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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.

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

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

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.

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 molar_mass is also known, the molecular formula. Masses come from the bundled NIST standard atomic weights, so the computation is offline and deterministic.

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 max_multiplier), and reduces to the empirical formula. Use balance to assign an unmeasured element (typically oxygen) the remainder up to 100%.

Returns the resolved_percentages (including any balance element), the empirical_formula and its weight, the molecular_formula (null without a molar mass) with its molecular_multiplier, and a fit block -- the predicted_percentages the returned formula actually implies, the per-element residuals, and the rms_error / max_abs_error in percentage points. Any data-quality warnings (percentages not summing to 100%, a poor fit, a molar mass far from a whole multiple) are listed.

Raises ValueError on an unknown element, a non-positive percentage, or percentages leaving no remainder for the balance element.

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

TDQS

A4.2/5.0

Scored across 5 tools

Disambiguation5/5

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.

Naming Consistency4/5

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.

Tool Count5/5

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.

Completeness4/5

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.

Maintenance

ActivityMaintained
ResponsivenessNo issues