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.

principal_moments(traj)

Compute the principal moments of a trajectory.

asphericity(traj)

Compute the asphericity of a trajectory.

acylindricity(traj)

Compute the acylindricity of a trajectory.

relative_shape_antisotropy(traj)

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_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