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molecular-optimization

Iterative lead optimization with analyze-reason-generate-verify-evaluate loop. Paper-backed (MT-Mol, DrugR, MultiMol).

59

Quality

74%

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SecuritybySnyk

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tessl review fix ./backend/cli/skills/chemistry/molecular-optimization/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

88%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.

The body is a strong, execution-first skill document: complete CLI examples for every workflow, a clearly sequenced protocol with real verification gates and an honest failure path, and correct references to the bundled scripts. Its weaknesses are mild — a little narrative padding in the overview and no separation of the protocol/threshold detail into reference files.

DimensionReasoningScore

Conciseness

The body is dominated by lean, high-value material — CLI invocations, a script table, and a compact six-step protocol with a thresholds table. There is minor over-explanation that could be trimmed (the overview sentence 'LLMs frequently generate invalid SMILES...', and 'datamol: Convenient molecular manipulation utilities'), placing it at 'efficient; minor instances of over-explanation' rather than the every-token-earns-its-place anchor 5.

4 / 5

Actionability

Four complete, copy-paste-ready CLI commands with realistic SMILES strings, targets, and flags cover the common cases (single, batch, verification-only, comparison), and all three referenced scripts exist in ./scripts/. The protocol adds executable specifics (Chem.MolFromSmiles() discard rule, ECFP4 Tanimoto < 0.4 gate, +1/-0.5 scoring formula), matching the fully-executable anchor.

5 / 5

Workflow Clarity

The 'Analyze → Identify Liabilities → Generate → Verify → Evaluate & Rank → Iterate' sequence is explicitly laid out with validation checkpoints in Step 4 (discard invalid SMILES, scaffold preservation, similarity flag, structural verification of claimed modifications) and a feedback/stop rule in Step 6 (halt after 3 non-improving iterations, 'return best found with honest assessment'). Batch operation guidance (Batch Optimization workflow) is also backed by these verification steps, so no cap applies.

5 / 5

Progressive Disclosure

The body is well-sectioned and its bundle references are real and clearly surfaced (each of the three scripts is invoked in a worked example and summarized in the Script Reference table). However, everything else — the protocol detail and the ADMET thresholds table — is inlined in a single ~150-line SKILL.md with no references/ split, leaving minor organization gaps ('good structure; most content appropriately placed') rather than the ideal split of anchor 5.

4 / 5

Total

18

/

20

Passed

Description

50%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.

The description is concise and technically accurate but reads like an internal method summary rather than a trigger. It states what the skill does at a high level but gives Claude no guidance on when to reach for it, and its only natural user keyword is 'lead optimization'.

Suggestions

Add an explicit 'Use when...' clause covering lead optimization, scaffold hopping, and multi-objective ADMET improvement of an existing hit compound.

Include natural trigger terms users would actually say: 'optimize a molecule', 'improve ADMET/potency', 'drug discovery', 'SMILES modification'.

Drop or shorten the paper acronym list ('MT-Mol, DrugR, MultiMol') in favor of one or two concrete capability verbs (e.g., 'generate and rank analog candidates with verified SMILES').

DimensionReasoningScore

Specificity

The description names the domain ('Iterative lead optimization') and one concrete action pattern ('analyze-reason-generate-verify-evaluate loop'), but does not enumerate the actual capabilities (e.g., improve ADMET properties, scaffold hopping, candidate ranking). It matches the 'names domain and 1-2 concrete actions, but not comprehensive' anchor rather than the several-specific-actions anchor above.

3 / 5

Completeness

The 'what' is clear (iterative lead optimization via a five-stage loop), but there is no 'Use when...' clause or any trigger guidance — the second sentence ('Paper-backed (MT-Mol, DrugR, MultiMol)') describes provenance, not when to invoke the skill. Per the judging guidelines a missing 'Use when' clause caps completeness at 3.

3 / 5

Trigger Term Quality

'lead optimization' is a natural phrase a medicinal chemist would say, but the description omits common variations and synonyms users would actually utter — 'optimize a molecule', 'ADMET', 'improve potency', 'drug discovery', 'SMILES'. Some relevant keywords exist, but coverage is incomplete, fitting the anchor-3 example ('Works with PDF files') better than the good-coverage anchor 4.

3 / 5

Distinctiveness Conflict Risk

'Iterative lead optimization' carves out a niche, but without a when-clause or differentiating triggers it could still be picked for adjacent tasks handled by sibling skills like admet-prediction or denovo design. It is 'somewhat specific but could still overlap with similar skills' (anchor 3) rather than 'mostly distinct' (anchor 4), which the paper acronyms do not remedy since users never say them.

3 / 5

Total

12

/

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

Path

backend/cli/skills/chemistry/molecular-optimization/SKILL.md

Reviewed

Table of Contents

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