I'm looking at one of the SmilesParserTest cases, specifically
testSFBug956921().
The function looks like:
String smiles = "[cH-]1cccc1";
IMolecule mol = sp.parseSmiles(smiles);
Assert.assertEquals(5, mol.getAtomCount());
// each atom should have 1 implicit hydrogen, and two neighbors
However when I look at the result of the SMILES parsing I see that
the first carbon has 1 implicit hydrogen (as returned by
atom.getHydrogenCount()) but all others are null - indicating that
they have not been set.
I'm using the code below:
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.smiles.SmilesParser;
public class junk {
public static void main(String[] args) throws
InvalidSmilesException {
SmilesParser sp = new SmilesParser
(DefaultChemObjectBuilder.getInstance());
String smiles = "[cH-]1cccc1";
IMolecule mol = sp.parseSmiles(smiles);
System.out.println("mol.getAtomCount() = " + mol.getAtomCount
());
for (int i = 0; i < mol.getAtomCount(); i++) {
Integer hc = mol.getAtom(i).getHydrogenCount();
System.out.println("mol.getAtom(i).getHydrogenCount() =
" +hc);
}
}
}
But, if in the above code I change the SMILES to c1ccccc1 and then
rerun, all the atoms are reported to have 0 implicit hydrogens,
whereas this should be for each atom.
I have been looking at the SmilesParser code and see 2 places where
implicit hydrogens are handled but can't really see what's going wrong.
If somebody could take a look or else point me in the right
direction, it would be much appreciated since this seems to be a very
fundamental error
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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Chemistry professors never die, they just fail to react.
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