No problem,
Your message actually prompted me to get it finished off yesterday so it should
be available relatively soon. Just trying to think of a name for it now.
J
On 28 Apr 2014, at 08:30, Oscar Mora <[email protected]> wrote:
> 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 <[email protected]>:
> 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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