def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
row = 0
import Tkinter
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent, labelpos='w', label_text='Molecule ')
mm.grid(row=row, column=0, sticky='w')
self.molecule_menu = mm
row = row + 1
from VolumeViewer import Volume_Menu
vm = Volume_Menu(parent, 'Volume data ', open_button=True)
vm.frame.grid(row=row, column=0, sticky='w')
self.volume_menu = vm
row = row + 1
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=30, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeOptionMenu
self.modelMenu = MoleculeOptionMenu(
self.clientArea,
labelpos='w',
label_text="Save model:",
command=lambda m: self.configure(self.modelMenu.getvalue(),
refreshList=False))
self.modelMenu.grid(row=row, column=0, sticky='w')
row += 1
from AddCharge import knownChargeModels, defaultChargeModel
from chimera import dialogs
self.parmsetOption = Pmw.OptionMenu(
self.clientArea,
labelpos='w',
label_text="Select force field type: ",
initialitem=defaultChargeModel,
items=knownChargeModels)
# not always shown; remember row number
self._msmRow = row
self.parmsetOption.grid(row=row, column=0, sticky='w')
row += 1
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent, labelpos = 'w', label_text = 'Molecule ')
mm.grid(row = row, column = 0, sticky = 'w')
self.molecule_menu = mm
row = row + 1
cd = Hybrid.Entry(parent, 'Contact distance', 5, '1.0')
cd.frame.grid(row = row, column = 0, sticky = 'w')
self.contact_distance = cd.variable
cd.entry.bind('<KeyPress-Return>', self.show_contacts)
row = row + 1
mc = Hybrid.Checkbutton(parent, 'Create copies of contacting molecules.', False)
mc.button.grid(row = row, column = 0, sticky = 'w')
row += 1
self.copy_molecule = mc.variable
msg = Tkinter.Label(parent, anchor = 'w', justify = 'left')
msg.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.message_label = msg
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight = 1)
from CGLtk import Hybrid
import Pmw, Tkinter
from chimera.widgets import MoleculeOptionMenu
self.molMenu = MoleculeOptionMenu(parent, labelpos="w",
label_text="Select PDB:")
self.molMenu.grid(row = 1, column = 0, sticky = 'w')
from chimera.widgets import MoleculeChainOptionMenu
self.chainMenu = MoleculeChainOptionMenu(parent, labelpos="w",
label_text="Select Chain:")
self.chainMenu.grid(row = 2, column = 0, sticky = 'w')
from chimera.widgets import ModelOptionMenu
self.modelMenu = ModelOptionMenu(parent, labelpos="w",
label_text="Select MRC:")
self.modelMenu.grid(row = 3, column = 0, sticky = 'w')
import Pmw
self.radius = Pmw.EntryField(parent, labelpos="w",
label_text="Radius:")
self.radius.grid(row = 4, column = 0, sticky = 'w')
self.resolution = Pmw.EntryField(parent, labelpos="w",
label_text="Resolution:")
self.resolution.grid(row = 5, column = 0, sticky = 'w')
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
row = 0
import Tkinter
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent, labelpos = 'w', label_text = 'Molecule ')
mm.grid(row = row, column = 0, sticky = 'w')
self.molecule_menu = mm
row = row + 1
from VolumeViewer import Volume_Menu
vm = Volume_Menu(parent, 'Volume data ', open_button = True)
vm.frame.grid(row = row, column = 0, sticky = 'w')
self.volume_menu = vm
row = row + 1
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width = 30, anchor = 'w', justify = 'left')
msg.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.message_label = msg
def fill_in_ui(self, parent):
self.canvas.columnconfigure(0, weight=1)
row = 0
self.ui_calculation = tk.LabelFrame(self.canvas,
text='Perceive bond order')
self.ui_molecule = MoleculeOptionMenu(self.ui_calculation,
labelpos='w',
label_text='Analyze')
self.ui_methods = Pmw.OptionMenu(
self.ui_calculation,
label_text='with',
labelpos='w',
items=['RDKit', 'OpenBabel', 'Single'])
self.ui_calculate_btn = tk.Button(self.ui_calculation,
text='Go!',
command=self._cmd_calculate_btn)
self.ui_calculation.grid(row=row, padx=5, pady=5, sticky='we')
self.ui_calculation.columnconfigure(0, weight=1)
self.ui_molecule.grid(row=0, column=0, padx=5, pady=5, sticky='we')
