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indigo_convert_molfile

indigo_convert_molfile
Read-onlyIdempotent

Converts a V2000 or V3000 molfile into SMILES, InChI, InChIKey, mol weight, or alternate molfile versions using Indigo toolkit endpoints.

Instructions

Convert a molfile using Indigo toolkit endpoints

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
molfileYesMolfile contents (V2000/V3000)
output_formatYesDesired transformation

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
valueYes
outputFormatYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.3.0

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already declare readOnly, idempotent, non-destructive and open-world behavior, so the safety profile is covered. The description adds nothing beyond noting an Indigo wrapper – no note on error behavior for invalid molfiles, unsupported conversions, or round-trip fidelity, which is the context an agent would actually want for a chemistry conversion tool.

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

Conciseness3/5

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

It is a single short sentence with no redundancy and the key resource is front-loaded, which is good structure. But the brevity reflects under-specification rather than efficient compression – the sentence carries almost no information beyond what the tool name already conveys.

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

Completeness3/5

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

With only two fully-documented parameters and an output schema present, the tool does not need return-value explanation. What is missing is the routing context – when this Indigo-based conversion is preferable to the OPSIN name converter or identifier resolution – leaving the definition minimally viable for a simple tool.

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 100% and the enum already enumerates the seven valid output formats with a description for each parameter. The description adds no additional meaning about the molfile string format or the semantic difference between mol_v2000 and mol_v3000 outputs, so the baseline 3 applies.

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

Purpose4/5

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

The description gives a specific verb ("Convert") and resource ("molfile"), which is clear enough to distinguish it from the wealth of search/get siblings. However, it does not differentiate itself from the equally conversion-oriented sibling opsin_convert_name or from resolve_chemical_identifier, so an agent cannot tell which converter applies from the text alone.

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

Usage Guidelines2/5

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

There is no guidance on when to use this tool versus alternatives such as opsin_convert_name or resolve_chemical_identifier, and no statement of prerequisites or supported input conditions. Usage must be inferred entirely from the name and the schema.

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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