def _get_selected_features(self, tree):
def get_child_chimera_obj(feat):
for child in feat.children:
o = child.chimera_obj
if o:
yield o
for obj in get_child_chimera_obj(child):
yield obj
def get_selection():
for f in tree.selectedIndexes():
feat = f.internalPointer()
obj = feat.chimera_obj
# Prefer to select pseudobonds (even from children)
if (obj is not None
and (not isinstance(obj, Atoms) or not feat.children)):
yield obj
else:
for obj in get_child_chimera_obj(feat):
yield obj
s = list(get_selection())
objs = Objects()
objs.add_pseudobonds(
Pseudobonds(x for x in s if isinstance(x, Pseudobond)))
for x in s:
if isinstance(x, Atoms):
objs.add_atoms(x)
return objs
def _filter_parts(self, model, atoms, num_atoms):
if not self.my_parts:
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,
None, self.my_attrs)
return atoms.filter(mask)
from ..objects import Objects
results = Objects()
for part in self.my_parts:
my_part = self.my_parts.__class__(part)
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,
my_part, self.my_attrs)
sub_atoms = atoms.filter(mask)
if len(sub_atoms) > 0:
results.add_atoms(sub_atoms)
return results.atoms
def _get_selected_chimera_objects(self, tree):
def _get_node_objects(node, objs):
o = node.chimera_obj
if o and not o.deleted:
objs.append(o)
for child in node._filtered_children:
_get_node_objects(child, objs)
objs = []
inds = tree.selectedIndexes()
for ind in inds:
_get_node_objects(ind.internalPointer(), objs)
# If empty selection, use the root instead
if not inds:
_get_node_objects(tree.model().rmf_hierarchy, objs)
objects = Objects()
objects.add_atoms(Atoms(x for x in objs if isinstance(x, Atom)))
objects.add_bonds(Bonds(x for x in objs if isinstance(x, Bond)))
return objects