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

[John M. <joh...@gm...>]

Ah, right just noticed… custom hydrogen adding.

> HydrogenAdderProcessor.convertImplicitToExplicitHydrogens(mol);


You need this : https://github.com/cdk/cdk/commit/3d61ec01c584cdef1b8d1ceb9110af56f13b555d

Note, the AtomContainerManipulators have also been updated to correctly handle hydrogen suppression / adding accounting for stereoelements.

J

On 13 Mar 2014, at 17:38, John May <joh...@gm...> wrote:

> Hi Nick,
> 
> This is expected, all implicit hydrogen counts must now be specified when generating SMILES. The hydrogen count is set to null if the atom typer doesn’t know the atom type - usually these are pseudo atoms and some metals. You can either see the nulls to 0, or avoid modifying them. You can still do atom typing but in generally CDKHydrogenAdder.addImplH is only needed if the count is not present. For Mol, Smiles and InChI the hydrogens are present and so the method is not needed.
> 
> You actually lose information, see the first code snippet here: http://efficientbits.blogspot.nl/2013/12/new-smiles-behaviour-parsing-cdk-154.html
> 
> Hope that helps,
> J
> 
> Here’s a correct version of your code, I should add SmilesParser/Generator are now thread safe so you don’t need a new instance all the time.
> 
>> public void testSmilesParser(String smiles) throws Exception
>> {
>> 	System.out.println("Testing smiles: " + smiles);
>> 	SmilesParser sp = new 
>> SmilesParser(SilentChemObjectBuilder.getInstance());
>> 	IAtomContainer mol = sp.parseSmiles(smiles);
>> 
>> 	HydrogenAdderProcessor.convertImplicitToExplicitHydrogens(mol);
>> 
>> 	SmilesGenerator smiGen = new SmilesGenerator();
>> 	String smiles2 = smiGen.create(mol);
>> 
>> 	System.out.println(smiles + "  --> " + smiles2);
>> }
> 
> On 13 Mar 2014, at 13:17, Nikolay Kochev <ni...@un...> wrote:
> 
>> 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
>> ----------------------------------------------------------
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/13534_NeoTech
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>