Thanks
On Mon, Sep 21, 2020 at 7:09 AM John Mayfield <john.wilkinson...@gmail.com>
wrote:
> The SMILES parser nor other IO (maybe CML) will assign atom types for you
> - you need to do this yourself with:
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(methane);
>
> Atom types are an annotation on top of a molecule. There are different
> atom types we could assign - CDK atom types are just on set, ALOGP is a
> different set (for example). In pre CDK 1.4 basically everything was built
> on top of the view that CDK atom types were present - this is no longer the
> case.
>
> On Sun, 20 Sep 2020 at 22:44, Rajarshi Guha <rajarshi.g...@gmail.com>
> wrote:
>
>> Hi, the following code is failing because the parsed molecule has no atom
>> type names. The calculate() method tries to identify atom types from the
>> atoms type name, but this seems circular. Unless I assign atom types, where
>> does the type name come from?
>>
>> public class CDKVolumeTest {
>> public static void main(String[] args) throws CDKException {
>> SmilesParser sp = new
>> SmilesParser(DefaultChemObjectBuilder.getInstance());
>> IAtomContainer mol = sp.parseSmiles("CCO");
>>
>> double vol = VABCVolume.calculate(mol);
>> }
>> }
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net | @rguha
>> <https://twitter.com/rguha>
>>
>> _______________________________________________
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
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>>
>
--
Rajarshi Guha | http://blog.rguha.net | @rguha <https://twitter.com/rguha>
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