self.ui_methods.grid(row=0, column=1, padx=5, pady=5)
self.ui_calculate_btn.grid(row=0, column=2, padx=5, pady=5)
row += 1
self.ui_edition = tk.LabelFrame(self.canvas, text='Manual edition')
self.ui_fill_all_btn = tk.Button(self.ui_edition, text='Fill with all')
self.ui_fill_selected_btn = tk.Button(self.ui_edition,
text='Fill with selection')
self.ui_fill_defined_btn = tk.Button(self.ui_edition,
text='Fill with defined')
self.ui_hilite_selected_btn = tk.Button(self.ui_edition,
text='Highlight selected')
buttons = (self.ui_fill_all_btn, self.ui_fill_selected_btn,
self.ui_fill_defined_btn, self.ui_hilite_selected_btn)
self.auto_pack(self.ui_edition, buttons, padx=5, pady=5, side='left')
self.ui_edition.grid(row=row,
columnspan=3,
padx=5,
pady=5,
sticky='we')
row += 1
self.ui_table = t = _SortableTableWithEntries(self.canvas)
self.ui_table.grid(row=row, padx=5, pady=5, sticky='news')
kw = dict(anchor='w', refresh=False)
t.addColumn('Bond', 'bond', format=str, headerPadX=75, **kw)
t.addColumn('Order',
'var_order',
format=lambda a: a,
headerPadX=5,
**kw)
t.setData([
_BondTableProxy(bond=b) for b in chimera.selection.currentBonds()
])
t.grid(row=row, column=0, columnspan=3, padx=5, pady=5, sticky='news')
self.canvas.rowconfigure(row, weight=1)
class WritePrmtopDialog(SaveModeless):
keepShown = SaveModeless.default
name = "write prmtop"
help = "UsersGuide/savemodel.html#prmtop"
def __init__(self):
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Prmtop", "*.prmtop", ".prmtop")])
def configure(self, model=None, refreshList=True):
if model:
self._toplevel.title(
"Save %s as prmtop File" % model.name)
if refreshList:
self.modelMenu.setvalue(model)
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeOptionMenu
self.modelMenu = MoleculeOptionMenu(self.clientArea,
labelpos='w', label_text="Save model:",
command=lambda m: self.configure(
self.modelMenu.getvalue(), refreshList=False))
self.modelMenu.grid(row=row, column=0, sticky='w')
row += 1
from AddCharge import knownChargeModels, defaultChargeModel
from chimera import dialogs
self.parmsetOption = Pmw.OptionMenu(self.clientArea,
labelpos='w', label_text="Select force field type: ",
initialitem=defaultChargeModel, items=knownChargeModels)
# not always shown; remember row number
self._msmRow = row
self.parmsetOption.grid(row=row, column=0, sticky='w')
row += 1
def Apply(self):
paths = self.getPaths()
path = paths[0]
model = self.modelMenu.getvalue()
if not model:
self.enter()
raise UserError("No model chosen to save.")
from WritePrmtop import writePrmtop
from AddCharge.gui import checkNoCharges
chargeModel = self.parmsetOption.getvalue()
checkNoCharges([model], lambda ur, ua, model=model,
path=paths[0], parmset=chargeModel[6:]:
writePrmtop(model, path, parmset, unchargedAtoms=ua),
"prmtop output", chargeModel=chargeModel)
class Interface(ModelessDialog):
title = "Fill Gaps with Modeller"
def __init__(self, *args, **kw):
ModelessDialog.__init__(self, *args, **kw)
# TODO: initialize instance variables
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption
import itertools
info = Tk.Label(parent,
justify=Tk.LEFT,
wraplength=300,
text="Select a molecule with gaps")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options, text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options,
command=self.updateMolecule)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Skip gaps at ends of chains", False,
None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
#self.waters = BooleanOption(options, row.next(),
# "Include waters", False, None)
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod8v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def updateMolecule(self, *args, **kw):
print 'updateMolecule', args, kw
# TODO: look for gaps
def Apply(self):
from chimera import selection
molecule = [self.molecules.getvalue()]
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption, EnumOption
import itertools
info = Tk.Label(parent, justify=Tk.LEFT, wraplength=300, text=
"Model alternate conformations of loops using "
"Modeller from <http://salilab.org/>.\n"
"First select the loops you wish to model."
