def _getMolecules(self, assignsel, usesel, restrict): if assignsel or usesel: sel = selection.currentMolecules() if usesel: for r in selection.currentResidues(): restrict[r] = True for a in selection.currentAtoms(): restrict[a] = True for m in sel: restrict[m] = True if assignsel: molecules = sel else: molecules = [] if not molecules: molecules = chimera.openModels.list( modelTypes=[chimera.Molecule]) return molecules
def selMolecules(noneReturnsAll=True, implied=False, create=False):
mol = selection.currentMolecules()
extendSelection(mol, 'molecules', noneReturnsAll, implied, create)
return mol
def _selectionChangedCB(self, trigger, closure, ignore): from chimera import selection mols = selection.currentMolecules() selected = [ m for m in mols if m in self.molList ] self.modBaseTable.highlight(selected)
def unselMolecules(): from chimera.selection import currentMolecules selMolecules = currentMolecules(asDict=True) return filter(lambda m: m not in selMolecules, chimera.openModels.list(modelTypes=[chimera.Molecule]))
def createHBonds(models=None, intramodel=True, intermodel=True, relax=True,
distSlop=recDistSlop, angleSlop=recAngleSlop, twoColors=False,
selRestrict=None, lineWidth=1.0, saveFile=None, batch=False,
interSubmodel=False, makePseudobonds=True, retainCurrent=False,
reveal=False, namingStyle=None, log=False, cacheDA=None,
color=(0.0, 0.8, 0.9, 1.0), slopColor=(0.95, 0.5, 0.0, 1.0)):
"""Wrapper to be called by gui and command line.
Use findHBonds for other programming applications.
"""
inColors = (color, slopColor)
outColors = []
for c in inColors:
if isinstance(c, basestring):
from chimera.colorTable import getColorByName
try:
outColors.append(getColorByName(c))
except KeyError:
raise "No known color named '%s'" % c
elif isinstance(c, tuple):
oc = chimera.MaterialColor()
oc.ambientDiffuse = c[:3]
if len(c) > 3:
oc.opacity = c[-1]
outColors.append(oc)
else:
outColors.append(c)
bondColor, slopColor = outColors
donors = acceptors = None
if selRestrict is not None:
selAtoms = currentAtoms(asDict=True)
if not selAtoms:
if batch:
return
raise UserError("No atoms in selection.")
if (not intermodel or selRestrict == "both") and models is None:
# intramodel only or both ends in selection
models = currentMolecules()
if selRestrict == "both":
# both ends in selection
donors = acceptors = selAtoms
if models is None:
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
if not relax:
distSlop = angleSlop = 0.0
if cacheDA == None:
# cache trajectories by default
cacheDA = len(models) == 1 and len(models[0].coordSets) > 1
hbonds = findHBonds(models, intermodel=intermodel,
intramodel=intramodel, distSlop=distSlop,
angleSlop=angleSlop, donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
hbonds = _filterBySel(hbonds, selAtoms, selRestrict)
outputInfo = (intermodel, intramodel, relax, distSlop, angleSlop,
models, hbonds)
if log:
import sys
# provide a separator from other output
print>>sys.stdout, ""
_fileOutput(sys.stdout, outputInfo, namingStyle)
if saveFile == '-':
from MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(outputInfo, _fileOutput,
initialfile="hbond.info",
title="Choose H-Bond Save File",
historyID="H-bond info")
elif saveFile is not None:
_fileOutput(saveFile, outputInfo, namingStyle)
replyobj.status("%d hydrogen bonds found\n"
% len(hbonds), log=1, blankAfter=120)
if not makePseudobonds:
return
if twoColors:
# color relaxed constraints differently
precise = findHBonds(models,
intermodel=intermodel, intramodel=intramodel,
donors=donors, acceptors=acceptors,
interSubmodel=interSubmodel, cacheDA=cacheDA)
if selRestrict and donors == None:
precise = _filterBySel(precise, selAtoms, selRestrict)
# give another opportunity to read the result...
replyobj.status("%d hydrogen bonds found\n" % len(hbonds),
blankAfter=120)
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup("hydrogen bonds", issueHint=True)
if not retainCurrent:
pbg.deleteAll()
pbg.lineWidth = lineWidth
for don, acc in hbonds:
if don.associated(acc, "hydrogen bonds"):
continue
pb = pbg.newPseudoBond(don, acc)
if twoColors:
if (don, acc) in precise:
color = bondColor
else:
color = slopColor
else:
color = bondColor
pb.color = color
if reveal:
for end in [don, acc]:
if end.display:
continue
for ea in end.residue.oslChildren():
ea.display = True
def lists(level="atom", mode="any", attribute=None):
import chimera
from chimera import replyobj, selection
mode = findBestMatch(mode, ["any", "all"])
level = findBestMatch(level, ["atom", "residue", "chain", "molecule"])
if level == "atom":
if attribute is None:
attribute = "idatmType"
_reportAtoms(selection.currentAtoms(), attribute)
elif level == "residue":
if mode == "any":
residues = selection.currentResidues()
else:
rMap = {}
for a in selection.currentAtoms():
l = rMap.setdefault(a.residue, [])
l.append(a)
residues = []
for r, aList in rMap.iteritems():
if len(r.atoms) == len(aList):
residues.append(r)
if attribute is None:
attribute = "type"
_reportResidues(residues, attribute)
elif level == "chain":
if mode == "any":
chains = selection.currentChains()
else:
rcMap = {}
cached = set([])
cMap = {}
for r in selection.currentResidues():
if r.molecule not in cached:
cached.add(r.molecule)
for seq in r.molecule.sequences():
for res in seq.residues:
rcMap[res] = seq
try:
seq = rcMap[r]
except KeyError:
pass
else:
l = cMap.setdefault(seq, [])
l.append(r)
chains = []
for seq, rList in cMap.iteritems():
if len(seq) == len(rList):
chains.append(seq)
if attribute is None:
attribute = "chain"
_reportChains(chains, attribute)
elif level == "molecule":
if mode == "any":
molecules = selection.currentMolecules()
else:
mMap = {}
for a in selection.currentAtoms():
l = mMap.setdefault(a.molecule, [])
l.append(a)
molecules = []
for m, aList in mMap.iteritems():
if len(m.atoms) == len(aList):
molecules.append(m)
if attribute is None:
attribute = "name"
_reportModels(molecules, attribute)
else:
raise chimera.UserError("\"%s\": unknown listselection level"
% level)
def unselMolecules():
from chimera.selection import currentMolecules
selMolecules = currentMolecules(asDict=True)
return filter(lambda m: m not in selMolecules,
chimera.openModels.list(modelTypes=[chimera.Molecule]))
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
def selMolecules(noneReturnsAll=True, implied=False, create=False): mol = selection.currentMolecules() extendSelection(mol, 'molecules', noneReturnsAll, implied, create) return mol