# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: gui.py 31917 2010-11-17 19:22:45Z pett $
from chimera.baseDialog import ModelessDialog
from chimera import dialogs
from prefs import prefs, defaults, INCOMPLETE_SC
class DockPrepDialog(ModelessDialog):
name = "dock prep dialog"
title = "Dock Prep"
buttons = ('OK', 'Cancel')
default = 'OK'
help = "ContributedSoftware/dockprep/dockprep.html"
def fillInUI(self, parent):
import Tkinter, Pmw
row=0
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(parent,
labelpos="nw", label_text="Molecules to prep:",
listbox_selectmode="extended")
self.molListBox.grid(row=row, sticky='ew')
row += 1
Tkinter.Label(parent, text="\nFor chosen molecules,"
" do the following:").grid(row=row, sticky='w')
row += 1
self.delSolventVar = Tkinter.IntVar(parent)
self.delSolventVar.set(True)
Tkinter.Checkbutton(parent, variable=self.delSolventVar, text=
"Delete solvent").grid(row=row, sticky='w')
row += 1
self.delIonsVar = Tkinter.IntVar(parent)
self.delIonsVar.set(False)
Tkinter.Checkbutton(parent, variable=self.delIonsVar, text=
"Delete non-complexed ions").grid(row=row, sticky='w')
row += 1
self.delAltLocsVar = Tkinter.IntVar(parent)
self.delAltLocsVar.set(True)
Tkinter.Checkbutton(parent, variable=self.delAltLocsVar, text=
"If alternate locations, keep only highest occupancy",
).grid(row=row, sticky='w')
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='w')
Tkinter.Label(f, text="Change:").grid(
row=0, column=0, rowspan=4)
self.mutMseVar = Tkinter.IntVar(parent)
self.mutMseVar.set(True)
Tkinter.Checkbutton(f, variable=self.mutMseVar, text=
"selenomethionine (MSE) to methionine (MET)"
).grid(row=0, column=1, sticky='w')
self.mut5buVar = Tkinter.IntVar(parent)
self.mut5buVar.set(True)
Tkinter.Checkbutton(f, variable=self.mut5buVar, text=
"bromo-UMP (5BU) to UMP (U)"
).grid(row=1, column=1, sticky='w')
self.mutUmsVar = Tkinter.IntVar(parent)
self.mutUmsVar.set(True)
Tkinter.Checkbutton(f, variable=self.mutUmsVar, text=
"methylselenyl-dUMP (UMS) to UMP (U)"
).grid(row=2, column=1, sticky='w')
self.mutCslVar = Tkinter.IntVar(parent)
self.mutCslVar.set(True)
Tkinter.Checkbutton(f, variable=self.mutCslVar, text=
"methylselenyl-dCMP (CSL) to CMP (C)"
).grid(row=3, column=1, sticky='w')
row += 1
self.incompleteVar = Tkinter.IntVar(parent)
self.incompleteVar.set(True)
f = Tkinter.Frame(parent)
Tkinter.Checkbutton(f, variable=self.incompleteVar,
text="Incomplete side chains:",
command=self._incompleteCB).grid(row=0, column=0)
from Rotamers import libraries
libraries.sort(lambda a, b: cmp(a.displayName, b.displayName))
from chimera.tkoptions import SymbolicEnumOption
labels = ["Replace using %s rotamer library" % lib.displayName
for lib in libraries]
labels.append("Mutate residues to ALA (if CB present) or GLY")
values = libraries + ["gly/ala"]
class IncompleteSCOption(SymbolicEnumOption):
pass
IncompleteSCOption.labels = labels
IncompleteSCOption.values = values
for possibleDefault in (prefs[INCOMPLETE_SC],
defaults[INCOMPLETE_SC]):
for val in IncompleteSCOption.values:
if type(val) == str:
if val == possibleDefault:
default = possibleDefault
break
elif val.importName == possibleDefault:
default = val
break
else:
continue
break
self.incompleteOpt = IncompleteSCOption(f, 0, "", default,
self._incompleteCB, startCol=1)
f.grid(row=row, sticky='w')
row += 1
self.addHydVar = Tkinter.IntVar(parent)
self.addHydVar.set(True)
Tkinter.Checkbutton(parent, variable=self.addHydVar,
text="Add hydrogens").grid(row=row, sticky='w')
row += 1
self.addChargesVar = Tkinter.IntVar(parent)
self.addChargesVar.set(True)
Tkinter.Checkbutton(parent, variable=self.addChargesVar,
text="Add charges").grid(row=row, sticky='w')
row += 1
self.writeMol2Var = Tkinter.IntVar(parent)
self.writeMol2Var.set(True)
Tkinter.Checkbutton(parent, variable=self.writeMol2Var,
text="Write Mol2 file").grid(row=row, sticky='w')
row += 1
self.applyKeywords = {}
self.citationWidgets = {}
self.citationRow = row
self._incompleteCB()
def Apply(self):
from DockPrep import prep
if self.addHydVar.get():
import AddH
addHFunc = AddH.hbondAddHydrogens
else:
addHFunc = None
kw = self.applyKeywords
self.applyKeywords = {}
rotamerLib = rotamerPreserve = None
if self.incompleteVar.get():
incompleteVal = self.incompleteOpt.get()
if type(incompleteVal) != str:
rotamerLib = incompleteVal.importName
rotamerPreserve = True
incompleteVal = "rotamers"
prefs[INCOMPLETE_SC] = incompleteVal
else:
incompleteVal = None
prep(self.molListBox.getvalue(), addHFunc=addHFunc,
addCharges=self.addChargesVar.get(),
runSaveMol2Dialog=self.writeMol2Var.get(),
mutateMSE=self.mutMseVar.get(),
mutate5BU=self.mut5buVar.get(),
mutateUMS=self.mutUmsVar.get(),
mutateCSL=self.mutCslVar.get(),
delSolvent=self.delSolventVar.get(),
delIons=self.delIonsVar.get(),
delAltLocs=self.delAltLocsVar.get(),
incompleteSideChains=incompleteVal,
rotamerLib=rotamerLib,
rotamerPreserve=rotamerPreserve, **kw)
def _incompleteCB(self, *args):
if 'showing' in self.citationWidgets:
self.citationWidgets['showing'].grid_forget()
del self.citationWidgets['showing']
if not self.incompleteVar.get():
return
lib = self.incompleteOpt.get()
if type(lib) == str:
return
if lib not in self.citationWidgets:
if lib.citation:
from CGLtk.Citation import Citation
citationWidget = Citation(self.uiMaster(),
lib.citation, prefix="Publications"
" using %s rotamers should cite:"
% lib.citeName, pubmedID=lib.citePubmedID)
else:
citationWidget = None
self.citationWidgets[lib] = citationWidget
else:
citationWidget = self.citationWidgets[lib]
if citationWidget:
citationWidget.grid(row=self.citationRow, column=0)
self.citationWidgets['showing'] = citationWidget
dialogs.register(DockPrepDialog.name, DockPrepDialog)