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
} |
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 |
| elemental_analysisA | Infer a chemical formula from elemental mass percentages (inverse analysis). The inverse of percent composition: given each element's mass percent -- what
a combustion / CHN elemental analyzer reports -- recover the best-fit
empirical formula, and, when Assumes a 100 g sample, converts each percentage to relative moles via the
atomic weights, normalises to whole-number atom ratios (searching integer
multipliers up to Returns the 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 5 tools
Each tool targets a clearly distinct task: compound lookup, molecular weight calculation, isotope distribution, inverse elemental analysis, and server info. Although molecular_weight_calculator and isotope_distribution both return mass-related values, their primary outputs and use cases are clearly separated by the descriptions.
All names use snake_case and are descriptive, but the pattern is not a uniform verb_noun: most are noun phrases (elemental_analysis, isotope_distribution, molecular_weight_calculator), one is verb-led (find_chemical_compound), and info is a bare meta name. The set remains readable and mostly predictable.
Five tools is well within the ideal 3–15 range for a focused chemistry server. Each tool serves a distinct, non-redundant function, so the count feels well-scoped rather than bloated or thin.
The surface covers lookup, molecular weight, isotope distribution, and inverse formula inference, which are the core formula-centric operations. Minor gaps remain, such as direct formula parsing, exact-mass-to-formula search, or batch calculations, but agents can work around these.