Hi Martin,
The Kekulization class replaces the FixBondOrderTool. You should invoke this on
read rather than on write - note again only certain formats will need it.
> SDFs like that is not deterministic
In what regard was the FixBondOrderTool non deterministic? Did it give
different Kekulé assignments for the same input or did it randomly fail.
Thanks,
J
On Sep 30, 2014, at 10:42 AM, Martin Guetlein <martin.guetl...@googlemail.com>
wrote:
> Hi John,
>
> my example is in the bug that I reported some time ago:
> https://sourceforge.net/p/cdk/bugs/1307
> I added the FixBondOrderTool to this example to make sure that, after
> writing compounds to SDF and reading them again, aromaticity can be
> detected correctly (thanks to kekulization). But then I found out that
> writing SDFs like that is not deterministic. This is why I am looking
> for a method that ensures a proper Kekule representation and, at the
> same time, is deterministic.
>
>> Are you reading from SMILES like in your example?
> My input data can be any format CDK is supporting (if your interested,
> see http://ches-mapper.org)
>
> Thanks for your help,
> Martin
>
>
>
>
>
>
>
> On 30 September 2014 11:15, John May <john.wilkinson...@gmail.com> wrote:
>> Hi Martin,
>>
>> I tried your mykekule-Method in this example (instead of
>> FixBondOrderTool) and it was able to detect aromaticity correctly
>>
>>
>> I’m not sure what you mean here - it is not detecting aromaticity at all.
>> The input to this method needs a structure with bond orders already
>> assigned, aromatic flags may be set but they are not utilised. Do you mean
>> aromaticity can be detected by the assigned structure.
>>
>> I do not fully understand. Is there a method to asign bond orders and
>> to make the mykekule a replacement for FixBondOrderTool?
>>
>>
>> Yes - but I think we’re on different pages. Are you reading from SMILES like
>> in your example? If so, the bond orders are automatically assigned on input
>> and no extra effort is needed to store the output in SDF.
>>
>> My understanding was you needed a way to assign a consistent Kekule
>> structure when there are multiple Kekule forms (i.e. in naphthalene)? This
>> is what the mykekule method does - it is less work to assign a Kekulé form.
>> It might be easier if you have an example of the unexpected behaviour.
>>
>> J
>>
>> On Sep 29, 2014, at 2:51 PM, Martin Guetlein
>> <martin.guetl...@googlemail.com> wrote:
>>
>> Hi John,
>>
>> Hmm, I was only using the FixBondOrderTool to make sure that
>> aromaticity is not lost when exporting compounds to molfiles/SDF (see
>> https://sourceforge.net/p/cdk/bugs/1307).
>> I tried your mykekule-Method in this example (instead of
>> FixBondOrderTool) and it was able to detect aromaticity correctly.
>>
>> The input to SMILES must already have bond orders assigned so it’s not a
>> drop in replacement for FixBondOrderTool if you have delocalized bonds.
>>
>> I do not fully understand. Is there a method to asign bond orders and
>> to make the mykekule a replacement for FixBondOrderTool?
>>
>>
>> Thanks for your help,
>> Martin
>>
>>
>> On 29 September 2014 15:35, John May <john.wilkinson...@gmail.com> wrote:
>>
>> Hi Martin,
>>
>> The mykekule() example as it is will preserve 3D coordinates. All properties
>> (except bond order) remain unchanged from the input. Using the SMILES output
>> just simplifies the code a little. The input to SMILES must already have
>> bond orders assigned so it’s not a drop in replacement for FixBondOrderTool
>> if you have delocalized bonds. Usual warning about aromatic bonds in
>> molfiles applies.
>>
>> J
>>
>> On Sep 29, 2014, at 1:12 PM, Martin Guetlein
>> <martin.guetl...@googlemail.com> wrote:
>>
>> Hi John,
>>
>> thanks for your email. Unfortunately, I cannot use the SMILES round
>> trip like that because my input molecules might include 3D
>> information, that will be lost. Could this be added to the mykekule
>> method? I would use this mykekule method instead of the
>> FixBondOrderTool, correct?
