def select(self, only=False):
from chimera.selection import setCurrent, addCurrent
if only:
setCurrent(self.bond)
else:
addCurrent(self.bond)
def selUp():
global _selChangeHandler, _atomChangeHandler
needHandlers = False
if not _selInfos[SELATOM:]:
needHandlers = True
_selInfos.append(_infoFromSel(selection.copyCurrent()))
# go up levels until the selection changes
global _IchangedSel, selLevel
_IchangedSel = False
while selLevel < SELALL:
selLevel += 1
try:
nextSel = _selInfos[selLevel][0]
if selLevel == SELALL \
and not _topValid:
raise IndexError, "new models present"
except IndexError:
nextSel = _nextSel()
_selInfos.append(_infoFromSel(nextSel))
if len(nextSel) != len(_selInfos[selLevel - 1][0]):
if not needHandlers:
_IchangedSel = True
selection.setCurrent(nextSel)
break
# delay the handlers until here in case setting the selection
# causes other things to get selected (e.g. axes/planes)
if needHandlers:
_atomChangeHandler = chimera.triggers.addHandler(
"Atom", _atomChangeCB, None)
_selChangeHandler = chimera.triggers.addHandler(
"selection changed", _selChangeCB, None)
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def select_atoms_outside_map():
from chimera.replyobj import status, info
from VolumeViewer import active_volume
dr = active_volume()
if dr is None:
status('No density map opened.')
return
if dr.surface_model() == None or not dr.surface_model().display:
status('No surface shown for map.')
return
levels = dr.surface_levels
if len(levels) == 0:
status('No surface shown for map.')
return
contour_level = min(levels)
from chimera import selection
atoms = selection.currentAtoms()
aolist = atoms_outside_map(atoms, dr, contour_level)
msg = ('%d of %d selected atoms outside %s at level %.5g' %
(len(aolist), len(atoms), dr.name, contour_level))
status(msg)
info(msg + '\n')
selection.setCurrent(aolist)
def select_markers(markers, only=True):
atoms = [m.atom for m in markers]
from chimera.selection import setCurrent, addCurrent
if only:
setCurrent(atoms)
else:
addCurrent(atoms)
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 restoreSelections(curSelIds, savedSels): from chimera import selection 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 _distTableSelCB(self, selDists): if self.distSelectsAtomsVar.get(): select = [] select.extend(selDists) for sd in selDists: select.extend(sd.atoms) selection.setCurrent(select) else: selection.removeCurrent(self.distances) selection.addCurrent(selDists)
def _angleTableSelCB(self, selAngles): if self.angleSelectsComponentsVar.get(): select = [] for atoms in selAngles: select.extend(atoms) atomSet = set(atoms) for a in atoms: for b in a.bonds: if b.otherAtom(a) in atomSet: select.append(b) selection.setCurrent(select)
def _itemsSelectAtoms(self, items, add=False): atoms = set() for item in items: atoms.update(item.atoms) if self.geomSelAtomsVar.get(): if add: selection.addCurrent(atoms) else: selection.setCurrent(atoms) elif set(atoms) == set(selection.currentAtoms()): selection.removeCurrent(atoms)
def selDown():
if not _selInfos[SELATOM:]:
return
# keep lowering level until selection changes
global _IchangedSel, selLevel
_IchangedSel = False
while selLevel > SELNONE:
selLevel -= 1
if len(_selInfos[selLevel][0]) != len(_selInfos[selLevel + 1][0]):
_IchangedSel = True
selection.setCurrent(_selInfos[selLevel][0])
break
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 select_connected():
'Select atoms and bonds connected to currently selected atoms and bnods'
from chimera import selection, Atom
atoms_and_bonds = selection.currentAtoms() + selection.currentBonds()
reached = set(atoms_and_bonds)
i = 0
while i < len(atoms_and_bonds):
ab = atoms_and_bonds[i]
if isinstance(ab, Atom):
n = ([b for b in ab.bonds if not b in reached] +
[a for a in ab.neighbors if not a in reached])
else:
n = [a for a in ab.atoms if not a in reached]
atoms_and_bonds.extend(n)
reached.update(set(n))
i += 1
selection.setCurrent(atoms_and_bonds)
def doApply(self, target, solid, track, selAtoms,
bias, prune, pruneDistance):
m1, m2 = target
if prune:
m1_list = SurfMaker.GetAtomList(m1, m2, pruneDistance)
m2_list = SurfMaker.GetAtomList(m2, m1, pruneDistance)
else:
m1_list = SurfMaker.GetAtomList(m1)
m2_list = SurfMaker.GetAtomList(m2)
if not m1_list or not m2_list:
raise chimera.UserError("No interface surface found")
p = SurfMaker.UnpackIntersurfData(m1_list, m2_list)
tetras = SurfMaker.ComputeTetrahedralization(p)
surfPoints, surfTriangles, surfAtoms = SurfMaker.ComputeSurface(p, tetras, bias)
surfMetric = [ getDistance(x[0], x[1]) for x in surfAtoms ]
lo = min(surfMetric)
hi = max(surfMetric)
scale = hi - lo
markers = [ (lo + m['xy'][0] * scale, m['rgba'])
for m in self.histogramMarkers ]
surfColors = [ getHistogramColor(x, markers)
for x in surfMetric ]
self.histogramData = (lo, hi, surfMetric)
def myMakeBars(numBins, data=self.histogramData):
return makeBars(numBins, data)
self.histogram["datasource"] = (lo, hi, myMakeBars)
self._show_geometry(surfPoints, surfTriangles, surfColors, solid, track)
if selAtoms:
from chimera import selection
atomSet = set([])
for a1, a2 in surfAtoms:
atomSet.add(a1)
atomSet.add(a2)
sel = selection.ItemizedSelection()
sel.add(atomSet)
sel.addImplied(vertices=False)
selection.setCurrent(sel)
# rc('aromatic disk')
# modify model to display double and triple bonds
rc('select #0')
atoms = currentAtoms()
bondsList = []
for a in atoms:
for b in bonds:
if b not in bondsList:
bondsList = bondsList + [b]
for bond in bondsList:
setCurrent(bond)
length = bond.length()
length = format(length, '.3f')
if float(length) in doubleBonds:
rc('setattr b radius 0.2 sel;wait')
elif float(length) in tripleBonds:
rc('setattr b radius 0.3 sel;wait')
rc('windowsize 800 800;wait')
rc('setzoom 30.0;wait')
rc('center;wait')
# take images of molecule
i = 0
def select_all():
'Select all models'
from chimera import selection, openModels
selection.setCurrent(openModels.list())
def clear_selection():
'Clear selection'
from chimera import selection
selection.setCurrent([])
