Syed Asad Rahman

This project uses CDK which is licensed under L-GPL.

Thanks, scripting is a way to go. We are exploring an inbuilt routine.

Below is the shell script which can be used in BASH environment on UNIX/LINUX. a) Store this in a file.. maybe ```run_recoder.sh``` b) change the jar file name in JAR...

Please refer to this thread https://github.com/asad/ReactionDecoder/issues/7

A robust reaction handling module would be wonderful. You might like to try the atom atom mapping module in the ECBlast http://www.ebi.ac.uk/thornton-srv/software/rbl/

Good idea!

The present version is compatible with CDK 2.1.1 https://github.com/asad/SMSD/core/pom.xml

Try these files a) query git clone git://gist.github.com/934995.git gist-934995 (1.mol) b) target git clone git://gist.github.com/934989.git gist-934989 (connected.sdf) java -Xms500M -Xmx500M -cp SMSD20110421.jar cmd.SMSDcmd -Q MOL -q 1.mol -T SDF -t...

Thanks Gilleain, Yes we need to think about label crowding and rewriting the options, but presently SMSD should throw some kind of error in handling unsupported options.