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)