mbuild_polybuild.aa_functional_groups.tmstb.TMSTB.from_trajectory

TMSTB.from_trajectory(traj, frame=-1, coords_only=False, infer_hierarchy=True)

Extract atoms and bonds from a md.Trajectory.

Will create sub-compounds for every chain if there is more than one and sub-sub-compounds for every residue.

Parameters:

• traj (mdtraj.Trajectory) – The trajectory to load.

• frame (int, optional, default=-1 (last)) – The frame to take coordinates from.

• coords_only (bool, optional, default=False) – Only read coordinate information

• infer_hierarchy (bool, optional, default=True) – If True, infer compound hierarchy from chains and residues

See also

mbuild.conversion.from_trajectory