def fillInUI(self, parent):
self.info = [
("Helix", HELIX_COLOR, 'isHelix'),
("Strand", SHEET_COLOR, 'isSheet'),
("Other", OTHER_COLOR, None)
]
header = Tkinter.Frame(parent)
header.grid(row=0, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
for i in range(len(self.info)):
parent.columnconfigure(i, weight=1)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(header,
selectioncommand=lambda: self.configure(
models=self.molListBox.getvalue()),
listbox_selectmode="extended",
labelpos="nw", label_text="Models")
self.molListBox.grid(row=0, column=0,
rowspan=len(self.info), sticky="nsew")
for i in range(3):
header.rowconfigure(i, weight=1)
header.columnconfigure(0, weight=1)
self.colorRibVar = Tkinter.IntVar(parent)
self.colorRibVar.set(True)
self.colorAtomVar = Tkinter.IntVar(parent)
self.colorAtomVar.set(False)
self.colorSurfVar = Tkinter.IntVar(parent)
self.colorSurfVar.set(False)
varFrame = Tkinter.Frame(parent)
varFrame.grid(row=1, column=0)
for i, info in enumerate([(self.colorRibVar, "Color ribbons"),
(self.colorAtomVar, "Color atoms"),
(self.colorSurfVar, "Color surfaces")]):
var, text = info
but = Tkinter.Checkbutton(varFrame, variable=var,
text=text)
but.grid(row=i, column=0, sticky='w')
self.wells = []
self.actVars = []
from CGLtk.color.ColorWell import ColorWell
from chimera.colorTable import getColorByName
for row, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
rgba = prefs[prefName]
if isinstance(rgba, basestring):
rgba = getColorByName(rgba).rgba()
well = ColorWell(header, color=rgba,
noneOkay=True)
self.wells.append(well)
well.grid(row=row, column=2)
actVar = Tkinter.IntVar(parent)
actVar.set(True)
self.actVars.append(actVar)
Tkinter.Checkbutton(header, variable=actVar,
text=ssType).grid(row=row,
column=1, sticky='w')
class mmmdDialog(ModelessDialog):
name = "Minimize Structure"
help = "ContributedSoftware/minimize/minimize.html"
buttons = ("Minimize", "Close")
keepShown = "Minimize"
def fillInUI(self, parent):
import Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
listbox_selectmode="extended")
self.molList.pack(expand=True, fill="both")
self.minimizeOptions = MinimizeOptions(parent)
self.minimizeOptions.pack(expand=False, fill="both")
def Apply(self):
molecules = self.molList.getvalue()
if not molecules:
from chimera import UserError
raise UserError("Please select a molecule to minimize")
import base
base.Minimizer(molecules, callback=self.run)
def run(self, minimizer):
self.minimizeOptions.setOptions(minimizer)
minimizer.run()
def Dynamics(self):
raise chimera.LimitationError("MD is unimplemented")
def fillInUI(self, parent):
self.parent = parent
Tkinter.Label(parent, text="Change color every:").grid(
row=0, rowspan=3, column=0, sticky='w')
self.colorChangeVar = Tkinter.StringVar(parent)
self.colorChangeVar.set("residues")
Tkinter.Radiobutton(parent, text='residue', value='residues',
variable=self.colorChangeVar).grid(
row=0, column=1, sticky='w')
Tkinter.Radiobutton(parent, text='chain', value='chains',
variable=self.colorChangeVar).grid(
row=1, column=1, sticky='w')
Tkinter.Radiobutton(parent, text='model', value='models',
variable=self.colorChangeVar).grid(
row=2, column=1, sticky='w')
group = Pmw.Group(parent, tag_text='Color range')
group.grid(row=3, column=0, columnspan=2)
self.wells = []
for i, color in enumerate(self.prefs["colors"]):
well = ColorWell(group.interior(), color=color,
noneOkay=1)
well.grid(row=0, column=i)
self.wells.append(well)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(parent,
listbox_selectmode="extended", labelpos="n",
label_text="Models")
self.molListBox.grid(row=0, column=2, rowspan=4, sticky="news")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(2, weight=1)
class mmmdDialog(ModelessDialog):
name = "Minimize Structure"
help = "ContributedSoftware/minimize/minimize.html"
buttons = ("Minimize", "Close")
keepShown = "Minimize"
def fillInUI(self, parent):
import Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
listbox_selectmode="extended")
self.molList.pack(expand=True, fill="both")
self.minimizeOptions = MinimizeOptions(parent)
self.minimizeOptions.pack(expand=False, fill="both")
def Apply(self):
molecules = self.molList.getvalue()
if not molecules:
from chimera import UserError
raise UserError("Please select a molecule to minimize")
import base
base.Minimizer(molecules, callback=self.run)
def run(self, minimizer):
self.minimizeOptions.setOptions(minimizer)
minimizer.run()
def Dynamics(self):
raise chimera.LimitationError("MD is unimplemented")
def fillInUI(self, parent):
import Pmw, Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(
parent,
labelpos='w',
label_text="Add hydrogens to:",
listbox_selectmode='extended',
selectioncommand=self._updateHisListing)
if self.startModels:
self.molList.setvalue(self.startModels)
self.molList.grid(row=0, column=0, sticky="news")
parent.columnconfigure(0, weight=1)
parent.rowconfigure(0, weight=1)
grp = Pmw.Group(parent, tag_text="Method", hull_padx=2)
grp.grid(row=1, column=0, sticky="ew")
self.useHBondsVar = Tkinter.IntVar(parent)
self.useHBondsVar.set(self.startUseHBonds)
Tkinter.Radiobutton(grp.interior(),
variable=self.useHBondsVar,
value=False,
text="steric only").grid(row=0, sticky='w')
Tkinter.Radiobutton(grp.interior(),
variable=self.useHBondsVar,
value=True,
text="also consider H-bonds (slower)").grid(
row=1, sticky='w')
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Histidine Protonation")
self.hisGroup.grid(row=2, column=0, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
Tkinter.Radiobutton(
interior,
variable=self.hisProtVar,
value="name",
text="Residue-name-based\n"
"(HIS/HID/HIE/HIP = unspecified/delta/epsilon/both)",
command=self._switchHisList,
justify="left").grid(row=0, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(
interior,
variable=self.hisProtVar,
value="pick",
textvariable=self._pickText,
command=self._switchHisList,
).grid(row=1, sticky='w')
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="default",
command=self._switchHisList,
text="Unspecified (determined by method)").grid(
row=3, sticky='w')
def fillInUI(self, parent):
import Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
listbox_selectmode="extended")
self.molList.pack(expand=True, fill="both")
self.minimizeOptions = MinimizeOptions(parent)
self.minimizeOptions.pack(expand=False, fill="both")
def fill_in_ui(self, parent):
input_frame = tk.LabelFrame(self.canvas,
text='Select a protein-ligand complex')
self.ui_molecules = MoleculeScrolledListBox(input_frame)
self.ui_molecules.filtFunc = lambda m: not m.name.startswith('PLIP-')
self.ui_molecules.refresh()
self.ui_molecules.pack(padx=5, pady=5, expand=True, fill='both')
input_frame.pack(padx=5, pady=5, expand=True, fill='both')
class AddAttrDialog(OpenModeless):
title = "Define Attribute"
provideStatus = True
name = "add/change attrs"
help = "ContributedSoftware/defineattrib/defineattrib.html"
def __init__(self):
OpenModeless.__init__(self, clientPos='s', clientSticky='nsew',
historyID="AddAttr")
def Apply(self):
mols = self.molListBox.getvalue()
if not mols:
self.enter()
replyobj.error("No models chosen in dialog\n")
return
for path in self.getPaths():
setAttrs = addAttributes(path, models=mols,
log=self.doLog.get(),
raiseAttrDialog=self.openDialog.get())
if setAttrs == []:
replyobj.error("No attributes were set from"
" file %s\n" % path)
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(self.clientArea,
listbox_selectmode="extended",
labelpos="w", label_text="Restrict to models:")
self.molListBox.grid(row=0, column=0, sticky="nsew")
self.clientArea.rowconfigure(0, weight=1)
self.clientArea.columnconfigure(0, weight=1)
checkButtonFrame = Tkinter.Frame(self.clientArea)
checkButtonFrame.grid(row=1, column=0)
self.openDialog = Tkinter.IntVar(parent)
self.openDialog.set(True)
Tkinter.Checkbutton(checkButtonFrame, variable=self.openDialog,
text="Open Render/Select by Attribute").grid(
row=0, column=0, sticky='w')
self.doLog = Tkinter.IntVar(parent)
self.doLog.set(False)
Tkinter.Checkbutton(checkButtonFrame,
text="Send match info to Reply Log",
variable=self.doLog).grid(row=1, column=0, sticky='w')
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
labelpos='w',
listbox_selectmode="extended",
label_text="Add ions : ")
self.molList.grid(row=0, column=0, sticky="nsew")
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
from Addions import ValidIontypes
self.iontype = "Cl-"
self.iontypeOption = Pmw.OptionMenu(rcf1,
label_text="Ion types:",
labelpos='w',
items=ValidIontypes,
initialitem=self.iontype,
command=self.changeIontype)
self.iontypeOption.grid(row=0, column=0)
rcf2 = Tkinter.Frame(parent)
rcf2.grid(row=3, column=0)
rcf2.columnconfigure(2, weight=1)
self.numionOption = Pmw.RadioSelect(rcf2,
buttontype='radiobutton',
command=self.changeNumion,
labelpos='w',
label_text="# of ions:")
self.numionOption.add("neutralize")
self.numionOption.add("specific number:")
self.numionOption.setvalue("neutralize")
self.numionOption.grid(row=0, column=0)
self.numion = "neutralize"
self.numionValue = Hybrid.StringVariable(rcf2)
self.numionEntry = Tkinter.Entry(
rcf2,
width=5,
textvariable=self.numionValue.tk_variable,
state='disabled')
self.numionEntry.grid(row=0, column=1)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def fillInUI(self, parent): import Tkinter from chimera.widgets import MoleculeScrolledListBox self.molList = MoleculeScrolledListBox(parent, listbox_selectmode="extended") self.molList.pack(expand=True, fill="both") self.minimizeOptions = MinimizeOptions(parent) self.minimizeOptions.pack(expand=False, fill="both")
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
titles = self.Servers.keys()
titles.sort()
self.serverChooser = Pmw.OptionMenu(parent,
labelpos="w",
label_text="Compute:",
items=titles,
command=self._changeServer)
self.serverChooser.pack(fill="x", expand=False)
self.paramHolder = Tkinter.Frame(parent, padx=10, pady=2)
self.paramHolder.pack(fill="x", expand=False)
self.paramFrames = {}
for name, val in self.Servers.iteritems():
self.paramFrames[name] = val[2](self, self.paramHolder)
self.propertyName = Pmw.EntryField(parent,
labelpos="w",
label_text="As attribute:",
value=self.Servers[titles[0]][0],
validate=self._validatePropName)
self.propertyName.pack(fill="x", expand=False)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("rba",
text="Open Render/Select by Attribute")
self.outputOptions.add("save",
text="Save server output to file")
self.outputOptions.add("show",
text="Show server output in browser")
self.outputOptions.setvalue(["rba"])
self._changeServer(titles[0])
def fill_in_ui(self, parent):
note_frame = tk.LabelFrame(self.canvas, text='How to run PoPMuSiC')
tk.Label(note_frame,
text="PoPMuSiC is a web service!\nYou must register "
"and run the jobs from:").pack(padx=5, pady=5)
self.ui_web_btn = tk.Button(
note_frame,
text="PoPMuSiC web interface",
command=lambda *a: web.open_new(r"http://soft.dezyme.com/"))
self.ui_web_btn.pack(padx=5, pady=5)
input_frame = tk.LabelFrame(
self.canvas, text='Select molecule and PoPMuSiC output files')
input_frame.rowconfigure(0, weight=1)
input_frame.columnconfigure(1, weight=1)
self.ui_molecules = MoleculeScrolledListBox(input_frame)
self.ui_molecules.grid(row=0,
columnspan=3,
padx=5,
pady=5,
sticky='news')
entries = [('popfile', 'POP file', '.pop'),
('popsfile', 'POPS file', '.pops')]
for i, (var, label, ext) in enumerate(entries):
# Label
tk.Label(input_frame, text=label).grid(row=i + 1,
column=0,
padx=3,
pady=3,
sticky='e')
# Field entry
stringvar = getattr(self, '_' + var)
entry = tk.Entry(input_frame, textvariable=stringvar)
entry.grid(row=i + 1, column=1, padx=3, pady=3, sticky='news')
setattr(self, 'ui_' + var + '_entry', entry)
# Button
button = tk.Button(
input_frame,
text='...',
command=lambda v=stringvar, e=ext: self._browse_cb(v, e))
button.grid(row=i + 1, column=2, padx=3, pady=3)
setattr(self, 'ui_' + var + '_button', button)
note_frame.pack(fill='x', padx=5, pady=5)
input_frame.pack(expand=True, fill='both', padx=5, pady=5)
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):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
labelpos='w',
listbox_selectmode="extended",
label_text='Add charges to:')
if self.startModels:
self.molList.setvalue(self.startModels)
self.molList.grid(row=0, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
import Pmw
from AddCharge import knownChargeModels, defaultChargeModel
self.chargeModel = Pmw.OptionMenu(parent,
labelpos='w',
label_text="Standard residues:",
items=knownChargeModels,
initialitem=self.initialChargeModel)
self.chargeModel.grid(row=1, column=0)
self.chargeMethod = ChargeMethodOption(parent, label="Other residues:")
self.chargeMethod.grid(row=2, column=0)
import Tkinter
labelFrame = Tkinter.Frame(parent)
labelFrame.grid(row=3, column=0)
Tkinter.Label(labelFrame,
text="Add labels showing charges"
" to atoms in:").grid(row=0, column=0, rowspan=2)
self.labelNonstandardVar = Tkinter.IntVar(parent)
self.labelNonstandardVar.set(False)
Tkinter.Checkbutton(labelFrame,
text="nonstandard residues",
variable=self.labelNonstandardVar).grid(row=0,
column=1,
sticky='w')
self.labelStandardVar = Tkinter.IntVar(parent)
self.labelStandardVar.set(False)
Tkinter.Checkbutton(labelFrame,
text="standard residues",
variable=self.labelStandardVar).grid(row=1,
column=1,
sticky='w')
class AttrFrame(Tkinter.Frame):
def __init__(self, master, **kw):
Tkinter.Frame.__init__(self, master, **kw)
self.rgbaOpt = RGBAOption(self,
1,
'Color',
prefs[COLOR],
None,
noneOkay=False)
self.associateVar = Tkinter.IntVar(self)
self.associateVar.set(0)
Tkinter.Checkbutton(self,
command=self.modelsActivity,
text="Associate with...",
variable=self.associateVar).grid(row=2,
column=0,
sticky='e')
self.moleculeList = MoleculeScrolledListBox(self,
autoselect='single',
listbox_state='disabled')
self.moleculeList.grid(row=2, column=1, sticky='w')
def modelsActivity(self):
if self.associateVar.get():
self.moleculeList.component('listbox').config(state='normal')
else:
self.moleculeList.component('listbox').config(state='disabled')
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
listbox_selectmode="extended",
label_text="Solvate: ")
self.molList.grid(row=0, column=0, sticky="nsew")
self.solvateMethod = Pmw.RadioSelect(parent,
buttontype='radiobutton', command=self.changeMethod,
labelpos='w', label_text="Solvate method:")
self.solvateMethod.add("Box")
self.solvateMethod.add("Cap")
self.solvateMethod.add("Oct")
self.solvateMethod.add("Shell")
self.solvateMethod.setvalue("Box")
self.solvateMethod.grid(row=1, column=0, sticky="nsew")
self.method = "Box"
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
self.solvent = prefs[SOLVENT_MODEL]
from Solvate import ValidSolventModels
self.solventModel = Pmw.OptionMenu(rcf1, label_text=
"Solvent Model:", labelpos = 'w', items=ValidSolventModels,
initialitem=self.solvent, command=self.changeSolvent)
self.solventModel.grid(row=0, column=0)
rcf2 = Tkinter.Frame(rcf1)
rcf2.grid(row=0, column=1)
rcf1.columnconfigure(1, weight=1)
self.extentLabel = Tkinter.Label(rcf2, text="Box size:" )
self.extentLabel.grid(row=0, column=0)
