mol2parser.py

#!/usr/bin/env python3
# -*- coding: UTF8 -*-

# Author: Guillaume Bouvier -- [email protected]
# https://research.pasteur.fr/en/member/guillaume-bouvier/
# 2020-03-06 13:17:44 (UTC+0100)

from pymol import cmd
from pymol import exporting

cmd.load('small03.mol2', 'mol2_in')
nstates = cmd.count_states('mol2_in')
for i in range(1, nstates + 1):
    cmd.split_states('mol2_in', i, i)
    molname = cmd.get_object_list()[-1]
# ------------------------------ Save a mol2 file ------------------------------
    cmd.save('out.mol2', molname)
# ---------------------------- or get a mol2 string ----------------------------
    mol2str = exporting.get_mol2str('mol2_in')
    print(mol2str)
# ------------------------------------- - --------------------------------------
    cmd.delete(molname)