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 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 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')
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):
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')
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')
def fillInUI(self, parent):
import Pmw, Tkinter
row = 0
Tkinter.Label(parent, text="Create axis for...").grid(row=row,
sticky='w')
row += 1
self.modeVar = Tkinter.IntVar(parent)
self.modeVar.set(self.MODE_HELICES)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='nsew')
row += 1
Tkinter.Radiobutton(f,
text="Each helix in:",
command=self._helixCB,
variable=self.modeVar,
value=self.MODE_HELICES).grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(f,
listbox_selectmode='extended')
self.molList.grid(row=0, column=1, sticky="nsew")
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
f.rowconfigure(0, weight=1)
f.columnconfigure(1, weight=1)
f = Tkinter.Frame(parent)
f.grid(row=row, sticky='w')
row += 1
Tkinter.Radiobutton(f,
text="Selected atoms (axis name:",
command=self._selCB,
variable=self.modeVar,
value=self.MODE_SELECTION).grid(row=0, column=0)
self.axisNameVar = Tkinter.StringVar(parent)
self.axisNameVar.set("axis")
Tkinter.Entry(f, textvariable=self.axisNameVar,
width=10).grid(row=0, column=1)
Tkinter.Label(f, text=")").grid(row=0, column=2)
paramGroup = Pmw.Group(parent, tag_text="Axis Parameters")
paramGroup.grid(row=row, column=0)
row += 1
paramFrame = paramGroup.interior()
prow = 0
butFrame = Tkinter.Frame(paramFrame)
butFrame.grid(row=prow, column=0, columnspan=3)
prow += 1
self.massWeighting = Tkinter.IntVar(parent)
self.massWeighting.set(False)
self._mwButton = Tkinter.Checkbutton(butFrame,
command=self._mwCB,
text="Mass weighting",
variable=self.massWeighting)
self._mwButton.grid(row=0, column=0, sticky='w')
self._mwButton.grid_remove()
self.helixCorrection = Tkinter.IntVar(parent)
self.helixCorrection.set(True)
Tkinter.Checkbutton(butFrame,
text="Use helical correction",
command=self._hcCB,
variable=self.helixCorrection).grid(row=1,
column=0,
sticky='w')
self.replaceExisting = Tkinter.IntVar(parent)
self.replaceExisting.set(True)
Tkinter.Checkbutton(butFrame,
text="Replace existing axes",
variable=self.replaceExisting).grid(row=2,
column=0,
sticky='w')
f = Tkinter.Frame(paramFrame)
f.grid(row=prow, column=0, columnspan=3)
prow += 1
from chimera.tkoptions import ColorOption, FloatOption
self.colorOpt = ColorOption(
f,
prow,
"Color",
None,
None,
balloon="Axis color. If No Color, then the axis"
" will be colored to match the structure")
Tkinter.Label(paramFrame, text="Radius:").grid(row=prow,
column=0,
rowspan=2)
self.fixedRadiusVar = Tkinter.IntVar(parent)
self.fixedRadiusVar.set(False)
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=False).grid(row=prow, column=1)
Tkinter.Label(paramFrame,
text="average axis-atom distance").grid(row=prow,
column=2,
sticky='w')
Tkinter.Radiobutton(paramFrame,
variable=self.fixedRadiusVar,
padx=0,
value=True).grid(row=prow + 1, column=1)
f = Tkinter.Frame(paramFrame)
f.grid(row=prow + 1, column=2, sticky='w')
self.radiusOpt = FloatOption(f,
0,
"angstroms",
prefs[AXIS_RADIUS],
None,
min=0.01)
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()
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 fill_in_ui(self, parent):
"""
This is the main part of the interface. With this method you code
the whole dialog, buttons, textareas and everything.
