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 do_rotation(self, drawing_area, rotation_angle, rotation_axis):
camera = context.application.camera
# Note that the camera must be rotated in the opposite direction to
# let the scene rotate in the right direction.
rotation = Rotation.from_properties(-rotation_angle, rotation_axis, False)
camera.rotation = camera.rotation * rotation
drawing_area.queue_draw()
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes(context.application.model.universe.children)
ScanForConnections = context.application.plugins.get_action("ScanForConnections")
rotation2 = Rotation.from_properties(1*numpy.pi, [0, 1, 0], False)
parameters = ScanForConnections.default_parameters()
parameters.connect_description1 = (
Expression("isinstance(node, Atom) and node.number == 8 and node.num_bonds() == 1"),
Expression("node.get_radius()"),
)
parameters.repulse_description1 = (
Expression("isinstance(node, Atom) and (node.number == 8 or node.number == 14)"),
Expression("node.get_radius()*1.5"),
)
parameters.action_radius = 4*angstrom
parameters.hit_tolerance = 0.1*angstrom
parameters.rotation2 = rotation2
assert ScanForConnections.analyze_selection(parameters)
ScanForConnections(parameters)
# Try to save the result to file an open it again.
context.application.model.file_save("test/output/tmp.zml")
FileNew = context.application.plugins.get_action("FileNew")
FileNew()
context.application.model.file_open("test/output/tmp.zml")
# Do some consistency tests on the connection scanner results:
for quality, transformation, pairs, inverse_pairs in context.application.model.folder.children[0].get_connections():
assert_arrays_almost_equal(transformation.r, rotation2.r)
assert len(pairs) >= 2
if len(inverse_pairs) > 0:
assert len(pairs) == len(inverse_pairs)
def fn():
context.application.model.file_open("test/input/core_objects.zml")
context.application.main.toggle_selection(context.application.model.universe.children[3], on=True)
parameters = Parameters()
parameters.rotation = Rotation.from_properties(1.0, numpy.array([0.1, 1.4, 0.3]), False)
RotateDialog = context.application.plugins.get_action("RotateDialog")
assert RotateDialog.analyze_selection(parameters)
RotateDialog(parameters)
def do_rotation(self, drawing_area, rotation_angle, rotation_axis):
camera = context.application.camera
# Note that the camera must be rotated in the opposite direction to
# let the scene rotate in the right direction.
rotation = Rotation.from_properties(-rotation_angle, rotation_axis,
False)
camera.rotation = camera.rotation * rotation
drawing_area.queue_draw()
def do_rotation(self, rotation_angle, rotation_axis):
rotation_axis = numpy.dot(self.eye_rotation, rotation_axis)
if self.rotation_axis is not None:
if numpy.dot(self.rotation_axis, rotation_axis) > 0:
rotation_axis = self.rotation_axis
else:
rotation_axis = -self.rotation_axis
rotation = Rotation.from_properties(rotation_angle, rotation_axis, False)
self.victim.set_transformation(self.rotation_center * (rotation * (self.rotation_center.inv * self.victim.transformation)))
context.application.main.drawing_area.queue_draw()
self.changed = True
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 test_pair_ego_precursor_rot():
geometry = Geometry(*get_precursor_model())
rot = Rotation.from_properties(-0.5*np.pi, [-1, 1, 0], False)
sender = Sender()
scanner = PairScanner(
send=sender,
geometry1=geometry,
geometry2=None,
action_radius=10.0,
hit_tolerance=0.1,
rotation2=rot,
)
scanner.run()
def do_rotation(self, rotation_angle, rotation_axis):
rotation_axis = numpy.dot(self.eye_rotation, rotation_axis)
if self.rotation_axis is not None:
if numpy.dot(self.rotation_axis, rotation_axis) > 0:
rotation_axis = self.rotation_axis
else:
