diff --git a/README.md b/README.md index a4f0478..fe3b185 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,67 @@ +[![DOI](https://zenodo.org/badge/687502368.svg)](https://zenodo.org/badge/latestdoi/687502368) +[![Javadoc](https://img.shields.io/badge/JavaDoc-Online-green)](https://jonasschaub.github.io/scaffold-graph-vis/javadoc/) +[![License: GPL v3](https://img.shields.io/badge/License-LGPL%20v2.1-blue.svg)](http://www.gnu.org/licenses/lgpl-2.1.html) +[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://GitHub.com/JonasSchaub/scaffold-graph-vis/graphs/commit-activity) +[![GitHub issues](https://img.shields.io/github/issues/JonasSchaub/scaffold-graph-vis.svg)](https://GitHub.com/JonasSchaub/scaffold-graph-vis/issues/) +[![GitHub contributors](https://img.shields.io/github/contributors/JonasSchaub/scaffold-graph-vis.svg)](https://GitHub.com/JonasSchaub/scaffold-graph-vis/graphs/contributors/) +[![GitHub release](https://img.shields.io/github/release/JonasSchaub/scaffold-graph-vis.svg)](https://github.com/JonasSchaub/scaffold-graph-vis/releases/) # scaffold-graph-vis -Basic utilities for visualising cdk-scaffold graphs using GraphStream +Basic utilities for visualising [cdk-scaffold](https://github.com/cdk/cdk-scaffold) graphs using the [GraphStream library](https://github.com/graphstream). + +## 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](https://github.com/cdk/cdk-scaffold). The open +[GraphStream](https://github.com/graphstream) dynamic graph library is used for visualisation. +The functionalities were part of the [Scaffold Generator](https://github.com/Julian-Z98/ScaffoldGenerator) 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)"](https://doi.org/10.1186/s13321-022-00656-x). +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](https://adoptium.net) (as one possible source of the JDK) +* Gradle version 8.2 + * [Gradle Build Tool](https://gradle.org) + +**Managed by Gradle:** +* JUnit Jupiter version 5.9.1 + * [JUnit ](https://junit.org/junit5/) + * License: Eclipse Public License - v 2.0 +* Spotless version 6.19 + * [Spotless GitHub repository](https://github.com/diffplug/spotless) + * License: Apache-2.0 license +* Javadoc-publisher version 2.4 + * [Javadoc-publisher GitHub repository](https://github.com/MathieuSoysal/Javadoc-publisher.yml) + * License: Apache-2.0 license \ No newline at end of file