"""
# Create all frames
frames = [('ui_input_frame', 'Model Topology'),
('ui_output_frame', 'Output'),
('ui_settings_frame', 'System & Simulation Settings'),
('ui_stage_frame', 'Stages')]
for attr, text in frames:
setattr(self, attr, tk.LabelFrame(self.canvas, text=text))
# Fill frames
# Fill Input frame
# Creating tabs
self.ui_input_note = ttk.Notebook(self.ui_input_frame, padding=5)
self.ui_tab_1 = tk.Frame(self.ui_input_note)
self.ui_tab_1.rowconfigure(0, weight=1)
self.ui_tab_1.columnconfigure(0, weight=1)
self.ui_tab_2 = tk.Frame(self.ui_input_note)
self.ui_tab_2.rowconfigure(0, weight=1)
self.ui_input_note.add(self.ui_tab_1,
text="Chimera",
state="normal",
sticky='news')
self.ui_input_note.add(self.ui_tab_2,
text="External Input",
state="normal",
sticky='news')
self.ui_input_note.pack(expand=True, fill='both')
# Input Frame
# Tab1
self.ui_chimera_models = MoleculeScrolledListBox(
self.ui_input_frame,
listbox_selectmode='single',
autoselect='single')
self.ui_chimera_models_options = tk.Button(
self.ui_input_frame,
text="Advanced\nOptions",
command=lambda: self.Open_window('ui_input_opt_window', self.
_fill_ui_input_opt_window))
self.ui_sanitize_chimera_model = tk.Button(self.ui_input_frame,
text="Sanitize\nModel",
command=self.sanitize_model)
chimera_input_grid = [[self.ui_chimera_models],
[(self.ui_chimera_models_options,
self.ui_sanitize_chimera_model)]]
self.auto_grid(self.ui_tab_1,
chimera_input_grid,
sticky='news',
padx=5,
pady=5)
# Tab 2
self.ui_model_extinput_add = tk.Button(self.ui_input_frame,
text='Add\nModel',
command=self._set_model)
self.ui_amber_model = tk.Listbox(
self.ui_input_frame,
height=5,
listvariable=self.var_path_extinput_top)
ui_amber_model_options = tk.Button(
self.ui_input_frame,
text="Advanced\nOptions",
command=lambda: self.Open_window('ui_input_opt_window', self.
_fill_ui_input_opt_window))
extinput_grid = [[self.ui_amber_model],
[(ui_amber_model_options, self.ui_model_extinput_add)]
]
self.auto_grid(self.ui_tab_2,
extinput_grid,
sticky='news',
padx=5,
pady=5)
# Output frame
self.ui_output_projectname_Entry = self.ui_output_entry = tk.Entry(
self.canvas, textvariable=self.var_output_projectname)
self.ui_output_reporters_md = ttk.Combobox(
self.canvas, textvariable=self.var_md_reporters, width=20)
self.ui_output_reporters_md.config(values=('PDB', 'DCD', 'None'))
self.ui_output_reporters_realtime = ttk.Combobox(
self.canvas, textvariable=self.var_verbose, width=20)
self.ui_output_reporters_realtime.config(values=('True', 'False'))
self.ui_output_trjinterval_Entry = tk.Entry(
self.canvas, textvariable=self.var_output_traj_interval, width=8)
self.ui_output_stdout_interval_Entry = tk.Entry(
self.canvas, textvariable=self.var_output_stdout_interval, width=8)
self.ui_output_options = tk.Button(
self.canvas,
text='Advanced options',
command=lambda: self.Open_window('ui_output_opt', self.
_fill_ui_output_opt_window))
self.ui_output_restart_Entry = tk.Entry(
self.canvas, textvariable=self.var_output_restart)
self.ui_output_restart_browse = tk.Button(
self.canvas,
text='...',
command=lambda: self._browse_file(self.var_output_restart, 'rst',
'xml'))
output_grid = [['Project name:', self.ui_output_projectname_Entry],
[
'Restart file:', self.ui_output_restart_Entry,
self.ui_output_restart_browse
], ['REPORTERS'],
[
'Trajectory:',
(self.ui_output_reporters_md, 'every',
self.ui_output_trjinterval_Entry, 'frames')
],
[
'Progress:',
(self.ui_output_reporters_realtime, 'every',
self.ui_output_stdout_interval_Entry, 'frames')
], ['', self.ui_output_options]]
self.auto_grid(self.ui_output_frame, output_grid, label_sep='')
# Settings frame
self.ui_forcefield_combo = ttk.Combobox(
self.canvas, textvariable=self.var_forcefield)
self.ui_forcefield_combo.config(values=('amber96', 'amber99sb',
'amber99sbildn',
'amber99sbnmr', 'amber03',
'amber10'))
self.ui_forcefield_add = tk.Button(
self.canvas,
text='+',
command=lambda: self.Open_window('ui_add_forcefields', self.
