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):
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 _menuCB(self, val):
newNum = int(val)
oldSettings = []
for well, entry in zip(self.wells, self.values):
entry.invoke()
oldSettings.append((well.rgba, float(entry.getvalue())))
well.grid_forget()
well.destroy()
entry.grid_forget()
entry.destroy()
import Pmw
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.values = []
scale = (len(oldSettings) - 1.0) / (newNum - 1.0)
f = self.interpFrame
for i in range(newNum):
index = i * scale
if index == int(index) \
or int(index) >= len(oldSettings):
color, value = oldSettings[int(index)]
else:
lowc, lowv = oldSettings[int(index)]
highc, highv = oldSettings[int(index) + 1]
frac = index - int(index)
color = []
for lowcomp, highcomp in zip(lowc, highc):
color.append((1.0 - frac) * lowcomp + frac * highcomp)
value = (1.0 - frac) * lowv + frac * highv
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
def color_surface_color_well():
global cscw
if cscw == None:
from CGLtk.color.ColorWell import ColorWell
from chimera.tkgui import app
cscw = ColorWell(app, callback=color_surface_cb)
return cscw
def fillInUI(self, parent):
import Tkinter, Pmw
row = 0
f = Tkinter.Frame(parent)
f.grid(row=row, column=0)
self.drawHbondsVar = Tkinter.IntVar(parent)
self.drawHbondsVar.set(prefs[DRAW_HBONDS])
Tkinter.Checkbutton(f, text="Draw H-bonds of color",
variable=self.drawHbondsVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.hbColorWell = ColorWell(f, noneOkay=False,
color=prefs[HBOND_COLOR])
self.hbColorWell.grid(row=0, column=1)
self.hbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
value=str(prefs[HBOND_WIDTH]))
self.hbWidthEntry.grid(row=0, column=2)
row += 1
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, column=0)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[HBOND_IGNORE_OTHERS])
Tkinter.Checkbutton(parent, text="Ignore H-bonds with other"
" models", variable=self.ignoreOthersVar).grid(row=row,
column=0, sticky='w')
row += 1
def fillInUI(self, parent):
row = 0
from DetectClash.gui import ClashDef, HbondAllow
self.clashDef = ClashDef(parent, value=prefs[CLASH_THRESHOLD])
self.clashDef.grid(row=row, column=0, sticky='w')
row += 1
self.hbondAllow = HbondAllow(parent,
value=prefs[HBOND_ALLOWANCE])
self.hbondAllow.grid(row=row, column=0, sticky='w')
row += 1
import Pmw, Tkinter
Tkinter.Button(parent, text="Default criteria",
pady=0, command=self._revertDefaults).grid(row=row)
row += 1
self.computeType = Pmw.RadioSelect(parent, pady=0,
buttontype='radiobutton', labelpos='w',
label_text="Column Value:", orient='vertical',
frame_borderwidth=2, frame_relief="ridge")
self.buttonInfo= [
("Number of clashes", "num"),
("Sum of overlaps", "sum"),
]
for label, short in self.buttonInfo:
self.computeType.add(label)
if prefs[CLASH_METHOD] == short:
default = label
self.computeType.invoke(default)
self.computeType.grid(row=row, column=0)
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
self.pbVar = Tkinter.IntVar(parent)
self.pbVar.set(prefs[CLASH_PBS])
Tkinter.Checkbutton(f, text="Draw pseudobonds of color",
variable=self.pbVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f, noneOkay=False,
color=prefs[CLASH_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
value=str(prefs[CLASH_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[CLASH_IGNORE_OTHERS])
Tkinter.Checkbutton(parent, text="Ignore clashes with other"
" models", variable=self.ignoreOthersVar).grid(row=row,
column=0, sticky='w')
row += 1
def _componentsCB(self, opt, update=True):
cf = self.componentsFrame
if hasattr(self, 'wells'):
for well in self.wells:
well.grid_forget()
well.destroy()
for label in self.labels:
label.frame.grid_forget()
self.reverseButton.grid_forget()
self.reverseButton.destroy()
else:
Tkinter.Label(cf, text="Colors").grid(row=0)
Tkinter.Label(cf, text="Labels").grid(row=0, column=1)
if isinstance(opt, int):
numComponents = opt
self.numComponents.set(opt)
else:
numComponents = opt.get()
wellSize = min(38, int((7 * 38) / numComponents))
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.labels = []
from CGLtk import Hybrid
for i in range(numComponents):
well = ColorWell(cf,
width=wellSize,
height=wellSize,
callback=self._keyChangeCB,
color='white')
well.grid(row=i + 1)
self.wells.append(well)
label = Hybrid.Entry(cf, "", 10)
label.variable.add_callback(self._keyTypingCB)
label.frame.grid(row=i + 1, column=1, sticky='ew')
self.labels.append(label)
self.reverseButton = Tkinter.Button(cf,
command=self.reverseKey,
text="Reverse ordering of above",
pady=0)
self.reverseButton.grid(row=numComponents + 1, column=0, columnspan=2)
self.notebook.setnaturalsize()
if update:
self._keyChangeCB()
def fillInUI(self, parent):
import Tkinter, Pmw
row = 0
f = Tkinter.Frame(parent)
f.grid(row=row, column=0)
self.drawHbondsVar = Tkinter.IntVar(parent)
self.drawHbondsVar.set(prefs[DRAW_HBONDS])
Tkinter.Checkbutton(f,
text="Draw H-bonds of color",
variable=self.drawHbondsVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.hbColorWell = ColorWell(f,
noneOkay=False,
color=prefs[HBOND_COLOR])
self.hbColorWell.grid(row=0, column=1)
self.hbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
value=str(prefs[HBOND_WIDTH]))
self.hbWidthEntry.grid(row=0, column=2)
row += 1
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, column=0)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[HBOND_IGNORE_OTHERS])
Tkinter.Checkbutton(parent,
text="Ignore H-bonds with other"
" models",
variable=self.ignoreOthersVar).grid(row=row,
column=0,
sticky='w')
row += 1
def _componentsCB(self, opt, update=True): cf = self.componentsFrame if hasattr(self, 'wells'): for well in self.wells: well.grid_forget() well.destroy() for label in self.labels: label.frame.grid_forget() self.reverseButton.grid_forget() self.reverseButton.destroy() else: Tkinter.Label(cf, text="Colors").grid(row=0) Tkinter.Label(cf, text="Labels").grid(row=0, column=1) if isinstance(opt, int): numComponents = opt self.numComponents.set(opt) else: numComponents = opt.get() wellSize = min(38, int( (7 * 38) / numComponents )) from CGLtk.color.ColorWell import ColorWell self.wells = [] self.labels = [] from CGLtk import Hybrid for i in range(numComponents): well = ColorWell(cf, width=wellSize, height=wellSize, callback=self._keyChangeCB, color='white') well.grid(row=i+1) self.wells.append(well) label = Hybrid.Entry(cf, "", 10) label.variable.add_callback(self._keyTypingCB) label.frame.grid(row=i+1, column=1, sticky='ew') self.labels.append(label) self.reverseButton = Tkinter.Button(cf, command=self.reverseKey, text="Reverse ordering of above", pady=0) self.reverseButton.grid(row=numComponents+1, column=0, columnspan=2) self.notebook.setnaturalsize() if update: self._keyChangeCB()
def _menuCB(self, val): newNum = int(val) oldSettings = [] for well, entry in zip(self.wells, self.values): entry.invoke() oldSettings.append((well.rgba, float(entry.getvalue()))) well.grid_forget() well.destroy() entry.grid_forget() entry.destroy() import Pmw from CGLtk.color.ColorWell import ColorWell self.wells = [] self.values = [] scale = (len(oldSettings) - 1.0) / (newNum - 1.0) f = self.interpFrame for i in range(newNum): index = i * scale if index == int(index) \ or int(index) >= len(oldSettings): color, value = oldSettings[int(index)] else: lowc, lowv = oldSettings[int(index)] highc, highv = oldSettings[int(index)+1] frac = index - int(index) color = [] for lowcomp, highcomp in zip(lowc, highc): color.append((1.0 - frac) * lowcomp + frac * highcomp) value = (1.0 - frac) * lowv + frac * highv well = ColorWell(f, color=color) well.grid(row=0, column=len(self.wells)) self.wells.append(well) entry = Pmw.EntryField(f, value=str(value), **self._entryOpts) entry.grid(row=1, column=len(self.values)) self.values.append(entry)
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(
parent,
labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew", columnspan=2)
Pmw.OptionMenu(parent,
command=self._menuCB,
initialitem="3",
items=[str(x) for x in range(2, 12)],
labelpos='w',
label_text="Number of colors/values:").grid(
row=1, column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(
parent,
3,
"Distance-dependent dielectric",
True,
None,
balloon="If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant", 4.0,
None)
self.surfDist = FloatOption(parent,
5,
"Distance from surface",
1.4,
None,
balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(
interior,
text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))), slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="name",
text="Residue name-based",
command=self._switchHisList).grid(row=1,
sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f,
text="HID/HIE/HIP = delta/epsilon/both").grid(row=0,
sticky='w')
self.hisDefault = Pmw.OptionMenu(
f,
initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"],
labelpos='w',
label_text="HIS = ",
command=lambda a, s=self: setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, 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=3,
sticky='w')
Tkinter.Button(parent,
pady=0,
command=self._colorKeyCB,
text="Create corresponding color key").grid(
row=7, column=0, columnspan=2)
self.hisChanged = False
class IlabelDialog(ModelessDialog):
name = "2D Labels/Color Key"
provideStatus = True
buttons = ("Delete", "Close")
LABELS = "Labels"
COLOR_KEY = "Color Key"
MOUSE_LABEL_TEXT = "Use mouse for label placement"
MOUSE_KEY_TEXT = "Use mouse for key placement"
EmphasisColor = "forest green"
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel,
None), icon=chimage.get(Image.open(os.path.join(myDir,
'ilabel.png')), tkgui.app))
addFunction('place key', (self._startOrGrabKey,
self._sizeOrMoveKey, None), icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
def fillInUI(self, parent):
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.fileMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Write...", command=self._writeFileCB)
self.fileMenu.add_command(label="Read...", command=self._readFileCB)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row=0)
from ColorKey import KeyModel
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
# _pageRaisedCB uses mouseModeVar, so define first
self.mouseLabelingVar = Tkinter.IntVar(parent)
self.mouseLabelingVar.set(True)
self.mlLabelVar = Tkinter.StringVar(parent)
self.mouseModeButton = Tkinter.Checkbutton(parent,
command=self._mouseFuncCB,
variable=self.mouseLabelingVar,
textvariable=self.mlLabelVar)
self.mouseModeButton.grid(row=2, column=0)
self.notebook = Pmw.NoteBook(parent,
raisecommand=self._pageRaisedCB)
self.notebook.add(self.LABELS, tab_text=self.LABELS)
self.notebook.add(self.COLOR_KEY, tab_text=self.COLOR_KEY)
self.notebook.grid(row=1, column=0, sticky="nsew")
self._fillLabelsPage(self.notebook.page(self.LABELS))
self.keyModel = KeyModel(self)
self.keyPosition = None
self._fillColorKeyPage(self.notebook.page(self.COLOR_KEY))
def _fillLabelsPage(self, page):
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
page.columnconfigure(2, weight=1)
row = 0
from CGLtk.Table import SortableTable
self.labelTable = SortableTable(page, automultilineHeaders=False)
self.labelTable.addColumn("Label [(x, y) text]", self._labelListing,
anchor='w')
self.labelTable.addColumn("Shown", "shown", format=bool)
self.labelTable.setData(self.model.labels)
self.labelTable.launch(browseCmd=self._tableCB, selectMode="single")
self.labelTable.grid(row=row, column=0, columnspan=3, sticky="nsew")
page.rowconfigure(row, weight=1)
row += 1
self.labelText = Pmw.ScrolledText(page, labelpos='w',
label_text="Text", text_height=3, text_width=20,
text_wrap='none', text_state='disabled',
text_exportselection=False)
text = self.labelText.component('text')
text.bind("<<Modified>>", self._textCB)
text.bind("<<Selection>>", self._updateTextAttrWidgets)
self.labelText.grid(row=row, column=0,
sticky='nsew', columnspan=3)
page.rowconfigure(row, weight=1)
row += 1
self.labelSymbolMenu = Pmw.OptionMenu(page, labelpos='w',
label_text="Insert symbol:", command=self._insertSymbol,
items=[
u'\N{GREEK SMALL LETTER ALPHA}',
u'\N{GREEK SMALL LETTER BETA}',
u'\N{GREEK SMALL LETTER GAMMA}',
u'\N{GREEK SMALL LETTER DELTA}',
u'\N{GREEK SMALL LETTER EPSILON}',
u'\N{GREEK SMALL LETTER PI}',
u'\N{GREEK SMALL LETTER PHI}',
u'\N{GREEK SMALL LETTER CHI}',
u'\N{GREEK SMALL LETTER PSI}',
u'\N{GREEK SMALL LETTER OMEGA}',
u'\N{LEFTWARDS ARROW}',
u'\N{RIGHTWARDS ARROW}',
u'\N{LEFT RIGHT ARROW}',
u'\N{UPWARDS ARROW}',
u'\N{DOWNWARDS ARROW}',
u'\N{SUPERSCRIPT TWO}',
u'\N{SUPERSCRIPT THREE}',
u'\N{DEGREE SIGN}',
u'\N{LATIN CAPITAL LETTER A WITH RING ABOVE}',
"more..."
