def do(self, cutoff):
cache = context.application.cache
parent = cache.common_root
def iter_translation_nodes(nodes):
for node in nodes:
if isinstance(node, GLTransformationMixin) and \
isinstance(node.transformation, Translation) and \
self.allow_node(node):
yield node
if isinstance(node, ContainerMixin):
for subnode in iter_translation_nodes(node.children):
yield subnode
nodes = []
coordinates = []
for node in iter_translation_nodes(cache.nodes_without_children):
nodes.append(node)
coordinates.append(node.get_frame_up_to(parent).t)
coordinates = numpy.array(coordinates)
unit_cell = None
if isinstance(parent, context.application.plugins.get_node("Universe")):
unit_cell = parent.cell
vector_counter = 1
for i0, i1, delta, distance in PairSearchIntra(coordinates, cutoff, unit_cell):
vector = self.get_vector(nodes[i0], nodes[i1], distance)
if vector is not None:
vector.name += " %i" % vector_counter
vector_counter += 1
primitive.Add(vector, common_parent([nodes[i0], nodes[i1]]))
def do(self, cutoff):
cache = context.application.cache
parent = cache.common_root
def iter_translation_nodes(nodes):
for node in nodes:
if isinstance(node, GLTransformationMixin) and \
isinstance(node.transformation, Translation) and \
self.allow_node(node):
yield node
if isinstance(node, ContainerMixin):
for subnode in iter_translation_nodes(node.children):
yield subnode
nodes = []
coordinates = []
for node in iter_translation_nodes(cache.nodes_without_children):
nodes.append(node)
coordinates.append(node.get_frame_up_to(parent).t)
coordinates = numpy.array(coordinates)
unit_cell = None
if isinstance(parent,
context.application.plugins.get_node("Universe")):
unit_cell = parent.cell
vector_counter = 1
for i0, i1, delta, distance in PairSearchIntra(coordinates, cutoff,
unit_cell):
vector = self.get_vector(nodes[i0], nodes[i1], distance)
if vector is not None:
vector.name += " %i" % vector_counter
vector_counter += 1
primitive.Add(vector, common_parent([nodes[i0], nodes[i1]]))
def connect(self, gl_object1, gl_object2):
try:
new = context.application.plugins.get_node(
self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)
)(targets=[gl_object1, gl_object2])
except TargetError:
return
if(self.vector_store.get_value(self.cb_vector.get_active_iter(), 0)=="Bond"):
new.set_bond_type(self.bondtype_store.get_value(self.cb_bondtype.get_active_iter(),1))
primitive.Add(new, common_parent([gl_object1.parent, gl_object2.parent]))
def connect(self, gl_object1, gl_object2):
try:
new = context.application.plugins.get_node(
self.vector_store.get_value(
self.cb_vector.get_active_iter(),
0))(targets=[gl_object1, gl_object2])
except TargetError:
return
if (self.vector_store.get_value(self.cb_vector.get_active_iter(),
0) == "Bond"):
new.set_bond_type(
self.bondtype_store.get_value(
self.cb_bondtype.get_active_iter(), 1))
primitive.Add(new,
common_parent([gl_object1.parent, gl_object2.parent]))
def connect_springs(self):
model, iter = self.tree_selection.get_selected()
Spring = context.application.plugins.get_node("Spring")
if self.cb_inverse.get_active() and len(model.get_value(iter,
3)[3]) > 0:
springs = [
Spring(targets=[node1(), node2()])
for node1, node2 in model.get_value(iter, 3)[3]
]
else:
springs = [
Spring(targets=[node1(), node2()])
for node1, node2 in model.get_value(iter, 3)[2]
]
parent = common_parent([self.frame1, self.frame2])
for spring in springs:
primitive.Add(spring, parent)
return springs
def connect_springs(self):
model, iter = self.tree_selection.get_selected()
Spring = context.application.plugins.get_node("Spring")
if self.cb_inverse.get_active() and len(model.get_value(iter, 3)[3]) > 0:
springs = [
Spring(targets=[node1(), node2()])
for node1, node2
in model.get_value(iter, 3)[3]
]
else:
springs = [
Spring(targets=[node1(), node2()])
for node1, node2
in model.get_value(iter, 3)[2]
]
parent = common_parent([self.frame1, self.frame2])
for spring in springs:
primitive.Add(spring, parent)
return springs
def get_frame_relative_to(self, other):
common = common_parent([self, other])
return other.get_frame_up_to(common).inv * self.get_frame_up_to(common)
def get_common_root(self):
return analysis.common_parent(self.nodes)
def get_common_parent(self):
return analysis.common_parent(self.parents)
def get_common_root(self):
return analysis.common_parent(self.nodes)
def get_common_parent(self):
return analysis.common_parent(self.parents)
def get_frame_relative_to(self, other):
common = common_parent([self, other])
return other.get_frame_up_to(common).inv * self.get_frame_up_to(common)
def get_frame_relative_to(self, other):
common = common_parent([self, other])
temp = self.get_frame_up_to(common)
temp.apply_inverse_after(other.get_frame_up_to(common))
return temp