mdtraj.geometry.squareform¶

mdtraj.geometry.squareform(distances, residue_pairs)¶

Reshape the contact distance to square contact maps

Parameters

distancesnp.ndarray, shape=(n_frames, n_pairs): Distances between pairs of residues, as computed by mdtraj.geometry.compute_contacts.
residue_pairsnp.ndarray, shape=(n_pairs, 2): The indices of the residues involved in each pair, as returned by mdtraj.geometry.compute_contacts

Returns

contact_mapsnp.ndarray, shape=(n_frames, n_residues, n_residues): Reshaped version of distances, such that the distance, in the k`th frame of the trajectory from residue `i to residue j is given by contact_maps[k, i, j]. All entries in contact_maps corresponding to the distance between residues that were not part of residue_pairs are 0.0.