self.extentValue = Hybrid.StringVariable(rcf2)
ev = Tkinter.Entry( rcf2, width=5, textvariable=self.extentValue.tk_variable)
ev.grid( row=0, column=1 )
rcf3 = Tkinter.Frame(parent)
rcf3.grid(row=3, column=0)
self.centerLabel = Tkinter.Label(rcf3, text="Cap center (in ambmask):", state='disabled' )
self.centerLabel.grid(row=0, column=0)
self.centerValue = Hybrid.StringVariable(rcf3)
self.centerEntry = Tkinter.Entry( rcf3, width=5, textvariable=self.centerValue.tk_variable, state='disabled')
self.centerEntry.grid( row=0, column=1 )
self.removeExisting = Hybrid.Checkbutton(parent,
"Remove existing ions/solvent", True)
self.removeExisting.button.grid(row=4, column=0)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def __init__(self, master, **kw): Tkinter.Frame.__init__(self, master, **kw) self.rgbaOpt = RGBAOption(self, 1, 'Color', prefs[COLOR], None, noneOkay=False) self.associateVar = Tkinter.IntVar(self) self.associateVar.set(0) Tkinter.Checkbutton(self, command=self.modelsActivity, text="Associate with...", variable=self.associateVar ).grid(row=2, column=0, sticky='e') self.moleculeList = MoleculeScrolledListBox(self, autoselect='single', listbox_state='disabled') self.moleculeList.grid(row=2, column=1, sticky='w')
def fillInUI(self, parent): OpenModeless.fillInUI(self, parent) from chimera.widgets import MoleculeScrolledListBox self.molListBox = MoleculeScrolledListBox(self.clientArea, listbox_selectmode="extended", labelpos="w", label_text="Restrict to models:") self.molListBox.grid(row=0, column=0, sticky="nsew") self.clientArea.rowconfigure(0, weight=1) self.clientArea.columnconfigure(0, weight=1) checkButtonFrame = Tkinter.Frame(self.clientArea) checkButtonFrame.grid(row=1, column=0) self.openDialog = Tkinter.IntVar(parent) self.openDialog.set(True) Tkinter.Checkbutton(checkButtonFrame, variable=self.openDialog, text="Open Render/Select by Attribute").grid( row=0, column=0, sticky='w') self.doLog = Tkinter.IntVar(parent) self.doLog.set(False) Tkinter.Checkbutton(checkButtonFrame, text="Send match info to Reply Log", variable=self.doLog).grid(row=1, column=0, sticky='w')
class PLIPInputDialog(TangramBaseDialog):
buttons = ('Run', 'Close')
def __init__(self, *args, **kwargs):
# GUI init
self.title = 'Tangram PLIP'
self.controller = None
# Fire up
super(PLIPInputDialog, self).__init__(*args, **kwargs)
def fill_in_ui(self, parent):
input_frame = tk.LabelFrame(self.canvas,
text='Select a protein-ligand complex')
self.ui_molecules = MoleculeScrolledListBox(input_frame)
self.ui_molecules.filtFunc = lambda m: not m.name.startswith('PLIP-')
self.ui_molecules.refresh()
self.ui_molecules.pack(padx=5, pady=5, expand=True, fill='both')
input_frame.pack(padx=5, pady=5, expand=True, fill='both')
def Apply(self):
pass
def Run(self):
self.Apply()
self.Close()
def Close(self):
global ui
ui = None
super(PLIPInputDialog, self).Close()
def load_controller(self):
pass
def fillInUI(self, parent):
import Pmw, Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
label_text="Add hydrogens to:",
listbox_selectmode='extended',
selectioncommand=self._updateHisListing)
if self.startModels:
self.molList.setvalue(self.startModels)
self.molList.grid(row=0, column=0, sticky="news")
parent.columnconfigure(0, weight=1)
parent.rowconfigure(0, weight=1)
grp = Pmw.Group(parent, tag_text="Method", hull_padx=2)
grp.grid(row=1, column=0, sticky="ew")
self.useHBondsVar = Tkinter.IntVar(parent)
self.useHBondsVar.set(self.startUseHBonds)
Tkinter.Radiobutton(grp.interior(), variable=self.useHBondsVar,
value=False, text="steric only"
).grid(row=0, sticky='w')
Tkinter.Radiobutton(grp.interior(), variable=self.useHBondsVar,
value=True, text="also consider H-bonds (slower)"
).grid(row=1, sticky='w')
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Histidine Protonation")
self.hisGroup.grid(row=2, column=0, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue-name-based\n"
"(HIS/HID/HIE/HIP = unspecified/delta/epsilon/both)",
command=self._switchHisList, justify="left").grid(
row=0, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList,
).grid(row=1, sticky='w')
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="default", command=self._switchHisList,
text="Unspecified (determined by method)"
).grid(row=3, sticky='w')
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
listbox_selectmode="extended",
label_text="Add ions : ")
self.molList.grid(row=0, column=0, sticky="nsew")
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
from Addions import ValidIontypes
self.iontype = "Cl-"
self.iontypeOption = Pmw.OptionMenu(rcf1, label_text=
"Ion types:", labelpos = 'w', items=ValidIontypes,
initialitem=self.iontype, command=self.changeIontype)
self.iontypeOption.grid(row=0, column=0)
rcf2 = Tkinter.Frame(parent)
rcf2.grid(row=3, column=0)
rcf2.columnconfigure(2, weight=1)
self.numionOption = Pmw.RadioSelect(rcf2,
buttontype='radiobutton', command=self.changeNumion,
labelpos='w', label_text="# of ions:")
self.numionOption.add("neutralize")
self.numionOption.add("specific number:")
self.numionOption.setvalue( "neutralize" )
self.numionOption.grid( row=0, column=0)
self.numion = "neutralize"
self.numionValue = Hybrid.StringVariable(rcf2)
self.numionEntry = Tkinter.Entry(rcf2, width=5, textvariable=self.numionValue.tk_variable, state='disabled')
self.numionEntry.grid( row=0, column=1 )
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def fillInUI(self, parent): from chimera.widgets import MoleculeScrolledListBox self.molList = MoleculeScrolledListBox(parent, labelpos='w', listbox_selectmode="extended", label_text='Add charges to:') if self.startModels: self.molList.setvalue(self.startModels) self.molList.grid(row=0, column=0, sticky="nsew") parent.rowconfigure(0, weight=1) parent.columnconfigure(0, weight=1) import Pmw from AddCharge import knownChargeModels, defaultChargeModel self.chargeModel = Pmw.OptionMenu(parent, labelpos='w', label_text="Standard residues:", items=knownChargeModels, initialitem=self.initialChargeModel) self.chargeModel.grid(row=1, column=0) self.chargeMethod = ChargeMethodOption(parent, label="Other residues:") self.chargeMethod.grid(row=2, column=0) import Tkinter labelFrame = Tkinter.Frame(parent) labelFrame.grid(row=3, column=0) Tkinter.Label(labelFrame, text="Add labels showing charges" " to atoms in:").grid(row=0, column=0, rowspan=2) self.labelNonstandardVar = Tkinter.IntVar(parent) self.labelNonstandardVar.set(False) Tkinter.Checkbutton(labelFrame, text="nonstandard residues", variable=self.labelNonstandardVar).grid(row=0, column=1, sticky='w') self.labelStandardVar = Tkinter.IntVar(parent) self.labelStandardVar.set(False) Tkinter.Checkbutton(labelFrame, text="standard residues", variable=self.labelStandardVar).grid(row=1, column=1, sticky='w')
class AddChargesDialog(ModelessDialog): name = "add charges" title = "Add Charges" help = "ContributedSoftware/addcharge/addcharge.html" default = 'OK' def __init__(self, process=None, models=None, chargeModel=None, cb=None, **kw): if process: self.title = "Assign Charges for %s" % process.title() else: from AddCharge import process self.process = process self.cb = cb self.startModels = models if not chargeModel: from AddCharge import defaultChargeModel chargeModel = defaultChargeModel self.initialChargeModel = chargeModel ModelessDialog.__init__(self, **kw) def fillInUI(self, parent): from chimera.widgets import MoleculeScrolledListBox self.molList = MoleculeScrolledListBox(parent, labelpos='w', listbox_selectmode="extended", label_text='Add charges to:') if self.startModels: self.molList.setvalue(self.startModels) self.molList.grid(row=0, column=0, sticky="nsew") parent.rowconfigure(0, weight=1) parent.columnconfigure(0, weight=1) import Pmw from AddCharge import knownChargeModels, defaultChargeModel self.chargeModel = Pmw.OptionMenu(parent, labelpos='w', label_text="Standard residues:", items=knownChargeModels, initialitem=self.initialChargeModel) self.chargeModel.grid(row=1, column=0) self.chargeMethod = ChargeMethodOption(parent, label="Other residues:") self.chargeMethod.grid(row=2, column=0) import Tkinter labelFrame = Tkinter.Frame(parent) labelFrame.grid(row=3, column=0) Tkinter.Label(labelFrame, text="Add labels showing charges" " to atoms in:").grid(row=0, column=0, rowspan=2) self.labelNonstandardVar = Tkinter.IntVar(parent) self.labelNonstandardVar.set(False) Tkinter.Checkbutton(labelFrame, text="nonstandard residues", variable=self.labelNonstandardVar).grid(row=0, column=1, sticky='w') self.labelStandardVar = Tkinter.IntVar(parent) self.labelStandardVar.set(False) Tkinter.Checkbutton(labelFrame, text="standard residues", variable=self.labelStandardVar).grid(row=1, column=1, sticky='w') def Apply(self): from AddCharge import initiateAddCharges from AddH.gui import checkNoHyds mols = self.molList.getvalue() chargeModel = self.chargeModel.getvalue() chargeMethod = self.chargeMethod.getvalue() checkNoHyds(mols, lambda mols=mols: initiateAddCharges( cb=self.cb, models=mols, chargeModel=chargeModel, method=chargeMethod, status=chimera.replyobj.status, labelStandard=self.labelStandardVar.get(), labelNonstandard=self.labelNonstandardVar.get()), self.process)
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)
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)
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
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)
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 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
class NCIPlotDialog(TangramBaseDialog):
buttons = ('Run', 'Save', 'Load', 'Close')
configure_dialog = None
help = "https://github.com/insilichem/tangram_nciplot"
VERSION = '0.0.1'
VERSION_URL = "https://api.github.com/repos/insilichem/tangram_nciplot/releases/latest"
def __init__(self, *args, **kwargs):
# GUI init
self.title = 'Tangram NCIPlot'
self._mouse_report_binding = None
# Variables
self.var_input_intermolecular_enabled = tk.IntVar()
self.var_input_intermolecular = tk.IntVar()
self.var_input_intermolecular.set(95)
self.var_input_summary = tk.StringVar()
self.var_input_summary.set('Please select your input.')
self.var_input_choice = tk.StringVar()
self.var_input_choice.set('molecules')
self.var_settings_isovalue_1 = tk.StringVar()
self.var_settings_isovalue_1.set('')
self.var_settings_isovalue_2 = tk.StringVar()
self.var_settings_isovalue_2.set('')
self.var_settings_report = tk.IntVar()
self.var_reported_value = tk.StringVar()
# Fire up
super(NCIPlotDialog, self).__init__(*args, **kwargs)
def fill_in_ui(self, parent):
# Select an input menu: Radio buttons
self.ui_input_frame = tk.LabelFrame(self.canvas, text='Input mode')
self.ui_input_frame.pack(expand=True, fill='x', padx=5, pady=5)
self.ui_input_frame.columnconfigure(0, weight=1)
self.ui_input_choice_frame = tk.Frame(self.ui_input_frame)
self.ui_input_choice_frame.grid(row=0, sticky='we')
self.ui_input_choice_molecules = tk.Radiobutton(
self.ui_input_choice_frame,
variable=self.var_input_choice,
text='Molecules',
value='molecules',
command=self._input_choice_cb)
self.ui_input_choice_selection = tk.Radiobutton(
self.ui_input_choice_frame,
variable=self.var_input_choice,
text='Selection',
value='selection',
command=self._input_choice_cb)
self.ui_input_choice_molecules.pack(side='left')
self.ui_input_choice_selection.pack(side='left')
self.ui_input_choice_molecules.select()
# Mode A: Opened molecules
self.ui_input_molecules_frame = tk.Frame(self.ui_input_frame)
self.ui_input_molecules_frame.grid(row=1, sticky='news')
self.ui_input_molecules_frame.columnconfigure(0, weight=1)
self.ui_input_molecules = MoleculeScrolledListBox(
self.ui_input_molecules_frame,
selectioncommand=self._on_selection_changed,
listbox_selectmode="extended")
self.ui_input_molecules.pack(expand=True, fill='x', padx=5)
# Mode B: Current selection
items = ['Current selection'] + sorted(
chimera.selection.savedSels.keys())
self.ui_input_named_selections = OptionMenu(
self.ui_input_molecules_frame, command=None, items=items)
self.input_new_named_atom_selection = None # Text field + 'Create button'
# More options
self.ui_input_intermolecular_frame = tk.Frame(self.ui_input_frame)
self.ui_input_intermolecular_frame.grid(row=2)
self.ui_input_intermolecular_check = tk.Checkbutton(
self.ui_input_intermolecular_frame,
text='Filter out % of intramolecular',
variable=self.var_input_intermolecular_enabled,
command=self._intermolecular_cb,
state='disabled')
self.ui_input_intermolecular_check.pack(side='left')
self.ui_input_intermolecular_field = tk.Entry(
self.ui_input_intermolecular_frame,
textvariable=self.var_input_intermolecular,
state='disabled',
width=3)
self.ui_input_intermolecular_field.pack(side='left')
# Review input data
self.ui_input_summary_label = tk.Label(
self.ui_input_frame, textvariable=self.var_input_summary)
self.ui_input_summary_label.grid(row=3)
# NCIPlot launcher
self.ui_nciplot_frame = tk.Frame(self.canvas)
self.ui_nciplot_frame.pack()
self.ui_config_btn = tk.Button(self.ui_nciplot_frame,
text='Configure',
command=self._configure_dialog)
self.ui_config_btn.pack(side='left')
# Configure Volume Viewer
self.ui_settings_frame = tk.LabelFrame(self.canvas,
text='Customize display',
padx=5,
pady=5)
self.ui_levels_lbl = tk.Label(self.ui_settings_frame, text='Levels: ')
self.ui_levels_lbl.grid(row=0, column=0)
self.ui_settings_isovalue_1 = tk.Entry(
self.ui_settings_frame,
textvariable=self.var_settings_isovalue_1,
width=10)
self.ui_settings_isovalue_1.grid(row=0, column=1, sticky='ew')
self.ui_settings_isovalue_2 = tk.Entry(
self.ui_settings_frame,
textvariable=self.var_settings_isovalue_2,
width=10)
self.ui_settings_isovalue_2.grid(row=0, column=2, sticky='ew')
self.ui_settings_update_btn = tk.Button(self.ui_settings_frame,
text='Update',
command=self._update_surface)
self.ui_settings_update_btn.grid(row=0,
column=3,
rowspan=2,
sticky='news')
self.ui_settings_color_palette = OptionMenu(
self.ui_settings_frame,
initialitem=3,
label_text='Colors: ',
labelpos='w',
items=sorted(standard_color_palettes.keys()))
self.ui_settings_color_palette.grid(row=1,
column=0,
columnspan=3,
sticky='we')
self.ui_report_btn = tk.Checkbutton(
self.ui_settings_frame,
text=u'Report \u03BB\u2082\u22C5\u03C1\u22C5100 value at cursor',
command=self._report_values_cb,
variable=self.var_settings_report)
self.ui_report_btn.grid(row=2, column=0, columnspan=3)
self.ui_reported_value = tk.Entry(self.ui_settings_frame,
textvariable=self.var_reported_value,
state='readonly',
width=8)
self.ui_reported_value.grid(row=2, column=3, sticky='we')
# Plot figure
self.ui_plot_frame = tk.LabelFrame(
self.canvas,
text=u'Plot RDG vs density (\u03BB\u2082\u22C5\u03C1)',
padx=5,
pady=5)
self.ui_plot_button = tk.Button(self.ui_plot_frame,
text='Plot',
command=self._plot)
self.ui_plot_button.grid(row=0)
self.ui_plot_figure = Figure(figsize=(5, 5),
dpi=100,
facecolor='#D9D9D9')
self.ui_plot_subplot = self.ui_plot_figure.add_subplot(111)
self.ui_plot_widget_frame = tk.Frame(self.ui_plot_frame)
self.ui_plot_widget_frame.grid(row=1)
self.ui_plot_widget = FigureCanvasTkAgg(
self.ui_plot_figure, master=self.ui_plot_widget_frame)
