
if x > 1e-6:
return 1
return 0
n = [fuzzySign(n.x), fuzzySign(n.y), fuzzySign(n.z)]
if n[axis[0]] == 0:
# should never happen with non-zero normal
n[axis[0]] = 1
if n[axis[1]] == 0:
n[axis[1]] = n[axis[0]] # mimic major axis
n = chimera.Vector(*n)
adjust = n.x * dx + n.y * dy
distance = 2 * viewer.camera.extent * adjust
p.moveOrigin(distance)
clipModel.clipPlane = p
class ClipFrame(Tkinter.Frame):
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 destroy(self):
delattr(self, 'model')
if self.mouseVar.get():
self.clipDialog.stopMouseClip()
Tkinter.Frame.destroy(self)
def _toggleClip(self):
if self.clipVar.get():
try:
initClip(self.model)
except ValueError:
replyobj.error("Model cannot currently be"
" clipped [no valid bounding box]\n")
self.clipVar.set(False)
return
self.slabThicknessVar.set(self.model.clipThickness)
for w in self.clipDependentWidgets:
w.config(state='normal')
else:
self.model.useClipPlane = False
if getClipModel() == self.model:
self.clipDialog.stopMouseClip()
self.mouseVar.set(False)
for w in self.clipDependentWidgets:
w.config(state='disabled')
def _toggleMouse(self):
if self.mouseVar.get():
self.clipDialog.startMouseClip(self.model)
else:
self.clipDialog.stopMouseClip()
def _changeSlab(self, event = None):
self.model.useClipThickness = self.slabVar.get()
try:
thick = float(self.slabThicknessVar.get())
except ValueError:
replyobj.error("Invalid slab thickness.\n")
return
self.model.clipThickness = thick
class ClipDialog(ModelessDialog):
name = "per-model clipping"
title = "Per-Model Clipping"
buttons = ("Close",)
help = 'ContributedSoftware/per-model/per-model.html'
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 Close(self):
if self.infoArea and self.infoArea.mouseVar.get():
self.infoArea.mouseVar.set(False)
self.stopMouseClip()
ModelessDialog.Close(self)
def setModel(self, model):
self.menu.setvalue(model)
def startMouseClip(self, model):
setClipModel(model)
if self.normMouse is not None: # clipping already ongoing
return
transVal = self.transMenu.getvalue()
pivotVal = self.pivotMenu.getvalue()
if transVal == pivotVal:
replyobj.error("Cannot assign both clip functions to"
" same button\n")
return
self.normMouse = [
mousemodes.getFuncName(*self.labelValues[transVal]),
mousemodes.getFuncName(*self.labelValues[pivotVal])
]
self._activateMouse(0, transVal)
self._activateMouse(1, pivotVal)
def stopMouseClip(self):
if self.normMouse is None: # already stopped
return
setClipModel(None)
self._restoreButton(0)
self._restoreButton(1)
self.normMouse = None
def _activateMouse(self, but, butName):
self.clipMouse[but] = butName
args = self.labelValues[butName] + (["plane translate",
"plane rotate"][but],)
mousemodes.setButtonFunction(*args)
def _align(self, refModel):
if not refModel.useClipPlane:
from chimera import LimitationError
raise LimitationError("Cannot align clip planes:"
" both models must have clipping on")
matchModel = self.menu.getvalue()
refMat = refModel.openState.xform
matchMat = matchModel.openState.xform
if refMat == matchMat:
matchModel.clipPlane = refModel.clipPlane
return
xf = matchMat.inverse()
xf.multiply(refMat)
refClip = refModel.clipPlane
matchModel.clipPlane = chimera.Plane(xf.apply(refClip.origin),
xf.apply(refClip.normal))
def _assignmentChange(self, pos, val):
if self.normMouse is None: # no ongoing clip
return
if val == self.clipMouse[1 - pos]:
replyobj.error("Cannot assign both clip functions to"
" same button\n")
[self.transMenu, self.pivotMenu][pos].setvalue(
self.clipMouse[pos])
return
# restore former function to button
self._restoreButton(pos)
# remember normal function of new button
self._rememberButton(pos, val)
# assign clip function to new button
self._activateMouse(pos, val)
def _flipPlane(self):
model = self.menu.getvalue()
p = model.clipPlane
normal = p.normal
normal.negate()
p.normal = normal
model.clipPlane = p
def _menuCB(self, model):
if self.infoArea:
self.infoArea.grid_forget()
if isinstance(self.infoArea, ClipFrame):
