On 4 September 2011 09:25, Egon Willighagen <[email protected]>wrote:
> cc:Sam (author of the CDK-InChI bridge)
>
> On Sun, Sep 4, 2011 at 7:52 AM, Nina Jeliazkova
> <[email protected]> wrote:
> > This usually happens, when the molecule does not contain explicit
> > hydrogens.
>
> I was not aware of that. Doesn't sound very useful. We don't have a
> unit test for this yet, right? That tests for InChI generation for a
> compound with and without explicit hydrogens, do we?
>
> Does this happen for any compound?
>
Aromatics only.
I came into this issue only recently, when working on metabolite generation
in Toxtree, haven't tested on a large scale.
>
> > e.g. the test below fails with exactly the same message : "Accepted
> unusual
> > valence(s): C(3); Cannot process aromatic bonds"
> > SmilesParser p = new
> > SmilesParser(NoNotificationChemObjectBuilder.getInstance());
> > IMolecule mol = p.parseSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C");
> > /*
> > CDKHydrogenAdder ha =
> >
> CDKHydrogenAdder.getInstance(NoNotificationChemObjectBuilder.getInstance());
> > ha.addImplicitHydrogens(mol);
> > AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
> > */
> > InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
> > InChIGenerator gen = factory.getInChIGenerator(mol);
> > INCHI_RET ret = gen.getReturnStatus();
> > if (ret != INCHI_RET.OKAY) {
> > throw new Exception(String.format("InChI failed: %s [%s]",
> > ret.toString(),gen.getMessage()));
> > }
> > String inchi = gen.getInchi();
> >
>
> Assert.assertEquals("InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3",
> > inchi);
>
> I'll try to use this to create a unit test. I'll also make one for
> methane... wondering how widespread this issue is...
>
Alkanes work fine.
Nina
>
> > Uncomment the hydrogen adder code and the test will succeed.
> > I haven't investigated whether the explicit H requirement is the normal
> > InChI behaviour or something in the cdk-inchi interaction, perhaps others
> > could help. Otherwise, I agree the current behaviour is not quite
> > convenient.
>
> Sam, do you know what is going on?
>
> Egon
>
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet (http://ki.se/imm)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
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