def save_mol_file()

in source/src/molecule-unfolding/utility/ResultProcess.py [0:0]

• 40 lines of code
• 5 McCabe index (conditional complexity)

    def save_mol_file(self, save_name):
        logging_info(f"save_mol_file {save_name}")
        raw_f = open(self.mol_file_name, "r")
        lines = raw_f.readlines()

        start_parse = 0

        def _update_atom_pos(line, atom_pos_data):
            atom_idx_name = re.findall(r"\d+ [A-Z]\d+", line)[0]
            logging.debug("atom id name is {}".format(atom_idx_name))
            atom_idx = atom_idx_name.split(' ')[0]

            regrex = re.compile(
                r"[-+]?\d+\.\d+ +[-+]?\d+\.\d+ +[-+]?\d+\.\d+", re.IGNORECASE)

            update_pos_x = atom_pos_data[atom_idx]['pts'][0]
            update_pos_y = atom_pos_data[atom_idx]['pts'][1]
            update_pos_z = atom_pos_data[atom_idx]['pts'][2]

            update_pos = "{}    {}    {}".format(
                update_pos_x, update_pos_y, update_pos_z)

            update_line = regrex.sub(update_pos, line)

            return update_line

        mol_save_name = f"{self.mol_file_name.split('mol2')[0][:-1]}_{self.method}_{save_name}.mol2"
        file_save_name = f"{self.mol_file_name.split('mol2')[0][:-1]}_{self.method}_{save_name}.json"

        update_f = open(mol_save_name, 'w')

        for line in lines:
            logging.debug(line)

            if line.startswith("@<TRIPOS>BOND"):
                logging.debug("finish atom part")
                start_parse = 0

            if start_parse == 1:
                update_line = _update_atom_pos(line, self.atom_pos_data)
                update_f.write(update_line)
            else:
                update_f.write(line)

            if line.startswith("@<TRIPOS>ATOM"):
                logging.debug("found atom start position")
                start_parse = 1

        raw_f.close()
        update_f.close()

        # update_parameters
        with open(file_save_name, "w") as outfile:
            json.dump(self.parameters, outfile)

        logging_info(f"finish save {mol_save_name} and {file_save_name}")

        return [mol_save_name, file_save_name]