def _selResidues(self, residues):
from chimera.selection import ItemizedSelection
from chimera.tkgui import selectionOperation
sel = ItemizedSelection()
sel.add(residues)
sel.addImplied(vertices=0)
selectionOperation(sel)
def _selResidues(self, residues): from chimera.selection import ItemizedSelection from chimera.tkgui import selectionOperation sel = ItemizedSelection() sel.add(residues) sel.addImplied(vertices=0) selectionOperation(sel)
def _mouseUpCB(self, event): canvas = self.seqCanvas.mainCanvas if not self._dragRegion: # maybe a region pick region = self._region(event) if region: self._toggleCurrent(region) else: # maybe a column pick col = self._columnPick(event) if col is not None: residues = self._residuesInBlock(( self.seqCanvas.seqs[0], self.seqCanvas.seqs[-1], col, col)) sel = ItemizedSelection() sel.add(residues) selectionOperation(sel) else: self._selectOnStructures() self._prevDrag = self._dragRegion self.seqCanvas.mav.status( "Shift-drag to add to region; " "control-drag to add new region\n" "Tools->Region Browser to change colors; " "control left/right arrow to realign region", blankAfter=120) self._startX, self._startY = None, None if self._afterID: canvas.after_cancel(self._afterID) self._afterID = None self._dragRegion = None self._clearDrag()
def _selectOnStructures(self, region=None): # highlight on chimera structures from chimera import getSelMode self._selChangeFromSelf = getSelMode() == "replace" sel = ItemizedSelection() sel.add(self.regionResidues(region)) sel.addImplied(vertices=False) selectionOperation(sel) self._selChangeFromSelf = False
def _instantiateAxis(self, number, name, color, radius, sourceModel, atoms,
center, vec, extents):
axis = Axis(number, name, color, radius, sourceModel, center, vec,
extents)
from chimera.selection import ItemizedSelection
sel = ItemizedSelection(selChangedCB=lambda a=axis: self.removeAxes(
[a], checkForChanges=False))
sel.add(atoms)
self.axisData[axis] = sel
from Geometry import geomManager
geomManager.addInterfaceItems([axis])
return axis
def _instantiatePlane(self, number, name, cmpVal, color, radius, thickness, sourceModel, atoms, chimeraPlane): plane = Plane(number, name, color, radius, thickness, sourceModel, chimeraPlane) from chimera.selection import ItemizedSelection sel = ItemizedSelection(selChangedCB=lambda pl=plane: self.removePlanes([pl], checkForChanges=False)) sel.add(atoms) self.planeData[plane] = sel from Geometry import geomManager geomManager.addInterfaceItems([plane]) return plane
def createHelices(m, **kw):
from chimera.specifier import evalSpec
sel = evalSpec(":/isHelix & backbone.minimal", models=[m])
residues = sel.residues()
if not residues:
return []
from chimera.misc import oslCmp
residues.sort(lambda r1, r2: oslCmp(r1.oslIdent(), r2.oslIdent()))
from chimera import bondsBetween
from chimera.selection import INTERSECT, ItemizedSelection
curHelix = []
axes = []
from Geometry import geomManager
geomManager.suspendUpdates()
while residues:
if not curHelix:
r = residues.pop(0)
curHelix.append(r)
helixNum = r.ssId
continue
if helixNum > -1:
if helixNum == residues[0].ssId:
curHelix.append(residues.pop(0))
continue
elif bondsBetween(curHelix[-1], residues[0], True):
curHelix.append(residues.pop(0))
continue
resSel = ItemizedSelection()
resSel.add(curHelix)
resSel.merge(INTERSECT, sel)
atoms = resSel.atoms()
if helixNum < 0:
created += 1
helixNum = created
hname = "%s H%d" % (m.name, helixNum)
axes.append(axisManager.createAxis(hname, atoms, **kw))
curHelix = []
if curHelix:
resSel = ItemizedSelection()
resSel.add(curHelix)
resSel.merge(INTERSECT, sel)
atoms = resSel.atoms()
if helixNum < 0:
created += 1
helixNum = created
hname = "%s H%d" % (m.name, helixNum)
axes.append(axisManager.createAxis(hname, atoms, **kw))
geomManager.enableUpdates()
return axes
def _writeParmchk(self, filename):
# generate Mol2 input file for parmchk
import WriteMol2
from chimera.selection import ItemizedSelection
from chimera import Bond
rSet = set(self.needParmchk)
for b in self.chimeraMolecule.bonds:
if b.display == Bond.Never:
continue
a0, a1 = b.atoms
r0 = a0.residue
r1 = a1.residue
if (r0 in self.needParmchk and r1 not in self.needParmchk):
rSet.add(r1)
elif (r0 not in self.needParmchk and r1 in self.needParmchk):
rSet.add(r0)
sel = ItemizedSelection()
sel.add(rSet)
WriteMol2.writeMol2(sel, filename, gaffType=True)
def gatherAtoms(bySerial, label, f, dicts):
for line in f:
line = line.strip()
if not line:
continue
# ignore altloc column...
if line.startswith("HETATM"):
# guarantee that atom serial number splits off...
line = "ATOM " + line[6:]
fields = line[:16].strip().split() + line[17:].split()
serial = int(fields[1])
try:
atom = bySerial[serial]
except KeyError:
raise ValueError("Non-existent serial number (%d) found"
" in %s file" % (serial, label))
from chimera.misc import chimeraLabel
if atom.name != fields[2] \
and atom.name != fields[2].replace("*", "'"):
raise ValueError(
"Atom with serial number %d (%s) does"
" not match name in %s file (%s)" %
(serial, chimeraLabel(atom, showModel=False,
modelName=False), label, fields[2]))
if atom.residue.type != fields[3]:
raise ValueError(
"Atom with serial number %d (%s) does"
" not match residue type in %s file (%s)" %
(serial, chimeraLabel(atom, showModel=False,
modelName=False), label, fields[3]))
id = int(fields[-2])
if id > len(dicts):
raise ValueError(
"%s ID (%d) in %s file greater than"
" number of %ss (%d) in %s info file" %
(label.capitalize(), id, label, label, len(dicts), label))
dicts[id - 1].setdefault("atoms", []).append(atom)
from chimera.selection import ItemizedSelection
for d in dicts:
sel = ItemizedSelection()
sel.add(d.get("atoms", []))
d["atoms"] = sel
def Apply(self): from operator import add from chimera.selection import ItemizedSelection, \ OSLSelection, REPLACE sel = ItemizedSelection() chainOSL = "" for codeInfo, var in self._codeVars.items(): model, code = codeInfo if var.get(): chainOSL = chainOSL + model.oslIdent() \ + ":." + code if chainOSL: sel.merge(REPLACE, OSLSelection(chainOSL)) for model, var, resList in self._physVars: if var.get(): sel.add(resList) sel.addImplied(vertices=0) chimera.tkgui.selectionOperation(sel)
def holdSteadyCB(self):
"""'hold steady' menu callback"""
from chimera.actions import selAtoms
from chimera.selection import ItemizedSelection
atoms = selAtoms()
if not atoms:
replyobj.error("No atoms selected\n")
return
self.status("Holding %d atoms steady" % len(atoms))
steadySel = ItemizedSelection(selChangedCB=self._steadySelCB)
steadySel.add(atoms)
identity = chimera.Xform.identity()
curFrame = self.currentFrame.get()
cs = self.model.activeCoordSet
self.holdingSteady = (atoms, steadySel, cs, identity)
self.transforms = {curFrame: (identity, identity)}
self.actionsMenu.entryconfigure(self.stopHoldingLabel, state='normal')
if self.volumeDialog:
# clear "no atoms held steady" error
self.volumeDialog.status("")
def Apply(self):
from operator import add
from chimera.selection import ItemizedSelection, \
OSLSelection, REPLACE
sel = ItemizedSelection()
chainOSL = ""
for codeInfo, var in self._codeVars.items():
model, code = codeInfo
if var.get():
chainOSL = chainOSL + model.oslIdent() \
+ ":." + code
if chainOSL:
sel.merge(REPLACE, OSLSelection(chainOSL))
for model, var, resList in self._physVars:
if var.get():
sel.add(resList)
sel.addImplied(vertices=0)
chimera.tkgui.selectionOperation(sel)
def _writeParmchk(self, filename): # generate Mol2 input file for parmchk import WriteMol2 from chimera.selection import ItemizedSelection from chimera import Bond rSet = set(self.needParmchk) for b in self.chimeraMolecule.bonds: if b.display == Bond.Never: continue a0, a1 = b.atoms r0 = a0.residue r1 = a1.residue if (r0 in self.needParmchk and r1 not in self.needParmchk): rSet.add(r1) elif (r0 not in self.needParmchk and r1 in self.needParmchk): rSet.add(r0) sel = ItemizedSelection() sel.add(rSet) WriteMol2.writeMol2(sel, filename, gaffType=True)
def holdSteadyCB(self):
"""'hold steady' menu callback"""
from chimera.actions import selAtoms
from chimera.selection import ItemizedSelection
atoms = selAtoms()
if not atoms:
replyobj.error("No atoms selected\n")
return
self.status("Holding %d atoms steady" % len(atoms))
steadySel = ItemizedSelection(selChangedCB=self._steadySelCB)
steadySel.add(atoms)
identity = chimera.Xform.identity()
curFrame = self.currentFrame.get()
cs = self.model.activeCoordSet
self.holdingSteady = (atoms, steadySel, cs, identity)
self.transforms = { curFrame: (identity, identity) }
self.actionsMenu.entryconfigure(self.stopHoldingLabel,