# self.plot_cursor = Cursor(self.plot_subplot, useblit=True, color='black', linewidth=1)
# self.plot_figure.canvas.mpl_connect('button_press_event', self._on_plot_click)
# Register and map triggers, callbacks...
chimera.triggers.addHandler('selection changed',
self._on_selection_changed, None)
self.nciplot_run = self.buttonWidgets['Run']
self.buttonWidgets['Save']['state'] = 'disabled'
def load_controller(self):
binary, dat = prefs.get_preferences()
return Controller(gui=self, nciplot_binary=binary, nciplot_dat=dat)
def input_options(self):
d = {}
if self.var_input_intermolecular_enabled.get():
d['intermolecular'] = self.var_input_intermolecular.get() / 100.0
return d
# All the callbacks
def _input_choice_cb(self):
"""
Change input mode
"""
if self.var_input_choice.get() == 'molecules':
self.ui_input_molecules.pack(expand=True, fill='x', padx=5)
self.ui_input_named_selections.pack_forget()
elif self.var_input_choice.get() == 'selection':
self.ui_input_molecules.pack_forget()
self.ui_input_named_selections.pack(expand=True, fill='x', padx=5)
self._on_selection_changed()
def _intermolecular_cb(self):
if self.var_input_intermolecular_enabled.get():
self.ui_input_intermolecular_field.config(state='normal')
else:
self.ui_input_intermolecular_field.config(state='disabled')
def _validate_input_data(self, *args):
atoms = self._on_selection_changed()
return atoms
def _configure_dialog(self, *args):
if self.configure_dialog is None:
self.configure_dialog = NCIPlotConfigureDialog(self.canvas)
self.configure_dialog.enter()
def Run(self, *args):
"""
Called at clicking 'Run' button.
"""
self._run_nciplot_clear_cb()
atoms = self._validate_input_data()
if atoms:
attr_getter = attrgetter('molecule')
groups = [
list(group) for k, group in groupby(atoms, key=attr_getter)
]
options = self.input_options()
self.controller = self.load_controller()
self.controller.run(groups=groups, **options)
self.nciplot_run.configure(state='disabled', text='Running...')
self.ui_settings_frame.pack_forget()
def Save(self, *args):
try:
grad = self.controller.data['grad_cube']
dens = self.controller.data['dens_cube']
xy = self.controller.data['xy_data']
except KeyError:
raise chimera.UserError("NCIPlot has not run yet!")
path = tkFileDialog.asksaveasfilename(
title='Choose destination (.cube)',
filetypes=[('Gaussian cube', '*.cube'), ('All', '*')],
defaultextension='.cube')
if not path:
return
data = self.controller.data.copy()
basename, ext = os.path.splitext(path)
data['grad_cube'] = newgradpath = '{fn}.grad{ext}'.format(fn=basename,
ext=ext)
shutil.copyfile(grad, newgradpath)
data['dens_cube'] = newdenspath = '{fn}.dens{ext}'.format(fn=basename,
ext=ext)
shutil.copyfile(dens, newdenspath)
data['xy_data'] = newdatpath = '{fn}.dat'.format(fn=basename, ext=ext)
shutil.copyfile(xy, newdatpath)
with open('{}.json'.format(basename), 'w') as f:
json.dump(data, f)
self.status('Saved at {}!'.format(os.path.dirname(path)),
color='blue',
blankAfter=4)
def Load(self, *args):
path = tkFileDialog.askopenfilename(title='Choose state file (*.json)',
filetypes=[('JSON file', '*.json'),
('All', '*')])
if not path:
return
with open(path) as f:
data = json.load(f)
self._run_nciplot_clear_cb()
self.controller = self.load_controller()
self.controller._after_cb(data)
self._run_nciplot_cb()
def Close(self): # Singleton mode
global ui
ui = None
super(NCIPlotDialog, self).Close()
def _run_nciplot_cb(self):
"""
Called after NCIPlot has successfully run
"""
self.nciplot_run.configure(state='normal', text='Run')
self.var_settings_isovalue_1.set(
self.controller.surface.surface_levels[0])
self.var_settings_isovalue_2.set(
self.controller.surface.surface_levels[1])
self.ui_settings_frame.pack()
self.ui_plot_frame.pack(expand=True, fill='both')
self.buttonWidgets['Save']['state'] = 'normal'
def _run_nciplot_clear_cb(self):
"""
Housecleaning method. Resets everything to original state
"""
self.nciplot_run.configure(state='normal', text='Run')
self.ui_plot_button.configure(state='normal')
self.ui_settings_frame.pack_forget()
self.var_settings_isovalue_1.set('')
self.var_settings_isovalue_2.set('')
self.ui_plot_frame.pack_forget()
self.ui_plot_widget.get_tk_widget().pack_forget()
self.controller = None
self.buttonWidgets['Save']['state'] = 'disabled'
def _update_surface(self):
"""
Gets GUI options, sets them and updates the surface
"""
# Levels
isovalue_1 = float(self.var_settings_isovalue_1.get())
isovalue_2 = float(self.var_settings_isovalue_2.get())
self.controller.isosurface(level_1=isovalue_1, level_2=isovalue_2)
# Update view
self.controller.update_surface()
# Colors
palette = self.ui_settings_color_palette.getvalue()
self.controller.colorize_by_volume(palette=palette)
# Update view
self.controller.update_surface()
def _plot(self):
"""
Draw density vs rdg with a hexbin
"""
self.controller.plot(self.ui_plot_subplot)
self.ui_plot_widget.get_tk_widget().pack(expand=True, fill='both')
self.ui_plot_widget.show()
self.ui_plot_button.configure(state='disabled')
def _report_values_cb(self):
"""
Binds mouse mouse callbacks to mouse movement events
"""
if self.var_settings_report.get(
) and self._mouse_report_binding is None:
self._mouse_report_binding = chimera.tkgui.app.graphics.bind(
'<Any-Motion>', self._report_values_event, add=True)
def _report_values_event(self, event):
"""
Report value of isosurface at cursor point
"""
if self.var_settings_report.get() and self.isVisible():
vpn = surface_value_at_window_position(event.x, event.y)
if vpn is None:
self.var_reported_value.set('')
else:
value, position, name = vpn
self.var_reported_value.set('{:8.5g}'.format(float(value)))
chimera.replyobj.status('{} at cursor: {:8.5g}'.format(
name, float(value)))
def _on_plot_click(self, event):
"""
Callback that sets isosurface values from plot X axis data.
Left click sets isovalue 1, right click sets isovalue 2
"""
if event.button == 1:
self.var_settings_isovalue_1.set(round(event.xdata, 2))
elif event.button == 3:
self.var_settings_isovalue_2.set(round(event.xdata, 2))
def _on_selection_changed(self, *args):
"""
Test if current selection is valid for running a new calculation,
reports number of atoms
"""
atoms = []
if self.var_input_choice.get() == 'selection':
atoms = chimera.selection.currentAtoms()
molecules = chimera.selection.currentMolecules()
elif self.var_input_choice.get() == 'molecules':
molecules = self.ui_input_molecules.getvalue()
atoms = [a for m in molecules for a in m.atoms]
color, state = ('black', 'normal') if atoms else ('red', 'disabled')
self.nciplot_run.configure(state=state)
self.ui_input_summary_label.configure(foreground=color)
self.var_input_summary.set('{} selected atoms'.format(len(atoms)))
if len(molecules) > 1:
self.ui_input_intermolecular_check.config(state='normal')
self.ui_input_intermolecular_check.select()
else:
self.ui_input_intermolecular_check.config(state='disabled')
self.ui_input_intermolecular_check.deselect()
self._intermolecular_cb()
return atoms
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("solid", text="Solid surface (rather than mesh)")
self.outputOptions.add("track", text="Reuse last surface (if any)")
self.outputOptions.add("atoms", text="Select interface atoms")
self.outputOptions.add("prune", text="Residue centroid distance pruning")
self.outputOptions.setvalue(["solid", "track"])
self.pruneDistance = Pmw.EntryField(parent,
labelpos="w",
label_text="Prune distance:",
value="30.0",
validate=self._validatePruneDistance)
self.pruneDistance.pack(fill="x", expand=False)
self.moleculeBias = Pmw.Counter(parent,
labelpos="w",
label_text="Molecule bias:",
datatype="real",
increment = 0.1,
entryfield_value="0.5",
entryfield_validate={'validator' : 'real',
'min' : '0.0', 'max' : '1.0',
'separator' : '.'})
self.moleculeBias.pack(fill="x", expand=False)
histKw = {
'minlabel': True,
'maxlabel': True,
'scaling': 'linear',
}
self.histogram = MarkedHistogram(parent, **histKw)
self.histogramMarkers = self.histogram.addmarkers(activate=True,
coordtype='relative')
self.histogramMarkers.extend([
((1.0, 0.0), (0.0, 0.0, 0.33, 1.0)),
((0.0, 0.0), (1.0, 0.0, 0.0, 1.0))])
self.histogram.pack(expand=True, fill="both")
self._trackedPiece = None
self._trackedModel = None
self.models = {}
chimera.openModels.addRemoveHandler(self._removeModel, None)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.saveSession, None)
chimera.triggers.addHandler("Molecule",
self._moleculeChanged, None)
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
class AddionsDialog(ModelessDialog):
name = "addions"
title = "Addions"
#help = "ContributedSoftware/addcharge/addcharge.html"
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
listbox_selectmode="extended",
label_text="Add ions : ")
self.molList.grid(row=0, column=0, sticky="nsew")
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
from Addions import ValidIontypes
self.iontype = "Cl-"
self.iontypeOption = Pmw.OptionMenu(rcf1, label_text=
"Ion types:", labelpos = 'w', items=ValidIontypes,
initialitem=self.iontype, command=self.changeIontype)
self.iontypeOption.grid(row=0, column=0)
rcf2 = Tkinter.Frame(parent)
rcf2.grid(row=3, column=0)
rcf2.columnconfigure(2, weight=1)
self.numionOption = Pmw.RadioSelect(rcf2,
buttontype='radiobutton', command=self.changeNumion,
labelpos='w', label_text="# of ions:")
self.numionOption.add("neutralize")
self.numionOption.add("specific number:")
self.numionOption.setvalue( "neutralize" )
self.numionOption.grid( row=0, column=0)
self.numion = "neutralize"
self.numionValue = Hybrid.StringVariable(rcf2)
self.numionEntry = Tkinter.Entry(rcf2, width=5, textvariable=self.numionValue.tk_variable, state='disabled')
self.numionEntry.grid( row=0, column=1 )
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def changeIontype(self, state):
self.iontype= state
def changeNumion(self, state):
if state=="neutralize":
self.numion = "neutralize"
self.numionEntry.config( state="disabled" )
else:
self.numion = "specific"
self.numionEntry.config( state="normal" )
def Apply(self):
from chimera import UserError, replyobj
if self.iontype=="":
self.enter()
raise UserError("No ion type chosen.")