])
self.labelSymbolMenu.grid(row=row, column=0, columnspan=3)
row += 1
colorHouse = Pmw.LabeledWidget(page, labelpos='w',
label_text="Color")
colorHouse.grid(row=row, column=0, rowspan=3)
from CGLtk.color.ColorWell import ColorWell
self.colorWell = ColorWell(colorHouse.interior(),
color=self._contrastWithBG(), callback=self._colorCB)
self.colorWell.grid()
from chimera.tkoptions import IntOption
self.labelFontSize = IntOption(page, row, "Font size", 24,
self._labelChangeCB, startCol=1, min=1,
attribute="size", width=3)
row += 1
self.labelFontStyle = FontStyle(page, row, "Font style",
oglFont.normal, self._labelChangeCB, startCol=1)
row += 1
self.labelFontTypeface = FontTypeface(page, row, "Font typeface",
FONT_TYPEFACE_VALUES[0],
self._labelChangeCB, startCol=1)
row += 1
if self.model.curLabel:
self.changeToLabel(self.model.curLabel, force=True)
def _fillColorKeyPage(self, page):
from chimera.tkoptions import IntOption, EnumOption, \
BooleanOption, RGBAOption
f = Tkinter.Frame(page)
f.grid(row=0, columnspan=2)
self.numComponents = IntOption(f, 0, "Number of colors/labels",
3, self._componentsCB, min=2, width=2)
self.componentsFrame = Tkinter.Frame(page)
self.componentsFrame.grid(row=1, column=0, sticky="nsew",
columnspan=2)
page.columnconfigure(0, weight=1)
self.componentsFrame.columnconfigure(1, weight=1)
class ColorTreatment(EnumOption):
values = ("distinct", "blended")
self.colorTreatment = ColorTreatment(page, 2,
"Color range depiction", "blended", self._keyChangeCB,
balloon="Should colors be shown as distinct rectangles"
" or as a continuous range")
class LabelPosition(EnumOption):
values = ("left/top", "right/bottom")
self.labelPos = LabelPosition(page, 3, "Label positions",
"right/bottom", self._keyChangeCB, balloon="Position of"
" labels relative to color key.\nLabels always"
" positioned adjacent to long side.")
self.labelColor = RGBAOption(page, 4, "Label color",
self._contrastWithBG(), self._keyChangeCB, balloob=
"Label color. If set to 'No color', use corresponding"
" key color", noneOkay=True)
class LabelJustification(EnumOption):
values = ("left", "decimal point", "right")
self.justification = LabelJustification(page, 5,
"Label justification", "decimal point",
self._keyChangeCB, balloon="Justification of label text"
" in a vertical key layout.\nHorizontal key labels will"
" always be center justified.")
self.labelOffset = IntOption(page, 6, "Label offset", 0,
self._keyChangeCB, width=3, balloon="Additional offset"
" of labels from color bar, in pixels")
self.keyFontSize = IntOption(page, 7, "Font size", 24,
self._keyChangeCB, width=3)
self.keyFontStyle = FontStyle(page, 8, "Font style",
oglFont.normal, self._keyChangeCB)
self.keyFontTypeface = FontTypeface(page, 9, "Font typeface",
FONT_TYPEFACE_VALUES[0], self._keyChangeCB)
self.borderColor = RGBAOption(page, 10, "Border color",
None, self._keyChangeCB, balloon="Color of border"
" around color key (not each individual color).\n"
"If 'no color', then no border is drawn.")
self.borderWidth = IntOption(page, 11, "Border width", 3,
self._keyChangeCB, balloon="in pixels")
self.tickMarks = BooleanOption(page, 12, "Show tick marks",
False, self._keyChangeCB, balloon="Show tick marks"
" pointing from key to labels")
self._componentsCB(self.numComponents)
def destroy(self, *args):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
chimera.triggers.deleteHandler(SAVE_SESSION,
self._sessionHandlerID)
chimera.triggers.deleteHandler(CLOSE_SESSION,
self._closeHandlerID)
chimera.triggers.deleteHandler(BEGIN_RESTORE_SESSION,
self._beginRestoreHandlerID)
chimera.openModels.close([self.model, self.keyModel])
ModelessDialog.destroy(self)
def map(self, e=None):
self._pageRaisedCB(self.notebook.getcurselection())
def unmap(self, e=None):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
def changeToLabel(self, nextLabel, force=False):
if nextLabel == self.model.curLabel and not force:
return
if self.model.curLabel and not unicode(self.model.curLabel) \
and self.model.curLabel != nextLabel:
# remove previous label if empty
self.removeLabel(self.model.curLabel)
self.model.changeToLabel(nextLabel)
self.labelText.component('text').configure(state='normal')
self.labelTable.select(nextLabel)
self.labelText.settext(unicode(nextLabel))
text = self.labelText.component('text')
lineIndex = 1
for line in self.model.curLabel.lines:
charIndex = 0
for c in line:
text.tag_add(id(c),
"%d.%d" % (lineIndex, charIndex))
charIndex += 1
text.tag_add(id(line), "%d.%d" % (lineIndex, charIndex))
lineIndex += 1
def Delete(self):
if self.notebook.getcurselection() == self.LABELS:
self.labelText.clear()
if not self.model.curLabel:
self.status("No label to delete", color="red",
blankAfter=10)
return
self.removeLabel(self.model.curLabel)
self.labelText.component('text').configure(
state='disabled')
else:
self.keyPosition = None
self._keyChangeCB()
def Help(self):
helpLoc = "ContributedSoftware/2dlabels/2dlabels.html"
if self.notebook.getcurselection() == self.COLOR_KEY:
helpLoc += "#colorkey"
chimera.help.display(helpLoc)
def keyConfigure(self, data, pageChange=True):
self._componentsCB(len(data), update=False)
for datum, well, label in zip(data, self.wells, self.labels):
color, text = datum
well.showColor(color, doCallback=False)
label.variable.set(text, invoke_callbacks=False)
self._keyChangeCB()
if pageChange:
self.notebook.selectpage(self.COLOR_KEY)
def makeChar(self, char, model):
attrs = {}
try:
attrs['rgba'] = self.colorWell.rgba
except AttributeError: # multi or None
if model:
attrs['rgba'] = model.rgba
size = self.labelFontSize.get()
if size is not None:
attrs['size'] = size
style = self.labelFontStyle.get()
if style is not None:
attrs['style'] = style
fontName = self.labelFontTypeface.get()
if fontName is not None:
attrs['fontName'] = fontName
return Character(char, **attrs)
def newLabel(self, pos):
label = self.model.newLabel(pos)
self.labelTable.setData(self.model.labels)
self.status("Mouse drag to reposition label",
color=self.EmphasisColor)
return label
def removeLabel(self, label):
self.model.removeLabel(label)
self.labelTable.setData(self.model.labels)
if self.model.curLabel is not None:
self.labelTable.select(self.model.curLabel)
def reverseKey(self):
data = zip([w.rgba for w in self.wells],
[l.variable.get() for l in self.labels])
data.reverse()
self.keyConfigure(data)
def setLabelFromText(self):
curLabel = self.model.curLabel
text = self.labelText.component('text')
# delete parts of label not in text...
#
# newlines first...
while len(curLabel.lines) > 1:
for i, line in enumerate(curLabel.lines[:-1]):
if not text.tag_ranges(id(line)):
curLabel.lines[i+1][:0] = line
del curLabel.lines[i]
break
else:
break
# characters...
for line in curLabel.lines:
for c in line[:]:
if not text.tag_ranges(id(c)):
line.remove(c)
# get new parts of text into label
model = None
targets = []
lines = curLabel.lines
for line in lines:
targets.extend([id(c) for c in line])
if not model and line:
model = line[0]
if line is not lines[-1]:
targets.append(id(line))
contents = self.labelText.get()[:-1] # drop trailing newline
if targets:
target = targets.pop(0)
else:
target = None
textLine = 1
textIndex = -1
curLine = lines[0]
for c in contents:
textIndex += 1
if str(target) in text.tag_names("%d.%d"
% (textLine, textIndex)):
if targets:
target = targets.pop(0)
else:
target = None
if c == '\n':
textLine += 1
textIndex = -1
curLine = lines[[id(l)
for l in lines].index(
id(curLine))+1]
elif curLine:
model = curLine[textIndex]
elif c == '\n':
insertLine = curLine[0:textIndex]
lines.insert(textLine-1, insertLine)
del curLine[0:textIndex]
text.tag_add(id(insertLine), "%d.%d"
% (textLine, textIndex))
textLine += 1
textIndex = -1
else:
labelChar = self.makeChar(c, model)
curLine.insert(textIndex, labelChar)
text.tag_add(id(labelChar), "%d.%d"
% (textLine, textIndex))
self.model.setMajorChange()
def updateGUI(self, source="gui"):
curLabel = self.model.curLabel
if curLabel and source == "gui":
self.setLabelFromText()
self.labelTable.setData(self.model.labels)
if curLabel:
self.labelTable.select(curLabel)
self._updateTextAttrWidgets()
def _colorCB(self, color):
curLabel = self.model.curLabel
if not curLabel:
self.status("No label to color", color='red')
return
self.model.setMajorChange()
for c in self._selChars():
c.rgba = color
def _componentsCB(self, opt, update=True):
cf = self.componentsFrame
if hasattr(self, 'wells'):
for well in self.wells:
well.grid_forget()
well.destroy()
for label in self.labels:
label.frame.grid_forget()
self.reverseButton.grid_forget()
self.reverseButton.destroy()
else:
Tkinter.Label(cf, text="Colors").grid(row=0)
Tkinter.Label(cf, text="Labels").grid(row=0, column=1)
if isinstance(opt, int):
numComponents = opt
self.numComponents.set(opt)
else:
numComponents = opt.get()
wellSize = min(38, int( (7 * 38) / numComponents ))
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.labels = []
from CGLtk import Hybrid
for i in range(numComponents):
well = ColorWell(cf, width=wellSize, height=wellSize,
callback=self._keyChangeCB, color='white')
well.grid(row=i+1)
self.wells.append(well)
label = Hybrid.Entry(cf, "", 10)
label.variable.add_callback(self._keyTypingCB)
label.frame.grid(row=i+1, column=1, sticky='ew')
self.labels.append(label)
self.reverseButton = Tkinter.Button(cf, command=self.reverseKey,
text="Reverse ordering of above", pady=0)
self.reverseButton.grid(row=numComponents+1, column=0,
columnspan=2)
self.notebook.setnaturalsize()
if update:
self._keyChangeCB()
def _contrastWithBG(self):
bg = chimera.viewer.background
if bg:
bgColor = bg.rgba()
else:
bgColor = (0, 0, 0)
if bgColor[0]*2 + bgColor[1]*3 + bgColor[2] < 0.417:
return (1, 1, 1)
else:
return (0, 0, 0)
def _eventToPos(self, viewer, event, offset = (0, 0)):
w, h = viewer.windowSize
return (event.x - offset[0]) / float(w), \
(h - event.y - offset[1]) / float(h)
def _handleTextChange(self):
self.updateGUI()
self.labelText.edit_modified(False)
def _insertSymbol(self, item):
if len(item) > 1:
from chimera import help
help.display("ContributedSoftware/2dlabels/symbols.html")
return
if not self.model.labels:
self.status("No labels have been created yet", color="red")
return
if not self.labelTable.selected():
self.status("No labels active", color="red")
self.labelText.insert("insert", item)
self.setLabelFromText()
def _keyChangeCB(self, *args):
self.keyModel.setMajorChange()
def _keyTypingCB(self, fromAfter=False):
# wait for a pause in typing before updating key...
if fromAfter:
self._typingHandler = None
self._keyChangeCB()
return
handle = getattr(self, '_typingHandler', None)
if handle:
self.componentsFrame.after_cancel(handle)
self._typingHandler = self.componentsFrame.after(500,
lambda: self._keyTypingCB(fromAfter=True))
def _labelChangeCB(self, option):
curLabel = self.model.curLabel
self.model.setMajorChange()
val = option.get()
attrName = option.attribute
for c in self._selChars():
setattr(c, attrName, val)
def _labelListing(self, label):
text = unicode(label)
if '\n' in text:
newline = text.index('\n')
text= text[:newline] + "..."
if not text:
text = "<empty>"
return "(%.2f, %.2f) %s" % (label.pos[0], label.pos[1], text)
def _mouseFuncCB(self):
self.status("")
if not self.mouseLabelingVar.get():
if hasattr(self, "_prevMouse"):
setButtonFunction("1", (), self._prevMouse)
delattr(self, "_prevMouse")
elif self.mlLabelVar.get() == self.MOUSE_LABEL_TEXT:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place text")
else:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place key")
def _moveLabel(self, viewer, event):
pos = self._eventToPos(viewer, event, self._moveOffset)
self.model.moveLabel(pos)
curLabel = self.model.curLabel
self.labelTable.setData(self.model.labels)
self.labelTable.select(curLabel)
def _pageRaisedCB(self, pageName):
if pageName == "Labels":
pageItem = self.MOUSE_LABEL_TEXT
if not self.model.labels:
self.status("Click mouse button 1 in graphics\n"
"window to place first label",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end')+1):
self.fileMenu.entryconfigure(index, state='normal')
else:
pageItem = self.MOUSE_KEY_TEXT
self.status("Drag mouse to position/size key",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end')+1):
self.fileMenu.entryconfigure(index, state='disabled')
self.mlLabelVar.set(pageItem)
# just setting the var doesn't cause the callback, and
# yet using invoke() toggles the var, so set it _opposite_
# to what's desired before calling invoke()
self.mouseLabelingVar.set(False)
self.mouseModeButton.invoke()
def _pickLabel(self, viewer, event):
w, h = viewer.windowSize
pos = self._eventToPos(viewer, event)
label, self._moveOffset = self.model.pickLabel(pos, w, h)
if label is None:
label = self.newLabel(pos)
self._moveOffset = (0, 0)
self.changeToLabel(label)
self.labelText.component('text').focus_set()
def _readFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import readFiles
readFiles(dialog.getPaths(), clear=dialog.deleteExistingVar.get())
def _readFileCB(self):
if not hasattr(self, "_readFileDialog"):
self._readFileDialog = ReadFileDialog(
command=self._readFile, clientPos='s')
self._readFileDialog.enter()
def _restoreSession(self, info):
if info["sel ranges"]:
self.labelText.tag_add("sel", *info["sel ranges"])
self._updateTextAttrWidgets()
self._suppressMap = True
self.labelText.edit_modified(False)
if "key position" not in info:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return
self.keyPosition = info["key position"]
self.colorTreatment.set(info["color depiction"])
self.labelPos.set(info["label positions"])
self.labelColor.set(info["label color"])
self.justification.set(info["label justification"])
self.labelOffset.set(info["label offset"])
self.keyFontSize.set(info["font size"])
self.keyFontStyle.set(info["font typeface"])
if "font name" in info:
self.keyFontTypeface.set(info["font name"])
self.borderColor.set(info["border color"])
self.borderWidth.set(info["border width"])
self.tickMarks.set(info["show ticks"])
self.keyConfigure(info["colors/labels"])
if self.keyPosition:
self.notebook.selectpage(self.COLOR_KEY)
else:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return info
def _saveSession(self, triggerName, myData, sessionFile):
print>>sessionFile, """
def restore2DLabelDialog(info):
from chimera.dialogs import find, display
from Ilabel.gui import IlabelDialog
dlg = find(IlabelDialog.name)
if dlg is not None:
dlg.destroy()
dlg = display(IlabelDialog.name)
dlg._restoreSession(info)
import SimpleSession
SimpleSession.registerAfterModelsCB(restore2DLabelDialog, %s)
""" % repr(self._sessionInfo())
def _selChars(self):
chars = []
curLabel = self.model.curLabel
if curLabel:
sel = self.labelText.tag_ranges("sel")
if sel:
sline, schar = [int(x)
for x in str(sel[0]).split('.')]
