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.
Thanks in advance for the help J
~Mark.
public static String getSmilesFromPubChem(String id, String type) throws
CDKException, IOException {
IMolecule mol = getPubChemMolecule(id,type);
SmilesGenerator generator = new SmilesGenerator();
return generator.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(new
InputStreamReader(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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