Skip to main content
Glama
berntpopp
by berntpopp

Compare Positions

compare_positions
Read-onlyIdempotent

Compare missense tolerance, domain annotations, and variant evidence across multiple residue positions in a single side-by-side table. Accepts a batch of positions and returns per-item results even if some positions are out of range.

Instructions

Return a side-by-side tolerance table (sw_dn_ds, ref_aa, domain ids, explicitly scoped variant evidence) 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
positionsYesA batch of 1-based protein residue positions to compare side by side.
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 already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint, indicating safe, idempotent reads. The description adds specific behavioral context beyond annotations: batch size cap, per-item error handling for out-of-range positions, and that the whole batch never fails. No contradictions with annotations.

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 extremely concise: two sentences plus a signature line. Every sentence adds value—main purpose, error handling behavior, and a clear function signature. No redundancy or fluff.

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?

Given the tool's complexity (batch comparison with error handling) and lack of output schema, the description reasonably covers key behaviors: return type (tolerance table with specific columns like sw_dn_ds, ref_aa, domain ids), error handling, batch cap, and parameters. It could elaborate slightly on the return structure, but the included column hints are sufficient.

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 coverage is 100% with descriptions for all three parameters. The description adds a signature line that mirrors the schema but does not provide additional semantic meaning beyond what is already in the schema. For example, the batch behavior is mentioned in the description but not tied specifically to the positions parameter beyond schema text.

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 specifies a clear verb ('Return') and resource ('side-by-side tolerance table ... for a batch of residue positions on a built landscape'). It distinguishes from sibling tools like get_position_tolerance by emphasizing batch processing and side-by-side comparison. Includes details about error handling and batch size cap, making the purpose unambiguous.

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 implies when to use this tool (for batch comparison of positions) and mentions behavioral safeguards ('batch never fails for one bad position'). It does not explicitly list alternative sibling tools for single-position queries, but the context of batch side-by-side comparison effectively differentiates from get_position_tolerance.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/berntpopp/metadome-link'

If you have feedback or need assistance with the MCP directory API, please join our Discord server