_fill_ui_add_forcefields))
self.ui_forcefield_charmmpar = tk.Button(
self.canvas,
text='...',
state='disabled',
command=lambda: self._browse_file(self.var_parametrize_forc, 'par',
''))
self.ui_forcefield_charmmpar_entry = tk.Entry(
self.canvas,
textvariable=self.var_parametrize_forc,
state='disabled')
self.ui_integrator = ttk.Combobox(
self.canvas,
textvariable=self.var_integrator,
values=('LangevinIntegrator', 'BrownianIntegrator',
'VerletIntegrator', 'VariableVerletIntegrator',
'VariableLangevinIntegrator'))
self.ui_timestep_entry = tk.Entry(self.canvas,
textvariable=self.var_tstep)
self.ui_advanced_options = tk.Button(
self.canvas,
text='More options',
command=lambda: self.Open_window('ui_advopt_window', self.
_fill_ui_advopt_window))
settings_grid = [[
'Forcefield', self.ui_forcefield_combo, self.ui_forcefield_add,
'Charmm Parameters',
(self.ui_forcefield_charmmpar_entry, self.ui_forcefield_charmmpar)
],
[
'Integrator', self.ui_integrator,
'Time Step (fs)', self.ui_timestep_entry,
self.ui_advanced_options
]]
self.auto_grid(self.ui_settings_frame, settings_grid)
# Stages Frame
self.ui_stages_up = tk.Button(self.canvas,
text='^',
command=self._move_stage_up)
self.ui_stages_down = tk.Button(self.canvas,
text='v',
command=self._move_stage_down)
self.ui_stages_add = tk.Button(
self.canvas,
text='+',
command=lambda: self.Open_window('ui_stages_window', self.
_fill_ui_stages_window))
self.ui_stages_listbox = tk.Listbox(self.ui_stage_frame,
height=18,
background='white')
self.ui_stages_remove = tk.Button(
self.canvas,
text='-',
command=lambda: self._remove_stage('ui_stages_listbox', self.stages
))
stage_frame_widgets = [
self.ui_stages_add, self.ui_stages_remove, self.ui_stages_up,
self.ui_stages_down
]
for row, item in enumerate(stage_frame_widgets):
item.grid(in_=self.ui_stage_frame,
row=row,
column=2,
sticky='news',
**self.style_option)
self.ui_stages_listbox.grid(in_=self.ui_stage_frame,
row=0,
column=0,
rowspan=4,
sticky='news',
**self.style_option)
# Grid Frames
self.ui_input_frame.grid(row=0,
column=0,
sticky='news',
padx=5,
pady=5)
self.ui_output_frame.grid(row=0,
column=1,
sticky='news',
padx=5,
pady=5)
self.ui_stage_frame.grid(row=0,
column=3,
rowspan=2,
sticky='news',
padx=5,
pady=5)
self.ui_settings_frame.grid(row=1,
columnspan=2,
sticky='ew',
padx=5,
pady=5)
# Events
self.ui_input_note.bind("<ButtonRelease-1>", self._forc_param)
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 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'
def fill_in_ui(self, parent):
self.canvas.columnconfigure(1, weight=1)
# Molecules
self.ui_molecules_frame = tk.LabelFrame(self.canvas,
text='Select a molecule')
self.ui_molecules_frame.grid(row=0,
column=0,
columnspan=2,
sticky='ew',
padx=5,
pady=5)
self.ui_molecules = MoleculeScrolledListBox(self.ui_molecules_frame)
self.ui_molecules.pack(expand=True, fill='both', padx=3, pady=3)
# Configuration
## Chains
self.ui_chains_frame = tk.Frame(self.canvas)
self.ui_chains_entry = tk.Entry(self.ui_chains_frame,
textvariable=self._chains,
width=15)
self.ui_chains_btn = tk.Button(self.ui_chains_frame, text='+')
self.ui_chains = [self.ui_chains_entry, self.ui_chains_btn]
