fingerprints from Instant JChem?

User 82d9f7eb00

28-08-2009 20:00:37

Can fingerprints be generated and exported from Instant JCHEM? If so, 

can you please provide the syntax for using GenerateMD?

java -cp 'C:\Program Files\ChemAxon\JChem\lib\jchem.jar;%CLASSPATH%" chemaxon.descriptors.GenerateMD c LOPAC.sdf -k CF -o desktop\test_jchem.MD

is my starting command. This needs to include the fingerprint length, as well as other


I also see that the chemaxon.descriptors.GenerateMD lists a unix-based specifications for input. Can these be done in GererateMD from the windows java application?








ChemAxon fa971619eb

29-08-2009 11:10:07

Fingerprint settings can be specified when creating a JChem table in Instant JChem, but there is no other support in Instant JChem for generating different molecular descriptors.

However, the GenerateMD command line application can genereate a wide range of descriptors, and output them in  number of different ways. I would suggest you study this page of the user guide: which provides a detailed description of how to use GenerateMD. Also, there are several examples towards the bottom.

Data from Instant JChem can easily be exported to a SD file, or you could directly access it from the database table using GenerateMD.

If you have further questions I suggest you post them to the "Library profiling: Virtual screening, clustering & molecular descriptors" forum whcih can be found here: