Inkscape Plugins

A small collection of Inkscape extensions for generating stylized scientific figures directly inside Inkscape — clustered point distributions, neural network schematics, 2D molecular graphs, and ray-traced 3D molecular images.

All plugins appear under Extensions → Generate after deployment.

Plugins

Plugin	What it does	Deps
make_clustered_points	Rectangle filled with Gaussian-clustered points using the Nord palette	inkex only
make_neural_network	Stylized neural-network schematic from a comma-separated layer topology	inkex only
make_mol_graph	2D molecular graph from SMILES with pastel CPK colors and gray bonds	rdkit
make_3d_molecular_structure	Ray-traced 3D ball-and-stick rendering with optional conformer ensembles	rdkit + pymol-open-source

The two molecular plugins call out to a shared pixi environment (shared_env/) for RDKit and PyMOL, since Inkscape's bundled Python cannot install those packages directly. The other two plugins have no external dependencies.

Installation

You'll need pixi installed (one-line install: curl -fsSL https://pixi.sh/install.sh | bash).

Then from the repo root:

./deploy.sh

The script prompts for your Inkscape User Extensions path. To find it:

Inkscape → Edit → Preferences → System → User extensions

Copy that path and paste it into the prompt. The script will:

1. Build the shared pixi environment (pixi install in shared_env/) — this pulls down RDKit and PyMOL on the first run and may take a few minutes.
2. Copy every plugin's .py and .inx files to your extensions folder.
3. Copy the shared .pixi/ directory alongside them so the molecular plugins can find their Python interpreter.

Restart Inkscape and the new menu items will be available under Extensions → Generate.

Re-deploying after changes

Run ./deploy.sh again. The script overwrites the deployed files in place; the shared .pixi/ is reused unless you've changed shared_env/pixi.toml.

Repository layout

inkscape_plugins/
├── deploy.sh                       Interactive deploy script
├── shared_env/pixi.toml            Shared rdkit + pymol-open-source environment
├── make_clustered_points/          Plugin (.py + .inx + README)
├── make_neural_network/            Plugin (.py + .inx + README)
├── make_mol_graph/                 Plugin (.py + .inx + README)
├── make_3d_molecular_structure/    Plugin (.py + .inx + README)
└── README.md                       This file