state='normal')
if self.volumeDialog:
# clear "no atoms held steady" error
self.volumeDialog.status("")
def _focusCB(self, event, pref=None): if pref == "residue": funcs = [self._residueCB, self._regionResiduesCB] else: funcs = [self._regionResiduesCB, self._residueCB] for func in funcs: residues = func(event) if residues is None: # no residue/region continue if not residues: # region with no structure residues return break if residues is None: return from Midas import cofr, window from chimera.selection import ItemizedSelection sel = ItemizedSelection() sel.add(residues) window(sel) cofr(sel)
class DetectClashDialog(ModelessDialog):
name = "detect clashes"
title = "Find Clashes/Contacts"
provideStatus = True
statusPosition = "above"
help = "ContributedSoftware/findclash/findclash.html"
FREQ_APPLY = "when OK/Apply clicked"
FREQ_MOTION = "after relative motions (until dialog closed)"
FREQ_CONTINUOUS = "continuously (until dialog closed)"
CHECK_SET = "second set of designated atoms"
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(), command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(), text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size-2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(), command=self._desig2CB,
pady=pady, text="Designate selection as second set"
).grid(row=3, column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size-4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(desigGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text="Check designated\natoms"
" against:", command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters", hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(
row=0, column=0)
Tkinter.Button(defaultsFrame, text="clash", pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame, text="contact", pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(
row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame, labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(prefs[BOND_SEPARATION]),
items=[str(i+2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(
row=0, column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(), text="Ignore intra-"
"residue contacts", variable=self.ignoreIntraResVar,
command=self._checkContinuous
).grid(row=4)
actionGroup = Pmw.Group(parent, tag_text=
"Treatment of Clash/Contact Atoms", hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(), text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f, text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f, noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f, text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f, noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f, labelpos='w',
label_text=" and width", validate={'validator': 'real',
'min': 0.01}, entry_width=4, entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" file", variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(), text="Write information to"
" reply log", variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent, tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0, orient='vertical', buttontype='radiobutton',
labelpos='w', label_text= "Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
def OK(self, *args):
# use main status line if dialog closing
from chimera.replyobj import status
self.status = status
ModelessDialog.OK(self, *args)
def Apply(self, *args):
# workaround: remove pseudobonds before recreating colors
# so C++ layer doesn't end up with pointers to deleted
# colors in obscure circumstances
from DetectClash import nukeGroup
nukeGroup()
from chimera import UserError
self.status("")
checkAtoms = self.designated.atoms()
if not checkAtoms:
self.enter()
raise UserError("No atoms designated for clash detection")
self.clashDef['command'] = None
self.clashDef.invoke()
self.clashDef['command'] = self._checkContinuous
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount"
" (in Clash/Contact Parameters)")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow['command'] = None
self.hbondAllow.invoke()
self.hbondAllow['command'] = self._checkContinuous
