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cheminem

Pharmaclaw Cheminformatics

by Cheminem · GitHub ↗ · v1.0.0 · MIT-0
cross-platform ✓ Security Clean
290
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Install in OpenClaw
/install pharmaclaw-cheminformatics
Description
Advanced cheminformatics agent for 3D molecular analysis, pharmacophore mapping, format conversion, RECAP fragmentation, and stereoisomer enumeration. The "s...
Usage Guidance
This appears to be a straightforward local cheminformatics toolkit. Before installing/using: (1) ensure RDKit (rdkit-pypi) and other dependencies (numpy, Pillow for images) are installed in a controlled environment; (2) be aware CPU/memory can be heavy for large conformer enumerations (the conformer generator uses all cores by default); (3) outputs are written to any output_dir you provide — chain_entry.py does not further sanitize output_dir, so choose directories you trust and have appropriate permissions; (4) no network calls or credentials are requested by the skill, so it won't exfiltrate data unless you run it in an environment that already exposes files or secrets; (5) as always, run untrusted code in an isolated environment (container/VM) if you are concerned about unexpected behavior.
Capability Analysis
Type: OpenClaw Skill Name: pharmaclaw-cheminformatics Version: 1.0.0 The pharmaclaw-cheminformatics bundle is a legitimate toolkit for molecular analysis and drug development workflows using the RDKit library. It provides functionality for 3D conformer generation, molecular format conversion, and pharmacophore mapping. The code includes basic security practices, such as path sanitization in `scripts/format_converter.py` to prevent path traversal, and uses controlled dynamic imports in `scripts/chain_entry.py`. No indicators of data exfiltration, malicious execution, or prompt injection were found.
Capability Assessment
Purpose & Capability
Name/description match the actual code. All modules implement the cheminformatics features described (conformers, pharmacophores, format conversion, RECAP fragmentation, stereoisomer enumeration) and rely on RDKit and standard scientific libs; no unrelated credentials, binaries, or services are requested.
Instruction Scope
SKILL.md and chain_entry.py confine operations to molecule inputs, local file outputs, and RDKit processing. Modules may write SDF/PDB/PNG/text files when an output path is provided. Two minor notes: (1) format_converter applies basic path sanitization for output file paths, but chain_entry.py writes into a user-supplied output_dir without additional sanitization, so outputs will be created wherever the caller points the skill; (2) some operations (conformer generation) use all CPU cores and can be resource-intensive.
Install Mechanism
There is no install spec (no downloads or installers). The code depends on RDKit, numpy, and optionally Pillow; missing dependencies cause the scripts to exit with a clear error. No remote URLs, extract operations, or package installs are embedded in the skill.
Credentials
The skill declares no required environment variables, credentials, or config paths. It uses RDKit internals (RDConfig.RDDataDir) to load feature definitions, which is expected. No secrets are requested or accessed.
Persistence & Privilege
always is false and the skill does not modify other skills or global agent settings. It writes outputs only to paths you supply; it does not attempt to persist credentials or alter runtime configuration beyond its own outputs.
How to Use
  1. Make sure OpenClaw is installed (local or Docker)
  2. Run the install command in chat: /install pharmaclaw-cheminformatics
  3. After installation, invoke the skill by name or use /pharmaclaw-cheminformatics
  4. Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.0
pharmaclaw-cheminformatics v1.0.0 - Initial release of an advanced cheminformatics agent for 3D molecular analysis and drug development workflows. - Adds 3D conformer generation, pharmacophore feature mapping, molecular format conversion (SMILES/SDF/MOL/InChI/PDB/XYZ), RECAP retrosynthetic fragmentation, and stereoisomer enumeration (R/S, E/Z). - Includes modules for ensemble conformer generation, pharmacophore extraction/fingerprints/comparison, retrosynthetic fragmentation, and stereochemistry analysis. - Provides a unified chain interface for integration with pharmacology, catalyst design, and IP expansion workflows. - Supports batch and single-molecule analysis; outputs 3D coordinates, SDF/PNG visualizations, and structured reports.
Metadata
Slug pharmaclaw-cheminformatics
Version 1.0.0
License MIT-0
All-time Installs 2
Active Installs 2
Total Versions 1
Frequently Asked Questions

What is Pharmaclaw Cheminformatics?

Advanced cheminformatics agent for 3D molecular analysis, pharmacophore mapping, format conversion, RECAP fragmentation, and stereoisomer enumeration. The "s... It is an AI Agent Skill for Claude Code / OpenClaw, with 290 downloads so far.

How do I install Pharmaclaw Cheminformatics?

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

Is Pharmaclaw Cheminformatics free?

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

Which platforms does Pharmaclaw Cheminformatics support?

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

Who created Pharmaclaw Cheminformatics?

It is built and maintained by Cheminem (@cheminem); the current version is v1.0.0.

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