Source code for icolos.utils.execute_external.openbabel

import os
import sys
from icolos.utils.enums.program_parameters import OpenBabelEnum
from icolos.utils.execute_external.execute import ExecutorBase

EE = OpenBabelEnum()


class OpenBabelExecutor(ExecutorBase):
    """For the execution of the "obabel" binary."""

    def __init__(self):
        # in case the environment is not activated, add the path to the binary here
        obabel_location = os.path.dirname(sys.executable)
        super().__init__(prefix_execution=None, binary_location=obabel_location)

    def execute(
        self, command: str, arguments: list, check=True, location=None, pipe_input=None
    ):
        # check, whether a proper executable is provided
        if command not in [EE.OBABEL]:
            raise ValueError(
                "Parameter command must be an element of the internal OpenBabel executable list."
            )

        return super().execute(
            command=command,
            arguments=arguments,
            check=check,
            location=location,
            pipe_input=pipe_input,
        )

    def is_available(self):
        # unfortunately, "obabel" does not return a meaningful return value (always '1'), so instead try to parse
        # the "stdout" of the standard message; note, that "OpenBabel" is part of the environment and should always work
        try:
            result = self.execute(command=EE.OBABEL, arguments=[], check=False)
            if EE.OBABEL_IDENTIFICATION_STRING in result.stdout:
                return True
            return False
        except Exception as e:
            return False