if self.numion =="specific":
self.numion = self.numionValue.get()
if self.numion=="":
self.enter()
raise UserError(" number of ion is not given." )
else:
assert self.numion=="neutralize"
from Addions import initiateAddions
mols = self.molList.getvalue()
from AddCharge.gui import checkNoCharges
checkNoCharges(mols, lambda ur, ua, mols=mols: initiateAddions(
mols, self.iontype, self.numion, replyobj.status),
"ion addition")
def fillInUI(self, parent):
self.refMolList = MoleculeScrolledListBox(
parent,
autoselect="single",
labelpos="nw",
label_text="Reference structure:")
self.refChainList = MoleculeChainScrolledListBox(
parent,
labelpos="nw",
label_text="Reference chain:",
listbox_selectmode='extended')
self.matchMolList = MoleculeScrolledListBox(
parent,
labelpos="nw",
label_text="Structure(s) to match:",
listbox_selectmode='extended')
self.matchChainList = ChainMenus(parent)
def doSync():
if self.chainMatchVar.get() != CP_SPECIFIC_SPECIFIC:
return
self.matchChainList.syncUp(self.refChainList)
self.refChainList.configure(selectioncommand=doSync)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
seqFrame = Tkinter.Frame(parent)
seqFrame.grid(row=1, column=0, columnspan=2, sticky="nsew")
seqFrame.columnconfigure(0, weight=1)
seqFrame.columnconfigure(1, weight=1)
pairingGroup = Pmw.Group(seqFrame, tag_text="Chain pairing")
pairingGroup.grid(row=0, column=0, columnspan=2, sticky="w", padx=2)
pairingGroup.interior().columnconfigure(0, weight=1)
self.chainMatchVar = Tkinter.StringVar(parent)
self.chainMatchVar.set(prefs[CHAIN_PAIRING])
radiobuttonInfo = [
(CP_BEST,
"Best-aligning pair of chains\n\tbetween reference and match structure"
),
(CP_SPECIFIC_BEST,
"Specific chain in reference structure\n\twith best-aligning chain in match structure"
),
(CP_SPECIFIC_SPECIFIC,
"Specific chain(s) in reference structure\n\twith specific chain(s) in match structure"
),
]
for i in range(len(radiobuttonInfo)):
val, text = radiobuttonInfo[i]
radio = Tkinter.Radiobutton(pairingGroup.interior(),
command=self._chainMatchCB,
text=text,
justify='left',
value=val,
variable=self.chainMatchVar)
radio.grid(row=i, column=0, sticky='w')
self._chainMatchCB()
self.seqAlgorithmMenu = Pmw.OptionMenu(
seqFrame,
initialitem=prefs[SEQUENCE_ALGORITHM],
labelpos='w',
label_text="Alignment algorithm:",
items=[SA_NEEDLEMAN_WUNSCH, SA_SMITH_WATERMAN])
self.seqAlgorithmMenu.grid(row=1, column=0, sticky='w')
matrixNames = SmithWaterman.matrices.keys()
matrixNames.sort()
if prefs[MATRIX] in SmithWaterman.matrices:
initialMatrix = prefs[MATRIX]
else:
if defaults[MATRIX] in SmithWaterman.matrices:
initialMatrix = defaults[MATRIX]
else:
initialMatrix = matrixNames[0]
prefs[MATRIX] = initialMatrix
self.matrixMenu = Pmw.OptionMenu(seqFrame,
initialitem=initialMatrix,
labelpos='w',
label_text="Matrix:",
items=matrixNames)
self.matrixMenu.grid(row=1, column=1, sticky='w')
gapFrame = Tkinter.Frame(seqFrame)
gapFrame.grid(row=2, column=0, columnspan=2, sticky='ew')
gapFrame.columnconfigure(0, weight=1)
gapFrame.columnconfigure(1, weight=1)
self.gapOpenEntry = Pmw.EntryField(gapFrame,
labelpos='w',
label_text="Gap opening penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_OPEN]))
self.gapOpenEntry.grid(row=0, column=0)
self.gapExtendEntry = Pmw.EntryField(
gapFrame,
labelpos='w',
label_text="Gap extension penalty",
validate='real',
entry_width=2,
entry_justify='right',
value="%g" % (prefs[GAP_EXTEND]))
self.gapExtendEntry.grid(row=0, column=1)
self._entries = [self.gapOpenEntry, self.gapExtendEntry]
self.ssParams = SSParams(seqFrame, prefs, useSSCB=self._useSSCB)
self.ssParams.grid(row=3, column=0, columnspan=2, sticky='ew')
self.computeSSVar = Tkinter.IntVar(parent)
self.computeSSVar.set(prefs[COMPUTE_SS])
self._computeSSButton = Tkinter.Checkbutton(
seqFrame,
text="Compute secondary structure assignments",
variable=self.computeSSVar)
self._computeSSGridArgs = {'row': 4, 'sticky': 'w', 'columnspan': 2}
if self.ssParams.useSSVar.get():
self._computeSSButton.grid(**self._computeSSGridArgs)
self.showSeqVar = Tkinter.IntVar(parent)
self.showSeqVar.set(prefs[SHOW_SEQUENCE])
Tkinter.Checkbutton(seqFrame,
text="Show pairwise alignment(s)",
variable=self.showSeqVar).grid(row=5,
column=0,
sticky='w',
columnspan=2)
matchGroup = Pmw.Group(parent, tag_text="Matching")
matchGroup.grid(row=2, column=0, columnspan=2, sticky="nsew", padx=2)
matchGroup.interior().columnconfigure(0, weight=1)
self.iterVar = Tkinter.IntVar(parent)
self.iterVar.set(prefs[ITERATE])
Tkinter.Checkbutton(matchGroup.interior(),
justify="left",
text="Iterate by pruning long atom pairs"
" until no pair exceeds:",
variable=self.iterVar).grid(row=0,
column=0,
sticky='w')
self.iterEntry = Pmw.EntryField(matchGroup.interior(),
validate='real',
entry_width=3,
entry_justify="right",
value="%.1f" % prefs[ITER_CUTOFF],
labelpos='e',
label_text="angstroms")
self.iterEntry.grid(row=1, column=0)
self._entries.append(self.iterEntry)
self.structSeqVar = Tkinter.IntVar(parent)
self.structSeqVar.set(False)
Tkinter.Checkbutton(parent,
text="After superposition, compute"
" structure-based multiple sequence alignment",
variable=self.structSeqVar).grid(row=3,
sticky='w',
columnspan=2)
f = Tkinter.Frame(parent)
f.grid(row=4, column=0, columnspan=2, sticky='ew')
from chimera import help
b = Tkinter.Button(f,
text="Save settings",
pady=0,
command=self._saveSettings)
b.grid(row=0, column=0)
help.register(b, balloon="Save current settings")
b = Tkinter.Button(f,
text="Reset to defaults",
pady=0,
command=self._restoreSettings)
b.grid(row=0, column=1)
help.register(b, balloon="Reset dialog to factory defaults")
f.columnconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
# set up state of gap-open entry
self._useSSCB()
class SolvateDialog(ModelessDialog):
name = "solvate"
title = "Solvate"
#help = "ContributedSoftware/addcharge/addcharge.html"
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
listbox_selectmode="extended",
label_text="Solvate: ")
self.molList.grid(row=0, column=0, sticky="nsew")
self.solvateMethod = Pmw.RadioSelect(parent,
buttontype='radiobutton', command=self.changeMethod,
labelpos='w', label_text="Solvate method:")
self.solvateMethod.add("Box")
self.solvateMethod.add("Cap")
self.solvateMethod.add("Oct")
self.solvateMethod.add("Shell")
self.solvateMethod.setvalue("Box")
self.solvateMethod.grid(row=1, column=0, sticky="nsew")
self.method = "Box"
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
self.solvent = prefs[SOLVENT_MODEL]
from Solvate import ValidSolventModels
self.solventModel = Pmw.OptionMenu(rcf1, label_text=
"Solvent Model:", labelpos = 'w', items=ValidSolventModels,
initialitem=self.solvent, command=self.changeSolvent)
self.solventModel.grid(row=0, column=0)
rcf2 = Tkinter.Frame(rcf1)
rcf2.grid(row=0, column=1)
rcf1.columnconfigure(1, weight=1)
self.extentLabel = Tkinter.Label(rcf2, text="Box size:" )
self.extentLabel.grid(row=0, column=0)
self.extentValue = Hybrid.StringVariable(rcf2)
ev = Tkinter.Entry( rcf2, width=5, textvariable=self.extentValue.tk_variable)
ev.grid( row=0, column=1 )
rcf3 = Tkinter.Frame(parent)
rcf3.grid(row=3, column=0)
self.centerLabel = Tkinter.Label(rcf3, text="Cap center (in ambmask):", state='disabled' )
self.centerLabel.grid(row=0, column=0)
self.centerValue = Hybrid.StringVariable(rcf3)
self.centerEntry = Tkinter.Entry( rcf3, width=5, textvariable=self.centerValue.tk_variable, state='disabled')
self.centerEntry.grid( row=0, column=1 )
self.removeExisting = Hybrid.Checkbutton(parent,
"Remove existing ions/solvent", True)
self.removeExisting.button.grid(row=4, column=0)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def changeMethod(self, state):
self.method = state
if state=="Box":
self.extentLabel.config( text="Box size: " )
self.centerLabel.config( state='disabled' )
self.centerEntry.config( state='disabled' )
elif state=="Cap":
self.extentLabel.config( text="Cap Radius: " )
self.centerLabel.config( state='normal' )
self.centerEntry.config( state='normal' )
elif state=="Oct":
self.extentLabel.config( text="Oct size: " )
self.centerLabel.config( state='disabled' )
self.centerEntry.config( state='disabled' )
else:
assert state=="Shell"
self.extentLabel.config( text="Shell extent: " )
self.centerLabel.config( state='disabled' )
self.centerEntry.config( state='disabled' )
def changeSolvent(self, solvent):
self.solvent = solvent
def Apply(self):
from chimera import UserError
if self.solvent=="":
self.enter()
raise UserError("No solvent model chosen.")
if self.extentValue.get()=="":
self.enter()
raise UserError(self.method + " size is not given." )
if self.method=="Cap" and self.centerValue.get()=="":
self.enter()
raise UserError("Center of cap is not given.")
prefs[SOLVENT_MODEL] = self.solvent
from Solvate import initiateSolvate
mols = self.molList.getvalue()
if self.removeExisting.variable.get():
from Midas import deleteAtomsBonds
deleteAtomsBonds(atoms=[a for m in mols
for a in m.atoms
if a.surfaceCategory in ["solvent", "ions"]])
# in case any models were _all_ solvent/ions...
mols = [m for m in mols if not m.__destroyed__]
noHyds = []
for mol in mols:
for a in mol.atoms:
if a.element.number == 1:
break
else:
noHyds.append(mol)
if noHyds:
from chimera.baseDialog import AskYesNoDialog
msg = "Hydrogens must be present for" \
" solvation to work correctly.\n"
if len(mols) == len(noHyds):
msg += "No models have hydrogens.\n"
else:
msg += "The following models have no" \
" hydrogens:\n"
for nh in noHyds:
msg += "\t%s (%s)\n" % (nh.name,
nh.oslIdent())
msg += "You can add hydrogens using the AddH tool.\n"
msg += "What would you like to do?"
from AddH.gui import NoHydsDialog
userChoice = NoHydsDialog(msg).run(chimera.tkgui.app)
if userChoice == "cancel":
return
elif userChoice == "add hydrogens":
from AddH.gui import AddHDialog
AddHDialog(title="Add Hydrogens for Solvate",
models=noHyds, useHBonds=True,
oneshot=True, cb=lambda mols=mols:
initiateSolvate(mols,self.method, self.solvent,
self.extentValue.get(), self.centerValue.get(),
chimera.replyobj.status))
return
initiateSolvate(mols, self.method, self.solvent, self.extentValue.get(), self.centerValue.get(), chimera.replyobj.status)
def fillInUI(self, parent):
# inter/intra-model; slop; colors; models; replace current;
# label
# for removing labels in subsequent passes...
# (use a selection so I don't have to track model closures)
self.labelSelection = ItemizedSelection()
self.labelMap = {}
self.callbacks = []
row = 0
cols = 3
self.bondColorOption = ColorOption(parent, row, 'H-bond color',
prefs[BOND_COLOR], None, noneOkay=0)
class HBLineWidthOption(LineWidthOption):
name = "Line width"
balloon = "Width of pseudobonds (in pixels)"
default = prefs[LINE_WIDTH]
self.lineWidth = HBLineWidthOption(parent, row+1,
None, None, None, width=4, sticky='w')
self.findMode = Pmw.RadioSelect(parent,
buttontype='radiobutton', labelpos='n', pady=0,
orient='vertical', label_text='Find these bonds:',
hull_borderwidth=2, hull_relief='ridge')
self.findMode.add('inter-model')
self.findMode.add('intra-model')
self.findMode.add('both')
self.findMode.invoke('both')
self.findMode.grid(row=row, column=2, rowspan=2)
row += 2
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, columnspan=cols,
sticky='nsew', padx=2)
row += 1
self.restrictModels = Tkinter.IntVar(parent)
self.restrictModels.set(0)
self.modelFrame = Tkinter.Frame(parent)
self.molTexts = ["Restrict to models...", "Restrict to models:"]
self.restrictCheckBox = Tkinter.Checkbutton(self.modelFrame,
variable=self.restrictModels,
text=self.molTexts[0], command=self._restrictModelsCB)
self.restrictCheckBox.grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(self.modelFrame,
listbox_selectmode="extended")
self.modelFrame.rowconfigure(0, weight=1)
self.modelFrame.grid(row=row, column=0, columnspan=cols,
sticky="nsw")
parent.rowconfigure(row, weight=1)
row += 1
self.inSelection = Tkinter.IntVar(parent)
self.inSelection.set(0)
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=cols, sticky="w")
Tkinter.Checkbutton(f, variable=self.inSelection,
text="Only find H-bonds with",
command=self._useSelChange).grid(
row=0, column=0, sticky="e")
self.selType = Pmw.OptionMenu(f, items=["at least one end",
"exactly one end", "both ends"], initialitem=0,
menubutton_state="disabled", labelpos="e",
label_text="selected")
self.selType.grid(row=0, column=1, sticky="w")
row += 1
self.revealEnds = Tkinter.IntVar(parent)
self.revealEnds.set(0)
Tkinter.Checkbutton(parent, variable=self.revealEnds,
text="If endpoint atom hidden, show endpoint residue"
).grid(row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.retainCurrent = Tkinter.IntVar(parent)
self.retainCurrent.set(0)
Tkinter.Checkbutton(parent, variable=self.retainCurrent,
text="Retain currently displayed H-bonds").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.interSubmodel = Tkinter.IntVar(parent)
self.interSubmodel.set(0)
# comment out the below since there seems to be no
# situations where cross-submodel-same-model hbonds
# are interesting. If reading pdbrun files occurs, this
# may change.
#Tkinter.Checkbutton(parent, variable=self.interSubmodel,
# text="Find H-bonds between submodels\n"
# "having same principal model number"
# ).grid(row=row, column=0, columnspan=cols, sticky="w")
#row += 1
self.writeFile = Tkinter.IntVar(parent)
self.writeFile.set(0)
Tkinter.Checkbutton(parent, variable=self.writeFile,
text="Write information to file").grid(row=row,
column=0, columnspan=cols, sticky="w")
self.fileName = None
row += 1
self.writeLog = Tkinter.IntVar(parent)
self.writeLog.set(0)
Tkinter.Checkbutton(parent, variable=self.writeLog,
text="Write information to reply log").grid(row=row,
column=0, columnspan=cols, sticky="w")
row += 1
class ColorSSDialog(ModelessDialog):
title = "Color Secondary Structure"
buttons = ('OK', 'Apply', 'Defaults', 'Close')
name = "color by SS"
help = "ContributedSoftware/colorss/colorss.html"
def __init__(self):
ModelessDialog.__init__(self)
def fillInUI(self, parent):
self.info = [
("Helix", HELIX_COLOR, 'isHelix'),
("Strand", SHEET_COLOR, 'isSheet'),
("Other", OTHER_COLOR, None)
]
header = Tkinter.Frame(parent)
header.grid(row=0, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
for i in range(len(self.info)):
parent.columnconfigure(i, weight=1)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(header,
selectioncommand=lambda: self.configure(
models=self.molListBox.getvalue()),
listbox_selectmode="extended",
labelpos="nw", label_text="Models")
self.molListBox.grid(row=0, column=0,
rowspan=len(self.info), sticky="nsew")
for i in range(3):
header.rowconfigure(i, weight=1)
header.columnconfigure(0, weight=1)
self.colorRibVar = Tkinter.IntVar(parent)
self.colorRibVar.set(True)
self.colorAtomVar = Tkinter.IntVar(parent)
self.colorAtomVar.set(False)
self.colorSurfVar = Tkinter.IntVar(parent)
self.colorSurfVar.set(False)
varFrame = Tkinter.Frame(parent)
varFrame.grid(row=1, column=0)
for i, info in enumerate([(self.colorRibVar, "Color ribbons"),
(self.colorAtomVar, "Color atoms"),
(self.colorSurfVar, "Color surfaces")]):
var, text = info
but = Tkinter.Checkbutton(varFrame, variable=var,
text=text)
but.grid(row=i, column=0, sticky='w')
self.wells = []
self.actVars = []
from CGLtk.color.ColorWell import ColorWell
from chimera.colorTable import getColorByName
for row, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
rgba = prefs[prefName]
if isinstance(rgba, basestring):
rgba = getColorByName(rgba).rgba()
well = ColorWell(header, color=rgba,
noneOkay=True)
self.wells.append(well)
well.grid(row=row, column=2)
actVar = Tkinter.IntVar(parent)
actVar.set(True)
self.actVars.append(actVar)
Tkinter.Checkbutton(header, variable=actVar,
text=ssType).grid(row=row,
column=1, sticky='w')
def Apply(self):
colors = {}
for i, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
rgba = self.wells[i].rgba
prefs[prefName] = rgba
if not self.actVars[i].get():
continue
if rgba is None:
color = None
else:
color = chimera.MaterialColor(*rgba)
colors[attrName] = color
mols = self.molListBox.getvalue()
# only the protein residues are relevant...
protein = {}
for m in mols:
for r in m.residues:
ratoms = r.atomsMap
if 'CA' not in ratoms:
continue
if len(ratoms) == 1:
# possible CA-only model
if ratoms['CA'][0].element.number == 6:
protein[r] = True
continue
if 'O' in ratoms \
and 'N' in ratoms \
and 'C' in ratoms:
protein[r] = True
atomAttrs = []
resAttrs = []
if self.colorRibVar.get():
resAttrs = ["ribbonColor"]
if self.colorAtomVar.get():
atomAttrs.append("color")
if self.colorSurfVar.get():
atomAttrs.append("surfaceColor")
from chimera.actions import changeSurfsFromCustom
changeSurfsFromCustom(mols)
if atomAttrs:
def colorAttrs(item, res, attrs):
for attrName, color in colors.items():
if attrName is None:
if not (res.isHelix
or res.isSheet):
break
elif getattr(res, attrName):
break
else:
return
for attr in attrs:
setattr(item, attr, color)
for m in mols:
for a in m.atoms:
res = a.residue
if res not in protein:
continue
colorAttrs(a, res, atomAttrs)
if resAttrs:
for m in mols:
for res in m.residues:
if res not in protein:
continue
for attrName, color in colors.items():
if attrName is None:
if not (res.isHelix
or res.isSheet):
break
elif getattr(res, attrName):
break
else:
continue
for attr in resAttrs:
setattr(res, attr, color)
def configure(self, models=None):
if models is not None:
self.molListBox.setvalue(models)
def Defaults(self):
from prefs import defaultColors
for i, ssInfo in enumerate(self.info):
ssType, prefName, attrName = ssInfo
self.wells[i].showColor(color=defaultColors[prefName])
class HBDialog(ModelessDialog):
title = "H-Bond Parameters"
buttons = ("OK", "Apply", "Close")
default = 'OK'
help = "ContributedSoftware/findhbond/findhbond.html"
def fillInUI(self, parent):
