QizhiSu / apps-ambit

Applications using AMBIT and examples how to call AMBIT modules

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!