eline, echar = [int(x)
for x in str(sel[1]).split('.')]
sline -= 1
eline -= 1
for li, line in enumerate(curLabel.lines):
if li < sline:
continue
if li > eline:
break
if sline == eline:
chars.extend(line[schar:echar])
elif li == sline:
chars.extend(line[schar:])
elif li == eline:
chars.extend(line[:echar])
else:
chars.extend(line)
else:
for l in curLabel.lines:
chars.extend(l)
return chars
def _sessionInfo(self):
info = {}
info["sel ranges"] = tuple([str(tr)
for tr in self.labelText.tag_ranges("sel")])
if self.mouseLabelingVar.get():
info["mouse func"] = "labeling"
else:
info["mouse func"] = "normal"
info["key position"] = self.keyPosition
info["colors/labels"] = [(w.rgba, l.variable.get())
for w, l in zip(self.wells, self.labels)]
info["color depiction"] = self.colorTreatment.get()
info["label positions"] = self.labelPos.get()
info["label color"] = self.labelColor.get()
info["label justification"] = self.justification.get()
info["label offset"] = self.labelOffset.get()
info["font size"] = self.keyFontSize.get()
info["font typeface"] = self.keyFontStyle.get()
info["font name"] = self.keyFontTypeface.get()
info["border color"] = self.borderColor.get()
info["border width"] = self.borderWidth.get()
info["show ticks"] = self.tickMarks.get()
return info
def _sizeOrMoveKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.grabPos:
deltas = [pos[axis] - self.grabPos[axis]
for axis in [0, 1]]
for posIndex in [0, 1]:
old = self.keyPosition[posIndex]
self.keyPosition[posIndex] = (
old[0] + deltas[0], old[1] + deltas[1])
self.grabPos = pos
elif len(self.keyPosition) == 1:
self.keyPosition.append(pos)
else:
self.keyPosition[1] = pos
self._keyChangeCB()
def _startOrGrabKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.keyPosition and len(self.keyPosition) == 2:
# possible grab;
# see if in middle third of long side...
p1, p2 = self.keyPosition
x1, y1 = p1
x2, y2 = p2
if abs(x2 - x1) < abs(y2 - y1):
longAxis = 1
ymin = min(y2, y1)
ymax = max(y2, y1)
b1 = (2* ymin + ymax) / 3.0
b2 = (2* ymax + ymin) / 3.0
o1 = min(x1, x2)
o2 = max(x1, x2)
else:
longAxis = 0
xmin = min(x2, x1)
xmax = max(x2, x1)
b1 = (2* xmin + xmax) / 3.0
b2 = (2* xmax + xmin) / 3.0
o1 = min(y1, y2)
o2 = max(y1, y2)
if b1 < pos[longAxis] < b2 \
and o1 < pos[1-longAxis] < o2:
self.grabPos = pos
return
self.grabPos = None
self.keyPosition = [pos]
self._keyChangeCB()
self.status("Grab middle of key to reposition",
color=self.EmphasisColor)
def _tableCB(self, sel):
if not sel:
return
self.changeToLabel(sel)
def _textCB(self, e):
text = self.labelText.component('text')
if not text.tk.call((text._w, 'edit', 'modified')):
#if not text.edit_modified():
return
# this callback can happen _before_ the change
# actually occurs, so do the processing after idle
text.after_idle(self._handleTextChange)
def _updateTextAttrWidgets(self, e=None):
rgba = None
multiple = False
for c in self._selChars():
if rgba is None:
rgba = c.rgba
elif rgba != c.rgba:
multiple = True
break
if rgba is not None:
self.colorWell.showColor(rgba, multiple=multiple,
doCallback=False)
self.labelFontSize.display(self._selChars())
self.labelFontStyle.display(self._selChars())
self.labelFontTypeface.display(self._selChars())
def _writeFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import writeFile
writeFile(dialog.getPaths()[0])
def _writeFileCB(self):
if not hasattr(self, "_writeFileDialog"):
from OpenSave import SaveModeless
self._writeFileDialog = SaveModeless(command=self._writeFile,
title="Write 2D Labels Info")
self._writeFileDialog.enter()
def _fillLabelsPage(self, page):
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
page.columnconfigure(2, weight=1)
row = 0
from CGLtk.Table import SortableTable
self.labelTable = SortableTable(page, automultilineHeaders=False)
self.labelTable.addColumn("Label [(x, y) text]",
self._labelListing,
anchor='w')
self.labelTable.addColumn("Shown", "shown", format=bool)
self.labelTable.setData(self.model.labels)
self.labelTable.launch(browseCmd=self._tableCB, selectMode="single")
self.labelTable.grid(row=row, column=0, columnspan=3, sticky="nsew")
page.rowconfigure(row, weight=1)
row += 1
self.labelText = Pmw.ScrolledText(page,
labelpos='w',
label_text="Text",
text_height=3,
text_width=20,
text_wrap='none',
text_state='disabled',
text_exportselection=False)
text = self.labelText.component('text')
text.bind("<<Modified>>", self._textCB)
text.bind("<<Selection>>", self._updateTextAttrWidgets)
self.labelText.grid(row=row, column=0, sticky='nsew', columnspan=3)
page.rowconfigure(row, weight=1)
row += 1
self.labelSymbolMenu = Pmw.OptionMenu(
page,
labelpos='w',
label_text="Insert symbol:",
command=self._insertSymbol,
items=[
u'\N{GREEK SMALL LETTER ALPHA}',
u'\N{GREEK SMALL LETTER BETA}',
u'\N{GREEK SMALL LETTER GAMMA}',
u'\N{GREEK SMALL LETTER DELTA}',
u'\N{GREEK SMALL LETTER EPSILON}',
u'\N{GREEK SMALL LETTER PI}', u'\N{GREEK SMALL LETTER PHI}',
u'\N{GREEK SMALL LETTER CHI}', u'\N{GREEK SMALL LETTER PSI}',
u'\N{GREEK SMALL LETTER OMEGA}', u'\N{LEFTWARDS ARROW}',
u'\N{RIGHTWARDS ARROW}', u'\N{LEFT RIGHT ARROW}',
u'\N{UPWARDS ARROW}', u'\N{DOWNWARDS ARROW}',
u'\N{SUPERSCRIPT TWO}', u'\N{SUPERSCRIPT THREE}',
u'\N{DEGREE SIGN}',
u'\N{LATIN CAPITAL LETTER A WITH RING ABOVE}', "more..."
])
self.labelSymbolMenu.grid(row=row, column=0, columnspan=3)
row += 1
colorHouse = Pmw.LabeledWidget(page, labelpos='w', label_text="Color")
colorHouse.grid(row=row, column=0, rowspan=3)
from CGLtk.color.ColorWell import ColorWell
self.colorWell = ColorWell(colorHouse.interior(),
color=self._contrastWithBG(),
callback=self._colorCB)
self.colorWell.grid()
from chimera.tkoptions import IntOption
self.labelFontSize = IntOption(page,
row,
"Font size",
24,
self._labelChangeCB,
startCol=1,
min=1,
attribute="size",
width=3)
row += 1
self.labelFontStyle = FontStyle(page,
row,
"Font style",
oglFont.normal,
self._labelChangeCB,
startCol=1)
row += 1
self.labelFontTypeface = FontTypeface(page,
row,
"Font typeface",
FONT_TYPEFACE_VALUES[0],
self._labelChangeCB,
startCol=1)
row += 1
if self.model.curLabel:
self.changeToLabel(self.model.curLabel, force=True)
class DetectClashDialog(ModelessDialog):
name = "detect clashes"
title = "Find Clashes/Contacts"
provideStatus = True
statusPosition = "above"
help = "ContributedSoftware/findclash/findclash.html"
FREQ_APPLY = "when OK/Apply clicked"
FREQ_MOTION = "after relative motions (until dialog closed)"
FREQ_CONTINUOUS = "continuously (until dialog closed)"
CHECK_SET = "second set of designated atoms"
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(),
command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(),
text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size - 2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(),
command=self._desig2CB,
pady=pady,
text="Designate selection as second set").grid(row=3,
column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size - 4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(
desigGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check designated\natoms"
" against:",
command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters",
hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(row=0, column=0)
Tkinter.Button(defaultsFrame,
text="clash",
pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame,
text="contact",
pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame,
labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(
prefs[BOND_SEPARATION]),
items=[str(i + 2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(row=0,
column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(),
text="Ignore intra-"
"residue contacts",
variable=self.ignoreIntraResVar,
command=self._checkContinuous).grid(row=4)
actionGroup = Pmw.Group(parent,
tag_text="Treatment of Clash/Contact Atoms",
hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(),
text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f,
text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f,
text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f,
noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" file",
variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" reply log",
variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent,
tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
def OK(self, *args):
# use main status line if dialog closing
from chimera.replyobj import status
self.status = status
ModelessDialog.OK(self, *args)
def Apply(self, *args):
# workaround: remove pseudobonds before recreating colors
# so C++ layer doesn't end up with pointers to deleted
# colors in obscure circumstances
from DetectClash import nukeGroup
nukeGroup()
from chimera import UserError
self.status("")
checkAtoms = self.designated.atoms()
if not checkAtoms:
self.enter()
raise UserError("No atoms designated for clash detection")
self.clashDef['command'] = None
self.clashDef.invoke()
self.clashDef['command'] = self._checkContinuous
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount"
" (in Clash/Contact Parameters)")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow['command'] = None
self.hbondAllow.invoke()
self.hbondAllow['command'] = self._checkContinuous
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount"
" (in Clash/Contact Parameters)")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[BOND_SEPARATION] = int(self.bondsApart.getvalue())
prefs[IGNORE_INTRA_RES] = self.ignoreIntraResVar.get()
checkVal = self.checkLocButtons.getvalue()
if checkVal == "themselves":
test = "self"
elif checkVal == "all other atoms":
test = "others"
elif checkVal == "other atoms in same model":
test = "model"
else:
test = self.designated2.atoms()
if not test:
self.enter()
raise UserError("No second-set atoms designated")
actionAttr = prefs[ACTION_ATTR] = self.actionAttrVar.get()
actionSelect = prefs[ACTION_SELECT] = self.actionSelVar.get()
actionColor = prefs[ACTION_COLOR] = self.actionColorVar.get()
actionPseudobonds = prefs[ACTION_PSEUDOBONDS] = \
self.actionPBVar.get()
actionWriteInfo = prefs[ACTION_WRITEINFO] = \
self.actionWriteInfoVar.get()
actionLogInfo = prefs[ACTION_REPLYLOG] = \
self.actionLogInfoVar.get()
if self.freqButtons.getvalue() != self.FREQ_APPLY:
actionAttr = actionWriteInfo = actionLogInfo = False
if not actionAttr and not actionSelect and not actionColor \
and not actionPseudobonds and not actionWriteInfo \
and not actionLogInfo:
self.enter()
raise UserError("No actions selected for clashes")
self.status("Checking for clashes")
clashColor = nonclashColor = None
if actionColor:
prefs[CLASH_COLOR] = self.clashColorWell.rgba
prefs[NONCLASH_COLOR] = self.nonclashColorWell.rgba
if prefs[CLASH_COLOR] == None:
clashColor = None
else:
clashColor = chimera.MaterialColor(*prefs[CLASH_COLOR])
if prefs[NONCLASH_COLOR] == None:
nonclashColor = None
else:
nonclashColor = chimera.MaterialColor(*prefs[NONCLASH_COLOR])
pbColor = None
if actionPseudobonds:
prefs[PB_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[PB_COLOR])
self.pbWidthEntry['command'] = None
self.pbWidthEntry.invoke()
self.pbWidthEntry['command'] = self._checkContinuous
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width "
"(in Treatment of Clash/Contact Atoms)")
prefs[PB_WIDTH] = float(self.pbWidthEntry.getvalue())
from DetectClash import cmdDetectClash
if actionWriteInfo:
saveFile = "-"
else:
saveFile = None
clashes = cmdDetectClash(checkAtoms,
test=test,
overlapCutoff=prefs[CLASH_THRESHOLD],
hbondAllowance=prefs[HBOND_ALLOWANCE],
bondSeparation=prefs[BOND_SEPARATION],
ignoreIntraRes=prefs[IGNORE_INTRA_RES],
setAttrs=actionAttr,
selectClashes=actionSelect,
colorClashes=actionColor,
clashColor=clashColor,
nonclashColor=nonclashColor,
makePseudobonds=actionPseudobonds,
pbColor=pbColor,
lineWidth=prefs[PB_WIDTH],
saveFile=saveFile,
log=actionLogInfo,
summary=self.status)
if actionAttr:
from ShowAttr import ShowAttrDialog
from chimera import dialogs
from DetectClash import attrName
d = dialogs.display(ShowAttrDialog.name)
d.configure(attrsOf="atoms", attrName=attrName, mode="Render")
def Close(self):
ModelessDialog.Close(self)
if self.freqButtons.getvalue() != self.FREQ_APPLY:
self.freqButtons.invoke(self.FREQ_APPLY)
def _checkContinuous(self, *args):
if self.freqButtons.getvalue() == self.FREQ_CONTINUOUS:
self.Apply()
def _clashDefaultsCB(self):
from prefs import defaults
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self._checkContinuous()
def _clearHandlers(self):
while self._handlers:
trigName, handler = self._handlers.popitem()
chimera.triggers.deleteHandler(trigName, handler)
def _contactDefaultsCB(self):
