def set_center_of_rotation():
'Set center of rotation to center of selected atoms or use center of models mode if no atoms are selected'
from chimera import selection
if selection.currentEmpty():
chimera.runCommand('~cofr')
else:
chimera.runCommand('cofr sel')
def transpSurf(amount):
if amount != -1:
aopacity = opacity = min(1.0, 1 - amount)
else:
opacity = 1
aopacity = -1
atoms = selAtoms()
import Midas
surfatoms = Midas.atomMSMSModels(atoms)
for s,atoms in surfatoms.items():
adjustMSMSTransparency(s, atoms, opacity, aopacity)
splist = selectedSurfacePieces(implied = True)
from chimera import MSMSModel
for p in splist:
s = p.model
if isinstance(s, MSMSModel) and s.molecule:
adjustMSMSTransparency(s, s.atoms, opacity, aopacity)
else:
adjustSurfacePieceTransparency(p, opacity)
if (len(atoms) > 0 and not selection.currentEmpty()
and len(surfatoms) == 0 and len(splist) == 0):
from replyobj import warning
warning('No surfaces shown for selected atoms.\n')
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 showSurface(warnLarge=True):
if warnLarge:
numSurfaces = len(selMolecules())
if numSurfaces > 20:
import tkgui
tkgui.SurfaceWarningDialog(numSurfaces,
lambda: showSurface(warnLarge=False))
return
empty = selection.currentEmpty()
atoms = selAtoms()
for a in atoms:
a.surfaceDisplay = True
import Midas
Midas.surfaceVisibilityByAtom(atoms)
plist = selectedSurfacePieces(implied=True)
if plist:
pa, pb = surfacePieceAtomsAndBonds(plist)
if pa:
# Don't surface atoms that have non-MSMS surface.
paset = set(pa)
atoms = [a for a in atoms if a not in paset]
for p in plist:
p.display = True
p.model.display = True
from Midas import surfaceNew
molcat = list(set([(a.molecule, a.surfaceCategory) for a in atoms]))
if empty:
# Only surface main category if nothing selected.
molcat = [mc for mc in molcat if mc[1] == 'main']
molcat.sort(lambda mc1, mc2: cmp(mc1[0].id, mc2[0].id))
for mol, cat in molcat:
surfaceNew(cat, models=[mol])
def showSurface(warnLarge=True): if warnLarge: numSurfaces = len(selMolecules()) if numSurfaces > 20: import tkgui tkgui.SurfaceWarningDialog(numSurfaces, lambda : showSurface(warnLarge=False)) return empty = selection.currentEmpty() atoms = selAtoms() for a in atoms: a.surfaceDisplay = True import Midas Midas.surfaceVisibilityByAtom(atoms) plist = selectedSurfacePieces(implied = True) if plist: pa, pb = surfacePieceAtomsAndBonds(plist) if pa: # Don't surface atoms that have non-MSMS surface. paset = set(pa) atoms = [a for a in atoms if a not in paset] for p in plist: p.display = True p.model.display = True from Midas import surfaceNew molcat = list(set([(a.molecule, a.surfaceCategory) for a in atoms])) if empty: # Only surface main category if nothing selected. molcat = [mc for mc in molcat if mc[1] == 'main'] molcat.sort(lambda mc1,mc2: cmp(mc1[0].id, mc2[0].id)) for mol, cat in molcat: surfaceNew(cat, models=[mol])
def transpSurf(amount):
if amount != -1:
aopacity = opacity = min(1.0, 1 - amount)
else:
opacity = 1
aopacity = -1
atoms = selAtoms()
import Midas
surfatoms = Midas.atomMSMSModels(atoms)
for s, atoms in surfatoms.items():
adjustMSMSTransparency(s, atoms, opacity, aopacity)
splist = selectedSurfacePieces(implied=True)
from chimera import MSMSModel
for p in splist:
s = p.model
if isinstance(s, MSMSModel) and s.molecule:
adjustMSMSTransparency(s, s.atoms, opacity, aopacity)
else:
adjustSurfacePieceTransparency(p, opacity)
if (len(atoms) > 0 and not selection.currentEmpty() and len(surfatoms) == 0
and len(splist) == 0):
from replyobj import warning
warning('No surfaces shown for selected atoms.\n')
def NDBColors(self):
from chimera import selection
if selection.currentEmpty():
import Midas
residues = Midas._selectedResidues('#')
else:
residues = selection.currentResidues()
NA.NDBColors(residues)
def extendSelection(objects,
objectName,
noneReturnsAll=True,
implied=False,
create=False):
if not objects and noneReturnsAll and selection.currentEmpty():
objects.extend(allObjects(objectName))
elif implied:
addImpliedSelection(objects, objectName, create, noneReturnsAll)
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box = not shown)
v.show()
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box=not shown)
