spyrmsd.graph module

spyrmsd.graph.adjacency_matrix_from_atomic_coordinates(aprops: ndarray, coordinates: ndarray) → ndarray

Compute adjacency matrix from atomic coordinates.

Parameters

• aprops (numpy.ndarray) – Atomic properties

• coordinates (numpy.ndarray) – Atomic coordinates

Returns

Adjacency matrix

Return type

numpy.ndarray

Notes

This function is based on an automatic bond perception algorithm: two atoms are considered to be bonded when their distance is smaller than the sum of their covalent radii plus a tolerance value. 3

Warning

The automatic bond perceptron rule implemented in this functions is very simple and only depends on atomic coordinates. Use with care!

3

E. C. Meng and R. A. Lewis, Determination of molecular topology and atomic hybridization states from heavy atom coordinates, J. Comp. Chem. 12, 891-898 (1991).