" Then choose the number of models "
"you wish to generate.")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options,
text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Restrict selections to turns", True, None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
self.waters = BooleanOption(options, row.next(),
"Include waters", False, None)
self.waters.disable()
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
self.count = IntOption(options, row.next(), "Number of models",
10, None, min=1, sticky=Tk.W)
#self.start = IntOption(options, row.next(),
# "Starting model number", 1, None, min=0)
class Refinement(EnumOption):
values = ('very fast', 'fast', 'slow', 'very slow',
'slow large', 'none')
self.refine = Refinement(options, row.next(), "Refinement",
'fast', None)
button = Tk.Button(options, text="Prune selection",
command=self.prune)
button.grid(row=row.next(), column=0, columnspan=2, pady=2)
self.start = 1
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod9v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1) # Allow scalebar to expand.
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent,
labelpos='w',
label_text='Molecule ',
command=self.show_cumulative_transform)
mm.grid(row=row, column=0, sticky='w')
self.molecule_menu = mm
row = row + 1
ea = Hybrid.Entry(parent, 'Euler angles ', 25, '0 0 0')
ea.frame.grid(row=row, column=0, sticky='e')
row = row + 1
self.euler_angles = ea.variable
tr = Hybrid.Entry(parent, 'Shift ', 25, '0 0 0')
tr.frame.grid(row=row, column=0, sticky='e')
row = row + 1
self.translation = tr.variable
cas = Tkinter.Label(parent, text='', justify='left')
cas.grid(row=row, column=0, sticky='w')
self.cumulative = cas
row = row + 1
el = Tkinter.Label(
parent,
text=
'Apply rotation and translation to atom coordinates\n using the molecule coordinate system.',
justify='left')
el.grid(row=row, column=0, sticky='w')
row = row + 1
self.show_cumulative_transform(None)
def fillInUI(self, parent): from chimera.widgets import MoleculeScrolledListBox self.molListBox = MoleculeScrolledListBox(parent, listbox_selectmode='extended', labelpos='w', label_text="Molecules to combine/copy:") if self.initModels: self.molListBox.setvalue(self.initModels) self.molListBox.grid(row=0, column=0, columnspan=2, sticky="nsew") parent.rowconfigure(0, weight=1) parent.columnconfigure(1, weight=1) from chimera.tkoptions import StringOption, IntOption self.molNameEntry = StringOption(parent, 1, "New model's" " name", "combination", None) curIDs = set([i1 for i1, i2 in openModels.listIds()]) mid = 0 while mid in curIDs: mid += 1 self.modelID = IntOption(parent, 2, "New model's ID", mid, None) from chimera.widgets import MoleculeOptionMenu self.refMolMenu = MoleculeOptionMenu(parent, labelpos='w', label_text="Coordinate system of:", initialitem=self.initModels[0]) self.refMolMenu.grid(row=3, column=0, columnspan=2, sticky='w') import Pmw chb = self.chainHandlingButtons = Pmw.RadioSelect(parent, buttontype="radiobutton", labelpos='w', label_text="If original molecules have duplicate\n" "single-letter chain IDs, then:", orient="vertical") self.buttonTexts = ["rename them uniquely", "retain them (residues may be renumbered)"] for bt in self.buttonTexts: chb.add(bt) chb.setvalue(self.buttonTexts[0]) chb.grid(row=4, column=0, columnspan=2) import Tkinter self.closeModelsVar = Tkinter.IntVar(parent) self.closeModelsVar.set(False) Tkinter.Checkbutton(parent, text="Close source models", variable=self.closeModelsVar).grid( row=5, column=0, columnspan=2)
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1) # Allow scalebar to expand.
