def _evaluate(f, models):
if f[0] is SIMPLE:
ks = knownSelection(f[1], models)
if ks is not None:
if ks == 1:
sel = selection.copyCurrent()
elif isinstance(ks, basestring):
sel = selection.OSLSelection(ks, models)
else:
sel = ks
else:
sel = selection.OSLSelection(f[1], models)
elif f[0] is ZONE:
sel = zone(_evaluate(f[1], chimera.openModels.list()), f[2], f[3],
f[4], models)
elif f[0] is UNION:
left = _evaluate(f[1], models)
right = _evaluate(f[2], models)
sel = selection.ItemizedSelection()
sel.merge(selection.REPLACE, left)
sel.merge(selection.EXTEND, right)
elif f[0] is INTERSECT:
left = _evaluate(f[1], models)
right = _evaluate(f[2], left.graphs())
sel = selection.ItemizedSelection()
sel.merge(selection.REPLACE, left)
sel.merge(selection.INTERSECT, right)
elif f[0] is COMPLEMENT:
sel = selection.ItemizedSelection()
sel.add(models)
operand = _evaluate(f[1], models)
sel.merge(selection.REMOVE, operand)
else:
raise ValueError, 'Unknown specifier function: %s' % str(f[0])
return sel
def analysisAtoms(movie, useSel, ignoreBulk, ignoreHyds):
mol = movie.model.Molecule()
if useSel:
selAtoms = selection.currentAtoms()
if selAtoms:
# reduce to just ours
sel1 = selection.ItemizedSelection()
sel1.add(selAtoms)
sel2 = selection.ItemizedSelection()
sel2.add(mol.atoms)
sel1.merge(selection.INTERSECT, sel2)
atoms = sel1.atoms()
if not atoms:
raise UserError("No selected atoms in" " trajectory!")
else:
atoms = mol.atoms
else:
atoms = mol.atoms
if ignoreBulk:
bulkSel = selection.OSLSelection("@/surfaceCategory="
"solvent or surfaceCategory=ions")
atomSel = selection.ItemizedSelection()
atomSel.add(atoms)
atomSel.merge(selection.REMOVE, bulkSel)
atoms = atomSel.atoms()
if not atoms:
raise UserError("No atoms remaining after ignoring"
" solvent/ions")
if ignoreHyds:
atoms = [a for a in atoms if a.element.number != 1]
if not atoms:
raise UserError("No atoms remaining after ignoring" " hydrogens")
return atoms
def _getSourceModel(self, atoms): sel = selection.ItemizedSelection() sel.add(atoms) mols = sel.molecules() if len(mols) == 1: return mols[0] return None
def apply(self, vFunc=None, eFunc=None):
sel = selection.ItemizedSelection()
sels = [] # used as a stack when selections get composited
funcGlobals = {
"__doc__": None,
"__name__": "CodeItemizedSelection",
"__builtins__": __builtins__
}
if self.models is None:
sm = chimera.openModels.list()
else:
sm = self.models
funcLocals = {
"models": sm,
"molecules": filter(lambda m, M=Molecule: isinstance(m, M), sm),
"sel": sel,
"sels": sels,
"selection": selection
}
try:
exec self.codeObj in funcGlobals, funcLocals
except:
from chimera import replyobj
replyobj.error(" CodeItemizedSelection failed\n")
s = apply(traceback.format_exception, sys.exc_info())
replyobj.message(string.join(s, ''))
sel.apply(vFunc, eFunc)
def focus():
disped = [x for x in selAtoms() + selBonds() if x.shown()]
ribbons = [
x for x in selResidues()
if x.ribbonDisplay and x.hasRibbon() and x.molecule.display
]
disped.extend(ribbons)
disped.extend([
p for p in selectedSurfacePieces()
if p.display and p.model.display and p.triangleCount > 0
])
if not disped:
from chimera import replyobj
replyobj.error(
"No target atoms/bonds/ribbons/surfaces currently shown\n")
return
sel = selection.ItemizedSelection()
sel.add(disped)
sel.addImplied(edges=False)
from Midas import window, cofr
window(sel)
from chimera import openModels as om
if selection.currentEmpty():
from chimera import viewing, viewer
om.cofrMethod = viewing.defaultCofrMethod
viewer.clipping = False
else:
om.cofrMethod = om.CenterOfView
def selectionFromText(self, enumText, models=None):
if enumText[0] in OSL_START_CHAR and '\n' not in enumText:
sel = selection.ItemizedSelection()
sel.merge(selection.REPLACE, selection.OSLSelection(enumText))
sel.addImplied(vertices=0)
return sel
else:
return CodeItemizedSelection(enumText, models=models)
def restoreSelections(curSelIds, savedSels):
selection.setCurrent(map(idLookup, curSelIds))
for selInfo in savedSels:
selName, ids = selInfo
sel = selection.ItemizedSelection()
sel.add(map(idLookup, ids))
chimera.selection.saveSel(selName, sel)
def restoreSelections(curSelOsls, savedSels): selection.setCurrent(weedOSLlist(curSelOsls)) for selInfo in savedSels: selName, osls = selInfo sel = selection.ItemizedSelection() sel.add(weedOSLlist(osls)) chimera.selection.saveSel(selName, sel)
def selBackbone(op=None):
