On 25 September 2013 08:03, Joos Kiener <j...@sunrise.ch> wrote:
> 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
>
The slow part is not reading molfile from the database, but loading it into
IAtomContainer. Actually it is rarely needed to load bunch of atom
containers in memory - especially in web based interface where
serialisation is to something web friendly, not Java objects.
http://apps.ideaconsult.net:8080/ambit2/dataset?page=0&pagesize=100
And of course check http://ambit.sf.net for full featured MySQL structure
searchable database + properties (no cartridge , no memory hog ORM, just
JDBC) with REST web service API ( i.e. OpenTox API).
Best regards,
Nina
> - 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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