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Molecular 3D Renderer
by
Zehua Zhao
· GitHub ↗
· v1.0.0
410
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Install in OpenClaw
/install mol-render
Description
Generate high-quality 3D ball-and-stick molecular renderings from SMILES strings or PDB structures using POV-Ray ray tracing.
Usage Guidance
This skill appears to do what it claims: convert SMILES or PDBs into POV‑Ray scenes and render PNGs. Before installing/running: (1) be aware it will invoke the system povray binary and pip packages (rdkit can be nontrivial to install; many environments prefer conda), (2) it will download PDB files from files.rcsb.org when given a PDB ID (network access required), and (3) it will write temp files and spawn subprocesses to run povray. If you are installing this on a sensitive host, run it in an isolated environment (container/VM) and ensure you trust the povray/rdkit packages you install. If you want extra assurance, you can review the full scripts (they are included) or run them on local sample inputs first.
Capability Analysis
Type: OpenClaw Skill
Name: mol-render
Version: 1.0.0
The skill bundle is benign. It provides functionality to render 3D molecular structures from SMILES strings or PDB files using POV-Ray. The `SKILL.md` instructions are purely functional, describing usage and dependencies without any prompt injection attempts. The Python scripts (`scripts/pdb_to_3d.py`, `scripts/smiles_to_3d.py`) use `subprocess.run` to execute the `povray` binary, but arguments are passed as a list, mitigating shell injection risks. PDB files are downloaded from the legitimate `files.rcsb.org` domain or read from user-specified local paths, which is appropriate for the skill's purpose. There is no evidence of data exfiltration, persistence mechanisms, or other malicious intent.
Capability Assessment
Purpose & Capability
The name/description (POV‑Ray molecular renderer) matches the declared binaries (povray, python3), pip deps (rdkit, numpy, optional biopython) and the included scripts. The code implements SMILES→3D and PDB parsing/rendering logic that justifies the dependencies.
Instruction Scope
SKILL.md and the scripts limit actions to parsing SMILES/PDB, optionally downloading PDB files from RCSB (files.rcsb.org), generating POV‑Ray scene files, and invoking povray to render PNGs. There are no instructions to read unrelated config, environment secrets, or to transmit results to any unexpected external endpoint.
Install Mechanism
This is instruction-only (no package download/install spec). SKILL.md suggests pip installs and apt-get for povray, which is a normal, proportional approach. Nothing is pulled from obscure URLs and the included source is plain Python (not obfuscated).
Credentials
The skill declares no required environment variables or credentials. The code does not access environment secrets or unrelated config paths; it uses temporary files and downloads PDBs from the public RCSB site, which is expected for PDB mode.
Persistence & Privilege
always:false and default autonomous invocation are used. The skill does not attempt to modify other skills or system-wide agent configs. It writes temporary files (PDB cache, POV scene, output PNG) which is normal for a renderer.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install mol-render - After installation, invoke the skill by name or use
/mol-render - Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.0
Initial release: SMILES + PDB → POV-Ray ball-and-stick 3D rendering. Features: aromatic bonds (solid+dashed), Kekulé mode, double bonds, PCA best-angle, PDB auto-download from RCSB, chain/residue filtering, metal ion support.
Metadata
Frequently Asked Questions
What is Molecular 3D Renderer?
Generate high-quality 3D ball-and-stick molecular renderings from SMILES strings or PDB structures using POV-Ray ray tracing. It is an AI Agent Skill for Claude Code / OpenClaw, with 410 downloads so far.
How do I install Molecular 3D Renderer?
Run "/install mol-render" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is Molecular 3D Renderer free?
Yes, Molecular 3D Renderer is completely free (open-source). You can download, install and use it at no cost.
Which platforms does Molecular 3D Renderer support?
Molecular 3D Renderer is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created Molecular 3D Renderer?
It is built and maintained by Zehua Zhao (@zhao-zehua); the current version is v1.0.0.
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