Since I have played around with this for a fairly long time, here some of
my observations:
- loading lots (thousands) of molfiles from relation databases is quiet slow
- converting and full configuring Atomcontainers from molfiles is a very
expensive operation
- AtomContainers use a lot of memory so it must be tightly controlled how
many are in memory and hence the point before comes into play again
This problem was also observed by the creators of OrChem, the Oracle
cartridge based on CDK. And hence they created a custom serialization
method that take less space than molfiles and stores configuration info of
atomcontainers:
http://orchem.cvs.sourceforge.net/viewvc/orchem/OrChem/src/uk/ac/ebi/orchem/search/OrchemMoleculeBuilder.java?view=markup
This is way faster (at least 10) than using the molfiles.
Also when talking about storing chemical structures in a database I can
gladly refer you below project of mine:
https://bitbucket.org/kienerj/moleculedatabaseframework
Best Regards,
Joos
2013/9/24 lochana menikarachchi <locha...@yahoo.com>
> What is the recommended method for storing IAtomContainers in a database.
> Serialize? MDL Strings?
> Is there anyway to get the MDLV2000 representation as a String from
> IAtomContainer??
>
>
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