def do(self):
for key, val in self.parameters.__dict__.iteritems():
if isinstance(val, Expression):
val.compile_as("<%s>" % key)
val.variables = (key[7:11], )
parent = context.application.cache.common_parent
if parent is None:
parent = context.application.model.universe
angles = []
graph = create_molecular_graph(context.application.cache.nodes)
match_definition = BendingAnglePattern(criteria_sets=[
CriteriaSet(
thing_criteria={
0: IndexToAtoms(self.parameters.filter_atom1),
1: IndexToAtoms(self.parameters.filter_atom2),
2: IndexToAtoms(self.parameters.filter_atom3),
},
relation_criteria={
0: IndexToBonds(self.parameters.filter_bond12),
1: IndexToBonds(self.parameters.filter_bond23),
},
)
], )
try:
atoms = graph.molecule.atoms
match_generator = GraphSearch(match_definition)
for match in match_generator(graph):
point1 = atoms[match.forward[0]].get_absolute_frame().t
point2 = atoms[match.forward[1]].get_absolute_frame().t
point3 = atoms[match.forward[2]].get_absolute_frame().t
delta1 = parent.shortest_vector(point2 - point1)
delta2 = parent.shortest_vector(point2 - point3)
if numpy.linalg.norm(delta1) > 1e-8 and \
numpy.linalg.norm(delta2) > 1e-8:
angles.append(angle(delta1, delta2))
except:
raise UserError(
"An error occured while sampling the bending angles.",
"If this is an error in one of the filter expressions,\n" +
"one should see the expression mentioned below as <filter_...>.\n\n"
)
comments = [
"atom 1 filter expression: %s" % self.parameters.filter_atom1.code,
"bond 1-2 filter expression: %s" %
self.parameters.filter_bond12.code,
"atom 2 filter expression: %s" % self.parameters.filter_atom2.code,
"bond 2-3 filter expression: %s" %
self.parameters.filter_bond23.code,
"atom 3 filter expression: %s" % self.parameters.filter_atom3.code,
]
if len(angles) > 0:
distribution_dialog = DistributionDialog()
distribution_dialog.run(numpy.array(angles), "Angle",
"Bending angle", comments)
else:
raise UserError("No bending angles match the given criteria.")
def express_out_of_plane_angle(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(
self.vectors[index4] - self.vectors[index3],
self.vectors[index2] - self.vectors[index3]
)
return express_measure(0.5*numpy.pi - angle(normal, delta), measure="Angle")
def do(self):
for key, val in self.parameters.__dict__.iteritems():
if isinstance(val, Expression):
val.compile_as("<%s>" % key)
val.variables = (key[7:11],)
parent = context.application.cache.common_parent
if parent is None:
parent = context.application.model.universe
angles = []
graph = create_molecular_graph(context.application.cache.nodes)
match_definition = BendingAnglePattern(
criteria_sets=[CriteriaSet(
thing_criteria={
0: IndexToAtoms(self.parameters.filter_atom1),
1: IndexToAtoms(self.parameters.filter_atom2),
2: IndexToAtoms(self.parameters.filter_atom3),
},
relation_criteria={
0: IndexToBonds(self.parameters.filter_bond12),
1: IndexToBonds(self.parameters.filter_bond23),
},
)],
)
try:
atoms = graph.molecule.atoms
match_generator = GraphSearch(match_definition)
for match in match_generator(graph):
point1 = atoms[match.forward[0]].get_absolute_frame().t
point2 = atoms[match.forward[1]].get_absolute_frame().t
point3 = atoms[match.forward[2]].get_absolute_frame().t
delta1 = parent.shortest_vector(point2 - point1)
delta2 = parent.shortest_vector(point2 - point3)
if numpy.linalg.norm(delta1) > 1e-8 and \
numpy.linalg.norm(delta2) > 1e-8:
angles.append(angle(delta1, delta2))
except:
raise UserError(
"An error occured while sampling the bending angles.",
"If this is an error in one of the filter expressions,\n" +
"one should see the expression mentioned below as <filter_...>.\n\n"
)
comments = [
"atom 1 filter expression: %s" % self.parameters.filter_atom1.code,
"bond 1-2 filter expression: %s" % self.parameters.filter_bond12.code,
"atom 2 filter expression: %s" % self.parameters.filter_atom2.code,
"bond 2-3 filter expression: %s" % self.parameters.filter_bond23.code,
"atom 3 filter expression: %s" % self.parameters.filter_atom3.code,
]
if len(angles) > 0:
distribution_dialog = DistributionDialog()
distribution_dialog.run(numpy.array(angles), "Angle", "Bending angle", comments)
else:
raise UserError("No bending angles match the given criteria.")
def express_dihedral_angle(index1, index2, index3, index4):
normal1 = numpy.cross(
self.vectors[index1] - self.vectors[index2],
self.vectors[index3] - self.vectors[index2]
)
normal2 = numpy.cross(
self.vectors[index2] - self.vectors[index3],
self.vectors[index4] - self.vectors[index3]
)
return express_measure(angle(normal1, normal2), measure="Angle")
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 express_out_of_plane_angle(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(self.vectors[index4] - self.vectors[index3],
self.vectors[index2] - self.vectors[index3])
return express_measure(0.5 * numpy.pi - angle(normal, delta),
measure="Angle")
def express_dihedral_angle(index1, index2, index3, index4):
normal1 = numpy.cross(self.vectors[index1] - self.vectors[index2],
self.vectors[index3] - self.vectors[index2])
normal2 = numpy.cross(self.vectors[index2] - self.vectors[index3],
self.vectors[index4] - self.vectors[index3])
return express_measure(angle(normal1, normal2), measure="Angle")
def express_angle(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index2]
return express_measure(angle(delta1, delta2), measure="Angle")
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 express_angle(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index2]
return express_measure(angle(delta1, delta2), measure="Angle")