Canonicalisation?

Red Hat Enterprise Linux AS release 3 (Taroon)


Kernel 2.4.21-4.ELsmp on an i686





Oracle version 10.1.0





Apache Tomcat/4.1.30





JChem version: 3.0.11


JChem Streams version: 3.0.11








Hello. I am confused as to what degree of canonicalisation is required to make Jchem’s jc_equals and jc_contains functions work correctly (and for best performance). I am only using the Cartridge and plain tables.





Should the smiles in my table be canonicalised using a Jchem function? If so, how?





Should I be passing some canonicalisation parameter when I build the index? If so, how.





Should I canonicalise the input smiles in the query? If so, how.





My testing seems to indicate that Jchem will work without any canonicalisation, but I want to know for definite one way or the other.





Thanks for your advice.


Mark

JChem Cartridge does not rely on your structures being canonicalised. So you can index them as they are.





Peter