search-species — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited search-species (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
When assisting users with chemical searches, you MUST adhere to the following step-by-step workflow. Note: Searching can be highly time-consuming; always prioritize efficiency.
pubchem, opsin, wikidata, or all) based on the query type. Avoid using all unless strictly necessary, to minimize search times.search command to query the database. You must set an appropriate max_cands limit to prevent excessively long processing times and reduce data noise.______________________________________________________________________
search-species integrates three distinct backends. Each serves a specific purpose in the chemical informatics workflow:
| Feature | OPSIN | PubChem | Wikidata |
|---|---|---|---|
| Core Method | Algorithmic Parser | Curated Database | Knowledge Graph |
| Primary Input | IUPAC English Names | Names, CIDs, SMILES | Common & Multilingual Names |
| Molecular Image | Supported (Rendered) | Supported (Stored) | Rarely Available |
| Mass/Formula | Calculated via RDKit | Database Metadata | Database Metadata |
| Key Strength | Handles theoretical molecules. | Highly standardized data. | Vernacular & Cross-lingual. |
(For more detailed engine capabilities, limitations, and data normalization behavior, see `reference/backends.md`)
Typical search syntax:
uvx search-species <engine> "<query>" [max_cands] -o <output_dir>
Output: Prints the retrieved species data summary and the file path where each candidate's JSON is saved (e.g., SpeciesCandidate(...) written -> ./cache/xyz.json).Typical render syntax:
uvx --from search-species render-species <candidate_files...> -o <output_dir>
Output: Prints the file path of the successfully generated image card (e.g., Successfully rendered -> ./gallery/xyz.png).PubChem (Standard database lookups):
uvx search-species pubchem "benzene" 5 -o ./results
OPSIN (Theoretical molecules & strict IUPAC):
uvx search-species opsin "2-acetyloxybenzoic acid"
Wikidata (Multilingual & common/trade names):
uvx search-species wikidata "Аспирин"
uvx search-species wikidata "TNT"
When using this toolkit for users, ensure you cross-check these points with the Core Workflow:
pubchem fails on a systematic name, fallback to opsin.<query> in quotes.reference/backends.md~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.