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 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 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 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 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 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
