mdtraj.chemical_shifts_spartaplus

mdtraj.chemical_shifts_spartaplus(trj, rename_HN=True)

Predict chemical shifts of a trajectory using SPARTA+.

Parameters

trjTrajectory

Trajectory to predict shifts for.

rename_HNbool, optional, default=True

SPARTA+ calls the amide proton “HN” instead of the standard “H”. When True, this option renames the output as “H” to match the PDB and BMRB nomenclature.

Returns

resultspandas.DataFrame

Dataframe containing results, with index consisting of (resSeq, atom_name) pairs and columns for each frame in trj.

Notes

You must have SPARTA+ available on your path; see (http://spin.niddk.nih.gov/bax/software/SPARTA+/). Also, the SPARTAP_DIR environment variable must be set so that SPARTA+ knows where to find its database files.

Chemical shift prediction is for PROTEIN atoms; trajectory objects with ligands, solvent, ions, or other non-protein components may give UNKNOWN RESULTS.

Please cite the appropriate reference below.

References

1

Shen, Y., and Bax, Ad. “SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network.” J. Biomol. NMR, 48, 13-22 (2010)