def addGeom(self, geom, parent=None, redo=False):
# add geometry to to geomContainer, create atom set and set pointer
# from geom to molecule
GeomContainer.addGeom(self, geom, parent, redo)
self.atoms[geom.name]=AtomSet([])
# FIXME we should use a weakreference to mol here
geom.mol = self.mol #need for backtracking picking
def __init__(self, mol, viewer):
"""constructor of the geometry container"""
GeomContainer.__init__(self)
self.mol = mol
mol.geomContainer = self
## Dictionary of AtomSets used to track which atoms are currently
## each mode
self.atoms = {}
## Dictionary of function to be called to expand an atomic
## property to the corresponding vertices in a geometry
## The function has to accept 4 arguments: a geometry name,
## a list of atoms, the name of the property and an optional argument
## the propIndex default is None, specifying the index of the property
## when needed.
## the key is the geometry name
self.atomPropToVertices = {}
## Dictionary of function to be called to convert a vertex into an atom
## if no function is registered, used default (1vertex to 1atom)
## mapping
## if None is registered: this geometry cannot represent atoms
## else, call the function registered for this geometry
self.geomPickToAtoms = {}
## Dictionary of function to be called when a part into a bond
## if no function is registered, used default (1vertex to 1bond)
## mapping
## if None is registered: this geometry cannot represent bonds
## else, call the function registered for this geometry
self.geomPickToBonds = {}
## this set of coordinates should really be shared by all geometries
self.allCoords = mol.allAtoms.coords
if viewer.hasGui:
self.VIEWER = viewer.GUI.VIEWER
# master Geometry
self.masterGeom = Geom(mol.name, shape=(0,0),
pickable=0, protected=True)
self.masterGeom.isScalable = 0
self.geoms['master'] = self.masterGeom
self.masterGeom.replace = True
self.VIEWER.AddObject( self.masterGeom )
# selection Geometry
if viewer.viewSelectionIcon=='cross':
self.geoms['selectionSpheres'] = CrossSet(
'selection', shape=(0,3), materials=((1.0, 1.0, 0.),),
lineWidth=2, inheritMaterial=0, protected=True)
elif viewer.viewSelectionIcon=='labels':
from DejaVu.glfLabels import GlfLabels
self.geoms['selectionSpheres'] = GlfLabels(
'selection', shape=(0,3),
font='times_new1.glf',
bilboard=True,
fontScales=(.5,.5,.5),
materials=((1.0, 1.0, 0.),),
inheritMaterial=0,
protected=True)
else:
self.geoms['selectionSpheres'] = Spheres(
'selection', shape=(0,3), radii=0.3, quality = 3,
materials = ((1.0, 1.0, 0.),), inheritMaterial=0, protected=True)
self.geoms['selectionSpheres'].pickable=0
self.VIEWER.AddObject(self.geoms['selectionSpheres'],
parent=self.masterGeom, redo=0 )