self.infoArea.destroy()
if model:
self.infoArea = ClipFrame(self, model)
self.infoArea.grid(row=1, sticky='nsew')
else:
self.infoArea = None
def _rememberButton(self, but, butName):
self.normMouse[but] = mousemodes.getFuncName(
*self.labelValues[butName])
def _restoreButton(self, but):
# restore former function of translation (but == 0) or
# pivot button (but == 1)
restoreFunc = self.normMouse[but]
restoreArgs = self.labelValues[self.clipMouse[but]] + (
restoreFunc,)
mousemodes.setButtonFunction(*restoreArgs)
def _planeRot(self, viewer, event):
xf = viewer.vsphere(event.time, event.x, event.y,
event.state % 2 == 1)
if xf.isIdentity():
return
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
axis, angle = clipModel.openState.xform.getRotation()
mxf = chimera.Xform.rotation(axis, angle)
mxfinv = chimera.Xform.rotation(axis, -angle)
mxfinv.multiply(xf)
mxfinv.multiply(mxf)
p.xformNormal(mxfinv)
clipModel.clipPlane = p
def _doPlaneAutospin(self, trigger, xform, frameNumber):
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
p.xformNormal(xform)
clipModel.clipPlane = p
def _planeStart(self, viewer, event, cursor):
viewer.recordPosition(event.time, event.x, event.y, cursor),
clipModel = getClipModel()
if not clipModel:
return
viewer.showPlaneModel = clipModel, .5
def _planeStop(self, viewer, event):
viewer.setCursor(None)
viewer.showPlaneModel = None, 0
def _planeTrans(self, viewer, event):
clipModel = getClipModel()
if not clipModel:
return
p = clipModel.clipPlane
dx, dy = viewer.delta(event.x, event.y, event.state % 2 == 1)
axis, angle = clipModel.openState.xform.getRotation()
mxf = chimera.Xform.rotation(axis, angle)
n = mxf.apply(p.normal)
# figure out major axis of normal in lab space
if abs(n.x) >= abs(n.y):
axis = (0, 1)
else:
axis = (1, 0)
# reassign normal so there are no zeros
# in mouse adjustment calculation
def fuzzySign(x):
if x < -1e-6:
return -1
if x > 1e-6:
return 1
return 0
n = [fuzzySign(n.x), fuzzySign(n.y), fuzzySign(n.z)]
if n[axis[0]] == 0:
# should never happen with non-zero normal
n[axis[0]] = 1
if n[axis[1]] == 0:
n[axis[1]] = n[axis[0]] # mimic major axis
n = chimera.Vector(*n)
adjust = n.x * dx + n.y * dy
distance = 2 * viewer.camera.extent * adjust
p.moveOrigin(distance)
clipModel.clipPlane = p
class Volume_Morph(ModelessDialog):
"""Class: Volume_Morph()
The main GUI dialog for morphing.
"""
title='Volume Morph'
name = 'volume morph'
buttons = ('Close',)
# @ help = 'ContributedSoftware/VolumeMorph/volmorph.html'
dir_pkg = os.path.dirname(__file__)
help_path = os.path.join(dir_pkg, 'volmorph.html')
help_url = 'file://' + help_path
help = help_url
provideStatus = True
statusPosition = 'above'
statusResizing = False
statusWidth = 40
morph_choices = {0: 'Simple', 1: 'Other'}
# ---------------------------------------------------------------------
# Fill in UI
# ---------------------------------------------------------------------
def fillInUI(self, parent):
"""fillInUI(parent)
"""
self.status('')
self.focus_region = None # current selection
self.data_item = None
self.output_item = None
self.data_shown = None
self.morph_dialog = vol_morph_dialog()
self.model = None
self.morph_init = None
self.morph_final = None
parent.columnconfigure(0, weight = 1)
# parent.rowconfigure(0, weight = 1)
self.toplevel_widget = parent.winfo_toplevel() # @ whatisthis
# panel buttons (pb)
row = 0
pb = Hybrid.Checkbutton_Row(parent, 'Panels ',
('Simple', ))
pb.frame.grid(row = row, column = 0, sticky = 'nw')
for b in pb.checkbuttons:
b.callback(self.allow_toplevel_resize_cb)
(self.morph_simple_panel_button,
) = pb.checkbuttons
# data menu frame (dmf)
row = row + 1
import SegmentMenu
from SegmentMenu import datamenuseg
dmf = datamenuseg.Segment_Open_Data(self, parent,
self.data_status_cb)
dmf.frame.grid(row = row, column = 0, sticky = 'nw', pady = 8)
self.data_panel = dmf
# morph model frame
row = row + 1
mmf = Tkinter.Frame(parent, padx=8, pady=8)
mmf.grid(row = row, column = 0, sticky = 'nw')
