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>
>
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>
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