rotation_axis = -self.rotation_axis
rotation = Rotation.from_properties(rotation_angle, rotation_axis,
False)
self.victim.set_transformation(
self.rotation_center *
(rotation *
(self.rotation_center.inv * self.victim.transformation)))
context.application.main.drawing_area.queue_draw()
self.changed = True
def test_pair_simple_rot():
geometry1 = Geometry(*get_simple_model1())
geometry2 = Geometry(*get_simple_model2())
rot = Rotation.from_properties(-0.5*np.pi, [0, 1, 0], False)
sender = Sender()
scanner = PairScanner(
send=sender,
geometry1=geometry1,
geometry2=geometry2,
action_radius=10.0,
hit_tolerance=0.1,
rotation2=rot,
)
scanner.run()
assert len(sender.connections) == 2
def default_parameters(cls):
rotation2 = Rotation.from_properties(0.0, [1, 0, 0], False)
result = Parameters()
result.connect_description1 = (Expression("True"), Expression("node.get_radius()"))
result.repulse_description1 = (Expression("True"), Expression("node.get_radius()"))
result.connect_description2 = (Expression("True"), Expression("node.get_radius()"))
result.repulse_description2 = (Expression("True"), Expression("node.get_radius()"))
result.action_radius = 7*angstrom
result.distance_tolerance = 0.1*angstrom
result.hit_tolerance = 0.1*angstrom
result.allow_inversions = True
result.minimum_triangle_size = 0.1*angstrom
result.rotation_tolerance = 0.05
result.rotation2 = Undefined(rotation2)
return result
def compute_transformations(self):
Scanner.compute_transformations(self)
if self.allow_inversions:
# derive the connections with inversion rotations, based on those
# without inversion rotations
new_connections = []
maximum = len(self.connections)
for progress, connection in enumerate(self.connections):
self.send(ProgressMessage("mirror", progress, maximum))
new = copy.deepcopy(connection)
mirror = (Translation(connection.triangle1.center) *
Rotation.from_properties(
numpy.pi, connection.triangle1.normal, True) *
Translation(-connection.triangle1.center))
new.set_transformation(mirror * new.transformation)
new_connections.append(new)
self.connections.extend(new_connections)
self.send(ProgressMessage("mirror", maximum, maximum))
def compute_transformations(self):
Scanner.compute_transformations(self)
if self.allow_inversions:
# derive the connections with inversion rotations, based on those
# without inversion rotations
new_connections = []
maximum = len(self.connections)
for progress, connection in enumerate(self.connections):
self.send(ProgressMessage("mirror", progress, maximum))
new = copy.deepcopy(connection)
mirror = (
Translation(connection.triangle1.center)
* Rotation.from_properties(numpy.pi, connection.triangle1.normal, True)
* Translation(-connection.triangle1.center)
)
new.set_transformation(mirror * new.transformation)
new_connections.append(new)
self.connections.extend(new_connections)
self.send(ProgressMessage("mirror", maximum, maximum))
def fn():
context.application.model.file_open("test/input/precursor.zml")
context.application.main.select_nodes(
context.application.model.universe.children)
ScanForConnections = context.application.plugins.get_action(
"ScanForConnections")
rotation2 = Rotation.from_properties(1 * numpy.pi, [0, 1, 0], False)
parameters = ScanForConnections.default_parameters()
parameters.connect_description1 = (
Expression(
"isinstance(node, Atom) and node.number == 8 and node.num_bonds() == 1"
),
Expression("node.get_radius()"),
)
parameters.repulse_description1 = (
Expression(
"isinstance(node, Atom) and (node.number == 8 or node.number == 14)"
),
Expression("node.get_radius()*1.5"),
)
parameters.action_radius = 4 * angstrom
parameters.hit_tolerance = 0.1 * angstrom
parameters.rotation2 = rotation2
assert ScanForConnections.analyze_selection(parameters)
ScanForConnections(parameters)
