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Scigantic

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surechembl_structure_search

Read-only

Search SureChEMBL's 31 million patent compounds by chemical structure.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "structure": "<structure>"
    },
    "name": "surechembl_structure_search"
  }
}

Input Schema

NameRequiredDescriptionDefault
modeNo"similarity" (Tanimoto at or above 0.8, default), "substructure" (at least 5 atoms; the server caps results at 10,000), "identical" (all features must match), or "connectivity" (same skeleton, any stereo/isotopes).
limitNoMax hits (default 20, max 500).
structureYesA SMILES.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • changedInput schema / properties / mode / description
      Previous value: -"\"similarity\" (Tanimoto, default), \"substructure\" (at least 5 atoms; the server caps results at 10,000), \"identical\" (all features must match), or \"connectivity\" (same skeleton, any stereo/isotopes)."New value: +"\"similarity\" (Tanimoto at or above 0.8, default), \"substructure\" (at least 5 atoms; the server caps results at 10,000), \"identical\" (all features must match), or \"connectivity\" (same skeleton, any stereo/isotopes)."
  2. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, so the safety profile is covered. The description adds useful dataset scope (31 million patent compounds), but says nothing about return shape, pagination, or that the 10,000 cap applies only to substructure mode — information the agent otherwise gets piecemeal from the schema.

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?

One sentence, front-loaded with the verb and corpus, with zero filler. It is arguably too terse for a tool whose behavior varies substantially by mode, but nothing in it is wasted.

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?

For a three-parameter read-only lookup with full schema coverage and no output schema, the definition is minimally sufficient. It does not convey result content (compound or patent identifiers) or the practical effect of the substructure cap, leaving the agent to rely entirely on the schema.

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%, so all three parameters, including the four-value mode enum and its defaults, are already documented in structured data. The description adds no interpretation, defaults, or format hints beyond the schema, which is exactly baseline for full coverage.

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 and resource (search patent compounds in SureChEMBL) plus the key qualifier 'by chemical structure', which separates it from the sibling text-based patent search tools. It stops short of naming a specific sibling, so an agent must still infer the split from names alone.

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

Usage Guidelines3/5

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

Usage is only implied by the phrase 'by chemical structure' — an agent can infer this is the structure-query tool, but there is no explicit when-to-use, when-not, or pointer to surechembl_search_patents or surechembl_compound for text-based lookups.

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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