self.hbondAllow.setvalue("0.0")
self.clashDef.setvalue("-0.4")
self._checkContinuous()
def _desigCB(self):
self.designated.clear()
self.designated.add(chimera.selection.currentAtoms())
self._updateDesigStatus()
def _desig2CB(self):
self.designated2.clear()
self.designated2.add(chimera.selection.currentAtoms())
self._locButtonCB()
self._updateDesig2Status()
def _freqChangeCB(self, freqVal):
self._clearHandlers()
if freqVal == self.FREQ_APPLY:
self.assignAttrButton.configure(state='normal')
self.writeInfoButton.configure(state='normal')
self.logInfoButton.configure(state='normal')
return
self.assignAttrButton.configure(state='disabled')
self.writeInfoButton.configure(state='disabled')
self.logInfoButton.configure(state='disabled')
def modCoordSets(trigName, myData, changes):
if changes.modified:
self.Apply()
self._handlers['CoordSet'] = chimera.triggers.addHandler(
'CoordSet', modCoordSets, None)
def justCoordSets(trigName, myData, changes):
if 'activeCoordSet changed' in changes.reasons:
self.Apply()
self._handlers['Molecule'] = chimera.triggers.addHandler(
'Molecule', justCoordSets, None)
if freqVal == self.FREQ_MOTION:
self._handlers[chimera.MOTION_STOP] = chimera.triggers\
.addHandler(chimera.MOTION_STOP,
self._motionCB, None)
elif freqVal == self.FREQ_CONTINUOUS:
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
self._motionCB()
self._handlers['OpenState'] = chimera.triggers\
.addHandler('OpenState', preCB, None)
self.Apply()
def _locButtonCB(self, butName=None):
checkSetBut = self.checkLocButtons.button(self.CHECK_SET)
if self.checkLocButtons.getvalue() == self.CHECK_SET \
and not self.designated2.atoms():
checkSetBut.config(fg="red", activeforeground="red")
else:
checkSetBut.config(fg="black", activeforeground="black")
self._updateDesig2Status()
def _motionCB(self, *args):
# if all molecule activities are the same (i.e. no possible
# relative motion), do nothing
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
self.Apply()
return
def _updateDesigStatus(self):
numAtoms = len(self.designated.atoms())
if numAtoms:
statusText = "%d atoms designated" % numAtoms
color = 'blue'
else:
statusText = "No atoms designated"
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desigStatus.config(text=statusText, fg=color)
self._checkContinuous()
def _updateDesig2Status(self):
numAtoms = len(self.designated2.atoms())
checkSet = self.checkLocButtons.getvalue() == self.CHECK_SET
color = 'black'
if numAtoms:
statusText = "Second set: %d atoms" % numAtoms
else:
statusText = "No second set"
if checkSet:
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desig2Status.config(text=statusText, fg=color)
if checkSet:
self._checkContinuous()
class IlabelDialog(ModelessDialog):
name = "2D Labels/Color Key"
provideStatus = True
buttons = ("Delete", "Close")
LABELS = "Labels"
COLOR_KEY = "Color Key"
MOUSE_LABEL_TEXT = "Use mouse for label placement"
MOUSE_KEY_TEXT = "Use mouse for key placement"
EmphasisColor = "forest green"
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel, None),
icon=chimage.get(
Image.open(os.path.join(myDir, 'ilabel.png')),
tkgui.app))
addFunction('place key',
(self._startOrGrabKey, self._sizeOrMoveKey, None),
icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
def fillInUI(self, parent):
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.fileMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Write...", command=self._writeFileCB)
self.fileMenu.add_command(label="Read...", command=self._readFileCB)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row=0)
from ColorKey import KeyModel
parent.rowconfigure(1, weight=1)
parent.columnconfigure(0, weight=1)
# _pageRaisedCB uses mouseModeVar, so define first
self.mouseLabelingVar = Tkinter.IntVar(parent)
self.mouseLabelingVar.set(True)
self.mlLabelVar = Tkinter.StringVar(parent)
self.mouseModeButton = Tkinter.Checkbutton(
parent,
command=self._mouseFuncCB,
variable=self.mouseLabelingVar,
textvariable=self.mlLabelVar)
self.mouseModeButton.grid(row=2, column=0)
self.notebook = Pmw.NoteBook(parent, raisecommand=self._pageRaisedCB)
self.notebook.add(self.LABELS, tab_text=self.LABELS)
self.notebook.add(self.COLOR_KEY, tab_text=self.COLOR_KEY)
self.notebook.grid(row=1, column=0, sticky="nsew")
self._fillLabelsPage(self.notebook.page(self.LABELS))
self.keyModel = KeyModel(self)
self.keyPosition = None
self._fillColorKeyPage(self.notebook.page(self.COLOR_KEY))
def _fillLabelsPage(self, page):
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
page.columnconfigure(2, weight=1)
row = 0
from CGLtk.Table import SortableTable
self.labelTable = SortableTable(page, automultilineHeaders=False)
self.labelTable.addColumn("Label [(x, y) text]",
self._labelListing,
anchor='w')
self.labelTable.addColumn("Shown", "shown", format=bool)
self.labelTable.setData(self.model.labels)
self.labelTable.launch(browseCmd=self._tableCB, selectMode="single")
self.labelTable.grid(row=row, column=0, columnspan=3, sticky="nsew")
page.rowconfigure(row, weight=1)
row += 1
self.labelText = Pmw.ScrolledText(page,
labelpos='w',
label_text="Text",
text_height=3,
text_width=20,
text_wrap='none',
text_state='disabled',
text_exportselection=False)
text = self.labelText.component('text')
text.bind("<<Modified>>", self._textCB)
text.bind("<<Selection>>", self._updateTextAttrWidgets)
self.labelText.grid(row=row, column=0, sticky='nsew', columnspan=3)
page.rowconfigure(row, weight=1)
row += 1
self.labelSymbolMenu = Pmw.OptionMenu(
page,
labelpos='w',
label_text="Insert symbol:",
command=self._insertSymbol,
items=[
u'\N{GREEK SMALL LETTER ALPHA}',
u'\N{GREEK SMALL LETTER BETA}',
u'\N{GREEK SMALL LETTER GAMMA}',
u'\N{GREEK SMALL LETTER DELTA}',
u'\N{GREEK SMALL LETTER EPSILON}',
u'\N{GREEK SMALL LETTER PI}', u'\N{GREEK SMALL LETTER PHI}',
u'\N{GREEK SMALL LETTER CHI}', u'\N{GREEK SMALL LETTER PSI}',
u'\N{GREEK SMALL LETTER OMEGA}', u'\N{LEFTWARDS ARROW}',
u'\N{RIGHTWARDS ARROW}', u'\N{LEFT RIGHT ARROW}',
u'\N{UPWARDS ARROW}', u'\N{DOWNWARDS ARROW}',
u'\N{SUPERSCRIPT TWO}', u'\N{SUPERSCRIPT THREE}',
u'\N{DEGREE SIGN}',
u'\N{LATIN CAPITAL LETTER A WITH RING ABOVE}', "more..."
])
self.labelSymbolMenu.grid(row=row, column=0, columnspan=3)
row += 1
colorHouse = Pmw.LabeledWidget(page, labelpos='w', label_text="Color")
colorHouse.grid(row=row, column=0, rowspan=3)
from CGLtk.color.ColorWell import ColorWell
self.colorWell = ColorWell(colorHouse.interior(),
color=self._contrastWithBG(),
callback=self._colorCB)
self.colorWell.grid()
from chimera.tkoptions import IntOption
self.labelFontSize = IntOption(page,
row,
"Font size",
24,
self._labelChangeCB,
startCol=1,
min=1,
attribute="size",
width=3)
row += 1
self.labelFontStyle = FontStyle(page,
row,
"Font style",
oglFont.normal,
self._labelChangeCB,
startCol=1)
row += 1
self.labelFontTypeface = FontTypeface(page,
row,
"Font typeface",
FONT_TYPEFACE_VALUES[0],
self._labelChangeCB,
startCol=1)
row += 1
if self.model.curLabel:
self.changeToLabel(self.model.curLabel, force=True)
def _fillColorKeyPage(self, page):
from chimera.tkoptions import IntOption, EnumOption, \
BooleanOption, RGBAOption
f = Tkinter.Frame(page)
f.grid(row=0, columnspan=2)
self.numComponents = IntOption(f,
0,
"Number of colors/labels",
3,
self._componentsCB,
min=2,
width=2)
self.componentsFrame = Tkinter.Frame(page)
self.componentsFrame.grid(row=1, column=0, sticky="nsew", columnspan=2)
page.columnconfigure(0, weight=1)
self.componentsFrame.columnconfigure(1, weight=1)
class ColorTreatment(EnumOption):
values = ("distinct", "blended")
self.colorTreatment = ColorTreatment(
page,
2,
"Color range depiction",
"blended",
self._keyChangeCB,
balloon="Should colors be shown as distinct rectangles"
" or as a continuous range")
class LabelPosition(EnumOption):
values = ("left/top", "right/bottom")
self.labelPos = LabelPosition(
page,
3,
"Label positions",
"right/bottom",
self._keyChangeCB,
balloon="Position of"
" labels relative to color key.\nLabels always"
" positioned adjacent to long side.")
self.labelColor = RGBAOption(
page,
4,
"Label color",
self._contrastWithBG(),
self._keyChangeCB,
balloob="Label color. If set to 'No color', use corresponding"
" key color",
noneOkay=True)
class LabelJustification(EnumOption):
values = ("left", "decimal point", "right")
self.justification = LabelJustification(
page,
5,
"Label justification",
"decimal point",
self._keyChangeCB,
balloon="Justification of label text"
" in a vertical key layout.\nHorizontal key labels will"
" always be center justified.")
self.labelOffset = IntOption(page,
6,
"Label offset",
0,
self._keyChangeCB,
width=3,
balloon="Additional offset"
" of labels from color bar, in pixels")
self.keyFontSize = IntOption(page,
7,
"Font size",
24,
self._keyChangeCB,
width=3)
self.keyFontStyle = FontStyle(page, 8, "Font style", oglFont.normal,
self._keyChangeCB)
self.keyFontTypeface = FontTypeface(page, 9, "Font typeface",
FONT_TYPEFACE_VALUES[0],
self._keyChangeCB)
self.borderColor = RGBAOption(
page,
10,
"Border color",
None,
self._keyChangeCB,
balloon="Color of border"
" around color key (not each individual color).\n"
"If 'no color', then no border is drawn.")
self.borderWidth = IntOption(page,
11,
"Border width",
3,
self._keyChangeCB,
balloon="in pixels")
self.tickMarks = BooleanOption(page,
12,
"Show tick marks",
False,
self._keyChangeCB,
balloon="Show tick marks"
" pointing from key to labels")
self._componentsCB(self.numComponents)
def destroy(self, *args):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
chimera.triggers.deleteHandler(SAVE_SESSION, self._sessionHandlerID)
chimera.triggers.deleteHandler(CLOSE_SESSION, self._closeHandlerID)
chimera.triggers.deleteHandler(BEGIN_RESTORE_SESSION,
self._beginRestoreHandlerID)
chimera.openModels.close([self.model, self.keyModel])
ModelessDialog.destroy(self)
def map(self, e=None):
self._pageRaisedCB(self.notebook.getcurselection())
def unmap(self, e=None):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
def changeToLabel(self, nextLabel, force=False):
if nextLabel == self.model.curLabel and not force:
return
if self.model.curLabel and not unicode(self.model.curLabel) \
and self.model.curLabel != nextLabel:
# remove previous label if empty
self.removeLabel(self.model.curLabel)
self.model.changeToLabel(nextLabel)
self.labelText.component('text').configure(state='normal')
self.labelTable.select(nextLabel)
self.labelText.settext(unicode(nextLabel))
text = self.labelText.component('text')
lineIndex = 1
for line in self.model.curLabel.lines:
charIndex = 0
for c in line:
text.tag_add(id(c), "%d.%d" % (lineIndex, charIndex))
charIndex += 1
text.tag_add(id(line), "%d.%d" % (lineIndex, charIndex))
lineIndex += 1
def Delete(self):
if self.notebook.getcurselection() == self.LABELS:
self.labelText.clear()
if not self.model.curLabel:
self.status("No label to delete", color="red", blankAfter=10)
return
self.removeLabel(self.model.curLabel)
self.labelText.component('text').configure(state='disabled')
else:
self.keyPosition = None
self._keyChangeCB()
def Help(self):
helpLoc = "ContributedSoftware/2dlabels/2dlabels.html"
if self.notebook.getcurselection() == self.COLOR_KEY:
helpLoc += "#colorkey"
chimera.help.display(helpLoc)
def keyConfigure(self, data, pageChange=True):
self._componentsCB(len(data), update=False)
for datum, well, label in zip(data, self.wells, self.labels):
color, text = datum
well.showColor(color, doCallback=False)
label.variable.set(text, invoke_callbacks=False)
self._keyChangeCB()
if pageChange:
self.notebook.selectpage(self.COLOR_KEY)
def makeChar(self, char, model):
attrs = {}
try:
attrs['rgba'] = self.colorWell.rgba
except AttributeError: # multi or None
if model:
attrs['rgba'] = model.rgba
size = self.labelFontSize.get()
if size is not None:
attrs['size'] = size
style = self.labelFontStyle.get()
if style is not None:
attrs['style'] = style
fontName = self.labelFontTypeface.get()
if fontName is not None:
attrs['fontName'] = fontName
return Character(char, **attrs)
def newLabel(self, pos):
label = self.model.newLabel(pos)
self.labelTable.setData(self.model.labels)
self.status("Mouse drag to reposition label", color=self.EmphasisColor)
return label
def removeLabel(self, label):
self.model.removeLabel(label)
self.labelTable.setData(self.model.labels)
if self.model.curLabel is not None:
self.labelTable.select(self.model.curLabel)
def reverseKey(self):
data = zip([w.rgba for w in self.wells],
[l.variable.get() for l in self.labels])
data.reverse()
self.keyConfigure(data)
def setLabelFromText(self):
curLabel = self.model.curLabel
text = self.labelText.component('text')
