4. scoria.Geometry module

class scoria.Geometry.Geometry(parent_molecule_object)

A class containing a few geometry functions. Note that numpy should be used for most geometry functions.

get_angle_between_three_points(pt1, pt2, pt3)

Computes the angle (in radians) formed by three points (numpy.array objects).

Should be called via the wrapper function get_angle_between_three_points()

Parameters:

• pt1 (numpy.array) – A numpy.array (x, y, z) representing the first of the three 3D points.
• pt2 (numpy.array) – A numpy.array (x, y, z) representing the second of the three 3D points.
• pt3 (numpy.array) – A numpy.array (x, y, z) representing the third of the three 3D points.

Returns:

A float containing the angle between the three points, in radians.

get_dihedral_angle(pt1, pt2, pt3, pt4)

Calculates the dihedral angle formed by four points (numpy.array objects).

Should be called via the wrapper function get_dihedral_angle()

Parameters:

• pt1 (numpy.array) – A numpy.array (x, y, z) representing the first 3D point.
• pt2 (numpy.array) – A numpy.array (x, y, z) representing the second 3D point.
• pt3 (numpy.array) – A numpy.array (x, y, z) representing the third 3D point.
• pt4 (numpy.array) – A numpy.array (x, y, z) representing the fourth 3D point.

Returns:

A float containing the dihedral angle between the four points, in radians.

get_planarity_deviation(pt1, pt2, pt3, pt4)

Determines how close four points (numpy.array objects) come to lying in a common plane.

Should be called via the wrapper function get_planarity_deviation()

Parameters:

• pt1 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt2 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt3 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt4 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.

Returns:

A float, the minimum distance between one point and the plane formed by the other three.

is_planar(pt1, pt2, pt3, pt4, planarity_cutoff=0.2)

Checks whether four points (numpy.array) lie in a common plane.

Should be called via the wrapper function is_planar()

Parameters:

• pt1 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt2 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt3 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• pt4 (numpy.array) – A numpy.array (x, y, z) representing a 3D point.
• planarity_cutoff (float) – An optional float. How much the points can deviate (in Angstroms) and still be considered planar. The default is 0.2.

Returns:

A boolean, whether the 4 points can be considered planar.