def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2 = self.hinge_atoms
direction = coordinates[atom1] - coordinates[atom2]
direction /= np.linalg.norm(direction)
direction *= np.random.uniform(-self.max_amplitude, self.max_amplitude)
result = Translation(direction)
return result
def get_transformation(self, molecule):
atom1, atom2 = self.hinge_atoms
direction = molecule.coordinates[atom1] - molecule.coordinates[atom2]
direction /= numpy.linalg.norm(direction)
direction *= numpy.random.uniform(-self.max_amplitude,
self.max_amplitude)
result = Translation()
result.t[:] = direction
return result
def get_transformation(self, coordinates):
"""Construct a transformation object"""
atom1, atom2, atom3, atom4 = self.hinge_atoms
a = coordinates[atom1] - coordinates[atom2]
a /= np.linalg.norm(a)
b = coordinates[atom3] - coordinates[atom4]
b /= np.linalg.norm(b)
direction = 0.5 * (a + b)
direction *= np.random.uniform(-self.max_amplitude, self.max_amplitude)
result = Translation(direction)
return result
def get_transformation(self, molecule):
atom1, atom2, atom3, atom4 = self.hinge_atoms
a = molecule.coordinates[atom1] - molecule.coordinates[atom2]
a /= numpy.linalg.norm(a)
b = molecule.coordinates[atom3] - molecule.coordinates[atom4]
b /= numpy.linalg.norm(b)
direction = 0.5 * (a + b)
direction *= numpy.random.uniform(-self.max_amplitude,
self.max_amplitude)
result = Translation()
result.t[:] = direction
return result
def randomize(self, center):
self.transform(Translation(-np.array(center)))
self.transform(Rotation.random())
self.transform(Translation(center))
def rotate(self, center, axis, angle):
self.transform(Translation(-np.array(center)))
self.transform(Rotation.from_properties(angle, axis, invert=False))
self.transform(Translation(center))
def translate(self, vector):
self.transform(Translation(vector))