## pH
self.ui_ph = tk.Scale(self.canvas,
from_=0,
to=14,
resolution=0.1,
orient='horizontal',
length=163,
variable=self._ph)
self.ui_ph_window_frame = tk.Frame(self.canvas)
self.ui_ph_window_0 = tk.Entry(self.ui_ph_window_frame,
textvariable=self._ph_window[0],
width=6)
self.ui_ph_window_1 = tk.Entry(self.ui_ph_window_frame,
textvariable=self._ph_window[1],
width=6)
self.ui_ph_window_2 = tk.Entry(self.ui_ph_window_frame,
textvariable=self._ph_window[2],
width=6)
self.ui_ph_window = [
self.ui_ph_window_0, self.ui_ph_window_1, self.ui_ph_window_2
]
self.ui_ph_grid_frame = tk.Frame(self.canvas)
self.ui_ph_grid_0 = tk.Entry(self.ui_ph_grid_frame,
textvariable=self._ph_grid[0],
width=6)
self.ui_ph_grid_1 = tk.Entry(self.ui_ph_grid_frame,
textvariable=self._ph_grid[1],
width=6)
self.ui_ph_grid_2 = tk.Entry(self.ui_ph_grid_frame,
textvariable=self._ph_grid[2],
width=6)
self.ui_ph_grid = [
self.ui_ph_grid_0, self.ui_ph_grid_1, self.ui_ph_grid_2
]
self.ui_ph_reference = Pmw.OptionMenu(
self.canvas,
menubutton_textvariable=self._ph_reference,
items=['neutral', 'low-pH'])
self.ui_titrate_frame = tk.Frame(self.canvas)
self.ui_titrate_entry = tk.Entry(self.ui_titrate_frame,
textvariable=self._titrate,
width=15)
self.ui_titrate_btn = tk.Button(self.ui_titrate_frame, text='+')
self.ui_titrate = [self.ui_titrate_entry, self.ui_titrate_btn]
self.ui_keep_protons = tk.Checkbutton(self.canvas,
variable=self._keep_protons,
anchor='w')
self.ui_mutations = tk.Entry(self.canvas, textvariable=self._mutations)
self.ui_mutations_method = tk.OptionMenu(self.canvas,
self._mutations_method,
'alignment', 'scwrl',
'jackal')
self.ui_mutations_options = tk.Entry(
self.canvas, textvariable=self._mutations_options)
labeled_widgets = {
(0, 'ui_chains_frame'): 'Chains',
(1, 'ui_ph'): 'pH',
(2, 'ui_ph_window_frame'): 'pH window',
(3, 'ui_ph_grid_frame'): 'pH grid',
(4, 'ui_ph_reference'): 'pH reference',
(5, 'ui_titrate_frame'): 'Titrate only',
(6, 'ui_keep_protons'): 'Keep protons',
# (7, 'ui_mutations'): 'Mutations',
# (8, 'ui_mutations_method'): 'Mutation method',
# (9, 'ui_mutations_options'): 'Mutation options',
}
for (i, attr), title in sorted(labeled_widgets.items()):
tk.Label(self.canvas, text=title).grid(row=i + 1,
column=0,
sticky='e',
padx=4,
pady=1)
getattr(self, attr).grid(row=i + 1,
column=1,
padx=4,
pady=1,
sticky='we')
left_packed = self.ui_ph_window + self.ui_ph_grid + self.ui_chains + self.ui_titrate
for widget in left_packed:
expand, fill = True, 'both'
if isinstance(widget, tk.Button):
expand, fill = False, None
widget.pack(side='left', padx=1, expand=expand, fill=fill)
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):
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 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 fill_in_ui(self, parent):
# Select molecules
self.ui_system_frame = tk.LabelFrame(self.canvas,
text='Configure system')
self.ui_system_frame.columnconfigure(0, weight=1)
self.ui_molecules = MoleculeScrolledListBox(
self.canvas, labelpos='n', label_text='Select molecule:')
self.ui_replicas_chk = tk.Checkbutton(