# inter/intra-model; slop; colors; models; replace current;
# label
# for removing labels in subsequent passes...
# (use a selection so I don't have to track model closures)
self.labelSelection = ItemizedSelection()
self.labelMap = {}
self.callbacks = []
row = 0
cols = 3
self.bondColorOption = ColorOption(parent,
row,
'H-bond color',
prefs[BOND_COLOR],
None,
noneOkay=0)
class HBLineWidthOption(LineWidthOption):
name = "Line width"
balloon = "Width of pseudobonds (in pixels)"
default = prefs[LINE_WIDTH]
self.lineWidth = HBLineWidthOption(parent,
row + 1,
None,
None,
None,
width=4,
sticky='w')
self.findMode = Pmw.RadioSelect(parent,
buttontype='radiobutton',
labelpos='n',
pady=0,
orient='vertical',
label_text='Find these bonds:',
hull_borderwidth=2,
hull_relief='ridge')
self.findMode.add('inter-model')
self.findMode.add('intra-model')
self.findMode.add('both')
self.findMode.invoke('both')
self.findMode.grid(row=row, column=2, rowspan=2)
row += 2
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, columnspan=cols, sticky='nsew', padx=2)
row += 1
self.restrictModels = Tkinter.IntVar(parent)
self.restrictModels.set(0)
self.modelFrame = Tkinter.Frame(parent)
self.molTexts = ["Restrict to models...", "Restrict to models:"]
self.restrictCheckBox = Tkinter.Checkbutton(
self.modelFrame,
variable=self.restrictModels,
text=self.molTexts[0],
command=self._restrictModelsCB)
self.restrictCheckBox.grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(self.modelFrame,
listbox_selectmode="extended")
self.modelFrame.rowconfigure(0, weight=1)
self.modelFrame.grid(row=row, column=0, columnspan=cols, sticky="nsw")
parent.rowconfigure(row, weight=1)
row += 1
self.inSelection = Tkinter.IntVar(parent)
self.inSelection.set(0)
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=cols, sticky="w")
Tkinter.Checkbutton(f,
variable=self.inSelection,
text="Only find H-bonds with",
command=self._useSelChange).grid(row=0,
column=0,
sticky="e")
self.selType = Pmw.OptionMenu(
f,
items=["at least one end", "exactly one end", "both ends"],
initialitem=0,
menubutton_state="disabled",
labelpos="e",
label_text="selected")
self.selType.grid(row=0, column=1, sticky="w")
row += 1
self.revealEnds = Tkinter.IntVar(parent)
self.revealEnds.set(0)
Tkinter.Checkbutton(
parent,
variable=self.revealEnds,
text="If endpoint atom hidden, show endpoint residue").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.retainCurrent = Tkinter.IntVar(parent)
self.retainCurrent.set(0)
Tkinter.Checkbutton(parent,
variable=self.retainCurrent,
text="Retain currently displayed H-bonds").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.interSubmodel = Tkinter.IntVar(parent)
self.interSubmodel.set(0)
# comment out the below since there seems to be no
# situations where cross-submodel-same-model hbonds
# are interesting. If reading pdbrun files occurs, this
# may change.
#Tkinter.Checkbutton(parent, variable=self.interSubmodel,
# text="Find H-bonds between submodels\n"
# "having same principal model number"
# ).grid(row=row, column=0, columnspan=cols, sticky="w")
#row += 1
self.writeFile = Tkinter.IntVar(parent)
self.writeFile.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeFile,
text="Write information to file").grid(
row=row, column=0, columnspan=cols, sticky="w")
self.fileName = None
row += 1
self.writeLog = Tkinter.IntVar(parent)
self.writeLog.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeLog,
text="Write information to reply log").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
def addCallback(self, callback):
self.callbacks.append(callback)
def Apply(self):
states = {}
for but in self.buttonWidgets.values():
states[but] = but.cget('state')
but.config(state='disabled')
try:
self._Apply()
finally:
for but, state in states.items():
but.config(state=state)
for cb in self.callbacks:
try:
cb()
except:
replyobj.reportException("H-bond callback function")
self.callbacks = []
def _Apply(self):
intramodel = intermodel = 1
cursel = self.findMode.getcurselection()
if cursel == 'inter-model':
intramodel = 0
elif cursel == 'intra-model':
intermodel = 0
distSlop = 0.0
angleSlop = 0.0
twoColors = False
relax = self.relaxParams.relaxConstraints
rc = self.relaxParams.relaxColor
if relax:
distSlop = self.relaxParams.relaxDist
angleSlop = self.relaxParams.relaxAngle
if self.relaxParams.useRelaxColor:
twoColors = True
prefs[RELAX_COLOR] = rc.rgba
if self.inSelection.get():
selRestrict = ["any", "cross",
"both"][self.selType.index(Pmw.SELECT)]
else:
selRestrict = None
lineWidth = self.lineWidth.get()
prefs[LINE_WIDTH] = lineWidth
bc = self.bondColorOption.get()
prefs[BOND_COLOR] = bc.rgba
if self.writeFile.get():
saveFile = '-'
else:
saveFile = None
if self.restrictModels.get():
models = self.molList.getvalue()
if not models:
raise ValueError, "No restriction models chosen"
else:
models = None
from base import createHBonds
createHBonds(models=models,
intramodel=intramodel,
intermodel=intermodel,
relax=relax,
distSlop=distSlop,
angleSlop=angleSlop,
twoColors=twoColors,
selRestrict=selRestrict,
lineWidth=lineWidth,
saveFile=saveFile,
log=self.writeLog.get(),
retainCurrent=self.retainCurrent.get(),
reveal=self.revealEnds.get(),
color=bc,
slopColor=rc)
def Close(self):
self.callbacks = []
ModelessDialog.Close(self)
def _restrictModelsCB(self):
restrict = self.restrictModels.get()
self.restrictCheckBox.config(text=self.molTexts[restrict])
if restrict:
self.molList.grid(row=0, column=1, sticky="ns")
else:
self.molList.grid_forget()
def _useSelChange(self):
if self.inSelection.get():
self.selType.component("menubutton").config(state="normal")
else:
self.selType.component("menubutton").config(state="disabled")
class Interface(ModelessDialog):
title = "Compute Surface Area and Volume"
help = "ContributedSoftware/surfvol/surfvol.html"
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
titles = self.Servers.keys()
titles.sort()
self.serverChooser = Pmw.OptionMenu(parent,
labelpos="w",
label_text="Compute:",
items=titles,
command=self._changeServer)
self.serverChooser.pack(fill="x", expand=False)
self.paramHolder = Tkinter.Frame(parent, padx=10, pady=2)
self.paramHolder.pack(fill="x", expand=False)
self.paramFrames = {}
for name, val in self.Servers.iteritems():
self.paramFrames[name] = val[2](self, self.paramHolder)
self.propertyName = Pmw.EntryField(parent,
labelpos="w",
label_text="As attribute:",
value=self.Servers[titles[0]][0],
validate=self._validatePropName)
self.propertyName.pack(fill="x", expand=False)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("rba",
text="Open Render/Select by Attribute")
self.outputOptions.add("save",
text="Save server output to file")
self.outputOptions.add("show",
text="Show server output in browser")
self.outputOptions.setvalue(["rba"])
self._changeServer(titles[0])
def _changeServer(self, name):
self.propertyName.setvalue(self.Servers[name][0])
for n, (frame, parts) in self.paramFrames.iteritems():
if n == name:
frame.pack(fill="x", expand=True)
else:
frame.forget()
def _validatePropName(self, text):
if len(text) == 0:
return Pmw.PARTIAL
if text[0] not in NameFirstChar:
return Pmw.ERROR
for c in text[1:]:
if c not in NameChar:
return Pmw.ERROR
return Pmw.OK
def Apply(self):
if not self.propertyName.valid():
raise chimera.UserError(
"Please enter valid attribute name")
propName = self.propertyName.getvalue()
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = self.chainChooser.getvalue()
if not target:
raise chimera.UserError(
"Please select molecule or chain")
opts = self.outputOptions.getvalue()
rba = "rba" in opts
save = "save" in opts
show = "show" in opts
serverName = self.serverChooser.getcurselection()
f = self.Servers[serverName][1]
parts = self.paramFrames[serverName][1]
opts = self.Servers[serverName][3](self, parts)
output = f(target, opts, propName, rba)
if save:
_save(output, show)
elif show:
# create temporary file and invoke browser
from OpenSave import osTemporaryFile
filename = osTemporaryFile(suffix=".html")
f = open(filename, "w")
f.write(output)
f.close()
import urllib
from chimera import help
help.display("file:" + urllib.pathname2url(filename))
_paramMsmsParams = [
( "Surface probe size:",
"msms_probe",
( ( "1.3", "1.3" ),
( "1.4", "1.4" ),
( "1.5", "1.5" ),
( "1.6", "1.6" ) ),
"1.5"
),
( "Atoms to use:",
"msms_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"No Hetatms"
),
]
_paramGersteinSurfaceParams = [
( "Surface probe size:",
"surf_Gerstein_probe",
( ( "1.3", "1.3" ),
( "1.4", "1.4" ),
( "1.5", "1.5" ),
( "1.6", "1.6" ) ),
"1.4"
),
( "Atoms to use:",
"surf_Gerstein_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"All atoms except waters"
),
]
_paramGersteinVolumeParams = [
( "Method:",
"vol_Gerstein_method",
( ( "Normal Voronoi", "1" ),
( "Method B", "2" ),
( "Radical Plane", "3" ),
( "Modified Method B", "4" ) ),
"Method B"
),
( "Radii:",
"vol_Gerstein_radii",
( ( "Chothia Radii", "" ),
( "Richards Radii", "-RichardsRadii" ) ),
"Chothia Radii"
),
( "Atoms to use:",
"vol_Gerstein_atoms",
( ( "No Hetatms", "HETATM" ),
( "Atoms + Hetatms", "ZZZZZZ" ),
( "All atoms except waters", "HOH" ) ),
"No Hetatms"
),
]
def _paramMakeMsms(self, group):
return self._paramMake(group, self._paramMsmsParams)
def _paramGetMsms(self, parts):
return self._paramGet(parts, self._paramMsmsParams)
def _paramMakeGersteinSurface(self, group):
return self._paramMake(group, self._paramGersteinSurfaceParams)
def _paramGetGersteinSurface(self, parts):
return self._paramGet(parts, self._paramGersteinSurfaceParams)
def _paramMakeGersteinVolume(self, group):
return self._paramMake(group, self._paramGersteinVolumeParams)
def _paramGetGersteinVolume(self, parts):
return self._paramGet(parts, self._paramGersteinVolumeParams)
def _paramMake(self, parent, params):
g = Pmw.Group(parent, tag_text="Parameters")
parts = []
for label, cgiTag, items, default in params:
m = Pmw.OptionMenu(g.interior(),
labelpos="w",
label_text=label,
items=[ item[0] for item in items ])
m.setvalue(default)
m.pack(fill="x", expand=False)
parts.append(m)
Pmw.alignlabels(parts)
return g, parts
def _paramGet(self, parts, params):
args = []
for i, m in enumerate(parts):
sel = m.getvalue()
label, cgiTag, items, default = params[i]
for name, value in items:
if name == sel:
args.append((cgiTag, None, value))
break
else:
raise ChimeraError("unexpected option value")
return args
Servers = {
"Surface Area (MSMS)":
( "msmsArea",
StrucTools.msms,
_paramMakeMsms,
_paramGetMsms,
),
"Accessible Surface (Gerstein)":
( "accessibleSurface",
StrucTools.surface,
_paramMakeGersteinSurface,
_paramGetGersteinSurface,
),
"Voronoi Volume (Gerstein)":
( "voronoiVolume",
StrucTools.volume,
_paramMakeGersteinVolume,
_paramGetGersteinVolume,
),
}
def fillInUI(self, parent):
# inter/intra-model; slop; colors; models; replace current;
# label
# for removing labels in subsequent passes...
# (use a selection so I don't have to track model closures)
self.labelSelection = ItemizedSelection()
self.labelMap = {}
self.callbacks = []
row = 0
cols = 3
self.bondColorOption = ColorOption(parent,
row,
'H-bond color',
prefs[BOND_COLOR],
None,
noneOkay=0)
class HBLineWidthOption(LineWidthOption):
name = "Line width"
balloon = "Width of pseudobonds (in pixels)"
default = prefs[LINE_WIDTH]
self.lineWidth = HBLineWidthOption(parent,
row + 1,
None,
None,
None,
width=4,
sticky='w')
self.findMode = Pmw.RadioSelect(parent,
buttontype='radiobutton',
labelpos='n',
pady=0,
orient='vertical',
label_text='Find these bonds:',
hull_borderwidth=2,
hull_relief='ridge')
self.findMode.add('inter-model')
self.findMode.add('intra-model')
self.findMode.add('both')
self.findMode.invoke('both')
self.findMode.grid(row=row, column=2, rowspan=2)
row += 2
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, columnspan=cols, sticky='nsew', padx=2)
row += 1
self.restrictModels = Tkinter.IntVar(parent)
self.restrictModels.set(0)
self.modelFrame = Tkinter.Frame(parent)
self.molTexts = ["Restrict to models...", "Restrict to models:"]
self.restrictCheckBox = Tkinter.Checkbutton(
self.modelFrame,
variable=self.restrictModels,
text=self.molTexts[0],
command=self._restrictModelsCB)
self.restrictCheckBox.grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(self.modelFrame,
listbox_selectmode="extended")
self.modelFrame.rowconfigure(0, weight=1)
self.modelFrame.grid(row=row, column=0, columnspan=cols, sticky="nsw")
parent.rowconfigure(row, weight=1)
row += 1
self.inSelection = Tkinter.IntVar(parent)
self.inSelection.set(0)
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=cols, sticky="w")
Tkinter.Checkbutton(f,
variable=self.inSelection,
text="Only find H-bonds with",
command=self._useSelChange).grid(row=0,
column=0,
sticky="e")
self.selType = Pmw.OptionMenu(
f,
items=["at least one end", "exactly one end", "both ends"],
initialitem=0,
menubutton_state="disabled",
labelpos="e",
label_text="selected")
self.selType.grid(row=0, column=1, sticky="w")
row += 1
self.revealEnds = Tkinter.IntVar(parent)
self.revealEnds.set(0)
Tkinter.Checkbutton(
parent,
variable=self.revealEnds,
text="If endpoint atom hidden, show endpoint residue").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.retainCurrent = Tkinter.IntVar(parent)
self.retainCurrent.set(0)
Tkinter.Checkbutton(parent,
variable=self.retainCurrent,
text="Retain currently displayed H-bonds").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.interSubmodel = Tkinter.IntVar(parent)
self.interSubmodel.set(0)
