Hi Mark
> I am parsing a PubChem SDF file into a smiles string but I can’t seem
> to remove the explicit hydrogens. I have tried using an
> AtomContainerManipulator but this does not appear to make a difference
> to the output (a very ugly smiles string). Code is below.
The AtomContainerManipulator.removeHydrogens doesn't remove the hydrogen
of the own atomcontainer but it creates a clone of the atomcontainer
without the hydrogens which is the return object.
in this case you can use:
mol = AtomContainerManipulator.removeHydrogens(mol);
the method removeHydrogens is static. It is not necessary to initiate
the constructor.
>
Best regards,
Miquel
>
>
> public static String getSmilesFromPubChem(String id, String type)
> throws CDKException, IOException {
>
> IMolecule mol = getPubChemMolecule(id,type);
>
> SmilesGenerator generator = new SmilesGenerator();
>
> returngenerator.createSMILES(mol);
>
> }
>
>
>
> public static IMolecule getPubChemMolecule(String id, String type)
> throws CDKException, IOException {
>
> IMolecule mol = null;
>
> URL url = new
> URL(String.format("http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?%s=%s&disopt=SaveSDF",type,id));
>
> // can't seem to get this to work with ReaderFactory
>
> Reader reader = new
> BufferedReader(newInputStreamReader(url.openStream()));
>
> IteratingMDLReader mdlReader = new IteratingMDLReader(reader,
> DefaultChemObjectBuilder.getInstance());
>
> if( mdlReader.hasNext() ) {
>
> mol = (IMolecule) mdlReader.next();
>
> AtomContainerManipulator manip = new
> AtomContainerManipulator();
>
> manip.removeHydrogens(mol);
>
> }
>
> return mol;
>
> }
>
>
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