peppr.find_all_matches

peppr.find_all_matches(reference: AtomArray, pose: AtomArray, min_sequence_identity: float = 0.95) → Iterator[tuple[ndarray[tuple[Any, ...], dtype[int64]], ndarray[tuple[Any, ...], dtype[int64]]]]

Find all possible atom mappings between the reference and the pose.

Each mappings gives corresponding atoms between the reference and the pose.

Parameters:

referenceAtomArray, shape=(p,)

The reference structure.

poseAtomArray, shape=(q,)

The pose structure.

min_sequence_identityfloat

The minimum sequence identity between two chains to be considered the same entity.

Yields:

list of tuple (np.ndarray, shape=(n,), dtype=int)

Atom indices that, when applied to the reference and pose, respectively, yield the corresponding atoms.

Notes

This functions tries all chain mappings of chain that are the same entity and within each small molecules tries all proper molecule permutations. For larger homomers this can quickly lead to a combinatorial explosion.