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Jean — Molecular Biology & Genomics

classify_grammar_part

Read-only

Which Golden Braid / MoClo / Yeast ToolKit grammar, position and level the open plasmid represents (or null).

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.
_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.

Output Schema

NameRequiredDescriptionDefault
levelYesassembly level
spansYesfor a COMPOSITE position, the slots it occupies end to end (YTK Type 234 spans 2, 3 and 4); empty otherwise
grammarYesgrammar name, or empty when unclassified
isVectorYestrue when a part at this position is also the acceptor backbone for its level (YTK Type 8, 8a, 678)
positionYesposition name within the grammar
releaseCutsYeshow many times the release enzyme cut. 2 for a clean excise; 3 for a GoldenBraid Level-0 module, whose pUPD backbone carries its own site, so the backbone is released in two pieces and the insert is identified by carrying no backbone marker
releaseEnzymeYesenzyme that releases the part
classificationYesthe full classification (null when no grammar matches)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already establish this is a safe, closed-world read, so the description is not carrying the safety burden. It usefully discloses that the result may be null when the plasmid matches no grammar, and that three grammar families are checked, but says nothing about how the classification is derived or what happens with input files.

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?

A single front-loaded sentence with no filler; the parenthetical '(or null)' efficiently conveys the failure case. Minor awkwardness in the phrasing 'which ... grammar ... the open plasmid represents' but nothing extraneous.

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?

For a read-only classifier with an output schema, the description is adequate: it names the outputs and the null case. It falls short on how the open plasmid and any supporting files participate, and gives no hint about what 'position' and 'level' values look like.

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% and both parameters are fully documented there, so the baseline is 3. The description adds only the framing that the target is 'the open plasmid', which slightly sharpens _subject semantics but does not explain the role of _files in classification.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

Names a specific action (classify) and the exact attributes returned: grammar family (Golden Braid / MoClo / Yeast ToolKit), position, and level. It is clearly distinguishable from siblings like check_golden_gate_parts or match_part_by_sequence, though it never explicitly contrasts itself with them.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no guidance on when to call this versus adjacent tools such as check_golden_gate_parts, match_part_by_sequence, or get_open_record, and no stated preconditions (e.g. that a plasmid must already be open). The implied context ('the open plasmid') is the only usage signal.

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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