rdkit_utilities.utilities

rdkit_utilities.utilities.compute_atom_distance_matrix(coordinates)[source]

Compute atom-to-atom distance for each conformer

Parameters: coordinates (numpy.ndarray) – 3D matrix of coordinates, with shape (n_conformers, n_atoms, 3)
Returns: distances – 3D matrix of distances, with shape (n_conformers, n_atoms, n_atoms)
Return type: numpy.ndarray
Parameters: coordinates (ndarray) –

rdkit_utilities.utilities.get_maximally_diverse_indices(distance_matrix, distance_threshold=0.05, n_indices=None)[source]

Greedily select maximally diverse indices from distance_matrix

Parameters

distance_matrix (numpy.ndarray) – 2D square distance matrix with shape (n_items, n_items)
distance_threshold (float) – If any item is below this threshold to any other item, they are considered too similar and only one will be included in the output
n_indices (int) – Number of items to output

Returns

indices – List of indices of maximally diverse items.

Return type

List[int]

Parameters