Hi all,
I'm attempting to use CDK for the first time, but am having problems with the
following code:
/**
*
* @param inchiTerm1
* @param inchiTerm2
* @return float
* @throws CDKException
*/
private float getScore( final String inchiTerm1, final String
inchiTerm2 ) throws CDKException
{
// System.out.println( inchiTerm1 + "\t" + inchiTerm2 );
//$NON-NLS-1$
final IAtomContainer molecule1 =
(IAtomContainer)getIChemObject( inchiTerm1 );
final IAtomContainer molecule2 =
(IAtomContainer)getIChemObject( inchiTerm2 );
final Fingerprinter fingerprinter = new Fingerprinter();
final BitSet fingerprint1 = fingerprinter.getFingerprint(
molecule1 );
final BitSet fingerprint2 = fingerprinter.getFingerprint(
molecule2 );
return Tanimoto.calculate( fingerprint1, fingerprint2 );
}
/**
* @param inchiTerm
* @return IChemObject
* @throws CDKException
*/
private IChemObject getIChemObject( final String inchiTerm ) throws
CDKException
{
return new INChIPlainTextReader( new ByteArrayInputStream(
inchiTerm.replace( "InChI", "INChI" ).getBytes() ) ).read( new ChemFile() ); //
Need to replace 'InChI' for 'INChI', unfortunately...
}
I'm wanting to generate BitSets from Inchi strings, but am failing in the
getIChemObject method. It seems that the reader doesn't like the following
Inchi string, despite the fact that it came from ChEBI and seems to be OK in
other applications.
InChI=1/C3H6N2O4/c4-3(9)5-1(6)2(7)8/h1,6H,(H,7,8)(H3,4,5,9)/t1-/m0/s1/f/h5,7H,4H2
I'm aware that there may be better ways of reading Inchis, but looking at the
API, this was the best that I can do.
Cheers,
Neil.
Neil Swainston
Experimental Officer
Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
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