# delete parts of label not in text...
#
# newlines first...
while len(curLabel.lines) > 1:
for i, line in enumerate(curLabel.lines[:-1]):
if not text.tag_ranges(id(line)):
curLabel.lines[i + 1][:0] = line
del curLabel.lines[i]
break
else:
break
# characters...
for line in curLabel.lines:
for c in line[:]:
if not text.tag_ranges(id(c)):
line.remove(c)
# get new parts of text into label
model = None
targets = []
lines = curLabel.lines
for line in lines:
targets.extend([id(c) for c in line])
if not model and line:
model = line[0]
if line is not lines[-1]:
targets.append(id(line))
contents = self.labelText.get()[:-1] # drop trailing newline
if targets:
target = targets.pop(0)
else:
target = None
textLine = 1
textIndex = -1
curLine = lines[0]
for c in contents:
textIndex += 1
if str(target) in text.tag_names("%d.%d" % (textLine, textIndex)):
if targets:
target = targets.pop(0)
else:
target = None
if c == '\n':
textLine += 1
textIndex = -1
curLine = lines[[id(l)
for l in lines].index(id(curLine)) + 1]
elif curLine:
model = curLine[textIndex]
elif c == '\n':
insertLine = curLine[0:textIndex]
lines.insert(textLine - 1, insertLine)
del curLine[0:textIndex]
text.tag_add(id(insertLine), "%d.%d" % (textLine, textIndex))
textLine += 1
textIndex = -1
else:
labelChar = self.makeChar(c, model)
curLine.insert(textIndex, labelChar)
text.tag_add(id(labelChar), "%d.%d" % (textLine, textIndex))
self.model.setMajorChange()
def updateGUI(self, source="gui"):
curLabel = self.model.curLabel
if curLabel and source == "gui":
self.setLabelFromText()
self.labelTable.setData(self.model.labels)
if curLabel:
self.labelTable.select(curLabel)
self._updateTextAttrWidgets()
def _colorCB(self, color):
curLabel = self.model.curLabel
if not curLabel:
self.status("No label to color", color='red')
return
self.model.setMajorChange()
for c in self._selChars():
c.rgba = color
def _componentsCB(self, opt, update=True):
cf = self.componentsFrame
if hasattr(self, 'wells'):
for well in self.wells:
well.grid_forget()
well.destroy()
for label in self.labels:
label.frame.grid_forget()
self.reverseButton.grid_forget()
self.reverseButton.destroy()
else:
Tkinter.Label(cf, text="Colors").grid(row=0)
Tkinter.Label(cf, text="Labels").grid(row=0, column=1)
if isinstance(opt, int):
numComponents = opt
self.numComponents.set(opt)
else:
numComponents = opt.get()
wellSize = min(38, int((7 * 38) / numComponents))
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.labels = []
from CGLtk import Hybrid
for i in range(numComponents):
well = ColorWell(cf,
width=wellSize,
height=wellSize,
callback=self._keyChangeCB,
color='white')
well.grid(row=i + 1)
self.wells.append(well)
label = Hybrid.Entry(cf, "", 10)
label.variable.add_callback(self._keyTypingCB)
label.frame.grid(row=i + 1, column=1, sticky='ew')
self.labels.append(label)
self.reverseButton = Tkinter.Button(cf,
command=self.reverseKey,
text="Reverse ordering of above",
pady=0)
self.reverseButton.grid(row=numComponents + 1, column=0, columnspan=2)
self.notebook.setnaturalsize()
if update:
self._keyChangeCB()
def _contrastWithBG(self):
bg = chimera.viewer.background
if bg:
bgColor = bg.rgba()
else:
bgColor = (0, 0, 0)
if bgColor[0] * 2 + bgColor[1] * 3 + bgColor[2] < 0.417:
return (1, 1, 1)
else:
return (0, 0, 0)
def _eventToPos(self, viewer, event, offset=(0, 0)):
w, h = viewer.windowSize
return (event.x - offset[0]) / float(w), \
(h - event.y - offset[1]) / float(h)
def _handleTextChange(self):
self.updateGUI()
self.labelText.edit_modified(False)
def _insertSymbol(self, item):
if len(item) > 1:
from chimera import help
help.display("ContributedSoftware/2dlabels/symbols.html")
return
if not self.model.labels:
self.status("No labels have been created yet", color="red")
return
if not self.labelTable.selected():
self.status("No labels active", color="red")
self.labelText.insert("insert", item)
self.setLabelFromText()
def _keyChangeCB(self, *args):
self.keyModel.setMajorChange()
def _keyTypingCB(self, fromAfter=False):
# wait for a pause in typing before updating key...
if fromAfter:
self._typingHandler = None
self._keyChangeCB()
return
handle = getattr(self, '_typingHandler', None)
if handle:
self.componentsFrame.after_cancel(handle)
self._typingHandler = self.componentsFrame.after(
500, lambda: self._keyTypingCB(fromAfter=True))
def _labelChangeCB(self, option):
curLabel = self.model.curLabel
self.model.setMajorChange()
val = option.get()
attrName = option.attribute
for c in self._selChars():
setattr(c, attrName, val)
def _labelListing(self, label):
text = unicode(label)
if '\n' in text:
newline = text.index('\n')
text = text[:newline] + "..."
if not text:
text = "<empty>"
return "(%.2f, %.2f) %s" % (label.pos[0], label.pos[1], text)
def _mouseFuncCB(self):
self.status("")
if not self.mouseLabelingVar.get():
if hasattr(self, "_prevMouse"):
setButtonFunction("1", (), self._prevMouse)
delattr(self, "_prevMouse")
elif self.mlLabelVar.get() == self.MOUSE_LABEL_TEXT:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place text")
else:
if not hasattr(self, "_prevMouse"):
self._prevMouse = getFuncName("1", ())
setButtonFunction("1", (), "place key")
def _moveLabel(self, viewer, event):
pos = self._eventToPos(viewer, event, self._moveOffset)
self.model.moveLabel(pos)
curLabel = self.model.curLabel
self.labelTable.setData(self.model.labels)
self.labelTable.select(curLabel)
def _pageRaisedCB(self, pageName):
if pageName == "Labels":
pageItem = self.MOUSE_LABEL_TEXT
if not self.model.labels:
self.status(
"Click mouse button 1 in graphics\n"
"window to place first label",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end') + 1):
self.fileMenu.entryconfigure(index, state='normal')
else:
pageItem = self.MOUSE_KEY_TEXT
self.status("Drag mouse to position/size key",
color=self.EmphasisColor)
for index in range(0, self.fileMenu.index('end') + 1):
self.fileMenu.entryconfigure(index, state='disabled')
self.mlLabelVar.set(pageItem)
# just setting the var doesn't cause the callback, and
# yet using invoke() toggles the var, so set it _opposite_
# to what's desired before calling invoke()
self.mouseLabelingVar.set(False)
self.mouseModeButton.invoke()
def _pickLabel(self, viewer, event):
w, h = viewer.windowSize
pos = self._eventToPos(viewer, event)
label, self._moveOffset = self.model.pickLabel(pos, w, h)
if label is None:
label = self.newLabel(pos)
self._moveOffset = (0, 0)
self.changeToLabel(label)
self.labelText.component('text').focus_set()
def _readFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import readFiles
readFiles(dialog.getPaths(), clear=dialog.deleteExistingVar.get())
def _readFileCB(self):
if not hasattr(self, "_readFileDialog"):
self._readFileDialog = ReadFileDialog(command=self._readFile,
clientPos='s')
self._readFileDialog.enter()
def _restoreSession(self, info):
if info["sel ranges"]:
self.labelText.tag_add("sel", *info["sel ranges"])
self._updateTextAttrWidgets()
self._suppressMap = True
self.labelText.edit_modified(False)
if "key position" not in info:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return
self.keyPosition = info["key position"]
self.colorTreatment.set(info["color depiction"])
self.labelPos.set(info["label positions"])
self.labelColor.set(info["label color"])
self.justification.set(info["label justification"])
self.labelOffset.set(info["label offset"])
self.keyFontSize.set(info["font size"])
self.keyFontStyle.set(info["font typeface"])
if "font name" in info:
self.keyFontTypeface.set(info["font name"])
self.borderColor.set(info["border color"])
self.borderWidth.set(info["border width"])
self.tickMarks.set(info["show ticks"])
self.keyConfigure(info["colors/labels"])
if self.keyPosition:
self.notebook.selectpage(self.COLOR_KEY)
else:
self.notebook.selectpage(self.LABELS)
if info["mouse func"] == "normal":
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
return info
def _saveSession(self, triggerName, myData, sessionFile):
print >> sessionFile, """
def restore2DLabelDialog(info):
from chimera.dialogs import find, display
from Ilabel.gui import IlabelDialog
dlg = find(IlabelDialog.name)
if dlg is not None:
dlg.destroy()
dlg = display(IlabelDialog.name)
dlg._restoreSession(info)
import SimpleSession
SimpleSession.registerAfterModelsCB(restore2DLabelDialog, %s)
""" % repr(self._sessionInfo())
def _selChars(self):
chars = []
curLabel = self.model.curLabel
if curLabel:
sel = self.labelText.tag_ranges("sel")
if sel:
sline, schar = [int(x) for x in str(sel[0]).split('.')]
eline, echar = [int(x) for x in str(sel[1]).split('.')]
sline -= 1
eline -= 1
for li, line in enumerate(curLabel.lines):
if li < sline:
continue
if li > eline:
break
if sline == eline:
chars.extend(line[schar:echar])
elif li == sline:
chars.extend(line[schar:])
elif li == eline:
chars.extend(line[:echar])
else:
chars.extend(line)
else:
for l in curLabel.lines:
chars.extend(l)
return chars
def _sessionInfo(self):
info = {}
info["sel ranges"] = tuple(
[str(tr) for tr in self.labelText.tag_ranges("sel")])
if self.mouseLabelingVar.get():
info["mouse func"] = "labeling"
else:
info["mouse func"] = "normal"
info["key position"] = self.keyPosition
info["colors/labels"] = [(w.rgba, l.variable.get())
for w, l in zip(self.wells, self.labels)]
info["color depiction"] = self.colorTreatment.get()
info["label positions"] = self.labelPos.get()
info["label color"] = self.labelColor.get()
info["label justification"] = self.justification.get()
info["label offset"] = self.labelOffset.get()
info["font size"] = self.keyFontSize.get()
info["font typeface"] = self.keyFontStyle.get()
info["font name"] = self.keyFontTypeface.get()
info["border color"] = self.borderColor.get()
info["border width"] = self.borderWidth.get()
info["show ticks"] = self.tickMarks.get()
return info
def _sizeOrMoveKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.grabPos:
deltas = [pos[axis] - self.grabPos[axis] for axis in [0, 1]]
for posIndex in [0, 1]:
old = self.keyPosition[posIndex]
self.keyPosition[posIndex] = (old[0] + deltas[0],
old[1] + deltas[1])
self.grabPos = pos
elif len(self.keyPosition) == 1:
self.keyPosition.append(pos)
else:
self.keyPosition[1] = pos
self._keyChangeCB()
def _startOrGrabKey(self, viewer, event):
pos = self._eventToPos(viewer, event)
if self.keyPosition and len(self.keyPosition) == 2:
