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
>>> t = md.load('trajectory.pdb')
>>> 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 [1].

Secondary Structure¶

compute_dssp(traj[, simplified])

Compute Dictionary of protein secondary structure (DSSP) secondary structure assignments

Shape Metrics¶

compute_gyration_tensor(traj)

Compute the gyration tensor 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_inertia_tensor`(traj)	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_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_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.
`chemical_shifts_ppm`(trj)	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.
`isothermal_compressability_kappa_T`(traj, …)	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