def __init__(self, parent):
from chimera.tkoptions import IntOption, FloatOption
Tkinter.Frame.__init__(self, parent)
self.nsteps = IntOption(self, 0, "Steps", 100, None)
self.stepsize = FloatOption(self,
1,
"Step size (A)",
0.02,
None,
min=0.0001,
max=1.0)
self.interval = IntOption(self, 2, "Update interval", 10, None)
self.freeze = FreezeOption(self, 3, "Fixed atoms", base.FreezeNone,
None)
def fillInUI(self, parent):
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption
Tkinter.Label(parent, text="Cluster trajectory", relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.useSel = BooleanOption(
parent, 4, "Cluster based on "
"current selection, if any", True, None)
self.ignoreBulk = BooleanOption(parent, 5, "Ignore solvent/"
"ions", True, None)
self.ignoreHyds = BooleanOption(parent, 6, "Ignore hydrogens", True,
None)
def fillInUI(self, parent):
from chimera.widgets import MoleculeOptionMenu
from chimera.tkoptions import IntOption, BooleanOption, \
InputFileOption, StringOption, EnumOption
import itertools
info = Tk.Label(parent, justify=Tk.LEFT, wraplength=300, text=
"Model alternate conformations of loops using "
"Modeller from <http://salilab.org/>.\n"
"First select the loops you wish to model."
" Then choose the number of models "
"you wish to generate.")
info.pack(ipadx=2, ipady=2)
options = Tk.Frame(parent)
options.columnconfigure(0, pad=2)
options.columnconfigure(1, pad=2)
row = itertools.count()
molRow = row.next()
text = Tk.Label(options,
text="Restrict selections to molecule:")
text.grid(row=molRow, column=0)
self.molecules = MoleculeOptionMenu(options)
self.molecules.grid(row=molRow, column=1, sticky=Tk.W)
self.turnsOnly = BooleanOption(options, row.next(),
"Restrict selections to turns", True, None)
self.hetatms = BooleanOption(options, row.next(),
"Include HETATM residues", False, None)
self.waters = BooleanOption(options, row.next(),
"Include waters", False, None)
self.waters.disable()
self.nucleic = BooleanOption(options, row.next(),
"Include nucleic acids", False, None)
self.nucleic.disable()
self.count = IntOption(options, row.next(), "Number of models",
10, None, min=1, sticky=Tk.W)
#self.start = IntOption(options, row.next(),
# "Starting model number", 1, None, min=0)
class Refinement(EnumOption):
values = ('very fast', 'fast', 'slow', 'very slow',
'slow large', 'none')
self.refine = Refinement(options, row.next(), "Refinement",
'fast', None)
button = Tk.Button(options, text="Prune selection",
command=self.prune)
button.grid(row=row.next(), column=0, columnspan=2, pady=2)
self.start = 1
hr = Tk.Frame(options, relief=Tk.GROOVE, borderwidth=1, height=2)
hr.grid(row=row.next(), columnspan=2, sticky='ew')
# modeller location
self.modeller = InputFileOption(options, row.next(),
"Modeller location", "mod9v2", None)
# temporary prefix -- TODO: add unique id
#self.tempdir = StringOption(options, row.next(),
# "Temporary file prefix", "modtmp", None)
options.pack()
def fillInUI(self, parent): SaveModal.fillInUI(self, parent) parent = self.clientArea parent.columnconfigure(0, weight=1) parent.columnconfigure(1, weight=1) parent = Tk.Frame(parent) parent.grid() self.quality = IntOption(parent, 0, 'JPEG quality', DEFAULT_JPEG_QUALITY, None, min=5, max=95, width=4, sticky=Tk.E) if self.millerBrowser.getFilter() != 'JPEG': self.quality.gridUnmanage()
