Source code for schrodinger.application.desmond.starter.ui.bpfep

"""
Binding-pose FEP command line UI

Copyright Schrodinger, LLC. All rights reserved.
"""

import argparse
import sys
from typing import List

from schrodinger.application.desmond import util
from schrodinger.structutils.analyze import validate_asl

from . import cmdline
from .cmdline import Option


class Args(cmdline.BaseArgs):

    def __init__(self, opt: argparse.Namespace):
        self.copy_parser_attributes(opt)
        if not self.mut_ligand_asl:
            self.mut_ligand_asl = self.ligand_asl
        super(Args, self).__init__(opt)

    def validate(self):
        if self.RESTART:
            if len(self.inp_file):
                sys.exit("ERROR: No positional arguments for a restart job.")
            return

        if 2 != len(self.inp_file):
            sys.exit("ERROR: Two MAE files are expected for a new job.")

        util.ensure_file_exists(self.inp_file[0])
        util.ensure_file_exists(self.inp_file[1])

        if not validate_asl(self.ligand_asl):
            sys.exit("ERROR: Invalid ASL expression for -ligand-asl: %s" %
                     self.ligand_asl)
        if self.mut_ligand_asl and not validate_asl(self.mut_ligand_asl):
            sys.exit("ERROR: Invalid ASL expression for -mut-ligand-asl: %s" %
                     self.mut_ligand_asl)
        if not validate_asl(self.receptor_asl):
            sys.exit("ERROR: Invalid ASL expression for -receptor-asl: %s" %
                     self.receptor_asl)
        super().validate()


def ui(argv: List[str]) -> Args:
    usage = """
Binding-pose FEP driver (experimental)
Report issues to Desmond.

* Run a new job:
    $SCHRODINGER/fep_binding_pose -HOST <compute-host> -JOBNAME <jobname> -ligand-asl <ASL> <ref-complex>.mae <mut-complex>.mae

* Restart a previously interrupted job:
    $SCHRODINGER/fep_binding_pose -HOST <compute-host> -JOBNAME <jobname> -RESTART -checkpoint <multisim-checkpoint-file>
  Note that the following options have no effects for a restart job:
    -ligand-asl, -mut-ligand-asl, -receptor-asl

* Prepare input files for multisim. Do NOT run job:
    $SCHRODINGER/fep_binding_pose -HOST <compute-host> -JOBNAME <jobname> -ligand-asl <ASL> <ref-complex>.mae <mut-complex>.mae -prepare
"""
    options = cmdline.get_common_options()
    options.extend([
        Option(
            "inp_file", None, "Two MAE files: The first is the reference "
            "complex structure, the second the mutant complex structure. Each "
            "file should contain exactly ONE CT block. This argument is "
            "required for a from-scratch new job, but should NOT be set for a "
            "restart job.", {
                "metavar": "<ref-complex>.mae <mut-complex>.mae",
                "nargs": "*"
            }),
        Option(
            "-ligand-asl", "",
            "ASL expression to specify the alchemical part of the ligand "
            "molecule in both complex structures. The selected atoms will be "
            "excluded from the atom mapping. If the alchemical part is "
            "different between the reference and the mutant ligands, use this "
            "option to specify only for the reference, and the -mut-ligand-asl "
            "option only for the mutant. This option is required for a "
            "from-scratch new job."),
        Option(
            "-mut-ligand-asl", "",
            "ASL expression to specify the alchemical part of the ligand "
            "molecule in the mutant complex structure. The selected atoms will "
            "be excluded from the atom mapping. Use this option ONLY when the "
            "alchemical part is different between the reference and the mutant "
            "ligands."),
        Option(
            "-receptor-asl", "not all",
            "ASL expression to specify the alchemical part of the receptor in "
            "both complex structures. The selected atoms will be excluded from "
            "the atom mapping. Default: All receptor atoms will be mapped."),
    ])
    cmdline.suppress_options(
        options,
        {"-ppj", "-seed", "-skip_traj", "-buffer", "-ffbuilder", '-ff-host'})
    opt = cmdline.parse_options(usage, options, argv[1:], add_subhost=False)
    return Args(opt)