#!/usr/bin/env python3

"""Module containing the FixSideChain class and the command line interface."""
import argparse
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.command_wrapper import cmd_wrapper
from biobb_common.tools.file_utils import launchlogger


class FixSideChain:
    """Class to model the missing atoms in amino acid side chains of a PDB.

    Args:
        input_pdb_path (str): Input PDB file path. `Sample file <https://github.com/bioexcel/biobb_model/blob/master/biobb_model/test/data/model/2ki5.pdb>`_. Accepted formats: pdb.
        output_pdb_path (str): Output PDB file path. `Sample file <https://github.com/bioexcel/biobb_model/blob/master/biobb_model/test/reference/model/output_pdb_path.pdb>`_. Accepted formats: pdb.
        properties (dic):
            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.    """

    def __init__(self, input_pdb_path: str, output_pdb_path: str,
                 properties: dict = None, **kwargs) -> None:
        properties = properties or {}

        # Input/Output files
        self.io_dict = {
            "in": {"input_pdb_path": input_pdb_path},
            "out": {"output_pdb_path": output_pdb_path}
        }

        # Properties specific for BB
        self.check_structure_path = properties.get('check_structure_path', 'check_structure')

        # Properties common in all BB
        self.can_write_console_log = properties.get('can_write_console_log', True)
        self.global_log = properties.get('global_log', None)
        self.prefix = properties.get('prefix', None)
        self.step = properties.get('step', None)
        self.path = properties.get('path', '')
        self.remove_tmp = properties.get('remove_tmp', True)
        self.restart = properties.get('restart', False)

        # Check the properties
        fu.check_properties(self, properties)

    @launchlogger
    def launch(self) -> int:
        """Model the missing atoms in side chains."""
        tmp_files = []

        # Get local loggers from launchlogger decorator
        out_log = getattr(self, 'out_log', None)
        err_log = getattr(self, 'err_log', None)

        # Restart if needed
        if self.restart:
            if fu.check_complete_files(self.io_dict["out"].values()):
                fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
                return 0

        cmd = [self.check_structure_path,
               '-i', self.io_dict["in"]["input_pdb_path"],
               '-o', self.io_dict["out"]["output_pdb_path"],
               '--force_save',
               'fixside', '--fix', 'ALL']

        returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()

        if self.remove_tmp:
            fu.rm_file_list(tmp_files, out_log=out_log)

        return returncode


def main():
    parser = argparse.ArgumentParser(description="Model the missing atoms in amino acid side chains of a PDB.",
                                     formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")

    # Specific args of each building block
    required_args = parser.add_argument_group('required arguments')
    required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input PDB file name")
    required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output PDB file name")

    args = parser.parse_args()
    config = args.config if args.config else None
    properties = settings.ConfReader(config=config, system=args.system).get_prop_dic()

    # Specific call of each building block
    FixSideChain(input_pdb_path=args.input_pdb_path,
                 output_pdb_path=args.output_pdb_path,
                 properties=properties).launch()


if __name__ == '__main__':
    main()
