Generate 2D and 3D molecular visualizations from PubChem or SMILES. RDKit and PyMOL based tool.

Originally developed for generating molecular structure images for Wikipedia, WikiMolGen provides a Python API, CLI, and a web interface for creating 2D SVG diagrams and 3D rendered structures.

Examples

2D structure (SVG)	3D render (ray-traced PNG)

Both images were generated with the tool itself:

wikimolgen 2d --compound aspirin --output aspirin.svg
wikimolgen 3d --compound aspirin --render --output-base aspirin

How it works

graph LR
    A["Compound Name"] --> D{Parse}
    B["PubChem CID"] --> D
    C["SMILES"] --> D
    D --> E["RDKit"]
    E --> F["2D SVG"]
    E --> G["SDF Conformer"]
    G --> H["PyMOL"]
    H --> I["3D PNG"]
    J["PDB ID"] --> H
    D --> K["PubChem Metadata"]
    K --> L["Wikipedia Templates"]
    style F stroke:#4caf50
    style I stroke:#4caf50
    style L stroke:#4caf50

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Features

• Three generation modes: 2D SVG, 3D ray-traced PNG, and protein cartoons from PDB
• Input as PubChem CID, compound name, or SMILES string
• Wikipedia tooling: Infobox drug/chembox templates, compound metadata, and Commons upload links
• Template and color-template systems for reproducible styling
• Python API, CLI, and Streamlit web interface

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Installation

Basic (2D only)

pip install wikimolgen

Full (2D + 3D with PyMOL)

conda create -n wikimolgen python=3.10
conda activate wikimolgen
conda install -c conda-forge rdkit pubchempy pymol-open-source
pip install wikimolgen

Web Interface

The Streamlit-based web interface provides an interactive dashboard for generating molecular visualizations with full control over rendering, styling, and Wikipedia metadata.

Features:

• 3 modes: 2D (SVG), 3D (ray-traced PNG), and Protein (PDB cartoon)
• Rich controls: atom coloring, lighting, transparency, ray tracing, conformer generation
• Wikipedia tooling: auto-generated Infobox drug/chembox templates, metadata, and Commons upload links

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CLI

The wikimolgen command provides three subcommands: 2d, 3d, and protein.

2d: generate 2D SVG structures

wikimolgen 2d --compound aspirin --output aspirin.svg
wikimolgen 2d --compound 24802108 --template wikipedia_2d --color-template cpk_standard

Flag	Description
--compound	PubChem CID, compound name, or SMILES string (required)
--output	Output SVG filename (default: molecule_2d.svg)
--template	Settings template (predefined name or JSON file path)
--color-template	Color template (predefined name or JSON file path)
--angle	Rotation angle in degrees (default: 180)
--auto-orient	Automatically optimize viewing angle using PCA
--scale	Pixels per coordinate unit (default: 30.0)
--use-bw	Use black and white atom palette
--transparent-bg	Use transparent background

3d: generate 3D structures with optional PyMOL rendering

wikimolgen 3d --compound 5284583 --render --output-base lsd
wikimolgen 3d --compound aspirin --render --x-rotation 10 --y-rotation 200 --z-rotation 0

Flag	Description
--compound	PubChem CID, compound name, or SMILES string (required)
--output-base	Base name for output files (default: compound name)
--template	Settings template (predefined name or JSON file path)
--color-template	Color template (predefined name or JSON file path)
--render	Render molecule with PyMOL (generates PNG)
--force-field	Force field for optimization: MMFF94 or UFF (default: MMFF94)
--ray-trace	Enable ray tracing mode
--bg-color	Background color: white, black, or gray (default: white)
--width / --height	Render size in pixels (default: 1800 × 1600)
--x-rotation / --y-rotation / --z-rotation	Rotation around each axis in degrees

protein: render protein structures from PDB

wikimolgen protein 8F7W --output 8f7w_protein.png --ray-trace

Flag	Description
pdb_id	PDB identifier, e.g. 8F7W (positional, required)
--output, -o	Output PNG filename
--color-scheme	secondary_structure, rainbow, chain, or hydrophobicity (default: secondary_structure)
--show-ligand	Show ligand/heteroatoms (default: on)
--no-ligand	Hide ligand/heteroatoms
--show-water	Show water molecules
--width / --height	Image size in pixels (default: 1920 × 1080)
--ray-trace	Enable ray tracing

Tech stack

Tool	Purpose
RDKit 2025.3+	2D structure generation, SMILES parsing, conformers
PyMOL (optional)	3D rendering and ray tracing
Streamlit 1.50+	Web interface
PubChemPy	PubChem compound lookup
Biotite	Protein structure parsing (PDB)
NumPy / Pillow / Requests	numerics, image post-processing, HTTP

Limitations

• 3D rendering requires the optional PyMOL dependency (pymol-open-source); the 2D path works without it.
• Compound metadata and PDB fetching need network access to the PubChem and RCSB APIs.
• Predefined templates cover common Wikipedia use cases; unusual molecule classes may need a custom JSON template.

Contributing

See CONTRIBUTING.md.

Security

See SECURITY.md.

License

PolyForm Noncommercial 1.0.0 - noncommercial use only. Commercial use and monetary gain require explicit written approval from the author. See LICENSE.