def fillInUI(self, parent):
import Tkinter, Pmw, Tix
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
selectMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Select", menu=selectMenu)
selectMenu.add_command(label="Current Rotamers",
command=self._selCurCB)
selectMenu.add_command(label="All Rotamers", command=self._selAllCB)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
self.addColumnMenu = Tkinter.Menu(self.columnMenu)
self.columnMenu.add_cascade(label="Add", menu=self.addColumnMenu)
for label, ddn in self.dependentDialogInfo:
self.addColumnMenu.add_command(
label=label + "...",
command=lambda name=ddn + "Dialog": self._showDialog(name))
self.columnMenu.add_separator()
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row=0)
self.numChis = len(self.rotamers[0].chis)
row = 1
Tkinter.Label(parent,
text="%s %s rotamers" %
(self.lib.displayName, self.resType)).grid(row=row,
column=0)
row += 1
self.buttonWidgets['OK'].config(state="disabled")
self.buttonWidgets['Apply'].config(state="disabled")
from CGLtk.Table import SortableTable
self.rotTable = SortableTable(parent,
menuInfo=(self.columnMenu, prefs, {},
True))
if not self.tableData:
for i in range(self.numChis):
self.rotTable.addColumn("Chi %d" % (i + 1),
"lambda r: r.chis[%d]" % i,
format="%6.1f")
self.rotTable.addColumn("Probability",
"rotamerProb",
format="%.6f",
font='TkFixedFont')
self.rotTable.setData(self.rotamers)
self.rotTable.launch(browseCmd=self._selRotamerCB,
restoreInfo=self.tableData)
delattr(self, 'tableData')
parent.rowconfigure(row, weight=1)
for tableColumn in range(1):
parent.columnconfigure(tableColumn, weight=1)
self.rotTable.grid(row=row, column=0, sticky="nsew")
row += 1
def fillInUI(self, parent):
from CGLtk.Table import SortableTable
self.blastTable = SortableTable(parent)
if not self.tableData:
self._addColumn("GI", "lambda m: m.gi",
format="%s ", anchor="w")
self._addColumn("PDB", "lambda m: m.pdb or '-'",
format="%s ", anchor="w")
self._addColumn("Evalue", "lambda m: m.evalue",
format="%s")
self._addColumn("Score", "lambda m: m.score",
format="%s")
self._addColumn("Description",
"lambda m: m.description",
format=" %s", anchor="w")
if self.parser:
self.blastTable.setData(self.parser.matches)
else:
self.blastTable.setData([])
self.blastTable.launch(browseCmd=self._selectHitCB,
restoreInfo=self.tableData)
self.blastTable.pack(expand=True, fill="both")
bw = self.buttonWidgets
bw["Show in MAV"].config(state="disabled")
bw["Load Structure"].config(state="disabled")
bw["Quit"].config(state="disabled")
def fillInUI(self, parent):
import Tkinter
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, pack = 'top')
self._makeActionGroup(parent)
from CGLtk.Table import SortableTable
from prefs import colAttr, colOrder, prefs, defaults
self.modBaseTable = SortableTable(parent, menuInfo=(
self.columnMenu,
prefs,
defaults,
False ))
if not self.tableData:
self._addColumn("Model",
"lambda m: m.oslIdent()",
format="%s",
shown=True)
for fieldName in colOrder:
keyName, format = colAttr[fieldName]
self._addColumn(fieldName,
"lambda m: m.modbaseInfo['%s']"
% keyName,
format=format)
self.modBaseTable.setData(self.molList)
chimera.triggers.addHandler("post-frame", self._launchTable,
None)
self.modBaseTable.pack(expand=True, fill="both")
def fillInUI(self, parent):
import Tkinter, Pmw, Tix
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
selectMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Select", menu=selectMenu)
selectMenu.add_command(label="Current Rotamers",
command=self._selCurCB)
selectMenu.add_command(label="All Rotamers",
command=self._selAllCB)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
self.addColumnMenu = Tkinter.Menu(self.columnMenu)
self.columnMenu.add_cascade(label="Add",
menu=self.addColumnMenu)
for label, ddn in self.dependentDialogInfo:
self.addColumnMenu.add_command(label=label + "...",
command=lambda name=ddn+"Dialog":
self._showDialog(name))
self.columnMenu.add_separator()
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row = 0)
self.numChis = len(self.rotamers[0].chis)
row = 1
Tkinter.Label(parent, text="%s %s rotamers" %
(self.lib.displayName, self.resType)).grid(
row=row, column=0)
row += 1
self.buttonWidgets['OK'].config(state="disabled")
self.buttonWidgets['Apply'].config(state="disabled")
from CGLtk.Table import SortableTable
self.rotTable = SortableTable(parent,
menuInfo=(self.columnMenu, prefs, {}, True))
if not self.tableData:
for i in range(self.numChis):
self.rotTable.addColumn("Chi %d" % (i+1),
"lambda r: r.chis[%d]" % i,
format="%6.1f")
self.rotTable.addColumn("Probability", "rotamerProb",
format="%.6f", font='TkFixedFont')
self.rotTable.setData(self.rotamers)
self.rotTable.launch(browseCmd=self._selRotamerCB,
restoreInfo=self.tableData)
delattr(self, 'tableData')
parent.rowconfigure(row, weight=1)
for tableColumn in range(1):
parent.columnconfigure(tableColumn, weight=1)
self.rotTable.grid(row=row, column=0, sticky="nsew")
row += 1
def fillInUI(self, parent):
self.distances = []
self.angleInfo = []
self.numMolecules = len(chimera.openModels.list(
modelTypes=[chimera.Molecule]))
chimera.triggers.addHandler('Molecule', self._molChange, None)
chimera.triggers.addHandler('PseudoBond', self._psbChange, None)
chimera.triggers.addHandler('Atom', self._atomChange, None)
chimera.triggers.addHandler('Model', self._modelChange, None)
distanceMonitor.updateCallbacks.append(self._distUpdateCB)
self.notebook = Pmw.NoteBook(parent,
raisecommand=self._nbRaiseCB,
lowercommand=self._nbLowerCB)
self.notebook.pack(fill='both', expand=1)
self.interfaces = {}
for pn in pageNames:
pageID = pn
## when more tabs shown, maybe do this...
#if '/' in pn:
# parts = pn.split('/')
# pn = "/ ".join(parts)
#if ' ' in pn:
# parts = pn.split(' ')
# pn = '\n'.join(parts)
self.notebook.add(pageID, tab_text=pn)
dp = self.notebook.page(DISTANCES)
from CGLtk.Table import SortableTable
self.distTable = SortableTable(dp)
self.distTable.grid(row=0, column=0, sticky='nsew', rowspan=7)
dp.columnconfigure(0, weight=1)
dp.rowconfigure(4, weight=1)
dp.rowconfigure(5, weight=1)
self.distTable.addColumn("ID", "id", format="%d")
self.distTable.addColumn("Atom 1",
lambda d, s=self: s.atomLabel(d.atoms[0]))
self.distTable.addColumn("Atom 2",
lambda d, s=self: s.atomLabel(d.atoms[1]))
self.distTable.addColumn("Distance", "distance", font="TkFixedFont")
self.distTable.setData(self.distances)
self.distTable.launch(browseCmd=self._distTableSelCB)
self.distButtons = Pmw.ButtonBox(dp, padx=0)
self.distButtons.add("Create", command=self._createDistance)
self.distButtons.add("Remove", command=self._removeDistance)
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.distButtons.numbuttons()):
self.distButtons.button(but).config(default='disabled')
self.distButtons.alignbuttons()
self.distButtons.grid(row=1, column=1)
self.distLabelChoice = Pmw.RadioSelect(dp, pady=0,
buttontype='radiobutton',
command=self._distLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.distLabelChoice.grid(row=2, column=1)
self.distLabelChoice.add("None", highlightthickness=0)
self.distLabelChoice.add("ID", highlightthickness=0)
self.distLabelChoice.add("Distance", highlightthickness=0)
self.distLabelChoice.invoke("Distance")
self.distPrecisionChoice = Pmw.Counter(dp, datatype={
'counter': self._distPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(precision()))
self.distPrecisionChoice.grid(row=3, column=1)
self.showUnitsVar = Tkinter.IntVar(dp)
self.showUnitsVar.set(showUnits())
Tkinter.Checkbutton(dp, text="Show Angstrom symbol",
variable=self.showUnitsVar,
command=self._showUnitsChangeCB).grid(row=4, column=1)
self.distSelectsAtomsVar = Tkinter.IntVar(dp)
self.distSelectsAtomsVar.set(False)
Tkinter.Checkbutton(dp, variable=self.distSelectsAtomsVar,
text="Choosing in table\nselects atoms\n(and pseudobond)"
).grid(row=5, column=1)
from chimera.pbgPanel import attributesCmd
Tkinter.Button(dp, text="Display options...", command=
lambda dm=distanceMonitor: attributesCmd([dm])
).grid(row=6, column=1)
for d in distanceMonitor.pseudoBonds:
self.newDistance(d)
atp = self.notebook.page(ANGLES)
from CGLtk.Table import SortableTable
self.angleTable = SortableTable(atp)
self.angleTable.grid(row=0, column=0, sticky='nsew', rowspan=4)
atp.columnconfigure(0, weight=1)
atp.rowconfigure(2, weight=1)
for i in range(4):
self.angleTable.addColumn("Atom %d" % (i+1), lambda atoms, s=self,
i=i: i >= len(atoms) and "N/A" or s.atomLabel(atoms[i]))
self.angleTable.addColumn("Angle/Torsion",
lambda atoms, s=self: s._angleLabel(atoms), font="TkFixedFont")
self.angleTable.setData(self.angleInfo)
self.angleTable.launch(browseCmd=self._angleTableSelCB)
self._osHandler = None
self.angleButtons = Pmw.ButtonBox(atp, padx=0)
self.angleButtons.add("Create", command=self._createAngle)
self.angleButtons.add("Remove", command=self._removeAngle,
state='disabled')
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.angleButtons.numbuttons()):
self.angleButtons.button(but).config(default='disabled')
self.angleButtons.alignbuttons()
self.angleButtons.grid(row=0, column=1)
self.anglePrecisionChoice = Pmw.Counter(atp, datatype={
'counter': self._anglePrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[ANGLE_PRECISION]))
self.anglePrecisionChoice.grid(row=1, column=1)
self.angleSelectsComponentsVar = Tkinter.IntVar(atp)
self.angleSelectsComponentsVar.set(True)
Tkinter.Checkbutton(atp, variable=self.angleSelectsComponentsVar,
text="Choosing in table selects\ncomponent atoms/bonds"
).grid(row=3, column=1)
brp = self.notebook.page(BONDROTS)
self.rotations = []
self.rotInfo = {}
labeledButton = Pmw.LabeledWidget(brp, labelpos="e",
label_text="selected bond as torsion")
labeledButton.grid(row=0, column=0, columnspan=2)
self.createRotButton = Tkinter.Button(labeledButton.interior(),
text="Activate", command=self._createRotation, pady=0)
self.createRotButton.grid()
tableFrame = Tkinter.Frame(brp, pady="0.1i")
tableFrame.grid(row=1, column=0, columnspan=2, sticky='ns')
from CGLtk.Table import ScrolledTable
self.rotTable = ScrolledTable(tableFrame, hscrollmode='none')
self.rotTable.setColumnTitle(0, "ID")
self.rotTable.setColumnTitle(1, "Near")
self.rotTable.setColumnTitle(2, "Bond")
self.rotTable.setColumnTitle(3, "Far")
self.angleTitle = Tkinter.StringVar(parent)
self.angleTitle.set("Torsion")
self.rotTable.setColumnTitle(4, self.angleTitle,
pyclass=Tkinter.Button, pady=0,
command=self._toggleAngleType)
brp.rowconfigure(1, weight=1)
brp.columnconfigure(0, weight=1)
brp.columnconfigure(1, weight=1)
tableFrame.rowconfigure(0, weight=1)
tableFrame.columnconfigure(0, weight=1)
self.rotTable.columnconfigure(4, weight=1)
self.rotTable.grid(row=0, column=0, sticky='news')
self.dialSizeLabels = ["small", "medium", "large"]
Pmw.OptionMenu(tableFrame,
items=self.dialSizeLabels, labelpos='w',
initialitem=self.dialSizeLabels[prefs[ROT_DIAL_SIZE]],
label_text="Dial size:", command=self._dialSizeChangeCB,
).grid(row=1, column=0, sticky='e')
f = Tkinter.Frame(brp)
f.grid(row=2, column=0, columnspan=2)
self.mouseModeVar = Tkinter.IntVar(f)
self.mouseModeVar.set(False)
self.needTorWidgets = []
self.needTorWidgets.append(Tkinter.Checkbutton(f, text="Rotate",
variable=self.mouseModeVar, command=self._mouseModeCB))
self.needTorWidgets[-1].grid(row=0, column=0)
self.rotModeTorsMenu = Pmw.OptionMenu(f)
self.rotModeTorsMenu.grid(row=0, column=1)
self.needTorWidgets.append(self.rotModeTorsMenu)
self.buttonLabels = []
self.labelValues = {}
for mod in ("",) + mousemodes.usedMods:
for but in mousemodes.usedButtons:
if mod:
self.buttonLabels.append(
mod.lower() + " button " + but)
self.labelValues[self.buttonLabels[-1]]\
= (but, (mod,))
else:
self.buttonLabels.append("button "+but)
self.labelValues[self.buttonLabels[-1]]\
= (but, ())
self._modeButton = self.buttonLabels[0]
self.rotModeButMenu = Pmw.OptionMenu(f, labelpos='w',
command=self._modeButtonCB,
label_text="using", items=self.buttonLabels)
self.rotModeButMenu.grid(row=0, column=2)
self.needTorWidgets.append(self.rotModeButMenu)
self.rotLabelChoice = Pmw.RadioSelect(brp, pady=0,
buttontype='radiobutton', hull_pady=".1i",
command=self._rotLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.rotLabelChoice.grid(row=3, rowspan=2, column=0)
self.rotLabelChoice.add("None", highlightthickness=0)
self.rotLabelChoice.add("ID", highlightthickness=0)
self.rotLabelChoice.add("Name", highlightthickness=0)
self.rotLabelChoice.add("Angle", highlightthickness=0)
self.rotLabelChoice.invoke(prefs[ROT_LABEL])
self.torsionPrecisionChoice = Pmw.Counter(brp, datatype={
'counter': self._torsionPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[TORSION_PRECISION]))
self.torsionPrecisionChoice.grid(row=3, column=1)
self.showDegreeSymbolVar = Tkinter.IntVar(brp)
self.showDegreeSymbolVar.set(prefs[SHOW_DEGREE_SYMBOL])
Tkinter.Checkbutton(brp, text="Show degree symbol",
variable=self.showDegreeSymbolVar,
command=self._showDegreeSymbolChangeCB).grid(
row=4, column=1)
self.setTorWidgetsState("disabled")
mousemodes.addFunction("rotate bond", (lambda v, e:
v.recordPosition(e.time, e.x, e.y, "rotate"),
self._mouseSphere,
lambda v, e: v.setCursor(None)))
if GEOMETRIES in pageNames:
gp = self.notebook.page(GEOMETRIES)
from Geometry import GeometryInterface
self.interfaces[GEOMETRIES] = GeometryInterface(gp, self.status)
if METALS in pageNames:
mp = self.notebook.page(METALS)
from Metals import MetalsInterface
self.interfaces[METALS] = MetalsInterface(mp,
self.status)
self.notebook.setnaturalsize()
class StructMeasure(ModelessDialog):
title="Structure Measurements"
buttons=("Close", "Save")
name="structure measurements"
provideStatus = True
statusPosition = "above"
dialSizes = [".1i", ".2i", ".3i"]
def fillInUI(self, parent):
self.distances = []
self.angleInfo = []
self.numMolecules = len(chimera.openModels.list(
modelTypes=[chimera.Molecule]))
chimera.triggers.addHandler('Molecule', self._molChange, None)
chimera.triggers.addHandler('PseudoBond', self._psbChange, None)
chimera.triggers.addHandler('Atom', self._atomChange, None)
chimera.triggers.addHandler('Model', self._modelChange, None)
distanceMonitor.updateCallbacks.append(self._distUpdateCB)
self.notebook = Pmw.NoteBook(parent,
raisecommand=self._nbRaiseCB,
lowercommand=self._nbLowerCB)
self.notebook.pack(fill='both', expand=1)
self.interfaces = {}
for pn in pageNames:
