jean — Molecular Biology & Genomics

number_antibody

Read-only

Find antibody and T-cell-receptor variable domains in a protein sequence, number them under IMGT, Kabat, Chothia, Martin, AHo or Wolfguy, call chain type and species, and assign the closest V and J germline with percent identity. Validated against ANARCI 2026.2.13.2 on every chain of its PDB benchmark.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`scheme`	No	numbering scheme. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), martin (Martin (enhanced Chothia)), aho (AHo), wolfguy (Wolfguy).	imgt
`protein`	Yes	the protein sequence (one-letter amino acids); may hold several domains, e.g. an scFv.
`species`	No	species whose HMMs are preferred for the hit and whose germlines are searched (ANARCI's default: human and mouse).
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`chainTypes`	No	chain types to number: H, K, L (antibody); A, B, G, D (TCR). Others are still listed in the hit table.
`cdrDefinition`	No	where CDR1-3 begin and end (abnumber's borders; North is read in Chothia numbering). Kabat, Chothia and North define H, K and L chains only; TCR domains keep IMGT's. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North).	imgt
`assignGermline`	No	assign the closest V and J germline genes.
`bitScoreThreshold`	No	minimum HMMER bit score for a domain to count (ANARCI's default 80).

Output Schema

TableJSON Schema

Name	Required	Description
`hits`	Yes	every HMM hit over the threshold: id, E-value, bit score, start, end
`domains`	Yes	one entry per domain: chain type, species, sequence span, numbering as [position, residue] pairs, framework and CDR regions (0-based residue spans) under cdrDefinition, germlines
`chainTypes`	Yes	the chain type of each domain, in sequence order

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.7/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered by structured data. The description adds a validation/quality signal (ANARCI 2026.2.13.2, benchmarked on PDB chains) but says nothing beyond the annotations about failure modes, sensitivity to short or non-Ig sequences, or what an unnumbered domain implies.

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?

Two sentences, no waste, and the primary capability is front-loaded before the backend validation caveat. The first sentence is clause-dense but every clause names a distinct capability rather than padding.

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?

With an output schema present and 100% parameter coverage, the description does not need to explain return values, and it adequately conveys the tool's full pipeline. The remaining gap is the lack of positioning against sibling antibody tools and of any input-type guidance for the record/_subject parameters.

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 every parameter (scheme, chainTypes, cdrDefinition, bitScoreThreshold, species, assignGermline) is already documented in the schema itself. The description restates the numbering scheme concept but adds no syntax, defaults, or edge-case meaning beyond the schema, so the baseline 3 applies.

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 opens with a precise verb+resource pair ('Find antibody and T-cell-receptor variable domains in a protein sequence') and then enumerates the full output scope: numbering under six schemes, chain-type/species calls, and V/J germline assignment with percent identity. This clearly separates it from siblings like humanize_antibody, graft_antibody_cdrs, antibody_liabilities, and antibody_molecule, which an agent can distinguish without opening any schema.

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?

The description states what the tool produces but gives no explicit when-to-use guidance, prerequisites, or named alternatives among the many sibling antibody tools. Usage is only implied by the domain ('variable domains in a protein sequence'), so an agent must infer the routing decision itself.

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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