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License: LGPL v2.1, see LICENSE.txt.
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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.
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:
<dependency>
<artifactId>cdk-scaffold</artifactId>
<groupId>org.openscience.cdk</groupId>
<version>2.8</version>
</dependency>For snapshot releases (currently 2.9-SNAPSHOT) include the following fragment to define the
snapshot repository:
<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:
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).