def show_surface():
'Show MSMS molecular surface'
from chimera.selection import currentAtoms
from Surface import selected_surface_pieces, show_surfaces
if len(currentAtoms()) > 0 or len(selected_surface_pieces()) == 0:
# If actions.showSurface() with no atoms selected and a SurfacePiece is
# selected then it shows a warning dialog. Suppress that.
from chimera import actions
actions.showSurface() # MSMSModel surfaces
show_surfaces(selected_surface_pieces()) # SurfaceModel surfaces
def record_movable_objects(self, event):
mode = self.mode
if mode == self.MOVE_SELECTION:
from chimera import selection
atoms = selection.currentAtoms()
chains = selected_multiscale_chains()
spieces = selected_surface_pieces()
self.movable_groups = objects_grouped_by_model(
atoms, chains, spieces)
elif mode in (self.MOVE_MOLECULE, self.MOVE_CHAIN,
self.MOVE_SECONDARY_STRUCTURE):
from chimera import viewer, Atom, Residue
# TODO: Appears to be a bug where picking 1a0m ribbon gives
# lists of many erroneous residues. It is caused by LensViewer
# pick(x,y) doing drag pick using previously set x,y! Not clear
# why since there is separate dragPick(x,y) method.
viewer.delta(event.x, event.y) # Sets lastx, lasty
objects = viewer.pick(event.x, event.y)
atoms = [a for a in objects if isinstance(a, Atom)]
residues = [r for r in objects if isinstance(r, Residue)]
if mode == self.MOVE_MOLECULE:
catoms = extend_to_molecules(atoms, residues)
mschains = multiscale_chain_pieces(objects,
full_molecules=True)
elif mode == self.MOVE_CHAIN:
catoms = extend_to_chains(atoms, residues)
mschains = multiscale_chain_pieces(objects)
elif mode == self.MOVE_SECONDARY_STRUCTURE:
catoms = extend_to_secondary_structure(atoms, residues)
mschains = []
self.movable_groups = objects_grouped_by_model(catoms, mschains)
else:
self.movable_groups = []
def mask_volume_using_selected_surfaces(axis=(0, 1, 0), pad=None):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
from Surface import selected_surface_pieces
plist = selected_surface_pieces()
from Matrix import xform_matrix, invert_matrix
tf = invert_matrix(xform_matrix(v.model_transform()))
surfaces = surface_geometry(plist, tf, pad)
if surfaces:
masked_volume(v, surfaces, axis)
def mask_volume_using_selected_surfaces(axis = (0,1,0), pad = None):
from VolumeViewer import active_volume
v = active_volume()
if v is None:
return
from Surface import selected_surface_pieces
plist = selected_surface_pieces()
from Matrix import xform_matrix, invert_matrix
tf = invert_matrix(xform_matrix(v.model_transform()))
surfaces = surface_geometry(plist, tf, pad)
if surfaces:
masked_volume(v, surfaces, axis)
def mask(volumes, surfaces, axis = None, fullMap = False,
pad = 0., slab = None, sandwich = True, invertMask = False):
from Commands import CommandError, filter_volumes, parse_floats
vlist = filter_volumes(volumes)
from Surface import selected_surface_pieces
glist = selected_surface_pieces(surfaces, include_outline_boxes = False)
if len(glist) == 0:
raise CommandError, 'No surfaces specified'
axis = parse_floats(axis, 'axis', 3, (0,1,0))
if not isinstance(fullMap, (bool,int)):
raise CommandError, 'fullMap option value must be true or false'
if not isinstance(invertMask, (bool,int)):
raise CommandError, 'invertMask option value must be true or false'
if not isinstance(pad, (float,int)):
raise CommandError, 'pad option value must be a number'
if isinstance(slab, (float,int)):
pad = (-0.5*slab, 0.5*slab)
elif not slab is None:
pad = parse_floats(slab, 'slab', 2)
if not isinstance(sandwich, bool):
raise CommandError, 'sandwich option value must be true or false'
from depthmask import surface_geometry, masked_volume
from Matrix import xform_matrix, invert_matrix
for v in vlist:
tf = invert_matrix(xform_matrix(v.model_transform()))
surfs = surface_geometry(glist, tf, pad)
masked_volume(v, surfs, axis, fullMap, sandwich, invertMask)
def selected_surfaces():
from Surface import selected_surface_pieces
splist = selected_surface_pieces()
splist.sort(lambda a, b: cmp(surface_name(a), surface_name(b)))
return splist
def selected_surface_pieces():
from Surface import selected_surface_pieces
from MultiScale import is_chain_piece
spieces = [p for p in selected_surface_pieces() if not is_chain_piece(p)]
return spieces
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