self.canvas, text='Frames', variable=self.var_molecule_replicas)
self.ui_connectivity = tk.Checkbutton(self.canvas,
variable=self.var_connectivity,
text='Connectivity')
self.ui_redundant_btn = tk.Button(self.canvas,
text='ModRedundant',
state='disabled')
self.ui_layers = tk.Button(self.canvas, text='Layers & Flex')
self.ui_charges_frame = tk.Frame(self.canvas)
self.ui_charges_qm = tk.Entry(self.canvas,
textvariable=self.var_charge_qm,
width=3)
self.ui_charges_mm = tk.Entry(self.canvas,
textvariable=self.var_charge_mm,
width=3)
self.ui_multiplicity_qm = tk.Entry(
self.canvas, textvariable=self.var_multiplicity_qm, width=3)
self.ui_multiplicity_mm = tk.Entry(
self.canvas, textvariable=self.var_multiplicity_mm, width=3)
charges_grid = [[
'Charge:', (self.ui_charges_qm, '(QM)'),
(self.ui_charges_mm, '(MM)')
],
[
'Mult:', (self.ui_multiplicity_qm, '(QM)'),
(self.ui_multiplicity_mm, '(MM)')
]]
self.auto_grid(self.ui_charges_frame,
charges_grid,
resize_columns=(1, 2),
label_sep='')
kw = dict(padx=5, pady=5)
self.ui_molecules.grid(in_=self.ui_system_frame,
row=0,
column=0,
rowspan=3,
sticky='news',
**kw)
self.ui_replicas_chk.grid(in_=self.ui_system_frame,
row=0,
column=1,
**kw)
self.ui_connectivity.grid(in_=self.ui_system_frame,
row=0,
column=2,
**kw)
self.ui_redundant_btn.grid(in_=self.ui_system_frame,
row=1,
column=1,
sticky='we',
**kw)
self.ui_layers.grid(in_=self.ui_system_frame,
row=1,
column=2,
sticky='we',
**kw)
self.ui_charges_frame.grid(in_=self.ui_system_frame,
row=2,
column=1,
columnspan=2,
sticky='news',
**kw)
# Modelization
self.ui_model_frame = tk.LabelFrame(self.canvas, text='Modelization')
self.ui_job = Pmw.OptionMenu(self.canvas,
items=JOB_TYPES,
initialitem=0,
menubutton_textvariable=self.var_job)
self.ui_job_options = Pmw.ComboBox(
self.canvas,
entry_textvariable=self.var_job_options,
history=True,
unique=True,
dropdown=True)
self.ui_calculation = Pmw.OptionMenu(
self.canvas,
items=['QM', 'ONIOM'],
initialitem=0,
menubutton_textvariable=self.var_calculation)
self.ui_qm_keywords = Pmw.ComboBox(
self.canvas,
entry_textvariable=self.var_qm_keywords,
history=True,
unique=True,
dropdown=True,
labelpos='w',
label_text='Extra keywords: ')
model_grid = [[('Model', self.ui_calculation, 'Job', self.ui_job,
self.ui_job_options)], [self.ui_qm_keywords]]
self.auto_grid(self.ui_model_frame, model_grid, padx=3, pady=3)
# QM configuration
self.ui_qm_frame = tk.LabelFrame(self.canvas, text='QM Settings')
self.ui_qm_methods = Pmw.OptionMenu(
self.canvas,
items=QM_METHODS,
initialitem=6,
menubutton_textvariable=self.var_qm_method)
self.ui_qm_functional_type = Pmw.OptionMenu(
self.canvas,
initialitem=0,
items=sorted(QM_FUNCTIONALS.keys()),
menubutton_textvariable=self.var_qm_functional_type)
self.ui_qm_functionals = Pmw.OptionMenu(
self.canvas,
initialitem=0,
items=QM_FUNCTIONALS['Pure'],
menubutton_textvariable=self.var_qm_functional)
self.ui_qm_basis_kind = Pmw.OptionMenu(
self.canvas,
items=QM_BASIS_SETS,
initialitem=0,
menubutton_textvariable=self.var_qm_basis_kind)
self.ui_qm_basis_ext = Pmw.OptionMenu(
self.canvas,
items=QM_BASIS_SETS_EXT,
initialitem=0,
menubutton_textvariable=self.var_qm_basis_ext)