# Try to save the result to file an open it again.
context.application.model.file_save("test/output/tmp.zml")
FileNew = context.application.plugins.get_action("FileNew")
FileNew()
context.application.model.file_open("test/output/tmp.zml")
# Do some consistency tests on the connection scanner results:
for quality, transformation, pairs, inverse_pairs in context.application.model.folder.children[
0].get_connections():
assert_arrays_almost_equal(transformation.r, rotation2.r)
assert len(pairs) >= 2
if len(inverse_pairs) > 0:
assert len(pairs) == len(inverse_pairs)
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
num_hydrogens = self.parameters.num_hydrogens
if len(existing_bonds) == 0:
t = atom.transformation.t + numpy.array([0, bond_length, 0])
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_hydrogens -= 1
main_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
main_direction += shortest_vector
main_direction /= numpy.linalg.norm(main_direction)
normal = random_orthonormal(main_direction)
rotation = Rotation.from_properties(
2 * numpy.pi / float(num_hydrogens), main_direction, False)
h_pos = bond_length * (
main_direction * numpy.cos(self.parameters.valence_angle) +
normal * numpy.sin(self.parameters.valence_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def default_parameters(cls):
rotation2 = Rotation.from_properties(0.0, [1, 0, 0], False)
result = Parameters()
result.connect_description1 = (Expression("True"),
Expression("node.get_radius()"))
result.repulse_description1 = (Expression("True"),
Expression("node.get_radius()"))
result.connect_description2 = (Expression("True"),
Expression("node.get_radius()"))
result.repulse_description2 = (Expression("True"),
Expression("node.get_radius()"))
result.action_radius = 7 * angstrom
result.distance_tolerance = 0.1 * angstrom
result.hit_tolerance = 0.1 * angstrom
result.allow_inversions = True
result.minimum_triangle_size = 0.1 * angstrom
result.rotation_tolerance = 0.05
result.rotation2 = Undefined(rotation2)
return result
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
num_hydrogens = self.parameters.num_hydrogens
if len(existing_bonds) == 0:
t = atom.transformation.t + numpy.array([0,bond_length,0])
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_hydrogens -= 1
main_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
main_direction += shortest_vector
main_direction /= numpy.linalg.norm(main_direction)
normal = random_orthonormal(main_direction)
rotation = Rotation.from_properties(2*numpy.pi / float(num_hydrogens), main_direction, False)
h_pos = bond_length*(
main_direction*numpy.cos(self.parameters.valence_angle) +
normal*numpy.sin(self.parameters.valence_angle)
)
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def convert_to_value(self, representation):
properties = ComposedInTable.convert_to_value(self, representation)
return MathRotation.from_properties(*properties)
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
num_bonds = len(existing_bonds)
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
if num_bonds == 0:
t = atom.transformation.t + numpy.array([0, bond_length, 0])
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_bonds = 1
used_valence = 0
oposite_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
oposite_direction -= shortest_vector
if bond.bond_type == BOND_SINGLE:
used_valence += 1
elif bond.bond_type == BOND_DOUBLE:
used_valence += 2
elif bond.bond_type == BOND_TRIPLE:
used_valence += 3
oposite_direction /= numpy.linalg.norm(oposite_direction)
num_hydrogens = valence_el(
atom.number) - 2 * lone_pairs(atom.number) - used_valence
if num_hydrogens <= 0:
return
hybride_count = num_hydrogens + lone_pairs(
atom.number) + num_bonds - (used_valence - num_bonds)
num_sites = num_hydrogens + lone_pairs(atom.number)
rotation = Rotation.from_properties(
2 * numpy.pi / float(num_sites), oposite_direction, False)
opening_key = (hybride_count, num_sites)
opening_angle = self.opening_angles.get(opening_key)
if opening_angle is None:
return
if num_bonds == 1:
first_bond = existing_bonds[0]
other_atom = first_bond.children[0].target
if other_atom == atom:
other_atom = first_bond.children[1].target
other_bonds = [
bond for bond in other_atom.iter_bonds()
if bond != first_bond
]
if len(other_bonds) > 0:
normal = other_bonds[0].shortest_vector_relative_to(
atom.parent)
normal -= numpy.dot(normal,
oposite_direction) * oposite_direction
normal /= numpy.linalg.norm(normal)
if other_bonds[0].children[0].target == other_atom:
normal *= -1
else:
normal = random_orthonormal(oposite_direction)
elif num_bonds == 2:
normal = numpy.cross(
oposite_direction,
existing_bonds[0].shortest_vector_relative_to(atom.parent))
normal /= numpy.linalg.norm(normal)
elif num_bonds == 3:
normal = random_orthonormal(oposite_direction)
else:
return
h_pos = bond_length * (oposite_direction * numpy.cos(opening_angle)
+ normal * numpy.sin(opening_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def align_cell(self, lcs=None, swap=True):
"""Align the unit cell with respect to the Cartesian Axes frame
**Optional Arguments:**
lcs
The linear combinations of the unit cell that must get aligned.
This is a 2x3 array, where each row represents a linear
combination of cell vectors. The first row is for alignment with
the x-axis, second for the z-axis. The default value is::
np.array([
[1, 0, 0],
[0, 0, 1],
])
swap
By default, the first alignment is done with the z-axis, then
with the x-axis. The order is reversed when swap is set to
False.
The alignment of the first linear combination is always perfect. The
alignment of the second linear combination is restricted to a plane.
The cell is always made right-handed. The coordinates are also
rotated with respect to the origin, but never inverted.
The attributes of the system are modified in-place. Note that this
method only works on 3D periodic systems.
