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berntpopp
by berntpopp

Compare Positions

compare_positions
Read-onlyIdempotent

Compare missense tolerance, domain annotations, and variant counts across multiple protein positions in a transcript with a side-by-side table.

Instructions

Return a side-by-side tolerance table (sw_dn_ds, ref_aa, domain ids, variant counts) for a batch of residue positions on a built landscape. Out-of-range positions get a per-item error row -- the whole batch never fails for one bad position; the batch size is capped. Signature: compare_positions(transcript_id=, positions=, response_mode=).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
transcript_idYesA versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first.
positionsYesA batch of 1-based protein residue positions to compare side by side.
response_modeNoVerbosity: minimal|compact|standard|full (default compact).compact

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
successYes
_metaNo
error_codeNo
messageNo
retryableNo
recovery_actionNo
fieldNo
hintNo
candidatesNo
recommended_citationNo
data_versionsNo
transcript_idNo
comparisonNo
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true. The description adds valuable behavioral details: out-of-range positions get error rows, no whole-batch failure, and batch size cap. No contradictions.

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?

The description is two sentences plus a signature line, all front-loaded and concise. Every sentence provides essential information without redundancy.

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

Completeness5/5

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

For a read-only batch tool with an output schema, the description covers purpose, error handling, batch size limits, and result components. No gaps.

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% with adequate descriptions. The description reinforces parameter names and mentions batch context but adds minimal new meaning beyond the schema.

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 tool returns a side-by-side tolerance table for a batch of residue positions, specifying the resource and action. It distinguishes from siblings like get_position_tolerance by highlighting batch processing and error handling.

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?

The description explains when to use the tool (batch comparison of positions) and notes error behavior (per-item errors, batch size cap). It does not explicitly compare to alternatives 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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