# comment out the below since there seems to be no
# situations where cross-submodel-same-model hbonds
# are interesting. If reading pdbrun files occurs, this
# may change.
#Tkinter.Checkbutton(parent, variable=self.interSubmodel,
# text="Find H-bonds between submodels\n"
# "having same principal model number"
# ).grid(row=row, column=0, columnspan=cols, sticky="w")
#row += 1
self.writeFile = Tkinter.IntVar(parent)
self.writeFile.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeFile,
text="Write information to file").grid(
row=row, column=0, columnspan=cols, sticky="w")
self.fileName = None
row += 1
self.writeLog = Tkinter.IntVar(parent)
self.writeLog.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeLog,
text="Write information to reply log").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
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 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 FitOpt_Dialog(ModelessDialog):
# Title of FitOpt plugin
title = 'FitOpt Flexible Fitting'
# Name of FitOpt plugin
name = 'FitOpt'
# Buttons of FitOpt GUI
buttons = ('Fit', 'Results', 'Close')
# Path of help guide of FitOpt plugin
help = ('fitopt.html', FitOpt)
# Name of the folder where FitOpt plugin is located
plugin_folder = 'FitOpt/'
# Path of the process of FitOpt
fitopt = plugin_folder + 'fitopt'
# Variable to keep the workspace
cwd = None
# Name of the fitted pdb generated after FitOpt process
fitted_molecule = "fitopt_fitted.pdb"
# Name of the trajectory movie
imovie = plugin_folder + "fitopt_movie.pdb"
# ---------------------------
# FitOpt Chimera Commands
# FitOpt in Chimera indicator
fitopt_chimera_opt = "--chimera"
# More PDBs
fitopt_chimera_morepdbs = "--morepdbs"
# PDB Reference
fitopt_chimera_pdb_ref = "--pdb_ref"
fitopt_chimera_pdb_ref_val = None
# Trajectory (movie)
fitopt_chimera_t = "-t"
# Fixing diagonalization
fitopt_chimera_r = "-r"
fitopt_chimera_r_val = "0"
# Rediagonalization
fitopt_chimera_re = "--rediag"
fitopt_chimera_re_val = "0"
# Coarse-grained model
fitopt_chimera_m = "-m"
fitopt_chimera_m_val = "2"
# Modes range
fitopt_chimera_n = "-n"
fitopt_chimera_n_val = "0.05"
# Advanced commands
fitopt_chimera_adv_commands = []
import tkFont
arialF = tkFont.Font(family='Arial', size=8)
arialBondF = tkFont.Font(family='Arial', size=7, weight=tkFont.BOLD)
# -------------------------------------------------
# Master function for dialog contents
#
def fillInUI(self, parent):
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
# Map selection (only Volumes)
fm = Volume_Menu(ff, 'Map: ')
fm.frame.grid(row=0, column=0, sticky='w')
self.map_menu = fm
# Resolution
rs = Hybrid.Entry(ff, 'Resolution ', 5)
rs.frame.grid(row=0, column=1, sticky='w')
self.resolution = rs.variable
# Cut-off
co = Hybrid.Entry(ff, 'Cut-off level ', 10)
co.frame.grid(row=0, column=2, sticky='w')
self.cutoff = co.variable
self.save_button = Tkinter.Button(ff,
text="From Volume Viewer",
font=self.arialBondF,
height=1,
command=self.get_cutoff)
self.save_button.grid(row=0, column=3, sticky='w')
hf = Tkinter.Frame(parent)
hf.grid(row=row, column=0, sticky='w')
row += 1
# Space
msg = Tkinter.Label(hf, anchor='w', justify='left')
msg.grid(row=2, column=0, sticky='ew')
row = row + 1
self.message_label = msg
# PDB's panel
self.pdbs = Tkinter.Frame(parent)
self.pdbs.grid(row=3, column=0, sticky='ew')
self.pdbs.columnconfigure(1, weight=1)
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fitted:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList.grid(row=row, column=0, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
self.modelList1 = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fixed:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList1.grid(row=row, column=1, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
row += 1
# Disable Results panel at first
self.results_button = self.buttonWidgets['Results']
self.results_button['state'] = 'disabled'
# ---------------------------------------------------------------------------
# Shows a message in FitOpt Plugin
#
def message(self, text):
self.message_label['text'] = text
self.message_label.update_idletasks()
# ---------------------------------------------------------------------------
# Map chosen to fit into base map.
#
def fit_map(self):
m = self.object_menu.getvalue()
from VolumeViewer import Volume
if isinstance(m, Volume):
return m
return None
# ---------------------------------------------------------------------------
# Atoms chosen in dialog for fitting.
#
def fit_atoms(self):
m = self.object_menu.getvalue()
if m == 'selected atoms':
from chimera import selection
atoms = selection.currentAtoms()
return atoms
from chimera import Molecule
if isinstance(m, Molecule):
return m.atoms
return []
# ---------------------------------------------------------------------------
# Gets the parameter values introduced by the user
#
def get_options_chimera(self):
# Model type
if 'atom' in self.model_type.get():
self.fitopt_chimera_m_val = "2"
elif '3BB2R' in self.model_type.get():
self.fitopt_chimera_m_val = "1"
else:
self.fitopt_chimera_m_val = "0"
# Number of models
if len(self.number_models.get()) > 0:
if self.mode_percentage.get() == 1:
mode = float(self.number_models.get()) / 100
if mode >= 0 and mode <= 1:
self.fitopt_chimera_n_val = str(mode)
else:
self.fitopt_chimera_n_val = str(self.number_models.get())
# Fix DoF
if '50' in self.fixing.variable.get():
self.fitopt_chimera_r_val = "0.5"
elif '75' in self.fixing.variable.get():
self.fitopt_chimera_r_val = "0.75"
elif '90' in self.fixing.variable.get():
self.fitopt_chimera_r_val = "0.9"
# Rediagonalization
if '0.1' in self.rediag.variable.get():
self.fitopt_chimera_re_val = "0.1"
elif '0.5' in self.rediag.variable.get():
self.fitopt_chimera_re_val = "0.5"
elif '1' in self.rediag.variable.get():
self.fitopt_chimera_re_val = "0.9"
# Advanced commands
if len(self.adv_commands.get()) > 0:
self.fitopt_chimera_adv_commands = self.adv_commands.get().split()
# ---------------------------------------------------------------------------
# Performs the FitOpt process
#
def Fit(self):
from chimera.replyobj import info
models = self.modelList.getvalue()
models1 = self.modelList1.getvalue()
if not models or not models1:
info('\n')
replyobj.error("No models chosen to save.\n")
return
else:
info('\n')
info('PDBs seleccionados a ajustar')
for m in models:
info('\n')
info(' - ' + m.name)
info('\n')
info('\n')
info('PDBs seleccionados a fijar')
for m in models1:
info('\n')
info(' - ' + m.name)
info('\n')
# # If a fitting is performed when Results panel is active, close it
# for widget in self.mmf.winfo_children():
# widget.destroy()
# self.results_panel.set(False)
#
# # Validation of the parameters introduced by the user
# if self.check_models() is False:
# return
#
# # Disable Fit, and Close buttons when FitOpt process is performed
# self.disable_process_buttons()
#
# # Retrieve the full plugin path
# self.plugin_path = __file__[:__file__.index(self.plugin_folder)]
#
# # -----------------------
# # Calling FitOpt process
# # -----------------------
# from subprocess import STDOUT, PIPE, Popen
# import os, sys
#
# # Get the full path of FitOpt process
# command = self.plugin_path + self.fitopt
# # Set the workspace
# self.cwd = self.plugin_path + self.plugin_folder
#
# # PDB selected in the menu
# pdbSelected = self.object_menu.getvalue()
# # Map selected in the menu
# mapSelected = self.map_menu.volume()
#
# # Get options values
# self.get_options_chimera()
#
# # Retrieve the full command to perform the fitting: fitopt + arguments
# cmd = [command, pdbSelected.openedAs[0], mapSelected.openedAs[0], self.resolution.get(), self.cutoff.get(),
# self.fitopt_chimera_m, self.fitopt_chimera_m_val,
# self.fitopt_chimera_t,
# self.fitopt_chimera_r, self.fitopt_chimera_r_val,
# self.fitopt_chimera_re, self.fitopt_chimera_re_val,
# self.fitopt_chimera_morepdbs,
# self.fitopt_chimera_n, self.fitopt_chimera_n_val] + self.fitopt_chimera_adv_commands
#
# # Execute the command with the respective arguments creating pipes between the process and Chimera
# # Pipes will be associated to the standard output and standard error required to show the process log
# # in the window
# from chimera.replyobj import info
# info('\n')
# info('Executing the FitOpt command:')
# info('\n')
# info(' '.join(cmd))
# fitopt_process = Popen(cmd, stdout=PIPE, stderr=PIPE, cwd=self.cwd, universal_newlines=True)
#
# # Text widget for process log that will showthe standard output of the process
# from Tkinter import *
# root = Tk()
# root.wm_title("FitOpt Process Log")
# S = Scrollbar(root)
# T = Text(root, height=30, width=85)
# S.pack(side=RIGHT, fill=Y)
# T.pack(side=LEFT, fill=Y)
# S.config(command=T.yview)
# T.config(yscrollcommand=S.set)
#
# # Read first line
# line = fitopt_process.stdout.readline()
# # Variables to check the process status and show its output in a friendly format to the user
# iter = False
# model_iter = False
# index_before_last_print = None
# first_ite_sec = True
#
# # Continue reading the standard output until FitOpt is finished
# # If the current line is an iteration for a model, replace in the widget the last showed
# # If it is a new model or is part of the FitOpt process, inserts the line at the end of the widget
# while line:
# if len(line.strip()) == 0:
# line = fitopt_process.stdout.readline()
# continue
# if iter is False or (iter is True and 'NMA' in line):
# T.insert(END, line)
# model_iter = True
# elif iter is True and 'sec' in line:
# if first_ite_sec is True:
# T.insert(END, line)
# model_iter = True
# else:
# T.delete(index_before_last_print + "-1c linestart", index_before_last_print)
# T.insert(END, line)
# first_ite_sec = False
# elif model_iter is True:
# index_before_last_print = T.index(END)
# T.insert(END, line)
# model_iter = False
# elif iter is True and 'sec' not in line:
# T.delete(index_before_last_print + "-1c linestart", index_before_last_print)
# T.insert(END, line)
# T.update()
# T.yview(END)
# line = fitopt_process.stdout.readline()
# if ('NMA_time' in line and 'Score' in line):
# iter = True
# if 'sec' in line and iter is True:
# first_ite_sec = True
# model_iter = True
# if index_before_last_print is not None:
# T.delete(index_before_last_print + "-1c linestart", index_before_last_print)
# index_before_last_print = T.index(END)
# if 'Convergence' in line:
# iter = False
#
# T.insert(END, "\n\n --> FitOpt Process has finished. Check 'Results' button to visualize solution. <--\n")
# T.update()
# T.yview(END)
#
# # When FitOpt process is finished, the results are set into the Results panel...
# self.fill_results()
# # and the plugin buttons are enabled again
# self.enable_process_buttons()
# ---------------------------------------------------------------------------
# Fill the Results panel with the corresponding components
#
def fill_results(self):
# Button to switch between the original molecule and the fitted one with FitOpt
import Tkinter
self.save_button = Tkinter.Button(self.mmf,
text="Show fitted molecule",
command=self.switch_original_fitted)
self.save_button.grid(row=0, column=0, sticky='w')
# Button to copy to the Model Panel the fitted molecule
self.save_fitted = Tkinter.Button(self.mmf,
text="Copy fitted molecule",
command=self.save_fitted_molecule)
self.save_fitted.grid(row=0, column=1, sticky='w')
self.save_fitted['state'] = 'disabled'
# Button to open the MD Movie created by iMODTFIT with the model trajectories
self.open_md_movie = Tkinter.Button(self.mmf,
text="Open movie",
command=self.open_movie)
self.open_md_movie.grid(row=1, column=0, sticky='w')
# ---------------------------------------------------------------------------
# Switchs between the original molecule and the fitted one with FitOpt
#
def switch_original_fitted(self):
if self.save_button["text"] == "Show fitted molecule":
# Show fitted molecule
self.show_fitted_molecule(True)
self.save_button["text"] = "Show original molecule"
self.save_fitted['state'] = 'normal'
else:
# Show original molecule
self.show_fitted_molecule(False)
self.save_button["text"] = "Show fitted molecule"
self.save_fitted['state'] = 'disabled'
# ---------------------------------------------------------------------------
# Reads the coordinates of the fitted molecule and updates the original
# molecule position to show the fitting made by FitOpt
#
def show_fitted_molecule(self, pdb_name):
from chimera.replyobj import info
info('\n')
info('Showing fitted ' + pdb_name + ' molecule')
# ---------------------------------------------------------------------------
# Makes a copy to the Model Panel of the fitted molecule
#
def save_fitted_molecule(self):
# Get opened molecule (the one selected in the menu)
m = self.object_menu.getvalue()
# Make copy using the copy_molecule native functionality from Chimera
from Molecule import copy_molecule
mc = copy_molecule(m)
# Set copy name
mc.name = m.name.split('.')[0] + '_fitopt.pdb'
# Add copy to list of open models
chimera.openModels.add([mc])
# ---------------------------------------------------------------------------
# Opens the MD movie created by iMODTFIT with the model trajectories
#
def open_movie(self):
# Import the native dialog MovieDialog from Chimera
from Movie.gui import MovieDialog
# import the loadEnsemble native functionality from Chimera to load the movie
from Trajectory.formats.Pdb import loadEnsemble
# Load the movie created by FitOpt
movie = self.plugin_path + self.imovie
loadEnsemble(("single", movie), None, None, MovieDialog)
# ---------------------------------------------------------------------------
# Disables the the FitOpt GUI Fit, Close and Results buttons
#
def disable_process_buttons(self):
self.fit_button = self.buttonWidgets['Fit']
self.fit_button['state'] = 'disabled'
self.options_button['state'] = 'disabled'
self.close_ch_button = self.buttonWidgets['Close']
self.close_ch_button['state'] = 'disabled'
self.results_button['state'] = 'disabled'
# ---------------------------------------------------------------------------
# Enables the the FitOpt GUI Fit, Close and Results buttons
#
def enable_process_buttons(self):
self.fit_button = self.buttonWidgets['Fit']
self.fit_button['state'] = 'normal'
self.options_button['state'] = 'normal'
self.close_ch_button = self.buttonWidgets['Close']
self.close_ch_button['state'] = 'normal'
self.results_button['state'] = 'normal'
# ---------------------------------------------------------------------------
# Results button is pressed
#
def Results(self):
self.results_panel.set(not self.results_panel.get())
# -----------------------------------------------------------------------------
# Gets the cut-off level value from the Volume Viewer dialog
# Useful when the user does not know an appropiate resolution and plays
# with the map density in this dialog.
#
def get_cutoff(self):
# validate if the map is loaded/choosed
bmap = self.map_menu.data_region()
if bmap is None:
self.message('Choose map.')
