#!/usr/bin/env python3 # (C) 2026 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. CADENCE 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. """Converts a CSV or SDF file into an HTML file with molecular depictions.""" import argparse import os import pathlib import sys import typing from openeye import oechem, oedepict from rich_argparse import HelpPreviewAction, RichHelpFormatter __SCRIPT_NAME__ = pathlib.Path(__file__).absolute().stem __SCRIPT_DESC__ = "Convert CSV or SDF files into HTML with molecular depictions" __SCRIPT_TOOLKITS__ = ["oechem", "oedepict"] __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]", ) io_group = parser.add_argument_group("Input/output options") io_group.add_argument( "--mol", metavar="MOL-FILE", type=str, required=True, help="input molecule file (.csv or .sdf)", ) io_group.add_argument( "--html", metavar="HTML-FILE", type=str, required=True, help="output HTML file (.html)", ) parser.add_argument("--help-image", action=HelpPreviewAction) parser.add_argument( "--save-console-svg", default=False, action="store_true", help=f"run command and capture console output in {__SCRIPT_NAME__}.svg file", ) return parser.parse_args() def main() -> int: """Convert molecule file to HTML with molecular depictions.""" args = parse_options() html_file = pathlib.Path(args.html) if html_file.suffix.lower() != ".html": oechem.OEThrow.Fatal("Invalid file extension expected .html!") mol_list: list[oechem.OEMolBase] = read_molecules(args.mol) tags = collect_data_tags(mol_list) width, height = 200, 200 opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) with html_file.open("w") as ofp: _write_html_file(ofp, mol_list, pathlib.Path(args.mol).name, tags, opts) return os.EX_OK def read_molecules(mol_filename: str) -> list[oechem.OEMolBase]: """Read molecules from a CSV or SDF file and return a list of OEMolBase objects.""" mol_path = pathlib.Path(mol_filename) if not mol_path.exists(): oechem.OEThrow.Fatal(f"Cannot open input file '{mol_path.name}'!") ifs = oechem.oemolistream() if not ifs.open(str(mol_path)): oechem.OEThrow.Fatal(f"Cannot open input file '{mol_path.name}'!") if ifs.GetFormat() not in [oechem.OEFormat_CSV, oechem.OEFormat_SDF]: oechem.OEThrow.Fatal("Input must be a CSV or SDF file!") mol_list: list[oechem.OEMolBase] = [ oechem.OEGraphMol(m) for m in ifs.GetOEGraphMols() ] return mol_list def collect_data_tags(mol_list: list[oechem.OEMolBase]) -> list[str]: """Collect all unique SD data tags from a list of molecules.""" tags: list[str] = [] for mol in mol_list: for dp in oechem.OEGetSDDataIter(mol): if dp.GetTag() not in tags: tags.append(dp.GetTag()) return tags def _write_html_file( ofp: typing.TextIO, mol_list: list[oechem.OEMolBase], filename: str, tags: list[str], opts: oedepict.OE2DMolDisplayOptions, ) -> None: """Write the full HTML file content.""" _write_html_header(ofp, filename, tags) for mol in mol_list: _write_html_table_row(ofp, mol, opts, tags) _write_html_footer(ofp) def _write_html_table_row( ofp: typing.TextIO, mol: oechem.OEMolBase, opts: oedepict.OE2DMolDisplayOptions, tags: list[str], ) -> None: """Write one table row with the molecule image and its SD data.""" ofp.write("\n") ofp.write(f" {_get_svg_image(mol, opts)}\n \n") for tag in tags: value = oechem.OEGetSDData(mol, tag) if oechem.OEHasSDData(mol, tag) else "N/A" ofp.write(f" {value} ") ofp.write("\n") def _get_svg_image(mol: oechem.OEMolBase, opts: oedepict.OE2DMolDisplayOptions) -> str: """Generate a bare SVG image string for a molecule.""" oedepict.OEPrepareDepiction(mol) disp = oedepict.OE2DMolDisplay(mol, opts) image_str = oedepict.OERenderMoleculeToString("bsvg", disp, False) return image_str.decode("utf-8") def _write_html_header(ofp: typing.TextIO, filename: str, tags: list[str]) -> None: """Write the HTML header including CSS styles and table header row.""" table_width = min(1800, (len(tags) + 1) * 200) ofp.write("\n") ofp.write(f"

{filename}

\n") ofp.write("\n") ofp.write("\n") ofp.write("\n") ofp.write("\n") ofp.write("") ofp.writelines(f"" for tag in tags) ofp.write("\n\n") def _write_html_footer(ofp: typing.TextIO) -> None: """Write the HTML closing tags.""" ofp.write("
Molecule {tag}
\n\n\n") 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())