laboratoire-de-chemoinformatique/chemspacecopilot/retrosynthesis-for-candidates

Retrosynthesis For Candidates

Use this skill when the user wants synthesis routes for a generated candidate, selected session molecule, SMILES string, or named compound.

Procedure

1. Resolve the target from the user prompt or session memory with session_resolve_session_reference when needed.
2. For generated-candidate references, resolve the candidate set and pass explicit selected SMILES. Ask for a candidate ID or selection when multiple candidates match.
3. Check that the SynPlanner runtime data is available before promising route generation.
4. Classify input with synplanner_identify_input; convert names with synplanner_convert_name_to_smiles when needed. If conversion fails, ask for SMILES.
5. Run synplanner_plan_synthesis and summarize with synplanner_describe_plan.
6. Save route figures with synplanner_get_route_visualizations when the user asks for visual artifacts or report-ready output. Present them in order using ![Route {route_index} - {caption}](png_path) with index/node_id/score in the caption.
7. If no route is found and an LLM fallback is allowed, label it explicitly as not SynPlanner-validated and do not present fallback chemistry as a SynPlanner result.
8. Include route artifacts in report_save_rich if a synthesis report is requested.

Expected Outputs

• Canonical target SMILES.
• Synthesis plan artifact.
• Optional route visualizations.
• Report-ready route summary.