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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.

Input Schema

NameRequiredDescriptionDefault
_filesNoThe 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.
schemeNonumbering scheme. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), martin (Martin (enhanced Chothia)), aho (AHo), wolfguy (Wolfguy).imgt
proteinYesthe protein sequence (one-letter amino acids); may hold several domains, e.g. an scFv.
speciesNospecies whose HMMs are preferred for the hit and whose germlines are searched (ANARCI's default: human and mouse).
_subjectNoThe 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.
chainTypesNochain types to number: H, K, L (antibody); A, B, G, D (TCR). Others are still listed in the hit table.
cdrDefinitionNowhere 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
assignGermlineNoassign the closest V and J germline genes.
bitScoreThresholdNominimum HMMER bit score for a domain to count (ANARCI's default 80).

Output Schema

NameRequiredDescriptionDefault
hitsYesevery HMM hit over the threshold: id, E-value, bit score, start, end
domainsYesone entry per domain: chain type, species, sequence span, numbering as [position, residue] pairs, framework and CDR regions (0-based residue spans) under cdrDefinition, germlines
chainTypesYesthe chain type of each domain, in sequence order

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety is covered. The description adds real behavioral detail beyond them: the tool both detects/numbering domains and performs secondary calls (chain type, species, closest V/J germline with % identity), telling the agent more will come back than just numbering. It does not mention failure modes when no domain passes the bit-score threshold, but the output schema carries return structure.

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 front-loaded sentence that leads with the core action and then enumerates the value-adds; every clause carries information. Minor redundancy in spelling out all six schemes, which the enum already lists, makes it slightly longer than necessary.

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 a 9-parameter tool with 100% schema coverage, full annotations, an output schema, and a single required input, the description covers the essential purpose and the pipeline outputs. An explicit note on behavior when no domain is found would complete it, but nothing needed to call it correctly is missing.

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, species, chainTypes, cdrDefinition, assignGermline, bitScoreThreshold, protein) is already documented. The description only restates the numbering schemes and germline assignment, adding no syntax, format, or interaction semantics beyond the schema; 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?

States a concrete verb+resource: find antibody/TCR variable domains in a protein sequence and number them. It additionally names the downstream outputs (chain type, species, V/J germline with percent identity), which clearly separates it from siblings like antibody_isotype, antibody_canonical_classes, or graft_antibody_cdrs.

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 implied rather than stated: an agent can infer it applies to an antibody/TCR protein sequence input, and the numbering-scheme enumeration hints at the choice to make. There is no explicit when-to-use/when-not or pointer to an alternative tool (e.g. compare_antibodies or antibody_molecule) for related tasks.

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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