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Jean — Molecular Biology & Genomics

screen_molecule_library

Read-only

Screen every structure of a library at once against drug-likeness rules and structural-alert catalogs, as the library grid does, and bin one rule property across it, split at the bound of a chosen rule.

Input Schema

NameRequiredDescriptionDefault
binsNohow many bins.
rulesNowhich drug-likeness rules to screen, by id. Every rule by default.
_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.
propertyNothe rule property to bin, at the value the rules judged. Values: mw (Monoisotopic mass), clogp (cLogP (Crippen)), hbd (H-bond donors), hba (H-bond acceptors), lipinskiHbd (Lipinski donors (NH + OH)), lipinskiHba (Lipinski acceptors (N + O)), hbonds (Donors + acceptors), tpsa (TPSA (N and O only)), rotatableBonds (Rotatable bonds), rings (Rings), heavyAtoms (Heavy atoms), numAtoms (Atoms in the graph), molarRefractivity (Molar refractivity (Crippen)), averageMw (Molecular weight (average)), totalAtoms (Atoms, hydrogens included), formalCharge (Net formal charge).mw
moleculesYesthe library: one SMILES or molfile per entry.
alert_setsNowhich structural-alert catalogs to screen against. Empty screens nothing.
split_ruleNothe rule whose bound on that property splits each bar; the first screened rule bounding it by default. Values: rule_of_five (Lipinski rule of five), rule_of_five_beyond (Beyond rule of five), rule_of_four (Rule of four (PPI inhibitors)), rule_of_three (Rule of three (fragments)), rule_of_three_extended (Rule of three, extended), rule_of_two (Rule of two (building blocks)), rule_of_ghose (Ghose filter), rule_of_veber (Veber filter), rule_of_reos (REOS), rule_of_chemaxon_druglikeness (ChemAxon drug-likeness), rule_of_egan (Egan filter), rule_of_pfizer_3_75 (Pfizer 3/75), rule_of_gsk_4_400 (GSK 4/400), rule_of_oprea (Oprea lead-likeness), rule_of_xu (Xu drug-like index), rule_of_cns (CNS penetration), rule_of_respiratory (Respiratory (inhaled/nasal)), rule_of_five_paper (Lipinski rule of five (paper: average MW)), rule_of_ghose_paper (Ghose filter (paper: all atoms, average MW)), rule_of_reos_paper (REOS (paper: net charge bounded, average MW)).

Output Schema

NameRequiredDescriptionDefault
rowsYesper structure: 0-based index, canonical SMILES, rules broken, alerts tripped
summaryYeshow many structures pass clean, and how many fall within the split bound
distributionYesthe bins (lo, hi, within, outside), the bounds on the property and the split

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
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. The description adds genuine behavioural context by disclosing that results are binned per rule property and split at a chosen rule's bound, but it says nothing about cost or limits on large libraries, nor about what happens when rules/alert_sets are empty (that only appears in the schema).

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 dense sentence that front-loads the screening action before the binning detail, with no wasted clauses. The one weak element is the parenthetical comparison 'as the library grid does', which spends words on an undefined reference.

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?

The presence of an output schema means return values need no explanation, and the read-only annotations cover safety. However, for an 8-parameter tool with nested _subject/_files structures, the description never indicates how the library is supplied (molecules array vs project record references), leaving a meaningful gap for a complex input surface.

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%, including per-value enum documentation for property, split_rule and the rule/alert catalogs, so the schema already carries the parameter burden. The description restates the property/split_rule relationship ('bin one rule property ... split at the bound of a chosen rule') but that interaction is also spelled out in the split_rule schema text, so it adds little beyond the baseline.

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 a specific verb ('screen') and resource ('every structure of a library'), and adds the secondary operation of binning one rule property. It is clearly distinct from single-molecule siblings like assess_small_molecule or compare_molecules, but it never names a sibling to contrast with, and the phrase 'as the library grid does' is opaque to an agent that has no grid context.

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 only implied by the phrase 'every structure of a library at once', which suggests bulk screening, but there is no explicit when-to-use or when-not-to-use guidance. Nothing routes the agent between this tool and near neighbours such as search_molecule_library, cluster_molecules, map_chemical_space, or assess_small_molecule.

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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