| rmsd(target, reference[, frame, ...]) | Compute RMSD of all conformations in target to a reference conformation. |
| baker_hubbard(traj[, freq, exclude_water]) | Identify hydrogen bonds based on cutoffs for the Donor-H...Acceptor distance and angle. |
| kabsch_sander(traj) | Compute the Kabsch-Sander hydrogen bond energy between each pair of residues in every frame. |
| shrake_rupley(traj[, probe_radius, ...]) | Compute the solvent accessible surface area of each atom in each simulation frame. |
| compute_distances(traj, atom_pairs[, ...]) | Compute the distances between pairs of atoms in each frame. |
| compute_contacts(traj[, contacts, scheme, ...]) | Compute the distance between pairs of residues in a trajectory. |
| geometry.squareform(distances, residue_pairs) | Reshape the contact distance to square contact maps |
| compute_displacements(traj, atom_pairs[, ...]) | Compute the displacement vector between pairs of atoms in each frame of a trajectory. |
| compute_angles(traj, angle_indices[, opt]) | Compute the bond angles between the supplied triplets of indices in each frame of a trajectory. |
| compute_dihedrals(traj, indices[, opt]) | Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory. |
| compute_phi(traj[, opt]) | Calculate the phi torsions of a trajectory. |
| compute_psi(traj[, opt]) | Calculate the psi torsions of a trajectory. |
| compute_chi1(traj[, opt]) | Calculate the chi1 torsions of a trajectory. |
| compute_chi2(traj[, opt]) | Calculate the chi2 torsions of a trajectory. |
| compute_chi3(traj[, opt]) | Calculate the chi3 torsions of a trajectory. |
| compute_chi4(traj[, opt]) | Calculate the chi4 torsions of a trajectory. |
| compute_omega(traj[, opt]) | Calculate the omega torsions of a trajectory. |
| compute_rg(traj[, masses]) | Compute the radius of gyration for every frame. |