Requirements
- Target platform
- OpenClaw
- Install method
- Manual import
- Extraction
- Extract archive
- Prerequisites
- OpenClaw
- Primary doc
- SKILL.md
Tencent SkillHub Β· AI
Molecular 3D Renderer
Generate high-quality 3D ball-and-stick molecular renderings from SMILES strings or PDB structures using POV-Ray ray tracing.
skill openclawclawhub Free
Generate high-quality 3D ball-and-stick molecular renderings from SMILES strings or PDB structures using POV-Ray ray tracing.
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Install for OpenClaw
Quick setup
- Download the package from Yavira.
- Extract the archive and review SKILL.md first.
- Import or place the package into your OpenClaw setup.
Package facts
- Download mode
- Yavira redirect
- Package format
- ZIP package
- Source platform
- Tencent SkillHub
- What's included
- SKILL.md, scripts/pdb_to_3d.py, scripts/smiles_to_3d.py
Validation
- Use the Yavira download entry.
- Review SKILL.md after the package is downloaded.
- Confirm the extracted package contains the expected setup assets.
Install with your agent
Agent handoff
Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.
- Download the package from Yavira.
- Extract it into a folder your agent can access.
- Paste one of the prompts below and point your agent at the extracted folder.
New install
I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete.
Upgrade existing
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Trust & source
Release facts
- Source
- Tencent SkillHub
- Verification
- Indexed source record
- Version
- 1.0.0
Provenance
- Publisher
- Zhao-Zehua
- Source page
- View original listing
- Canonical URL
- Open canonical page
Documentation
mol-render
Generate high-quality 3D ball-and-stick model PNG images from SMILES strings or PDB structures, rendered with POV-Ray ray tracing.
Dependencies
Required: rdkit β SMILES parsing & 3D conformer generation numpy β coordinate transforms povray β ray tracing renderer Optional (PDB mode only): biopython β PDB file parsing Install: pip install rdkit numpy apt-get install -y povray # For PDB support: pip install biopython
SMILES Mode
python3 scripts/smiles_to_3d.py "SMILES" -o output.png Arguments: SMILES β (positional) SMILES string (required) -o, --output β output PNG path (default: molecule.png) --bg β background color: black / white / blue (default: blue) --no-hydrogen β hide hydrogen atoms --kekulize β convert aromatic bonds to alternating single/double bonds Examples: # Ethanol python3 scripts/smiles_to_3d.py "CCO" -o ethanol.png # Benzene (white background, KekulΓ© style) python3 scripts/smiles_to_3d.py "c1ccccc1" -o benzene.png --bg white --kekulize # Caffeine python3 scripts/smiles_to_3d.py "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -o caffeine.png # Aspirin (no hydrogens) python3 scripts/smiles_to_3d.py "CC(=O)OC1=CC=CC=C1C(=O)O" -o aspirin.png --no-hydrogen
PDB Mode
python3 scripts/pdb_to_3d.py --pdb <PDB_ID_or_file> -o output.png Arguments: --pdb β PDB file path or 4-character PDB ID (auto-downloads from RCSB) (required) -o, --output β output PNG path (default: pdb_molecule.png) --chain β select specific chain (e.g., A) --residues β residue range (e.g., 1-50 or 10,20,30-40) --ligand-only β render only ligands (HETATM, excluding water) --no-hydrogen β hide hydrogen atoms --no-water / --keep-water β filter/keep water molecules (default: filter) --bg β background color: black / white / blue (default: blue) --view β viewing angle: auto / side / top / front or ΞΈ,Ο in degrees (default: auto) --resolution β resolution multiplier, e.g., 0.5 for half, 2.0 for double (default: 1.0) --sphere-scale β override sphere scale factor (default: auto) --bond-radius β override bond radius (default: auto) Examples: # Download and render G-quadruplex from RCSB python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen -o g4.png # Side view python3 scripts/pdb_to_3d.py --pdb 1KF1 --no-hydrogen --view side -o g4_side.png # Ligands only python3 scripts/pdb_to_3d.py --pdb 1KF1 --ligand-only -o ligands.png # Specific chain and residues python3 scripts/pdb_to_3d.py --pdb 1KF1 --chain A --residues 1-12 -o partial.png # Local PDB file python3 scripts/pdb_to_3d.py --pdb structure.pdb -o out.png # Large protein at lower resolution python3 scripts/pdb_to_3d.py --pdb 2HYY --no-hydrogen --resolution 0.5 -o protein.png
Output
1200Γ1200 PNG with POV-Ray ray tracing CPK color scheme (C=dark gray, O=red, N=blue, H=white, P=orange, S=yellow, K=purple, ...) Aromatic bonds rendered as solid + dashed lines (SMILES mode) Double bonds rendered as two parallel solid lines --kekulize option converts aromatic bonds to alternating single/double Metal ions displayed with ionic radius (large spheres), no coordination bonds drawn Auto-selects best viewing angle (PCA-based) Auto-scales sphere/bond sizes for large molecules Water molecules filtered by default (PDB mode)
Known Limitations
Very large molecules (>2000 atoms) may be slow to render (use --resolution 0.5) PDB mode renders all bonds as single bonds (no double/aromatic distinction) Metal coordination bonds are not rendered POV-Ray must be installed (which povray) biopython required only for PDB mode (optional dependency)
License
MIT
Category context
Agent frameworks, memory systems, reasoning layers, and model-native orchestration.
Source: Tencent SkillHub
Largest current source with strong distribution and engagement signals.
Package contents
Included in package
2 Scripts1 Docs
- SKILL.md
- scripts/pdb_to_3d.py
- scripts/smiles_to_3d.py