pageID = pn
## when more tabs shown, maybe do this...
#if '/' in pn:
# parts = pn.split('/')
# pn = "/ ".join(parts)
#if ' ' in pn:
# parts = pn.split(' ')
# pn = '\n'.join(parts)
self.notebook.add(pageID, tab_text=pn)
dp = self.notebook.page(DISTANCES)
from CGLtk.Table import SortableTable
self.distTable = SortableTable(dp)
self.distTable.grid(row=0, column=0, sticky='nsew', rowspan=7)
dp.columnconfigure(0, weight=1)
dp.rowconfigure(4, weight=1)
dp.rowconfigure(5, weight=1)
self.distTable.addColumn("ID", "id", format="%d")
self.distTable.addColumn("Atom 1",
lambda d, s=self: s.atomLabel(d.atoms[0]))
self.distTable.addColumn("Atom 2",
lambda d, s=self: s.atomLabel(d.atoms[1]))
self.distTable.addColumn("Distance", "distance", font="TkFixedFont")
self.distTable.setData(self.distances)
self.distTable.launch(browseCmd=self._distTableSelCB)
self.distButtons = Pmw.ButtonBox(dp, padx=0)
self.distButtons.add("Create", command=self._createDistance)
self.distButtons.add("Remove", command=self._removeDistance)
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.distButtons.numbuttons()):
self.distButtons.button(but).config(default='disabled')
self.distButtons.alignbuttons()
self.distButtons.grid(row=1, column=1)
self.distLabelChoice = Pmw.RadioSelect(dp, pady=0,
buttontype='radiobutton',
command=self._distLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.distLabelChoice.grid(row=2, column=1)
self.distLabelChoice.add("None", highlightthickness=0)
self.distLabelChoice.add("ID", highlightthickness=0)
self.distLabelChoice.add("Distance", highlightthickness=0)
self.distLabelChoice.invoke("Distance")
self.distPrecisionChoice = Pmw.Counter(dp, datatype={
'counter': self._distPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(precision()))
self.distPrecisionChoice.grid(row=3, column=1)
self.showUnitsVar = Tkinter.IntVar(dp)
self.showUnitsVar.set(showUnits())
Tkinter.Checkbutton(dp, text="Show Angstrom symbol",
variable=self.showUnitsVar,
command=self._showUnitsChangeCB).grid(row=4, column=1)
self.distSelectsAtomsVar = Tkinter.IntVar(dp)
self.distSelectsAtomsVar.set(False)
Tkinter.Checkbutton(dp, variable=self.distSelectsAtomsVar,
text="Choosing in table\nselects atoms\n(and pseudobond)"
).grid(row=5, column=1)
from chimera.pbgPanel import attributesCmd
Tkinter.Button(dp, text="Display options...", command=
lambda dm=distanceMonitor: attributesCmd([dm])
).grid(row=6, column=1)
for d in distanceMonitor.pseudoBonds:
self.newDistance(d)
atp = self.notebook.page(ANGLES)
from CGLtk.Table import SortableTable
self.angleTable = SortableTable(atp)
self.angleTable.grid(row=0, column=0, sticky='nsew', rowspan=4)
atp.columnconfigure(0, weight=1)
atp.rowconfigure(2, weight=1)
for i in range(4):
self.angleTable.addColumn("Atom %d" % (i+1), lambda atoms, s=self,
i=i: i >= len(atoms) and "N/A" or s.atomLabel(atoms[i]))
self.angleTable.addColumn("Angle/Torsion",
lambda atoms, s=self: s._angleLabel(atoms), font="TkFixedFont")
self.angleTable.setData(self.angleInfo)
self.angleTable.launch(browseCmd=self._angleTableSelCB)
self._osHandler = None
self.angleButtons = Pmw.ButtonBox(atp, padx=0)
self.angleButtons.add("Create", command=self._createAngle)
self.angleButtons.add("Remove", command=self._removeAngle,
state='disabled')
# remove the extra space around buttons allocated to indicate
# which button is the 'default', so that buttons stack closely
for but in range(self.angleButtons.numbuttons()):
self.angleButtons.button(but).config(default='disabled')
self.angleButtons.alignbuttons()
self.angleButtons.grid(row=0, column=1)
self.anglePrecisionChoice = Pmw.Counter(atp, datatype={
'counter': self._anglePrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[ANGLE_PRECISION]))
self.anglePrecisionChoice.grid(row=1, column=1)
self.angleSelectsComponentsVar = Tkinter.IntVar(atp)
self.angleSelectsComponentsVar.set(True)
Tkinter.Checkbutton(atp, variable=self.angleSelectsComponentsVar,
text="Choosing in table selects\ncomponent atoms/bonds"
).grid(row=3, column=1)
brp = self.notebook.page(BONDROTS)
self.rotations = []
self.rotInfo = {}
labeledButton = Pmw.LabeledWidget(brp, labelpos="e",
label_text="selected bond as torsion")
labeledButton.grid(row=0, column=0, columnspan=2)
self.createRotButton = Tkinter.Button(labeledButton.interior(),
text="Activate", command=self._createRotation, pady=0)
self.createRotButton.grid()
tableFrame = Tkinter.Frame(brp, pady="0.1i")
tableFrame.grid(row=1, column=0, columnspan=2, sticky='ns')
from CGLtk.Table import ScrolledTable
self.rotTable = ScrolledTable(tableFrame, hscrollmode='none')
self.rotTable.setColumnTitle(0, "ID")
self.rotTable.setColumnTitle(1, "Near")
self.rotTable.setColumnTitle(2, "Bond")
self.rotTable.setColumnTitle(3, "Far")
self.angleTitle = Tkinter.StringVar(parent)
self.angleTitle.set("Torsion")
self.rotTable.setColumnTitle(4, self.angleTitle,
pyclass=Tkinter.Button, pady=0,
command=self._toggleAngleType)
brp.rowconfigure(1, weight=1)
brp.columnconfigure(0, weight=1)
brp.columnconfigure(1, weight=1)
tableFrame.rowconfigure(0, weight=1)
tableFrame.columnconfigure(0, weight=1)
self.rotTable.columnconfigure(4, weight=1)
self.rotTable.grid(row=0, column=0, sticky='news')
self.dialSizeLabels = ["small", "medium", "large"]
Pmw.OptionMenu(tableFrame,
items=self.dialSizeLabels, labelpos='w',
initialitem=self.dialSizeLabels[prefs[ROT_DIAL_SIZE]],
label_text="Dial size:", command=self._dialSizeChangeCB,
).grid(row=1, column=0, sticky='e')
f = Tkinter.Frame(brp)
f.grid(row=2, column=0, columnspan=2)
self.mouseModeVar = Tkinter.IntVar(f)
self.mouseModeVar.set(False)
self.needTorWidgets = []
self.needTorWidgets.append(Tkinter.Checkbutton(f, text="Rotate",
variable=self.mouseModeVar, command=self._mouseModeCB))
self.needTorWidgets[-1].grid(row=0, column=0)
self.rotModeTorsMenu = Pmw.OptionMenu(f)
self.rotModeTorsMenu.grid(row=0, column=1)
self.needTorWidgets.append(self.rotModeTorsMenu)
self.buttonLabels = []
self.labelValues = {}
for mod in ("",) + mousemodes.usedMods:
for but in mousemodes.usedButtons:
if mod:
self.buttonLabels.append(
mod.lower() + " button " + but)
self.labelValues[self.buttonLabels[-1]]\
= (but, (mod,))
else:
self.buttonLabels.append("button "+but)
self.labelValues[self.buttonLabels[-1]]\
= (but, ())
self._modeButton = self.buttonLabels[0]
self.rotModeButMenu = Pmw.OptionMenu(f, labelpos='w',
command=self._modeButtonCB,
label_text="using", items=self.buttonLabels)
self.rotModeButMenu.grid(row=0, column=2)
self.needTorWidgets.append(self.rotModeButMenu)
self.rotLabelChoice = Pmw.RadioSelect(brp, pady=0,
buttontype='radiobutton', hull_pady=".1i",
command=self._rotLabelModeChange, orient='vertical',
labelpos='w', label_text="Labels")
self.rotLabelChoice.grid(row=3, rowspan=2, column=0)
self.rotLabelChoice.add("None", highlightthickness=0)
self.rotLabelChoice.add("ID", highlightthickness=0)
self.rotLabelChoice.add("Name", highlightthickness=0)
self.rotLabelChoice.add("Angle", highlightthickness=0)
self.rotLabelChoice.invoke(prefs[ROT_LABEL])
self.torsionPrecisionChoice = Pmw.Counter(brp, datatype={
'counter': self._torsionPrecisionChange}, labelpos='w',
label_text="Decimal places", entry_width=1,
entry_pyclass=PrecisionEntry,
entryfield_value=str(prefs[TORSION_PRECISION]))
self.torsionPrecisionChoice.grid(row=3, column=1)
self.showDegreeSymbolVar = Tkinter.IntVar(brp)
self.showDegreeSymbolVar.set(prefs[SHOW_DEGREE_SYMBOL])
Tkinter.Checkbutton(brp, text="Show degree symbol",
variable=self.showDegreeSymbolVar,
command=self._showDegreeSymbolChangeCB).grid(
row=4, column=1)
self.setTorWidgetsState("disabled")
mousemodes.addFunction("rotate bond", (lambda v, e:
v.recordPosition(e.time, e.x, e.y, "rotate"),
self._mouseSphere,
lambda v, e: v.setCursor(None)))
if GEOMETRIES in pageNames:
gp = self.notebook.page(GEOMETRIES)
from Geometry import GeometryInterface
self.interfaces[GEOMETRIES] = GeometryInterface(gp, self.status)
if METALS in pageNames:
mp = self.notebook.page(METALS)
from Metals import MetalsInterface
self.interfaces[METALS] = MetalsInterface(mp,
self.status)
self.notebook.setnaturalsize()
def setCategoryMenu(self, category):
# avoid unnecessary page raises; they interfere with
# the bond rotation mouse mode (graphics window loses
# focus)
if self.notebook.getcurselection() != category:
self.notebook.selectpage(category)
def atomLabel(self, atom, diffWith=None):
if self.numMolecules > 1:
showModel = 1
else:
showModel = 0
from chimera.misc import chimeraLabel
lab = chimeraLabel(atom, showModel=showModel,
diffWith=diffWith)
if lab == "":
lab = atom.name
return lab
def _angleLabel(self, atoms):
pts = tuple([a.xformCoord() for a in atoms])
if len(pts) == 3:
val = chimera.angle(*pts)
else:
val = chimera.dihedral(*pts)
return "%.*f" % (prefs[ANGLE_PRECISION], val)
def _anglePrecisionChange(self, *args):
newPrecision = self._checkPrecision(*args)
prefs[ANGLE_PRECISION] = newPrecision
self.angleTable.refresh()
return str(newPrecision)
def _angleTableSelCB(self, selAngles):
if self.angleSelectsComponentsVar.get():
select = []
for atoms in selAngles:
select.extend(atoms)
atomSet = set(atoms)
for a in atoms:
for b in a.bonds:
if b.otherAtom(a) in atomSet:
select.append(b)
selection.setCurrent(select)
def _atomChange(self, trigName, myData, trigData):
if not trigData.deleted:
return
remove = []
for atoms in self.angleInfo:
for a in atoms:
if a.__destroyed__:
remove.append(atoms)
break
if remove:
self._removeAngle(remove=remove)
def _checkPrecision(self, text, plusMinus, increment):
newPrecision = int(text) + plusMinus
if newPrecision < 0:
raise ValueError("decimal places must be non-negative")
if newPrecision > 9:
raise ValueError("9 decimal places is enough")
return newPrecision
def _createAngle(self, atoms=None):
"""'Create angle' callback"""
if atoms is None:
atoms = selection.currentAtoms(ordered=True)
if len(atoms) not in [3,4]:
replyobj.error("Either three or four atoms must be"
" selected in graphics window\n")
return
if not self.angleInfo:
from SimpleSession import SAVE_SESSION
self._angleSesTrigID = chimera.triggers.addHandler(SAVE_SESSION,
self._sessionAngleSaveCB, None)
self.angleInfo.append(atoms)
self.angleTable.setData(self.angleInfo)
self.angleButtons.button("Remove").config(state='normal')
if self._osHandler is None:
models = set([a.molecule for a in atoms])
if len(models) > 1:
self._osHandler = chimera.triggers.addHandler(
'OpenState', self._osChange, None)
def _createDistance(self):
"""'Create distance' callback"""
selAtoms = selection.currentAtoms()
if len(selAtoms) != 2:
replyobj.error("Exactly two atoms must be selected "
"in graphics window\n")
return
addDistance(*tuple(selAtoms))
def _createRotation(self):
selBonds = selection.currentBonds()
if len(selBonds) == 1:
addRotation(selBonds[0])
return
replyobj.error("Exactly one bond must be selected "
"in graphics window\n")
def deadDistances(self):
"""Remove deleted distances from the table"""
pre = len(self.distances)
self.distances = [d for d in self.distances
if not d.__destroyed__]
if len(self.distances) != pre:
self.distTable.setData(self.distances)
return True
return False
def _dialSizeChangeCB(self, dialSizeLabel):
dialSize = self.dialSizeLabels.index(dialSizeLabel)
prefs[ROT_DIAL_SIZE] = dialSize
for info in self.rotInfo.values():
for angleCounter in info[0][-2:]:
angleCounter.configure(dial_radius=
self.dialSizes[dialSize])
self.notebook.setnaturalsize()
def dihedEndAtoms(self, br):
widgets, nearIndex, nearAtoms, farIndex, farAtoms = \
self.rotInfo[br]
return nearAtoms[nearIndex], farAtoms[farIndex]
def _distPrecisionChange(self, text, plusMinus, increment):
setPrecision(int(text) + plusMinus)
if precision() > 9:
setPrecision(9)
raise ValueError, "9 decimal places is enough"
return str(precision())
def _distTableSelCB(self, selDists):
if self.distSelectsAtomsVar.get():
select = []
select.extend(selDists)
for sd in selDists:
select.extend(sd.atoms)
selection.setCurrent(select)
else:
selection.removeCurrent(self.distances)
selection.addCurrent(selDists)
def _distUpdateCB(self):
"""Distances just updated"""
self.distTable.refresh()
def _distLabelModeChange(self, mode):
if mode == "None":
distanceMonitor.fixedLabels = 1
for d in self.distances:
d.label = ""
elif mode == "ID":
distanceMonitor.fixedLabels = 1
for d in self.distances:
d.label = "%d" % d.id
else:
distanceMonitor.fixedLabels = 0
for d in self.distances:
d.label = d.distance
def Help(self):
anchor = self.notebook.getcurselection().lower().split()[0]
if "/" in anchor:
anchor = anchor.split('/')[0]
chimera.help.display("ContributedSoftware/structuremeas/"
"structuremeas.html#" + anchor)
def _labelRot(self, br, mode=None):
if mode is None:
mode = self.rotLabelChoice.getvalue()
if mode == "None":
for br in self.rotations:
br.bond.label = ""
elif mode == "Name":
for br in self.rotations:
br.bond.label = self.rotLabel(br)
elif mode == "Angle":
isDihed = self.angleTitle.get() == "Torsion"
if prefs[SHOW_DEGREE_SYMBOL]:
suffix = "\260"
else:
suffix = ""
for br in self.rotations:
if isDihed:
val = self.dihedral(br)
else:
val = br.get()
while val < -180.0:
val += 180.0
while val > 180.0:
val -= 180.0
br.bond.label = "%.*f%s" % (
prefs[TORSION_PRECISION],
val, suffix)
elif mode == "ID":
br.bond.label = str(br.id)
def _modelChange(self, trigName, myData, trigData):
if not trigData.modified:
return
# both Coord and CoordSet changes fire the Model trigger
self._updateAngles()
def _molChange(self, trigName, myData, trigData):
n = len(chimera.openModels.list(modelTypes=[chimera.Molecule]))
if n == 1 and self.numMolecules > 1 \
or n > 1 and self.numMolecules == 1:
# don't want to remake atom labels right away since
# some of the distances may have gone away, and that
# won't get cleaned up until the Pseudobond trigger
# fires, so register for the monitorChanges trigger and
# update the labels there
chimera.triggers.addHandler(
'monitor changes', self.monitorCB, None)
self.numMolecules = n
def _modeButtonCB(self, but):
if self.mouseModeVar.get():
# "manually" turn off, then on with new value
self.mouseModeVar.set(False)
self._mouseModeCB()
self._modeButton = but
self.mouseModeVar.set(True)
self._mouseModeCB()
else:
self._modeButton = but
def _mouseModeCB(self):
but, mods = self.labelValues[self._modeButton]
if self.mouseModeVar.get():
self._formerMouseMode = mousemodes.getFuncName(but,mods)
mousemodes.setButtonFunction(but, mods, "rotate bond")
else:
mousemodes.setButtonFunction(but, mods,
self._formerMouseMode)
def _mouseSphere(self, viewer, event):
xf = viewer.vsphere(event.time, event.x, event.y,
event.state % 2 == 1)
if xf.isIdentity():
return
axis, angle = xf.getRotation()
br = self.rotations[self.rotModeTorsMenu.index(Pmw.SELECT)]
rotVec = br.atoms[1].xformCoord() - br.atoms[0].xformCoord()
axis.normalize()
rotVec.normalize()
turn = angle * (axis * rotVec)
br.set(turn + br.get())
def newDistance(self, d):
if self.distances:
d.id = self.distances[-1].id + 1
else:
d.id = 1
if not hasattr(d, 'distance'):
d.distance = ""
self.distances.append(d)
self.distTable.setData(self.distances)
def monitorCB(self, trigName, myData, trigData):
from chimera.triggerSet import ONESHOT
self.mcHandlerID = None
self.remakeAtomLabels()
return ONESHOT
def _nbLowerCB(self, pageName):
if pageName in self.interfaces:
interface = self.interfaces[pageName]
try:
interface._lowerCmd()
except AttributeError:
self.status("")
else:
self.status("")
def _nbRaiseCB(self, pageName):
if pageName in self.interfaces:
interface = self.interfaces[pageName]
try:
interface._raiseCmd()
except AttributeError:
pass
def _osChange(self, trigName, myData, trigData):
if 'transformation change' not in trigData.reasons:
return
self._updateAngles()
def _psbChange(self, trigName, myData, trigData):
"""Callback from PseudoBond trigger"""
change = False
# clean up deleted distances
if trigData.deleted:
change = self.deadDistances()
# insert new distances
for psb in trigData.created:
if psb in distanceMonitor.pseudoBonds:
self.newDistance(psb)
change = True
if change:
self.notebook.setnaturalsize()
def remakeAtomLabels(self):
self.distTable.refresh()
self.angleTable.refresh()
newLabels = []
for br in self.rotations:
newLabels.append(self.rotLabel(br))
rotMenu = self.rotInfo[br][0][2]
rotMenu.configure(text=newLabels[-1])
if newLabels:
modeTors = self.rotModeTorsMenu.index(Pmw.SELECT)
if not modeTors:
modeTors = None
else:
modeTors = None
self.rotModeTorsMenu.setitems(newLabels, index=modeTors)
def _removeAngle(self, remove=None):
if len(self.angleInfo) == 0:
replyobj.error("No angles to remove\n")
return
if remove is None:
if len(self.angleInfo) == 1:
remove = self.angleInfo
else:
remove = self.angleTable.selected()
if not remove:
replyobj.error("Must select angle(s) in table\n")
return
for rm in remove:
self.angleInfo.remove(rm)
self.angleTable.setData(self.angleInfo)
if len(self.angleInfo) == 0:
self.angleButtons.button("Remove").config(
state='disabled')
from SimpleSession import SAVE_SESSION
chimera.triggers.deleteHandler(SAVE_SESSION, self._angleSesTrigID)
if self._osHandler:
stillNeedHandler = False
for info in self.angleInfo:
models = dict.fromkeys([a.molecule
for a in info[0]])
if len(models) > 1:
stillNeedHandler = True
break
if not stillNeedHandler:
chimera.triggers.deleteHandler('OpenState',
self._osHandler)
self._osHandler = None
def _removeDistance(self):
if len(self.distances) == 1:
removeDistance(self.distances[0])
return
if len(self.distances) == 0:
replyobj.error("No distances to remove\n")
return
if not self.distTable.selected():
replyobj.error("Must select distance in table\n")
return
for d in self.distTable.selected():
removeDistance(d)
def rotLabel(self, br):
return "%s -> %s" % (self.atomLabel(br.atoms[0]),
self.atomLabel(br.atoms[1], diffWith=br.atoms[0]))
def _rotLabelModeChange(self, mode):
prefs[ROT_LABEL] = mode
for br in self.rotations:
self._labelRot(br, mode)
def Save(self):
"""Save the displayed info to file"""
if not hasattr(self, '_saveDialog'):
self._saveDialog = _SaveStructInfo(self, clientPos='s',
title='Save Structure Measurements')
self._saveDialog.enter()
def setTorWidgetsState(self, state):
for w in self.needTorWidgets:
if isinstance(w, Pmw.OptionMenu):
if w['labelpos']:
w.configure(label_state=state)
w.configure(menubutton_state=state)
else:
w.configure(state=state)
def _showDegreeSymbolChangeCB(self):
prefs[SHOW_DEGREE_SYMBOL] = self.showDegreeSymbolVar.get()
if self.rotLabelChoice.getvalue() == "Angle":
for br in self.rotations:
self._labelRot(br)
def _showUnitsChangeCB(self):
showUnits(self.showUnitsVar.get())
def _syncUI(self, br, side):
"""Called from the Bond trigger callback, to correct the
dihedral angle menus if possible"""
start = 1+2*side
index, atoms = self.rotInfo[br][start:start+2]
newIndex, newNames, newAtoms = \
self.dihedChoices(br.atoms[side], br.atoms[1-side])
if not newAtoms:
# when gnats 243 is fixed, this bond rotation will
# already have been destroyed and we won't get here
return None
if atoms == newAtoms:
return None
atom = atoms[index]
if atom in newAtoms:
newIndex = newAtoms.index(atom)
menu = self.rotInfo[br][0][1+2*side]
menu.setitems(newNames, newNames[newIndex])
self.rotInfo[br][start:start+2] = [newIndex, newAtoms]
return menu
def _torsionPrecisionChange(self, *args):
newPrecision = self._checkPrecision(*args)
prefs[TORSION_PRECISION] = newPrecision
for br in self.rotations:
self._updateRot(br)
return str(newPrecision)
def rotChange(self, trigger, brInfo):
needResize = False
if trigger == bondRotMgr.DELETED:
self._delRots(brInfo)
needResize = True
elif trigger == bondRotMgr.CREATED:
self._addRot(brInfo)