return
# Import the native dialog Volume Viewer from Chimera
from chimera import dialogs
vdlg = dialogs.find("volume viewer")
# Get the cut-off level from the Volume Viewer dialog
cutoff_panel = vdlg.thresholds_panel.threshold.get()
# Set the cut-off value in FitOpt with the previous value
self.cutoff.set(cutoff_panel)
self.message("")
# -----------------------------------------------------------------------------
# Validates the values of the parameteres introduced by the users.
# Moreover, check if molecule and maps are loaded
#
def check_models(self):
fatoms = self.fit_atoms()
fmap = self.fit_map()
bmap = self.map_menu.data_region()
if (len(fatoms) == 0 and fmap is None) or bmap is None:
self.message('Choose model and map.')
return False
if fmap == bmap:
self.message('Chosen maps are the same.')
return False
if len(self.cutoff.get()) == 0:
self.message('Cutoff must be defined.')
return False
if len(self.resolution.get()) == 0:
self.message('Resolution must be defined.')
return False
if float(self.resolution.get()) < 0 or float(
self.resolution.get()) >= 60:
self.message('Resolution must be less than 100.')
return False
self.message("")
return True
# ----------------------------------------------
# Validates if a string represents an integer
#
def representsInt(self, number):
try:
int(number)
return True
except ValueError:
return False
# ----------------------------------------------
# Validates if a string represents an integer
#
def representsFloat(self, number):
try:
float(number)
return True
except ValueError:
return False
class AddHDialog(ModelessDialog):
name = "add hydrogens"
help = "ContributedSoftware/addh/addh.html"
buttons = ('OK', 'Close')
default = 'OK'
def __init__(self, title="Add Hydrogens", models=None,
useHBonds=None, cb=None, **kw):
self.title = title
self.cb = cb
self.startModels = models
if useHBonds is None:
self.startUseHBonds = prefs[HBOND_GUIDED]
else:
self.startUseHBonds = useHBonds
ModelessDialog.__init__(self, **kw)
def fillInUI(self, parent):
import Pmw, Tkinter
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent, labelpos='w',
label_text="Add hydrogens to:",
listbox_selectmode='extended',
selectioncommand=self._updateHisListing)
if self.startModels:
self.molList.setvalue(self.startModels)
self.molList.grid(row=0, column=0, sticky="news")
parent.columnconfigure(0, weight=1)
parent.rowconfigure(0, weight=1)
grp = Pmw.Group(parent, tag_text="Method", hull_padx=2)
grp.grid(row=1, column=0, sticky="ew")
self.useHBondsVar = Tkinter.IntVar(parent)
self.useHBondsVar.set(self.startUseHBonds)
Tkinter.Radiobutton(grp.interior(), variable=self.useHBondsVar,
value=False, text="steric only"
).grid(row=0, sticky='w')
Tkinter.Radiobutton(grp.interior(), variable=self.useHBondsVar,
value=True, text="also consider H-bonds (slower)"
).grid(row=1, sticky='w')
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Histidine Protonation")
self.hisGroup.grid(row=2, column=0, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue-name-based\n"
"(HIS/HID/HIE/HIP = unspecified/delta/epsilon/both)",
command=self._switchHisList, justify="left").grid(
row=0, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList,
).grid(row=1, sticky='w')
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="default", command=self._switchHisList,
text="Unspecified (determined by method)"
).grid(row=3, sticky='w')
def _clearAll(self):
for v, cmd in self._vars:
if v.get():
v.set(0)
cmd()
def _selectAll(self):
for v, cmd in self._vars:
if not v.get():
v.set(1)
cmd()
def _switchHisList(self):
if not hasattr(self, 'hisListing'):
if self.hisProtVar.get() != "pick":
return
self.hisListingData = {}
import Tix, Tkinter
self.hisFrame = Tkinter.Frame(self.hisGroup.interior())
Tkinter.Label(self.hisFrame, text="If neither delta"
" nor epsilon is selected\nthen chosen method"
" determines protonation").grid(row=0,
column=0, columnspan=2)
self.hisListing = Tix.ScrolledHList(self.hisFrame,
width="3i",
options="""hlist.columns 4
hlist.header 1
hlist.indicator 1""")
self.hisListing.hlist.configure(
selectbackground=self.hisListing['background'],
selectborderwidth=0)
self.hisListing.grid(row=1, column=0, columnspan=2,
sticky="nsew")
self.hisFrame.rowconfigure(1, weight=1)
self.hisFrame.columnconfigure(0, weight=1)
self.hisFrame.columnconfigure(1, weight=1)
hlist = self.hisListing.hlist
hlist.header_create(0, itemtype="text", text="Model")
hlist.header_create(1, itemtype="text", text="Residue")
hlist.header_create(2, itemtype="text", text="Delta")
hlist.header_create(3, itemtype="text", text="Epsilon")
self._checkButtonStyle = Tix.DisplayStyle("window",
background=hlist['background'],
refwindow=self.hisListing, anchor='center')
self._updateHisListing()
Tkinter.Button(self.hisFrame, text="Select All",
pady=0, highlightthickness=0,
command=self._selectAll).grid(row=2, column=0)
Tkinter.Button(self.hisFrame, text="Clear All",
pady=0, highlightthickness=0,
command=self._clearAll).grid(row=2, column=1)
if self.hisProtVar.get() == "pick":
self._pickText.set("Individually chosen:")
self.hisFrame.grid(row=2, sticky="nsew")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
interior.rowconfigure(2, weight=1)
self.uiMaster().rowconfigure(2, weight=4)
else:
self._pickText.set("Individually chosen...")
self.hisFrame.grid_forget()
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=0)
interior.rowconfigure(2, weight=0)
self.uiMaster().rowconfigure(2, weight=0)
def _toggleDelta(self, res):
old = self.hisListingData[res]
if old == "HIS":
new = "HID"
elif old == "HID":
new = "HIS"
elif old == "HIE":
new = "HIP"
else:
new = "HIE"
self.hisListingData[res] = new
def _toggleEpsilon(self, res):
old = self.hisListingData[res]
if old == "HIS":
new = "HIE"
elif old == "HID":
new = "HIP"
elif old == "HIE":
new = "HIS"
else:
new = "HID"
self.hisListingData[res] = new
def _updateHisListing(self):
if not hasattr(self, 'hisListing'):
return
self._updateHisListingData()
hlist = self.hisListing.hlist
on = self.hisListing.tk.call('tix', 'getimage', 'ck_on')
off = self.hisListing.tk.call('tix', 'getimage', 'ck_off')
hlist.delete_all()
import Tkinter
row = 0
self._vars = []
for m in self.molList.getvalue():
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
hisType = self.hisListingData[r]
except KeyError:
self.hisListingData[r] = hisType = "HIS"
hlist.add(row, itemtype="text", text="%s (%s)"
% (m.name, m.oslIdent()))
hlist.item_create(row, 1, itemtype="text",
text=r.oslIdent(
start=chimera.SelResidue))
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HID", "HIP"])
cmd = lambda r=r: self._toggleDelta(r)
self._vars.append((var, cmd))
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 2, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HIE", "HIP"])
cmd = lambda r=r: self._toggleEpsilon(r)
self._vars.append((var, cmd))
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 3, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
row += 1
def _updateHisListingData(self):
newData = {}
for m in self.molList.getvalue():
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
newData[r] = self.hisListingData[r]
except KeyError:
newData[r] = r.type
self.hisListingData = newData
def Apply(self):
from chimera import openModels, Molecule
from AddH import simpleAddHydrogens, hbondAddHydrogens
from unknownsGUI import initiateAddHyd
prefs[HBOND_GUIDED] = self.useHBondsVar.get()
method = [simpleAddHydrogens, hbondAddHydrogens][
prefs[HBOND_GUIDED]]
if self.hisProtVar.get() == "name":
hisScheme = None
elif self.hisProtVar.get() == "pick":
hisScheme = self.hisListingData
else:
hisScheme = {}
initiateAddHyd(self.molList.getvalue(), addFunc=method,
hisScheme=hisScheme, okCB=self.cb)
def fillInUI(self, parent):
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
# Map selection (only Volumes)
fm = Volume_Menu(ff, 'Map: ')
fm.frame.grid(row=0, column=0, sticky='w')
self.map_menu = fm
# Resolution
rs = Hybrid.Entry(ff, 'Resolution ', 5)
rs.frame.grid(row=0, column=1, sticky='w')
self.resolution = rs.variable
# Cut-off
co = Hybrid.Entry(ff, 'Cut-off level ', 10)
co.frame.grid(row=0, column=2, sticky='w')
self.cutoff = co.variable
self.save_button = Tkinter.Button(ff,
text="From Volume Viewer",
font=self.arialBondF,
height=1,
command=self.get_cutoff)
self.save_button.grid(row=0, column=3, sticky='w')
hf = Tkinter.Frame(parent)
hf.grid(row=row, column=0, sticky='w')
row += 1
# Space
msg = Tkinter.Label(hf, anchor='w', justify='left')
msg.grid(row=2, column=0, sticky='ew')
row = row + 1
self.message_label = msg
# PDB's panel
self.pdbs = Tkinter.Frame(parent)
self.pdbs.grid(row=3, column=0, sticky='ew')
self.pdbs.columnconfigure(1, weight=1)
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fitted:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList.grid(row=row, column=0, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
self.modelList1 = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fixed:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList1.grid(row=row, column=1, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
row += 1
# Disable Results panel at first
self.results_button = self.buttonWidgets['Results']
self.results_button['state'] = 'disabled'
class Interface(ModelessDialog):
title = "Compute Interface Surface"
help = "ContributedSoftware/intersurf/intersurf.html"
def fillInUI(self, parent):
self.notebook = Pmw.NoteBook(parent)
self.notebook.pack(fill="both", expand=True)
page = self.notebook.add("Molecules")
self.molChooser = MoleculeScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.molChooser.pack(fill="both", expand=True)
page = self.notebook.add("Chains")
self.chainChooser = MoleculeChainScrolledListBox(page,
listbox_selectmode="extended",
autoselect="single")
self.chainChooser.pack(fill="both", expand=True)
self.outputOptions = Pmw.RadioSelect(parent,
pady=0,
buttontype="checkbutton",
orient="vertical")
self.outputOptions.pack(fill="x", expand=False)
self.outputOptions.add("solid", text="Solid surface (rather than mesh)")
self.outputOptions.add("track", text="Reuse last surface (if any)")
self.outputOptions.add("atoms", text="Select interface atoms")
self.outputOptions.add("prune", text="Residue centroid distance pruning")
self.outputOptions.setvalue(["solid", "track"])
self.pruneDistance = Pmw.EntryField(parent,
labelpos="w",
label_text="Prune distance:",
value="30.0",
validate=self._validatePruneDistance)
self.pruneDistance.pack(fill="x", expand=False)
self.moleculeBias = Pmw.Counter(parent,
labelpos="w",
label_text="Molecule bias:",
datatype="real",
increment = 0.1,
entryfield_value="0.5",
entryfield_validate={'validator' : 'real',
'min' : '0.0', 'max' : '1.0',
'separator' : '.'})
self.moleculeBias.pack(fill="x", expand=False)
histKw = {
'minlabel': True,
'maxlabel': True,
'scaling': 'linear',
}
self.histogram = MarkedHistogram(parent, **histKw)
self.histogramMarkers = self.histogram.addmarkers(activate=True,
coordtype='relative')
self.histogramMarkers.extend([
((1.0, 0.0), (0.0, 0.0, 0.33, 1.0)),
((0.0, 0.0), (1.0, 0.0, 0.0, 1.0))])
self.histogram.pack(expand=True, fill="both")
self._trackedPiece = None
self._trackedModel = None
self.models = {}
chimera.openModels.addRemoveHandler(self._removeModel, None)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.saveSession, None)
chimera.triggers.addHandler("Molecule",
self._moleculeChanged, None)
def _validatePruneDistance(self, text):
if len(text) == 0:
return Pmw.PARTIAL
try:
float(text)
except:
return Pmw.ERROR
return Pmw.OK
def _show_geometry(self, vertices, triangles, vertex_colors, solid=0, track=0):
import numpy
varray = numpy.array(vertices, numpy.float32)
tarray = numpy.array(triangles, numpy.int32)
carray = numpy.array(vertex_colors, numpy.float32)
import chimera
if track and self._trackedPiece:
sm = self._trackedModel
g = self._trackedPiece
g.geometry = varray, tarray
g.vertexColors = carray
if solid:
g.displayStyle = g.Solid
else:
g.displayStyle = g.Mesh
else:
import _surface
sm = _surface.SurfaceModel()
g = sm.addPiece(varray, tarray, (1, 1, 1, 1))
g.vertexColors = carray
if solid:
g.displayStyle = g.Solid
else:
g.displayStyle = g.Mesh
sm.name = "Interface Surface"
chimera.openModels.add([sm])
self._trackedPiece = g
self._trackedModel = sm
sm.openState.xform = chimera.Xform.identity()
self.models[sm] = (vertices, triangles, vertex_colors, solid)
return sm, g
def Apply(self):
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = self.chainChooser.getvalue()
if not target:
raise chimera.UserError("Please select two molecules/chains")
if len(target) != 2:
raise chimera.UserError("Please select exactly two molecules/chains")
opts = self.outputOptions.getvalue()
solid = "solid" in opts
prune = "prune" in opts
track = "track" in opts
selAtoms = "atoms" in opts
if not self.moleculeBias.valid():
raise chimera.UserError("Please enter a valid bias toward the second molecule")
bias = float(self.moleculeBias.getvalue())
if prune:
if not self.pruneDistance.valid():
raise chimera.UserError("Please enter a valid prune distance")
pruneDistance = float(self.pruneDistance.getvalue())
else:
pruneDistance = 0
self.doApply(target, solid, track, selAtoms,
bias, prune, pruneDistance)
def doApply(self, target, solid, track, selAtoms,
bias, prune, pruneDistance):
m1, m2 = target
if prune:
m1_list = SurfMaker.GetAtomList(m1, m2, pruneDistance)
m2_list = SurfMaker.GetAtomList(m2, m1, pruneDistance)
else:
m1_list = SurfMaker.GetAtomList(m1)
m2_list = SurfMaker.GetAtomList(m2)
if not m1_list or not m2_list:
raise chimera.UserError("No interface surface found")
p = SurfMaker.UnpackIntersurfData(m1_list, m2_list)
tetras = SurfMaker.ComputeTetrahedralization(p)
surfPoints, surfTriangles, surfAtoms = SurfMaker.ComputeSurface(p, tetras, bias)
surfMetric = [ getDistance(x[0], x[1]) for x in surfAtoms ]
lo = min(surfMetric)
