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 _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 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)
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 _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 _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 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 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)
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 fillInUI(self, parent):
# inter/intra-model; slop; colors; models; replace current;
# label
# for removing labels in subsequent passes...
# (use a selection so I don't have to track model closures)
self.labelSelection = ItemizedSelection()
self.labelMap = {}
self.callbacks = []
row = 0
cols = 3
self.bondColorOption = ColorOption(parent,
row,
'H-bond color',
prefs[BOND_COLOR],
None,
noneOkay=0)
class HBLineWidthOption(LineWidthOption):
name = "Line width"
balloon = "Width of pseudobonds (in pixels)"
default = prefs[LINE_WIDTH]
self.lineWidth = HBLineWidthOption(parent,
row + 1,
None,
None,
None,
width=4,
sticky='w')
self.findMode = Pmw.RadioSelect(parent,
buttontype='radiobutton',
labelpos='n',
pady=0,
orient='vertical',
label_text='Find these bonds:',
hull_borderwidth=2,
hull_relief='ridge')
self.findMode.add('inter-model')
self.findMode.add('intra-model')
self.findMode.add('both')
self.findMode.invoke('both')
self.findMode.grid(row=row, column=2, rowspan=2)
row += 2
self.relaxParams = RelaxParams(parent, prefs[RELAX_COLOR])
self.relaxParams.grid(row=row, columnspan=cols, sticky='nsew', padx=2)
row += 1
self.restrictModels = Tkinter.IntVar(parent)
self.restrictModels.set(0)
self.modelFrame = Tkinter.Frame(parent)
self.molTexts = ["Restrict to models...", "Restrict to models:"]
self.restrictCheckBox = Tkinter.Checkbutton(
self.modelFrame,
variable=self.restrictModels,
text=self.molTexts[0],
command=self._restrictModelsCB)
self.restrictCheckBox.grid(row=0, column=0)
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(self.modelFrame,
listbox_selectmode="extended")
self.modelFrame.rowconfigure(0, weight=1)
self.modelFrame.grid(row=row, column=0, columnspan=cols, sticky="nsw")
parent.rowconfigure(row, weight=1)
row += 1
self.inSelection = Tkinter.IntVar(parent)
self.inSelection.set(0)
f = Tkinter.Frame(parent)
f.grid(row=row, column=0, columnspan=cols, sticky="w")
Tkinter.Checkbutton(f,
variable=self.inSelection,
text="Only find H-bonds with",
command=self._useSelChange).grid(row=0,
column=0,
sticky="e")
self.selType = Pmw.OptionMenu(
f,
items=["at least one end", "exactly one end", "both ends"],
initialitem=0,
menubutton_state="disabled",
labelpos="e",
label_text="selected")
self.selType.grid(row=0, column=1, sticky="w")
row += 1
self.revealEnds = Tkinter.IntVar(parent)
self.revealEnds.set(0)
Tkinter.Checkbutton(
parent,
variable=self.revealEnds,
text="If endpoint atom hidden, show endpoint residue").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.retainCurrent = Tkinter.IntVar(parent)
self.retainCurrent.set(0)
Tkinter.Checkbutton(parent,
variable=self.retainCurrent,
text="Retain currently displayed H-bonds").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
self.interSubmodel = Tkinter.IntVar(parent)
self.interSubmodel.set(0)
# comment out the below since there seems to be no
# situations where cross-submodel-same-model hbonds
# are interesting. If reading pdbrun files occurs, this
# may change.
#Tkinter.Checkbutton(parent, variable=self.interSubmodel,
# text="Find H-bonds between submodels\n"
# "having same principal model number"
# ).grid(row=row, column=0, columnspan=cols, sticky="w")
#row += 1
self.writeFile = Tkinter.IntVar(parent)
self.writeFile.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeFile,
text="Write information to file").grid(
row=row, column=0, columnspan=cols, sticky="w")
self.fileName = None
row += 1
self.writeLog = Tkinter.IntVar(parent)
self.writeLog.set(0)
Tkinter.Checkbutton(parent,
variable=self.writeLog,
text="Write information to reply log").grid(
row=row, column=0, columnspan=cols, sticky="w")
row += 1
def _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):
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 writeMol2(models, fileName, status=None, anchor=None, relModel=None,
hydNamingStyle="sybyl", multimodelHandling="individual",
skip=None, resNum=True, gaffType=False, gaffFailError=None):
"""Write a Mol2 file.
'models' are the models to write out into a file named 'fileName'.