needResize = True
elif trigger == bondRotMgr.REVERSED:
# since the bond has reversed, need to switch
# near/far labels as well
widgets, nearIndex, nearAtoms, farIndex, farAtoms = \
self.rotInfo[brInfo]
row = self.rotations.index(brInfo)
self.rotInfo[brInfo] = [widgets, farIndex, farAtoms,
nearIndex, nearAtoms]
# swap torsion-end menus
widgets[1], widgets[3] = widgets[3], widgets[1]
widgets[2].configure(text=self.rotLabel(brInfo))
if self.angleTitle.get() == "Torsion":
widgets[1].grid_forget()
widgets[3].grid_forget()
widgets[1].grid(row=row, column=1, sticky='ew')
widgets[3].grid(row=row, column=3, sticky='ew')
self.rotModeTorsMenu.setitems([self.rotLabel(r)
for r in self.rotations],
index=self.rotModeTorsMenu.index(Pmw.SELECT))
else:
self._updateRot(brInfo)
self._updateAngles()
if needResize:
self.notebook.setnaturalsize()
def dihedChoices(self, baseAtom, otherAtom):
# sort choices so they are always in the same order
default = None
info = []
for a in baseAtom.neighbors:
if a is otherAtom:
continue
name = self.atomLabel(a, diffWith=baseAtom)
info.append((name, a))
if a.element.number > 1:
default = a
info.sort()
names = map(lambda items: items[0], info)
bonded = map(lambda items: items[1], info)
if default is None:
default = 0
else:
default = bonded.index(default)
return default, names, bonded
def dihedral(self, br):
near, far = self.dihedEndAtoms(br)
widgets, nearIndex, nearAtoms, farIndex, farAtoms = \
self.rotInfo[br]
return dihedral(near.xformCoord(), br.atoms[0].xformCoord(),
br.atoms[1].xformCoord(), far.xformCoord())
def _addRot(self, br, row=-1):
self.setTorWidgetsState("normal")
if row == -1:
# by default, append bond rotation
row = len(self.rotInfo)
else:
# insert bond rotation at given row, so make room
for i in range(len(self.rotations), row, -1):
nbr = self.rotations[i - 1]
widgets = self.rotInfo[nbr][0]
for w in widgets:
gi = w.grid_info()
if gi.has_key('column'):
# otherwise presumably unmapped
column = gi['column']
w.grid_forget()
w.grid(row=i, column=column,
sticky='ew')
self.rotations.insert(row, br)
a1, a2 = br.atoms
nearIndex, nearNames, nearAtoms = self.dihedChoices(a1, a2)
farIndex, farNames, farAtoms = self.dihedChoices(a2, a1)
# need to do this here so that self.dihedral(br) works
widgets = []
self.rotInfo[br] = [widgets,
nearIndex, nearAtoms, farIndex, farAtoms]
ID = Tkinter.Label(self.rotTable.interior(), text=str(br.id))
widgets.append(ID)
ID.grid(row=row, column=0)
near = Pmw.OptionMenu(self.rotTable.interior(),
menubutton_highlightthickness=0,
initialitem=nearIndex, items=nearNames)
near.configure(command=lambda x, br=br, n=near, s=self:
s._setDihedEnd(br, n))
widgets.append(near)
if self.angleTitle.get() == "Torsion":
near.grid(row=row, column=1, sticky='ew')
actions = PmwableMenuButton(self.rotTable.interior(),
text=self.rotLabel(br), indicatoron=1,
relief='raised', bd=2, justify='right',
states=['normal', 'normal', 'normal', 'normal'],
items=['Revert', 'Reverse', 'Deactivate', 'Select'],
command=lambda c, s=self, br=br: s._menuCB(c, br))
widgets.append(actions)
actions.grid(row=row, column=2, sticky='ew')
far = Pmw.OptionMenu(self.rotTable.interior(),
menubutton_highlightthickness=0,
initialitem=farIndex, items=farNames)
far.configure(command=lambda x, br=br, n=far, s=self:
s._setDihedEnd(br, n))
widgets.append(far)
if self.angleTitle.get() == "Torsion":
far.grid(row=row, column=3, sticky='ew')
from CGLtk.AngleCounter import AngleCounter
delta = AngleCounter(self.rotTable.interior(), dialpos='e',
angle=float("%.*f" % (prefs[TORSION_PRECISION],
br.get())),
dial_zeroAxis='y', dial_radius=self.dialSizes[
prefs[ROT_DIAL_SIZE]], dial_rotDir='clockwise',
command=lambda d, s=self, br=br: s._deltaCB(br, d))
dihed = AngleCounter(self.rotTable.interior(), dialpos='e',
angle=float("%.*f" % (prefs[TORSION_PRECISION],
self.dihedral(br))),
dial_zeroAxis='y', dial_radius=self.dialSizes[
prefs[ROT_DIAL_SIZE]], dial_rotDir='clockwise',
command=lambda d, s=self, br=br: s._dihedCB(br, d))
if self.angleTitle.get() == "Delta":
delta.grid(row=row, column=4, sticky='ew')
widgets.extend([delta, dihed])
else:
dihed.grid(row=row, column=4, sticky='ew')
widgets.extend([dihed, delta])
modeTors = self.rotModeTorsMenu.getvalue()
if not modeTors:
modeTors = None
items = map(self.rotLabel, self.rotations)
self.rotModeTorsMenu.setitems(items, index=modeTors)
self._labelRot(br)
def _delRots(self, brs):
for br in brs:
row = self.rotations.index(br)
widgets = self.rotInfo[br][0]
for w in widgets:
w.grid_forget()
w.destroy()
del self.rotInfo[br]
for i in range(row + 1, len(self.rotations)):
nbr = self.rotations[i]
widgets = self.rotInfo[nbr][0]
for w in widgets:
gi = w.grid_info()
if gi.has_key('column'):
# otherwise presumably unmapped
column = gi['column']
w.grid_forget()
w.grid(row=i-1, column=column,
sticky='ew')
self.rotations.remove(br)
modeTors = self.rotModeTorsMenu.getvalue()
items = [self.rotLabel(br) for br in self.rotations]
if modeTors in items:
self.rotModeTorsMenu.setitems(items, index=modeTors)
else:
self.rotModeTorsMenu.setitems(items)
if self.mouseModeVar.get():
self.mouseModeVar.set(False)
self._mouseModeCB()
if not items:
self.setTorWidgetsState("disabled")
def _updateRot(self, br):
if self.angleTitle.get() == "Torsion":
dihed, delta = self.rotInfo[br][0][-2:]
else:
delta, dihed = self.rotInfo[br][0][-2:]
delta.configure(angle = float("%.*f" %
(prefs[TORSION_PRECISION], br.get())))
dihed.configure(angle = float("%.*f" %
(prefs[TORSION_PRECISION], self.dihedral(br))))
if self.rotLabelChoice.getvalue() == "Angle":
self._labelRot(br, "Angle")
def _dihedCB(self, br, degrees):
# callback from dihedral AngleCounter
curDihed = self.dihedral(br)
br.set(br.get() + degrees - curDihed)
def _counterAngle(self, text, updown, incr, **kw):
angle = float(text)
if updown > 0:
angle = angle + incr
else:
angle = angle - incr
while angle < -180.0:
angle = angle + 360.0
while angle > 180.0:
angle = angle - 360.0
self._deltaCB(kw['br'], angle=angle)
return str(angle)
def _deltaCB(self, br, degrees):
# callback from delta AngleCounter
br.set(degrees)
def _menuCB(self, cmdText, br):
# callback from angle pull-down menu
if cmdText == "Revert":
br.set(0)
elif cmdText == "Deactivate":
br.bond.label = ""
br.destroy()
elif cmdText == "Select":
selectables = []
selectables.extend(br.atoms)
selectables.append(br.bond)
if self.angleTitle.get() == "Torsion":
near, far = self.dihedEndAtoms(br)
selectables.extend([near, far])
selectables.append(br.atoms[0].bondsMap[near])
selectables.append(br.atoms[1].bondsMap[far])
from chimera.tkgui import selectionOperation
sel = selection.ItemizedSelection()
sel.add(selectables)
selectionOperation(sel)
elif cmdText == "Reverse":
br.anchorSide = br.bond.otherAtom(br.anchorSide)
def _sessionAngleSaveCB(self, trigName, myData, sessionFile):
from SimpleSession import sessionID, sesRepr
sesData = []
for atoms in self.angleInfo:
sesData.append([sessionID(a) for a in atoms])
print>>sessionFile, "angleInfo = %s" % sesRepr(sesData)
print>>sessionFile, """
try:
from StructMeasure.gui import restoreAngles
restoreAngles(angleInfo)
except:
reportRestoreError("Error restoring angle monitors in session")
"""
def _setDihedEnd(self, br, dihedMenu):
"""callback when a 'near atoms' menu is set"""
widgets, nearIndex, nearAtoms, farIndex, farAtoms = \
self.rotInfo[br]
index = dihedMenu.index(Pmw.SELECT)
if dihedMenu is widgets[1]:
nearIndex = index
else:
farIndex = index
self.rotInfo[br] = [widgets, nearIndex, nearAtoms,
farIndex, farAtoms]
widgets[4].configure(angle=float("%.*f" %
(prefs[TORSION_PRECISION], self.dihedral(br))))
self._labelRot(br)
def _toggleAngleType(self):
if self.angleTitle.get() == "Torsion":
self.angleTitle.set("Delta")
self.rotTable.setColumnTitle(1, None)
self.rotTable.setColumnTitle(3, None)
for i in range(len(self.rotations)):
br = self.rotations[i]
ID, near, menu, far, dihed, delta = \
self.rotInfo[br][0]
dihed.grid_forget()
near.grid_forget()
far.grid_forget()
delta.grid(row=i, column=4, sticky='ew')
self.rotInfo[br][0][-2:] = delta, dihed
else:
self.angleTitle.set("Torsion")
self.rotTable.setColumnTitle(1, "Near")
self.rotTable.setColumnTitle(3, "Far")
for i in range(len(self.rotations)):
br = self.rotations[i]
ID, near, menu, far, delta, dihed = \
self.rotInfo[br][0]
delta.grid_forget()
dihed.grid(row=i, column=4, sticky='ew')
near.grid(row=i, column=1, sticky='ew')
far.grid(row=i, column=3, sticky='ew')
self.rotInfo[br][0][-2:] = dihed, delta
if self.rotLabelChoice.getvalue() == "Angle":
for br in self.rotations:
self._labelRot(br, "Angle")
def _updateAngles(self):
self.angleTable.refresh()
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):
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 __init__(self, parent, status):
self.status = status
self.parent = parent
import Pmw, Tkinter
row = 0
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
Tkinter.Button(parent, text="Define axes...", pady=0,
command=self._createAxesCB).grid(row=row, column=0)
Tkinter.Button(parent, text="Define plane...", pady=0,
command=self._createPlaneCB).grid(row=row, column=1)
row += 1
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.grid(row=row, column=0, columnspan=2, sticky="nsew")
parent.rowconfigure(row, weight=1)
self.table.addColumn("Name", "name", format="%s ")
self.table.addColumn(" ", "model.color", format=(False, True))
idCol = self.table.addColumn("ID", "id")
self.table.addColumn("Shown", "model.display", format=bool)
self.table.addColumn("Length", "length", format="%4.1f", font="TkFixedFont")
self.table.addColumn("Radius", "radius", format="%4.1f", font="TkFixedFont")
self.table.setData(geomManager.items)
self.table.sortBy(idCol)
self.table.launch(browseCmd=self._tableCB)
row += 1
selGroup = Pmw.Group(parent, tag_text="Choosing in table...")