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount"
" (in Clash/Contact Parameters)")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[BOND_SEPARATION] = int(self.bondsApart.getvalue())
prefs[IGNORE_INTRA_RES] = self.ignoreIntraResVar.get()
checkVal = self.checkLocButtons.getvalue()
if checkVal == "themselves":
test = "self"
elif checkVal == "all other atoms":
test = "others"
elif checkVal == "other atoms in same model":
test = "model"
else:
test = self.designated2.atoms()
if not test:
self.enter()
raise UserError("No second-set atoms designated")
actionAttr = prefs[ACTION_ATTR] = self.actionAttrVar.get()
actionSelect = prefs[ACTION_SELECT] = self.actionSelVar.get()
actionColor = prefs[ACTION_COLOR] = self.actionColorVar.get()
actionPseudobonds = prefs[ACTION_PSEUDOBONDS] = \
self.actionPBVar.get()
actionWriteInfo = prefs[ACTION_WRITEINFO] = \
self.actionWriteInfoVar.get()
actionLogInfo = prefs[ACTION_REPLYLOG] = \
self.actionLogInfoVar.get()
if self.freqButtons.getvalue() != self.FREQ_APPLY:
actionAttr = actionWriteInfo = actionLogInfo = False
if not actionAttr and not actionSelect and not actionColor \
and not actionPseudobonds and not actionWriteInfo \
and not actionLogInfo:
self.enter()
raise UserError("No actions selected for clashes")
self.status("Checking for clashes")
clashColor = nonclashColor = None
if actionColor:
prefs[CLASH_COLOR] = self.clashColorWell.rgba
prefs[NONCLASH_COLOR] = self.nonclashColorWell.rgba
if prefs[CLASH_COLOR] == None:
clashColor = None
else:
clashColor = chimera.MaterialColor(
*prefs[CLASH_COLOR])
if prefs[NONCLASH_COLOR] == None:
nonclashColor = None
else:
nonclashColor = chimera.MaterialColor(
*prefs[NONCLASH_COLOR])
pbColor = None
if actionPseudobonds:
prefs[PB_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[PB_COLOR])
self.pbWidthEntry['command'] = None
self.pbWidthEntry.invoke()
self.pbWidthEntry['command'] = self._checkContinuous
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width "
"(in Treatment of Clash/Contact Atoms)")
prefs[PB_WIDTH] = float(self.pbWidthEntry.getvalue())
from DetectClash import cmdDetectClash
if actionWriteInfo:
saveFile = "-"
else:
saveFile = None
clashes = cmdDetectClash(checkAtoms, test=test,
overlapCutoff=prefs[CLASH_THRESHOLD],
hbondAllowance=prefs[HBOND_ALLOWANCE],
bondSeparation=prefs[BOND_SEPARATION],
ignoreIntraRes=prefs[IGNORE_INTRA_RES],
setAttrs=actionAttr,
selectClashes=actionSelect,
colorClashes=actionColor,
clashColor=clashColor, nonclashColor=nonclashColor,
makePseudobonds=actionPseudobonds,
pbColor=pbColor, lineWidth=prefs[PB_WIDTH],
saveFile=saveFile, log=actionLogInfo,
summary=self.status)
if actionAttr:
from ShowAttr import ShowAttrDialog
from chimera import dialogs
from DetectClash import attrName
d = dialogs.display(ShowAttrDialog.name)
d.configure(attrsOf="atoms", attrName=attrName,
mode="Render")
def Close(self):
ModelessDialog.Close(self)
if self.freqButtons.getvalue() != self.FREQ_APPLY:
self.freqButtons.invoke(self.FREQ_APPLY)
def _checkContinuous(self, *args):
if self.freqButtons.getvalue() == self.FREQ_CONTINUOUS:
self.Apply()
def _clashDefaultsCB(self):
from prefs import defaults
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self._checkContinuous()
def _clearHandlers(self):
while self._handlers:
trigName, handler = self._handlers.popitem()
chimera.triggers.deleteHandler(trigName, handler)
def _contactDefaultsCB(self):
self.hbondAllow.setvalue("0.0")
self.clashDef.setvalue("-0.4")
self._checkContinuous()
def _desigCB(self):
self.designated.clear()
self.designated.add(chimera.selection.currentAtoms())
self._updateDesigStatus()
def _desig2CB(self):
self.designated2.clear()
self.designated2.add(chimera.selection.currentAtoms())
self._locButtonCB()
self._updateDesig2Status()
def _freqChangeCB(self, freqVal):
self._clearHandlers()
if freqVal == self.FREQ_APPLY:
self.assignAttrButton.configure(state='normal')
self.writeInfoButton.configure(state='normal')
self.logInfoButton.configure(state='normal')
return
self.assignAttrButton.configure(state='disabled')
self.writeInfoButton.configure(state='disabled')
