noctis 1.0.2

What is NOCTIS?

NOCTIS is a Python package for modeling and analyzing chemical reaction data as graph structures.

It allows you to build and explore complex reaction networks — beyond just molecules and chemical equations — by supporting additional node types, metadata, and relationships.

NOCTIS provides tools to:

• Preprocess and validate chemical reaction datasets

• Build graph representations from reaction data

• Query and navigate reaction networks

• Mine synthesis routes using a custom Java plugin

• Interact programmatically with graph databases

• Transform query results into formats suitable for further analysis (e.g., NetworkX, Pandas)

To learn more, visit the documentation.

Try it interactively with our example notebook! 📓 Example Notebook

Installation

Create a dedicated Python environment for this package with your favorite environment manager.

conda create -n noctis python=3.9
conda activate noctis

• Option 1: Install the package from the GitHub repository:

pip install git+ssh://git@github.com/syngenta/noctis.git@main

• Option 2: Install the package from the Python Package Index (PyPI):

pip install noctis

Configuration

Both NOCTIS and its companion package Linchemin need a small on-disk configuration before you can use them.

After installation, and before the first usage, run the following command:

noctis_configure && linchemin_configure

What each command does

settings.yaml – default runtime settings (edit as needed)

.secrets.yaml – placeholders for credentials (replace with the real values)

schema.yaml – description of the graph schema used by the database

settings.toml – default settings you may tweak

.secrets.toml – placeholders for the required secrets

For more details:

Development Installation

If you’re working on the development of NOCTIS and want to run directly from source:

git clone git@gitlab.com:syngentagroup/scientific-computing-team/noctis.git
pip install -e noctis/[dev]