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Jean — Molecular Biology & Genomics

digest_reaction_conditions

Read-only

The reaction a digest needs, from NEB's own data: the NEBuffer that serves every enzyme together (scored on the WORST enzyme's percent activity, a star-activity buffer disqualified at any percent), the incubation temperature(s), any cofactor that must be added (SAM or ATP), and each product's heat-inactivation step, or the products NEB cannot heat-inactivate.

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.
enzymesYesenzymes or NEB product names in one tube (EcoRI, BamHI-HF). A name NEB does not sell is returned under `unknown`, never dropped. Left unset, the run uses your active enzyme collection.
_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
bufferYesthe recommended NEBuffer, or null when every buffer is starred or at 0% for one of the enzymes
buffersYesevery NEBuffer scored, best first: worst percent, star-active enzymes, usable, per-enzyme activity
unknownYesnames NEB does not sell, so no conditions exist for them
cofactorsYescofactors the reaction requires (SAM, ATP), from REBASE
singleTubeYestrue when one buffer AND one temperature serve every enzyme
temperaturesCYesincubation temperatures required, ascending; more than one means more than one step
heatInactivationYeswhether the tube can be heat-killed, each product's NEB step (temperature, minutes), and the products that need a column or gel cleanup instead

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint true, destructiveHint false, closed-world), so the description is free to add real substance — and it does: it discloses the data source (NEB's own tables), the selection rule (buffer scored on the WORST enzyme's percent activity, star-activity buffer disqualified at any percent), and that un-heat-inactivatable products are reported rather than omitted. That scoring rule is decision-relevant behavior no structured field carries.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

It is a single sentence, front-loaded with the outcome, and every clause maps to a returned field, so little is wasted. However, the nested parentheticals about worst-enzyme scoring and star-activity disqualification make it dense enough to require a second read; a short lead plus a bulleted list of the four outputs would scan better.

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?

An output schema exists, so the description needn't document return shapes, and it still characterizes the payload well enough for the agent to trust the result. With annotations covering safety and the schema covering parameters, the only real gap is the absence of any cue about ordering this call relative to digest setup or thermocycler planning.

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 the enzymes parameter already documents the unknown-name fallback and the active-collection default, so the schema does the heavy lifting. The description adds only the indirect notion of 'every enzyme together' in one tube, which reinforces that enzymes are pooled rather than individually buffered. Baseline 3 is appropriate.

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?

The description names the resource precisely — reaction conditions for a restriction digest drawn from NEB's own data — and enumerates the four outputs (NEBuffer, incubation temperature, required cofactor, heat-inactivation step). It is clearly distinguishable from siblings like digest_fragments or enzyme_cut_counts. It falls short of 5 because it is written as a noun phrase describing the payload rather than a verb stating the operation.

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 explicit when-to-use or when-not-to-use guidance and no named alternative. The agent must infer that this is a lookup to run before setting up a digest, and nothing routes it away from enzyme_cut_counts, digest_fragments, or plan_thermocycler_program, which overlap in domain.

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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