# Analysis Reference¶

Trajectory analysis is the heart of MDTraj. These functions can be used to run a variety of analyses on mdtraj.Trajectory objects. It’s usually as simple as

>>> import mdtraj as md
>>> print(md.compute_phi(t))


## Root-mean-square deviation (RMSD)¶

 rmsd(target, reference[, frame, …]) Compute RMSD of all conformations in target to a reference conformation. rmsf(target, reference[, frame, …]) Compute RMSF 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(self, reference[, …]) Superpose each conformation in this trajectory upon a reference

## Hydrogen Bonding¶

 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, …]) Identify hydrogen bonds based on cutoffs for the Donor-H…Acceptor distance and angle according to the criterion outlined in .

## Secondary Structure¶

 compute_dssp(traj[, simplified]) Compute Dictionary of protein secondary structure (DSSP) secondary structure assignments

## Shape Metrics¶

 Compute the gyration tensor of a trajectory. Compute the principal moments of a trajectory. asphericity(traj) Compute the asphericity of a trajectory. acylindricity(traj) Compute the acylindricity of a trajectory. Compute the acylindricity of a trajectory.

## Surface Area, Radius of Gyration and Inertia¶

 shrake_rupley(traj[, probe_radius, …]) Compute the solvent accessible surface area of each atom or residue in each simulation frame. compute_rg(traj[, masses]) Compute the radius of gyration for every frame. Compute the inertia tensor of a trajectory.

## Distances¶

 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_neighbors(traj, cutoff, query_indices) Find (spatially) neighboring atoms in 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 of an MD trajectory Compute the center of mass for each frame. geometry.squareform(distances, residue_pairs) Reshape the contact distance to square contact maps compute_rdf(traj, pairs[, r_range, …]) Compute radial distribution functions for pairs in every frame.

## Bond Angles and Dihedrals¶

 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.

## NMR Observables¶

 compute_J3_HN_C(traj[, model]) Calculate the scalar coupling between HN and C_prime. compute_J3_HN_CB(traj[, model]) Calculate the scalar coupling between HN and C_beta. compute_J3_HN_HA(traj[, model]) Calculate the scalar coupling between HN and H_alpha. chemical_shifts_shiftx2(trj[, pH, temperature]) Predict chemical shifts of a trajectory using ShiftX2. Predict chemical shifts of a trajectory using ppm. chemical_shifts_spartaplus(trj[, rename_HN]) Predict chemical shifts of a trajectory using SPARTA+. reindex_dataframe_by_atoms(trj, frame) Reindex chemical shift output to use atom number (serial) indexing.

## Thermodynamic Quantities¶

 dipole_moments(traj, charges) Calculate the dipole moments of each frame in a trajectory. static_dielectric(traj, charges, temperature) Calculate the static dielectric constant from a trajectory. Calculate the isothermal compressability. thermal_expansion_alpha_P(traj, temperature, …) Calculate the thermal expansion coefficient. density(traj[, masses]) Calculate the mass density of each frame in a trajectory.

## Order Parameters¶

 compute_nematic_order(traj[, indices]) Compute the nematic order parameter of a group in every frame. compute_directors(traj[, indices]) Compute the characteristic vector describing the orientation of each group