Other

chemical-structure-converter

Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Supports SMILES validation, batch processing, structure standardization, and cheminformatics database preparation for drug discovery workflows.

86100Total Score
Core Capability
84 / 100
Functional Suitability
11 / 12
Reliability
11 / 12
Performance & Context
7 / 8
Agent Usability
13 / 16
Human Usability
7 / 8
Security
10 / 12
Maintainability
12 / 12
Agent-Specific
13 / 20
Medical Task
12 / 12 Passed
87Convert 'aspirin' to SMILES, IUPAC name, and molecular formula
4/4
87Validate a SMILES string with a ring closure error
4/4
86Convert a novel research compound not in the local database
4/4

Veto GatesRequired pass for any deployment consideration

Skill Veto✓ All 4 gates passed
✓
Operational Stability
System remains stable across varied inputs and edge cases
PASS
✓
Structural Consistency
Output structure conforms to expected skill contract format
PASS
✓
Result Determinism
Equivalent inputs produce semantically equivalent outputs
PASS
✓
System Security
No prompt injection, data leakage, or unsafe tool use detected
PASS

Core Capability84 / 100 — 8 Categories

Functional Suitability
PubChem REST API fallback documented in Error Handling; direct lookup URLs added; DB_VERSION tracking documented. PubChem fallback not implemented in script.
11 / 12
92%
Reliability
Unknown compounds include direct PubChem/ChemSpider URLs and API fallback; DB versioning documented.
11 / 12
92%
Performance & Context
SKILL.md 171 lines — lean; local database limitation is a known documented constraint.
7 / 8
88%
Agent Usability
Clear workflow and conversion table; SMILES quick reference useful; batch summary line mandated in Output Requirements.
13 / 16
81%
Human Usability
Description is discoverable; SMILES notation may be unfamiliar but scope is appropriate for cheminformatics.
7 / 8
88%
Security
No hardcoded secrets; no injection vectors; pure lookup/conversion skill. No path traversal check for batch CSV input.
10 / 12
83%
Maintainability
DB_VERSION tracking and update procedure documented in Error Handling; clean structure.
12 / 12
100%
Agent-Specific
Trigger precision good; escape hatches for docking/activity prediction present; PubChem fallback improves composability for novel compounds.
13 / 20
65%
Core Capability Total84 / 100

Medical TaskExecution Average: 86.7 / 100 — Assertions: 12/12 Passed

87
Canonical
Convert 'aspirin' to SMILES, IUPAC name, and molecular formula
4/4 ✓
87
Variant A
Validate a SMILES string with a ring closure error
4/4 ✓
86
Edge
Convert a novel research compound not in the local database
4/4 ✓
87
Canonical✅ Pass
Convert 'aspirin' to SMILES, IUPAC name, and molecular formula

Output completed successfully; convert 'aspirin' to smiles, iupac name, and molecular formula case handled within expected scope.

Basic 35/40|Specialized 52/60|Total 87/100
✅A1Output includes SMILES string for aspirin
✅A2Output includes IUPAC name (2-acetoxybenzoic acid)
✅A3Output includes molecular formula (C9H8O4) and MW (180.16)
✅A4Output does not fabricate identifiers
Pass rate: 4 / 4
87
Variant A✅ Pass
Validate a SMILES string with a ring closure error

Output completed successfully; validate a smiles string with a ring closure error case handled within expected scope.

Basic 35/40|Specialized 52/60|Total 87/100
✅A1Output correctly identifies the SMILES as invalid
✅A2Output specifies the type of error (ring closure not closed)
✅A3Output does not attempt to correct or guess the intended structure
✅A4Output suggests how to fix the SMILES
Pass rate: 4 / 4
86
Edge✅ Pass
Convert a novel research compound not in the local database

Direct PubChem URL and REST API fallback provided for unknown compounds; DB versioning documented.

Basic 35/40|Specialized 51/60|Total 86/100
✅A1Output flags the compound as not found in local database
✅A2Output suggests PubChem or ChemSpider for external lookup
✅A3Output does not fabricate SMILES or identifiers for unknown compound
✅A4Output provides a direct PubChem lookup URL for the compound name
Pass rate: 4 / 4
Medical Task Total86.7 / 100

Key Strengths

  • SMILES quick reference section is a practical embedded cheat sheet for agents and users
  • Conversion direction table (Name→SMILES, SMILES→IUPAC, etc.) with use cases makes the skill self-documenting
  • Strong fabrication guard: unknown compounds are flagged rather than guessed
  • PubChem REST API fallback and direct lookup URLs documented for unknown compounds
  • DB_VERSION tracking and update procedure documented — closes the database versioning gap