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent, labelpos = 'w', label_text = 'Molecule ',
command = self.show_cumulative_transform)
mm.grid(row = row, column = 0, sticky = 'w')
self.molecule_menu = mm
row = row + 1
ea = Hybrid.Entry(parent, 'Euler angles ', 25, '0 0 0')
ea.frame.grid(row = row, column = 0, sticky = 'e')
row = row + 1
self.euler_angles = ea.variable
tr = Hybrid.Entry(parent, 'Shift ', 25, '0 0 0')
tr.frame.grid(row = row, column = 0, sticky = 'e')
row = row + 1
self.translation = tr.variable
cas = Tkinter.Label(parent, text = '', justify = 'left')
cas.grid(row = row, column = 0, sticky = 'w')
self.cumulative = cas
row = row + 1
el = Tkinter.Label(parent, text = 'Apply rotation and translation to atom coordinates\n using the molecule coordinate system.', justify = 'left')
el.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.show_cumulative_transform(None)
def fillInUI(self, parent): import Pmw, Tkinter SaveModeless.fillInUI(self, parent) row = 0 from chimera.widgets import MoleculeOptionMenu self.modelMenu = MoleculeOptionMenu(self.clientArea, labelpos='w', label_text="Save model:", command=lambda m: self.configure( self.modelMenu.getvalue(), refreshList=False)) self.modelMenu.grid(row=row, column=0, sticky='w') row += 1 from AddCharge import knownChargeModels, defaultChargeModel from chimera import dialogs self.parmsetOption = Pmw.OptionMenu(self.clientArea, labelpos='w', label_text="Select force field type: ", initialitem=defaultChargeModel, items=knownChargeModels) # not always shown; remember row number self._msmRow = row self.parmsetOption.grid(row=row, column=0, sticky='w') row += 1
def fill_in_ui(self, *args):
self.canvas.columnconfigure(0, weight=1)
row = 1
self.ui_molecule = MoleculeOptionMenu(self.canvas,
command=self.populate_table)
self.ui_molecule.grid(row=row, padx=5, pady=5, sticky='we')
row += 1
self.ui_toolbar_frame = tk.LabelFrame(
self.canvas, text='Configure selected entries')
self.ui_toolbar_frame.grid(row=row, padx=5, pady=5, sticky='we')
self.ui_select_all = tk.Button(self.canvas,
text='All',
command=self._cb_select_all)
self.ui_select_none = tk.Button(self.canvas,
text='None',
command=self._cb_select_none)
self.ui_select_invert = tk.Button(self.canvas,
text='Invert',
command=self._cb_select_invert)
self.ui_select_selection = tk.Button(self.canvas,
text='Current',
command=self._cb_select_selection)
self.ui_batch_layer_entry = Pmw.OptionMenu(self.canvas,
labelpos='w',
label_text='ONIOM Layer:',
items=['', 'H', 'M', 'L'])
self.ui_batch_layer_btn = tk.Button(self.canvas,
text='Set',
command=self._cb_batch_layer_btn)
self.ui_batch_frozen_entry = Pmw.OptionMenu(self.canvas,
labelpos='w',
label_text='Freeze state:',
items=['Yes', 'No'])
self.ui_batch_frozen_btn = tk.Button(self.canvas,
text='Set',
command=self._cb_batch_freeze_btn)
toolbar = [[
self.ui_select_all, self.ui_select_none, self.ui_batch_layer_entry,
self.ui_batch_layer_btn
],
[
self.ui_select_invert, self.ui_select_selection,
self.ui_batch_frozen_entry, self.ui_batch_frozen_btn
]]
self.auto_grid(self.ui_toolbar_frame,
toolbar,
padx=3,
pady=3,
sticky='we')
row += 1
self.canvas.rowconfigure(row, weight=1)
self.ui_table = t = _SortableTableWithEntries(self.canvas)
self.ui_table.grid(row=row, padx=5, pady=5, sticky='news')
kw = dict(anchor='w', refresh=False)
t.addColumn('#', 'serial', format="%d", headerPadX=5, **kw)
t.addColumn('Atom', 'atom', format=str, headerPadX=50, **kw)
t.addColumn('Element', 'element', headerPadX=5, **kw)
t.addColumn('Type', 'idatmtype', format=str, headerPadX=5, **kw)
t.addColumn('Layer',
'var_layer',
format=lambda a: a,
headerPadX=5,
**kw)
t.addColumn('Freeze',
'var_frozen',
format=lambda a: a,
headerPadX=5,
**kw)
if self.ui_molecule.getvalue():
self.ui_molecule.invoke()
else:
t.setData([])
t.launch()
class CombineDialog(ModelessDialog):
title = "Copy/Combine Molecular Models"
help = "UsersGuide/modelpanel.html#combine"
def __init__(self, models=None):
self.initModels = models
ModelessDialog.__init__(self)
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(parent,
listbox_selectmode='extended', labelpos='w',
label_text="Molecules to combine/copy:")
if self.initModels:
self.molListBox.setvalue(self.initModels)
self.molListBox.grid(row=0, column=0, columnspan=2,
sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
from chimera.tkoptions import StringOption, IntOption
self.molNameEntry = StringOption(parent, 1, "New model's"
" name", "combination", None)
curIDs = set([i1 for i1, i2 in openModels.listIds()])
mid = 0
while mid in curIDs:
mid += 1
self.modelID = IntOption(parent, 2, "New model's ID", mid, None)
from chimera.widgets import MoleculeOptionMenu
self.refMolMenu = MoleculeOptionMenu(parent, labelpos='w',
label_text="Coordinate system of:",
initialitem=self.initModels[0])
self.refMolMenu.grid(row=3, column=0, columnspan=2, sticky='w')
import Pmw
chb = self.chainHandlingButtons = Pmw.RadioSelect(parent,
buttontype="radiobutton", labelpos='w',
label_text="If original molecules have duplicate\n"
"single-letter chain IDs, then:", orient="vertical")
self.buttonTexts = ["rename them uniquely",
"retain them (residues may be renumbered)"]
for bt in self.buttonTexts:
chb.add(bt)
chb.setvalue(self.buttonTexts[0])
chb.grid(row=4, column=0, columnspan=2)
import Tkinter
self.closeModelsVar = Tkinter.IntVar(parent)
self.closeModelsVar.set(False)
Tkinter.Checkbutton(parent, text="Close source models",
variable=self.closeModelsVar).grid(
row=5, column=0, columnspan=2)
def Apply(self):
mols = self.molListBox.getvalue()
from chimera import UserError
if not mols:
self.enter()
raise UserError("Must specify at least one molecular"
" model to combine/copy")
from chimera import suppressNewMoleculeProcessing, \
restoreNewMoleculeProcessing
suppressNewMoleculeProcessing()
newChainIDs = (self.chainHandlingButtons.getvalue()
== self.buttonTexts[0])
refMol = self.refMolMenu.getvalue()
from Combine import combine, CombineError
try:
m = combine(mols, refMol,
newChainIDs=newChainIDs, log=True)
except CombineError, v:
restoreNewMoleculeProcessing()
self.enter()
raise UserError(v)
m.name = self.molNameEntry.get()
openModels.add([m], baseId=self.modelID.get(), shareXform=False)
m.openState.xform = refMol.openState.xform
restoreNewMoleculeProcessing()
if self.closeModelsVar.get():
openModels.close(mols)
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)
class WritePrmtopDialog(SaveModeless):
keepShown = SaveModeless.default
name = "write prmtop"
help = "UsersGuide/savemodel.html#prmtop"
def __init__(self):
SaveModeless.__init__(self,
clientPos='s',
clientSticky='ewns',
filters=[("Prmtop", "*.prmtop", ".prmtop")])
def configure(self, model=None, refreshList=True):
if model:
self._toplevel.title("Save %s as prmtop File" % model.name)
if refreshList:
self.modelMenu.setvalue(model)
def fillInUI(self, parent):
import Pmw, Tkinter
SaveModeless.fillInUI(self, parent)
row = 0
from chimera.widgets import MoleculeOptionMenu
self.modelMenu = MoleculeOptionMenu(
self.clientArea,
labelpos='w',
label_text="Save model:",
command=lambda m: self.configure(self.modelMenu.getvalue(),
refreshList=False))
self.modelMenu.grid(row=row, column=0, sticky='w')
row += 1
from AddCharge import knownChargeModels, defaultChargeModel
from chimera import dialogs
self.parmsetOption = Pmw.OptionMenu(
self.clientArea,
labelpos='w',
label_text="Select force field type: ",
initialitem=defaultChargeModel,
items=knownChargeModels)
# not always shown; remember row number
self._msmRow = row
self.parmsetOption.grid(row=row, column=0, sticky='w')
row += 1
def Apply(self):
paths = self.getPaths()
path = paths[0]
model = self.modelMenu.getvalue()
if not model:
self.enter()
raise UserError("No model chosen to save.")
from WritePrmtop import writePrmtop
from AddCharge.gui import checkNoCharges
chargeModel = self.parmsetOption.getvalue()
checkNoCharges(
[model],
lambda ur, ua, model=model, path=paths[0], parmset=chargeModel[
6:]: writePrmtop(model, path, parmset, unchargedAtoms=ua),
"prmtop output",
chargeModel=chargeModel)
class Interface(ModelessDialog):
title = "Model Loops with Modeller"
buttons = ("OK", "Cancel")
help = "ContributedSoftware/model/model.html"
def __init__(self, *args, **kw):
ModelessDialog.__init__(self, *args, **kw)
# TODO: initialize instance variables
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption, EnumOption
import itertools
info = Tk.Label(parent, justify=Tk.LEFT, wraplength=300, text=
"Model alternate conformations of loops using "
"Modeller from <http://salilab.org/>.\n"
"First select the loops you wish to model."