selGroup.grid(row=row, column=0, columnspan=3, sticky='ew')
row += 1
cbFrame = selGroup.interior()
cbFrame.columnconfigure(0, weight=1)
cbFrame.columnconfigure(1, weight=1)
self.geomSelObjVar = Tkinter.IntVar(parent)
self.geomSelObjVar.set(prefs[AXIS_SEL_OBJ])
Tkinter.Checkbutton(cbFrame, variable=self.geomSelObjVar,
text="selects object").grid(row=0, column=0)
self.geomSelObjVar.trace_variable("w", self._selModeChangeCB)
self.geomSelAtomsVar = Tkinter.IntVar(parent)
self.geomSelAtomsVar.set(prefs[AXIS_SEL_ATOMS])
Tkinter.Checkbutton(cbFrame, variable=self.geomSelAtomsVar,
text="selects atoms").grid(row=0, column=1)
self.geomSelAtomsVar.trace_variable("w", self._selModeChangeCB)
self.buttons = []
self.buttons.append(Tkinter.Button(parent, text="Delete", pady=0,
state='disabled', command=self._deleteItemsCB))
self.buttons[-1].grid(row=row, column=0, sticky='e')
self.buttons.append(Tkinter.Button(parent, text="Rename", pady=0,
state='disabled', command=self._renameItems))
self.buttons[-1].grid(row=row, column=1, sticky='w')
self.renameDialogs = {}
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=2)
row += 1
self.buttons.append(Tkinter.Button(f, text="Report distance", pady=0,
state='disabled', command=self._atomsDistanceCB))
self.buttons[-1].grid(row=0, column=0)
Tkinter.Label(f, text="to selected atoms"
).grid(row=0, column=1)
geomManager.registerInterface(self)
if geomManager.items:
self._selHandlerID = triggers.addHandler("selection changed",
self._selChangeCB, None)
class RotamerDialog(ModelessDialog):
buttons = ('OK', 'Apply', 'Close',)
oneshot = True
help = "ContributedSoftware/rotamers/rotamers.html#rotamerlist"
def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(SAVE_SESSION,
self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True, lib=lib, resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule, hidden=True, noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'),
('H-Bonds', 'hbond'), ('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter, Pmw, Tix
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
selectMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Select", menu=selectMenu)
selectMenu.add_command(label="Current Rotamers",
command=self._selCurCB)
selectMenu.add_command(label="All Rotamers",
command=self._selAllCB)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
self.addColumnMenu = Tkinter.Menu(self.columnMenu)
self.columnMenu.add_cascade(label="Add",
menu=self.addColumnMenu)
for label, ddn in self.dependentDialogInfo:
self.addColumnMenu.add_command(label=label + "...",
command=lambda name=ddn+"Dialog":
self._showDialog(name))
self.columnMenu.add_separator()
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row = 0)
self.numChis = len(self.rotamers[0].chis)
row = 1
Tkinter.Label(parent, text="%s %s rotamers" %
(self.lib.displayName, self.resType)).grid(
row=row, column=0)
row += 1
self.buttonWidgets['OK'].config(state="disabled")
self.buttonWidgets['Apply'].config(state="disabled")
from CGLtk.Table import SortableTable
self.rotTable = SortableTable(parent,
menuInfo=(self.columnMenu, prefs, {}, True))
if not self.tableData:
for i in range(self.numChis):
self.rotTable.addColumn("Chi %d" % (i+1),
"lambda r: r.chis[%d]" % i,
format="%6.1f")
self.rotTable.addColumn("Probability", "rotamerProb",
format="%.6f", font='TkFixedFont')
self.rotTable.setData(self.rotamers)
self.rotTable.launch(browseCmd=self._selRotamerCB,
restoreInfo=self.tableData)
delattr(self, 'tableData')
parent.rowconfigure(row, weight=1)
for tableColumn in range(1):
parent.columnconfigure(tableColumn, weight=1)
self.rotTable.grid(row=row, column=0, sticky="nsew")
row += 1
def addClashColumn(self, *args):
from Rotamers import processClashes
format = processClashes(self.residue, self.rotamers, *args)
self.rotTable.addColumn("Clashes", "clashScore", format=format,
display=True)
registerAttribute(chimera.Molecule, "clashScore")
def addHbondColumn(self, *args):
from Rotamers import processHbonds
processHbonds(self.residue, self.rotamers, *args)
self.rotTable.addColumn("H-Bonds", "numHbonds", format="%d",
display=True)
registerAttribute(chimera.Molecule, "numHbonds")
def addVolumeColumn(self, columnName, *args):
from Rotamers import processVolume
format = processVolume(self.rotamers, columnName, *args)
self.rotTable.addColumn(columnName,
"lambda r: r.volumeScores[%s]" % repr(columnName),
format=format, display=True)
registerAttribute(chimera.Molecule, "volumeScores")
def Apply(self):
from Rotamers import useRotamer
useRotamer(self.residue, self.rotamerSel, log=True)
def destroy(self):
chimera.triggers.deleteHandler('Residue', self.resHandlerID)
chimera.triggers.deleteHandler(SAVE_SESSION, self._sesHandlerID)
chimera.openModels.close(self.rotamers)
for label, ddn in self.dependentDialogInfo:
dd = getattr(self, ddn + 'Dialog', None)
if dd:
dd.destroy()
ModelessDialog.destroy(self)
def selectRotamers(self, rotamers):
from chimera import selectionOperation
from chimera.selection import ItemizedSelection
rotSel = ItemizedSelection()
rotSel.add(rotamers)
selectionOperation(rotSel)
def _resChangeCB(self, trigName, myData, trigData):
if self.residue in trigData.deleted:
self.destroy()
def _selAllCB(self):
self.selectRotamers(self.rotamers)
def _selCurCB(self):
self.selectRotamers([r for r in self.rotamers if r.display])
def _selRotamerCB(self, tableSel):
tableSet = set(tableSel)
if tableSet == set([r for r in self.rotamers if r.display]):
return
self.rotamerSel = tableSel
for rot in self.rotamers:
rot.display = rot in tableSet
if len(tableSel) > 0:
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK'].config(state=state)
self.buttonWidgets['Apply'].config(state=state)
def _sessionCB(self, trigName, myData, sesFile):
from SimpleSession import sessionID
data = (1, sessionID(self.residue), self.resType,
[sessionID(rot) for rot in self.rotamers], self.bbdep,
self.lib.displayName, self.rotTable.getRestoreInfo())
print>>sesFile, """
try:
from Rotamers.gui import sessionRestore
sessionRestore(%s)
except:
reportRestoreError('Error restoring Rotamers')
""" % repr(data)
def _showDialog(self, dialogName):
d = getattr(self, dialogName, None)
if d:
d.enter()
else:
importName = dialogName[0].upper() + dialogName[1:]
exec("from %s import %s" % (importName, importName))
exec("self.%s = %s(self)" % (dialogName, importName))
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)
def fillInUI(self, parent):
# scaleWidget allows user to scale the displacement
# vector for display purposes.
# addColumn arguments are: (column title, attribute associated
# with column, layout format). format=None means use default
# display string. format=bool means display using checkbutton
# that can be used to change the value of the variable.
self.modesTable = t = SortableTable(parent, automultilineHeaders=False)
t.pack(expand=True, fill="both")
t.addColumn("#", "index", format="%d")
t.addColumn("Active", "active", format=bool)
t.addColumn(u"Frequency (cm\u207B\u00b9)", "frequency", format=None)
t.setData(self.modeData)
t.launch()
#self.hydro = False
#self.resid = False
self.representation = 1
# self.scaleWidget = Tkinter.Scale(parent,
# label="Scale Factor",
# from_=1.0, to=50.0, orient="horizontal", resolution = 1.0,
# command = self.__scaleCB)
# self.scaleWidget.set(0.1)
# self.scaleWidget.pack(expand=True, fill="both")
self.scaleWidget = Pmw.Counter(parent,
entryfield_command=self.__scaleCB,
autorepeat=True,
entryfield_value=1,
entryfield_validate=self._validate)
self.scaleWidget.pack(expand=True, fill="both")
self.optionVector = Pmw.RadioSelect(
parent,
buttontype='checkbutton',
labelpos='w',
label_text='Show displacement Vectors:',
command=self._show)
self.optionVector.add("")
self.optionVector.pack(expand=False, fill='both')
self.vectorGroup = Pmw.Group(parent, tag_text='Displacement Vectors')
self.vectorGroup.pack(expand=False, fill='both')
self.vectorGroup.pack_forget()
# test for drawing vectors
self.__vecTypeDef = Tkinter.StringVar()
self.__vecTypeDef.set('all atoms')
self.vecType = Pmw.OptionMenu(
self.vectorGroup.interior(),
labelpos='w',
label_text='Representation :',
menubutton_textvariable=self.__vecTypeDef,
items=('all atoms', 'no hydrogens', 'by residues'),
command=self.__vecType)
self.vecType.pack(anchor='w', fill="both")
self.vectorType = Pmw.RadioSelect(self.vectorGroup.interior(),
buttontype='radiobutton',
orient='vertical',
command=self.__scaleCB2)
self.vectorType.add("Positive Displacement")
self.vectorType.add("Negative Displacement")
self.vectorType.setvalue("Positive Displacement")
self.vectorType.pack(expand=False, fill="both")
# defining the arrows
self.sf = Pmw.ScrolledFrame(self.vectorGroup.interior(),
labelpos='n',
label_text='Modifying Arrows',
usehullsize=1,
hull_width=400,
hull_height=220)
self.arrow = Pmw.RadioSelect(self.vectorGroup.interior(),
buttontype='checkbutton',
labelpos='w',
label_text='Configuration arrows',
command=self._arrowShow)
self.arrow.add("")
self.arrow.pack(expand=False, fill='both')
# function per entrar infos sobre les amplituds de les flexes
self.__vectorCyl = Pmw.Counter(self.sf.interior(),
entryfield_command=self.__cylCB,
autorepeat=True,
label_text="Radius of the cylinder",
labelpos="w",
entryfield_value=0.03,
datatype={
'counter': 'real',
'separator': '.'
},
increment=0.01,
entryfield_validate=self._validateCyl)
self.__vectorCyl.pack(expand=False, fill="both")
self.__vectorCon = Pmw.Counter(
self.sf.interior(),
entryfield_command=self.__conCB,
autorepeat=True,
label_text="Radius of the base of the cone",
labelpos="w",
entryfield_value=0.3,
datatype={
'counter': 'real',
'separator': '.'
},
increment=0.01,
entryfield_validate=self._validateCon)
self.__vectorCon.pack(expand=False, fill="both")
self.__vectorRel = Pmw.Counter(
self.sf.interior(),
entryfield_command=self.__relCB,
autorepeat=True,
label_text="Relative size of the cylinder",
labelpos="w",
entryfield_value=0.8,
datatype={
'counter': 'real',
'separator': '.'