self._make_morph_models_panel(mmf)
# simple morph frame
row = row + 1
smf = Tkinter.Frame(parent, padx=8, pady=8)
smf.grid(row = row, column = 0, sticky = 'nw')
self._make_morph_simple_panel(smf)
self.morph_simple_panel_button.popup_frame(smf,
row=row, column=0, sticky='nw')
self.morph_simple_panel_button.variable.set(1)
# morph output frame
row = row + 1
mof = Tkinter.Frame(parent, padx=8, pady=8)
mof.grid(row = row, column = 0, sticky = 'nw')
self._make_morph_output_panel(mof)
# output menu frame
row = row + 1
import SegmentMenu
from SegmentMenu import datamenuseg
omf = datamenuseg.Segment_Open_Output(self, parent,
self.output_status_cb)
omf.frame.grid(row = row, column = 0, sticky = 'nw', pady=8)
self.output_panel = omf
# create initial data menu list
self.data_panel.data_items_refresh()
# @ do we need to do stuff before closing Chimera session
# or this segmentation dialog
# ---------------------------------------------------------------------
# Panels
# ---------------------------------------------------------------------
def _make_morph_models_panel(self, frame):
"""_make_morph_models_panel(frame)
Make a panel in the GUI for morph models.
"""
row = 0
# morph models label (mmL)
mmL = Tkinter.Label(frame,
text = 'Morph Models ')
mmL.grid(row = row, column = 0, sticky = 'nw')
# morph models frame
row = row + 1
mmf = Tkinter.Frame(frame, padx=40)
mmf.grid(row = row, column = 0, sticky = 'nw')
from chimera.widgets import ModelOptionMenu
# morph model init menu and label
self.morph_init_menu = ModelOptionMenu(mmf,
command=self.morph_model_menu_cb,
labelpos='w',
label_text=' Inital model: ')
self.morph_init_menu.grid(row=0, column=0, sticky='w')
miL = Tkinter.Label(mmf, text = ' (PDB) ')
miL.grid(row=0, column=1, sticky = 'nw')
# morph model final menu and label
self.morph_final_menu = ModelOptionMenu(mmf,
command=self.morph_model_menu_cb,
labelpos='w',
label_text=' Final model: ')
self.morph_final_menu.grid(row=1, column=0, sticky='w')
mfL = Tkinter.Label(mmf, text = ' (PDB) ')
mfL.grid(row=1, column=1, sticky = 'nw')
return
def _make_morph_simple_panel(self, frame):
"""_make_morph_simple_panel(frame)
Make a panel in the GUI for simple morphing.
"""
row = 0
# simple morph label (smL)
smL = Tkinter.Label(frame,
text = 'Simple Morph ')
smL.grid(row = row, column = 0, sticky = 'nw')
# simple morph fraction frame
row = row + 1
smfrf = Tkinter.Frame(frame, padx=40)
smfrf.grid(row = row, column = 0, sticky = 'nw')
# simple morph fraction
smfr_e = Hybrid.Entry(smfrf, 'Fraction :', '6', '1.0')
smfr_e.frame.grid(row=0, column=0, sticky = 'nw')
self.sm_fraction_value = smfr_e
# simple morph threshold frame
row = row + 1
smtf = Tkinter.Frame(frame, padx=40)
smtf.grid(row = row, column = 0, sticky = 'nw')
# simple morph threshold
smt_c = Hybrid.Checkbutton_Row(smtf, 'Threshold : ',
('Use ',))
smt_c.frame.grid(row=0, column=0, sticky = 'nw')
(threshold_button,) = smt_c.checkbuttons
threshold_button.callback(self.sm_threshold_button_cb)
self.sm_threshold_button = threshold_button
smt_e = Hybrid.Entry(smtf, ' ', '8', '0.0')
smt_e.frame.grid(row=0, column=1, sticky = 'nw')
self.sm_threshold_value = smt_e
# simple morph filter frame
row = row + 1
smff = Tkinter.Frame(frame, padx=40)
smff.grid(row = row, column = 0, sticky = 'nw')
# simple morph filter
smf_c = Hybrid.Checkbutton_Row(smff, 'Filter : ',
('Use ',))
smf_c.frame.grid(row=0, column=0, sticky = 'nw')
(filter_button,) = smf_c.checkbuttons
filter_button.callback(self.sm_filter_button_cb)
self.sm_filter_button = filter_button
smf_e = Hybrid.Entry(smff, ' lowpass ', '8', '0.0')
smf_e.frame.grid(row=0, column=1, sticky = 'nw')
self.sm_filter_value = smf_e
smfL = Tkinter.Label(smff, text = ' (Ang) ')
smfL.grid(row=0, column=2, sticky = 'nw')
# default options
self.sm_threshold_button.variable.set(0)
self.sm_filter_button.variable.set(0)
return
def _make_morph_output_panel(self, frame):
"""_make_morph_output_panel(frame)
Make a panel in the GUI for output.
