Hi John,
Thank you very much for your fast and very helpful response. Just to be
sure: I have to imagine the electron pair between the "@" and the "]",
right? So it is always the first "substituent" after the central atom.
Thank you for the link and the comment to our code!
Best regards,
Lina
On 11/24/2015 10:45 AM, John M wrote:
> 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):
> 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 <mailto:john.wilkinson...@gmail.com>
>
> On 24 November 2015 at 08:34, Lina Humbeck <lina.humb...@tu-dortmund.de
> <mailto: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 <tel:%2B49%20231-755%2047%2013>
> lina.humb...@tu-dortmund.de <mailto:lina.humb...@tu-dortmund.de>
> www.ccb.tu-dortmund.de <http://www.ccb.tu-dortmund.de>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for
> multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net <mailto:Cdk-user@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
--
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
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