},
increment=0.01,
entryfield_validate=self._validateRel)
self.__vectorRel.pack(expand=False, fill="both")
self.__var = Tkinter.StringVar()
self.__var.set('medium purple')
self.__vectorColor = Pmw.OptionMenu(
self.sf.interior(),
labelpos='w',
label_text='Choose Color:',
menubutton_textvariable=self.__var,
items=('red', 'blue', 'cyan', 'medium purple', 'yellow', 'grey',
'green'),
command=self.__colorCB,
)
self.__vectorColor.pack(anchor='w', fill="both")
self.__vectorScale = Pmw.Counter(self.sf.interior(),
entryfield_command=self.__scaleCB,
autorepeat=True,
label_text="Vector Scale Factor",
labelpos="w",
entryfield_value=50,
datatype={'counter': 'numeric'},
increment=1,
entryfield_validate=self._validateSf)
self.__vectorScale.pack(expand=False, fill="both")
self.saveOptionVector = Pmw.RadioSelect(
parent,
buttontype='checkbutton',
labelpos='w',
label_text='Save Modes in Session:',
command=self._showsave)
self.saveOptionVector.add("")
self.saveOptionVector.pack(expand=False, fill='both')
self.vecSaveGroup = Pmw.Group(parent,
tag_text='Modes to save in session')
self.vecSaveGroup.pack(expand=False, fill='both')
self.modeText = Pmw.EntryField(self.vecSaveGroup.interior(),
label_text=" modes",
labelpos='e',
validate={"validator": "real"})
self.modeText.pack(expand=False, fill="both")
self.vecSaveGroup.pack_forget()
class BlastResultsDialog(ModelessDialog):
buttons = ( "Show in MAV", "Load Structure", "Hide", "Quit" )
help = "UsersGuide/blast.html#results"
def __init__(self, mol=None, seq=None, blastData=None, sessionData=None):
self.loaded = {}
self.reference = mol
if isinstance(self.reference, StructureSequence):
self.molecule = self.reference.molecule
elif isinstance(self.reference, Molecule):
self.molecule = self.reference
self.sequence = seq # for session data only
if seq is None:
self.seq, self.refResList = self._makeSeq(mol)
else:
self.seq = seq
if self.reference:
seq, resList = self._makeSeq(mol)
self.refResList = self._getResidues(self.seq,
seq, resList)
if blastData:
self.initBlast(*blastData)
else:
self.initSession(*sessionData)
self.title = "Blast: %s" % self.basename
ModelessDialog.__init__(self)
if not blastData:
self._updateLoadButton()
if self.molecule:
self.closeHandler = chimera.openModels.addRemoveHandler(
self._modelClosedCB, None)
else:
self.closeHandler = None
self.sesHandler = chimera.triggers.addHandler(
SAVE_SESSION,
self._sessionCB, None)
chimera.extension.manager.registerInstance(self)
def _makeSeq(self, mol):
if isinstance(mol, StructureSequence):
if not mol.hasProtein():
raise UserError("No protein sequence found "
"in %s %s\n" % (
mol.molecule.name,
mol.name))
return ''.join(mol.sequence), mol.residues
elif isinstance(mol, Molecule):
from chimera import resCode
seq = []
refResList = []
for r in mol.residues:
try:
seq.append(resCode.protein3to1[r.type])
except KeyError:
pass
else:
refResList.append(r)
if len(seq) == 0:
raise UserError("No protein sequence "
"found in %s\n" % mol.name)
return ''.join(seq), refResList
else:
raise ValueError("Blast Protein not called with "
"molecule or chain\n")
def initBlast(self, prog, db, evalue, matrix, passes, showOne):
import os.path
self.program = prog
if self.molecule is not None:
base = os.path.basename(self.molecule.name)
else:
try:
base = self.seq.name
except AttributeError:
base = "query"
self.basename = base.replace(' ', '_')
self.showOne = showOne
self.parser = None
from Parser import BlastproteinService
self.service = BlastproteinService(self._finish, params=(
prog, db,
self.basename,
self.seq, evalue,
matrix, passes))
self.tableData = None
def initSession(self, program, name, showOne, parserData,
serviceData, tableData):
self.basename = name
self.program = program
self.showOne = showOne
if parserData:
from Parser import restoreParser
self.parser = restoreParser(parserData)
else:
self.parser = None
if serviceData:
from Parser import BlastproteinService
self.service = BlastproteinService(self._finish,
sessionData=serviceData)
else:
self.service = None
self.tableData = tableData
def fillInUI(self, parent):
from CGLtk.Table import SortableTable
self.blastTable = SortableTable(parent)
if not self.tableData:
self._addColumn("GI", "lambda m: m.gi",
format="%s ", anchor="w")
self._addColumn("PDB", "lambda m: m.pdb or '-'",
format="%s ", anchor="w")
self._addColumn("Evalue", "lambda m: m.evalue",
format="%s")
self._addColumn("Score", "lambda m: m.score",
format="%s")
self._addColumn("Description",
"lambda m: m.description",
format=" %s", anchor="w")
if self.parser:
self.blastTable.setData(self.parser.matches)
else:
self.blastTable.setData([])
self.blastTable.launch(browseCmd=self._selectHitCB,
restoreInfo=self.tableData)
self.blastTable.pack(expand=True, fill="both")
bw = self.buttonWidgets
bw["Show in MAV"].config(state="disabled")
bw["Load Structure"].config(state="disabled")
bw["Quit"].config(state="disabled")
def _finish(self, results):
if self.blastTable is None:
# We already quit, so UI is gone
return
from Parser import Parser
import os.path
try:
self.parser = Parser(self.basename, results,
self.program == "psiblast")
except SyntaxError, s:
replyobj.error("BLAST error: %s\n" % s)
return
except:
class RotamerDialog(ModelessDialog):
buttons = (
'OK',
'Apply',
'Close',
)
oneshot = True
help = "ContributedSoftware/rotamers/rotamers.html#rotamerlist"
def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True,
lib=lib,
resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule,
hidden=True,
noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'), ('H-Bonds', 'hbond'),
('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def fillInUI(self, parent):
import Tkinter, Pmw, Tix
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
selectMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Select", menu=selectMenu)
selectMenu.add_command(label="Current Rotamers",
command=self._selCurCB)
selectMenu.add_command(label="All Rotamers", command=self._selAllCB)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
self.addColumnMenu = Tkinter.Menu(self.columnMenu)
self.columnMenu.add_cascade(label="Add", menu=self.addColumnMenu)
for label, ddn in self.dependentDialogInfo:
self.addColumnMenu.add_command(
label=label + "...",
command=lambda name=ddn + "Dialog": self._showDialog(name))
self.columnMenu.add_separator()
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row=0)
self.numChis = len(self.rotamers[0].chis)
row = 1
Tkinter.Label(parent,
text="%s %s rotamers" %
(self.lib.displayName, self.resType)).grid(row=row,
column=0)
row += 1
self.buttonWidgets['OK'].config(state="disabled")
self.buttonWidgets['Apply'].config(state="disabled")
from CGLtk.Table import SortableTable
self.rotTable = SortableTable(parent,
menuInfo=(self.columnMenu, prefs, {},
True))
if not self.tableData:
for i in range(self.numChis):
self.rotTable.addColumn("Chi %d" % (i + 1),
"lambda r: r.chis[%d]" % i,
format="%6.1f")
self.rotTable.addColumn("Probability",
"rotamerProb",
format="%.6f",
font='TkFixedFont')
self.rotTable.setData(self.rotamers)
self.rotTable.launch(browseCmd=self._selRotamerCB,
restoreInfo=self.tableData)
delattr(self, 'tableData')
parent.rowconfigure(row, weight=1)
for tableColumn in range(1):
parent.columnconfigure(tableColumn, weight=1)
self.rotTable.grid(row=row, column=0, sticky="nsew")
row += 1
def addClashColumn(self, *args):
from Rotamers import processClashes
format = processClashes(self.residue, self.rotamers, *args)
self.rotTable.addColumn("Clashes",
"clashScore",
format=format,
display=True)
registerAttribute(chimera.Molecule, "clashScore")
def addHbondColumn(self, *args):
from Rotamers import processHbonds
processHbonds(self.residue, self.rotamers, *args)
self.rotTable.addColumn("H-Bonds",
"numHbonds",
format="%d",
display=True)
registerAttribute(chimera.Molecule, "numHbonds")
def addVolumeColumn(self, columnName, *args):
from Rotamers import processVolume
format = processVolume(self.rotamers, columnName, *args)
self.rotTable.addColumn(columnName,
"lambda r: r.volumeScores[%s]" %
repr(columnName),
format=format,
display=True)
registerAttribute(chimera.Molecule, "volumeScores")
def Apply(self):
from Rotamers import useRotamer
useRotamer(self.residue, self.rotamerSel, log=True)
def destroy(self):
chimera.triggers.deleteHandler('Residue', self.resHandlerID)
chimera.triggers.deleteHandler(SAVE_SESSION, self._sesHandlerID)
chimera.openModels.close(self.rotamers)
for label, ddn in self.dependentDialogInfo:
dd = getattr(self, ddn + 'Dialog', None)
if dd:
dd.destroy()
ModelessDialog.destroy(self)
def selectRotamers(self, rotamers):
from chimera import selectionOperation
from chimera.selection import ItemizedSelection
rotSel = ItemizedSelection()
rotSel.add(rotamers)
selectionOperation(rotSel)
def _resChangeCB(self, trigName, myData, trigData):
if self.residue in trigData.deleted:
self.destroy()
def _selAllCB(self):
self.selectRotamers(self.rotamers)
def _selCurCB(self):
self.selectRotamers([r for r in self.rotamers if r.display])
def _selRotamerCB(self, tableSel):
tableSet = set(tableSel)
if tableSet == set([r for r in self.rotamers if r.display]):
return
self.rotamerSel = tableSel
for rot in self.rotamers:
rot.display = rot in tableSet
if len(tableSel) > 0:
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK'].config(state=state)
self.buttonWidgets['Apply'].config(state=state)
def _sessionCB(self, trigName, myData, sesFile):
from SimpleSession import sessionID
data = (1, sessionID(self.residue), self.resType,
[sessionID(rot) for rot in self.rotamers], self.bbdep,
self.lib.displayName, self.rotTable.getRestoreInfo())
print >> sesFile, """
try:
from Rotamers.gui import sessionRestore
sessionRestore(%s)
except:
reportRestoreError('Error restoring Rotamers')
""" % repr(data)
def _showDialog(self, dialogName):
d = getattr(self, dialogName, None)
if d:
d.enter()
else:
importName = dialogName[0].upper() + dialogName[1:]
exec("from %s import %s" % (importName, importName))
exec("self.%s = %s(self)" % (dialogName, importName))
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
# load needed coord sets...
frameNums = range(self.startFrame, self.endFrame+1, self.stride)
for frameNum in frameNums:
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum,
makeCurrent=False)
# compute RMSDs
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel,
self.ignoreBulk, self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
numFrames = len(frameNums)
self.status("Fetching %d coordinate arrays" % numFrames)
numpyArrays = {}
from time import time
t0 = time()
for i, fn in enumerate(frameNums):
numpyArrays[fn] = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(fn))
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
if i == numFrames - 1:
self.status("Fetched %d coordinate arrays"
% (i+1))
else:
elapsed = time() - t0
perSec = elapsed / (i+1)
remaining = perSec * (numFrames - (i+1))
self.status("Fetched %d of %d coordinate arrays"
"\nAbout %.1f minutes remaining" %
(i+1, numFrames, remaining / 60.0))
t0 = time()
totalRMSDs = numFrames * (numFrames - 1) / 2
self.status("Computing %d RMSDs" % totalRMSDs)
from EnsembleMatch.distmat import DistanceMatrix
fullDM = DistanceMatrix(numFrames)
sameAs = {}
for i, frame1 in enumerate(frameNums):
na1 = numpyArrays[frame1]
for j, frame2 in enumerate(frameNums[i+1:]):
na2 = numpyArrays[frame2]
rmsd = matchPositions(na1, na2)[1]
fullDM.set(i, i+j+1, rmsd)
if rmsd == 0.0:
sameAs[frame2] = frame1
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
numComputed = totalRMSDs - ((numFrames - (i+1)) *
(numFrames - (i+2))) / 2
if numComputed == totalRMSDs:
self.status("Computed %d RMSDs" % totalRMSDs)
else:
elapsed = time() - t0
perSec = elapsed / numComputed
remaining = perSec * (totalRMSDs - numComputed)
if remaining < 50:
timeEst = "%d seconds" % int(
remaining + 0.5)
else:
timeEst = "%.1f minutes" % (
remaining / 60.0)
self.status("Computed %d of %d RMSDs\n"
"About %s remaining" % (numComputed,
totalRMSDs, timeEst))
self.status("Generating clusters")
self.buttonWidgets['Close'].configure(text="Close")
if not sameAs:
dm = fullDM
reducedFrameNums = frameNums
indexMap = range(len(frameNums))
elif len(sameAs) == numFrames - 1:
raise UserError("All frames to cluster are identical!")
self.Close()
else:
dm = DistanceMatrix(numFrames - len(sameAs))
reducedFrameNums = []
indexMap = []
for i, fn in enumerate(frameNums):
if fn in sameAs:
continue
reducedFrameNums.append(fn)
indexMap.append(i)
for i in range(len(reducedFrameNums)):
mapi = indexMap[i]
for j in range(i+1, len(reducedFrameNums)):
mapj = indexMap[j]
dm.set(i, j, fulldm.get(mapi, mapj))
from EnsembleMatch.nmrclust import NMRClust
clustering = NMRClust(dm)
self.clusterMap = {}
self.representatives = []
self.clusters = []
unsortedClusters = [(c, clustering.representative(c))
for c in clustering.clusters]
# sort the clusters so that the coloring is reproducible
# while trying to avoid using adjacent colors for
# adjacent clusters
clusters = [unsortedClusters.pop()]
while unsortedClusters:
bestCluster = bestVal = None
for uc in unsortedClusters:
val = abs(uc[-1] - clusters[-1][-1])
if len(clusters) > 1:
val += 0.5 * abs(uc[-1]
- clusters[-2][-1])
if len(clusters) > 2:
val += 0.25 * abs(uc[-1]
- clusters[-3][-1])
if bestVal == None or val > bestVal:
bestCluster = uc
bestVal = val
unsortedClusters.remove(bestCluster)
clusters.append(bestCluster)
colors = colorRange(len(clusters))
for c, rep in clusters:
cluster = Cluster()
cluster.color = colors.pop()
self.clusters.append(cluster)
cluster.representative = reducedFrameNums[rep]
cluster.members = []
for m in c.members():
f = reducedFrameNums[m]
self.clusterMap[f] = cluster
cluster.members.append(f)
for dup, base in sameAs.items():
c = self.clusterMap[base]
self.clusterMap[dup] = c
c.members.append(dup)
self.status("%d clusters" % len(self.clusters))
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.addColumn("Color", "color", format=(False, False),
titleDisplay=False)
membersCol = self.table.addColumn("Members",
"lambda c: len(c.members)", format="%d")
self.table.addColumn("Representative Frame", "representative",
format="%d")
self.table.setData(self.clusters)
self.table.launch(browseCmd=self.showRep)
self.table.sortBy(membersCol)
self.table.sortBy(membersCol) # to get descending order
self.table.grid(sticky="nsew")
self.timeLine = Pmw.ScrolledCanvas(parent, canvas_height="0.5i")
self.timeLine.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
self.zoom = 2.0
self.drawTimeLine()
def fillInUI(self, parent):
self.sel_handler = None
self.last_selected = set()
import Tkinter
from CGLtk import Hybrid
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
file_menu_entries = (('Export...', self.export_cb), )
fmenu = Hybrid.cascade_menu(menubar, 'File', file_menu_entries)
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
columns = (
('region', lambda r: r.rid),
('grid points', lambda r: r.point_count()),
('grouped', lambda r: len(r.children())),
('has surface', lambda r: 1 if r.has_surface() else 0),
('contacts', lambda r: len(r.contacting_regions())),
('edge distance', lambda r: r.edge_distance()),
('bounds', lambda r: tuple(r.bounds()[0]) + tuple(r.bounds()[1]),
'%d,%d,%d,%d,%d,%d', False),
)
self.computed_attributes = dict([c[:2] for c in columns])
self.keys = set([c[0] for c in columns])
defaults = dict([(c[0], True) for c in columns])
prefs = {}
mi = (self.columnMenu, prefs, defaults, True)
from CGLtk.Table import SortableTable
self.attribute_table = t = SortableTable(parent, menuInfo=mi)
for cspec in columns:
name, func = cspec[:2]
format = cspec[2] if len(cspec) >= 3 else format_item
display = cspec[3] if len(cspec) >= 4 else True
t.addColumn(name,
func,
format=format,
display=display,
font='TkFixedFont',
refresh=False)
self.add_columns() # Additional region attributes.