"""
row = 0
# morph output label (moL)
moL = Tkinter.Label(frame,
text = 'Morph Output ')
moL.grid(row = 0, column = 0, sticky = 'nw')
# morph output paramters frame (mopf)
row = row + 1
mopf = Tkinter.Frame(frame, padx=32)
mopf.grid(row = 1, column = 0, sticky = 'nw')
# chose morph type (cmt)
cmt = Hybrid.Radiobutton_Row(mopf, 'Choose Morph type ',
(self.morph_choices[0],),
self.morph_type_cb)
cmt.frame.grid(row = 0, column = 0, columnspan = 2,
sticky = 'nw', padx=8)
self.morph_type = cmt
# output data file entry (odfE)
odfE = Hybrid.Entry(mopf, 'File MRC ', '16', 'temp.mrc')
odfE.frame.grid(row = 1, column=0, sticky = 'w', padx=8)
self.data_output = odfE
# @ how to update entry - callback
# buttons
mb = Hybrid.Button_Row(mopf, '',
(('Apply', self.morph_apply_cb),))
mb.frame.grid(row = 1, column = 1, sticky = 'w', padx=8)
self.morph_type.variable.set(self.morph_choices[0])
return
# ---------------------------------------------------------------------
# Data menu related functions
# ---------------------------------------------------------------------
def data_status_cb(self, data_item, data_status):
"""data_status_cb(data_item, data_status) - callback.
Callback function for data status, used by datamenuseg's
Data menu. Activates and deactivates mouse buttons.
"""
self.data_shown = data_status
self.data_item = data_item
# display a message
if data_status == self.data_panel.DATA_NOT_SHOWN:
msg = 'Data item %s not shown\n' % (data_item.name)
elif data_status == self.data_panel.DATA_SHOWN:
msg = 'Data item %s shown\n'% (data_item.name)
else:
msg = 'No data items present\n'
# self.status(msg, color='blue', blankAfter=15)
# if data_status == self.data_panel.DATA_EMPTY:
# replyobj.info(msg)
# activate/deactivate mouse selection
# if data_status == self.data_panel.DATA_NOT_SHOWN:
# self.selection_hide_cb()
# self.sel_mouse_button['state'] = 'disabled'
# elif data_status == self.data_panel.DATA_SHOWN:
# self.selection_show_cb()
# self.sel_mouse_button['state'] = 'normal'
# else:
# self.selection_delete_cb()
# self.sel_mouse_button['state'] = 'disabled'
return
# ---------------------------------------------------------------------
# Output menu related functions
# ---------------------------------------------------------------------
def output_status_cb(self, output_item, output_status):
"""output_status_cb(output_item, output_status) - callback
Callback function for output status, used by datamenuseg's
Output menu.
