Source code for schrodinger.application.bioluminate.run_propka

"""
PROPKA wrapper functions
"""

import os
import platform
import subprocess
import sys

PROPKA_SCRIPT = "propka_run_wrapper.py"


def run_propka(files, **kwargs):
    """
    Runs the propka job.

    All kwargs will be added to the command line arguments. They must
    be taken from the help arguments. The prepended dash is automatically
    added to the key. For example, this::

       propka.run(files, pH=6.8)

    will run propka with "-pH 6.8" added to the command line.

    :param files: The pdb files to operate on
    :type  files: The filename (as string) or list/tuple of filenames (strings)
    """
    try:
        schro = os.environ['SCHRODINGER']
        if sys.platform.startswith("win32"):
            cmd = ["%s/run.exe" % schro, PROPKA_SCRIPT]
        else:
            cmd = ['%s/run' % schro, PROPKA_SCRIPT]
    except KeyError:
        # In case SCHRODINGER is not defined
        cmd = ["python", PROPKA_SCRIPT]
    if type(files) in [list, tuple]:
        cmd.extend([f for f in files])
    else:
        cmd.append(files)

    for key, val in kwargs.items():
        new_key = '-%s' % key
        cmd.append(new_key)
        cmd.append(val)

    # Suppress DeprecationWarning from __main__ when running
    env = os.environ.copy()
    env["PYTHONWARNINGS"] = "ignore::DeprecationWarning"
    proc = subprocess.run(cmd, text=True, env=env, capture_output=True)

    return proc.stdout, proc.stderr


if __name__ == '__main__':
    # Pass all the arguments to the PROPKA backend

    schro = os.environ['SCHRODINGER']
    if platform.system() == 'Windows':
        cmd = ["%s/run.exe" % schro, PROPKA_SCRIPT]
    else:
        cmd = ['%s/run' % schro, PROPKA_SCRIPT]

    cmd += sys.argv[1:]
    subprocess.call(cmd)