#!/usr/bin/env python3
# (C) 2026 Cadence Design Systems, Inc. (Cadence)
# All rights reserved.
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# subject to these terms. Cadence claims no rights to Customer's
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# 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
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# liable for any damages or liability in connection with the Sample Code
# or its use.


"""Depict MDL reactions with colored highlights by component and map index."""


import argparse
import io
import os
import pathlib
import sys

from openeye import oechem, oedepict
from PIL import Image
from rich_argparse import HelpPreviewAction, RichHelpFormatter

__SCRIPT_NAME__ = pathlib.Path(__file__).absolute().stem
__SCRIPT_DESC__ = (
    "Depict MDL reactions with colored highlights by component and map index."
)
__SCRIPT_TOOLKITS__ = ["oechem", "oedepict"]
__SCRIPT_KEYWORDS__ = ["monomer", "reaction", "depiction"]
__SCRIPT_CATEGORIES__ = ["depiction"]


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

    input_group = parser.add_argument_group("Input reaction")
    input_group.add_argument(
        "--rxn",
        metavar="RXN-FILE",
        type=str,
        required=True,
        help="input reaction file (rxn)",
    )

    image_group = parser.add_argument_group("Image options")
    image_group.add_argument(
        "--image",
        type=str,
        required=False,
        metavar="IMAGE-FILE",
        help="output image file (PNG, SVG) (required: %(required)s) -- if no output is provided the image will be displayed on the  screen",
    )
    image_group.add_argument(
        "--width",
        type=int,
        default=900,
        help="width of output image (default: %(default)s)",
    )
    image_group.add_argument(
        "--height",
        type=int,
        default=300,
        help="height of output image (default: %(default)s)",
    )

    parser.add_argument("--help-image", action=HelpPreviewAction)
    return parser.parse_args()


def main() -> int:
    """Render an MDL reaction file with component highlighting."""
    args = parse_args()

    _check_image_file(args)

    ifs = oechem.oemolistream()
    if not ifs.open(args.rxn):
        oechem.OEThrow.Fatal("Cannot open input file!")

    reaction_mol = oechem.OEGraphMol()
    if not oechem.OEReadMDLReactionQueryFile(ifs, reaction_mol):
        oechem.OEThrow.Fatal("Cannot read reaction file!")

    image = oedepict.OEImage(args.width, args.height)

    opts = oedepict.OE2DMolDisplayOptions(
        args.width, args.height, oedepict.OEScale_AutoScale
    )
    opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)

    # # depict reaction with component highlights

    reaction_display = oedepict.OE2DMolDisplay(reaction_mol, opts)
    color_reaction_by_components(reaction_display)
    oedepict.OERenderMolecule(image, reaction_display)

    if args.image:
        oedepict.OEWriteImage(args.image, image)
    else:
        image_view = Image.open(io.BytesIO(oedepict.OEWriteImageToBytes("png", image)))
        image_view.show()

    return os.EX_OK


def color_reaction_by_components(
    reaction_display: oedepict.OE2DMolDisplay,
) -> None:
    """Highlight reaction components with distinct colors."""
    reaction_mol = reaction_display.GetMolecule()
    num_parts, parts = oechem.OEDetermineComponents(reaction_mol)
    part_pred = oechem.OEPartPredAtom(parts)

    colors = list(oechem.OEGetLightColors())
    highlight_style = oedepict.OEHighlightStyle_BallAndStick

    for part_idx, color in zip(range(1, num_parts + 1), colors, strict=False):

        part_pred.SelectPart(part_idx)

        if is_reactant_component(reaction_mol, part_pred):

            reactant = oechem.OEAtomBondSet(reaction_mol.GetAtoms(part_pred))
            add_bonds_between_atoms(reaction_mol, reactant)
            oedepict.OEAddHighlighting(
                reaction_display, color, highlight_style, reactant
            )

            product = get_product_atoms(reaction_mol, reactant)
            add_bonds_between_atoms(reaction_mol, product)
            oedepict.OEAddHighlighting(
                reaction_display, color, highlight_style, product
            )


def get_product_atoms(
    reaction_mol: oechem.OEMolBase,
    reactant: oechem.OEAtomBondSet,
) -> oechem.OEAtomBondSet:
    """Retrieve product atoms corresponding to reactant atoms by map index."""
    product = oechem.OEAtomBondSet()
    for reactant_atom in reactant.GetAtoms():
        map_idx = reactant_atom.GetMapIdx()
        if map_idx != 0:
            product_atom = reaction_mol.GetAtom(
                oechem.OEAndAtom(
                    oechem.OEHasMapIdx(map_idx), oechem.OEAtomIsInProduct()
                )
            )
            if product_atom is not None:
                product.AddAtom(product_atom)

    return product


def is_reactant_component(
    reaction_mol: oechem.OEMolBase, part_pred: oechem.OEUnaryAtomPred
) -> bool:
    """Check if a component is part of the reaction reactants."""
    atom = reaction_mol.GetAtom(
        oechem.OEAndAtom(part_pred, oechem.OEAtomIsInReactant())
    )
    return atom is not None


def add_bonds_between_atoms(
    reaction_mol: oechem.OEMolBase,
    atom_bond_set: oechem.OEAtomBondSet,
) -> None:
    """Add bonds between atoms in a set."""
    pred = oechem.OEIsAtomMember(atom_bond_set.GetAtoms())
    for bond in reaction_mol.GetBonds():
        if pred(bond.GetBgn()) and pred(bond.GetEnd()):
            atom_bond_set.AddBond(bond)


def _check_image_file(args: argparse.Namespace) -> None:
    # script will terminate if there are some issues
    if not args.image:
        # image will be displayed on the screen
        return
    ext = pathlib.Path(args.image).suffix[1:].upper()
    if not oedepict.OEIsRegisteredImageFile(ext):
        oechem.OEThrow.Fatal("Unknown image output type!")

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


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


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