laszlopere/mcp-molecules

**Atoms and molecules for the artificial minds — trustworthy chemistry tools,
computed for real and backed by authoritative data.**
Atoms combine into molecules, and a language model asked about them should not
have to recall facts from memory; it should *compute* answers it can trust.
mcp-molecules is a growing toolbox for working with chemical elements and
molecules — offline, deterministic, and backed by authoritative sources such as
the NIST Atomic Weights and Isotopic Compositions database.
For example, it can already take a chemical formula and return its molecular
weight: ask "what does C₆H₁₂O₆ weigh?" and it parses the formula, looks every
element up in NIST data, and computes the molar mass rather than guessing it.
More molecule-oriented tools are planned.
You can ask things like:
- *"What does a mole of glucose weigh?"* — resolves the name to C₆H₁₂O₆ and
computes the molar mass.
- *"How much of Fe₂(SO₄)₃'s mass is iron?"* — per-element percent composition.
- *"What's the molar mass of caffeine, with uncertainty?"* — propagates the NIST
standard uncertainties.
- *"What does the mass spectrum of chloroform look like?"* — the natural chlorine
isotope pattern (the M, M+2, M+4 … peaks).
- *"What's the [M+H]⁺ m/z for caffeine?"* — the protonated-ion mass.
- *"Which compound has the formula C₉H₈O₄?"* — formula → name (aspirin, among its
isomers).
- *"What are the isomers of C₂H₆O?"* — one formula, several names (ethanol and
dimethyl ether).
What it gives you
- **molecular_weight_calculator** — *(one example of what's here today)*
compute the molecular weight (molar mass) of a chemical formula. Parameters:
- formula — element symbols, integer multipliers, arbitrarily nested
parentheses, and the isotope labels D (deuterium) and T (tritium).
Examples: H2O, C6H12O6, Ca(OH)2, Fe2(SO4)3, ((CH3)2CH)2, D2O, Tc.
- unit — g/mol *(default)*, kg/mol, Da, u, or kDa.
- uncertainty — propagate the per-element NIST standard uncertainties in
quadrature and report value ± sigma.
- monoisotopic — use the most abundant isotope of each element
(mass-spectrometry monoisotopic mass) instead of the standard atomic weight.
- composition — return the per-element percent composition by mass.
- **isotope_distribution** — compute the natural isotopic pattern (the peaks a
mass spectrometer would see) for a formula, with each peak's mass, m/z, and
relative intensity, plus the monoisotopic and average masses. Parameters:
- formula — same syntax as molecular_weight_calculator.
- charge — 0 *(default)* reports neutral masses; a non-zero n reports m/z
for the [M+nH]/[M-nH] ion.
- threshold — drop peaks below this percent of the base peak *(default 0.1)*.
- limit — maximum peaks to return, most intense first *(default 10)*.
- grouping — unit *(default)* collapses to nominal integer masses; exact
keeps every resolved isotopologue.
- **find_chemical_compound** — look up a compound by name or molecular
formula. Searches a bundled offline database (a PubChem subset) and a writable