mdtraj.reindex_dataframe_by_atoms

mdtraj.reindex_dataframe_by_atoms(trj, frame)

Reindex chemical shift output to use atom number (serial) indexing.

Parameters
trjTrajectory

Trajectory to predict shifts for.

framepandas.DataFrame

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

Returns
new_framepandas.DataFrame

Dataframe containing results, with index consisting of atom indices (AKA the ‘serial’ entry in a PDB). Columns correspond to each frame in trj.

Notes

Be aware that this function may DROP predictions if the atom naming is different between the input trajectory and the output of various chemical shift prediction tools.