pylipid.api.LipidInteraction.save_coordinate¶

LipidInteraction.save_coordinate(item, save_dir=None, fn_coord=None)[source]¶

Save protein coordinates in PDB format with interaction data in the B factor column.

In this method, the receptor coordinates, which are taken from the first frame of the trajectory, are written out in the PDB format with the specified interaction data stored in the B factor column. Supported interaction data include: Residence Time, Duration, Occupancy and Lipid Count. These are interaction data for residues.

By default, the coordinates will be saved in the directory of Coordinate_{lipid} under the root directory defined when the class LipidInteraction was initiated. It can be changed by providing to path to save_dir.

By default, the coordinates file is saved as Coordinate_{lipid}_{item}.pdb. This can be changed by providing a file name to fn_coord.

Parameters

item ({"Residence Time", "Duration", "Occupancy", "Lipid Count"}) – Interaction data to be stored in the B factor column.
save_dir (str or None, default=None) – The directory for saving the coordinate file. By default, the coordinate file is saved at the directory of Coordinate_{lipid} under the root directory defined at the initialization of LipidInteraction.
fn_coord (str or None, default=None) – The file name of the written coordinate file. By default, the file is named as Coordinate_{lipid}_{item}.pdb