self.logInfoButton.configure(state='disabled')
def modCoordSets(trigName, myData, changes):
if changes.modified:
self.Apply()
self._handlers['CoordSet'] = chimera.triggers.addHandler(
'CoordSet', modCoordSets, None)
def justCoordSets(trigName, myData, changes):
if 'activeCoordSet changed' in changes.reasons:
self.Apply()
self._handlers['Molecule'] = chimera.triggers.addHandler(
'Molecule', justCoordSets, None)
if freqVal == self.FREQ_MOTION:
self._handlers[chimera.MOTION_STOP] = chimera.triggers\
.addHandler(chimera.MOTION_STOP,
self._motionCB, None)
elif freqVal == self.FREQ_CONTINUOUS:
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
self._motionCB()
self._handlers['OpenState'] = chimera.triggers\
.addHandler('OpenState', preCB, None)
self.Apply()
def _locButtonCB(self, butName=None):
checkSetBut = self.checkLocButtons.button(self.CHECK_SET)
if self.checkLocButtons.getvalue() == self.CHECK_SET \
and not self.designated2.atoms():
checkSetBut.config(fg="red", activeforeground="red")
else:
checkSetBut.config(fg="black", activeforeground="black")
self._updateDesig2Status()
def _motionCB(self, *args):
# if all molecule activities are the same (i.e. no possible
# relative motion), do nothing
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
self.Apply()
return
def _updateDesigStatus(self):
numAtoms = len(self.designated.atoms())
if numAtoms:
statusText = "%d atoms designated" % numAtoms
color = 'blue'
else:
statusText = "No atoms designated"
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desigStatus.config(text=statusText, fg=color)
self._checkContinuous()
def _updateDesig2Status(self):
numAtoms = len(self.designated2.atoms())
checkSet = self.checkLocButtons.getvalue() == self.CHECK_SET
color = 'black'
if numAtoms:
statusText = "Second set: %d atoms" % numAtoms
else:
statusText = "No second set"
if checkSet:
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desig2Status.config(text=statusText, fg=color)
if checkSet:
self._checkContinuous()
def selectRotamers(self, rotamers): from chimera import selectionOperation from chimera.selection import ItemizedSelection rotSel = ItemizedSelection() rotSel.add(rotamers) selectionOperation(rotSel)
def selectRotamers(self, rotamers):
from chimera import selectionOperation
from chimera.selection import ItemizedSelection
rotSel = ItemizedSelection()
rotSel.add(rotamers)
selectionOperation(rotSel)
class DetectClashDialog(ModelessDialog):
name = "detect clashes"
title = "Find Clashes/Contacts"
provideStatus = True
statusPosition = "above"
help = "ContributedSoftware/findclash/findclash.html"
FREQ_APPLY = "when OK/Apply clicked"
FREQ_MOTION = "after relative motions (until dialog closed)"
FREQ_CONTINUOUS = "continuously (until dialog closed)"
CHECK_SET = "second set of designated atoms"
def fillInUI(self, parent):
self._handlers = {}
desigGroup = Pmw.Group(parent, tag_text="Atoms to Check", hull_padx=2)
desigGroup.grid(row=0, sticky="ew")
from chimera.tkgui import windowSystem
Tkinter.Button(desigGroup.interior(),
command=self._desigCB,
text="Designate").grid(row=0, column=0, sticky='e')
Tkinter.Label(desigGroup.interior(),
text="currently selected"
" atoms for checking").grid(row=0, column=1, sticky='w')
self.desigStatus = Tkinter.Label(desigGroup.interior())
from tkFont import Font
font = Font(font=self.desigStatus.cget('font'))
size = int(font.cget('size'))
if size > 2:
font.config(size=size - 2)
font.config(weight='normal')
self.desigStatus.config(font=font)
from chimera.selection import ItemizedSelection
self.designated = ItemizedSelection(
selChangedCB=self._updateDesigStatus)
self.desigStatus.grid(row=1, column=0, columnspan=2)
self.designated2 = ItemizedSelection(selChangedCB=self._locButtonCB)
if windowSystem == 'aqua':
pady = None
else:
pady = 0
Tkinter.Button(desigGroup.interior(),
command=self._desig2CB,
pady=pady,
text="Designate selection as second set").grid(row=3,
column=1)
self.desig2Status = Tkinter.Label(desigGroup.interior())
if size > 4:
font2 = Font(font=font)
font2.config(size=size - 4)
else:
font2 = font
self.desig2Status.config(font=font2)
self.desig2Status.grid(row=4, column=1)
