[Cdk-devel] SmilesGenerator and implicit H atoms converted to explicit

[Nikolay K. <ni...@un...>]

Hi,

I obtain Null pointer exception when I try to generate the smiles code 
for a molecule with hydrogen atoms converted from implicit to explicit.
Am I missing something in the explicit hydrogens manipulation?
The exception is in thrown by the Beem package.

I use CDK 1.5.6
Here is the java code:


public void testSmilesParser(String smiles) throws Exception
{
	System.out.println("Testing smiles: " + smiles);
	SmilesParser sp = new 
SmilesParser(SilentChemObjectBuilder.getInstance());
	IAtomContainer mol = sp.parseSmiles(smiles);

	AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
	CDKHydrogenAdder adder = 
CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance());
	adder.addImplicitHydrogens(mol);
	HydrogenAdderProcessor.convertImplicitToExplicitHydrogens(mol);

	SmilesGenerator smiGen = new SmilesGenerator();
	String smiles2 = smiGen.create(mol);

	System.out.println(smiles + "  --> " + smiles2);
}


testSmilesParser("CC");


And here is the output.

Testing smiles: CC
Exception in thread "main" java.lang.NullPointerException: One or more 
atoms had an undefined number of implicit hydrogens
	at 
com.google.common.base.Preconditions.checkNotNull(Preconditions.java:208)
	at org.openscience.cdk.smiles.CDKToBeam.toBeamAtom(CDKToBeam.java:200)
	at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:148)
	at 
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:376)
	at 
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:332)
	at 
ambit2.smarts.test.TestUtilities.testSmilesParser(TestUtilities.java:1534)
	at ambit2.smarts.test.TestUtilities.main(TestUtilities.java:2127)


Analogously in the molecule is read from a MOL file the same exception 
is thrown.

If the input smiles is defined with explicit hydrogen there is no 
problem.


testSmilesParser("[H]C([H])([H])C([H])([H])[H]");

outputs:
Testing smiles: [H]C([H])([H])C([H])([H])[H]
[H]C([H])([H])C([H])([H])[H]  --> [H]C([H])([H])C([H])([H])[H]


With best regards
Nick


----------------------------------------------------------
Dr. Nikolay Kochev
University of Plovdiv
Department of Analytical Chemistry and Computer Chemistry
----------------------------------------------------------