def fillInUI(self, parent):
OpenModeless.fillInUI(self, parent)
group = Pmw.Group(self.clientArea, tag_text='Further info')
group.grid(row=0, column=0, sticky='nsew')
self.catName = StringOption(group.interior(), 0, "group name", None,
None)
class PBLineWidthOption(LineWidthOption):
default = prefs["line width"]
balloon = "Width of pseudobonds (in pixels)"
self.lineWidth = PBLineWidthOption(group.interior(), 1, None, None,
None)
self.clearCat = BooleanOption(group.interior(), 2,
"clear group of previous pseudobonds", 1,
None)
self.leftModel = IntOption(group.interior(), 3,
"first column specifiers default to model",
0, None)
self.rightModel = IntOption(
group.interior(), 4, "second column specifiers default to model",
0, None)
def fillInUI(self, parent): from chimera.widgets import MoleculeScrolledListBox self.molListBox = MoleculeScrolledListBox(parent, listbox_selectmode='extended', labelpos='w', label_text="Molecules to combine/copy:") if self.initModels: self.molListBox.setvalue(self.initModels) self.molListBox.grid(row=0, column=0, columnspan=2, sticky="nsew") parent.rowconfigure(0, weight=1) parent.columnconfigure(1, weight=1) from chimera.tkoptions import StringOption, IntOption self.molNameEntry = StringOption(parent, 1, "New model's" " name", "combination", None) curIDs = set([i1 for i1, i2 in openModels.listIds()]) mid = 0 while mid in curIDs: mid += 1 self.modelID = IntOption(parent, 2, "New model's ID", mid, None) from chimera.widgets import MoleculeOptionMenu self.refMolMenu = MoleculeOptionMenu(parent, labelpos='w', label_text="Coordinate system of:", initialitem=self.initModels[0]) self.refMolMenu.grid(row=3, column=0, columnspan=2, sticky='w') import Pmw chb = self.chainHandlingButtons = Pmw.RadioSelect(parent, buttontype="radiobutton", labelpos='w', label_text="If original molecules have duplicate\n" "single-letter chain IDs, then:", orient="vertical") self.buttonTexts = ["rename them uniquely", "retain them (residues may be renumbered)"] for bt in self.buttonTexts: chb.add(bt) chb.setvalue(self.buttonTexts[0]) chb.grid(row=4, column=0, columnspan=2) import Tkinter self.closeModelsVar = Tkinter.IntVar(parent) self.closeModelsVar.set(False) Tkinter.Checkbutton(parent, text="Close source models", variable=self.closeModelsVar).grid( row=5, column=0, columnspan=2)
def _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 fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
self.clientArea.columnconfigure(1, weight=1)
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(self.clientArea,
0,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(self.clientArea,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(self.clientArea,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.roundtrip = BooleanOption(
self.clientArea,
4, "Encode"
' forward then backward ("roundtrip")',
prefs[RECORDER_ROUNDTRIP],
None,
balloon="Encode the frames in forward and then reverse\n"
"order so that if the movie is played as a loop\n"
"the motion seems continuous")
class FrameQuality(BooleanOption):
labels = ["screen", "supersampled"]
self.supersample = FrameQuality(
self.clientArea,
5,
"Frame quality",
prefs[RECORDER_SUPERSAMPLE],
self.supersampleCB,
balloon="Whether each frame should be taken as is from\n"
"the screen (fast) or redrawn at higher quality\n"
"with several samples per pixel.")