self.checkLocButtons = Pmw.RadioSelect(
desigGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check designated\natoms"
" against:",
command=self._locButtonCB)
self.checkLocButtons.grid(row=2, column=0, columnspan=2)
self.checkLocButtons.add("themselves")
self.checkLocButtons.add("all other atoms")
self.checkLocButtons.add("other atoms in same model")
self.checkLocButtons.add(self.CHECK_SET)
self.checkLocButtons.invoke(1)
defGroup = Pmw.Group(parent,
tag_text="Clash/Contact Parameters",
hull_padx=2)
defGroup.grid(row=1, sticky='ew')
self.clashDef = ClashDef(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[CLASH_THRESHOLD]))
self.clashDef.grid(row=0, sticky='w')
self.hbondAllow = HbondAllow(defGroup.interior(),
command=self._checkContinuous,
value=str(prefs[HBOND_ALLOWANCE]))
self.hbondAllow.grid(row=1, sticky='w')
defaultsFrame = Tkinter.Frame(defGroup.interior())
defaultsFrame.grid(row=2)
Tkinter.Label(defaultsFrame, text="Default").grid(row=0, column=0)
Tkinter.Button(defaultsFrame,
text="clash",
pady=pady,
command=self._clashDefaultsCB).grid(row=0, column=1)
Tkinter.Label(defaultsFrame, text="/").grid(row=0, column=2)
Tkinter.Button(defaultsFrame,
text="contact",
pady=pady,
command=self._contactDefaultsCB).grid(row=0, column=3)
Tkinter.Label(defaultsFrame, text="criteria").grid(row=0, column=4)
bondsFrame = Tkinter.Frame(defGroup.interior())
bondsFrame.grid(row=3, sticky='w')
self.bondsApart = Pmw.OptionMenu(bondsFrame,
labelpos='w',
label_text="Ignore contacts of pairs",
command=self._checkContinuous,
initialitem=str(
prefs[BOND_SEPARATION]),
items=[str(i + 2) for i in range(4)])
self.bondsApart.grid(row=0, column=0)
Tkinter.Label(bondsFrame, text="or fewer bonds apart").grid(row=0,
column=1)
self.ignoreIntraResVar = Tkinter.IntVar(parent)
self.ignoreIntraResVar.set(prefs[IGNORE_INTRA_RES])
Tkinter.Checkbutton(defGroup.interior(),
text="Ignore intra-"
"residue contacts",
variable=self.ignoreIntraResVar,
command=self._checkContinuous).grid(row=4)
actionGroup = Pmw.Group(parent,
tag_text="Treatment of Clash/Contact Atoms",
hull_padx=2)
actionGroup.grid(row=2, sticky='ew')
self.actionSelVar = Tkinter.IntVar(parent)
self.actionSelVar.set(prefs[ACTION_SELECT])
Tkinter.Checkbutton(actionGroup.interior(),
text="Select",
command=self._checkContinuous,
variable=self.actionSelVar).grid(row=0, sticky='w')
self.actionColorVar = Tkinter.IntVar(parent)
self.actionColorVar.set(prefs[ACTION_COLOR])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=1, sticky='w')
Tkinter.Checkbutton(f,
text="Color",
command=self._checkContinuous,
variable=self.actionColorVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.clashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[CLASH_COLOR])
self.clashColorWell.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms").grid(row=0,
column=2)
self.nonclashColorWell = ColorWell(f,
noneOkay=True,
callback=self._checkContinuous,
color=prefs[NONCLASH_COLOR])
self.nonclashColorWell.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.actionPBVar = Tkinter.IntVar(parent)
self.actionPBVar.set(prefs[ACTION_PSEUDOBONDS])
f = Tkinter.Frame(actionGroup.interior())
f.grid(row=2, sticky='w')
Tkinter.Checkbutton(f,
text="Draw pseudobonds of color",
command=self._checkContinuous,
variable=self.actionPBVar).grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pbColorWell = ColorWell(f,
noneOkay=False,
callback=self._checkContinuous,
color=prefs[PB_COLOR])
self.pbColorWell.grid(row=0, column=1)
self.pbWidthEntry = Pmw.EntryField(f,
labelpos='w',
label_text=" and width",
validate={
'validator': 'real',
'min': 0.01
},
entry_width=4,
entry_justify="center",
command=self._checkContinuous,
value=str(prefs[PB_WIDTH]))
self.pbWidthEntry.grid(row=0, column=2)
self.actionAttrVar = Tkinter.IntVar(parent)
self.actionAttrVar.set(prefs[ACTION_ATTR])
self.assignAttrButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Assign 'overlap' attribute",
variable=self.actionAttrVar)
self.assignAttrButton.grid(row=3, sticky='w')
self.actionWriteInfoVar = Tkinter.IntVar(parent)
self.actionWriteInfoVar.set(prefs[ACTION_WRITEINFO])
