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