scaffold-graph-vis

Basic utilities for visualising cdk-scaffold graphs using the GraphStream library.

Description

This repository contains very basic but easy-to-use visualisation functionalities for molecular scaffold networks and scaffold trees generated using the cdk-scaffold module. The open GraphStream dynamic graph library is used for visualisation. The functionalities were part of the Scaffold Generator library earlier and are described in the accompanying scientific publication "Schaub, J., Zander, J., Zielesny, A. et al. Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). J Cheminform 14, 79 (2022)". Please note that this is a very basic functionality primarily meant for visual inspection and debugging. GraphStream might also throw errors in some cases where the problem lies with the library, not this functionality here.

Example initialization and usage of ART2a-Clustering-for-Java

See the wiki of this repository.

JavaDoc

The JavaDoc of this library can be found here.

Installation

Scaffold-graph-vis is hosted as a package/artifact on the sonatype maven central repository. See the artifact page for installation guidelines using build tools like maven or gradle.
To install Scaffold-graph-vis via its JAR archive, you can get it from the releases. Note that other dependencies will need to be installed via JAR archives as well this way.
In order to open the project locally, e.g. to extend it, download or clone the repository and open it in a Gradle-supporting IDE (e.g. IntelliJ) as a Gradle project and execute the build.gradle file. Gradle will then take care of installing all dependencies. A Java Development Kit (JDK) of version 17 or higher must also be pre-installed.

Contents of this repository

Sources

The "src" subfolder contains all source code files including JUnit tests.

Tests

The test class GraphStreamUtilityTest mainly contains executable demo code for how to use the library functionalities.

Dependencies for local installation

Needs to be pre-installed:

• Java Development Kit (JDK) version 17
  • Adoptium OpenJDK (as one possible source of the JDK)
• Gradle version 8.2
  • Gradle Build Tool

Managed by Gradle:

• JUnit Jupiter version 5.9.1
  • JUnit
  • License: Eclipse Public License - v 2.0
• Spotless version 6.19
  • Spotless GitHub repository
  • License: Apache-2.0 license
• Javadoc-publisher version 2.4
  • Javadoc-publisher GitHub repository
  • License: Apache-2.0 license