self.writeInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" file",
variable=self.actionWriteInfoVar)
self.writeInfoButton.grid(row=4, sticky='w')
self.actionLogInfoVar = Tkinter.IntVar(parent)
self.actionLogInfoVar.set(prefs[ACTION_REPLYLOG])
self.logInfoButton = Tkinter.Checkbutton(
actionGroup.interior(),
text="Write information to"
" reply log",
variable=self.actionLogInfoVar)
self.logInfoButton.grid(row=5, sticky='w')
freqGroup = Pmw.Group(parent,
tag_text="Frequency of Checking",
hull_padx=2)
freqGroup.grid(row=3, sticky="ew")
self.freqButtons = Pmw.RadioSelect(freqGroup.interior(),
pady=0,
orient='vertical',
buttontype='radiobutton',
labelpos='w',
label_text="Check...",
command=self._freqChangeCB)
self.freqButtons.grid(sticky='w')
self.freqButtons.add(self.FREQ_APPLY)
self.freqButtons.add(self.FREQ_MOTION)
self.freqButtons.add(self.FREQ_CONTINUOUS)
self.freqButtons.invoke(0)
self._updateDesigStatus()
def OK(self, *args):
# use main status line if dialog closing
from chimera.replyobj import status
self.status = status
ModelessDialog.OK(self, *args)
def Apply(self, *args):
# workaround: remove pseudobonds before recreating colors
# so C++ layer doesn't end up with pointers to deleted
# colors in obscure circumstances
from DetectClash import nukeGroup
nukeGroup()
from chimera import UserError
self.status("")
checkAtoms = self.designated.atoms()
if not checkAtoms:
self.enter()
raise UserError("No atoms designated for clash detection")
self.clashDef['command'] = None
self.clashDef.invoke()
self.clashDef['command'] = self._checkContinuous
if not self.clashDef.valid():
self.enter()
raise UserError("Invalid clash amount"
" (in Clash/Contact Parameters)")
prefs[CLASH_THRESHOLD] = float(self.clashDef.getvalue())
self.hbondAllow['command'] = None
self.hbondAllow.invoke()
self.hbondAllow['command'] = self._checkContinuous
if not self.hbondAllow.valid():
self.enter()
raise UserError("Invalid H-bond overlap amount"
" (in Clash/Contact Parameters)")
prefs[HBOND_ALLOWANCE] = float(self.hbondAllow.getvalue())
prefs[BOND_SEPARATION] = int(self.bondsApart.getvalue())
prefs[IGNORE_INTRA_RES] = self.ignoreIntraResVar.get()
checkVal = self.checkLocButtons.getvalue()
if checkVal == "themselves":
test = "self"
elif checkVal == "all other atoms":
test = "others"
elif checkVal == "other atoms in same model":
test = "model"
else:
test = self.designated2.atoms()
if not test:
self.enter()
raise UserError("No second-set atoms designated")
actionAttr = prefs[ACTION_ATTR] = self.actionAttrVar.get()
actionSelect = prefs[ACTION_SELECT] = self.actionSelVar.get()
actionColor = prefs[ACTION_COLOR] = self.actionColorVar.get()
actionPseudobonds = prefs[ACTION_PSEUDOBONDS] = \
self.actionPBVar.get()
actionWriteInfo = prefs[ACTION_WRITEINFO] = \
self.actionWriteInfoVar.get()
actionLogInfo = prefs[ACTION_REPLYLOG] = \
self.actionLogInfoVar.get()
if self.freqButtons.getvalue() != self.FREQ_APPLY:
actionAttr = actionWriteInfo = actionLogInfo = False
if not actionAttr and not actionSelect and not actionColor \
and not actionPseudobonds and not actionWriteInfo \
and not actionLogInfo:
self.enter()
raise UserError("No actions selected for clashes")
self.status("Checking for clashes")
clashColor = nonclashColor = None
if actionColor:
prefs[CLASH_COLOR] = self.clashColorWell.rgba
prefs[NONCLASH_COLOR] = self.nonclashColorWell.rgba
if prefs[CLASH_COLOR] == None:
clashColor = None
else:
clashColor = chimera.MaterialColor(*prefs[CLASH_COLOR])
if prefs[NONCLASH_COLOR] == None:
nonclashColor = None
else:
nonclashColor = chimera.MaterialColor(*prefs[NONCLASH_COLOR])
pbColor = None
if actionPseudobonds:
prefs[PB_COLOR] = self.pbColorWell.rgba
pbColor = chimera.MaterialColor(*prefs[PB_COLOR])
self.pbWidthEntry['command'] = None
self.pbWidthEntry.invoke()
self.pbWidthEntry['command'] = self._checkContinuous
if not self.pbWidthEntry.valid():
self.enter()
raise UserError("Invalid pseudobond width "
"(in Treatment of Clash/Contact Atoms)")
prefs[PB_WIDTH] = float(self.pbWidthEntry.getvalue())
from DetectClash import cmdDetectClash
if actionWriteInfo:
saveFile = "-"
