WARNING! starting from verion 3.2.0 (Aug 22, 2022), DENOPTIM provides all the functionality of GM3DFragmenter in a more user-friendly framework that includes a graphical user interface. A number of other improvements to the fragmentation algorithm are available in the DENOPTIM-integrated implementation. Therefore, GM3DFragmenter is discontinued.

GM3DFragmenter

GM3DFragmenter is a molecular fragmentation tool meant to support peculiar chemical features, such as multihapto bonds and situations beyond standard valence rules.

This fragmenter takes chemical objects containing formally defined bonds (i.e., a connectivity table) and generates 2D and 3D fragments according to the principles of the class-based approach described in these papers:

1. Foscato, M.; Occhipinti, G.; Venkatraman, V.; Alsberg, B. K.; Jensen, V. R.; Automated Design of Realistic Organometallic, Molecules from Fragments; J. Chem. Inf. Model. 2014, 54, 767–780.
2. Foscato, M.; Venkatraman, V.; Occhipinti, G.; Alsberg, B. K.; Jensen, V. R.; Automated Building of Organometallic Complexes from 3D Fragments; J. Chem. Inf. Model. 2014, 54, 1919–1931.

Overview of the folder tree

• data: contains various versions of cutting rules
• doc: contains the user manual and, after running the createDoc.sh, the API documentation
• jar: after building (see below), contains the JAR archive files
• lib: contains the third parties library used by GM3DFragmenter
• src: source code of GM3DFragmenter
• test: input and data required to run the functionality tests
• utils: utilities associated with the generation and management of fragments libraries

Compile GM3DFragmenter

Building scripts are made available for Unix systems. These scripts assume java and javac commands are in your $PATH. To verify this condition, please see if you get a reasonable output from the following commands.

    java -version
    javac -version

To build GM3DFragmenter run:

    ./build_GM3DFragmenter.sh

Now, you are ready to go. Happy fragmenting!

User Manual

The user manual is available under the doc folder. An online version is also available.

WARNING! starting from verion 3.2.0 (Aug 22, 2022), DENOPTIM provides all the functionality of GM3DFragmenter in a more user-friendly framework that includes a graphical user interface. A number of other improvements to the fragmentation algorithm are available in the DENOPTIM-integrated implementation. Therefore, GM3DFragmenter is discontinued.

License

The software is distributed under the GNU Affero General Public License version 3. Modifications of the CDK library (affecting org/openscience/cdk/smiles/smarts/SMARTSQueryTool, org/openscience/cdk/smiles/FixBondOrdersTool, org/openscience/cdk/tools/periodictable/PeriodicTable) are discributed under the GNU Lesser General Public License version 2.1. See under the lib.