mdtraj.geometry.squareform

mdtraj.geometry.squareform(distances, residue_pairs)[source]

Reshape the contact distance to square contact maps

Parameters:
  • distances (np.ndarray, shape=(n_frames, n_pairs)) – Distances between pairs of residues, as computed by mdtraj.geometry.compute_contacts.

  • residue_pairs (np.ndarray, shape=(n_pairs, 2)) – The indices of the residues involved in each pair, as returned by mdtraj.geometry.compute_contacts

Returns:

contact_maps – 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.

Return type:

np.ndarray, shape=(n_frames, n_residues, n_residues)

See also

mdtraj.compute_contacts

Compute the array of contact distances