self.ui_qm_basis_per_atom = tk.Button(self.canvas, text='Per-element')
self.ui_qm_basis_custom_set = tk.Entry(
self.canvas, textvariable=self.var_qm_basis_set)
self.ui_solvent_btn = tk.Button(self.canvas,
text='Configure solvent',
state='disabled')
qm_grid = [[
'Method',
(self.ui_qm_methods, 'Functional', self.ui_qm_functional_type,
self.ui_qm_functionals)
],
[
'Basis set',
(self.ui_qm_basis_kind, self.ui_qm_basis_ext,
self.ui_qm_basis_custom_set, self.ui_qm_basis_per_atom)
], ['Solvent', self.ui_solvent_btn]]
self.auto_grid(self.ui_qm_frame, qm_grid)
# MM Configuration
self.ui_mm_frame = tk.LabelFrame(self.canvas, text='MM Settings')
self.ui_mm_forcefields = Pmw.OptionMenu(
self.canvas,
initialitem=0,
items=MM_FORCEFIELDS['General'],
menubutton_textvariable=self.var_mm_forcefield)
self.ui_mm_water_forcefield = Pmw.OptionMenu(
self.canvas,
initialitem=0,
items=MM_FORCEFIELDS['Water'],
menubutton_textvariable=self.var_mm_water_forcefield)
self.ui_mm_frcmod = tk.Entry(self.canvas,
textvariable=self.var_mm_frcmod)
self.ui_mm_frcmod_btn = tk.Button(self.canvas, text='...')
self.ui_mm_types_btn = tk.Button(self.canvas, text='Set MM Atom Types')
mm_grid = [[('Forcefield', self.ui_mm_forcefields),
('Waters', self.ui_mm_water_forcefield)],
[('Frcmod', self.ui_mm_frcmod, self.ui_mm_frcmod_btn),
self.ui_mm_types_btn]]
self.auto_grid(self.ui_mm_frame, mm_grid)
# Hardware
self.ui_hw_frame = tk.LabelFrame(self.canvas, text='Output')
self.ui_title = tk.Entry(self.canvas, textvariable=self.var_title)
self.ui_title_btn = tk.Button(
self.canvas,
text='Random',
command=lambda: self.var_title.set(''.join(
choice(ascii_letters) for i in range(8))))
self.ui_checkpoint = tk.Checkbutton(self.canvas,
variable=self.var_checkpoint,
text='Check:')
self.ui_checkpoint_fld = tk.Entry(
self.canvas, textvariable=self.var_checkpoint_path)
self.ui_checkpoint_btn = tk.Button(self.canvas, text='Browse')
self.ui_nproc = tk.Entry(self.canvas,
textvariable=self.var_nproc,
width=5)
self.ui_nproc_btn = tk.Button(
self.canvas,
text='Get',
command=lambda: self.var_nproc.set(cpu_count()))
self.ui_memory = tk.Entry(self.canvas,
textvariable=self.var_memory,
width=5)
self.ui_memory_units = Pmw.OptionMenu(
self.canvas,
items=MEM_UNITS,
initialitem=2,
menubutton_textvariable=self.var_memory_units)
hw_grid = [[
'Job title', self.ui_title, self.ui_title_btn, '# CPUs',
self.ui_nproc, self.ui_nproc_btn
],
[
self.ui_checkpoint, self.ui_checkpoint_fld,
self.ui_checkpoint_btn, 'Memory', self.ui_memory,
self.ui_memory_units
]]
self.auto_grid(self.ui_hw_frame, hw_grid, sticky='news')
# Live output
self.ui_preview_frame = tk.LabelFrame(self.canvas,
text='Preview output')
self.ui_preview = Pmw.ScrolledText(self.canvas,
text_state='disabled',
text_padx=4,
text_pady=4,
usehullsize=True,
hull_width=300,
hull_height=200,
text_font='Monospace')
self.ui_preview.pack(in_=self.ui_preview_frame,
expand=True,
fill='both',
padx=5,
pady=5)
kw = dict(sticky='news', padx=5, pady=5)
self.ui_system_frame.grid(row=0, column=0, **kw)
self.ui_qm_frame.grid(row=0, column=1, **kw)
self.ui_model_frame.grid(row=1, column=0, **kw)
self.ui_mm_frame.grid(row=1, column=1, **kw)
