mdtraj.chemical_shifts_spartaplus

mdtraj.chemical_shifts_spartaplus(trj, rename_HN=True)

Predict chemical shifts of a trajectory using SPARTA+.

Parameters:

trj : Trajectory

Trajectory to predict shifts for.

rename_HN : bool, 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:

results : pandas.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

[R24]

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)