"""
from molmod import Rotation, deg
# define the target
target = np.array([
[1, 0, 0],
[0, 0, 1],
])
# default value for linear combination
if lcs is None:
lcs = target.copy()
# The starting values
pos = self.pos
rvecs = self.cell.rvecs.copy()
if rvecs.shape != (3, 3):
raise TypeError(
'The align_cell method only supports 3D periodic systems.')
# Optionally swap a cell vector if the cell is not right-handed.
if np.linalg.det(rvecs) < 0:
# Find a reasonable vector to swap...
index = rvecs.sum(axis=1).argmin()
rvecs[index] *= -1
# Define the source
source = np.dot(lcs, rvecs)
# Do the swapping
if swap:
target = target[::-1]
source = source[::-1]
# auxiliary function
def get_angle_axis(t, s):
cos = np.dot(s, t) / np.linalg.norm(s) / np.linalg.norm(t)
angle = np.arccos(np.clip(cos, -1, 1))
axis = np.cross(s, t)
return angle, axis
# first alignment
angle, axis = get_angle_axis(target[0], source[0])
if np.linalg.norm(axis) > 0:
r1 = Rotation.from_properties(angle, axis, False)
pos = r1 * pos
rvecs = r1 * rvecs
source = r1 * source
# second alignment
# Make sure the source is orthogonal to target[0]
s1p = source[1] - target[0] * np.dot(target[0], source[1])
angle, axis = get_angle_axis(target[1], s1p)
r2 = Rotation.from_properties(angle, axis, False)
pos = r2 * pos
rvecs = r2 * rvecs
# assign
self.pos = pos
self.cell = Cell(rvecs)
def align_cell(self, lcs=None, swap=True):
"""Align the unit cell with respect to the Cartesian Axes frame
**Optional Arguments:**
lcs
The linear combinations of the unit cell that must get aligned.
This is a 2x3 array, where each row represents a linear
combination of cell vectors. The first row is for alignment with
the x-axis, second for the z-axis. The default value is::
np.array([
[1, 0, 0],
[0, 0, 1],
])
swap
By default, the first alignment is done with the z-axis, then
with the x-axis. The order is reversed when swap is set to
False.
The alignment of the first linear combination is always perfect. The
alignment of the second linear combination is restricted to a plane.
The cell is always made right-handed. The coordinates are also
rotated with respect to the origin, but never inverted.
The attributes of the system are modified in-place. Note that this
method only works on 3D periodic systems.
"""
from molmod import Rotation, deg
# define the target
target = np.array([
[1, 0, 0],
[0, 0, 1],
])
# default value for linear combination
if lcs is None:
lcs = target.copy()
# The starting values
pos = self.pos
rvecs = self.cell.rvecs.copy()
if rvecs.shape != (3,3):
raise TypeError('The align_cell method only supports 3D periodic systems.')
# Optionally swap a cell vector if the cell is not right-handed.
if np.linalg.det(rvecs) < 0:
# Find a reasonable vector to swap...
index = rvecs.sum(axis=1).argmin()
rvecs[index] *= -1
# Define the source
source = np.dot(lcs, rvecs)
# Do the swapping
if swap:
target = target[::-1]
source = source[::-1]
# auxiliary function
def get_angle_axis(t, s):
cos = np.dot(s, t)/np.linalg.norm(s)/np.linalg.norm(t)
angle = np.arccos(np.clip(cos, -1, 1))
axis = np.cross(s, t)
return angle, axis
# first alignment
angle, axis = get_angle_axis(target[0], source[0])
if np.linalg.norm(axis) > 0:
r1 = Rotation.from_properties(angle, axis, False)
pos = r1*pos
rvecs = r1*rvecs
source = r1*source
# second alignment
# Make sure the source is orthogonal to target[0]
s1p = source[1] - target[0]*np.dot(target[0], source[1])
angle, axis = get_angle_axis(target[1], s1p)
r2 = Rotation.from_properties(angle, axis, False)
pos = r2*pos
rvecs = r2*rvecs
# assign
self.pos = pos
self.cell = Cell(rvecs)
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 compute_transformation(self, connection):
# print connection.pairs
triangle1 = connection.triangle1
triangle2 = connection.triangle2
triangles = [triangle1, triangle2]
# print "BEFORE TRANSFORMING\n"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# print "---------"
# *** t1: translation of triangle in geometry2 to origin
t1 = Translation(-triangle2.center)
# print triangle2.center
triangle2.apply_to_coordinates(t1)
# also move triangle1 to the origin
t_tmp = Translation(-triangle1.center) # was t0
triangle1.apply_to_coordinates(t_tmp)
# print "AFTER CENTERING (T1 and T0)"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# *** r2: make the two triangles coplanar
# print "NORMALS"
# print triangle1.normal
# print triangle2.normal
rotation_axis = numpy.cross(triangle2.normal, triangle1.normal)
if numpy.dot(rotation_axis, rotation_axis) < 1e-8:
rotation_axis = random_orthonormal(triangle2.normal)
rotation_angle = angle(triangle2.normal, triangle1.normal)
# print "R2 %s, %s" % (rotation_angle/numpy.pi*180, rotation_axis)
r2 = Rotation.from_properties(rotation_angle, rotation_axis, False)
triangle2.apply_to_coordinates(r2)
# print "AFTER R2"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# bring both triangles in the x-y plane, by a rotation around an axis