else:
saveFile = None
clashes = cmdDetectClash(checkAtoms,
test=test,
overlapCutoff=prefs[CLASH_THRESHOLD],
hbondAllowance=prefs[HBOND_ALLOWANCE],
bondSeparation=prefs[BOND_SEPARATION],
ignoreIntraRes=prefs[IGNORE_INTRA_RES],
setAttrs=actionAttr,
selectClashes=actionSelect,
colorClashes=actionColor,
clashColor=clashColor,
nonclashColor=nonclashColor,
makePseudobonds=actionPseudobonds,
pbColor=pbColor,
lineWidth=prefs[PB_WIDTH],
saveFile=saveFile,
log=actionLogInfo,
summary=self.status)
if actionAttr:
from ShowAttr import ShowAttrDialog
from chimera import dialogs
from DetectClash import attrName
d = dialogs.display(ShowAttrDialog.name)
d.configure(attrsOf="atoms", attrName=attrName, mode="Render")
def Close(self):
ModelessDialog.Close(self)
if self.freqButtons.getvalue() != self.FREQ_APPLY:
self.freqButtons.invoke(self.FREQ_APPLY)
def _checkContinuous(self, *args):
if self.freqButtons.getvalue() == self.FREQ_CONTINUOUS:
self.Apply()
def _clashDefaultsCB(self):
from prefs import defaults
self.hbondAllow.setvalue(str(defaults[HBOND_ALLOWANCE]))
self.clashDef.setvalue(str(defaults[CLASH_THRESHOLD]))
self._checkContinuous()
def _clearHandlers(self):
while self._handlers:
trigName, handler = self._handlers.popitem()
chimera.triggers.deleteHandler(trigName, handler)
def _contactDefaultsCB(self):
self.hbondAllow.setvalue("0.0")
self.clashDef.setvalue("-0.4")
self._checkContinuous()
def _desigCB(self):
self.designated.clear()
self.designated.add(chimera.selection.currentAtoms())
self._updateDesigStatus()
def _desig2CB(self):
self.designated2.clear()
self.designated2.add(chimera.selection.currentAtoms())
self._locButtonCB()
self._updateDesig2Status()
def _freqChangeCB(self, freqVal):
self._clearHandlers()
if freqVal == self.FREQ_APPLY:
self.assignAttrButton.configure(state='normal')
self.writeInfoButton.configure(state='normal')
self.logInfoButton.configure(state='normal')
return
self.assignAttrButton.configure(state='disabled')
self.writeInfoButton.configure(state='disabled')
self.logInfoButton.configure(state='disabled')
def modCoordSets(trigName, myData, changes):
if changes.modified:
self.Apply()
self._handlers['CoordSet'] = chimera.triggers.addHandler(
'CoordSet', modCoordSets, None)
def justCoordSets(trigName, myData, changes):
if 'activeCoordSet changed' in changes.reasons:
self.Apply()
self._handlers['Molecule'] = chimera.triggers.addHandler(
'Molecule', justCoordSets, None)
if freqVal == self.FREQ_MOTION:
self._handlers[chimera.MOTION_STOP] = chimera.triggers\
.addHandler(chimera.MOTION_STOP,
self._motionCB, None)
elif freqVal == self.FREQ_CONTINUOUS:
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
self._motionCB()
self._handlers['OpenState'] = chimera.triggers\
.addHandler('OpenState', preCB, None)
self.Apply()
def _locButtonCB(self, butName=None):
checkSetBut = self.checkLocButtons.button(self.CHECK_SET)
if self.checkLocButtons.getvalue() == self.CHECK_SET \
and not self.designated2.atoms():
checkSetBut.config(fg="red", activeforeground="red")
else:
checkSetBut.config(fg="black", activeforeground="black")
self._updateDesig2Status()
def _motionCB(self, *args):
# if all molecule activities are the same (i.e. no possible
# relative motion), do nothing
activity = None
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
if activity is None:
activity = m.openState.active
elif activity != m.openState.active:
self.Apply()
return
def _updateDesigStatus(self):
numAtoms = len(self.designated.atoms())
if numAtoms:
statusText = "%d atoms designated" % numAtoms
color = 'blue'
else:
statusText = "No atoms designated"
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desigStatus.config(text=statusText, fg=color)
self._checkContinuous()
def _updateDesig2Status(self):
numAtoms = len(self.designated2.atoms())
checkSet = self.checkLocButtons.getvalue() == self.CHECK_SET
color = 'black'
if numAtoms:
statusText = "Second set: %d atoms" % numAtoms
else:
statusText = "No second set"
if checkSet:
color = 'red'
self.freqButtons.invoke(self.FREQ_APPLY)
self.desig2Status.config(text=statusText, fg=color)
if checkSet:
self._checkContinuous()