interactions

This module contains functions to analyze interactions between ligands and proteins in PDB.

Note Install chimerax before running

Add hydrogen using ChimeraX

import os
import logging
import subprocess

def protonate_structure(structure: str, out_dir:str) -> tuple[bool, str]:
        """Uses ChimeraX to add hydrogens to the input structure.
        The command being used is `addh hbond true`.

        Args:
            structure: Path to the input structure
            out_dir: Directory where the protonated structure will be saved

        Returns:
            A tuple (success, protonated), where success indicates whether the protonation
            was succcessful or not , and protonated is the path to protonated structure
        """
        logging.info("Protonation started.")

        chimerax_success = False
        protonated_cif = os.path.join(
            out_dir, f'{os.path.basename(structure).split(".")[0]}_h.cif'
        )

        cmd_file = os.path.join(out_dir, "chimera_config.cxc")
        structure = os.path.realpath(structure)
        protonated_cif = os.path.realpath(protonated_cif)

        with open(cmd_file, "w") as f:
            f.write(
                f"""
                open {structure}
                addh hbond true
                save {protonated_cif} format mmcif
                exit
                """
            )
        try:
            subprocess.call(
                ["chimerax", "--nogui", "--cmd", f"open {cmd_file}", "--silent"]
            )
            logging.info("Protonation finished.")
        except Exception:
            return (chimerax_success, protonated_cif)

        if not os.path.isfile(protonated_cif):
            return (chimerax_success, protonated_cif)

        return (chimerax_success, protonated_cif)