#!/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 # SaaS offerings (each a "Customer"). # Customer is hereby permitted to use, copy, and modify the Sample Code, # subject to these terms. Cadence claims no rights to Customer's # modifications. Modification of Sample Code is at Customer's sole and # exclusive risk. Sample Code may require Customer to have a then # 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 the unpaired and clash interactions of an active site.""" import argparse import io import os import sys from pathlib import Path from openeye import oechem, oedepict, oegrapheme from PIL import Image from rich_argparse import HelpPreviewAction, RichHelpFormatter __SCRIPT_NAME__ = Path(__file__).absolute().stem __SCRIPT_DESC__ = "Depict the unpaired and clash interactions of an active site." __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=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=600, help="height of output image (default: %(default)s)", ) image_group.add_argument( "--interactive-legend", default=False, action="store_true", help="visualize legend on mouse hover (SVG-only feature) (default: %(default)s)", ) return parser.parse_args() def main() -> int: """Depict the unpaired and clash interactions of an active site.""" 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!") # depict unpaired interaction map image = oedepict.OEImage(args.width, args.height) cell_width, cell_height = args.width, args.height if not args.interactive_legend: cell_width = cell_width * 0.8 opts = oegrapheme.OE2DActiveSiteDisplayOptions(cell_width, cell_height) opts.SetRenderInteractiveLegend(args.interactive_legend) if args.interactive_legend: depict_unpaired_map(image, protein, ligand, opts) else: main_frame = oedepict.OEImageFrame( image, args.width * 0.80, args.height, oedepict.OE2DPoint(args.width * 0.2, 0.0), ) legend_frame = oedepict.OEImageFrame( image, args.width * 0.20, args.height, oedepict.OE2DPoint(args.width * 0.0, 0.0), ) depict_unpaired_map(main_frame, protein, ligand, opts, legend_frame) if ( args.image and Path(args.image).suffix[1:].lower() == "svg" and args.interactive_legend ): icon_scale = 0.5 oedepict.OEAddInteractiveIcon( image, oedepict.OEIconLocation_TopRight, icon_scale ) oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0) 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 depict_unpaired_map( image: oedepict.OEImageBase, protein: oechem.OEMolBase, ligand: oechem.OEMolBase, depict_options: oegrapheme.OE2DActiveSiteDisplayOptions, legend_frame: oedepict.OEImageBase | None = None, ) -> None: """Depict unpaired interaction map.""" # 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) active_site_disp = oegrapheme.OE2DActiveSiteDisplay(active_site, depict_options) oegrapheme.OERenderUnpairedInteractionMap(image, active_site_disp) if legend_frame: legend_options = oegrapheme.OE2DActiveSiteLegendDisplayOptions(12, 1) oegrapheme.OEDrawUnpairedInteractionMapLegend( legend_frame, active_site_disp, legend_options ) def get_protein_and_ligand_from_pdb( pdb_filename: str, ) -> tuple[oechem.OEMolBase, oechem.OEMolBase]: """Read protein and and ligand from 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 and ligand from 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 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!") 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())