scaffold-graph-vis
Basic utilities for visualising cdk-scaffold graphs using GraphStream
Science Score: 67.0%
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Low similarity (11.6%) to scientific vocabulary
Repository
Basic utilities for visualising cdk-scaffold graphs using GraphStream
Basic Info
- Host: GitHub
- Owner: JonasSchaub
- License: lgpl-2.1
- Language: Java
- Default Branch: main
- Size: 197 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
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
Owner
- Name: Jonas Schaub
- Login: JonasSchaub
- Kind: user
- Location: Jena, Germany
- Company: Friedrich-Schiller-University
- Website: https://cheminf.uni-jena.de/members/jonas-schaub/
- Repositories: 1
- Profile: https://github.com/JonasSchaub
Doctoral candidate of Steinbeck research group for cheminformatics and computational metabolomics. ORCID: 0000-0003-1554-6666
Citation (CITATION.cff)
cff-version: 1.2.0
title: scaffold-graph-vis
version: 1.0.0.0
message: "If you use this software, please cite it as below."
type: software
authors:
- family-names: "Zander"
given-names: "Julian"
orcid: "https://orcid.org/0000-0001-8197-076X"
- family-names: "Schaub"
given-names: "Jonas"
orcid: "https://orcid.org/0000-0003-1554-6666"
- family-names: "Zielesny"
given-names: "Achim"
orcid: "https://orcid.org/0000-0003-0722-4229"
- family-names: "Steinbeck"
given-names: "Christoph"
orcid: "https://orcid.org/0000-0001-6966-0814"
url: "https://github.com/JonasSchaub/scaffold-graph-vis"
license: LGPL-2.1
doi: "10.5281/zenodo.10043527"
date-released: 2023-10-26
references:
- authors:
- family-names: "Schaub"
given-names: "Jonas"
orcid: "https://orcid.org/0000-0003-1554-6666"
- family-names: "Zander"
given-names: "Julian"
orcid: "https://orcid.org/0000-0001-8197-076X"
- family-names: "Zielesny"
given-names: "Achim"
orcid: "https://orcid.org/0000-0003-0722-4229"
- family-names: "Steinbeck"
given-names: "Christoph"
orcid: "https://orcid.org/0000-0001-6966-0814"
doi: "10.1186/s13321-022-00656-x"
journal: "J Cheminform"
scope: "Cite this article if you want to reference the general concepts of the software."
title: "Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)"
type: article
year: 2022
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