hi = max(surfMetric)
scale = hi - lo
markers = [ (lo + m['xy'][0] * scale, m['rgba'])
for m in self.histogramMarkers ]
surfColors = [ getHistogramColor(x, markers)
for x in surfMetric ]
self.histogramData = (lo, hi, surfMetric)
def myMakeBars(numBins, data=self.histogramData):
return makeBars(numBins, data)
self.histogram["datasource"] = (lo, hi, myMakeBars)
self._show_geometry(surfPoints, surfTriangles, surfColors, solid, track)
if selAtoms:
from chimera import selection
atomSet = set([])
for a1, a2 in surfAtoms:
atomSet.add(a1)
atomSet.add(a2)
sel = selection.ItemizedSelection()
sel.add(atomSet)
sel.addImplied(vertices=False)
selection.setCurrent(sel)
def _removeModel(self, trigger, data, models):
for m in models:
if self._trackedModel is m:
self._trackedModel = None
self._trackedPiece = None
try:
del self.models[m]
except KeyError:
pass
def _moleculeChanged(self, trigger, data, models):
if 'activeCoordSet changed' not in models.reasons:
return
pageName = self.notebook.getcurselection()
if pageName == "Molecules":
target = self.molChooser.getvalue()
elif pageName == "Chains":
target = [ c.molecule for c in self.chainChooser.getvalue() ]
else:
return
for m in models.modified:
if m in target:
break
else:
return
self.Apply()
def saveSession(self, trigger, data, file):
isMapped = self.uiMaster().winfo_ismapped()
if not isMapped and not self.models:
# Not visible and no displayed surfaces
return
from SessionUtil import stateclasses, objecttree
restoring_code = \
"""
def restoreIntersurfSession(state):
import SimpleSession
from Intersurf import Intersurf
SimpleSession.registerAfterModelsCB(Intersurf.restoreSession, state)
risArgs = (%s)
try:
restoreIntersurfSession(risArgs)
except:
reportRestoreError("Error restoring Intersurf extension")
"""
pageName = self.notebook.getcurselection()
chosenMolecules = self.molChooser.getcurselection()
chosenChains = self.chainChooser.getcurselection()
opts = self.outputOptions.getvalue()
pruneDistance = self.pruneDistance.getvalue()
bias = self.moleculeBias.getvalue()
if isinstance(self.histogram["datasource"], basestring):
histogramData = self.histogram["datasource"]
else:
histogramData = self.histogramData
markerValues = []
markers, selectedMarker = self.histogram.currentmarkerinfo()
if markers:
for m in markers:
markerValues.append((m["xy"], m["rgba"]))
ms = stateclasses.Model_State()
modelData = []
trackedIndex = -1
n = 0
for m, v in self.models.iteritems():
if self._trackedModel is m:
trackedIndex = n
ms.state_from_model(m)
bt = objecttree.instance_tree_to_basic_tree(ms)
modelData.append((v, bt))
n += 1
state = (pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
histogramData, markerValues,
modelData, trackedIndex, isMapped)
file.write(restoring_code % repr(state))
def restoreSession(self, state):
from SessionUtil import stateclasses, objecttree
if len(state) == 10:
(pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
dataSource, markerValues,
modelData, trackedIndex) = state
if modelData:
isMapped = True
else:
isMapped = False
else:
(pageName, chosenMolecules, chosenChains, opts,
pruneDistance, bias,
histogramData, markerValues,
modelData, trackedIndex, isMapped) = state
# Call get method to make sure items are updated
self.molChooser.get()
self.molChooser.setvalue(chosenMolecules)
self.chainChooser.get()
self.chainChooser.setvalue(chosenChains)
self.notebook.selectpage(pageName)
self.outputOptions.setvalue(list(opts))
self.pruneDistance.setvalue(pruneDistance)
self.moleculeBias.setvalue(bias)
if isinstance(histogramData, basestring):
dataSource = histogramData
else:
lo, hi, surfMetric = histogramData
self.histogramData = (lo, hi, surfMetric)
def myMakeBars(numBins, data=self.histogramData):
return makeBars(numBins, data)
dataSource = (lo, hi, myMakeBars)
self.histogram["datasource"] = dataSource
if markerValues:
oldMarkers = self.histogram.currentmarkerinfo()[0]
newMarkers = self.histogram.addmarkers()
newMarkers.extend(markerValues)
self.histogram.deletemarkers(oldMarkers)
self.histogramMarkers = newMarkers
trackedModel = None
trackedPiece = None
nameToClass = {
"Model_State": stateclasses.Model_State,
"Xform_State": stateclasses.Xform_State,
}
for n, mState in enumerate(modelData):
if len(mState) == 2:
v, bt = mState
else:
v = mState
bt = None
sm, g = self._show_geometry(*v)
if trackedIndex == n:
trackedModel = sm
trackedPiece = g
if bt is not None:
ms = objecttree.basic_tree_to_instance_tree(bt,
nameToClass)
ms.restore_state(sm)
if trackedModel:
self._trackedModel = trackedModel
self._trackedPiece = trackedPiece
if not isMapped:
self.Close()
class PoPMuSiCExtension(TangramBaseDialog):
buttons = ('Run', 'Close')
def __init__(self, *args, **kwargs):
# GUI init
self.title = 'Tangram PoPMuSiC input'
self.controller = None
# Variables
self._popsfile = tk.StringVar()
self._popfile = tk.StringVar()
# Fire up
super(PoPMuSiCExtension, self).__init__(*args, **kwargs)
def fill_in_ui(self, parent):
note_frame = tk.LabelFrame(self.canvas, text='How to run PoPMuSiC')
tk.Label(note_frame,
text="PoPMuSiC is a web service!\nYou must register "
"and run the jobs from:").pack(padx=5, pady=5)
self.ui_web_btn = tk.Button(
note_frame,
text="PoPMuSiC web interface",
command=lambda *a: web.open_new(r"http://soft.dezyme.com/"))
self.ui_web_btn.pack(padx=5, pady=5)
input_frame = tk.LabelFrame(
self.canvas, text='Select molecule and PoPMuSiC output files')
input_frame.rowconfigure(0, weight=1)
input_frame.columnconfigure(1, weight=1)
self.ui_molecules = MoleculeScrolledListBox(input_frame)
self.ui_molecules.grid(row=0,
columnspan=3,
padx=5,
pady=5,
sticky='news')
entries = [('popfile', 'POP file', '.pop'),
('popsfile', 'POPS file', '.pops')]
for i, (var, label, ext) in enumerate(entries):
# Label
tk.Label(input_frame, text=label).grid(row=i + 1,
column=0,
padx=3,
pady=3,
sticky='e')
# Field entry
stringvar = getattr(self, '_' + var)
entry = tk.Entry(input_frame, textvariable=stringvar)
entry.grid(row=i + 1, column=1, padx=3, pady=3, sticky='news')
setattr(self, 'ui_' + var + '_entry', entry)
# Button
button = tk.Button(
input_frame,
text='...',
command=lambda v=stringvar, e=ext: self._browse_cb(v, e))
button.grid(row=i + 1, column=2, padx=3, pady=3)
setattr(self, 'ui_' + var + '_button', button)
note_frame.pack(fill='x', padx=5, pady=5)
input_frame.pack(expand=True, fill='both', padx=5, pady=5)
def Run(self):
pass
def Close(self):
global ui
ui = None
super(PoPMuSiCExtension, self).Close()
def _browse_cb(self, var, extension):
path = askopenfilename()
if os.path.isfile(path):
var.set(path)
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')
class RainbowDialog(ModelessDialog):
title = 'Rainbow'
buttons = ('OK', 'Apply', 'Defaults', 'Close',)
default = 'OK'
name = "rainbow models"
help = "UsersGuide/modelpanel.html#rainbow"
def __init__(self):
self.prefs = preferences.addCategory("Rainbow models",
preferences.HiddenCategory,
optDict={ "colors": defaultColors })
ModelessDialog.__init__(self)
def configure(self, models=[], target=None):
self.molListBox.setvalue(models)
if target:
self.colorChangeVar.set(target)
def fillInUI(self, parent):
self.parent = parent
Tkinter.Label(parent, text="Change color every:").grid(
row=0, rowspan=3, column=0, sticky='w')
self.colorChangeVar = Tkinter.StringVar(parent)
self.colorChangeVar.set("residues")
Tkinter.Radiobutton(parent, text='residue', value='residues',
variable=self.colorChangeVar).grid(
row=0, column=1, sticky='w')
Tkinter.Radiobutton(parent, text='chain', value='chains',
variable=self.colorChangeVar).grid(
row=1, column=1, sticky='w')
Tkinter.Radiobutton(parent, text='model', value='models',
variable=self.colorChangeVar).grid(
row=2, column=1, sticky='w')
group = Pmw.Group(parent, tag_text='Color range')
group.grid(row=3, column=0, columnspan=2)
self.wells = []
for i, color in enumerate(self.prefs["colors"]):
well = ColorWell(group.interior(), color=color,
noneOkay=1)
well.grid(row=0, column=i)
self.wells.append(well)
from chimera.widgets import MoleculeScrolledListBox
self.molListBox = MoleculeScrolledListBox(parent,
listbox_selectmode="extended", labelpos="n",
label_text="Models")
self.molListBox.grid(row=0, column=2, rowspan=4, sticky="news")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(2, weight=1)
def Apply(self):
colors = []
allColors = []
for well in self.wells:
color = well.rgba
allColors.append(color)
if color is None:
continue
colors.append(color)
if not colors:
replyobj.error("No colors for rainbow")
return
rainbowModels(self.molListBox.getvalue(),
changeAt=self.colorChangeVar.get(),
colors=colors)
self.prefs["colors"] = allColors
def Defaults(self):
for i, color in enumerate(defaultColors):
self.wells[i].showColor(color=color)
def fill_in_ui(self, parent):
# Select an input menu: Radio buttons
self.ui_input_frame = tk.LabelFrame(self.canvas, text='Input mode')
self.ui_input_frame.pack(expand=True, fill='x', padx=5, pady=5)
self.ui_input_frame.columnconfigure(0, weight=1)
self.ui_input_choice_frame = tk.Frame(self.ui_input_frame)
self.ui_input_choice_frame.grid(row=0, sticky='we')
self.ui_input_choice_molecules = tk.Radiobutton(
self.ui_input_choice_frame,
variable=self.var_input_choice,
text='Molecules',
value='molecules',
command=self._input_choice_cb)
self.ui_input_choice_selection = tk.Radiobutton(
self.ui_input_choice_frame,
variable=self.var_input_choice,
text='Selection',
value='selection',
command=self._input_choice_cb)
self.ui_input_choice_molecules.pack(side='left')
self.ui_input_choice_selection.pack(side='left')
self.ui_input_choice_molecules.select()
# Mode A: Opened molecules
self.ui_input_molecules_frame = tk.Frame(self.ui_input_frame)
self.ui_input_molecules_frame.grid(row=1, sticky='news')
self.ui_input_molecules_frame.columnconfigure(0, weight=1)
self.ui_input_molecules = MoleculeScrolledListBox(
self.ui_input_molecules_frame,
selectioncommand=self._on_selection_changed,
listbox_selectmode="extended")
self.ui_input_molecules.pack(expand=True, fill='x', padx=5)
# Mode B: Current selection
items = ['Current selection'] + sorted(
chimera.selection.savedSels.keys())
self.ui_input_named_selections = OptionMenu(
self.ui_input_molecules_frame, command=None, items=items)
self.input_new_named_atom_selection = None # Text field + 'Create button'
# More options
self.ui_input_intermolecular_frame = tk.Frame(self.ui_input_frame)
self.ui_input_intermolecular_frame.grid(row=2)
self.ui_input_intermolecular_check = tk.Checkbutton(
self.ui_input_intermolecular_frame,
text='Filter out % of intramolecular',
variable=self.var_input_intermolecular_enabled,
command=self._intermolecular_cb,
state='disabled')
self.ui_input_intermolecular_check.pack(side='left')
self.ui_input_intermolecular_field = tk.Entry(
self.ui_input_intermolecular_frame,
textvariable=self.var_input_intermolecular,
state='disabled',
width=3)
self.ui_input_intermolecular_field.pack(side='left')
# Review input data
self.ui_input_summary_label = tk.Label(
self.ui_input_frame, textvariable=self.var_input_summary)
self.ui_input_summary_label.grid(row=3)
# NCIPlot launcher
self.ui_nciplot_frame = tk.Frame(self.canvas)
self.ui_nciplot_frame.pack()
self.ui_config_btn = tk.Button(self.ui_nciplot_frame,
text='Configure',
command=self._configure_dialog)
self.ui_config_btn.pack(side='left')
# Configure Volume Viewer
self.ui_settings_frame = tk.LabelFrame(self.canvas,
text='Customize display',
padx=5,
pady=5)
self.ui_levels_lbl = tk.Label(self.ui_settings_frame, text='Levels: ')
self.ui_levels_lbl.grid(row=0, column=0)
self.ui_settings_isovalue_1 = tk.Entry(
self.ui_settings_frame,
textvariable=self.var_settings_isovalue_1,
width=10)
self.ui_settings_isovalue_1.grid(row=0, column=1, sticky='ew')
self.ui_settings_isovalue_2 = tk.Entry(
self.ui_settings_frame,
textvariable=self.var_settings_isovalue_2,
width=10)
self.ui_settings_isovalue_2.grid(row=0, column=2, sticky='ew')
self.ui_settings_update_btn = tk.Button(self.ui_settings_frame,
text='Update',
command=self._update_surface)
self.ui_settings_update_btn.grid(row=0,
column=3,
rowspan=2,
sticky='news')
self.ui_settings_color_palette = OptionMenu(
self.ui_settings_frame,
initialitem=3,
label_text='Colors: ',
labelpos='w',
items=sorted(standard_color_palettes.keys()))
self.ui_settings_color_palette.grid(row=1,
column=0,
columnspan=3,
sticky='we')
self.ui_report_btn = tk.Checkbutton(
self.ui_settings_frame,
text=u'Report \u03BB\u2082\u22C5\u03C1\u22C5100 value at cursor',
command=self._report_values_cb,
variable=self.var_settings_report)
self.ui_report_btn.grid(row=2, column=0, columnspan=3)
self.ui_reported_value = tk.Entry(self.ui_settings_frame,
textvariable=self.var_reported_value,
state='readonly',
width=8)
self.ui_reported_value.grid(row=2, column=3, sticky='we')
# Plot figure
self.ui_plot_frame = tk.LabelFrame(
self.canvas,
text=u'Plot RDG vs density (\u03BB\u2082\u22C5\u03C1)',
padx=5,
pady=5)
self.ui_plot_button = tk.Button(self.ui_plot_frame,
text='Plot',
command=self._plot)
self.ui_plot_button.grid(row=0)
self.ui_plot_figure = Figure(figsize=(5, 5),
dpi=100,
facecolor='#D9D9D9')
self.ui_plot_subplot = self.ui_plot_figure.add_subplot(111)
self.ui_plot_widget_frame = tk.Frame(self.ui_plot_frame)
self.ui_plot_widget_frame.grid(row=1)
self.ui_plot_widget = FigureCanvasTkAgg(
self.ui_plot_figure, master=self.ui_plot_widget_frame)
# self.plot_cursor = Cursor(self.plot_subplot, useblit=True, color='black', linewidth=1)
# self.plot_figure.canvas.mpl_connect('button_press_event', self._on_plot_click)
# Register and map triggers, callbacks...
chimera.triggers.addHandler('selection changed',
self._on_selection_changed, None)
self.nciplot_run = self.buttonWidgets['Run']
self.buttonWidgets['Save']['state'] = 'disabled'
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)
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()