README.md

examples

This project consists of examples how to call AMBIT modules from Java code.

AMBIT source code and site is at Sourceforge.net

AMBIT publications http://ambit.sourceforge.net/pubs_citeambit.html

AMBIT Web REST services

• Publication doi:10.1186/1758-2946-3-18

• Download http://ambit.sourceforge.net/download_ambitrest.html

• ambit2-www.war at Maven repository

• OpenTox API examples

• Ambit JSON extension of OpenTox API

• Ambit/OpenTox REST API client library https://github.com/ideaconsult/opentox-cli

• Ambit API documentation

SMARTS (and SMIRKS)

• Publication doi:10.1002/minf.201100028

• Ambit2-SMARTS examples at http://ambit.sourceforge.net/AMBIT2-LIBS/ambit2-smarts/index.html

• ambit2-smarts.jar at Maven repository

Tautomers generation

• Publication doi:10.1002/minf.201200133 and EuroQSAR 2012 poster

• Code example and a command line application at tautomers-example

• Ambit2-tautomer module at Sourceforge.net.

• ambit2-tautomer.jar download

• ambit2-tautomer.jar at Maven repository

Chemical structure standardization

• Code example : Jupyter notebook standardize/ambit_standardize_demo.ipynb

Applicability domain command line appliction

• https://github.com/ideaconsult/examples-ambit/tree/master/appdomain-example

JavaScript Molecular browser

• Publishing a chemical dataset online is easy - just convert SDF file to JSON and a folder of images with molbrowser command line application.

• Try it at http://ideaconsult.github.io/examples-ambit/molbrowser/

More examples

• Coming soon!