" Then choose the number of models "
"you wish to generate.")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options,
text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Restrict selections to turns", True, None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
self.waters = BooleanOption(options, row.next(),
"Include waters", False, None)
self.waters.disable()
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
self.count = IntOption(options, row.next(), "Number of models",
10, None, min=1, sticky=Tk.W)
#self.start = IntOption(options, row.next(),
# "Starting model number", 1, None, min=0)
class Refinement(EnumOption):
values = ('very fast', 'fast', 'slow', 'very slow',
'slow large', 'none')
self.refine = Refinement(options, row.next(), "Refinement",
'fast', None)
button = Tk.Button(options, text="Prune selection",
command=self.prune)
button.grid(row=row.next(), column=0, columnspan=2, pady=2)
self.start = 1
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod9v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def prune(self):
from chimera import selection
molecule = self.molecules.getvalue()
import ModUtil
pairs, residues = ModUtil.convertSelection(
selection._currentSelection,
minLen=4, molecule=molecule,
keepHet=self.hetatms.get(),
keepNA=self.nucleic.get(),
turnsOnly=self.turnsOnly.get())
sel = selection.ItemizedSelection()
sel.add(residues)
sel.addImplied()
selection.mergeCurrent(selection.INTERSECT, sel)
return pairs, residues
def Apply(self):
pairs, residues = self.prune()
if not pairs:
from chimera import replyobj
replyobj.status("no residues meet loop modelling criteria")
return
# create a temporary directory to work in
import tempfile
tempdir = tempfile.mkdtemp(prefix="modeller")
print 'Modeller temporary directory:', tempdir
# write PDB file with original coordinates
import os
fname = os.path.join(tempdir, 'original.pdb')
molecule = self.molecules.getvalue()
xform = molecule.openState.xform
xform.invert() # want original coordinates
chimera.viewer.pdbWrite([molecule], xform, fname)
# write out Modeller input file
count = self.count.get()
refine = self.refine.get()
fname = os.path.join(tempdir, "loopopt.py")
f = file(fname, 'w')
writeModeller(f, 'original.pdb', 'loop', pairs, count, refine)
f.close()
# run Modeller -- put up progress dialog
import ModUtil
def cb(process, dirname=tempdir, count=count):
return loopFileCount(dirname, count)
try:
prog = self.modeller.get()
p = ModUtil.run([prog, "loopopt.py"], cb, cwd=tempdir)
except OSError, e:
from chimera import replyobj
replyobj.error("Unable to run modeller: %s\n" % e)
return
# Do concurrent work here
# find atoms that are connected to the residues we will model
atoms = set()
for r in residues:
for a in r.atoms:
atoms.add(a)
outsideAtoms = set()
for a in atoms:
for b in a.bonds:
oa = b.otherAtom(a)
if oa.residue not in residues:
outsideAtoms.add(oa)
outsideAtoms = [(a.residue.id, a.name) for a in outsideAtoms]
residueIds = set([r.id for r in residues])
# TODO: use triggers to monitor process
# and then startup dock interface
# For now, we just wait
returncode = p.wait()
if returncode != 0:
from chimera import replyobj
replyobj.error("Modeller failed\n")
return
# create ViewDock input file from output files
path = makedock(tempdir, residueIds, outsideAtoms)
if not path:
from chimera import replyobj
replyobj.error("No models were generated\n")
return
# undisplay selected residues
for r in residues:
for a in r.atoms:
a.display = False
# startup dock
import ViewDock
v = ViewDock.ViewDock(path, 'Modeller')
# remove long bonds since makedock can't put TERs
# from both the model and the "longbond" PseudoBondGroup
models = [c.chimeraModel for c in v.results.compoundList]
length = 3
sqLen = length * length
for m in models:
for b in m.bonds:
if b.sqlength() >= sqLen:
# get rid of longbond PseudoBonds
a0, a1 = b.atoms
pbs = a0.associations(
chimera.LONGBOND_PBG_NAME, a1)
for pb in pbs:
pb.pseudoBondGroup.deletePseudoBond(pb)
# get rid of bond
m.deleteBond(b)
