xyz2xtb

#!/usr/bin/env python3

# xyz2xtb -- A small python script to run xtb on xyz files found in a directory
# Nicholas Hadler - nhadler@berkeley.edu
# March 20th, 2022

import os
from pathlib import Path
import shutil
import time
import argparse


def xyz_to_xtb(com_file, cores):

    # Gets current directory
    dir = os.getcwd()

    # Open XTB command file
    with open(com_file, "r") as file:
        com = file.read().rstrip("\n")

    for file in os.listdir(dir):

        if file.endswith(".xyz") or file.endswith(".sdf"):

            # Creates a folder for each XYZ file and copies the XYZ into them.
            new_dir = file.split(".")[0] + "_dir"
            path = Path(new_dir)
            path.mkdir(parents=True, exist_ok=True)
            shutil.copy(file, new_dir)

            # Formats and writes the complete com file
            new_com = file + " " + com + " > out_" + file.split(".")[0]
            f_name = new_dir + "/com_" + file.split(".")[0]
            f = open(f_name, "w")
            f.write(new_com)
            f.close()

            # Runs the MGCF xtb command
            xtb_run = (
                "cd " + new_dir + " && "
                "run_xtb " + "com_" + file.split(".")[0] + " " + cores
            )
            os.system(xtb_run)

            # Waits 3 seconds for file to be submitted
            time.sleep(3)


if __name__ == "__main__":

    parser = argparse.ArgumentParser(
        description="""A small python script to run xtb on xyz files found in a directory""",
    )
    parser.add_argument(
        "com",
        help="Com file for XTB arguments. This needs to only include the run arguments.",
    )
    parser.add_argument("cores", help="Number of cores to use.")
    args = vars(parser.parse_args())

    xyz_to_xtb(args["com"], args["cores"])