self.ui_hw_frame.grid(row=2, columnspan=2, sticky='ew', padx=5, pady=5)
self.canvas.columnconfigure(0, weight=1)
self.canvas.columnconfigure(1, weight=1)
self.canvas.columnconfigure(2, weight=1)
self.canvas.rowconfigure(100, weight=1)
self.ui_preview_frame.grid(row=100, columnspan=3, **kw)
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_Prody(self, parent):
#
# Algorithm selection
#
self.canvas.columnconfigure(1, weight=1)
row = 0
self.ui_algorithms_menu_lbl = tk.Label(self.canvas,
text='Algorithm:',
anchor='e')
self.ui_algorithms_menu = Pmw.OptionMenu(
self.canvas,
items=[
'Full atom', 'Extend from C-alpha', 'Group by residues',
'Group by mass', 'Group by graph'
],
command=self._algorithms_menu_cb)
self.ui_algorithms_param = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'integer',
'min': 1
},
labelpos='w',
label_text='#:')
self.ui_algorithms_param.setvalue(1)
self.ui_algorithms_menu_lbl.grid(row=row,
column=0,
sticky='we',
padx=3,
pady=3)
self.ui_algorithms_menu.grid(row=row,
column=1,
sticky='we',
padx=3,
pady=3,
columnspan=2)
#
# Number of modes & Molecule Minimization
#
row += 1
self.ui_n_modes_lbl = tk.Label(self.canvas,
text='# Modes:',
anchor='e')
self.ui_n_modes = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'integer',
'min': 1
})
self.ui_n_modes.setvalue(20)
self.ui_n_modes_lbl.grid(column=0,
row=row,
sticky='we',
padx=3,
pady=3)
self.ui_n_modes.grid(column=1, row=row, sticky='news', padx=3)
self.ui_minimize_btn = tk.Button(
self.canvas,
text="Minimize",
) #command=lambda: chimera.dialogs.display(mmmdDialog.name))
self.ui_minimize_btn.grid(column=2,
row=row,
sticky='we',
padx=3,
pady=3)
#
# Cutoff
#
row += 1
self.ui_cutoff_lbl = tk.Label(self.canvas, text='Cutoff:', anchor='e')
self.ui_cutoff = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'real',
'min': 4.0
})
self.ui_cutoff.setvalue(15.0)
self.ui_cutoff_lbl.grid(column=0, row=row, sticky='we', padx=3, pady=3)
self.ui_cutoff.grid(column=1, row=row, sticky='news', padx=3)
#
# Cutoff
#
row += 1
self.ui_gamma_lbl = tk.Label(self.canvas, text='Gamma LJ:', anchor='e')
self.ui_gamma = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'real',
'min': 0.0
})
self.ui_gamma.setvalue(1.0)
self.ui_gamma_lbl.grid(column=0, row=row, sticky='we', padx=3, pady=3)
self.ui_gamma.grid(column=1, row=row, sticky='news', padx=3)
#
# Optional Selections: Lennard-Jones and mass-weighted hessian
#
row += 1
self.ui_extra_options = Pmw.Group(self.canvas, tag_text='Options')
self.ui_extra_options.grid(column=0,
row=row,
columnspan=3,
sticky='nsew',
padx=5,
pady=5)
self.ui_extra_options_chk = Pmw.RadioSelect(
self.ui_extra_options.interior(), buttontype='checkbutton')
self.ui_extra_options_chk.add('Mass-Weighted')
self.ui_extra_options_chk.grid(column=0, row=0, sticky='we')
#
# Model selection
#
row += 1
self.ui_molecules_lbl = tk.Label(self.canvas,
text="Select model:",
anchor='e')
self.ui_molecules_lbl.grid(column=0, row=row, padx=3)
self.ui_molecules = MoleculeScrolledListBox(
self.canvas, listbox_selectmode="single")
self.ui_molecules.grid(column=1,
row=row,
columnspan=3,
sticky='nsew',
padx=3,
pady=3)