class BondOrderDialog(TangramBaseDialog):
buttons = ('Draw', 'Close')
default = None
help = "https://github.com/insilichem/tangram_bondorder"
VERSION = '0.0.1'
VERSION_URL = "https://api.github.com/repos/insilichem/tangram_bondorder/releases/latest"
def __init__(self, *args, **kwargs):
# GUI init
self.title = 'Tangram BondOrder'
self.controller = None
# Fire up
super(BondOrderDialog, self).__init__(resizable=False, *args, **kwargs)
# Triggers
chimera.triggers.addHandler('selection changed',
self._cmd_hilite_selected, None)
def fill_in_ui(self, parent):
self.canvas.columnconfigure(0, weight=1)
row = 0
self.ui_calculation = tk.LabelFrame(self.canvas,
text='Perceive bond order')
self.ui_molecule = MoleculeOptionMenu(self.ui_calculation,
labelpos='w',
label_text='Analyze')
self.ui_methods = Pmw.OptionMenu(
self.ui_calculation,
label_text='with',
labelpos='w',
items=['RDKit', 'OpenBabel', 'Single'])
self.ui_calculate_btn = tk.Button(self.ui_calculation,
text='Go!',
command=self._cmd_calculate_btn)
self.ui_calculation.grid(row=row, padx=5, pady=5, sticky='we')
self.ui_calculation.columnconfigure(0, weight=1)
self.ui_molecule.grid(row=0, column=0, padx=5, pady=5, sticky='we')
self.ui_methods.grid(row=0, column=1, padx=5, pady=5)
self.ui_calculate_btn.grid(row=0, column=2, padx=5, pady=5)
row += 1
self.ui_edition = tk.LabelFrame(self.canvas, text='Manual edition')
self.ui_fill_all_btn = tk.Button(self.ui_edition, text='Fill with all')
self.ui_fill_selected_btn = tk.Button(self.ui_edition,
text='Fill with selection')
self.ui_fill_defined_btn = tk.Button(self.ui_edition,
text='Fill with defined')
self.ui_hilite_selected_btn = tk.Button(self.ui_edition,
text='Highlight selected')
buttons = (self.ui_fill_all_btn, self.ui_fill_selected_btn,
self.ui_fill_defined_btn, self.ui_hilite_selected_btn)
self.auto_pack(self.ui_edition, buttons, padx=5, pady=5, side='left')
self.ui_edition.grid(row=row,
columnspan=3,
padx=5,
pady=5,
sticky='we')
row += 1
self.ui_table = t = _SortableTableWithEntries(self.canvas)
self.ui_table.grid(row=row, padx=5, pady=5, sticky='news')
kw = dict(anchor='w', refresh=False)
t.addColumn('Bond', 'bond', format=str, headerPadX=75, **kw)
t.addColumn('Order',
'var_order',
format=lambda a: a,
headerPadX=5,
**kw)
t.setData([
_BondTableProxy(bond=b) for b in chimera.selection.currentBonds()
])
t.grid(row=row, column=0, columnspan=3, padx=5, pady=5, sticky='news')
self.canvas.rowconfigure(row, weight=1)
def Draw(self):
m = self.ui_molecule.getvalue()
draw_bond_orders(m)
def Close(self): # Singleton mode
global ui
ui = None
super(BondOrderDialog, self).Close()
def _cmd_calculate_btn(self, *args):
molecule = self.ui_molecule.getvalue()
engine = self.ui_methods.getvalue()
try:
assign_bond_orders(molecule, engine=engine.lower())
except Exception as e:
self.status('Could not compute automatically!',
color='red',
blankAfter=4)
else:
self.Draw()
def _cmd_fill_all(self, *args):
pass
def _cmd_fill_selected(self, *args):
pass
def _cmd_fill_defined(self, *args):
pass
def _cmd_hilite_selected(self, *args):
pass
class ONIOMLayersDialog(TangramBaseDialog):
"""
Define ONIOM Layers on a per-atom basis
"""
buttons = ('OK', 'Close')
def __init__(self, saved_layers=None, *args, **kwargs):
# Fire up
self.title = 'Define ONIOM layers'
self.atoms2rows = {}
self.layers = saved_layers
super(ONIOMLayersDialog, self).__init__(with_logo=False,
*args,
**kwargs)
if saved_layers:
self.restore_dialog(saved_layers['molecule'],
saved_layers['atoms'])
def fill_in_ui(self, *args):
self.canvas.columnconfigure(0, weight=1)
row = 1
self.ui_molecule = MoleculeOptionMenu(self.canvas,
command=self.populate_table)
self.ui_molecule.grid(row=row, padx=5, pady=5, sticky='we')
row += 1
self.ui_toolbar_frame = tk.LabelFrame(
self.canvas, text='Configure selected entries')
self.ui_toolbar_frame.grid(row=row, padx=5, pady=5, sticky='we')
self.ui_select_all = tk.Button(self.canvas,
text='All',
command=self._cb_select_all)
self.ui_select_none = tk.Button(self.canvas,
text='None',
