-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
f213b9f
commit d1dfde1
Showing
1 changed file
with
66 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,67 @@ | ||
| [](https://zenodo.org/badge/latestdoi/687502368) | ||
| [](https://jonasschaub.github.io/scaffold-graph-vis/javadoc/) | ||
| [](http://www.gnu.org/licenses/lgpl-2.1.html) | ||
| [](https://GitHub.com/JonasSchaub/scaffold-graph-vis/graphs/commit-activity) | ||
| [](https://GitHub.com/JonasSchaub/scaffold-graph-vis/issues/) | ||
| [](https://GitHub.com/JonasSchaub/scaffold-graph-vis/graphs/contributors/) | ||
| [](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 <a href="https://github.com/JonasSchaub/scaffold-graph-vis/wiki">wiki</a> of this repository. | ||
|
|
||
| ## JavaDoc | ||
| The JavaDoc of this library can be found <a href="https://jonasschaub.github.io/scaffold-graph-vis/javadoc/latest">here</a>. | ||
|
|
||
| ## Installation | ||
| Scaffold-graph-vis is hosted as a package/artifact on the sonatype maven central repository. See the | ||
| <a href="https://central.sonatype.com/artifact/io.github.jonasschaub/scaffold-graph-vis/">artifact page</a> for installation | ||
| guidelines using build tools like maven or gradle. | ||
| <br> | ||
| To install Scaffold-graph-vis via its JAR archive, you can get it from the | ||
| <a href="https://github.com/JonasSchaub/scaffold-graph-vis/releases">releases</a>. Note that other dependencies | ||
| will need to be installed via JAR archives as well this way. | ||
| <br> | ||
| 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 <a href="https://github.com/JonasSchaub/scaffold-graph-vis/tree/main/src">"src"</a> subfolder contains | ||
| all source code files including JUnit tests. | ||
|
|
||
| ### Tests | ||
| The test class | ||
| <a href="https://github.com/JonasSchaub/scaffold-graph-vis/blob/main/src/test/java/de/unijena/cheminf/scaffolds/GraphStreamUtilityTest.java"> | ||
| <i>GraphStreamUtilityTest</i></a> 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 |