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. |
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 |
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 |
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 |
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 |