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 <[email protected]> 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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