geometry_analysis package

Submodules

geometry_analysis.measure module

measure.py A python package for the MolSSI Software Summer School. Contains a functions for measuring bonds and angles.

geometry_analysis.measure.calculate_angle(rA, rB, rC, degrees=False)

Calculate angle between points A, B, and C

Parameters

• rA (numpy array) – The x, y, z coordinates of point A

• rB (numpy array) – The x, y, z coordinates of point B

• degrees (bool, optional) – Return the calculated angle in degrees.

Returns

angle – The distance between points A and B.

Return type

float

geometry_analysis.measure.calculate_distance(rA, rB)

Calculate the distance between points A and B.

Parameters

• rA (numpy array) – The x, y, z coordinates of point A

• rB (numpy array) – The x, y, z coordinates of point B

Returns

distance – The distance between points A and B.

Return type

float

Examples

>>> r1 = np.array([0, 0, 0])
>>> r2 = np.array([0, 0.1, 0])
>>> calculate_distance(r1, r2)
0.1

geometry_analysis.molecule module

molecule.py A python package for the MolSSI Software Summer School. Contains a molecule class

class geometry_analysis.molecule.Molecule(name, symbols, coordinates)

Bases: object

build_bond_list(max_bond=2.93, min_bond=0)

Build a list of bonds based on a distance criteria. Atoms within a specified distance of one another will be considered bonded. :param max_bond: :type max_bond: float, optional :param min_bond: :type min_bond: float, optional

Returns

bond_list – List of bonded atoms. Returned as list of tuples where the values are the atom indices.

Return type

list

property coordinates

property num_atoms

Module contents

geometry_analysis A python package for the MolSSI Software Summer School.