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berntpopp
by berntpopp

Get Position Tolerance

get_position_tolerance
Read-onlyIdempotent

Retrieve missense tolerance, Pfam domain membership, and variant evidence for a single protein residue position. Provide transcript ID and residue position.

Instructions

Return one residue's missense tolerance (sw_dn_ds + sliding-window coverage), its Pfam/meta-domain membership, and explicitly scoped variant evidence on a built tolerance landscape. Out-of-range positions raise invalid_input; a not-yet-built landscape raises not_found (request_tolerance_landscape first). Signature: get_position_tolerance(transcript_id=, position=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
positionYes1-based protein residue position.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact
transcript_idYesA versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first.
Behavior5/5

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

Annotations declare readOnlyHint=true and idempotentHint=true. Description adds behavioral details: specific error types (invalid_input, not_found) and the dependency on a built landscape, which annotations do not cover. No contradiction.

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

Conciseness5/5

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

Two sentences plus a concise signature. No wasted words; key information front-loaded. Every sentence adds value.

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?

Description summarizes main outputs but lacks details on return structure, especially for variant evidence and response_mode modes. Without output schema, more specificity would improve completeness.

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 has 100% description coverage for all 3 parameters. Description provides the signature and mentions response_mode verbosity, but adds little beyond schema. Baseline 3 is appropriate.

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 clearly states the verb 'Return' and resource: one residue's missense tolerance, domain membership, and variant evidence. It distinguishes from siblings like get_tolerance_landscape by specifying 'on a built tolerance landscape'.

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?

Explicitly describes error conditions for out-of-range positions and not-yet-built landscapes, guiding the agent to call request_tolerance_landscape first. Could contrast more with siblings but provides clear context.

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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