"""
self.output_shown = output_status
self.output_item = output_item
# display a message
if output_status == self.output_panel.DATA_NOT_SHOWN:
msg = 'Output item %s not shown\n' % (output_item.name)
elif output_status == self.output_panel.DATA_SHOWN:
msg = 'Output item %s shown\n'% (output_item.name)
else:
msg = 'No output items present\n'
# self.status(msg, color='blue', blankAfter=15)
# if output_status == self.output_panel.DATA_EMPTY:
# replyobj.info(msg)
return
# ---------------------------------------------------------------------
# Morph related callback functions
# ---------------------------------------------------------------------
def morph_model_menu_cb(self, val):
"""morph_model_menu_cb(val) - callback for morph model menu
"""
return
def morph_type_cb(self):
"""morph_type_cb() - callback for morph type
"""
return
# ---------------------------------------------------------------------
# Simple Morph related callback functions
# ---------------------------------------------------------------------
def sm_threshold_button_cb(self):
"""sm_threshold_button_cb() - callback for simple morph
callback for threshold parameter in simple morph
"""
if self.sm_threshold_button.variable.get():
self.sm_threshold_value.entry['state'] = 'normal'
else:
self.sm_threshold_value.entry['state'] = 'readonly'
return
def sm_filter_button_cb(self):
"""sm_filter_button_cb() - callback for simple morph
callback for filter parameter in simple morph
"""
if self.sm_filter_button.variable.get():
self.sm_filter_value.entry['state'] = 'normal'
else:
self.sm_filter_value.entry['state'] = 'readonly'
return
# ---------------------------------------------------------------------
# Morph related functions.
# ---------------------------------------------------------------------
def morph_apply_cb(self):
"""morph_apply_cb() - callback for Apply button.
"""
self.morph_apply()
return
def morph_apply(self):
"""morph_apply() - applies appropriate morphing
Applies appropriate morphing after Apply button
is specified. Checks values and passes a message if
incorrect parameters.
"""
# check input data exists
if self.data_item == None:
name = '%s' % (self.data_panel.data_menu.variable.get())
msg = 'Input data %s not found!\n' % name
self.status(msg, color='red', blankAfter=15)
replyobj.error(msg)
return
# get input file path, name, and size in pixels
infile_path = str(self.data_item.path)
infile = str(self.data_item.name)
infile_size = self.data_item.size
# get morph models
morph0, morph1 = self.get_morph_models()
if (morph0 == None or morph1 == None):
return
# get morph parameters
morph_type = self.morph_type.variable.get()
if morph_type == self.morph_choices[0]:
frac, thr, filt = self.get_simple_morph_param()
# check and set output name
self.output_item = None
outfile = str(self.data_output.variable.get())
if (outfile == '') or (outfile == infile):
first_part, last_part = self.name_and_dot_suffix(infile)
outfile = '%s-m%s' % (first_part, last_part)
msg = 'Using default output file %s\n'% outfile
replyobj.info(msg)
self.data_output.variable.set(outfile)
# output
out_dir = os.getcwd()
out_files = [outfile]
# run morph command
seg_sucess = 0
if morph_type == self.morph_choices[0]:
seg_success = self.morph_apply_simple(self.data_item,
morph0, morph1, outfile, frac, thr, filt)
# open output
if seg_success:
self.open_output_data_items(out_dir, out_files)
self.enter()
return
def check_morph_model(self, model):
"""check_morph_model(model) - get morph model if valid
Output:
model morph model
"""
from chimera import Molecule
if model is None or not isinstance(model, Molecule):
print model.__class__
msg = 'Select a PDB model as morph model!\n'
self.status(msg, color='red', blankAfter=10)
replyobj.error(msg)
return None
return model
def get_morph_models(self):
"""get_morph_models() - get init and final morph models
Output:
model0 morph model initial (None if invalid)
model1 morph model final (None if invalid)
Return the inital and final morph models,
after checking.
"""
morph0 = self.morph_init_menu.getvalue()
morph1 = self.morph_final_menu.getvalue()
morph0 = self.check_morph_model(morph0)
morph1 = self.check_morph_model(morph1)
if morph0 == None or morph1 == None:
return None, None
morph0_path = morph0.openedAs[0]
morph1_path = morph1.openedAs[0]
if morph0_path == morph1_path:
msg = 'Select 2 different PDB models!\n'
self.status(msg, color='red', blankAfter=10)
replyobj.error(msg)
return None, None
return morph0, morph1
def get_simple_morph_param(self):
"""get_simple_morph_param() - simple morph parameters
Output:
thr
filt
frac
Returns parameters to be used for simple morph,
after checking.
