Re: [Cdk-devel] [Cdk-user] restriction of CDKAromaticityDetector (getHybridization returns null)

[Rajarshi G. <rg...@in...>]

On Dec 9, 2007, at 1:35 AM, Nina Jeliazkova wrote:

> Hi,
>
> I think I've found the reason - when a molecule is created via
> SmilesParser, the hybridization of atoms is correctly set. If a  
> molecule
> is read from a file, atom.getHybridization() method returns null.   
> Thus
> for aromaticity detection to work properly, we need some preprocessing
> after the molecule is read, or/and some exception thrown if  
> aromaticity
> detector encounters nulls in getHybridization method.

Have you tried perform atom typing before the aromaticity detection?  
I think the method is detectAndConfigureAtomTypes or something like that

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Rajarshi Guha  <rg...@in...>
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