'status', if not None, is a function that takes a string -- used
to report the progress of the write.
'anchor' is a selection (i.e. instance of a subclass of
chimera.selection.Selection) containing atoms/bonds that should
be written out to the @SETS section of the file as the rigid
framework for flexible ligand docking.
'hydNamingStyle' controls whether hydrogen names should be
"Sybyl-like" (value: sybyl) or "PDB-like" (value: pdb)
-- e.g. HG21 vs. 1HG2.
'multimodelHandling' controls whether multiple models will be
combined into a single @MOLECULE section (value: combined) or
each given its own section (value: individual).
'skip' is a list of atoms to not output
'resNum' controls whether residue sequence numbers are included
in the substructure name. Since Sybyl Mol2 files include them,
this defaults to True.
If 'gaffType' is True, outout GAFF atom types instead of Sybyl
atom types. 'gaffFailError', if specified, is the type of error
to throw (e.g. UserError) if there is no gaffType attribute for
an atom, otherwise throw the standard AttributeError.
"""
# open the given file name for writing
from OpenSave import osOpen
f = osOpen(fileName, "w")
sortFunc = serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
if isinstance(models, chimera.Molecule):
models = [models]
elif isinstance(models, Selection):
# create a fictitious jumbo model
if isinstance(models, ItemizedSelection):
sel = models
else:
sel = ItemizedSelection()
sel.merge(models)
sel.addImplied()
class Jumbo:
def __init__(self, sel):
self.atoms = sel.atoms()
self.residues = sel.residues()
self.bonds = sel.bonds()
self.name = "(selection)"
models = [Jumbo(sel)]
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
multimodelHandling = "individual"
# transform...
if relModel is None:
xform = chimera.Xform.identity()
else:
xform = relModel.openState.xform
xform.invert()
# need to find amide moieties since Sybyl has an explicit amide type
if status:
status("Finding amides\n")
from ChemGroup import findGroup
amides = findGroup("amide", models)
amideNs = dict.fromkeys([amide[2] for amide in amides])
amideCNs = dict.fromkeys([amide[0] for amide in amides])
amideCNs.update(amideNs)
amideOs = dict.fromkeys([amide[1] for amide in amides])
substructureNames = None
if multimodelHandling == "combined":
# create a fictitious jumbo model
class Jumbo:
def __init__(self, models):
self.atoms = []
self.residues = []
self.bonds = []
self.name = models[0].name + " (combined)"
for m in models:
self.atoms.extend(m.atoms)
self.residues.extend(m.residues)
self.bonds.extend(m.bonds)
# if combining single-residue models,
# can be more informative to use model name
# instead of residue type for substructure
if len(models) == len(self.residues):
rtypes = [r.type for r in self.residues]
if len(set(rtypes)) < len(rtypes):
mnames = [m.name for m in models]
if len(set(mnames)) == len(mnames):
self.substructureNames = dict(
zip(self.residues, mnames))
models = [Jumbo(models)]
if hasattr(models[-1], 'substructureNames'):
substructureNames = models[-1].substructureNames
delattr(models[-1], 'substructureNames')
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
# write out models
for mol in models:
if hasattr(mol, 'mol2comments'):
for m2c in mol.mol2comments:
print>>f, m2c
if hasattr(mol, 'solventInfo' ):
print>>f, mol.solventInfo
# molecule section header
print>>f, "%s" % MOLECULE_HEADER
# molecule name
print>>f, "%s" % mol.name
ATOM_LIST = mol.atoms
BOND_LIST = mol.bonds
if skip:
skip = set(skip)
ATOM_LIST = [a for a in ATOM_LIST if a not in skip]
BOND_LIST = [b for b in BOND_LIST
if b.atoms[0] not in skip
and b.atoms[1] not in skip]
RES_LIST = mol.residues
# Chimera has an unusual internal order for its atoms, so
# sort them by input order
if status:
status("Putting atoms in input order")
ATOM_LIST.sort(sortFunc)
# if anchor is not None, then there will be two entries in
# the @SETS section of the file...
if anchor:
sets = 2
else:
