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laszlopere

mcp-molecules

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
MCP_MOLECULES_ONLINENoSet to a falsy value (0/false/no/off) to keep lookups fully offline. Default is enabled.
MCP_MOLECULES_EPA_API_KEYNoFree CCTE API key for EPA CompTox source. Without it, that source is skipped.

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": false
}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
infoA

Report mcp-molecules server availability, version, and environment information.

molecular_weight_calculatorA

Compute the molecular weight (molar mass) of a chemical formula.

Parses formula into an atom tally, looks up each element's mass in the bundled NIST Atomic Weights and Isotopic Compositions database, and returns the total weight in the requested unit. Every call reports all three distinct mass flavors under masses so callers never conflate them or have to re-ask:

  • nominal -- sum of the integer mass numbers of the most abundant isotopes,

  • average -- the standard atomic weight (average molar mass),

  • monoisotopic -- the exact mass of the most abundant isotopes.

The monoisotopic flag selects which of these is mirrored at the top level (weight / uncertainty / formatted) and named by primary. Optionally propagates NIST uncertainties (uncertainty) and/or reports percent composition by mass (composition).

Raises ValueError for an unparseable formula or an unknown element.

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 mass (and mz when charge is non-zero), its intensity relative to the base peak, and its absolute abundance. Also reports the monoisotopic_mass (most-abundant isotope of each element) and the average_mass. Backed by the bundled NIST Atomic Weights and Isotopic Compositions database -- offline and deterministic.

Peaks below threshold percent of the base peak are dropped; at most limit are returned. grouping selects nominal-mass (unit) or fully resolved (exact) peaks.

Raises ValueError for an unparseable formula or an unknown element.

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 by. Returns the query, how it was interpreted (interpreted_as), the normalized Hill-system canonicalization of the query whenever it parses as a formula (e.g. 'O6C6H12' -> 'C6H12O6'; null when it is not a parseable formula), the matches (each {"name", "formula"}, the preferred result first), and the resolving source / license.

Raises ValueError if nothing matches.

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

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