Geometry Utilities#

cgbind.geom.calc_com(atoms)#

Calculate the centre of mass for a list of xyzs

Parameters:

atoms – (list(cgbind.atoms.Atom))

Returns:

(np.ndarray) shape: 3

cgbind.geom.calc_normalised_vector(coord1, coord2)#
cgbind.geom.is_geom_reasonable(molecule)#

For an xyz list check to ensure the geometry is sensible, before an optimisation is carried out. There should be no distances smaller than

0.7 Å

Parameters:

molecule – (cgbind.molecule.BaseStruct)

Returns:

(bool)

cgbind.geom.rotation_matrix(axis, theta)#

Return the rotation matrix associated with counterclockwise rotation about the given axis by theta radians.

Parameters:

  • axis – (np.ndarray) Unit vector in 3D to rotate around

  • theta – (float) Angle in radians

cgbind.geom.get_rot_mat_kabsch(p_matrix, q_matrix)#

Get the optimal rotation matrix with the Kabsch algorithm. Notation is from https://en.wikipedia.org/wiki/Kabsch_algorithm

Parameters:

  • p_matrix – (np.ndarray)

  • q_matrix – (np.ndarray)

Returns:

(np.ndarray) rotation matrix

cgbind.geom.get_centered_matrix(mat)#

For a list of coordinates n.e. a n_atoms x 3 matrix as a np array translate to the center of the coordinates

Parameters:

mat – (np.ndarray)

Returns:

(np.ndarray) translated coordinates

cgbind.geom.spherical_to_cart(r, theta, phi)#