t.setData([])
t.launch(browseCmd=self.table_line_selected)
t.grid(row=row, column=0, sticky="nsew")
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
naf = Tkinter.Frame(parent)
naf.grid(row=row, column=0, sticky='new')
naf.columnconfigure(1, weight=1)
row += 1
ke = Hybrid.Entry(naf, 'Set attribute ', 15)
ke.frame.grid(row=0, column=0, sticky='w')
self.key_name = ke.variable
ke.entry.bind('<KeyPress-Return>', self.new_value_cb)
ve = Hybrid.Entry(naf, ' to value ', 15)
ve.frame.grid(row=0, column=1, sticky='ew')
self.value = ve.variable
ve.entry.bind('<KeyPress-Return>', self.new_value_cb)
ol = Tkinter.Label(naf, text=' or ')
ol.grid(row=0, column=2, sticky='e')
sb = Tkinter.Button(naf, text='snapshot', command=self.snapshot_cb)
sb.grid(row=0, column=3, sticky='e')
fl = Hybrid.Checkbutton_Entries(parent, False, 'Filter list ',
(50, 'grid_points > 1000'))
fl.frame.grid(row=row, column=0, sticky='new')
row += 1
self.use_filter, self.filter_text = fl.variables
self.use_filter.add_callback(self.filter_cb)
e = fl.entries[0]
fl.frame.columnconfigure(1, weight=1)
e.grid(sticky='ew')
e.bind('<KeyPress-Return>', self.filter_cb)
op = Hybrid.Popup_Panel(parent, resize_dialog=False)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.optionsPanel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=0, sticky='e')
l = Tkinter.Label(opf, text='Options', font='TkCaptionFont')
l.grid(column=0, row=orow, sticky='w', pady=5)
orow += 1
ss = Hybrid.Checkbutton(opf, 'Show selected region surface', False)
ss.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.show_selected = ss.variable
msg = Tkinter.Label(parent, width=60, anchor='w', justify='left')
msg.grid(column=0, row=row, sticky='ew')
self.msg = msg
self.Update()
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()
class ModBaseDialog(ModelessDialog):
buttons = ( "Hide", "Quit" )
help = "UsersGuide/modbase.html"
def __init__(self, name, molList, tableData=None):
self.title = "ModBase: %s" % name
self.molList = molList
self.tableData = tableData
ModelessDialog.__init__(self)
self.closeHandler = chimera.openModels.addRemoveHandler(
self._modelClosedCB, None)
self.selHandler = chimera.triggers.addHandler(
"selection changed",
self._selectionChangedCB, None)
self.sesHandler = chimera.triggers.addHandler(
SAVE_SESSION,
self._sessionCB, None)
chimera.extension.manager.registerInstance(self)
def fillInUI(self, parent):
import Tkinter
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, pack = 'top')
self._makeActionGroup(parent)
from CGLtk.Table import SortableTable
from prefs import colAttr, colOrder, prefs, defaults
self.modBaseTable = SortableTable(parent, menuInfo=(
self.columnMenu,
prefs,
defaults,
False ))
if not self.tableData:
self._addColumn("Model",
"lambda m: m.oslIdent()",
format="%s",
shown=True)
for fieldName in colOrder:
keyName, format = colAttr[fieldName]
self._addColumn(fieldName,
"lambda m: m.modbaseInfo['%s']"
% keyName,
format=format)
self.modBaseTable.setData(self.molList)
chimera.triggers.addHandler("post-frame", self._launchTable,
None)
self.modBaseTable.pack(expand=True, fill="both")
def _makeActionGroup(self, parent):
from prefs import prefs
from chimera import chimage
import Tkinter, Pmw
d = prefs.get("treatment", {})
self.treatmentShow = d.get("show", 0)
selAtoms = d.get("selectAtoms", 0)
selModels = d.get("selectModels", 0)
hideOthers = d.get("hideOthers", 1)
self.rightArrow = chimage.get("rightarrow.png", parent)
self.downArrow = chimage.get("downarrow.png", parent)
if self.treatmentShow:
relief = "groove"
image = self.downArrow
else:
relief = "flat"
image = self.rightArrow
self.treatmentGroup = Pmw.Group(parent,
collapsedsize=0,
tagindent=0,
ring_relief=relief,
tag_pyclass=Tkinter.Button,
tag_text=" Treatment of Chosen Models",
tag_relief="flat",
tag_compound="left",
tag_image=image,
tag_command=self._treatmentCB)
if not self.treatmentShow:
self.treatmentGroup.collapse()
self.treatmentGroup.pack(side="top", fill="x", padx=3)
interior = self.treatmentGroup.interior()
self.treatmentSelAtom = Tkinter.IntVar(parent)
self.treatmentSelAtom.set(selAtoms)
b = Tkinter.Checkbutton(interior,
text="Select atoms",
onvalue=1, offvalue=0,
variable=self.treatmentSelAtom,
command=self._treatmentChangedCB)
b.pack(side="left")
self.treatmentSelModel = Tkinter.IntVar(parent)
self.treatmentSelModel.set(selModels)
b = Tkinter.Checkbutton(interior,
text="Choose in Model Panel",
onvalue=1, offvalue=0,
variable=self.treatmentSelModel,
command=self._treatmentChangedCB)
b.pack(side="left")
self.treatmentHideOthers = Tkinter.IntVar(parent)
self.treatmentHideOthers.set(hideOthers)
b = Tkinter.Checkbutton(interior,
text="Hide others",
onvalue=1, offvalue=0,
variable=self.treatmentHideOthers,
command=self._treatmentChangedCB)
b.pack(side="left")
def _treatmentCB(self):
self.treatmentShow = not self.treatmentShow
if self.treatmentShow:
self.treatmentGroup.configure(ring_relief="groove",
tag_image=self.downArrow)
self.treatmentGroup.expand()
else:
self.treatmentGroup.configure(ring_relief="flat",
tag_image=self.rightArrow)
self.treatmentGroup.collapse()
self._savePrefs()
def _addColumn(self, title, attrFetch, format="%s", shown=None):
if title in [c.title for c in self.modBaseTable.columns]:
return
if title in ["Model Score", "Sequence Identity"]:
# try to align decimal points
kw = {'font': 'TkFixedFont'}
else:
kw = {}
c = self.modBaseTable.addColumn(title, attrFetch, format=format,
display=shown, **kw)
self.modBaseTable.columnUpdate(c)
def _launchTable(self, trigger, closure, mols):
self.modBaseTable.launch(browseCmd=self._selectModelCB,
restoreInfo=self.tableData)
return chimera.triggerSet.ONESHOT
def _modelClosedCB(self, trigger, closure, mols):
remainder = [ m for m in self.molList if m not in mols ]
if len(remainder) == 0:
self.molList = []
self.exit()
elif len(remainder) != len(self.molList):
self.molList = remainder
self.modBaseTable.setData(self.molList)
self.modBaseTable.refresh(rebuild=True)
def _selectionChangedCB(self, trigger, closure, ignore):
from chimera import selection
mols = selection.currentMolecules()
selected = [ m for m in mols if m in self.molList ]
self.modBaseTable.highlight(selected)
def _selectModelCB(self, tableSel):
if self.treatmentSelAtom.get():
from chimera import selection
selection.clearCurrent()
selection.addCurrent(tableSel)
selection.addImpliedCurrent()
if self.treatmentSelModel.get():
from ModelPanel import ModelPanel
from chimera import dialogs
d = dialogs.display(ModelPanel.name)
d.selectionChange(tableSel)
shown = {}
if self.treatmentHideOthers.get():
for m in self.molList:
key = (m.id, m.subid)
shown[key] = m in tableSel or not tableSel
else:
for m in tableSel:
key = (m.id, m.subid)
shown[key] = True
for m in chimera.openModels.list():
key = (m.id, m.subid)
try:
m.display = shown[key]
except KeyError:
pass
def _treatmentChangedCB(self):
self._selectModelCB(self.modBaseTable.selected())
self._savePrefs()
def _savePrefs(self):
from prefs import prefs
prefs["treatment"] = {
"show": self.treatmentShow,
"selectAtoms": self.treatmentSelAtom.get(),
"selectModels": self.treatmentSelModel.get(),
"hideOthers": self.treatmentHideOthers.get(),
}
prefs.save()
def _sessionCB(self, trigger, myData, sesFile):
from SimpleSession import sessionID
data = (1, # version
self.title, # title
[ sessionID(m) for m in self.molList ], # molecules
[ m.modbaseInfo for m in self.molList ],# stats
self.modBaseTable.getRestoreInfo()) # GUI
print >> sesFile, """
try:
from ModBase.gui import sessionRestore
sessionRestore(%s)
except:
reportRestoreError("Error restoring ModBase")
""" % repr(data)
def exit(self):
if self.molList:
chimera.openModels.close(self.molList)
if self.closeHandler:
chimera.openModels.deleteRemoveHandler(
self.closeHandler)
self.closeHandler = None
if self.selHandler:
chimera.triggers.deleteHandler("selection changed",
self.selHandler)
self.selHandler = None
if self.sesHandler:
chimera.triggers.deleteHandler(SAVE_SESSION,
self.sesHandler)
self.sesHandler = None
chimera.extension.manager.deregisterInstance(self)
self.destroy()
def emName(self):
return self.title
def emRaise(self):
self.enter()
def emHide(self):
self.Close()
Hide = emHide
def emQuit(self):
self.exit()
Quit = emQuit
def fillInUI(self, parent):
top = parent.winfo_toplevel()
row = 0
from CGLtk.Table import SortableTable
rt = SortableTable(parent, automultilineHeaders = False)
self.resultsTable = rt
columns = {}
fval = "lambda e: float(e['%s'])"
sval = "lambda e: ' '.join(e['%s'].split())"
lval = "lambda e: ', '.join(e['%s'])"
val= "lambda e: e.get('%s','')"
def cite(e):
return ('%s\n%s\n%s %s (%s) %s-%s' %
(' '.join(e['title'].split()),
e.get('citationAuthorList',''),
e.get('citationJournalName',''),
e.get('citationJournalYear',''),
e.get('citationJournalVolume',''),
e.get('citationJournalFirstPage',''),
e.get('citationJournalLastPage','')))
headings = (('ID', sval % 'accessionCode', 'nw', 0),
('Sample Name', sval % 'sampleName', 'nw', '6c'),
('Reference', cite, 'nw', '10c'),
('Resolution', fval % 'resolution', 'n', 0),
('Release Date', val % 'mapReleaseDate', 'n', 0),
('Fit PDBs', val % 'fittedPDBidList', 'nw', '6c'),
)
for h, vfunc, a, w in headings:
c = rt.addColumn(h, vfunc, format="%s", wrapLength = w,
anchor = a, entryPadX = 10, entryPadY = 5,
headerPadX = 10, headerPadY = 5, font = 'TkTextFont')
columns[h] = c
rt.sortBy(columns["ID"])
rt.setData(self.results)
rt.grid(row=row, column=0, sticky="nsew")
rt.launch()
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
class GeometryInterface:
crossingPrompt = "Show angles/distances by choosing two objects" \
" from table"
def __init__(self, parent, status):
self.status = status
self.parent = parent
import Pmw, Tkinter
row = 0
parent.columnconfigure(0, weight=1)
parent.columnconfigure(1, weight=1)
Tkinter.Button(parent, text="Define axes...", pady=0,
command=self._createAxesCB).grid(row=row, column=0)
Tkinter.Button(parent, text="Define plane...", pady=0,
command=self._createPlaneCB).grid(row=row, column=1)
row += 1
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.grid(row=row, column=0, columnspan=2, sticky="nsew")
parent.rowconfigure(row, weight=1)
self.table.addColumn("Name", "name", format="%s ")
self.table.addColumn(" ", "model.color", format=(False, True))
idCol = self.table.addColumn("ID", "id")
self.table.addColumn("Shown", "model.display", format=bool)
self.table.addColumn("Length", "length", format="%4.1f", font="TkFixedFont")
self.table.addColumn("Radius", "radius", format="%4.1f", font="TkFixedFont")
self.table.setData(geomManager.items)
self.table.sortBy(idCol)
self.table.launch(browseCmd=self._tableCB)
row += 1
selGroup = Pmw.Group(parent, tag_text="Choosing in table...")
