ChemGlyph MCP server

ChemGlyph

Publication-quality chemical structure and reaction rendering for AI agents. ChemGlyph is the KaTeX of chemistry: a rendering layer, a validation layer, and an MCP interface on top of RDKit.

Install

pip install chemglyph

Render a molecule

import chemglyph

result = chemglyph.render_molecule("c1ccccc1")  # benzene
open("benzene.svg", "w").write(result.data)

rendermolecule takes SMILES, InChI, or molblock and returns SVG (or PNG) plus canonicalsmiles, molformula, molweight, and warnings.

Styles

Three styles, same molecule (benzoic acid, caffeine, (S)-ibuprofen):

chemglyph.render_molecule(smiles, style="acs")  # black/white, ACS journal
chemglyph.render_molecule(smiles, style="modern")  # colored heteroatoms, screens
chemglyph.render_molecule(smiles, style="textbook-cn")  # bold monochrome, textbook

All styles default to a transparent background (transparent=True) and support fmt="png".

Reactions

spec = {
    "steps": [
        {
            "reactants": ["OC(=O)c1ccccc1O", "CC(=O)OC(C)=O"],
            "products": ["CC(=O)Oc1ccccc1C(=O)O", "CC(=O)O"],
            "conditions": {"above": "H₂SO₄ (cat.)", "below": "rt, 15 min"},
            "yield": "89%",
            "arrow": "forward",
        }
    ],
    "style": "modern",
}
svg = chemglyph.render_reaction(spec)

Conditions are pre-formatted Unicode text, so pass H₂SO₄, not H2SO4. ChemGlyph does not parse formulas out of text. The full schema (multi-step chains, equilibrium and retro arrows, line wrapping) is in docs/reaction_schema.md.

The aspirin demo writes a two-step route:

python examples/aspirin_synthesis.py  # writes examples/aspirin_synthesis.svg

Validation

validate_structure reports parse errors and applies four quick fixes: unmatched brackets and ring closures (reported, not guessed), kekulization failures of lowercase aromatic atoms, and nitrogen valence errors via a formal [N+]. Anything else passes RDKit's message through unchanged.

report = chemglyph.validate_structure("c1cccc1")
report.fixes[0].description  # 'lowercase aromatic atoms could not be kekulized...'
report.fixes[0].fixed_smiles  # 'C1CCCC1'

Naming

chemglyph.parse_name("aspirin")  # 'CC(=O)Oc1ccccc1C(=O)O'

English IUPAC and common names resolve offline through OPSIN (pip install 'chemglyph[opsin]', plus a Java runtime). Chinese names use the built-in dictionary, and the library API accepts a translator callable for names that are not in it:

chemglyph.parse_name("阿司匹林")  # 'CC(=O)Oc1ccccc1C(=O)O'
chemglyph.parse_name("六甲基苯", translator=to_english)

ChemGlyph itself never calls an online service, including for translation.

MCP server

Run the bundled console script (stdio transport):

<!-- mcp-name: io.github.random-orbit/chemglyph -->

chemglyph-mcp

Claude Desktop registration (macOS: ~/Library/Application Support/Claude/claudedesktopconfig.json):

{
  "mcpServers": {
    "chemglyph": {
      "command": "chemglyph-mcp"
    }
  }
}

Shortened. The full README is on GitHub.