# Define a regular expression for matching the names of protein backbone
# atoms (we do not include the carbonyl oxygens because they tend to
# clutter up the graphics display without adding much information).
MAINCHAIN = re.compile("^(N|CA|C)$", re.I)
# The 'list' method of chimera.openModels will return a list of
# currently open models, and takes several optional keyword arguments
# to restrict this list to models matching certain criteria.
# When called with no arguments, this method will
# return a list of all visible models, essentially models that
# were created by the user. Internally managed ('hidden') models,
# such as the distance monitor pseudobondgroup, do not show up in this
# list. A list of hidden models can be obtained by setting the
# optional keyword argument 'hidden' to True.
# The 'all' argument (True/False) can be used to return a list of all open models
# (including both hidden and visible). Other optional arguments include:
# 'id' and 'subid', which restrict the returned list to models with the given
# id and subid, respectively, while 'modelTypes' (a list of model types,
# i.e. '[chimera.Molecule]') will restrict the returned list to models
# of a particular type.
bbAtoms = []
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if MAINCHAIN.match(a.name):
bbAtoms.append(a)
# Create a selection instance that we can use to hold the protein
# backbone atoms. We could have added the atoms one by one to the
# selection while we were in the above loop, but it is more efficient
# to add items in bulk to selections if possible.
backboneSel = selection.ItemizedSelection()
backboneSel.add(bbAtoms)
# Add the connecting bonds to the selection. The 'addImplied' method
# of Selection adds bonds if both bond endpoint atoms are in the
# selection, and adds atoms if any of the atom's bonds are in the
# selection. We use that method here to add the connecting bonds.
backboneSel.addImplied()
# Change the selection in the main Chimera window in the manner
# indicated by this function's 'op' keyword argument. If op is
# 'None', then use whatever method is indicated by the 'Selection Mode'
# item in Chimera's Select menu. Otherwise, op should
# be one of: 'selection.REPLACE', 'selection.INTERSECT',
# 'selection.EXTEND' or 'selection.REMOVE'.
# - 'REPLACE' causes the Chimera selection to be replaced with
# 'backboneSel'.
# - 'INTERSECT' causes the Chimera selecion to be intersected
# with 'backboneSel'.
# - 'EXTEND' causes 'backboneSel' to be appended to the Chimera
# selection.
# - 'REMOVE' causes 'backboneSel' to be unselected in the
# Chimera window.
if op is None:
chimera.tkgui.selectionOperation(backboneSel)
else:
selection.mergeCurrent(op, backboneSel)
def zoomModel(self, model):
self.manipulateModel(model)
sel = selection.ItemizedSelection()
for m in self.refModels:
if m.openState.active:
sel.add(m.atoms)
for m in self.altModels:
if m.openState.active:
sel.add(m.atoms)
Midas.window(sel)
def setPivot():
atoms = selAtoms(noneReturnsAll=False)
plist = selectedSurfacePieces(noneReturnsAll=False)
sel = selection.ItemizedSelection()
sel.add(atoms)
sel.add(plist)
from Midas import cofr, uncofr
if len(sel) > 0:
cofr(sel)
else:
uncofr()
def _zoneResidue(orig, floor, ceiling, modelList):
coordList = _getCoordList(orig)
if not coordList:
return orig
if floor is None:
fSq = None
fbbox = None
else:
fSq = floor * floor
valid, fbbox = chimera.find_minimum_bounding_sphere(coordList)
if valid:
fbbox.radius += floor
else:
fbbox = None
if ceiling is None:
cSq = None
cbbox = None
else:
cSq = ceiling * ceiling
valid, cbbox = chimera.find_minimum_bounding_sphere(coordList)
if valid:
cbbox.radius += ceiling
else:
cbbox = None
zone = selection.ItemizedSelection()
for m in modelList:
try:
residueList = m.residues
except AttributeError:
continue
for r in residueList:
atomList = r.oslChildren()
keep = ceiling is None
for a in atomList:
try:
c = a.xformCoord()
except AttributeError:
continue
if cbbox and not cbbox.inside(c):
continue
isIn = _inZone(c, coordList, fSq, cSq, fbbox)
if isIn < 0:
keep = 0
break
elif isIn > 0:
keep = 1
if keep:
zone.add(atomList)
if floor is None:
zone.merge(selection.EXTEND, orig)
return zone
def select_atoms_and_chains(atoms, cplist):
