def ask_parameters(self):
cache = context.application.cache
nodes = cache.nodes
last = cache.last
next_to_last = cache.next_to_last
if isinstance(last, Vector):
if (len(nodes) >= 2) and isinstance(next_to_last, Vector):
parent = nodes[-2].parent
b1 = last.children[0].translation_relative_to(parent)
e1 = last.children[1].translation_relative_to(parent)
b2 = next_to_last.children[0].translation_relative_to(parent)
e2 = next_to_last.children[1].translation_relative_to(parent)
if (b1 is not None) and (e1 is not None) and (b2 is not None) and (e2 is not None):
angle = compute_angle(e1 - b1, e2 - b2)
axis = numpy.cross(e1 - b1, e2 - b2)
self.parameters.center = Translation(0.5*(b1+b2))
self.parameters.rotation = Rotation.from_properties(angle, axis, False)
else:
parent = next_to_last.parent
b = last.children[0].translation_relative_to(parent)
e = last.children[1].translation_relative_to(parent)
if (b is not None) and (e is not None):
self.parameters.center = Translation(b)
self.parameters.rotation = Rotation.from_properties(numpy.pi*0.25, e - b, False)
elif isinstance(last, GLTransformationMixin) and isinstance(last.transformation, Translation):
parent = last.parent
self.parameters.center = Translation(last.get_frame_relative_to(parent).t)
self.parameters.rotation = Rotation.identity()
else:
self.parameters.center = Translation(calculate_center(cache.translations))
if self.parameters_dialog.run(self.parameters) != gtk.RESPONSE_OK:
self.parameters.clear()
def ask_parameters(self):
cache = context.application.cache
nodes = cache.nodes
last = cache.last
next_to_last = cache.next_to_last
if isinstance(last, Vector):
if (len(nodes) >= 2) and isinstance(next_to_last, Vector):
parent = nodes[-2].parent
b1 = last.children[0].translation_relative_to(parent)
e1 = last.children[1].translation_relative_to(parent)
b2 = next_to_last.children[0].translation_relative_to(parent)
e2 = next_to_last.children[1].translation_relative_to(parent)
if (b1 is not None) and (e1 is not None) and (
b2 is not None) and (e2 is not None):
angle = compute_angle(e1 - b1, e2 - b2)
axis = numpy.cross(e1 - b1, e2 - b2)
self.parameters.center = Translation(0.5 * (b1 + b2))
self.parameters.rotation = Rotation.from_properties(
angle, axis, False)
else:
parent = next_to_last.parent
b = last.children[0].translation_relative_to(parent)
e = last.children[1].translation_relative_to(parent)
if (b is not None) and (e is not None):
self.parameters.center = Translation(b)
self.parameters.rotation = Rotation.from_properties(
numpy.pi * 0.25, e - b, False)
elif isinstance(last, GLTransformationMixin) and isinstance(
last.transformation, Translation):
parent = last.parent
self.parameters.center = Translation(
last.get_frame_relative_to(parent).t)
self.parameters.rotation = Rotation.identity()
else:
self.parameters.center = Translation(
calculate_center(cache.translations))
if self.parameters_dialog.run(self.parameters) != gtk.RESPONSE_OK:
self.parameters.clear()
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if (self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if (self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(
gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(
new.children[1].number,
bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1 / old_length *
(new_length - old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if (self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action(
"UnframeAbsolute")
UnframeAbsolute([new])
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if(self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if(self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(new.children[1].number, bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1/old_length*(new_length-old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if(self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action("UnframeAbsolute")
UnframeAbsolute([new])