# possible grab;
# see if in middle third of long side...
p1, p2 = self.keyPosition
x1, y1 = p1
x2, y2 = p2
if abs(x2 - x1) < abs(y2 - y1):
longAxis = 1
ymin = min(y2, y1)
ymax = max(y2, y1)
b1 = (2 * ymin + ymax) / 3.0
b2 = (2 * ymax + ymin) / 3.0
o1 = min(x1, x2)
o2 = max(x1, x2)
else:
longAxis = 0
xmin = min(x2, x1)
xmax = max(x2, x1)
b1 = (2 * xmin + xmax) / 3.0
b2 = (2 * xmax + xmin) / 3.0
o1 = min(y1, y2)
o2 = max(y1, y2)
if b1 < pos[longAxis] < b2 \
and o1 < pos[1-longAxis] < o2:
self.grabPos = pos
return
self.grabPos = None
self.keyPosition = [pos]
self._keyChangeCB()
self.status("Grab middle of key to reposition",
color=self.EmphasisColor)
def _tableCB(self, sel):
if not sel:
return
self.changeToLabel(sel)
def _textCB(self, e):
text = self.labelText.component('text')
if not text.tk.call((text._w, 'edit', 'modified')):
#if not text.edit_modified():
return
# this callback can happen _before_ the change
# actually occurs, so do the processing after idle
text.after_idle(self._handleTextChange)
def _updateTextAttrWidgets(self, e=None):
rgba = None
multiple = False
for c in self._selChars():
if rgba is None:
rgba = c.rgba
elif rgba != c.rgba:
multiple = True
break
if rgba is not None:
self.colorWell.showColor(rgba, multiple=multiple, doCallback=False)
self.labelFontSize.display(self._selChars())
self.labelFontStyle.display(self._selChars())
self.labelFontTypeface.display(self._selChars())
def _writeFile(self, okayed, dialog):
if not okayed:
return
from Ilabel import writeFile
writeFile(dialog.getPaths()[0])
def _writeFileCB(self):
if not hasattr(self, "_writeFileDialog"):
from OpenSave import SaveModeless
self._writeFileDialog = SaveModeless(command=self._writeFile,
title="Write 2D Labels Info")
self._writeFileDialog.enter()
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(),
command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(),
text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size - 2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(),
command=self._desig2CB,
pady=pady,
text="Designate selection as second set").grid(row=3,
column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size - 4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(
desigGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check designated\natoms"
" against:",
command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters",
hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(row=0, column=0)
Tkinter.Button(defaultsFrame,
text="clash",
pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame,
text="contact",
pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame,
labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(
prefs[BOND_SEPARATION]),
items=[str(i + 2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(row=0,
column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(),
text="Ignore intra-"
"residue contacts",
variable=self.ignoreIntraResVar,
command=self._checkContinuous).grid(row=4)
actionGroup = Pmw.Group(parent,
tag_text="Treatment of Clash/Contact Atoms",
hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(),
text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f,
text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f,
text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f,
noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" file",
variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" reply log",
variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent,
tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
def fillInUI(self, parent):
from sys import getrefcount
import Tkinter, Pmw
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row = 0)
row = 1
from CGLtk.Table import SortableTable
self.cavityTable = SortableTable(parent, menuInfo=
(self.columnMenu, prefs, dict.fromkeys(
defaults[SHOWN_COLS], True), False))
if not self.tableData:
from CASTp import mouthFieldNames, pocketFieldNames
# add preferred columns first
shownCols = prefs[SHOWN_COLS]
for fn in ("ID", "MS volume", "SA volume",
"pocket MS area", "pocket SA area",
"# openings"):
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
self.cavityTable.addColumn(fn, "lambda c: "
"c.pocketInfo['%s']" % fn, **kw)
for fn in ("mouth MS area", "mouth SA area",
"MS circumference sum",
"SA circumference sum"):
self.cavityTable.addColumn(fn, "lambda c: "
"c.mouthInfo['%s']" % fn,
format="%6.1f", font='TkFixedFont')
for fieldNames, attrName in [
(pocketFieldNames, "pocketInfo"),
(mouthFieldNames, "mouthInfo")]:
for fn in fieldNames:
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
c = self.cavityTable.addColumn(fn,
"lambda c: "
"getattr(c, '%s')['%s']" %
(attrName, fn), **kw)
if fn == "ID":
self.cavityTable.sortBy(c)
self.cavityTable.sortBy(c)
self.cavityTable.setData(self.cavities)
self.cavityTable.launch(browseCmd=self._selCavityCB,
restoreInfo=self.tableData)
self.cavityTable.grid(row=row, column=0, sticky="nsew")
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
grp = Pmw.Group(parent,
tag_text="Treatment of Chosen Pocket Atoms")
grp.grid(row=row)
checkFrame = grp.interior()
from CGLtk import Hybrid
def buttonCB(s=self):
self._selCavityCB(self.cavityTable.selected())
self.doSelect = Hybrid.Checkbutton(checkFrame, "Select",
prefs[DO_SELECT])
self.doSelect.variable.add_callback(buttonCB)
self.doSelect.button.grid(row=0, sticky='w')
f = Tkinter.Frame(checkFrame)
f.grid(row=1, sticky='w')
self.doColor = Hybrid.Checkbutton(f, "Color",
prefs[DO_COLOR])
self.doColor.variable.add_callback(buttonCB)
self.doColor.button.grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pocketColor = ColorWell(f, color=prefs[POCKET_COLOR],
noneOkay=True)
self.pocketColor.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms ").grid(
row=0, column=2)
self.nonpocketColor = ColorWell(f, color=prefs[NONPOCKET_COLOR],
noneOkay=True)
self.nonpocketColor.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.doSurface = Hybrid.Checkbutton(checkFrame, "Surface",
prefs[DO_SURFACE])
self.doSurface.variable.add_callback(buttonCB)
self.doSurface.button.grid(row=2, sticky='w')
self.doZoom = Hybrid.Checkbutton(checkFrame, "Zoom in on",
prefs[DO_ZOOM])
self.doZoom.variable.add_callback(buttonCB)
self.doZoom.button.grid(row=3, sticky='w')
self.excludeMouth = Hybrid.Checkbutton(checkFrame,
"Exclude mouth atoms", prefs[EXCLUDE_MOUTH])
self.excludeMouth.variable.add_callback(buttonCB)
self.excludeMouth.button.grid(row=4, sticky='w')
row += 1
class CastpDialog(ModelessDialog):
help = "UsersGuide/castp.html"
buttons = ("Quit", "Hide")
def __init__(self, name, cavities, sessionData=None):
self.title = "CASTp: %s" % name
self.cavities = cavities
from weakref import proxy
def wrapper(s=proxy(self)):
s._cavityChangeCB()
for cav in cavities:
cav.pocketInfo["atoms"].selChangedCB = wrapper
cav.mouthInfo["atoms"].selChangedCB = wrapper
if sessionData:
self.tableData = sessionData
else:
self.tableData = None
ModelessDialog.__init__(self)
chimera.extension.manager.registerInstance(self)
def fillInUI(self, parent):
from sys import getrefcount
import Tkinter, Pmw
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row = 0)
row = 1
from CGLtk.Table import SortableTable
self.cavityTable = SortableTable(parent, menuInfo=
(self.columnMenu, prefs, dict.fromkeys(
defaults[SHOWN_COLS], True), False))
if not self.tableData:
from CASTp import mouthFieldNames, pocketFieldNames
# add preferred columns first
shownCols = prefs[SHOWN_COLS]
for fn in ("ID", "MS volume", "SA volume",
"pocket MS area", "pocket SA area",
"# openings"):
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
self.cavityTable.addColumn(fn, "lambda c: "
"c.pocketInfo['%s']" % fn, **kw)
for fn in ("mouth MS area", "mouth SA area",
"MS circumference sum",
"SA circumference sum"):
self.cavityTable.addColumn(fn, "lambda c: "
"c.mouthInfo['%s']" % fn,
format="%6.1f", font='TkFixedFont')
for fieldNames, attrName in [
(pocketFieldNames, "pocketInfo"),
(mouthFieldNames, "mouthInfo")]:
for fn in fieldNames:
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
c = self.cavityTable.addColumn(fn,
"lambda c: "
"getattr(c, '%s')['%s']" %
(attrName, fn), **kw)
if fn == "ID":
self.cavityTable.sortBy(c)
self.cavityTable.sortBy(c)
self.cavityTable.setData(self.cavities)
self.cavityTable.launch(browseCmd=self._selCavityCB,
restoreInfo=self.tableData)
self.cavityTable.grid(row=row, column=0, sticky="nsew")
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
grp = Pmw.Group(parent,
tag_text="Treatment of Chosen Pocket Atoms")
grp.grid(row=row)
checkFrame = grp.interior()
from CGLtk import Hybrid
def buttonCB(s=self):
self._selCavityCB(self.cavityTable.selected())
self.doSelect = Hybrid.Checkbutton(checkFrame, "Select",
prefs[DO_SELECT])
self.doSelect.variable.add_callback(buttonCB)
self.doSelect.button.grid(row=0, sticky='w')
f = Tkinter.Frame(checkFrame)
f.grid(row=1, sticky='w')
self.doColor = Hybrid.Checkbutton(f, "Color",
prefs[DO_COLOR])
self.doColor.variable.add_callback(buttonCB)
self.doColor.button.grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pocketColor = ColorWell(f, color=prefs[POCKET_COLOR],
noneOkay=True)
self.pocketColor.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms ").grid(
row=0, column=2)
self.nonpocketColor = ColorWell(f, color=prefs[NONPOCKET_COLOR],
noneOkay=True)
self.nonpocketColor.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.doSurface = Hybrid.Checkbutton(checkFrame, "Surface",
prefs[DO_SURFACE])
self.doSurface.variable.add_callback(buttonCB)
self.doSurface.button.grid(row=2, sticky='w')
self.doZoom = Hybrid.Checkbutton(checkFrame, "Zoom in on",
prefs[DO_ZOOM])
self.doZoom.variable.add_callback(buttonCB)
self.doZoom.button.grid(row=3, sticky='w')
self.excludeMouth = Hybrid.Checkbutton(checkFrame,
"Exclude mouth atoms", prefs[EXCLUDE_MOUTH])
self.excludeMouth.variable.add_callback(buttonCB)
self.excludeMouth.button.grid(row=4, sticky='w')
row += 1
def destroy(self):
if self.cavities:
cav1 = self.cavities[0]
atoms = (cav1.mouthInfo["atoms"].atoms()
or cav1.pocketInfo["atoms"].atoms())
if atoms:
# close surface too...
from chimera import openModels
mol = atoms[0].molecule
openModels.close(openModels.list(
id=mol.id, subid=mol.subid))
for chk in [self.doSelect, self.doColor, self.doSurface,
self.doZoom, self.excludeMouth]:
chk.destroy()
chimera.extension.manager.deregisterInstance(self)
ModelessDialog.destroy(self)
def emHide(self):
"""Extension manager method"""
self.Close()
Hide = emHide
def emName(self):
"""Extension manager method"""
return self.title
def emQuit(self):
"""Extension manager method"""
self.destroy()
Quit = emQuit
def emRaise(self):
"""Extension manager method"""
self.enter()
def _cavityChangeCB(self):
newCavities = [cav for cav in self.cavities
if len(cav.mouthInfo["atoms"]) > 0
or len(cav.pocketInfo["atoms"]) > 0]
if len(newCavities) == len(self.cavities):
return
if not newCavities:
self.destroy()
return
self.cavities = newCavities
self.cavityTable.setData(self.cavities)
def _colDispChange(self, col):
self.cavityTable.columnUpdate(col, display=not col.display)
prefs[SHOWN_COLS] = [c.title for c in self.cavityTable.columns
if c.display]
def _selCavityCB(self, tableSel):
prefs[EXCLUDE_MOUTH] = self.excludeMouth.variable.get()
from chimera.selection import ItemizedSelection, mergeCurrent, \
EXTEND, REMOVE
cavitySel = ItemizedSelection()
for cavity in tableSel:
cavitySel.merge(EXTEND, cavity.pocketInfo["atoms"])
if prefs[EXCLUDE_MOUTH]:
cavitySel.merge(REMOVE,
cavity.mouthInfo["atoms"])
cavitySel.addImplied()
# might be no cavities selected...
cav1 = self.cavities[0]
someA = (cav1.mouthInfo["atoms"].atoms()
or cav1.pocketInfo["atoms"].atoms())[0]
if someA.__destroyed__:
return
mol = someA.molecule
cavitySet = set(cavitySel.atoms())
from chimera import selectionOperation
doSelect = self.doSelect.variable.get()
if doSelect != prefs[DO_SELECT]:
#if not doSelect:
# mergeCurrent(REMOVE, cavitySel)
prefs[DO_SELECT] = doSelect
doColor = self.doColor.variable.get()
if doColor != prefs[DO_COLOR]:
if not doColor and hasattr(self, '_prevColors'):
for a, c, sc in self._prevColors:
if a.__destroyed__:
continue
a.color = c
a.surfaceColor = sc
delattr(self, '_prevColors')
prefs[DO_COLOR] = doColor
if doColor:
prefs[POCKET_COLOR] = self.pocketColor.rgba
prefs[NONPOCKET_COLOR] = self.nonpocketColor.rgba
doSurface = self.doSurface.variable.get()
if doSurface != prefs[DO_SURFACE]:
if not doSurface:
for a in cavitySet:
a.surfaceDisplay = False
prefs[DO_SURFACE] = doSurface
doZoom = self.doZoom.variable.get()
if doZoom != prefs[DO_ZOOM]:
if not doZoom:
from Midas import focus, uncofr
focus([mol])
uncofr()
prefs[DO_ZOOM] = doZoom
if doSelect:
selectionOperation(cavitySel)
if doColor:
if prefs[POCKET_COLOR] == None:
pocketColor = None
else:
pocketColor = chimera.MaterialColor(
*prefs[POCKET_COLOR])
if prefs[NONPOCKET_COLOR] == None:
nonpocketColor = None
else:
nonpocketColor = chimera.MaterialColor(
*prefs[NONPOCKET_COLOR])
if not hasattr(self, '_prevColors'):
self._prevColors = [(a, a.color, a.surfaceColor)
for a in mol.atoms]
for a in mol.atoms:
if a in cavitySet:
a.surfaceColor = a.color = pocketColor
else:
a.surfaceColor = a.color = nonpocketColor
if doSurface:
for a in mol.atoms:
a.surfaceDisplay = a in cavitySet
surfs = chimera.openModels.list(mol.id, mol.subid,
modelTypes=[chimera.MSMSModel])
catsurfs = [s for s in surfs if s.category == "main"]
if not catsurfs:
from Midas import surfaceNew
surfaceNew("main", models=[mol])
if doZoom and tableSel:
from Midas import align, focus
align(cavitySel, mol.atoms)
focus(cavitySel)
def fillInUI(self, parent):
row = 0
from DetectClash.gui import ClashDef, HbondAllow
self.clashDef = ClashDef(parent, value=prefs[CLASH_THRESHOLD])
self.clashDef.grid(row=row, column=0, sticky='w')
row += 1
self.hbondAllow = HbondAllow(parent, value=prefs[HBOND_ALLOWANCE])
self.hbondAllow.grid(row=row, column=0, sticky='w')
row += 1
import Pmw, Tkinter
Tkinter.Button(parent,
text="Default criteria",
pady=0,
command=self._revertDefaults).grid(row=row)
row += 1
self.computeType = Pmw.RadioSelect(parent,
pady=0,
buttontype='radiobutton',
labelpos='w',
label_text="Column Value:",
orient='vertical',
frame_borderwidth=2,
frame_relief="ridge")
self.buttonInfo = [
("Number of clashes", "num"),
("Sum of overlaps", "sum"),
]
for label, short in self.buttonInfo:
self.computeType.add(label)
if prefs[CLASH_METHOD] == short:
default = label
self.computeType.invoke(default)
self.computeType.grid(row=row, column=0)
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
self.pbVar = Tkinter.IntVar(parent)
self.pbVar.set(prefs[CLASH_PBS])
Tkinter.Checkbutton(f,
text="Draw pseudobonds of color",
variable=self.pbVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f,
noneOkay=False,
color=prefs[CLASH_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
value=str(prefs[CLASH_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[CLASH_IGNORE_OTHERS])
