chemanim 0.1.3

A Manim-based library for chemistry and biochemistry animations

Chemanim

A Python library extended from ManimGL for creating chemistry and biochemistry animations.

Features

• Core Chemistry: Visualize Atoms, Bonds, and Molecules.
• Trusted Data: Fetch molecular structures directly from PubChem.
• Biochemistry: Parse and visualize PDB structures (Proteins/DNA).
• 3D Molecules: Render ball-and-stick, space-filling, and wireframe structures.
• Protein Visualization: Cartoon ribbon diagrams with secondary structure coloring.
• Reactions: Animate chemical reactions simply.

Installation

Install from PyPI:

pip install chemanim

Interactive Setup (Recommended)

After installation, run the setup wizard to install optional features:

chemanim-setup

This will show an interactive menu to choose what you need:

• All Features ⭐ - ManimGL + RDKit + ChemPy + Biotite + py3Dmol
• Animations Only - Just ManimGL
• Chemistry Analysis - RDKit + ChemPy + ChemFormula
• Protein Analysis - Just Biotite
• 3D Viewer - Just py3Dmol

Manual Installation

Or install optional dependencies directly:

Command	What it adds
pip install chemanim[vis]	ManimGL for animations
pip install chemanim[chem]	RDKit + ChemPy + ChemFormula for molecular analysis
pip install chemanim[bio]	Biotite for protein secondary structure analysis
pip install chemanim[viewer]	py3Dmol for interactive 3D viewing
pip install chemanim[all]	All optional dependencies

Core Dependencies (installed automatically)

• numpy - Numerical operations
• requests - HTTP requests for PubChem
• pubchempy - PubChem API wrapper
• biopython - PDB file parsing
• networkx - Molecular graph operations

Development Installation

For local development:

git clone https://github.com/Wachirawut2023/Chemanim.git
cd Chemanim
pip install -e .[all]

Usage

See examples/ folder for demo scripts.

Basic Animation

manimgl examples/demo_reaction.py SimpleReactionScene

3D Molecule Visualization

manimgl examples/demo_3d_molecule.py Molecule3DDemo

Protein Visualization

manimgl examples/demo_protein_styles.py ProteinStylesDemo

Interactive 3D Viewer (py3Dmol)

from chemanim.connect import fetch_molecule_data
from chemanim.viewer_3d import show_py3dmol, write_xyz

data = fetch_molecule_data("benzene")
view = show_py3dmol(data, style="ball_and_stick")
view.write_html("benzene.html")
write_xyz("benzene.xyz", data)

Examples

Example	Description
demo_pubchem.py	Fetch and display molecules from PubChem
demo_reaction.py	Simple chemical reaction animation
demo_render_styles.py	Ball-and-stick, space-filling, wireframe
demo_protein_styles.py	Protein cartoon, backbone, and atom views
demo_py3dmol_viewer.py	Interactive HTML 3D viewer

License

MIT License - see LICENSE for details.

Author

Wachirawut Raksawat (@Wachirawut2023)