sets = 0
# number of entries for various sections...
print>>f, "%d %d %d 0 %d" % (len(ATOM_LIST), len(BOND_LIST),
len(RES_LIST), sets)
# type of molecule
if hasattr(mol, "mol2type"):
mtype = mol.mol2type
else:
mtype = "SMALL"
from chimera.resCode import nucleic3to1, protein3to1
for r in mol.residues:
if r.type in protein3to1:
mtype = "PROTEIN"
break
if r.type in nucleic3to1:
mtype = "NUCLEIC_ACID"
break
print>>f, mtype
# indicate type of charge information
if hasattr(mol, 'chargeModel'):
print>>f, mol.chargeModel
else:
print>>f, "NO_CHARGES"
if hasattr(mol, 'mol2comment'):
print>>f, "\n%s" % mol.mol2comment
else:
print>>f, "\n"
if status:
status("writing atoms\n")
# atom section header
print>>f, "%s" % ATOM_HEADER
# make a dictionary of residue indices so that we can do
# quick look ups
resIndices = {}
for i, r in enumerate(RES_LIST):
resIndices[r] = i+1
for i, atom in enumerate(ATOM_LIST):
# atom ID, starting from 1
print>>f, "%7d" % (i+1),
# atom name, possibly rearranged if it's a hydrogen
if hydNamingStyle == "sybyl" \
and not atom.name[0].isalpha():
atomName = atom.name[1:] + atom.name[0]
else:
atomName = atom.name
print>>f, "%-8s" % atomName,
# untransformed coordinate position
coord = xform.apply(atom.xformCoord())
print>>f, "%9.4f %9.4f %9.4f" % (
coord.x, coord.y, coord.z),
# atom type
if gaffType:
try:
atomType = atom.gaffType
except AttributeError:
if not gaffFailError:
raise
raise gaffFailError("%s has no Amber/GAFF type assigned.\n"
"Use the AddCharge tool to assign Amber/GAFF types."
% atom)
elif hasattr(atom, 'mol2type'):
atomType = atom.mol2type
elif atom in amideNs:
atomType = "N.am"
elif atom.residue.id.chainId == "water":
if atom.element.name == "O":
atomType = "O.t3p"
else:
atomType = "H.t3p"
elif atom.element.name == "N" and len(
[r for r in atom.minimumRings() if r.aromatic()]) > 0:
atomType = "N.ar"
elif atom.idatmType == "C2" and len([nb for nb in atom.neighbors
if nb.idatmType == "Ng+"]) > 2:
atomType = "C.cat"
else:
try:
atomType = chimera2sybyl[atom.idatmType]
except KeyError:
chimera.replyobj.warning("Atom whose"
" IDATM type has no equivalent"
" Sybyl type: %s (type: %s)\n"
% (atom.oslIdent(),
atom.idatmType))
atomType = str(atom.element)
print>>f, "%-5s" % atomType,
# residue-related info
res = atom.residue
# residue index
print>>f, "%5d" % resIndices[res],
# substructure identifier and charge
if hasattr(atom, 'charge'):
charge = atom.charge
else:
charge = 0.0
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-5d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print>>f, "%s %9.4f" % (rname, charge)
if status:
status("writing bonds\n")
# bond section header
print>>f, "%s" % BOND_HEADER
# make an atom-index dictionary to speed lookups
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i+1
for i, bond in enumerate(BOND_LIST):
a1, a2 = bond.atoms
# ID
print>>f, "%6d" % (i+1),
# atom IDs
print>>f, "%4d %4d" % (
atomIndices[a1], atomIndices[a2]),
# bond order; give it our best shot...
amideA1 = a1 in amideCNs
amideA2 = a2 in amideCNs
if amideA1 and amideA2:
print>>f, "am"
continue
if amideA1 or amideA2:
if a1 in amideOs or a2 in amideOs:
print>>f, "2"
else:
print>>f, "1"
continue
aromatic = False
for ring in bond.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
print>>f, "ar"
continue
try:
geom1 = typeInfo[a1.idatmType].geometry
except KeyError:
print>>f, "1"
continue
try:
geom2 = typeInfo[a2.idatmType].geometry
except KeyError:
print>>f, "1"
continue
if geom1 not in [2,3] or geom2 not in [2,3]:
print>>f, "1"