Tkinter.Checkbutton(parent,
text="Ignore clashes with other"
" models",
variable=self.ignoreOthersVar).grid(row=row,
column=0,
sticky='w')
row += 1
class ClashDialog(ModelessDialog):
title = "Rotamer Clash Params"
buttons = ("OK", "Apply", "Close")
help = "ContributedSoftware/rotamers/rotamers.html#clashes"
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
row = 0
from DetectClash.gui import ClashDef, HbondAllow
self.clashDef = ClashDef(parent, value=prefs[CLASH_THRESHOLD])
self.clashDef.grid(row=row, column=0, sticky='w')
row += 1
self.hbondAllow = HbondAllow(parent,
value=prefs[HBOND_ALLOWANCE])
self.hbondAllow.grid(row=row, column=0, sticky='w')
row += 1
import Pmw, Tkinter
Tkinter.Button(parent, text="Default criteria",
pady=0, command=self._revertDefaults).grid(row=row)
row += 1
self.computeType = Pmw.RadioSelect(parent, pady=0,
buttontype='radiobutton', labelpos='w',
label_text="Column Value:", orient='vertical',
frame_borderwidth=2, frame_relief="ridge")
self.buttonInfo= [
("Number of clashes", "num"),
("Sum of overlaps", "sum"),
]
for label, short in self.buttonInfo:
self.computeType.add(label)
if prefs[CLASH_METHOD] == short:
default = label
self.computeType.invoke(default)
self.computeType.grid(row=row, column=0)
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
self.pbVar = Tkinter.IntVar(parent)
self.pbVar.set(prefs[CLASH_PBS])
Tkinter.Checkbutton(f, text="Draw pseudobonds of color",
variable=self.pbVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f, noneOkay=False,
color=prefs[CLASH_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
value=str(prefs[CLASH_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[CLASH_IGNORE_OTHERS])
Tkinter.Checkbutton(parent, text="Ignore clashes with other"
" models", variable=self.ignoreOthersVar).grid(row=row,
column=0, sticky='w')
row += 1
def Apply(self):
from chimera import UserError
self.clashDef.invoke()
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow.invoke()
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[CLASH_PBS] = self.pbVar.get()
if prefs[CLASH_PBS]:
prefs[CLASH_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[CLASH_COLOR])
self.pbWidthEntry.invoke()
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width")
prefs[CLASH_WIDTH] = float(self.pbWidthEntry.getvalue())
else:
pbColor = None
prefs[CLASH_METHOD] = self.buttonInfo[self.computeType.index(
self.computeType.getvalue())][1]
prefs[CLASH_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addClashColumn(prefs[CLASH_THRESHOLD],
prefs[HBOND_ALLOWANCE], prefs[CLASH_METHOD],
prefs[CLASH_PBS], pbColor, prefs[CLASH_WIDTH],
prefs[CLASH_IGNORE_OTHERS])
def destroy(self):
self.rotDialog = None
if prefs[CLASH_PBS]:
from DetectClash import nukeGroup
nukeGroup()
ModelessDialog.destroy(self)
def _revertDefaults(self):
from prefs import defaults
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(), command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(), text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size-2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(), command=self._desig2CB,
pady=pady, text="Designate selection as second set"
).grid(row=3, column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size-4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(desigGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text="Check designated\natoms"
" against:", command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters", hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(
row=0, column=0)
Tkinter.Button(defaultsFrame, text="clash", pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame, text="contact", pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(
row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame, labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(prefs[BOND_SEPARATION]),
items=[str(i+2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(
row=0, column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(), text="Ignore intra-"
"residue contacts", variable=self.ignoreIntraResVar,
command=self._checkContinuous
).grid(row=4)
actionGroup = Pmw.Group(parent, tag_text=
"Treatment of Clash/Contact Atoms", hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(), text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f, text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f, text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f, noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" file", variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" reply log", variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent, tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text= "Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
class HbondDialog(ModelessDialog):
title = "Hydrogen Bond Params"
buttons = ("OK", "Apply", "Close")
help = "ContributedSoftware/rotamers/rotamers.html#hbonds"
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter, Pmw
row = 0
f = Tkinter.Frame(parent)
f.grid(row=row, column=0)
self.drawHbondsVar = Tkinter.IntVar(parent)
self.drawHbondsVar.set(prefs[DRAW_HBONDS])
Tkinter.Checkbutton(f,
text="Draw H-bonds of color",
variable=self.drawHbondsVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.hbColorWell = ColorWell(f,
noneOkay=False,
color=prefs[HBOND_COLOR])
self.hbColorWell.grid(row=0, column=1)
self.hbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
value=str(prefs[HBOND_WIDTH]))
self.hbWidthEntry.grid(row=0, column=2)
row += 1
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, column=0)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[HBOND_IGNORE_OTHERS])
Tkinter.Checkbutton(parent,
text="Ignore H-bonds with other"
" models",
variable=self.ignoreOthersVar).grid(row=row,
column=0,
sticky='w')
row += 1
def Apply(self):
dhb = self.drawHbondsVar.get()
prefs[DRAW_HBONDS] = dhb
prefs[HBOND_COLOR] = self.hbColorWell.rgba
bc = chimera.MaterialColor(*prefs[HBOND_COLOR])
self.hbWidthEntry.invoke()
if not self.hbWidthEntry.valid():
self.enter()
raise UserError("Invalid H-bond width")
lw = prefs[HBOND_WIDTH] = float(self.hbWidthEntry.getvalue())
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()
self.groupName = "H-bonds for rotamers of %s" % (
self.rotDialog.residue)
prefs[HBOND_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addHbondColumn(dhb, bc, lw, relax, distSlop, angleSlop,
twoColors, rc, self.groupName,
prefs[HBOND_IGNORE_OTHERS])
def destroy(self):
self.rotDialog = None
if hasattr(self, 'groupName'):
from Rotamers import nukeGroup
nukeGroup(self.groupName)
ModelessDialog.destroy(self)
def _addRegionsPage(self, page):
def showSelChange(opt):
self.mav.prefs[SHOW_SEL] = opt.get()
self.mav.regionBrowser._showSelCB()
tkoptions.BooleanOption(page, 0, "Show Chimera selection as region",
self.mav.prefs[SHOW_SEL], showSelChange)
def selColorChange(opt, prefName):
val = opt.get()
self.mav.prefs[prefName] = val
from RegionBrowser import SEL_REGION_NAME
selRegion = self.mav.regionBrowser.getRegion(SEL_REGION_NAME)
if selRegion:
if prefName == SEL_REGION_BORDER:
selRegion.setBorderRGBA(val)
else:
selRegion.setInteriorRGBA(val)
tkoptions.RGBAOption(page, 1, "Chimera selection region border color",
self.mav.prefs[SEL_REGION_BORDER],
lambda o: selColorChange(o, SEL_REGION_BORDER))
tkoptions.RGBAOption(page, 2,
"Chimera selection region interior color",
self.mav.prefs[SEL_REGION_INTERIOR],
lambda o: selColorChange(o, SEL_REGION_INTERIOR))
tkoptions.RGBAOption(
page, 3, "New region border color",
self.mav.prefs[NEW_REGION_BORDER],
lambda o: self.mav.prefs.update({NEW_REGION_BORDER: o.get()}))
tkoptions.RGBAOption(
page, 4, "New region interior color",
self.mav.prefs[NEW_REGION_INTERIOR],
lambda o: self.mav.prefs.update({NEW_REGION_INTERIOR: o.get()}))
tkoptions.IntOption(page,
5,
"Use ellipsis for names longer than",
self.mav.prefs[REGION_NAME_ELLIPSIS],
self._newRegionEllipsis,
width=3,
min=4)
widgetData = [
("successful matches", MATCH_REG_ACTIVE, MATCH_REG_EDGE,
MATCH_REG_FILL),
("mismatches", ERROR_REG_ACTIVE, ERROR_REG_EDGE, ERROR_REG_FILL),
("structure gaps", GAP_REG_ACTIVE, GAP_REG_EDGE, GAP_REG_FILL)
]
assocGroup = Pmw.Group(page, tag_text="Structure association")
assocGroup.grid(row=6, column=0, columnspan=2)
from CGLtk.color.ColorWell import ColorWell
inside = assocGroup.interior()
inside.columnconfigure(0, weight=1)
inside.columnconfigure(3, weight=1)
for i, regPrefs in enumerate(widgetData):
descript, activePref, edgePref, fillPref = regPrefs
rv = Tkinter.IntVar(inside)
rv.set(self.mav.prefs[activePref])
Tkinter.Checkbutton(
inside,
variable=rv,
text="Draw region depicting %s" % descript,
command=lambda var=rv, prefName=activePref: self.mav.prefs.
update({prefName: var.get()})).grid(row=2 * i,
column=0,
columnspan=4,
sticky='w')
Tkinter.Label(inside, text="Border:").grid(row=2 * i + 1,
column=0,
sticky='e')
ColorWell(inside,
color=self.mav.prefs[edgePref],
noneOkay=True,
wantAlpha=False,
callback=lambda c, prefName=edgePref: self.mav.prefs.
update({prefName: c})).grid(row=2 * i + 1,
column=1,
sticky='w')
Tkinter.Label(inside, text=" Interior:").grid(row=2 * i + 1,
column=2,
sticky='e')
ColorWell(inside,
color=self.mav.prefs[fillPref],
noneOkay=True,
wantAlpha=False,
callback=lambda c, prefName=fillPref: self.mav.prefs.
update({prefName: c})).grid(row=2 * i + 1,
column=3,
sticky='w')
def _hlistKw(self, model, colNum):
vt = _valueTypes[self.columnMap[colNum]]
vf = _valueFuncs[self.columnMap[colNum]]
kw = {'itemtype': vt}
txt = None
img = None
if vt == 'text':
txt = vf(model)
if not isinstance(txt, basestring):
txt, bcolor = txt
if bcolor is not None:
if not isinstance(bcolor, basestring):
if hasattr(bcolor, 'rgba'):
rgba = bcolor.rgba()
else:
rgba = bcolor
from CGLtk.color import rgba2tk
bcolor = rgba2tk(rgba)
fcolor = CGLtk.textForeground(bcolor, self.modelTable)
kw['style'] = Tix.DisplayStyle("text",
refwindow=self.modelTable,
background=bcolor,
foreground=fcolor,
selectforeground=bcolor)
else:
kw['style'] = self.textStyle
elif vt == 'image':
img = vf(model)
elif vt == 'imagetext':
img, txt = vf(model)
elif vt == 'toggle':
kw['itemtype'] = 'window'
bool, cb = vf(model)
togKw = {
'command':
# avoid holding references to model
lambda cb=cb, i=self.models.index(model), b=not bool: cb(
self.models[i], b),
'indicatoron':
0,
'borderwidth':
0
}
if bool:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_on')
else:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_off')
toggle = Tkinter.Checkbutton(self.modelTable.hlist, **togKw)
kw['window'] = toggle
kw['style'] = self.checkButtonStyle
elif vt == 'well':
color, noneOkay, alphaOkay, cb = vf(model)
if color is False:
kw['itemtype'] = 'text'
txt = ""
else:
kw['itemtype'] = 'window'
if isinstance(color, chimera.MaterialColor):
color = color.rgba()
def wellCB(clr, cb=cb, mdl=model):
if clr is not None:
clr = chimera.MaterialColor(*clr)
cb(mdl, clr)
from CGLtk.color.ColorWell import ColorWell
kw['window'] = ColorWell(self.modelTable.hlist,
color,
callback=wellCB,
width=18,
height=18,
noneOkay=noneOkay,
wantAlpha=alphaOkay)
kw['style'] = self.colorWellStyle
else:
raise ValueError("Unknown column type: '%s'" % vt)
if txt != None:
kw['text'] = str(txt)
if img != None:
kw['image'] = self.modelTable.tk.call('tix', 'getimage', img)
return kw
class HbondDialog(ModelessDialog):
title = "Hydrogen Bond Params"
buttons = ("OK", "Apply", "Close")
help = "ContributedSoftware/rotamers/rotamers.html#hbonds"
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter, Pmw
row = 0
f = Tkinter.Frame(parent)
f.grid(row=row, column=0)
self.drawHbondsVar = Tkinter.IntVar(parent)
self.drawHbondsVar.set(prefs[DRAW_HBONDS])
Tkinter.Checkbutton(f, text="Draw H-bonds of color",
variable=self.drawHbondsVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.hbColorWell = ColorWell(f, noneOkay=False,
color=prefs[HBOND_COLOR])
self.hbColorWell.grid(row=0, column=1)
self.hbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
value=str(prefs[HBOND_WIDTH]))
self.hbWidthEntry.grid(row=0, column=2)
row += 1
from FindHBond.gui import RelaxParams
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, column=0)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[HBOND_IGNORE_OTHERS])
Tkinter.Checkbutton(parent, text="Ignore H-bonds with other"
" models", variable=self.ignoreOthersVar).grid(row=row,
column=0, sticky='w')
row += 1
def Apply(self):
dhb = self.drawHbondsVar.get()
prefs[DRAW_HBONDS] = dhb
prefs[HBOND_COLOR] = self.hbColorWell.rgba
bc = chimera.MaterialColor(*prefs[HBOND_COLOR])
self.hbWidthEntry.invoke()
if not self.hbWidthEntry.valid():
self.enter()
raise UserError("Invalid H-bond width")
lw = prefs[HBOND_WIDTH] = float(self.hbWidthEntry.getvalue())
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()
self.groupName = "H-bonds for rotamers of %s" % (
self.rotDialog.residue)
prefs[HBOND_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addHbondColumn(dhb, bc, lw, relax, distSlop,
angleSlop, twoColors, rc, self.groupName,
prefs[HBOND_IGNORE_OTHERS])
def destroy(self):
self.rotDialog = None
if hasattr(self, 'groupName'):
from Rotamers import nukeGroup
nukeGroup(self.groupName)
ModelessDialog.destroy(self)
def _fillLabelsPage(self, page):
page.columnconfigure(0, weight=1)
page.columnconfigure(1, weight=1)
page.columnconfigure(2, weight=1)
row = 0
from CGLtk.Table import SortableTable
self.labelTable = SortableTable(page, automultilineHeaders=False)
self.labelTable.addColumn("Label [(x, y) text]", self._labelListing,
anchor='w')
self.labelTable.addColumn("Shown", "shown", format=bool)
self.labelTable.setData(self.model.labels)
self.labelTable.launch(browseCmd=self._tableCB, selectMode="single")
self.labelTable.grid(row=row, column=0, columnspan=3, sticky="nsew")
page.rowconfigure(row, weight=1)
row += 1
self.labelText = Pmw.ScrolledText(page, labelpos='w',
label_text="Text", text_height=3, text_width=20,
text_wrap='none', text_state='disabled',
text_exportselection=False)
text = self.labelText.component('text')
text.bind("<<Modified>>", self._textCB)
text.bind("<<Selection>>", self._updateTextAttrWidgets)
self.labelText.grid(row=row, column=0,
sticky='nsew', columnspan=3)
page.rowconfigure(row, weight=1)
row += 1
self.labelSymbolMenu = Pmw.OptionMenu(page, labelpos='w',
label_text="Insert symbol:", command=self._insertSymbol,
items=[
u'\N{GREEK SMALL LETTER ALPHA}',
u'\N{GREEK SMALL LETTER BETA}',
u'\N{GREEK SMALL LETTER GAMMA}',
u'\N{GREEK SMALL LETTER DELTA}',
u'\N{GREEK SMALL LETTER EPSILON}',
u'\N{GREEK SMALL LETTER PI}',
u'\N{GREEK SMALL LETTER PHI}',
u'\N{GREEK SMALL LETTER CHI}',
u'\N{GREEK SMALL LETTER PSI}',
u'\N{GREEK SMALL LETTER OMEGA}',
u'\N{LEFTWARDS ARROW}',
u'\N{RIGHTWARDS ARROW}',
u'\N{LEFT RIGHT ARROW}',
u'\N{UPWARDS ARROW}',
u'\N{DOWNWARDS ARROW}',
u'\N{SUPERSCRIPT TWO}',
u'\N{SUPERSCRIPT THREE}',
u'\N{DEGREE SIGN}',
u'\N{LATIN CAPITAL LETTER A WITH RING ABOVE}',
"more..."