# orthogonal to the Z-axis.
rotation_axis = numpy.array([triangle1.normal[1], -triangle1.normal[0], 0.0], float)
if numpy.dot(rotation_axis, rotation_axis) < 1e-8:
rotation_axis = numpy.array([1.0, 0.0, 0.0], float)
cos_angle = triangle1.normal[2]
if cos_angle >= 1.0:
rotation_angle = 0
elif cos_angle <= -1.0:
rotation_angle = numpy.pi
else:
rotation_angle = numpy.arccos(cos_angle)
# print "RT %s, %s" % (rotation_angle/numpy.pi*180, rotation_axis)
r_flat = Rotation.from_properties(rotation_angle, rotation_axis, False)
triangle1.apply_to_coordinates(r_flat)
triangle2.apply_to_coordinates(r_flat)
# print "AFTER RT"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# *** r3: second rotation that makes both triangle coinced
H = lambda a, b, c, d: a * c + b * d + (a + b) * (c + d)
c = H(
triangle1.coordinates[0][0],
triangle1.coordinates[1][0],
triangle2.coordinates[0][0],
triangle2.coordinates[1][0],
) + H(
triangle1.coordinates[0][1],
triangle1.coordinates[1][1],
triangle2.coordinates[0][1],
triangle2.coordinates[1][1],
)
s = H(
triangle1.coordinates[0][1],
triangle1.coordinates[1][1],
triangle2.coordinates[0][0],
triangle2.coordinates[1][0],
) - H(
triangle1.coordinates[0][0],
triangle1.coordinates[1][0],
triangle2.coordinates[0][1],
triangle2.coordinates[1][1],
)
# if c > s: c, s = -c, -s
# print "cos=%f sin=%f" % (c, s)
rotation_angle = numpy.arctan2(s, c)
# print "R3 %s, %s" % (rotation_angle/numpy.pi*180, triangle1.normal)
r3 = Rotation.from_properties(rotation_angle, triangle1.normal, False)
r_tmp = Rotation.from_properties(rotation_angle, numpy.array([0, 0, 1], float), False)
triangle2.apply_to_coordinates(r_tmp)
# print "AFTER R3"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# t4: translate the triangle to the definitive coordinate
t4 = Translation(triangle1.center)
# print "AFTER T4"
# for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
return t4 * r3 * r2 * t1
def compute_transformation(self, connection):
#print connection.pairs
triangle1 = connection.triangle1
triangle2 = connection.triangle2
triangles = [triangle1, triangle2]
#print "BEFORE TRANSFORMING\n"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
#print "---------"
# *** t1: translation of triangle in geometry2 to origin
t1 = Translation(-triangle2.center)
#print triangle2.center
triangle2.apply_to_coordinates(t1)
# also move triangle1 to the origin
t_tmp = Translation(-triangle1.center) # was t0
triangle1.apply_to_coordinates(t_tmp)
#print "AFTER CENTERING (T1 and T0)"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# *** r2: make the two triangles coplanar
#print "NORMALS"
#print triangle1.normal
#print triangle2.normal
rotation_axis = numpy.cross(triangle2.normal, triangle1.normal)
if numpy.dot(rotation_axis, rotation_axis) < 1e-8:
rotation_axis = random_orthonormal(triangle2.normal)
rotation_angle = angle(triangle2.normal, triangle1.normal)
#print "R2 %s, %s" % (rotation_angle/numpy.pi*180, rotation_axis)
r2 = Rotation.from_properties(rotation_angle, rotation_axis, False)
triangle2.apply_to_coordinates(r2)
#print "AFTER R2"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# bring both triangles in the x-y plane, by a rotation around an axis