# Don't select chains where atoms are selected.
rlist = list(set([a.residue for a in atoms]))
import MultiScale
ac = set(MultiScale.containing_chain_pieces(cplist, rlist))
splist = [cp.surface_piece for cp in cplist
if not cp in ac and cp.surface_piece != None]
from chimera import selection
sel = selection.ItemizedSelection()
sel.add(atoms + splist)
sel.addImplied(vertices = False, edges = True) # Select bonds
selection.setCurrent(sel)
def prune(self): from chimera import selection molecule = self.molecules.getvalue() import ModUtil pairs, residues = ModUtil.convertSelection( selection._currentSelection, minLen=4, molecule=molecule, keepHet=self.hetatms.get(), keepNA=self.nucleic.get(), turnsOnly=self.turnsOnly.get()) sel = selection.ItemizedSelection() sel.add(residues) sel.addImplied() selection.mergeCurrent(selection.INTERSECT, sel) return pairs, residues
def localFit(input_map_path,input_pdb_path):
chimera.openModels.open(input_map_path)
chimera.openModels.open(input_pdb_path)
import FitMap
from chimera import selection
from FitMap import fitcmd
mapid = chimera.openModels.list(id = 0)[0]
pdbid = chimera.openModels.list(id = 1)[0]
s1 = selection.ItemizedSelection([pdbid])
fit_list=FitMap.fitcmd.fitmap(s1,mapid,search=30 ,listFits = False,resolution=20)
for fit in fit_list:
va = fit.correlation()
print va
return fit_list
def _zoneAtom(orig, floor, ceiling, modelList):
coordList = _getCoordList(orig)
if not coordList:
return orig
if floor is None:
fSq = None
fbbox = None
else:
fSq = floor * floor
valid, fbbox = chimera.find_minimum_bounding_sphere(coordList)
if valid:
fbbox.radius += floor
else:
fbbox = None
if ceiling is None:
cSq = None
cbbox = None
else:
cSq = ceiling * ceiling
valid, cbbox = chimera.find_minimum_bounding_sphere(coordList)
if valid:
cbbox.radius += ceiling
else:
cbbox = None
zone = selection.ItemizedSelection()
for m in modelList:
try:
atomList = m.atoms
except AttributeError:
continue
for a in atomList:
try:
c = a.xformCoord()
except AttributeError:
continue
if cbbox and not cbbox.inside(c):
continue
if _inZone(c, coordList, fSq, cSq, fbbox) > 0:
zone.add(a)
if floor is None:
zone.merge(selection.EXTEND, orig)
return zone
def path_length(operation, path, group='all'):
from chimera import selection
if isinstance(path, selection.OSLSelection):
# OSLSelection never includes bonds. Use bonds between selected atoms.
atoms = path.contents()[0]
path = selection.ItemizedSelection(atoms)
path.addImplied()
bonds = path.bonds()
if len(bonds) == 0:
raise CommandError('No bonds specified')
if group == 'all':
groups = [bonds]
elif group == 'models':
groups = bonds_per_molecule(bonds)
elif group == 'connected':
groups = connected_bonds(bonds)
else:
raise CommandError('Group must be "all", "models", or "connected"')
lines = []
totlen = 0
import PathLength
for g in groups:
length = PathLength.path_length(g)
totlen += length
lines.append('%s ... %s path, %d segments, length = %.5g' %
(g[0].atoms[0].oslIdent(), g[-1].atoms[1].oslIdent(),
len(g), length))
avelen = totlen / len(groups)
t = '\n'.join(lines) + '\n'
s = lines[0] if len(lines) == 1 else '%d paths, average length = %.5g' % (
len(groups), avelen)
from chimera import replyobj
replyobj.info(t)
replyobj.status(s)
def _menuCB(self, cmdText, br): # callback from angle pull-down menu if cmdText == "Revert": br.set(0) elif cmdText == "Deactivate": br.bond.label = "" br.destroy() elif cmdText == "Select": selectables = [] selectables.extend(br.atoms) selectables.append(br.bond) if self.angleTitle.get() == "Torsion": near, far = self.dihedEndAtoms(br) selectables.extend([near, far]) selectables.append(br.atoms[0].bondsMap[near]) selectables.append(br.atoms[1].bondsMap[far]) from chimera.tkgui import selectionOperation sel = selection.ItemizedSelection() sel.add(selectables) selectionOperation(sel) elif cmdText == "Reverse": br.anchorSide = br.bond.otherAtom(br.anchorSide)
