Chemanim

A Python library extended from Manim 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 structures with PubChem or RDKit conformers.
• Reactions: Animate chemical reactions simply.

Installation

1. Basic (Logic & Data only)

Use this if you don't need animations or cannot install Manim dependencies.

pip install -e .

2. Full (With Animations)

First, ensure you have Manim's system dependencies installed (FFmpeg, etc.).

pip install -e .[vis]

Usage

See examples/ folder for demo scripts.

manim -pql examples/demo_reaction.py SimpleReactionScene

3D quickstart

Install with Manim and RDKit (optional) and run the sample:

manim -pql examples/demo_3d_molecule.py Molecule3DDemo

External 3D viewers (py3Dmol / XYZ)

Optional dependency: pip install py3Dmol

• Generate interactive HTML and XYZ: python examples/demo_py3dmol_viewer.py
• Styles supported: ball, stick, ball-and-stick (default). Files land in media/py3dmol/.

Programmatic use:

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)