from chimera.printer import SupersampleOption
self.samples = SupersampleOption(self.clientArea, 6, "Samples",
prefs[RECORDER_SAMPLES], None)
self.supersampleCB()
self.raytrace = BooleanOption(self.clientArea, 7, "Raytrace"
" with POV-Ray",
prefs[RECORDER_RAYTRACE], None)
def povOptCB():
from chimera.dialogs import display
d = display("preferences")
from chimera.printer import POVRAY_SETUP
d.setCategoryMenu(POVRAY_SETUP)
Tkinter.Button(self.clientArea,
text="POV-Ray Options",
pady=0,
command=povOptCB).grid(row=8, column=0, columnspan=2)
self.recordArgs = StringOption(
self.clientArea,
9,
"Additional recording options",
prefs[RECORDER_RECORD_ARGS],
None,
balloon="Options (other than 'supersample' and 'raytrace')\n"
"for recording frames as per Chimera's 'movie record'"
" command")
self.encodeArgs = StringOption(
self.clientArea,
10,
"Additional encoding options",
prefs[RECORDER_ENCODE_ARGS],
None,
balloon="Options (other than 'mformat', 'output', and\n"
"'roundtrip') for composing the frames into the\n"
"final animation as per Chimera's 'movie encode'\n"
"command")
Tkinter.Label(self.clientArea,
text="On some computers it may be necessary to make sure"
" that no\nwindows occlude the main Chimera graphics"
" window (even\npartially) during non-raytraced movie"
" recording").grid(row=11, column=0, columnspan=2)
def fillInUI(self, master):
self._ModelTrigger = None
#self._SetupTrigger = None
self._SizeTrigger = None
self.raytrace = None
# Image Size
imageSetup = Tix.LabelFrame(master, label="Image Size")
imageSetup.pack(fill=Tk.X, ipadx=2, ipady=2)
subframe = imageSetup.frame
#subframe = Tk.Frame(imageSetup.frame)
#subframe.pack(fill=Tk.BOTH, expand=1)
# add in conversion factor for pixels and graphics screen
from chimera import tkgui
win = tkgui.app.graphics
res = tkgui.getScreenMMWidth() / win.winfo_screenwidth()
convert['pixels'] = mm2pt(res)
self.matchAspect = Tk.BooleanVar(master)
self.matchAspect.set(1)
self.usePrint = Tk.BooleanVar(master)
self.usePrint.set(preferences.get(IMAGE_SETUP, USE_PRINT_UNITS))
import itertools
row = itertools.count()
self.showUsePrint = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.usePrint, highlightthickness=0,
text=USE_PRINT_UNITS,
command=self._updateUsePrint)
self.showUsePrint.grid(columnspan=2, row=row.next(), sticky=Tk.W)
w, h = chimera.viewer.windowSize
self.units = ImageUnitsOption(subframe, row.next(), UNITS,
'pixels', self.updateImageUnits)
self.iWidth = FloatOption(subframe, row.next(), 'Image width',
w, self.updateImageWidth, min=1e-10)
self.iHeight = FloatOption(subframe, row.next(), 'Image height',
h, self.updateImageHeight, min=1e-10)
matchAspect = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.matchAspect, highlightthickness=0,
text="Maintain current aspect ratio",
command=self.updateMatchAspect)
matchAspect.grid(columnspan=2, row=row.next(), sticky=Tk.W)
self.grow = Tk.Button(imageSetup.frame, text="Grow to Fit",
command=self.Resize, state=Tk.DISABLED)
fitrow = row.next()
self.grow.grid(row=fitrow, column=0, padx=2, pady=2,
sticky=Tk.NSEW)
self.shrink = Tk.Button(imageSetup.frame, text="Shrink to Fit",
command=lambda f=self.Resize: f(False),
state=Tk.DISABLED)
self.shrink.grid(row=fitrow, column=1, padx=2, pady=2,
sticky=Tk.NSEW)
#fetch = Tk.Button(imageSetup.frame, text="Get Pixels",
# command=self.fetchWindowSize)
#fetch.grid(row=row.next(), column=0, padx=2, pady=2, sticky=Tk.NSEW)
#calc = Tk.Button(imageSetup.frame, text="Image Setup",
# command=self.showImageSetupDialog)
#calc.grid(row=row.next(), column=1, padx=2, pady=2, sticky=Tk.NSEW)
self.printRes = FloatOption(subframe, row.next(), DPI,
preferences.get(IMAGE_SETUP, DPI),
self._updatePrint, min=1)
# Image Information
info = Tix.LabelFrame(master, label="Image Information")
info.pack(fill=Tk.X)
