MolGarden

An interactive 3D molecule viewer and builder, with support for querying any 3D molecular generative model. Below is a demo with Symphony:

Built on top of JSmol for 3D visualization.

Quick Start

1. Start the Backend

The backend corresponds to the model server, which will be queried for generation.

# Install dependencies (in your symphony environment)
pip install flask flask-cors

# Run with your trained checkpoint
python src/symphony/server.py \
    --checkpoint /path/to/checkpoint.ckpt \
    --device cuda \
    --port 5000

2. Serve the Frontend

# From the project root
python -m http.server 8000

Then open http://localhost:8000 in your browser.

How Generation Works

1. Click Generate Step to grow a molecule one atom at a time.
2. Enable Auto-generate to loop until the model emits a STOP token (molecule is complete).
3. Adjust inverse temperature parameters to control generation diversity:
   • Focus τ — controls which existing atom gets selected as the focus (anchor) for the new atom.
   • Radial τ — controls the distance of the new atom from the focus.
   • Angular τ — controls the direction of the new atom relative to the focus.
   • Higher values: more deterministic, lower values: more random.

Other Features

• Load structures from PDB, Materials Project, and PubChem.
• Upload files in .xyz, .pdb, .mol, .sdf, .cif formats.
• Manipulate atoms: select, delete, expand selection.
• Visualization controls: display types, color schemes, isosurfaces, labels.
• Export as .png, .xyz, .pdb, .mol, .sdf, .cif.