cdxml-toolkit-community: Instructions file for Claude Code

cdxml-toolkit — Agent Reference

What this is

A chemistry office automation toolkit with 15 compatible core MCP tools and a 35-tool community profile. Agents use these tools to draw molecules, render reaction schemes, parse ELN exports, analyze LCMS/NMR data, complete lab books, and manipulate ChemDraw files in PowerPoint/Word.

All structure output is CDXML (ChemDraw XML). Uses ACS Document 1996 style.

Key rules

1. Ground every molecule. Connectivity may come from a trusted value supplied by the user or from resolve_name, modify_molecule, parse_reaction, or an OCSR tool. Never invent a SMILES from model knowledge or visual inspection.
2. Verify structural edits. Route intentional changes through modify_molecule; inspect its MCS diff before drawing. A trusted SMILES that requires no modification can be passed to draw_molecule.
3. Never return large output inline. Tools write files and return {ok, output_path, size}. Use summarize_reaction to view parse_reaction output — do not read the full JSON.
4. CDXML is the interchange format. Binary CDX files must be converted via convert_cdx_cdxml.

MCP server

python -m cdxml_toolkit.mcp_runtime                              # stdio
python -m cdxml_toolkit.mcp_runtime --profile office             # smaller profile
python -m cdxml_toolkit.mcp_runtime --transport streamable-http  # network service

Tool reference

Read docs/mcp-tools.md for all generated signatures. The sections below describe the compatible core tools.

resolve_name

Resolve any chemical identifier to a rich molecule descriptor.

resolve_name(query="aspirin")
resolve_name(query="Cs2CO3")
resolve_name(query="534-17-8")       # CAS number
resolve_name(query="CF3")            # fragment → prefix form

Returns: {ok, name, smiles, formula, mw, exact_mass, iupac_name, source, role, display_text, prefix_form}

5-tier chain: curated reagent DB (186 entries) → condensed formula parser → ChemScript IUPAC (preferred) → OPSIN (bundled offline fallback) → PubChem.