On Nov 21, 2007, at 6:42 AM, Javi Muriel Zafra wrote:
> Hi.
>
> I'm working with molecules in an application, and I want to store
> them in a database. So, I would like to know how I can to store a
> molecule what I have in a Molecule (or AtomContainer) object. The
> type in which I store the molecule in the database table is a Long
> Row, so I need to use the method PreparedStatement.setBinaryStream
> (JDBC).
>
> To read a molecule from de db I use the following code:
>
> ResultSet rset = stmt.executeQuery(" .... ");
>
> ...
>
> IChemObjectReader reader = new ReaderFactory().createReader(
>
> rset.getBinaryStream("structure"));
>
> ChemObject cmol = (ChemObject) reader.read( new
> org.openscience.cdk.Molecule());
>
> IAtomContainer iaTemp = (IAtomContainer) cmol;
>
> I've tried to "reverse" the code to adapt for write a molecule, but
> I've not obtained it. Any idea??
You could store molecules in a variety of ways
* SMILES
* SDF
* a binary object (Postgres+Tigress supports this)
On the hand, it looks like you want Java object serialization. See
http://www.devx.com/tips/Tip/12439 for an example
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