selGroup.grid(row=row, column=0, columnspan=3, sticky='ew')
row += 1
cbFrame = selGroup.interior()
cbFrame.columnconfigure(0, weight=1)
cbFrame.columnconfigure(1, weight=1)
self.geomSelObjVar = Tkinter.IntVar(parent)
self.geomSelObjVar.set(prefs[AXIS_SEL_OBJ])
Tkinter.Checkbutton(cbFrame, variable=self.geomSelObjVar,
text="selects object").grid(row=0, column=0)
self.geomSelObjVar.trace_variable("w", self._selModeChangeCB)
self.geomSelAtomsVar = Tkinter.IntVar(parent)
self.geomSelAtomsVar.set(prefs[AXIS_SEL_ATOMS])
Tkinter.Checkbutton(cbFrame, variable=self.geomSelAtomsVar,
text="selects atoms").grid(row=0, column=1)
self.geomSelAtomsVar.trace_variable("w", self._selModeChangeCB)
self.buttons = []
self.buttons.append(Tkinter.Button(parent, text="Delete", pady=0,
state='disabled', command=self._deleteItemsCB))
self.buttons[-1].grid(row=row, column=0, sticky='e')
self.buttons.append(Tkinter.Button(parent, text="Rename", pady=0,
state='disabled', command=self._renameItems))
self.buttons[-1].grid(row=row, column=1, sticky='w')
self.renameDialogs = {}
row += 1
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=2)
row += 1
self.buttons.append(Tkinter.Button(f, text="Report distance", pady=0,
state='disabled', command=self._atomsDistanceCB))
self.buttons[-1].grid(row=0, column=0)
Tkinter.Label(f, text="to selected atoms"
).grid(row=0, column=1)
geomManager.registerInterface(self)
if geomManager.items:
self._selHandlerID = triggers.addHandler("selection changed",
self._selChangeCB, None)
def addItems(self, items):
if len(items) == len(geomManager.items):
self._selHandlerID = triggers.addHandler("selection changed",
self._selChangeCB, None)
self.table.setData(geomManager.items)
def feedback(self, sels):
if not self.parent.winfo_viewable():
return
if len(sels) == 2:
words1 = sels[0].name.split()
words2 = sels[1].name.split()
if len(words2) < len(words1):
words1, words2 = words2, words1
for i, word in enumerate(words1):
if word != words2[i]:
break
diff = " ".join(words2[i:])
infos = geomManager.infoTexts(sels)
message = "%s/%s %s\n" % (" ".join(words1), diff, ", ".join(infos))
self.status(message, log=True)
else:
self.status(self.crossingPrompt)
def removeItems(self, items):
self.table.setData(geomManager.items)
for item in items:
if item in self.renameDialogs:
self.renameDialogs[item].destroy()
del self.renameDialogs[item]
if items and not geomManager.items:
triggers.deleteHandler("selection changed", self._selHandlerID)
def _atomsDistanceCB(self):
atoms = selection.currentAtoms()
if not atoms:
self.status("No atoms selected", color="red")
return
items = self.table.selected()
if not items:
self.status("No objects chosen", color="red")
return
for item in items:
points = []
dists = item.pointDistances([a.xformCoord()
for a in atoms])
if len(dists) == 1:
self.status("Distance from %s to %s: %.1f\n" %
(atoms[0], item, dists[0]), log=True)
continue
import numpy
dists = numpy.array(dists)
imin = dists.argmin()
imax = dists.argmax()
self.status("Distance from %d atoms to %s: "
"min: %.1f (%s), mean: %.1f, max: %.1f (%s)\n"
% (len(atoms), item, dists[imin], atoms[imin],
dists.mean(), dists[imax], atoms[imax]),
log=True)
def _createAxesCB(self):
if not hasattr(self, 'createAxesDialog'):
from Axes import CreateAxesDialog
self.createAxesDialog = CreateAxesDialog()
self.createAxesDialog.enter()
def _createPlaneCB(self):
if not hasattr(self, 'createPlaneDialog'):
from Planes import CreatePlaneDialog
self.createPlaneDialog = CreatePlaneDialog()
self.createPlaneDialog.enter()
def _deleteItemsCB(self):
items = self.table.selected()
if not items:
self.status("No objects chosen", color="red")
return
geomManager.removeItems(items)
def _itemsSelectAtoms(self, items, add=False):
atoms = set()
for item in items:
atoms.update(item.atoms)
if self.geomSelAtomsVar.get():
if add:
selection.addCurrent(atoms)
else:
selection.setCurrent(atoms)
elif set(atoms) == set(selection.currentAtoms()):
selection.removeCurrent(atoms)
def _lowerCmd(self):
for rd in self.renameDialogs.values():
rd.destroy()
self.renameDialogs.clear()
self.status("")
def _raiseCmd(self):
self.status(self.crossingPrompt)
def _renameItems(self):
for item in self.table.selected():
if item in self.renameDialogs:
self.renameDialogs[item].enter()
else:
self.renameDialogs[item] = RenameDialog(self, item)
def _renameItemCB(self, item, name):
item.name = name
self.table.refresh()
self.renameDialogs[item].destroy()
del self.renameDialogs[item]
def _selChangeCB(self, *args):
selGraphs = set(selection.currentGraphs())
itemModels = set([item.model for item in geomManager.items])
selItems = selGraphs & itemModels
chosenItems = set([item.model for item in self.table.selected()])
if chosenItems != selItems:
items = [item for item in geomManager.items
if item.model in selItems]
self.table.select(items)
if self.geomSelAtomsVar.get():
self._itemsSelectAtoms(items, add=True)
self.feedback(items)
def _selModeChangeCB(self, *args):
self._tableCB(self.table.selected(), modeChange=True)
def _tableCB(self, sels, modeChange=False):
if self.geomSelAtomsVar.get() or modeChange:
self._itemsSelectAtoms(sels)
if self.geomSelObjVar.get():
items = set(geomManager.items)
# avoid affecting the selection if models are
# being destroyed...
removable = [a.model
for a in items.difference(sels)
if not a.model.__destroyed__]
if removable:
selection.removeCurrent(removable)
addable = [a.model for a in sels if not a.model.__destroyed__]
if addable:
selection.addCurrent(addable)
if modeChange:
return
butState = 'normal'
if not sels:
butState = 'disabled'
for but in self.buttons:
but.configure(state=butState)
self.feedback(sels)
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 ClusterDialog(ModelessDialog):
oneshot = True
provideStatus = True
buttons = ("Close", )
title = "Clustering"
def __init__(self, movie, startFrame, stride, endFrame, useSel, ignoreBulk,
ignoreHyds):
self.movie = movie
self.movie.subdialogs.append(self)
self.startFrame = startFrame
self.stride = stride
self.endFrame = endFrame
self.useSel = useSel
self.ignoreBulk = ignoreBulk
self.ignoreHyds = ignoreHyds
ModelessDialog.__init__(self)
def Close(self):
if self._computing:
self._abort = True
return
self.movie.subdialogs.remove(self)
ModelessDialog.Close(self)
def destroy(self):
# calling ModelessDialog.Close causes recursion
ModelessDialog.destroy(self)
def fillInUI(self, parent):
from chimera.match import matchPositions
from chimera import numpyArrayFromAtoms
from chimera import selection, UserError
self._computing = False
# load needed coord sets...
frameNums = range(self.startFrame, self.endFrame + 1, self.stride)
for frameNum in frameNums:
if not self.movie.findCoordSet(frameNum):
self.status("loading frame %d" % frameNum)
self.movie._LoadFrame(frameNum, makeCurrent=False)
# compute RMSDs
from analysis import analysisAtoms
try:
atoms = analysisAtoms(self.movie, self.useSel, self.ignoreBulk,
self.ignoreHyds)
except UserError:
self.Close()
raise
self.buttonWidgets['Close'].configure(text="Abort")
numFrames = len(frameNums)
self.status("Fetching %d coordinate arrays" % numFrames)
numpyArrays = {}
from time import time
t0 = time()
for i, fn in enumerate(frameNums):
numpyArrays[fn] = numpyArrayFromAtoms(atoms,
self.movie.findCoordSet(fn))
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
if i == numFrames - 1:
self.status("Fetched %d coordinate arrays" % (i + 1))
else:
elapsed = time() - t0
perSec = elapsed / (i + 1)
remaining = perSec * (numFrames - (i + 1))
self.status("Fetched %d of %d coordinate arrays"
"\nAbout %.1f minutes remaining" %
(i + 1, numFrames, remaining / 60.0))
t0 = time()
totalRMSDs = numFrames * (numFrames - 1) / 2
self.status("Computing %d RMSDs" % totalRMSDs)
from EnsembleMatch.distmat import DistanceMatrix
fullDM = DistanceMatrix(numFrames)
sameAs = {}
for i, frame1 in enumerate(frameNums):
na1 = numpyArrays[frame1]
for j, frame2 in enumerate(frameNums[i + 1:]):
na2 = numpyArrays[frame2]
rmsd = matchPositions(na1, na2)[1]
fullDM.set(i, i + j + 1, rmsd)
if rmsd == 0.0:
sameAs[frame2] = frame1
self._computing = True
self._abort = False
parent.update() # allow Abort button to function
self._computing = False
if self._abort:
parent.after_idle(self.Close)
return
numComputed = totalRMSDs - ((numFrames - (i + 1)) * (numFrames -
(i + 2))) / 2
if numComputed == totalRMSDs:
self.status("Computed %d RMSDs" % totalRMSDs)
else:
elapsed = time() - t0
perSec = elapsed / numComputed
remaining = perSec * (totalRMSDs - numComputed)
if remaining < 50:
timeEst = "%d seconds" % int(remaining + 0.5)
else:
timeEst = "%.1f minutes" % (remaining / 60.0)
self.status("Computed %d of %d RMSDs\n"
"About %s remaining" %
(numComputed, totalRMSDs, timeEst))
self.status("Generating clusters")
self.buttonWidgets['Close'].configure(text="Close")
if not sameAs:
dm = fullDM
reducedFrameNums = frameNums
indexMap = range(len(frameNums))
elif len(sameAs) == numFrames - 1:
raise UserError("All frames to cluster are identical!")
self.Close()
else:
dm = DistanceMatrix(numFrames - len(sameAs))
reducedFrameNums = []
indexMap = []
for i, fn in enumerate(frameNums):
if fn in sameAs:
continue
reducedFrameNums.append(fn)
indexMap.append(i)
for i in range(len(reducedFrameNums)):
mapi = indexMap[i]
for j in range(i + 1, len(reducedFrameNums)):
mapj = indexMap[j]
dm.set(i, j, fulldm.get(mapi, mapj))
from EnsembleMatch.nmrclust import NMRClust
clustering = NMRClust(dm)
self.clusterMap = {}
self.representatives = []
self.clusters = []
unsortedClusters = [(c, clustering.representative(c))
for c in clustering.clusters]
# sort the clusters so that the coloring is reproducible
# while trying to avoid using adjacent colors for
# adjacent clusters
clusters = [unsortedClusters.pop()]
while unsortedClusters:
bestCluster = bestVal = None
for uc in unsortedClusters:
val = abs(uc[-1] - clusters[-1][-1])
if len(clusters) > 1:
val += 0.5 * abs(uc[-1] - clusters[-2][-1])
if len(clusters) > 2:
val += 0.25 * abs(uc[-1] - clusters[-3][-1])
if bestVal == None or val > bestVal:
bestCluster = uc
bestVal = val
unsortedClusters.remove(bestCluster)
clusters.append(bestCluster)
colors = colorRange(len(clusters))
for c, rep in clusters:
cluster = Cluster()
cluster.color = colors.pop()
self.clusters.append(cluster)
cluster.representative = reducedFrameNums[rep]
cluster.members = []
for m in c.members():
f = reducedFrameNums[m]
self.clusterMap[f] = cluster
cluster.members.append(f)
for dup, base in sameAs.items():
c = self.clusterMap[base]
self.clusterMap[dup] = c
c.members.append(dup)
self.status("%d clusters" % len(self.clusters))
from CGLtk.Table import SortableTable
self.table = SortableTable(parent)
self.table.addColumn("Color",
"color",
format=(False, False),
titleDisplay=False)
membersCol = self.table.addColumn("Members",
"lambda c: len(c.members)",
format="%d")
self.table.addColumn("Representative Frame",
"representative",
format="%d")
self.table.setData(self.clusters)
self.table.launch(browseCmd=self.showRep)
self.table.sortBy(membersCol)
self.table.sortBy(membersCol) # to get descending order
self.table.grid(sticky="nsew")
self.timeLine = Pmw.ScrolledCanvas(parent, canvas_height="0.5i")
self.timeLine.grid(row=1, column=0, sticky="nsew")
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
self.zoom = 2.0
self.drawTimeLine()
def drawTimeLine(self, width=None):
if width == None:
width = 3.0
tl = self.timeLine
for item in tl.find_all():
tl.delete(item)
for c in self.clusters:
c.canvasItems = []
c.canvas = tl
frameNums = range(self.startFrame, self.endFrame + 1, self.stride)
cluster = startFrame = None
f2x = self._frame2x
height = 22
for fn in frameNums:
c = self.clusterMap[fn]
if c == cluster:
continue
if cluster != None:
tkColor = rgba2tk(cluster.color)
cluster.canvasItems.append(
tl.create_rectangle(f2x(startFrame),
0,
f2x(fn) - 1,
height,
fill=tkColor,
outline=tkColor))
cluster = c
startFrame = fn
tkColor = rgba2tk(cluster.color)
cluster.canvasItems.append(
tl.create_rectangle(f2x(startFrame),
0,
f2x(frameNums[-1] + self.stride) - 1,
height,
fill=tkColor,
outline=tkColor))
for c in self.clusters:
rep = c.representative
tkColor = rgba2tk(c.color)
c.canvasItems.append(
tl.create_rectangle(f2x(rep),
0,
f2x(rep + self.stride) - 1,
-0.5 * height,
fill=tkColor,
outline=tkColor))
tl.resizescrollregion()
def showRep(self, clusters):
self.movie.currentFrame.set(clusters[0].representative)
self.movie.LoadFrame()
def _frame2x(self, fn):
return int(self.zoom * (fn - self.startFrame) / self.stride + 0.5)