v.show()
def selectedSurfacePieces(excludeMSMS = False, noneReturnsAll = True, implied = False): import Surface if noneReturnsAll and selection.currentEmpty(): plist = Surface.all_surface_pieces() else: plist = Surface.selected_surface_pieces() if implied and surfacesWithAtomsAndBonds(): atoms = selAtoms(noneReturnsAll) bonds = selBonds(noneReturnsAll) pset = set(plist) pab = atomAndBondSurfacePieces(atoms, bonds) plist.extend([p for p in pab if p not in pset]) if excludeMSMS: plist = [p for p in plist if (not isinstance(p.model, chimera.MSMSModel) or p.model.molecule is None)] return plist
def selectedSurfacePieces(excludeMSMS=False,
noneReturnsAll=True,
implied=False):
import Surface
if noneReturnsAll and selection.currentEmpty():
plist = Surface.all_surface_pieces()
else:
plist = Surface.selected_surface_pieces()
if implied and surfacesWithAtomsAndBonds():
atoms = selAtoms(noneReturnsAll)
bonds = selBonds(noneReturnsAll)
pset = set(plist)
pab = atomAndBondSurfacePieces(atoms, bonds)
plist.extend([p for p in pab if p not in pset])
if excludeMSMS:
plist = [
p for p in plist if (not isinstance(p.model, chimera.MSMSModel)
or p.model.molecule is None)
]
return plist
def setFixed(self, which): from chimera import selection if which == "none" or selection.currentEmpty(): for ma in self.universe.atomList(): ma.fixed = False elif which == "selected": import chimera for ma in self.universe.atomList(): ma.fixed = False for a in selection.currentAtoms(): if a.molecule in self.mols: ma = self.atomMap[a] ma.fixed = True else: import chimera for ma in self.universe.atomList(): ma.fixed = True for a in selection.currentAtoms(): if a.molecule in self.mols: ma = self.atomMap[a] ma.fixed = False
def setFixed(self, which):
from chimera import selection
if which == "none" or selection.currentEmpty():
for ma in self.universe.atomList():
ma.fixed = False
elif which == "selected":
import chimera
for ma in self.universe.atomList():
ma.fixed = False
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = True
else:
import chimera
for ma in self.universe.atomList():
ma.fixed = True
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = False
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 extendSelection(objects, objectName, noneReturnsAll=True, implied=False, create=False): if not objects and noneReturnsAll and selection.currentEmpty(): objects.extend(allObjects(objectName)) elif implied: addImpliedSelection(objects, objectName, create, noneReturnsAll)
def Apply(self):
from chimera import selection
if not self.restrict.get() or selection.currentEmpty():
molecules = chimera.openModels.list(
modelTypes=[chimera.Molecule])
residues = []
for mol in molecules:
residues.extend(mol.residues)
else:
residues = selection.currentResidues()
molecules = tuple(set(r.molecule for r in residues))
residues = [r for r in residues
if r.ribbonResidueClass.isNucleic()]
backbone = self.showBackbone.get()
display = backbone != 'atoms & bonds'
for r in residues:
r.ribbonDisplay = display
side = self.showSide.get()
if side == 'ladder':
distSlop = 0.0
angleSlop = 0.0
relax = self.relaxParams.relaxConstraints
if relax:
distSlop = self.relaxParams.relaxDist
angleSlop = self.relaxParams.relaxAngle
NA.set_ladder(molecules, residues,
rungRadius=self.rungRadius.get(),
showStubs=self.showStubs.get(),
skipNonBaseHBonds=self.skipNonBase.get(),
useExisting=self.useExisting.get(),
distSlop=distSlop, angleSlop=angleSlop)
return
if side.endswith('slab'):
if self.currentStyle is None:
info = self._getInfo()
NA.addStyle(None, info)
showGly = self.anchor.get() != NA.SUGAR
if showGly and side.startswith('tube'):
showGly = self.showGlycosidic.get()
NA.set_slab(side, molecules, residues,
style=self.currentStyle,
thickness=self.thickness.get(),
orient=self.showOrientation.get(),
shape=self.shape.get(), showGly=showGly,
hide=self.hideBases.get())
if side.startswith('fill'):
for r in residues:
r.fillDisplay = True
else:
for r in residues:
r.fillDisplay = False
if side.endswith('fill'):
if self.showOrientation.get():
NA.set_orient(molecules, residues)
else:
NA.set_normal(molecules, residues)
elif side.startswith('atoms'):
NA.set_normal(molecules, residues)
return