mcp-molecules
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| MCP_MOLECULES_ONLINE | No | Set to a falsy value (0/false/no/off) to keep lookups fully offline. Default is enabled. | |
| MCP_MOLECULES_EPA_API_KEY | No | Free CCTE API key for EPA CompTox source. Without it, that source is skipped. |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| infoA | Report mcp-molecules server availability, version, and environment information. |
| molecular_weight_calculatorA | Compute the molecular weight (molar mass) of a chemical formula. Parses
The Raises |
| isotope_distributionA | Compute the natural isotopic pattern (isotope distribution) of a formula. Returns the set of isotopologue peaks a mass spectrometer would see: each
peak's neutral Peaks below Raises |
| find_chemical_compoundA | Look up a chemical compound by name or molecular formula. Searches the bundled name<->formula database (a PubChem subset) first, then
the writable user cache, then -- unless disabled -- the online fallback
(PubChem, Wikidata, and, when an API key is set, EPA CompTox). A name
resolves to its molecular formula(e); a formula resolves to the compound
name(s) sharing it (isomers), ordered with the preferred name first. The
direction is chosen by Raises |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 4 tools
Each tool has a clearly distinct purpose: lookup compounds, report server info, compute isotope distribution, and calculate molecular weight. There is no functional overlap, and the detailed descriptions prevent confusion.
Tool names mix patterns: 'find_chemical_compound' follows verb_noun, while 'info', 'isotope_distribution', and 'molecular_weight_calculator' are noun phrases. The inconsistent verb usage and the terse 'info' name break a predictable pattern.
With 4 tools, the server is well-scoped for its purpose of chemical compound lookup and calculation. Each tool earns its place without feeling sparse or bloated.
The server covers core workflows: compound lookup, molecular weight, and isotope distribution. Minor gaps exist, such as missing tools for property lookup or cache management, but the domain is well-served by the current set.