])
self.labelSymbolMenu.grid(row=row, column=0, columnspan=3)
row += 1
colorHouse = Pmw.LabeledWidget(page, labelpos='w',
label_text="Color")
colorHouse.grid(row=row, column=0, rowspan=3)
from CGLtk.color.ColorWell import ColorWell
self.colorWell = ColorWell(colorHouse.interior(),
color=self._contrastWithBG(), callback=self._colorCB)
self.colorWell.grid()
from chimera.tkoptions import IntOption
self.labelFontSize = IntOption(page, row, "Font size", 24,
self._labelChangeCB, startCol=1, min=1,
attribute="size", width=3)
row += 1
self.labelFontStyle = FontStyle(page, row, "Font style",
oglFont.normal, self._labelChangeCB, startCol=1)
row += 1
self.labelFontTypeface = FontTypeface(page, row, "Font typeface",
FONT_TYPEFACE_VALUES[0],
self._labelChangeCB, startCol=1)
row += 1
if self.model.curLabel:
self.changeToLabel(self.model.curLabel, force=True)
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(parent, labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew",
columnspan=2)
Pmw.OptionMenu(parent, command=self._menuCB, initialitem="3",
items=[str(x) for x in range(2, 12)], labelpos='w',
label_text="Number of colors/values:").grid(row=1,
column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(parent, 3,
"Distance-dependent dielectric", True, None, balloon=
"If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant",
4.0, None)
self.surfDist = FloatOption(parent, 5, "Distance from surface",
1.4, None, balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(interior, text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))),
slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue name-based", command=
self._switchHisList).grid(row=1, sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f, text="HID/HIE/HIP = delta/epsilon/both").grid(
row=0, sticky='w')
self.hisDefault = Pmw.OptionMenu(f, initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"], labelpos='w',
label_text="HIS = ", command=lambda a, s=self:
setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, 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=3, sticky='w')
Tkinter.Button(parent, pady=0, command=self._colorKeyCB,
text="Create corresponding color key").grid(row=7,
column=0, columnspan=2)
self.hisChanged = False
class ClashDialog(ModelessDialog):
title = "Rotamer Clash Params"
buttons = ("OK", "Apply", "Close")
help = "ContributedSoftware/rotamers/rotamers.html#clashes"
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def fillInUI(self, parent):
row = 0
from DetectClash.gui import ClashDef, HbondAllow
self.clashDef = ClashDef(parent, value=prefs[CLASH_THRESHOLD])
self.clashDef.grid(row=row, column=0, sticky='w')
row += 1
self.hbondAllow = HbondAllow(parent, value=prefs[HBOND_ALLOWANCE])
self.hbondAllow.grid(row=row, column=0, sticky='w')
row += 1
import Pmw, Tkinter
Tkinter.Button(parent,
text="Default criteria",
pady=0,
command=self._revertDefaults).grid(row=row)
row += 1
self.computeType = Pmw.RadioSelect(parent,
pady=0,
buttontype='radiobutton',
labelpos='w',
label_text="Column Value:",
orient='vertical',
frame_borderwidth=2,
frame_relief="ridge")
self.buttonInfo = [
("Number of clashes", "num"),
("Sum of overlaps", "sum"),
]
for label, short in self.buttonInfo:
self.computeType.add(label)
if prefs[CLASH_METHOD] == short:
default = label
self.computeType.invoke(default)
self.computeType.grid(row=row, column=0)
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, sticky='w')
self.pbVar = Tkinter.IntVar(parent)
self.pbVar.set(prefs[CLASH_PBS])
Tkinter.Checkbutton(f,
text="Draw pseudobonds of color",
variable=self.pbVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f,
noneOkay=False,
color=prefs[CLASH_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
value=str(prefs[CLASH_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
row += 1
self.ignoreOthersVar = Tkinter.IntVar(parent)
self.ignoreOthersVar.set(prefs[CLASH_IGNORE_OTHERS])
Tkinter.Checkbutton(parent,
text="Ignore clashes with other"
" models",
variable=self.ignoreOthersVar).grid(row=row,
column=0,
sticky='w')
row += 1
def Apply(self):
from chimera import UserError
self.clashDef.invoke()
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow.invoke()
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[CLASH_PBS] = self.pbVar.get()
if prefs[CLASH_PBS]:
prefs[CLASH_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[CLASH_COLOR])
self.pbWidthEntry.invoke()
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width")
prefs[CLASH_WIDTH] = float(self.pbWidthEntry.getvalue())
else:
pbColor = None
prefs[CLASH_METHOD] = self.buttonInfo[self.computeType.index(
self.computeType.getvalue())][1]
prefs[CLASH_IGNORE_OTHERS] = self.ignoreOthersVar.get()
self.rotDialog.addClashColumn(prefs[CLASH_THRESHOLD],
prefs[HBOND_ALLOWANCE],
prefs[CLASH_METHOD], prefs[CLASH_PBS],
pbColor, prefs[CLASH_WIDTH],
prefs[CLASH_IGNORE_OTHERS])
def destroy(self):
self.rotDialog = None
if prefs[CLASH_PBS]:
from DetectClash import nukeGroup
nukeGroup()
ModelessDialog.destroy(self)
def _revertDefaults(self):
from prefs import defaults
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
class DetectClashDialog(ModelessDialog):
name = "detect clashes"
title = "Find Clashes/Contacts"
provideStatus = True
statusPosition = "above"
help = "ContributedSoftware/findclash/findclash.html"
FREQ_APPLY = "when OK/Apply clicked"
FREQ_MOTION = "after relative motions (until dialog closed)"
FREQ_CONTINUOUS = "continuously (until dialog closed)"
CHECK_SET = "second set of designated atoms"
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(), command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(), text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size-2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(), command=self._desig2CB,
pady=pady, text="Designate selection as second set"
).grid(row=3, column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size-4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(desigGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text="Check designated\natoms"
" against:", command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters", hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(
row=0, column=0)
Tkinter.Button(defaultsFrame, text="clash", pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame, text="contact", pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(
row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame, labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(prefs[BOND_SEPARATION]),
items=[str(i+2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(
row=0, column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(), text="Ignore intra-"
"residue contacts", variable=self.ignoreIntraResVar,
command=self._checkContinuous
).grid(row=4)
actionGroup = Pmw.Group(parent, tag_text=
"Treatment of Clash/Contact Atoms", hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(), text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f, text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f, text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f, noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" file", variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" reply log", variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent, tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text= "Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
def OK(self, *args):
# use main status line if dialog closing
from chimera.replyobj import status
self.status = status
ModelessDialog.OK(self, *args)
def Apply(self, *args):
# workaround: remove pseudobonds before recreating colors
# so C++ layer doesn't end up with pointers to deleted
# colors in obscure circumstances
from DetectClash import nukeGroup
nukeGroup()
from chimera import UserError
self.status("")
checkAtoms = self.designated.atoms()
if not checkAtoms:
self.enter()
raise UserError("No atoms designated for clash detection")
self.clashDef['command'] = None
self.clashDef.invoke()
self.clashDef['command'] = self._checkContinuous
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount"
" (in Clash/Contact Parameters)")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow['command'] = None
self.hbondAllow.invoke()
self.hbondAllow['command'] = self._checkContinuous
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount"
" (in Clash/Contact Parameters)")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[BOND_SEPARATION] = int(self.bondsApart.getvalue())
prefs[IGNORE_INTRA_RES] = self.ignoreIntraResVar.get()
checkVal = self.checkLocButtons.getvalue()
if checkVal == "themselves":
test = "self"
elif checkVal == "all other atoms":
test = "others"
elif checkVal == "other atoms in same model":
test = "model"
else:
test = self.designated2.atoms()
if not test:
self.enter()
raise UserError("No second-set atoms designated")
actionAttr = prefs[ACTION_ATTR] = self.actionAttrVar.get()
actionSelect = prefs[ACTION_SELECT] = self.actionSelVar.get()
actionColor = prefs[ACTION_COLOR] = self.actionColorVar.get()
actionPseudobonds = prefs[ACTION_PSEUDOBONDS] = \
self.actionPBVar.get()
actionWriteInfo = prefs[ACTION_WRITEINFO] = \
self.actionWriteInfoVar.get()
actionLogInfo = prefs[ACTION_REPLYLOG] = \
self.actionLogInfoVar.get()
if self.freqButtons.getvalue() != self.FREQ_APPLY:
actionAttr = actionWriteInfo = actionLogInfo = False
if not actionAttr and not actionSelect and not actionColor \
and not actionPseudobonds and not actionWriteInfo \
and not actionLogInfo:
self.enter()
raise UserError("No actions selected for clashes")
self.status("Checking for clashes")
clashColor = nonclashColor = None
if actionColor:
prefs[CLASH_COLOR] = self.clashColorWell.rgba
prefs[NONCLASH_COLOR] = self.nonclashColorWell.rgba
if prefs[CLASH_COLOR] == None:
clashColor = None
else:
clashColor = chimera.MaterialColor(
*prefs[CLASH_COLOR])
if prefs[NONCLASH_COLOR] == None:
nonclashColor = None
else:
nonclashColor = chimera.MaterialColor(
*prefs[NONCLASH_COLOR])
pbColor = None
if actionPseudobonds:
prefs[PB_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[PB_COLOR])
self.pbWidthEntry['command'] = None
self.pbWidthEntry.invoke()
self.pbWidthEntry['command'] = self._checkContinuous
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width "
"(in Treatment of Clash/Contact Atoms)")
prefs[PB_WIDTH] = float(self.pbWidthEntry.getvalue())
from DetectClash import cmdDetectClash
if actionWriteInfo:
saveFile = "-"
else:
saveFile = None
clashes = cmdDetectClash(checkAtoms, test=test,
overlapCutoff=prefs[CLASH_THRESHOLD],
hbondAllowance=prefs[HBOND_ALLOWANCE],
bondSeparation=prefs[BOND_SEPARATION],
ignoreIntraRes=prefs[IGNORE_INTRA_RES],
setAttrs=actionAttr,
selectClashes=actionSelect,
colorClashes=actionColor,
clashColor=clashColor, nonclashColor=nonclashColor,
makePseudobonds=actionPseudobonds,
pbColor=pbColor, lineWidth=prefs[PB_WIDTH],
saveFile=saveFile, log=actionLogInfo,
summary=self.status)
if actionAttr:
from ShowAttr import ShowAttrDialog
from chimera import dialogs
from DetectClash import attrName
d = dialogs.display(ShowAttrDialog.name)
d.configure(attrsOf="atoms", attrName=attrName,
mode="Render")
def Close(self):
ModelessDialog.Close(self)
if self.freqButtons.getvalue() != self.FREQ_APPLY:
self.freqButtons.invoke(self.FREQ_APPLY)
def _checkContinuous(self, *args):
if self.freqButtons.getvalue() == self.FREQ_CONTINUOUS:
self.Apply()
def _clashDefaultsCB(self):
from prefs import defaults
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self._checkContinuous()
def _clearHandlers(self):
while self._handlers:
trigName, handler = self._handlers.popitem()
chimera.triggers.deleteHandler(trigName, handler)
def _contactDefaultsCB(self):
self.hbondAllow.setvalue("0.0")
self.clashDef.setvalue("-0.4")
self._checkContinuous()
def _desigCB(self):
self.designated.clear()
self.designated.add(chimera.selection.currentAtoms())
self._updateDesigStatus()
def _desig2CB(self):
self.designated2.clear()
self.designated2.add(chimera.selection.currentAtoms())
self._locButtonCB()
self._updateDesig2Status()
def _freqChangeCB(self, freqVal):
self._clearHandlers()
if freqVal == self.FREQ_APPLY:
self.assignAttrButton.configure(state='normal')
self.writeInfoButton.configure(state='normal')
self.logInfoButton.configure(state='normal')
return
self.assignAttrButton.configure(state='disabled')
self.writeInfoButton.configure(state='disabled')
self.logInfoButton.configure(state='disabled')
def modCoordSets(trigName, myData, changes):
if changes.modified:
self.Apply()
self._handlers['CoordSet'] = chimera.triggers.addHandler(
'CoordSet', modCoordSets, None)
def justCoordSets(trigName, myData, changes):
if 'activeCoordSet changed' in changes.reasons:
self.Apply()
self._handlers['Molecule'] = chimera.triggers.addHandler(
'Molecule', justCoordSets, None)
if freqVal == self.FREQ_MOTION:
self._handlers[chimera.MOTION_STOP] = chimera.triggers\
.addHandler(chimera.MOTION_STOP,
self._motionCB, None)
elif freqVal == self.FREQ_CONTINUOUS:
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
self._motionCB()
self._handlers['OpenState'] = chimera.triggers\
.addHandler('OpenState', preCB, None)
self.Apply()
def _locButtonCB(self, butName=None):
checkSetBut = self.checkLocButtons.button(self.CHECK_SET)
if self.checkLocButtons.getvalue() == self.CHECK_SET \
and not self.designated2.atoms():
checkSetBut.config(fg="red", activeforeground="red")
else:
checkSetBut.config(fg="black", activeforeground="black")
self._updateDesig2Status()
def _motionCB(self, *args):
# if all molecule activities are the same (i.e. no possible
# relative motion), do nothing
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
self.Apply()
return
def _updateDesigStatus(self):
numAtoms = len(self.designated.atoms())
if numAtoms:
statusText = "%d atoms designated" % numAtoms
color = 'blue'
else:
statusText = "No atoms designated"
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desigStatus.config(text=statusText, fg=color)
self._checkContinuous()
def _updateDesig2Status(self):
numAtoms = len(self.designated2.atoms())
checkSet = self.checkLocButtons.getvalue() == self.CHECK_SET
color = 'black'
if numAtoms:
statusText = "Second set: %d atoms" % numAtoms
else:
statusText = "No second set"
if checkSet:
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desig2Status.config(text=statusText, fg=color)
if checkSet:
self._checkContinuous()