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zinc-database

Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.

55

Quality

63%

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SecuritybySnyk

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tessl review fix ./backend/cli/skills/databases/zinc-database/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

57%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-organized, highly actionable skill body whose main weaknesses are redundancy (duplicated tranche/output-field/publication content, boilerplate disclaimers), inlined API detail that duplicates the bundled reference file, and workflows that lack validation steps despite involving batch operations. Actionability is strong, with only a few malformed example URLs.

Suggestions

Add validation checkpoints to each workflow, e.g. after each API query check the result is non-empty and well-formed before parsing/downloading ("if df.empty: refine the search"), which is required to lift workflow clarity above the batch-operation cap.

Move the endpoint catalog, Output Fields, and Tranche System sections into references/api_reference.md, keeping only one concise example per capability in SKILL.md to remove duplication and tighten the token budget.

Fix the malformed example URLs (Search by ZINC ID, Search by SMILES, and the query_zinc_by_id Python function) so every shown command is copy-paste executable, and drop the boilerplate disclaimer/citation duplication.

DimensionReasoningScore

Conciseness

The bulk is concrete, executable material, but there is real tightening opportunity: the tranche format is explained twice (Workflow 1 comment plus the Tranche System section), output fields are listed twice (capability 1 response fields plus the Output Fields section), publications appear in both Additional Resources and Citations, and the "Important Disclaimers"/"Appropriate Use" sections are padded boilerplate. This is 'mostly efficient but includes some unnecessary explanation or could be tightened' rather than the level-2 'several unnecessary explanations', since the core content is dense with usable commands.

3 / 5

Actionability

Nearly all guidance is copy-paste ready: concrete curl URLs with real values ("c1ccccc1", ZINC000000000001), parameter tables, and complete Python functions. Not a 5 because several endpoint examples are malformed — e.g. the Search-by-ZINC-ID, Search-by-SMILES, and query_zinc_by_id examples contain URLs like "cartblanche22.docking.org/[email protected]_fields=..." that are not executable as written, which is a minor but real gap.

4 / 5

Workflow Clarity

The four workflows have clear numbered sequences with concrete commands, but none include validation checkpoints — no check that the response is non-empty/valid before parsing, no verification step before downloading 10,000-compound libraries, and step 4 of Workflow 1 ("Download 3D structures") is vague with no command. Since these are batch operations (bulk retrieval, bulk 3D downloads), the rubric guideline capping workflow clarity at 3 without validation applies; the sequences themselves are better than the level-2 anchor, so 3 rather than lower.

3 / 5

Progressive Disclosure

The body is well-sectioned and points to a real one-level-deep bundle file (references/api_reference.md, 692 lines, clearly listed in a Resources section). However, roughly a third of the body — the endpoint catalog, Output Fields section, and Tranche System section — duplicates content that already lives in api_reference.md and should be pushed there, leaving SKILL.md as a leaner overview. That matches the level-3 anchor 'content that should be separate is inline' better than level 4, where most content is appropriately placed.

3 / 5

Total

13

/

20

Passed

Description

70%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A domain-specific, capability-rich description that clearly states what the skill does with concrete actions and strong trigger vocabulary. Its main deficiency is the absence of any explicit 'use when' guidance, which caps completeness at 3.

Suggestions

Append an explicit trigger clause, e.g. "Use when the user mentions ZINC, needs purchasable/analog compounds for docking or virtual screening, or asks to look up molecules by ZINC ID or SMILES."

Mention the supplier-code and random-sampling capabilities to round out coverage in the description.

Add one or two natural user phrasings (e.g. "find purchasable analogs of this compound") to strengthen trigger terms.

DimensionReasoningScore

Specificity

"Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery" lists several concrete actions in a named domain. It falls short of the 5 anchor because supplier-code lookup, random sampling, and batch retrieval — all documented in the body — are absent, which matches 'several specific actions; minor gaps in coverage' rather than comprehensive coverage.

4 / 5

Completeness

The "what" is clear ("Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES..."), but there is no "Use when..." or equivalent trigger guidance anywhere in the description — the trailing "for virtual screening and drug discovery" is a purpose clause, not an explicit when-to-use condition. Per the rubric guideline, a missing 'Use when...' clause caps completeness at 3.

3 / 5

Trigger Term Quality

Natural terms users would say are present: "ZINC", "SMILES", "docking", "similarity searches", "analog discovery", "virtual screening", "drug discovery", "purchasable compounds". Not a 5: common variations such as "compound lookup/database", "supplier", and concrete user phrasings like "find analogs of this compound" are missing.

4 / 5

Distinctiveness Conflict Risk

ZINC is a specific named database with distinct domain triggers (ZINC ID, SMILES, purchasable compounds, docking libraries). The phrase "3D-ready structures for docking" has minor adjacency to docking-tool skills, but the named-source framing makes conflict risk minimal, matching the 5 anchor 'clear niche with distinct triggers'.

5 / 5

Total

16

/

20

Passed

Validation

87%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

14

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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