#!/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. 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. """Print monomers to console.""" import argparse import json import os import pathlib import sys import rich.console import rich.markup import rich.table import rich.text from openeye import oechem from rich_argparse import HelpPreviewAction, RichHelpFormatter __SCRIPT_NAME__ = pathlib.Path(__file__).absolute().stem __SCRIPT_DESC__ = "Print monomers to console." __SCRIPT_TOOLKITS__ = ["oechem"] __SCRIPT_KEYWORDS__ = ["monomer", "peptide", "peptide-informatics"] __SCRIPT_CATEGORIES__ = ["peptide-informatics"] def parse_options() -> argparse.Namespace: """Set up command line options.""" parser = argparse.ArgumentParser( add_help=True, formatter_class=RichHelpFormatter, description="[yellow]" + __SCRIPT_DESC__ + "[/yellow]", ) monomers_group = parser.add_argument_group("Monomer set options") _add_monomer_collection(monomers_group) 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: """Print monomers to console.""" args = parse_options() monomers = _get_monomer_collection(args) console = rich.console.Console(record=args.save_console_svg) console.print(monomers) if args.save_console_svg: console.save_svg(f"{__SCRIPT_NAME__}.svg", title="output") return os.EX_OK class MonomerSetParameter: # noqa: PLW1641 """Utility class to handle both built-in and user defined monomer sets.""" def __init__(self) -> None: # noqa: D107 self._monomer_sets = ["Standard", "OpenEye", "JSON-FILENAME"] def __repr__(self) -> str: # noqa: D105 return ",".join(self._monomer_sets) def __eq__(self, param: object) -> bool: # noqa: D105 if not isinstance(param, str): return False if param in ["Standard", "OpenEye"]: return True console = rich.console.Console() monomer_set_filepath = pathlib.Path(param) if ( not monomer_set_filepath.exists() or monomer_set_filepath.suffix.lower() != ".json" ): console.print(f"[red]Invalid monomer set file '{param}' ![/red]") return False try: with monomer_set_filepath.open("r") as json_file: json.load(json_file) except json.JSONDecodeError as e: console.print(f"[red]Invalid monomer set file '{param}' ![/red]") console.print(f"[red]Error decoding JSON: {e} ![/red]") return False return True def _add_monomer_collection(arg_group: argparse._ArgumentGroup) -> None: arg_group.add_argument( "-m", "--monomers", type=str, default="Standard", choices=[MonomerSetParameter()], help="built-in monomer-set type or json file of monomers", ) def _get_monomer_collection(args: argparse.Namespace) -> oechem.OEMonomerSet: monomers = oechem.OEMonomerSet() match args.monomers: case "Standard": oechem.OELoadStandardMonomerSet(monomers) case "OpenEye": oechem.OELoadOpenEyeMonomerSet(monomers) case _: oechem.OEReadMonomerSet(monomers, args.monomers) return monomers def monomer_set_rich_console( self, # noqa: ANN001 console: rich.console.Console, options: rich.console.ConsoleOptions, ) -> rich.console.RenderResult: """Rich representation of the monomer set.""" primary_code_set = self.GetPrimaryCodeSet() code_sets: list[str] = [ primary_code_set, *[c for c in self.GetCodeSets() if c != primary_code_set], ] columns: list[tuple[str, str, str]] = [ # (header, justified, footer ("idx", "right", "Total"), *[(c, "left", f"{self.NumMonomers(c)}") for c in code_sets], *[(str(r), "right", "") for r in range(1, 4)], ("polymer", "center", ""), ("monomer", "center", ""), ("amino types", "center", ""), ("analogue", "center", ""), ("SMILES", "left", ""), ] table = rich.table.Table( title=f"[bold]Number of monomers: {self.NumMonomers()} Version={self.GetVersion()} [/bold]", show_footer=True, ) for header, justify, footer in columns: table.add_column(header, justify=justify, footer=footer) # type: ignore[arg-type] for idx, monomer in enumerate(self.GetMonomers()): codes: list[rich.text.Text] = [ ( rich.text.Text( monomer.GetCode(code_set), style=( "" if code_set != "PDB" else f"link https://www.rcsb.org/ligand/{monomer.GetCode(code_set)}" ), ) if monomer.HasCode(code_set) else rich.text.Text("-", style="dim") ) for code_set in code_sets ] polymer_type = oechem.OEPolymerTypeToString(monomer.GetPolymerType()) row_data = [ str(idx + 1), *codes, *[_get_r_group_repr(monomer, r) for r in range(1, 4)], polymer_type, _get_monomer_type_repr(monomer), _get_amino_acid_type_repr(monomer), _get_standard_analog_repr(monomer), f"{rich.markup.escape(monomer.GetSmiles())}", ] table.add_row(*row_data) yield from table.__rich_console__(console, options) def _get_r_group_repr(monomer: oechem.OEMonomer, rgroup_idx: int) -> rich.text.Text: if not monomer.HasRGroup(rgroup_idx): return rich.text.Text("") if monomer.GetPolymerType() == oechem.OEPolymerType_Peptide: match rgroup_idx: case 1: return rich.text.Text("R1", style="bold rgb(100,120,240)") case 2: return rich.text.Text("R2", style="bold rgb(240,100,120)") case 3: return rich.text.Text("R3", style="bold rgb(45,110,40)") return rich.text.Text(f"R{rgroup_idx}", style="bold rgb(240,140,80)") def _get_monomer_type_repr(monomer: oechem.OEMonomer) -> rich.text.Text: if monomer.GetMonomerType() == oechem.OEMonomerType_Backbone: return rich.text.Text("backbone") if ( monomer.GetMonomerType() == oechem.OEMonomerType_Terminal and monomer.IsNTerminal() ): return rich.text.Text("🅝", style="bold white") + rich.text.Text( "-terminal", style="not bold" ) if ( monomer.GetMonomerType() == oechem.OEMonomerType_Terminal and monomer.IsCTerminal() ): return rich.text.Text("🅒", style="bold white") + rich.text.Text( "-terminal", style="not bold" ) return rich.text.Text("N/A", style="bold on red") def _get_amino_acid_type_repr(monomer: oechem.OEMonomer) -> rich.text.Text: amino_acid_type = monomer.GetAminoAcidType() amino_acid_dict = { oechem.OEAminoAcidType_Alpha: "α", # noqa: RUF001 oechem.OEAminoAcidType_Beta: "β", oechem.OEAminoAcidType_Gamma: "γ", # noqa: RUF001 oechem.OEAminoAcidType_Delta: "δ", oechem.OEAminoAcidType_NMethylated: "N-me", oechem.OEAminoAcidType_AlphaMethylated: "α-me", # noqa: RUF001 oechem.OEAminoAcidType_BetaMethylated: "β-me", } amino_types = [] for amino, amino_repr in amino_acid_dict.items(): if amino_acid_type & amino == amino: amino_types.append(amino_repr) return rich.text.Text(",".join(amino_types), style="bold") def _get_standard_analog_repr(monomer: oechem.OEMonomer) -> rich.text.Text: if monomer.GetPolymerType() != oechem.OEPolymerType_Peptide: return rich.text.Text("-", style="bold") analog = oechem.OEGetStandardAnalog(monomer.GetCanonicalSmiles()) if analog == oechem.OEResidueIndex_UNK: return rich.text.Text("-", style="bold") return rich.text.Text(oechem.OEGetAminoAcidCode(analog), style="bold") oechem.OEMonomerSet.__rich_console__ = monomer_set_rich_console # type: ignore[attr-defined] 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())