mdtraj.reindex_dataframe_by_atoms

mdtraj.reindex_dataframe_by_atoms(trj, frame)[source]

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

Parameters:
  • trj (Trajectory) – Trajectory to predict shifts for.

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

Returns:

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

Return type:

pandas.DataFrame

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.