continue
# if either endpoint atom is in an aromatic ring and
# the bond isn't, it's a single bond...
for endp in [a1, a2]:
aromatic = False
for ring in endp.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
break
else:
# neither endpoint in aromatic ring
print>>f, "2"
continue
print>>f, "1"
if status:
status("writing residues")
# residue section header
print>>f, "%s" % SUBSTR_HEADER
for i, res in enumerate(RES_LIST):
# residue id field
print>>f, "%6d" % (i+1),
# residue name field
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-4d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print>>f, rname,
# ID of the root atom of the residue
from chimera.misc import principalAtom
chainAtom = principalAtom(res)
if chainAtom is None:
if hasattr(res, 'atomsMap'):
chainAtom = res.atoms[0]
else:
chainAtom = res.atoms.values()[0][0]
print>>f, "%5d" % atomIndices[chainAtom],
print>>f, "RESIDUE 4",
# Sybyl seems to use chain 'A' when chain ID is blank,
# so run with that
chainID = res.id.chainId
if len(chainID.strip()) != 1:
chainID = 'A'
print>>f, "%s %3s" % (chainID, res.type),
# number of out-of-substructure bonds
crossResBonds = 0
if hasattr(res, "atomsMap"):
atoms = res.atoms
for a in atoms:
for oa in a.bondsMap.keys():
if oa.residue != res:
crossResBonds += 1
else:
atoms = [a for aList in res.atoms.values()
for a in aList]
for a in atoms:
for oa in a.bonds.keys():
if oa.residue != res:
crossResBonds += 1
print>>f, "%5d" % crossResBonds,
# print "ROOT" if first or only residue of a chain
if a.molecule.rootForAtom(a, True).atom.residue == res:
print>>f, "ROOT"
else:
print>>f
# write flexible ligand docking info
if anchor:
if status:
status("writing anchor info")
print>>f, "%s" % SET_HEADER
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i+1
bondIndices = {}
for i, b in enumerate(BOND_LIST):
bondIndices[b] = i+1
print>>f, "ANCHOR STATIC ATOMS <user> **** Anchor Atom Set"
atoms = anchor.atoms()
print>>f, len(atoms),
for a in atoms:
if a in atomIndices:
print>>f, atomIndices[a],
print>>f
print>>f, "RIGID STATIC BONDS <user> **** Rigid Bond Set"
bonds = anchor.bonds()
print>>f, len(bonds),
for b in bonds:
if b in bondIndices:
print>>f, bondIndices[b],
print>>f
f.close()
def selectRotamers(self, rotamers): from chimera import selectionOperation from chimera.selection import ItemizedSelection rotSel = ItemizedSelection() rotSel.add(rotamers) selectionOperation(rotSel)
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 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()
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 writeMol2(models,
fileName,
status=None,
anchor=None,
relModel=None,
hydNamingStyle="sybyl",
multimodelHandling="individual",
skip=None,
resNum=True,
gaffType=False,
gaffFailError=None):
"""Write a Mol2 file.
'models' are the models to write out into a file named 'fileName'.
'status', if not None, is a function that takes a string -- used
to report the progress of the write.
'anchor' is a selection (i.e. instance of a subclass of
chimera.selection.Selection) containing atoms/bonds that should
be written out to the @SETS section of the file as the rigid
framework for flexible ligand docking.
'hydNamingStyle' controls whether hydrogen names should be
"Sybyl-like" (value: sybyl) or "PDB-like" (value: pdb)
-- e.g. HG21 vs. 1HG2.
'multimodelHandling' controls whether multiple models will be
combined into a single @MOLECULE section (value: combined) or
each given its own section (value: individual).
'skip' is a list of atoms to not output
'resNum' controls whether residue sequence numbers are included
in the substructure name. Since Sybyl Mol2 files include them,
this defaults to True.
If 'gaffType' is True, outout GAFF atom types instead of Sybyl
atom types. 'gaffFailError', if specified, is the type of error
to throw (e.g. UserError) if there is no gaffType attribute for
an atom, otherwise throw the standard AttributeError.
"""
# open the given file name for writing
from OpenSave import osOpen
f = osOpen(fileName, "w")
sortFunc = serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
if isinstance(models, chimera.Molecule):
models = [models]
elif isinstance(models, Selection):
# create a fictitious jumbo model
if isinstance(models, ItemizedSelection):
sel = models
else:
sel = ItemizedSelection()
sel.merge(models)
sel.addImplied()
class Jumbo:
def __init__(self, sel):
self.atoms = sel.atoms()
self.residues = sel.residues()
self.bonds = sel.bonds()
self.name = "(selection)"
models = [Jumbo(sel)]
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
multimodelHandling = "individual"
