#!/usr/bin/env python3
# (C) 2023 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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# or its use.


"""Calculates XLogP and visualizes atom contributions using property map."""

import argparse
import io
import os
import sys
from pathlib import Path

from openeye import oechem, oedepict, oegrapheme, oemolprop, oequacpac
from PIL import Image
from rich_argparse import HelpPreviewAction, RichHelpFormatter

__SCRIPT_NAME__ = Path(__file__).absolute().stem
__SCRIPT_DESC__ = "Depict XLogP of molecule (atom based)."
__SCRIPT_TOOLKITS__ = ["oechem", "oedepict", "oegrapheme", "oemolprop", "oequacpac"]
__SCRIPT_CATEGORIES__ = ["depiction"]


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_group = parser.add_argument_group("Input options")
    input_group.add_argument(
        "--mol",
        type=str,
        required=True,
        metavar="MOL-FILE",
        help="input molecule file (oeb, sdf)",
    )

    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=800,
        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:
    """Visualizes XLogP atom contributions."""
    args = parse_options()

    _check_image_file(args)
    mol = _get_molecule(args)

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

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

    # depict molecule with XLogP atom contributions

    oedepict.OEPrepareDepiction(mol)
    depict_molecule_xlogp(image, mol, opts)

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

    return os.EX_OK


def set_atom_properties(mol: oechem.OEMolBase, tag: int) -> None:
    """Attach the XLogP atom contribution to each atom with the given tag."""
    oequacpac.OERemoveFormalCharge(mol)

    atom_values = oechem.OEFloatArray(mol.GetMaxAtomIdx())
    xlogp = oemolprop.OEGetXLogP(mol, atom_values)

    mol.SetTitle(f"{mol.GetTitle()} -- OEXLogP = {xlogp:.2f}")

    for atom in mol.GetAtoms():
        val = atom_values[atom.GetIdx()]
        atom.SetData(tag, val)


def depict_molecule_xlogp(
    image: oedepict.OEImageBase,
    mol: oechem.OEMolBase,
    opts: oedepict.OE2DMolDisplayOptions,
) -> None:
    """Generate an image of a molecule depicting the atom contribution of XLogP."""
    scale = oegrapheme.OEGetMoleculeSurfaceScale(mol, opts)
    opts.SetScale(scale)

    str_tag = "XLogP"
    int_tag = oechem.OEGetTag(str_tag)
    set_atom_properties(mol, int_tag)

    disp = oedepict.OE2DMolDisplay(mol, opts)

    prop_map = oegrapheme.OE2DPropMap(opts.GetBackgroundColor())
    prop_map.SetNegativeColor(oechem.OEDarkGreen)
    prop_map.SetPositiveColor(oechem.OEDarkPurple)
    prop_map.SetLegendLocation(oegrapheme.OELegendLocation_Left)
    prop_map.Render(disp, str_tag)

    oedepict.OERenderMolecule(image, disp)


def _check_image_file(args: argparse.Namespace) -> None:
    # script will terminate if there is some issues
    if not args.image:
        # image will be displayed on the screen
        return
    ext = 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!")


def _get_molecule(args: argparse.Namespace) -> oechem.OEMolBase:
    ifs = oechem.oemolistream()
    if not ifs.open(args.mol):
        oechem.OEThrow.Fatal(f"Cannot open {args.mol} input file!")

    mol = oechem.OEGraphMol()
    if not oechem.OEReadMolecule(ifs, mol):
        oechem.OEThrow.Fatal(f"Cannot read molecule from {args.mol} input file!")

    return mol


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())