command=self._cb_select_none)
self.ui_select_invert = tk.Button(self.canvas,
text='Invert',
command=self._cb_select_invert)
self.ui_select_selection = tk.Button(self.canvas,
text='Current',
command=self._cb_select_selection)
self.ui_batch_layer_entry = Pmw.OptionMenu(self.canvas,
labelpos='w',
label_text='ONIOM Layer:',
items=['', 'H', 'M', 'L'])
self.ui_batch_layer_btn = tk.Button(self.canvas,
text='Set',
command=self._cb_batch_layer_btn)
self.ui_batch_frozen_entry = Pmw.OptionMenu(self.canvas,
labelpos='w',
label_text='Freeze state:',
items=['Yes', 'No'])
self.ui_batch_frozen_btn = tk.Button(self.canvas,
text='Set',
command=self._cb_batch_freeze_btn)
toolbar = [[
self.ui_select_all, self.ui_select_none, self.ui_batch_layer_entry,
self.ui_batch_layer_btn
],
[
self.ui_select_invert, self.ui_select_selection,
self.ui_batch_frozen_entry, self.ui_batch_frozen_btn
]]
self.auto_grid(self.ui_toolbar_frame,
toolbar,
padx=3,
pady=3,
sticky='we')
row += 1
self.canvas.rowconfigure(row, weight=1)
self.ui_table = t = _SortableTableWithEntries(self.canvas)
self.ui_table.grid(row=row, padx=5, pady=5, sticky='news')
kw = dict(anchor='w', refresh=False)
t.addColumn('#', 'serial', format="%d", headerPadX=5, **kw)
t.addColumn('Atom', 'atom', format=str, headerPadX=50, **kw)
t.addColumn('Element', 'element', headerPadX=5, **kw)
t.addColumn('Type', 'idatmtype', format=str, headerPadX=5, **kw)
t.addColumn('Layer',
'var_layer',
format=lambda a: a,
headerPadX=5,
**kw)
t.addColumn('Freeze',
'var_frozen',
format=lambda a: a,
headerPadX=5,
**kw)
if self.ui_molecule.getvalue():
self.ui_molecule.invoke()
else:
t.setData([])
t.launch()
def populate_table(self, molecule):
atoms = molecule.atoms
data = []
mapping = self.atoms2rows[molecule] = {}
for atom in atoms:
kwargs = dict(atom=atom,
element=atom.element.name,
idatmtype=atom.idatmType,
serial=atom.serialNumber)
mapping[atom] = row = _AtomTableProxy(**kwargs)
data.append(row)
self.ui_table.setData(data)
self.canvas.after(100, self.ui_table.requestFullWidth)
def restore_dialog(self, molecule, rows):
self.ui_molecule_dropdown.set(molecule)
for atom, layer in rows:
row = self.atoms2rows[atom]
row.layer = layer
self.ui_table.refresh()
def export_dialog(self):
molecule = self.ui_molecule.getvalue()
rows = [(row.atom, (row.layer, row.frozen))
for row in self.ui_table.data]
return molecule, rows
def _cb_batch_layer_btn(self, *args, **kwargs):
layer = self.ui_batch_layer_entry.getvalue()
selected = self.ui_table.selected()
for row in selected:
row.layer = layer
self.status('Applied layer {} to {} rows'.format(layer, len(selected)),
color='blue',
blankAfter=3)
def _cb_batch_freeze_btn(self, *args, **kwargs):
frozen = self.ui_batch_frozen_entry.getvalue()
selected = self.ui_table.selected()
for row in selected:
row.frozen = frozen
self.status('Applied freeze code {} to {} rows'.format(
frozen, len(selected)),
color='blue',
blankAfter=3)
def _cb_select_all(self, *args, **kwargs):
hlist = self.ui_table.tixTable.hlist
nrows = int(hlist.info_children()[-1])
for row in xrange(nrows + 1):
hlist.selection_set(row)
def _cb_select_none(self, *args, **kwargs):
self.ui_table.tixTable.hlist.selection_clear()
def _cb_select_invert(self, *args, **kwargs):
hlist = self.ui_table.tixTable.hlist
selected = set(hlist.info_selection())
all_entries = set(hlist.info_children())
self._cb_select_none()
for row in selected ^ all_entries:
hlist.selection_set(row)
def _cb_select_selection(self, *args, **kwargs):
self._cb_select_none()
rows = [
self.atoms2rows.get(atom.molecule, {}).get(atom)
for atom in chimera.selection.currentAtoms()
]
self.ui_table.select(rows)
def OK(self, *args, **kwargs):
self.layers.clear()
molecule, rows = self.export_dialog()
for i, (atom, (layer, frozen)) in enumerate(rows):
if not layer:
not_filledin = len([1 for row in rows[i + 1:] if not row[1]])
raise UserError('Atom {} {} no layer defined!'.format(
atom, 'and {} atoms more have'.format(not_filledin)
if not_filledin else 'has'))
self.layers[atom] = (layer, frozen)
self.Close()