Thanks for your message.
You are right, the 'AtomTypeAwareSaturationChecker' solves these cases.
I'll use it until the new kekulisation process will be ready
Thanks
Oscar
2014-04-26 20:36 GMT+02:00 John May <john...@ebi.ac.uk>:
> Hi Oscar,
>
> I have an improved kekulisation almost done that handles a lot more cases
> but it's not ready yet I’m afraid.
>
> AtomTypeAwareSaturationChecker is probably your best bet but there are
> known issues with it.
>
> I thought it might be possible to go via SMILES and use the atom typer to
> add hydrogens. Unfortunately this doesn’t work as the atom type doesn’t
> seem to be defined and a hydrogen is added when it should not be.
>
> [nH+]1(ccccc1)[O-]
>
>
> when it should be
>
> [n+]1(ccccc1)[O-]
>
>
> J
>
> On 26 Apr 2014, at 11:03, Oscar Mora <oscarmorape...@gmail.com> wrote:
>
> Hi!
>
> I am experiencing a problem trying to kekulise a set of molecules with
> aromatic rings and atoms with formal charge defined.
>
> I use CDK 1.5.5 to read and process a set molecules (SDF/Mol). I would
> like to kekulise all the aromatic rings in order to transform those bonds
> which are specified (mis)using bond order = 4 to an alternate set of bonds
> with order 1 and 2. In order to do this I use the tool 'FixBondOrdersTool'.
>
> I use the same piece of code specified in
> http://blueobelisk.shapado.com/questions/detect-aromatic-rings-using-bond-order-4-in-a-sdf-file-with-cdk#answer52299d9597cfef16df00952f
>
> String input = "C:\\Users\\Oscar\\Desktop\\problem.sdf";
>
> String output = "C:\\Users\\Oscar\\Desktop\\problem2.sdf";
>
> IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
>
> IteratingSDFReader sdfr = new IteratingSDFReader(new
> FileReader(input),
> builder);
>
> SDFWriter sdfw = new SDFWriter(new FileWriter(output));
>
> FixBondOrdersTool fbot = new FixBondOrdersTool();
>
> while (sdfr.hasNext()) {
> IAtomContainer container = sdfr.next();
>
> AtomContainerManipulator
> .percieveAtomTypesAndConfigureAtoms(container);
>
> container = fbot.kekuliseAromaticRings(container);
> sdfw.write(container);
> }
>
> sdfr.close();
>
> sdfw.close();
>
>
> It works fine in most cases. But I have found that when one of the atoms
> of the ring has a formal charge specified in the input SDF/Mol, the
> transformation is not performed correctly. Example:
>
> Input molecule:
>
> 7 7 0 0 0 0 999 V2000
> -0.2947 3.3589 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
> 0.4198 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4198 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.2947 1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0091 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0091 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.2947 4.1839 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
> 1 2 4 0 0 0 0
> 1 6 4 0 0 0 0
> 2 3 4 0 0 0 0
> 3 4 4 0 0 0 0
> 4 5 4 0 0 0 0
> 5 6 4 0 0 0 0
> 1 7 1 0 0 0 0
> M CHG 2 1 1 7 -1
> M END
> $$$$
>
> Processed molecule (using FixBondOrdersTool):
>
>
> CDK 0426141124
>
> 7 7 0 0 0 0 0 0 0 0999 V2000
> -0.2947 3.3589 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4198 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4198 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.2947 1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0091 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0091 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.2947 4.1839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 0 0 0 0 0
> 1 6 0 0 0 0 0
> 2 3 0 0 0 0 0
> 3 4 0 0 0 0 0
> 4 5 0 0 0 0 0
> 5 6 0 0 0 0 0
> 1 7 1 0 0 0 0
> M CHG 1 1 1
> M CHG 1 7 -1
> M END
> > <cdk:Title>
> null
>
> > <cdk:Remark>
> null
>
> $$$$
>
> As you can see the bond type of the bonds which belong to the ring are
> specified with bond order = 0.
>
> Am I doing something wrong ? How could I manage these cases in order to
> obtain a kekulised structure ?
>
> I have attached both SDF files.
>
> Thanks in advance
>
> Oscar
>
> <INPUT.sdf><PROCESSED.sdf>
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