Hi all,
I gave it a try, it cause a NullPointerException when writing the
deprotonated result back to SMILES. What am I doing wrong?
Kind regards,
Martin
Code:
String smi = "CCC(O)=O";
IAtomContainer mol = Converter.parseSmiles(smi);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
String carboxylSMARTS = "C(O)=O";
int oIndexInSMARTS = 1;
SMARTSQueryTool smartsMatch = new
SMARTSQueryTool(carboxylSMARTS, SilentChemObjectBuilder.getInstance());
if (smartsMatch.matches(mol))
{
for (List<Integer> match : smartsMatch.getMatchingAtoms())
{
IAtom oAtom = mol.getAtom(match.get(oIndexInSMARTS));
for (IAtom neighborToO : mol.getConnectedAtomsList(oAtom))
{
if (neighborToO.getSymbol().equals("H"))
{
System.out.println("removing H");
mol.removeAtom(neighborToO);
}
}
}
}
System.out.println(new SmilesGenerator().create(mol));
Output:
removing H
Exception in thread "main" java.lang.NullPointerException
at org.openscience.cdk.smiles.CDKToBeam.toBeamEdge(CDKToBeam.java:244)
at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:153)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:374)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:330)
Am 06.10.2015 um 16:51 schrieb Schmid Emanuel (ID SIS):
Hi
Is there an easy way to deprotonate all carboxyl groups of a molecule?
It's because I need the salts rather than the acids.
Greetings,
Emanuel
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