"""
frac_value = 1.0
thr_value = None
filt_value = None
# read fraction
frac = str(self.sm_fraction_value.variable.get())
try:
frac_value = float(frac)
except:
frac_value = 1.0
msg = 'Reset fraction value!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
self.sm_fraction_value.variable.set('%5.2f' % frac_value)
if ((frac_value < 0.1) or (frac_value > 1.0)):
frac_value = 1.0
msg = 'Reset fraction value!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
self.sm_fraction_value.variable.set('%5.2f' % frac_value)
# read threshold
if self.sm_threshold_button.variable.get():
thr = str(self.sm_threshold_value.variable.get())
try:
thr_value = float(thr)
except:
thr_value = 0.0
msg = 'Reset threshold value!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
self.sm_threshold_value.variable.set('%5.2f' % thr_value)
# read filter value
if self.sm_filter_button.variable.get():
filt = str(self.sm_filter_value.variable.get())
try:
filt_value = float(filt)
except:
filt_value = 0.0
msg = 'Reset filter value!\n'
self.status(msg, color='red', blankAfter=15)
replyobj.warning(msg)
self.sm_filter_value.variable.set('%5.2f' % filt_value)
return frac_value, thr_value, filt_value
# ---------------------------------------------------------------------
# Morph simple
# ---------------------------------------------------------------------
def morph_apply_simple(self, inputdata, morph0, morph1, outputfile,
frac=1.0, thr=None, filt=None):
"""morph_apply_simple(inputdata, morph0, morph1, outputfile,
frac=1.0, thr=None, filt=None)
Input:
inputdata input volume data
morph0 PDB model for morph initial state
morph1 PDB model for morph final state
outputfile output file path
frac fraction of morphing (0.1 to 1)
thr threshold, default=None = no thr
filt lowpass filter in Angstroms
Output:
1/0 success
Apply simple morph.
Assumes that the input parmaeters are all valid.
"""
infile_path = str(inputdata.path)
msg = 'Applying simple morph on %s\n' % infile_path
replyobj.info(msg)
import morphsimple
morphsimple.simple_morph(inputdata.data, morph0, morph1,
outputfile, frac, thr, filt)
msg = 'Applied simple morphing on %s\n' \
% os.path.basename(infile_path)
self.status(msg, color='blue', blankAfter=10)
replyobj.info(msg)
return 1
# ---------------------------------------------------------------------
# Output functions.
# ---------------------------------------------------------------------
def open_output_data_items(self, outdir, outfiles):
"""open_output_data_items(outdir, outfiles) - output menu.
Input:
outdir output file directory
outfiles output file
Add output data items in outfiles in outdir directory, to
output data menu.
"""
if len(outfiles) == 0:
return
filepaths = map(lambda outfile: os.path.join(outdir, outfile),
outfiles)
filepaths_valid = filter(lambda p: os.path.isfile(p), filepaths)
self.output_panel.data_open_cb(filepaths_valid)
if len(filepaths_valid) < len(outfiles):
msg = 'Some or all output files not found!\n'
self.status(msg, color='red', blankAfter=10)
replyobj.error(msg)
return
# ---------------------------------------------------------------------
# Misc functions.
# ---------------------------------------------------------------------
# ---------------------------------------------------------------------
# After user resizes dialog by hand it will not resize automatically
# when panels are added or deleted. This allows the automatic resize
# to happen
#
def allow_toplevel_resize_cb(self):
self.toplevel_widget.geometry('')
# ---------------------------------------------------------------------
# Returns first part and dot suffix from file name or path.
# Note that the suffix includes last '.'
#
def name_and_dot_suffix(self, name):
try:
dot_position = name.rindex('.')
except ValueError:
return name, ''
first_part = name[:dot_position]
last_part = name[dot_position:]
return first_part, last_part
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()
class Vol_Cut_Dialog(ModelessDialog):
title = 'Volume_Cut'
name = 'Volume_Cut'
buttons = ('Cut Volume', 'Close',)
help = 'https://github.com/nissensonm/VolumeCut/'
# -----------------------------------------------------------------------------
#
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 CutVolume(self):
#print ' mode: ' + str(self.mode.get())
import VolCut as vc
if self.molMenu.getvalue() is None or self.modelMenu.getvalue() is None \
or self.chainMenu.getvalue() is None:
warnings.warn('Must load valid PDB, MRC, or select a chain.')
return
if type(self.modelMenu.getvalue()) is not VolumeViewer.volume.Volume:
warnings.warn('Must select a valid MRC for the mrc')
return
try:
float(self.radius.getvalue())
except ValueError:
warnings.warn('Radius must be a valid float value')
return
try:
float(self.resolution.getvalue())
except ValueError:
warnings.warn('Resolution must be a valid float value')
return
vc.cutvol(self.molMenu.getvalue().id, self.modelMenu.getvalue().id, \
float(self.radius.getvalue()), \
float(self.resolution.getvalue()), \
self.chainMenu.getvalue().chain)