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cheminem

Pharmaclaw Chemistry Query

by Cheminem · GitHub ↗ · v2.0.1 · MIT-0
cross-platform ✓ Security Clean
823
Downloads
3
Stars
4
Active Installs
6
Versions
Install in OpenClaw
/install pharmaclaw-chemistry-query
Description
Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMIL...
Usage Guidance
This skill appears coherent and implements what it claims: PubChem/ChEMBL/PubMed queries plus RDKit-based analysis, drawing, and retrosynthesis. Before installing or running it, consider: (1) it can generate multi-step synthesis routes and contains named reaction templates and experimental conditions — if your organization restricts assistance for lab synthesis, review the content carefully; (2) the OPSIN JAR is downloaded at runtime from a GitHub release but the script verifies a pinned SHA-256 (good practice); (3) the skill runs multiple Python scripts as subprocesses and writes visualization files into a viz directory under the skill — check file-write locations and sanitize any sensitive environment where you run it; and (4) no secrets are required. If you need higher assurance, review the included files (particularly templates.json and rdkit_reaction.py) for content you consider sensitive and run in an isolated environment (container or sandbox).
Capability Analysis
Type: OpenClaw Skill Name: pharmaclaw-chemistry-query Version: 2.0.1 The pharmaclaw-chemistry-query bundle is a legitimate chemistry toolkit for PubChem data retrieval and RDKit analysis. It demonstrates strong security practices, including explicit input sanitization (null-byte rejection, length limits) and path traversal protections in scripts like `rdkit_mol.py` and `advanced_chem.py`. While `opsin_name_to_smiles.py` downloads an external JAR file, it implements SHA-256 checksum verification to ensure file integrity, and all subprocess calls are handled using list-based arguments to prevent shell injection.
Capability Assessment
Purpose & Capability
Name/description match the included scripts: PubChem/ChEMBL/PubMed queries, RDKit processing, visualization, retrosynthesis, and reaction templates. Declared external APIs and system dependency (optional Java/OPSIN) are used by the code, and there are no unrelated credentials or surprising binaries requested.
Instruction Scope
SKILL.md instructs use for compound lookups, RDKit analysis, and retrosynthesis, which the scripts implement. It also mentions chaining outputs to a 'pharma-pharmacology-agent' (a usage suggestion rather than an autonomy requirement). The scripts run subprocesses and access only local skill files, call public APIs (PubChem/ChEMBL/NCBI), and write visualizations under a local viz directory; they do not attempt to read or exfiltrate unrelated system files or require secrets.
Install Mechanism
There is no formal install spec; code runs as-is. One runtime behavior worth noting: opsin_name_to_smiles.py will auto-download an OPSIN JAR from a GitHub release on first use. The download is verified with a pinned SHA-256 checksum in the script, reducing risk. No other remote arbitrary downloads or unverified installers are present.
Credentials
The skill declares no required environment variables or credentials and the code does not attempt to access hidden tokens. External APIs used are public (no key required). The lack of requested secrets is proportionate to its stated functionality.
Persistence & Privilege
always is false and the skill does not request permanent system-wide presence or modify other skills' configurations. It writes images/reports into its own viz/scripts directories and runs local subprocesses — expected for this type of tool.
How to Use
  1. Make sure OpenClaw is installed (local or Docker)
  2. Run the install command in chat: /install pharmaclaw-chemistry-query
  3. After installation, invoke the skill by name or use /pharmaclaw-chemistry-query
  4. Provide required inputs per the skill's parameter spec and get structured output
Version History
v2.0.1
PharmaClaw drug discovery suite - full agent team launch
v2.0.0
Full release: PubChem + RDKit + retrosynthesis + multi-step synth planning
v1.4.1
v1.4.1: Security hardening — input sanitization, path traversal prevention, null-byte rejection, shell metachar blocking. Addresses VirusTotal suspicious flag.
v1.4.0
v1.4.0: Fixed PubChem SMILES/InChI endpoints, fixed chain_entry HTML entity corruption, fixed BRICS retro string handling, added 15s timeouts, graceful error handling for invalid SMILES, 21 reaction templates, multi-step synthesis planning, comprehensive e2e testing, CLI integration support
v1.0.3
- Initial public release of the skill as a code module (v1.0.3). - Added all source scripts and resources required for PubChem querying and RDKit-based chemistry analysis. - Included sample scripts for compound lookup, property calculation, molecular visualization, and retrosynthesis. - OPSIN auto-download and checksum verification for IUPAC name conversion now documented. - Expanded install and dependency documentation for Python, Java, and third-party APIs. - Removed legacy virtual environment configuration file (venv/pyvenv.cfg).
v1.0.2
pharmaclaw-chemistry-query v1.0.2 - Added comprehensive chemistry toolkit combining PubChem API queries and RDKit cheminformatics. - Supports compound info retrieval, structure visualization, synthesis references, molecular properties, retrosynthesis, reaction simulation, and synthesis planning. - Includes multi-format data output (JSON, images), name and SMILES resolution, and handling for errors/invalid inputs. - Structured chaining interface for downstream workflows. - Thoroughly tested with representative compounds and robust error handling. - Refer to SKILL.md for usage examples and detailed script documentation.
Metadata
Slug pharmaclaw-chemistry-query
Version 2.0.1
License MIT-0
All-time Installs 4
Active Installs 4
Total Versions 6
Frequently Asked Questions

What is Pharmaclaw Chemistry Query?

Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMIL... It is an AI Agent Skill for Claude Code / OpenClaw, with 823 downloads so far.

How do I install Pharmaclaw Chemistry Query?

Run "/install pharmaclaw-chemistry-query" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.

Is Pharmaclaw Chemistry Query free?

Yes, Pharmaclaw Chemistry Query is completely free, licensed under MIT-0. You can download, install and use it at no cost.

Which platforms does Pharmaclaw Chemistry Query support?

Pharmaclaw Chemistry Query is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).

Who created Pharmaclaw Chemistry Query?

It is built and maintained by Cheminem (@cheminem); the current version is v2.0.1.

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