Computational Chemistry Agent Skills
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search-species

tools
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.
v0.1.0 Requires `uv` installed. repository source

Installation

Install folder: search-species · Repo path: tools/search-species
Copy/paste this message to your OpenClaw agent. 
Please install the OpenClaw skill "search-species" on the OpenClaw host.

Steps:
- Download: https://skills.computchem.cn/skill-zips/search-species.zip
- Unzip it to get search-species/
- Copy search-species/ into the workspace skills directory (<workspace>/skills/)
- Start a NEW OpenClaw session so the skill is loaded

Then verify:
openclaw skills list --eligible
openclaw skills info search-species
Prerequisites: Requires `uv` installed.

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.

Search Backend Overview

search-species integrates three distinct backends. Each serves a specific purpose in the chemical informatics workflow:

FeatureOPSINPubChemWikidata
Core MethodAlgorithmic ParserCurated DatabaseKnowledge Graph
Primary InputIUPAC English NamesNames, CIDs, SMILESCommon & Multilingual Names
Molecular ImageSupported (Rendered)Supported (Stored)Rarely Available
Mass/FormulaCalculated via RDKitDatabase MetadataDatabase Metadata
Key StrengthHandles 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.

References

  • Engine Details & Limitations: reference/backends.md