d = Tk.Label(info.frame, text="Description:")
d.grid(columnspan=2, row=0, column=0, sticky=Tk.W, padx=2,
pady=1)
self.description = Tk.Entry(info.frame)
info.frame.grid_columnconfigure(0, weight=1)
info.frame.grid_columnconfigure(1, weight=1)
self.description.grid(columnspan=2, row=1, column=0,
sticky=Tk.EW, padx=2, pady=2)
imageCredits = Tk.Button(info.frame,
text="Image Credits",
command=self.showImageCreditsDialog)
imageCredits.grid(row=2, column=0, padx=2, pady=2)
credit = Tk.Button(info.frame, text="Citing Chimera",
command=lambda: help.display("credits.html"))
credit.grid(row=2, column=1, padx=2, pady=2)
# Image camera
self.raytrace = BooleanOption(master, -1,
'Raytrace with POV-Ray', False,
self._updateRaytrace)
self.raytraceOptions = Tk.Button(master, text=POVRAY_SETUP,
command=self.showPOVRayOptions)
self.raytraceOptions.pack()
self.raytraceOptions.pack_forget()
self.supersample = SupersampleOption(master, -1, SUPERSAMPLE,
preferences.get(IMAGE_SETUP, SUPERSAMPLE),
self._updateSS)
self.adjustFOV = AdjustFOVOption(master, -1, ADJUST_FOV,
preferences.get(IMAGE_SETUP, ADJUST_FOV),
self._updateAdjustFOV)
self.printMode = _PrintModeOption(master, -1,
'Image camera mode', _PrintModeOption.SAME,
self._updatePrintMode)
self.lenticular = IntOption(master, -1,
'Number of lenticular images',
chimera.Camera.lenticularImageCount(),
self._updateLenticular, min=2, width=4)
self.lenticular.forget()
# switch to user's prefered units
self.adjust = convert['pixels']
units = preferences.get(IMAGE_SETUP, UNITS)
self._updateUsePrint()
self.units.set(units)
self.updateImageUnits()
def fillInUI(self, parent):
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption
Tkinter.Label(parent,
text="Create RMSD map of trajectory "
"against itself",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.minRmsd = FloatOption(parent,
4, "Lower RMSD threshold"
" (white)",
prefs[RMSD_MIN],
None,
width=6)
self.maxRmsd = FloatOption(parent,
5, "Upper RMSD threshold"
" (black)",
prefs[RMSD_MAX],
None,
width=6)
self.useSel = BooleanOption(
parent, 6, "Restrict map to "
"current selection, if any", True, None)
self.ignoreBulk = BooleanOption(parent, 7, "Ignore solvent/"
"ions", True, None)
self.ignoreHyds = BooleanOption(parent, 8, "Ignore hydrogens", True,
None)
self.recolor = BooleanOption(parent, 9, "Auto-recolor for"
" contrast", prefs[RMSD_AUTOCOLOR], None)
def fillInUI(self, parent):
Tkinter.Label(parent,
text="Collect positions of selected"
" atoms over trajectory",
relief="ridge",
bd=4).grid(row=0, column=0, columnspan=2, sticky="ew")
startFrame = self.movie.startFrame
endFrame = self.movie.endFrame
from chimera.tkoptions import IntOption, BooleanOption, \
FloatOption, StringOption
self.startFrame = IntOption(parent,
1,
"Starting frame",
startFrame,
None,
min=startFrame,
max=endFrame,
width=6)
numFrames = endFrame - startFrame + 1
defStride = 1 + int(numFrames / 300)
self.stride = IntOption(parent,
2,
"Step size",
defStride,
None,
min=1,
max=numFrames,
width=3)
self.endFrame = IntOption(parent,
3,
"Ending frame",
endFrame,
None,
min=startFrame,
max=endFrame,
width=6)
self.doCutoff = BooleanOption(
parent, 4, 'Limit data collection'
' to within cutoff distance of any "held steady" atoms', True,
None)
self.cutoff = FloatOption(parent,
5,
"Cutoff distance",
prefs[VOLUME_CUTOFF],
None,
width=4)
self.resolution = FloatOption(parent,
6,
"Volume grid spacing",
prefs[VOLUME_RESOLUTION],
None,
min=0.0001,
width=4)
self.volumeName = StringOption(parent,
7,
"Volume data name",
self.movie.ensemble.name,
None,
width=20)
self.byAtomType = BooleanOption(
parent,
8, "Collect data"
" separately for each atom type in selection",
True,
None,
balloon="Create a volume data set for"
" each type of atom type\n(sp2 oxygen, aromatic carbon,"
" etc.) in current selection")