pylipid.util.write_pymol_script¶

pylipid.util.write_pymol_script(fname, pdb_fname, data_fname, lipid, n_binding_site)[source]¶

Write Python script that opens a PyMol session with binding site information.

This function will generate a Python script which opens a PyMol session in which the binding site information stored in the interaction data file (a csv file provided by data_fname) is mapped onto the receptor structure (loaded from a PDB coordinate file provided by pdb_fname). In this PyMol session, residues from the same binding site are colored in the same color and shown in spheres with scales corresponding to their residence times.

The PDB coordinate of the receptor need to have the same topology as in the simulations (i.e. the same as shown in the data_fname). A warning will show up and break the PyMol seesion, if residue names are different or residue indices are different.

As PyMol only recognizes atomistic structures, the PDB coordinates of the receptor (provided by pdb_fname) needs to be an atomistic structure. For coarse-grained simulation results, this pdb_fname needs to be a PDB coordinates before the coarse-graining step.

Parameters

fname (str) – The filename of the PyMol script to be written.
pdb_fname (str) – The PDB coordinate file of the receptor.
data_fname (str) – The csv file of the interaction data.
lipid (str) – Lipid residue name
n_binding_site (int) – Number of binding site detected (shown in the csv file).