# orthogonal to the Z-axis.
rotation_axis = numpy.array(
[triangle1.normal[1], -triangle1.normal[0], 0.0], float)
if numpy.dot(rotation_axis, rotation_axis) < 1e-8:
rotation_axis = numpy.array([1.0, 0.0, 0.0], float)
cos_angle = triangle1.normal[2]
if cos_angle >= 1.0: rotation_angle = 0
elif cos_angle <= -1.0: rotation_angle = numpy.pi
else: rotation_angle = numpy.arccos(cos_angle)
#print "RT %s, %s" % (rotation_angle/numpy.pi*180, rotation_axis)
r_flat = Rotation.from_properties(rotation_angle, rotation_axis, False)
triangle1.apply_to_coordinates(r_flat)
triangle2.apply_to_coordinates(r_flat)
#print "AFTER RT"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# *** r3: second rotation that makes both triangle coinced
H = lambda a, b, c, d: a * c + b * d + (a + b) * (c + d)
c = (H(triangle1.coordinates[0][0], triangle1.coordinates[1][0],
triangle2.coordinates[0][0], triangle2.coordinates[1][0]) +
H(triangle1.coordinates[0][1], triangle1.coordinates[1][1],
triangle2.coordinates[0][1], triangle2.coordinates[1][1]))
s = (H(triangle1.coordinates[0][1], triangle1.coordinates[1][1],
triangle2.coordinates[0][0], triangle2.coordinates[1][0]) -
H(triangle1.coordinates[0][0], triangle1.coordinates[1][0],
triangle2.coordinates[0][1], triangle2.coordinates[1][1]))
#if c > s: c, s = -c, -s
#print "cos=%f sin=%f" % (c, s)
rotation_angle = numpy.arctan2(s, c)
#print "R3 %s, %s" % (rotation_angle/numpy.pi*180, triangle1.normal)
r3 = Rotation.from_properties(rotation_angle, triangle1.normal, False)
r_tmp = Rotation.from_properties(rotation_angle,
numpy.array([0, 0, 1], float), False)
triangle2.apply_to_coordinates(r_tmp)
#print "AFTER R3"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
# t4: translate the triangle to the definitive coordinate
t4 = Translation(triangle1.center)
#print "AFTER T4"
#for triangle in triangles:
# #print "-------"
# for coordinate in triangle.coordinates:
# #print coordinate
return t4 * r3 * r2 * t1
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 convert_to_value(self, representation):
properties = ComposedInTable.convert_to_value(self, representation)
return MathRotation.from_properties(*properties)
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
num_bonds = len(existing_bonds)
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
if num_bonds == 0:
t = atom.transformation.t + numpy.array([0,bond_length,0])
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_bonds = 1
used_valence = 0
oposite_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
oposite_direction -= shortest_vector
if bond.bond_type == BOND_SINGLE:
used_valence += 1
elif bond.bond_type == BOND_DOUBLE:
used_valence += 2
elif bond.bond_type == BOND_TRIPLE:
used_valence += 3
oposite_direction /= numpy.linalg.norm(oposite_direction)
num_hydrogens = valence_el(atom.number) - 2*lone_pairs(atom.number) - used_valence
if num_hydrogens <= 0:
return
hybride_count = num_hydrogens + lone_pairs(atom.number) + num_bonds - (used_valence - num_bonds)
num_sites = num_hydrogens + lone_pairs(atom.number)
rotation = Rotation.from_properties(2*numpy.pi / float(num_sites), oposite_direction, False)
opening_key = (hybride_count, num_sites)
opening_angle = self.opening_angles.get(opening_key)
if opening_angle is None:
return
if num_bonds == 1:
first_bond = existing_bonds[0]
other_atom = first_bond.children[0].target
if other_atom == atom:
other_atom = first_bond.children[1].target
other_bonds = [bond for bond in other_atom.iter_bonds() if bond != first_bond]
if len(other_bonds) > 0:
normal = other_bonds[0].shortest_vector_relative_to(atom.parent)
normal -= numpy.dot(normal, oposite_direction) * oposite_direction
normal /= numpy.linalg.norm(normal)
if other_bonds[0].children[0].target == other_atom:
normal *= -1
else:
normal = random_orthonormal(oposite_direction)
elif num_bonds == 2:
normal = numpy.cross(oposite_direction, existing_bonds[0].shortest_vector_relative_to(atom.parent))
normal /= numpy.linalg.norm(normal)
elif num_bonds == 3:
normal = random_orthonormal(oposite_direction)
else:
return
h_pos = bond_length*(oposite_direction*numpy.cos(opening_angle) + normal*numpy.sin(opening_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
