#!/usr/bin/env python3
# (C) 2023 Cadence Design Systems, Inc. (Cadence)
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of Cadence products or
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# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
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# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

"""Depict active site maps."""

import argparse
import os
import sys
from pathlib import Path

from openeye import oechem, oedepict, oegrapheme
from rich_argparse import HelpPreviewAction, RichHelpFormatter

__SCRIPT_NAME__ = Path(__file__).absolute().stem
__SCRIPT_DESC__ = "Depict active site maps."
__SCRIPT_TOOLKITS__ = ["oechem", "oedepict", "oegrapheme"]
__SCRIPT_CATEGORIES__ = ["visualization", "ligand-protein interactions"]


def parse_options() -> argparse.Namespace:
    """Set up command line options."""
    parser = argparse.ArgumentParser(
        add_help=True,
        formatter_class=RichHelpFormatter,
        description="[yellow]" + __SCRIPT_DESC__ + "[/yellow]",
    )
    parser.add_argument("--help-image", action=HelpPreviewAction)

    # input options
    input_group = parser.add_argument_group("Input ligand-protein complex")
    exclusive_input_group = input_group.add_mutually_exclusive_group(required=True)
    exclusive_input_group.add_argument(
        "--complex",
        type=str,
        required=False,
        metavar="PDB-FILE",
        help="input PDB file of the ligand-protein complex",
    )
    exclusive_input_group.add_argument(
        "--design-unit",
        "--du",
        type=str,
        metavar="DU-FILE",
        help="input design unit file",
    )
    image_group = parser.add_argument_group("Image options")
    image_group.add_argument(
        "--image",
        type=str,
        required=True,
        metavar="IMAGE-FILE",
        help="output image file (SVG)",
    )
    image_group.add_argument(
        "--width",
        type=int,
        default=600,
        help="width of output image (default: %(default)s)",
    )
    image_group.add_argument(
        "--height",
        type=int,
        default=400,
        help="height of output image (default: %(default)s)",
    )
    return parser.parse_args()


def main() -> int:
    """Depict active site maps."""
    args = parse_options()

    _check_image_file(args)

    if args.complex:
        protein, ligand = get_protein_and_ligand_from_pdb(args.complex)
    elif args.design_unit:
        protein, ligand = get_protein_and_ligand_from_design_unit(args.design_unit)
    else:
        oechem.OEThrow.Fatal("Invalid input option!")

    image = oedepict.OEImage(args.width, args.height)
    depict_active_site_maps(image, protein, ligand)

    icon_scale = 0.5
    oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight, icon_scale)
    oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
    oedepict.OEWriteImage(args.image, image)

    return os.EX_OK


def depict_active_site_maps(
    image: oedepict.OEImageBase, protein: oechem.OEMolBase, ligand: oechem.OEMolBase
) -> None:
    """Depict active site maps."""
    # perceive interactions
    active_site = oechem.OEInteractionHintContainer(protein, ligand)
    if not active_site.IsValid():
        oechem.OEThrow.Fatal("Cannot initialize active site!")
    active_site.SetTitle(ligand.GetTitle())

    oechem.OEPerceiveInteractionHints(active_site)

    # depiction
    oegrapheme.OEPrepareActiveSiteDepiction(active_site)
    oegrapheme.OERenderActiveSiteMaps(image, active_site)


def get_protein_and_ligand_from_pdb(
    pdb_filename: str,
) -> tuple[oechem.OEMolBase, oechem.OEMolBase]:
    """Read protein and ligand from pdb/cif file."""
    ifs = oechem.oemolistream()
    if not ifs.open(pdb_filename):
        oechem.OEThrow.Fatal(f"Unable to open {pdb_filename} for reading")

    complex_mol = oechem.OEGraphMol()
    if not oechem.OEReadMolecule(ifs, complex_mol):
        oechem.OEThrow.Fatal(f"Unable to read complex from {pdb_filename}")

    if not oechem.OEHasResidues(complex_mol):
        oechem.OEPerceiveResidues(complex_mol, oechem.OEPreserveResInfo_All)

    # separate ligand and protein
    split_opts = oechem.OESplitMolComplexOptions()
    ligand = oechem.OEGraphMol()
    protein = oechem.OEGraphMol()
    water = oechem.OEGraphMol()
    other = oechem.OEGraphMol()

    split_opts.SetProteinFilter(
        oechem.OEOrRoleSet(split_opts.GetProteinFilter(), split_opts.GetWaterFilter())
    )
    split_opts.SetWaterFilter(
        oechem.OEMolComplexFilterFactory(oechem.OEMolComplexFilterCategory_Nothing)
    )

    oechem.OESplitMolComplex(ligand, protein, water, other, complex_mol, split_opts)

    if ligand.NumAtoms() == 0:
        oechem.OEThrow.Fatal("Cannot separate complex!")

    return protein, ligand


def get_protein_and_ligand_from_design_unit(
    filename: str,
) -> tuple[oechem.OEMolBase, oechem.OEMolBase]:
    """Read protein and ligand from design unit file."""
    du = oechem.OEDesignUnit()
    if not oechem.OEIsReadableDesignUnit(filename) or not oechem.OEReadDesignUnit(
        filename, du
    ):
        oechem.OEThrow.Fatal("Cannot read design unit.")

    protein = oechem.OEGraphMol()
    if not du.GetComponents(protein, oechem.OEDesignUnitComponents_TargetComplex):
        oechem.OEThrow.Fatal("Could not extract protein from the design unit.")

    ligand = oechem.OEGraphMol()
    if not du.GetLigand(ligand):
        oechem.OEThrow.Fatal("Could not extract ligand from the design unit.")

    return (protein, ligand)


def _check_image_file(args: argparse.Namespace) -> None:
    # script will terminate if there is an issue
    if Path(args.image).suffix[1:].upper() != "SVG":
        oechem.OEThrow.Fatal(
            "This script only accepts SVG as the output image file format!"
        )

    ofs = oechem.oeofstream()
    if not ofs.open(args.image):
        oechem.OEThrow.Fatal(f"Cannot open output image file {args.image}!")


setattr(main, "__SCRIPT_NAME__", __SCRIPT_NAME__)
setattr(main, "__SCRIPT_DESC__", __SCRIPT_DESC__)
setattr(main, "__SCRIPT_TOOLKITS__", __SCRIPT_TOOLKITS__)
setattr(main, "__SCRIPT_CATEGORIES__", __SCRIPT_CATEGORIES__)

if __name__ == "__main__":
    sys.exit(main())