cdk-scaffold
Chemistry Development Kit module for scaffold functionalities
Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
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○Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary
Repository
Chemistry Development Kit module for scaffold functionalities
Basic Info
Statistics
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
CDK-Scaffold Module
Scaffold Functionalities for the Chemistry Development Kit (CDK)
Copyright © 2023 The CDK Development Team, especially Julian Zander, Jonas Schaub, Achim Zielesny, Christoph Steinbeck
License: LGPL v2.1, see LICENSE.txt.
CDK Home Page | JavaDoc | Wiki | Issues | CDK Users Mailing List
Introduction
The Chemistry Development Kit (CDK) is an open-source Java library for cheminformatics and bioinformatics. For more details, visit the main CDK repository at https://github.com/cdk/cdk.
The cdk-scaffold module makes versatile molecular scaffold functionalities available for integration with CDK-based workflows and software.
It was initially based on the "Scaffold Generator" project which is described in detail in Schaub et al. "Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)" (J Cheminform 14, 79, 2022).
Detailed code examples can be found in the repository wiki.
Some of the cdk-scaffold functionalities are also implemented in the MORTAR (MOlecule fRagmenTAtion fRamework) rich client Graphical User Interface (GUI) application (GitHub repository, article).
The (very basic) visualisation functionalities for scaffold trees and networks described in the Scaffold Generator article linked above can be found in this repository.
Install
The library is built with Apache Maven and currently requires Java 1.8 or later.
You can download a pre-built library JAR from releases.
If you are using Maven, you can install the cdk-scaffold package using:
xml
<dependency>
<artifactId>cdk-scaffold</artifactId>
<groupId>org.openscience.cdk</groupId>
<version>2.8</version>
</dependency>
Snapshot releases
For snapshot releases (currently 2.9-SNAPSHOT) include the following fragment to define the
snapshot repository:
xml
<repositories>
<repository>
<id>ossrh</id>
<url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
</repository>
</repositories>
Further details on building the project in integrated development environments (IDEs) are available on the wiki: * Building the CDK * Maven Reporting Plugins
Getting Help
The Toolkit-Rosetta Wiki Page provides some examples for common tasks. If you need help using the CDK and have questions please use the user mailing list, cdk-user@lists.sf.net (you must subscribe here first to post).
Owner
- Name: The Chemistry Development Kit
- Login: cdk
- Kind: organization
- Website: https://cdk.github.io/
- Repositories: 19
- Profile: https://github.com/cdk
Chem- and bioinformatics library
Citation (CITATION.cff)
cff-version: 1.2.0
title: cdk-scaffold
version: 2.8
message: "If you use this software, please cite it as below and also cite the accompanying scientific publication referenced 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"
doi: "10.5281/zenodo.7940339"
date-released: 2023-09-11
url: "https://github.com/cdk/cdk-scaffold"
license: LGPL-2.1
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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Dependencies
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/setup-java v3 composite
- org.openscience.cdk:cdk-core 2.9
- org.openscience.cdk:cdk-fragment 2.9
- org.openscience.cdk:cdk-interfaces 2.9
- org.openscience.cdk:cdk-standard 2.9
- org.hamcrest:hamcrest 2.2 test
- org.hamcrest:hamcrest-core 2.2 test
- org.junit.jupiter:junit-jupiter-api 5.9.3 test
- org.junit.jupiter:junit-jupiter-engine 5.9.3 test
- org.junit.jupiter:junit-jupiter-params 5.9.3 test
- org.openscience.cdk:cdk-data 2.9 test
- org.openscience.cdk:cdk-depict 2.9 test
- org.openscience.cdk:cdk-io 2.9 test
- org.openscience.cdk:cdk-test 2.9 test