Skip to main content
Glama

jean — Molecular Biology & Genomics

enzyme_cut_counts

Read-only

Per-enzyme cut counts on the open plasmid (the EcoRI² superscript-badge numbers).

Input Schema

TableJSON 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.
enzymesYesenzyme names to scope the scan to — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows). 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

TableJSON Schema
NameRequiredDescriptionDefault
totalYestotal cuts across every enzyme asked about
countsYesenzyme → cut-count map; an enzyme with no sites is present with 0, never omitted
singleYeshow many cut EXACTLY once: the enzymes that linearise this molecule
cuttersYeshow many of the enzymes cut at least once
zero_cuttersYeshow many were scanned for and have no site here

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

C2.9/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=false, and destructiveHint=false, so the safety profile is covered. The description adds useful behavioral context: it operates on the open plasmid and corresponds to the EcoRI² superscript-badge numbers in the editor UI.

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?

The description is a single, front-loaded fragment with no wasted words. It is appropriately terse for a simple read-only count tool, though the parenthetical jargon may not be meaningful to an agent without UI context.

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?

An output schema exists, so return values need not be explained, and annotations cover safety. However, the description omits usage guidance and sibling differentiation, leaving gaps for an agent deciding between similar restriction-analysis tools.

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 the schema already documents all three parameters in detail. The description adds no additional parameter meaning beyond implying that counts are per enzyme, making the baseline of 3 appropriate.

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

Purpose3/5

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

The description names a specific resource and output type: per-enzyme cut counts on the open plasmid. However, it is a fragment without a clear verb, and it does not distinguish itself from sibling tools such as find_restriction_sites, digest_fragments, or enzyme_collection, leaving the agent to infer the exact 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 guidance on when to use this tool versus alternatives. The phrase 'on the open plasmid' implies the tool acts on the currently open record, but no alternatives or exclusions are named.

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

Try in Browser

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources