On Sat, 2007-04-14 at 09:44 -0400, Bala B K wrote: > Hi all, > I have a question regarding generating SMILES strings for fragments of > a molecule. Say I have a molecule for which I have already generated > the SMILES string, which means that ring perception, canonicalization > etc. have been done. Now during the course of a reaction, I split the > molecule into two and want to generate the SMILES string for both > pieces. Does the SMILESGenerator do ring perception again or does it > use the previous information. If it doesn't use the information > computed in the previous calculation, how can I make it use that > information so that it runs faster.
AFAICS, it will have to do aromaticity detection etc again. Note that you can specify your own AllRingsFinder object at construction time. However it's not clear to me whether the generator could make use of prior information at all. More specifically, if you have an IAtomContainer X and then fragment it to an IAtomContainer[] Y. Say you had an ARF for X, there is no guarantee that the atoms/bonds in the ARF for X would map to Y (especially if the elements of Y are deep copy's) especially, if the fragmentation occurred at ring bonds (unlikely) So I think the generator will just redo the aromaticity/ring perception. ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "355/113 -- Not the famous irrational number PI, but an incredible simulation!" ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
