Noctis Route Miner is part of NOCTIS package. In this repository, you will find a tool designed to extract all possible synthetic routes from a reaction network. Consider a chemical network consisting of chemical equations (reactions) and molecules (compounds). In this network, a molecule produced by one reaction might serve as an ingredient for another reaction. A "route" is defined as a sufficient subgraph required to produce a given compound. The algorithm uses a breadth-first search approach to systematically mine routes—from the target compound to the starting materials. The tool is implemented as a Java plugin and is accessible via a dedicated Neo4j query either directly through Neo4j Desktop or through Noctis. For more details about the design and workflow, we invite you to read the article.
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Java Development Kit (JDK) 17
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Gradle (or use the included Gradle wrapper)
Download the Latest Release:
Grab the latest JAR file from the Releases page.
Install in Neo4j:
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Drop the JAR file into your Neo4j plugins folder.
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Restart your Neo4j database.
If you prefer to build the project yourself:
Clone the Repository:
$ bash git clone https://github.com/your_username/noctis-route-miner.git cd noctis-route-miner
Build with Gradle (Windows Example):
$ bash .\gradlew build
This will compile the project and produce the JAR file for use in ./build/libs folder
After installation, you can use the following Cypher query to invoke the route extraction functionality:
Directly through Neo4j Desktop:
$ cypher
MATCH (paracetamol: {smiles: 'CC(=O)Nc1ccc(O)cc1'})
CALL noctis.route.miner(
paracetamol,
'Molecule',
'ChemicalEquation',
'<REACTANT',
'<PRODUCT',
{maxNumberReactions: 4, nodeStopProperty:'TOXIC' }
)
YIELD relationships
WITH relationships,
[ rel in relationships | startNode(rel)] AS startNodes,
[ rel in relationships | endNode(rel)] AS endNodes
WITH relationships, startNodes + endNodes AS allNodes
RETURN
relationships,
apoc.coll.toSet(allNodes) AS nodes
Replace the MATCH statement with any other query to fetch the desired molecule, and adjust node labels, relationship types, and parameters as needed.
Through NOCTIS:
$ python
repo = Neo4jRepository(uri=YOUR_URI, username=USER, password=SECUREPASSWORD, database=DB)
routes = repo.execute_query('get_routes', root_node_uid="UID1", max_number_reactions=7, node_stop_property='REDFLAG')
For more details, we invite you to check NOCTIS repo or the publication.
Attention!!!: A uid property is required on all Molecule and ChemicalEquation nodes for the algorithm to run correctly.
Contributions are welcome! If you have ideas for improvements or encounter issues, please feel free to fork the repository and submit a pull request. For major changes, it is recommended to open an issue first to discuss what you would like to change.