global _selInfos, selLevel
sel, info = _selInfos[selLevel]
if _countsFromSel(sel) == info:
return
chimera.triggers.deleteHandler("selection changed", _selChangeHandler)
chimera.triggers.deleteHandler("Atom", _atomChangeHandler)
_selInfos = _selInfos[:SELATOM]
selLevel = SELATOM
def _addModelHandler(*args):
# adding a model invalidates the 'all' selection
global _topValid
_topValid = False
def _infoFromSel(sel):
return (sel, _countsFromSel(sel))
def _countsFromSel(sel):
mols = sel.molecules()
sortable = [(m.oslIdent(), m) for m in mols]
from chimera.misc import oslModelCmp
sortable.sort(oslModelCmp)
return [len(s[1].atoms) for s in sortable]
_selInfos = [_infoFromSel(selection.ItemizedSelection())]
_selAllHandler = None
def _nextSel():
sel = selection.ItemizedSelection()
sel.add(selection.currentBarrenGraphs())
if selLevel == SELRES:
items = []
addResidues = {}
for r in selection.currentResidues():
addResidues[r] = 1
selPseudoBonds = filter(
lambda e, PB=chimera.PseudoBond: isinstance(e, PB),
selection.currentEdges())
# for currently selected chain-trace pseudobonds
# act as if they select their residues
for ct in filter(
lambda e: isinstance(e.pseudoBondGroup, chimera.ChainTrace),
selPseudoBonds):
addResidues[ct.atoms[0].residue] = 1
addResidues[ct.atoms[1].residue] = 1
for r in addResidues.keys():
items.extend(r.atoms)
sel.add(items)
sel.addImplied(vertices=0)
sel.add(selPseudoBonds)
# add chain trace pseudobonds that should be selected
sel.add(selChainTrace(sel))
elif selLevel == SELCHAIN:
chainIDs = {}
for a in selection.currentAtoms():
chainID = a.residue.id.chainId
try:
chainIDs[a.molecule][chainID] = 1
except KeyError:
chainIDs[a.molecule] = {chainID: 1}
items = []
for m, ids in chainIDs.items():
for a in m.atoms:
if not ids.has_key(a.residue.id.chainId):
continue
items.append(a)
items.extend(a.bonds)
pbgs = {}
for pb in filter(lambda b, PB=chimera.PseudoBond: isinstance(b, PB),
selection.currentEdges()):
pbgs[pb.pseudoBondGroup] = 1
for pbg in pbgs.keys():
if isinstance(pbg, chimera.ChainTrace):
continue
items.extend(pbg.pseudoBonds)
sel.add(items)
sel.add(selChainTrace(sel))
elif selLevel == SELSUBMODEL:
items = []
for m in selection.currentMolecules():
items.extend(m.atoms)
items.extend(m.bonds)
items.extend(
filter(lambda e, PB=chimera.PseudoBond: isinstance(e, PB),
selection.currentEdges()))
sel.add(items)
sel.add(selChainTrace(sel))
elif selLevel == SELMODEL:
molDict = {}
for m in selection.currentMolecules():
osl = m.oslIdent()
if '.' in osl:
molDict[osl[:osl.index('.')]] = 1
else:
molDict[m] = 1
items = []
for mosl in molDict.keys():
if isinstance(mosl, basestring):
for m in selection.OSLSelection(mosl).molecules():
items.extend(m.atoms)
items.extend(m.bonds)
else:
items.extend(mosl.atoms)
items.extend(mosl.bonds)
items.extend(
filter(lambda e, PB=chimera.PseudoBond: isinstance(e, PB),
selection.currentEdges()))
sel.add(items)
sel.add(selChainTrace(sel))
elif selLevel == SELALL:
global _topValid
_topValid = True
items = []
if selection.currentMolecules():
for m in chimera.openModels.list():
if hasattr(m, 'atoms'):
items.extend(m.atoms)
items.extend(m.bonds)
for e in selection.currentEdges():
if isinstance(e, chimera.PseudoBond):
pbsSelected = True
break
else:
pbsSelected = False
if pbsSelected:
mgr = chimera.PseudoBondMgr.mgr()
for grp in mgr.pseudoBondGroups:
items.extend(grp.pseudoBonds)
sel.add(items)
sel.add(selChainTrace(sel))
global _selAllHandler
if _selAllHandler is not None:
_selAllHandler = \
chimera.openModels.addAddHandler(
_addModelHandler, None)
else:
raise ValueError, "Bad selection level"
# Handle selected surface pieces
from Surface import selected_surface_pieces
plist = selected_surface_pieces()
mlist = set([p.model for p in plist])
if selLevel == SELALL and len(mlist) > 0:
from _surface import SurfaceModel
mlist = chimera.openModels.list(modelTypes=[SurfaceModel])
sel.add(mlist)
return sel
