Hi,
I'm not entirely sure what the question was but -
The lone-pair is treated like an implicit hydrogen and is placed where the
central atom is. In the internal representation this means one of the
neighbours will also be the central atom.
For example in (your email client might cut the tail off with this inline
image):
[image: Inline images 1]
We have
central atom: 7
neighbours: {6, 7, 8, 9 } // note 7 appears in the neighbour list
winding: clockwise
The winding is looking from 6 towards {7,8,9}.
Try these in http://cdkdepict-openchem.rhcloud.com/depict.html:
Cc1cnc(C[S@@](=O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC
> Cc1cnc(C[S@](=O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC
Cc1cnc(C[C@@H](O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC
> Cc1cnc(C[C@H](O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC
PS, you don't need this for your code if you ditch the CDK aromaticity:
// prepare atom types
> try {
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
> } catch (CDKException e) {
> e.printStackTrace();
> }
>
> // add implicit hydrogens
> try {
>
> CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol);
> } catch (CDKException e) {
> e.printStackTrace();
> }
Then you can use this -
new Aromaticity(ElectronDonation.daylight(), Cycles.or(Cycles.all(),
> Cycles.edgeShort()));
Regards,
John W May
john.wilkinson...@gmail.com
On 24 November 2015 at 08:34, Lina Humbeck <lina.humb...@tu-dortmund.de>
wrote:
> Hi all,
>
>
> we used the attached java code utilizing CDK 1.5. to create a canonical
> chiral smiles from the input which was the attached Esomeprazol.sdf. The
> result is:
> Cc1cnc(C[S@@](=O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC
> To determine an explicit chirality from the smiles you need the four
> different substituents of the sulfur atom. Therefore, we miss the
> explicit representation of the free electron pair of sulfur. I have no
> representation of electron pairs in smiles in mind. Is there a rule
> where the free electron pair implicitly is placed? Such as for example:
> The free electron pair is always implicitly placed as first or last
> substituent of the chiral atom?
>
> Best regards,
>
> Lina
>
>
> --
> Dipl.-Pharm.
> Lina Humbeck
>
> TU Dortmund University
> Faculty of Chemistry and Chemical Biology
> Otto-Hahn-Str. 6
> D-44227 Dortmund
>
> Phone: +49 231-755 47 13
> lina.humb...@tu-dortmund.de
> www.ccb.tu-dortmund.de
>
>
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