Question concerning atom typing

I am currently using JChem Base for calculating chemical hased fingerprints and I have a question concerning the atom typing used for calculation of these fingerprints? Do you use internal atom types or something like SYBYL from mol2? Thanks for reply!

Hi Philipp,

The chemical hashed fingerprint is a truly chemical descriptor, so it uses the literal atom types. (Carbon, Nitrogen, Oxygen, etc) 

However, JChem Screen can also calculate pharmacophore fingerprints where instead of atom types pharmacophoric properties are used. See more details here:

http://www.chemaxon.com/jchem/doc/user/PFp2D.html

 

Best regards,

Szabolcs