CovaSyn Chemistry Tools

covabasic_iupac_name

Get the IUPAC name of a structure — generating one when it is unknown to any database.

Two sources, tried in order, and the response always says which one answered:
  - `source="pubchem"`  — the curated, human-checked IUPAC name. Authoritative,
    but only exists for compounds PubChem indexes.
  - `source="openclatura"` — a name constructed from the molecular graph by a
    deterministic IUPAC Blue Book (2013) rule engine. Works on any valid
    structure, including novel compounds, intermediates and analogues.

Parameters:
  prefer_pubchem — check PubChem first (default true). Set false to force
    generation, or to keep the call purely offline and ~100x faster: the
    rule engine takes ~5 ms, the PubChem round-trip 0.6-1 s.
  explain — also return `rules_hit`, the Blue Book rules that fired
    (e.g. P-44, P-61). Costs ~5x the naming time; off by default.
  verify — round-trip the generated name through OPSIN and report whether it
    parses back to the same structure. Needs a Java runtime; without one the
    result reports `verification="skipped_no_java"` instead of failing.

Returns: `{name, smiles, source, generated, engine}` (+ `rules_hit`,
`verification` when requested), or `{error, smiles}`.

A generated name is a systematic construction, not a database record —
treat `generated=true` accordingly.

Input Schema

Name	Required	Description	Default
`smiles`	Yes
`verify`	No
`api_key`	No
`explain`	No
`prefer_pubchem`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 9, 2026

TDQS

A4.3/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full behavioral burden and does so well: it discloses source order, speed difference (~5 ms vs 0.6–1 s), explain cost (~5x), verify's Java dependency and graceful fallback, and the meaning of generated=true. It also states the error return shape.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The definition is front-loaded and organized with source bullets, parameter bullets, and a short returns note. It is appropriately sized for a tool with five parameters and no schema descriptions, though including return fields is somewhat redundant given the output schema.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with no annotations, zero schema descriptions, and complex behavior, the description is largely complete: it covers source precedence, performance, dependencies, and generated-name caveats. It stops short of full completeness because api_key and the exact smiles input expectation are unexplained.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must define all five parameters. It explains prefer_pubchem, explain, and verify in useful detail, but never explains the required smiles input format or the api_key parameter, leaving real gaps.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb+resource: 'Get the IUPAC name of a structure,' and immediately extends it to generation when no database entry exists. This is clear enough to distinguish it from sibling tools like covabasic_pubchem or covabasic_analyze by output, even though it does not explicitly name an alternative tool.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explains the two source modes and gives concrete conditions for setting prefer_pubchem=false: force generation, keep the call offline, or gain ~100x speed. It does not explicitly route the agent away from sibling tools or state when not to use this tool, so it falls short of full alternative-routing guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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