# transform...
if relModel is None:
xform = chimera.Xform.identity()
else:
xform = relModel.openState.xform
xform.invert()
# need to find amide moieties since Sybyl has an explicit amide type
if status:
status("Finding amides\n")
from ChemGroup import findGroup
amides = findGroup("amide", models)
amideNs = dict.fromkeys([amide[2] for amide in amides])
amideCNs = dict.fromkeys([amide[0] for amide in amides])
amideCNs.update(amideNs)
amideOs = dict.fromkeys([amide[1] for amide in amides])
substructureNames = None
if multimodelHandling == "combined":
# create a fictitious jumbo model
class Jumbo:
def __init__(self, models):
self.atoms = []
self.residues = []
self.bonds = []
self.name = models[0].name + " (combined)"
for m in models:
self.atoms.extend(m.atoms)
self.residues.extend(m.residues)
self.bonds.extend(m.bonds)
# if combining single-residue models,
# can be more informative to use model name
# instead of residue type for substructure
if len(models) == len(self.residues):
rtypes = [r.type for r in self.residues]
if len(set(rtypes)) < len(rtypes):
mnames = [m.name for m in models]
if len(set(mnames)) == len(mnames):
self.substructureNames = dict(
zip(self.residues, mnames))
models = [Jumbo(models)]
if hasattr(models[-1], 'substructureNames'):
substructureNames = models[-1].substructureNames
delattr(models[-1], 'substructureNames')
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
# write out models
for mol in models:
if hasattr(mol, 'mol2comments'):
for m2c in mol.mol2comments:
print >> f, m2c
if hasattr(mol, 'solventInfo'):
print >> f, mol.solventInfo
# molecule section header
print >> f, "%s" % MOLECULE_HEADER
# molecule name
print >> f, "%s" % mol.name
ATOM_LIST = mol.atoms
BOND_LIST = mol.bonds
if skip:
skip = set(skip)
ATOM_LIST = [a for a in ATOM_LIST if a not in skip]
BOND_LIST = [
b for b in BOND_LIST
if b.atoms[0] not in skip and b.atoms[1] not in skip
]
RES_LIST = mol.residues
# Chimera has an unusual internal order for its atoms, so
# sort them by input order
if status:
status("Putting atoms in input order")
ATOM_LIST.sort(sortFunc)
# if anchor is not None, then there will be two entries in
# the @SETS section of the file...
if anchor:
sets = 2
else:
sets = 0
# number of entries for various sections...
print >> f, "%d %d %d 0 %d" % (len(ATOM_LIST), len(BOND_LIST),
len(RES_LIST), sets)
# type of molecule
if hasattr(mol, "mol2type"):
mtype = mol.mol2type
else:
mtype = "SMALL"
from chimera.resCode import nucleic3to1, protein3to1
for r in mol.residues:
if r.type in protein3to1:
mtype = "PROTEIN"
break
if r.type in nucleic3to1:
mtype = "NUCLEIC_ACID"
break
print >> f, mtype
# indicate type of charge information
if hasattr(mol, 'chargeModel'):
print >> f, mol.chargeModel
else:
print >> f, "NO_CHARGES"
if hasattr(mol, 'mol2comment'):
print >> f, "\n%s" % mol.mol2comment
else:
print >> f, "\n"
if status:
status("writing atoms\n")
# atom section header
print >> f, "%s" % ATOM_HEADER
# make a dictionary of residue indices so that we can do
# quick look ups
resIndices = {}
for i, r in enumerate(RES_LIST):
resIndices[r] = i + 1
for i, atom in enumerate(ATOM_LIST):
# atom ID, starting from 1
print >> f, "%7d" % (i + 1),
# atom name, possibly rearranged if it's a hydrogen
if hydNamingStyle == "sybyl" \
and not atom.name[0].isalpha():
atomName = atom.name[1:] + atom.name[0]
else:
atomName = atom.name
print >> f, "%-8s" % atomName,
# untransformed coordinate position
coord = xform.apply(atom.xformCoord())
print >> f, "%9.4f %9.4f %9.4f" % (coord.x, coord.y, coord.z),
# atom type
if gaffType:
try:
atomType = atom.gaffType
except AttributeError:
if not gaffFailError:
raise
raise gaffFailError(
"%s has no Amber/GAFF type assigned.\n"
"Use the AddCharge tool to assign Amber/GAFF types." %
atom)
elif hasattr(atom, 'mol2type'):
atomType = atom.mol2type
elif atom in amideNs:
atomType = "N.am"
elif atom.residue.id.chainId == "water":
if atom.element.name == "O":
atomType = "O.t3p"
else:
atomType = "H.t3p"
elif atom.element.name == "N" and len(
[r for r in atom.minimumRings() if r.aromatic()]) > 0:
atomType = "N.ar"
elif atom.idatmType == "C2" and len(
[nb for nb in atom.neighbors if nb.idatmType == "Ng+"]) > 2:
atomType = "C.cat"
else:
try:
atomType = chimera2sybyl[atom.idatmType]
except KeyError:
chimera.replyobj.warning("Atom whose"
" IDATM type has no equivalent"
" Sybyl type: %s (type: %s)\n" %
(atom.oslIdent(), atom.idatmType))
atomType = str(atom.element)
print >> f, "%-5s" % atomType,
# residue-related info
res = atom.residue
# residue index
print >> f, "%5d" % resIndices[res],
# substructure identifier and charge
if hasattr(atom, 'charge'):
charge = atom.charge
else:
charge = 0.0
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-5d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print >> f, "%s %9.4f" % (rname, charge)
if status:
status("writing bonds\n")
# bond section header
print >> f, "%s" % BOND_HEADER
# make an atom-index dictionary to speed lookups
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i + 1
for i, bond in enumerate(BOND_LIST):
