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

"""
Constant pH command line UI

Copyright Schrodinger, LLC. All rights reserved.
"""
import argparse
from typing import List
import sys

from schrodinger.application.desmond import util

from . import cmdline
from .cmdline import Option


class Args(cmdline.BaseArgs):

    def __init__(self, opt: argparse.Namespace):
        """
        :param opt: Command line options with corresponding values.
        """
        from schrodinger.application.scisol.packages.fep import utils as scisol_utils
        self.copy_parser_attributes(opt)
        # Flatten list to simplify parsing
        self.titratable_sites = list(
            scisol_utils.flattened(self.titratable_sites))
        super().__init__(opt)

    def validate(self):
        """
        :raise SystemExit: For invalid parameters.
        """
        util.ensure_file_exists(self.inp_file)
        if not self.titratable_sites and not (self.checkpoint or self.extend):
            sys.exit(
                "-titratable-site must be specified. "
                "Use '-titratable-site all' to titrate all titratable sites.")
        super().validate()


def ui(argv: List[str]) -> Args:
    """
    Parse the arguments and return an object containing the values.
    """

    usage = """
Runs a constant-pH simulation. This only works with the S-OPLS forcefield.

* Run a new job:
    $SCHRODINGER/constant_ph input.mae -time 5000.0 -HOST <job-host> -JOBNAME <jobname> -titratable-site all

* Restart a previously interrupted job:
    $SCHRODINGER/constant_ph input.mae -HOST <job-host> -JOBNAME <jobname> -RESTART

* Extend a completed job:
    $SCHRODINGER/constant_ph input.mae -time 1000.0 -HOST <job-host> -JOBNAME <jobname> -extend
"""

    options = cmdline.get_common_options()
    options.extend([
        # name           default    help                    [dest]
        Option("inp_file", None, "A Maestro structure file"),
        Option(
            "-time", 5000.0,
            "Specify time (in ps) for the production simulation stage."
            " Default: %(default)s. "),
        Option(
            "-titratable-site", [], "Specify the titratable site to consider "
            "in the format 'A:2B' or 'chain:resnum[inscode]'. "
            "If no insertion code is present, just leave it off 'A:2'. "
            " '_' can be used to indicate an blank chain letter in '_:2'."
            " Only ASP/GLU/HIS residues may be titrated. Use 'all' "
            " to mark all supported residues as titratable. "
            " You may pass in the argument multiple times for multiple sites. ",
            {
                'nargs': 1,
                'action': 'extend',
                'dest': 'titratable_sites'
            }),
        Option(
            "-skip-sidechain-mapping", False, argparse.SUPPRESS
            # "Set to skip mapping the side chains"
        ),  # Probably will become default True once the backend supports this
        Option("-ph-lower-limit", 0.5,
               "Set to the lower limit of pH's to run simulations at."),
        Option("-ph-upper-limit", 9.0,
               "Set to the upper limit of pH's to run simulations at."),
        Option("-ph-interval", 0.5,
               "Set to the interval in pH units to run the simulations at."),
        Option("-extend", False,
               "Set to True to run an extension for the original job."),
    ])

    cmdline.suppress_options(
        options, {
            "-skip_traj", "-checkpoint", "-buffer", "-no_concat", "-m", "-ff",
            "-lambda-windows", "-ffbuilder", "-ff-host"
        })

    args = cmdline.parse_options(usage, options, argv[1:], add_subhost=False)
    return Args(args)