| rmsd(target, reference[, frame, ...]) | Compute RMSD of all conformations in target to a reference conformation. |
| lprmsd(target, reference[, frame, ...]) | Compute Linear-Programming Root-Mean-Squared Deviation (LP-RMSD) of all conformations in target to a reference conformation. |
| Trajectory.superpose(reference[, frame, ...]) | Superpose each conformation in this trajectory upon a reference |
| 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. |
| wernet_nilsson(traj[, exclude_water, periodic]) | Identify hydrogen bonds based on cutoffs for the Donor-H...Acceptor distance and angle according to the criterion outlined in [1]. |
| shrake_rupley(traj[, probe_radius, ...]) | Compute the solvent accessible surface area of each atom in each simulation frame. |
| compute_rg(traj[, masses]) | Compute the radius of gyration for every frame. |
| compute_distances(traj, atom_pairs[, ...]) | Compute the distances between pairs of atoms in each frame. |
| compute_displacements(traj, atom_pairs[, ...]) | Compute the displacement vector between pairs of atoms in each frame of a trajectory. |
| compute_contacts(traj[, contacts, scheme, ...]) | Compute the distance between pairs of residues in a trajectory. |
| compute_drid(traj[, atom_indices]) | Distribution of reciprocal interatomic distances (DRID) representation |
| compute_center_of_mass(traj) | Compute the center of mass for each frame. |
| geometry.squareform(distances, residue_pairs) | Reshape the contact distance to square contact maps |
| compute_angles(traj, angle_indices[, ...]) | Compute the bond angles between the supplied triplets of indices in each frame of a trajectory. |
| compute_dihedrals(traj, indices[, periodic, opt]) | Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory. |
| compute_phi(traj[, periodic, opt]) | Calculate the phi torsions of a trajectory. |
| compute_psi(traj[, periodic, opt]) | Calculate the psi torsions of a trajectory. |
| compute_chi1(traj[, periodic, opt]) | Calculate the chi1 torsions of a trajectory. |
| compute_chi2(traj[, periodic, opt]) | Calculate the chi2 torsions of a trajectory. |
| compute_chi3(traj[, periodic, opt]) | Calculate the chi3 torsions of a trajectory. |
| compute_chi4(traj[, periodic, opt]) | Calculate the chi4 torsions of a trajectory. |
| compute_omega(traj[, periodic, opt]) | Calculate the omega torsions of a trajectory. |
| chemical_shifts_shiftx2(trj) | Predict chemical shifts of a trajectory using ShiftX2. |
| chemical_shifts_ppm(trj) | Predict chemical shifts of a trajectory using ppm. |
| chemical_shifts_spartaplus(trj) | Predict chemical shifts of a trajectory using SPARTA+. |
| reindex_dataframe_by_atoms(trj, frame) | Reindex chemical shift output to use atom number (serial) indexing. |