search-species

name	search-species
description	USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. You MUST actively retrieve the data using this skill; DO NOT hallucinate or generate structures yourself. DO NOT USE WHEN asking for physical properties (melting point, solubility), safety/toxicity data (MSDS), or synthesis pathways.
compatibility	Requires `uv` installed.
license	GPL-3.0-only
metadata	{"author":"light-cyan","version":"0.1.0","repository":"https://github.com/light-cyan/search-species"}

Search Species

🔄 Core Workflow (CRITICAL)

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.

1. Acquire Target: Identify the chemical name, identifier, or SMILES the user wants to query.
2. Select Engine: Choose the most targeted search backend (pubchem, opsin, wikidata, or all) based on the query type. Avoid using all unless strictly necessary, to minimize search times.
3. Execute Search: Use the search command to query the database. You must set an appropriate max_cands limit to prevent excessively long processing times and reduce data noise.
4. Evaluate Results: Carefully review the returned summary data in the output.
5. Confirm & Iterate: Present the retrieved data to the user for confirmation. If the result is ambiguous or incorrect, communicate with the user to adjust the search keywords and restart the process.

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Search Backend Overview

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)

Quick Start & Command Outputs

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).

Example

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"

Agent Checklist

When using this toolkit for users, ensure you cross-check these points with the Core Workflow:

• Engine Match: Match the engine to the query type based on the overview table.
• Data Scope: Remember this tool only retrieves structural identity (Name, Formula, Mass, SMILES, 2D Image).
• Fallback: If pubchem fails on a systematic name, fallback to opsin.
• Quoting: Always wrap the chemical <query> in quotes.

GPUMD integration

Use search-species to look up molecular SMILES before generating 3D structures with openbabel or rdkit-conf for Packmol packing into GPUMD liquid simulations. Also useful for verifying species identities when building multi-component NEP training datasets.

References

• Engine Details & Limitations: reference/backends.md