a1, a2 = bond.atoms
# ID
print >> f, "%6d" % (i + 1),
# atom IDs
print >> f, "%4d %4d" % (atomIndices[a1], atomIndices[a2]),
# bond order; give it our best shot...
amideA1 = a1 in amideCNs
amideA2 = a2 in amideCNs
if amideA1 and amideA2:
print >> f, "am"
continue
if amideA1 or amideA2:
if a1 in amideOs or a2 in amideOs:
print >> f, "2"
else:
print >> f, "1"
continue
aromatic = False
for ring in bond.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
print >> f, "ar"
continue
try:
geom1 = typeInfo[a1.idatmType].geometry
except KeyError:
print >> f, "1"
continue
try:
geom2 = typeInfo[a2.idatmType].geometry
except KeyError:
print >> f, "1"
continue
if geom1 not in [2, 3] or geom2 not in [2, 3]:
print >> f, "1"
continue
# if either endpoint atom is in an aromatic ring and
# the bond isn't, it's a single bond...
for endp in [a1, a2]:
aromatic = False
for ring in endp.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
break
else:
# neither endpoint in aromatic ring
print >> f, "2"
continue
print >> f, "1"
if status:
status("writing residues")
# residue section header
print >> f, "%s" % SUBSTR_HEADER
for i, res in enumerate(RES_LIST):
# residue id field
print >> f, "%6d" % (i + 1),
# residue name field
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-4d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print >> f, rname,
# ID of the root atom of the residue
from chimera.misc import principalAtom
chainAtom = principalAtom(res)
if chainAtom is None:
if hasattr(res, 'atomsMap'):
chainAtom = res.atoms[0]
else:
chainAtom = res.atoms.values()[0][0]
print >> f, "%5d" % atomIndices[chainAtom],
print >> f, "RESIDUE 4",
# Sybyl seems to use chain 'A' when chain ID is blank,
# so run with that
chainID = res.id.chainId
if len(chainID.strip()) != 1:
chainID = 'A'
print >> f, "%s %3s" % (chainID, res.type),
# number of out-of-substructure bonds
crossResBonds = 0
if hasattr(res, "atomsMap"):
atoms = res.atoms
for a in atoms:
for oa in a.bondsMap.keys():
if oa.residue != res:
crossResBonds += 1
else:
atoms = [a for aList in res.atoms.values() for a in aList]
for a in atoms:
for oa in a.bonds.keys():
if oa.residue != res:
crossResBonds += 1
print >> f, "%5d" % crossResBonds,
# print "ROOT" if first or only residue of a chain
if a.molecule.rootForAtom(a, True).atom.residue == res:
print >> f, "ROOT"
else:
print >> f
# write flexible ligand docking info
if anchor:
if status:
status("writing anchor info")
print >> f, "%s" % SET_HEADER
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i + 1
bondIndices = {}
for i, b in enumerate(BOND_LIST):
bondIndices[b] = i + 1
print >> f, "ANCHOR STATIC ATOMS <user> **** Anchor Atom Set"
atoms = anchor.atoms()
print >> f, len(atoms),
for a in atoms:
if a in atomIndices:
print >> f, atomIndices[a],
print >> f
print >> f, "RIGID STATIC BONDS <user> **** Rigid Bond Set"
bonds = anchor.bonds()
print >> f, len(bonds),
for b in bonds:
if b in bondIndices:
print >> f, bondIndices[b],
print >> f
f.close()