>>
>> Kind regards,
>> Martin
>>
>>
>> On 29 September 2014 12:54, John May <john.wilkinson...@gmail.com> wrote:
>>
>> Hi Martin,
>>
>> I can’t speak for the FixBondOrdersTool but Kekulization is deterministic
>> and will generate the Kekulé assignment depending on atom order. To generate
>> a uniform assignment first canonicalize the molecule by sorting the atoms
>> and bonds but a canonical label (e.g. from Canon or InChINumbersTools).
>>
>> For something out of the box you could round trip through SMILES.
>>
>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>> SmilesParser smipar = new SmilesParser(bldr);
>> SmilesGenerator smigen = SmilesGenerator.unique();
>>
>> System.out.println(smigen.create(smipar.parseSmiles("c1cc2c(cc1)cccc2")));
>> System.out.println(smigen.create(smipar.parseSmiles("C1=CC2=C(C=C1)C=CC=C2")));
>> System.out.println(smigen.create(smipar.parseSmiles("C=1C=C2C(=CC=1)C=CC=C2")));
>> System.out.println(smigen.create(smipar.parseSmiles("C1=CC=2C(C=C1)=CC=CC=2")));
>>
>>
>> Gives the output
>>
>> C1=CC=C2C=CC=CC2=C1
>>
>> C1=CC=C2C=CC=CC2=C1
>>
>> C1=CC=C2C=CC=CC2=C1
>>
>> C1=CC=C2C=CC=CC2=C1
>>
>>
>> It is possible to do it without reordering the molecule permanently but it
>> is quite tricky to explain so I’ll just provide the code.
>>
>> static IAtomContainer mykekule(IAtomContainer org) throws Exception {
>>
>> final IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>> final SmilesParser smipar = new SmilesParser(bldr);
>> final SmilesGenerator smigen = SmilesGenerator.unique();
>>
>> final int n = org.getAtomCount();
>> int[] ordering = new int[n];
>>
>> // generate a kekule assignment via SMILES and store the output order (a
>> permutation of
>> // atom indices)
>> IAtomContainer cpy = smipar.parseSmiles(smigen.create(org, ordering));
>>
>> // index atoms for lookup
>> final Map<IAtom,Integer> atomIndexMap = new HashMap<>();
>> for (IAtom atom : org.atoms())
>> atomIndexMap.put(atom, atomIndexMap.size());
>>
>> // util to get atom index -> bond map
>> EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(cpy);
>> GraphUtil.toAdjList(cpy, bondMap);
>>
>> for (IBond bond : org.bonds()) {
>>
>> // atom indices
>> int u = atomIndexMap.get(bond.getAtom(0));
>> int v = atomIndexMap.get(bond.getAtom(1));
>>
>> // atom indices in 'cpy'
>> int uCpy = ordering[u];
>> int vCpy = ordering[v];
>>
>> // propagate the assigned bond order
>> bond.setOrder(bondMap.get(uCpy, vCpy).getOrder());
>>
>> // note the following would also work to get the cpy bond
>> // cpy.getBond(cpy.getAtom(uCpy), cpy.getAtom(vCpy));
>> }
>>
>> return org;
>> }
>>
>>
>> https://gist.github.com/johnmay/cf1d3767d04eb424557f
>>
>> You can use that method to consistently kekulise molecules and maintain the
>> atom order. I use SMILES again but would work the same with molfiles.
>>
>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>> SmilesParser smipar = new SmilesParser(bldr);
>> SmilesGenerator smigen = SmilesGenerator.generic(); // note not unique
>> smiles now!
>>
>> System.out.println(smigen.create(mykekule(smipar.parseSmiles("c1cc2c(cc1)cccc2"))));
>> System.out.println(smigen.create(mykekule(smipar.parseSmiles("C1=CC2=C(C=C1)C=CC=C2"))));
>> System.out.println(smigen.create(mykekule(smipar.parseSmiles("C=1C=C2C(=CC=1)C=CC=C2"))));
>> System.out.println(smigen.create(mykekule(smipar.parseSmiles("C1=CC=2C(C=C1)=CC=CC=2"))));
>>
>>
>> C=1C=C2C(=CC1)C=CC=C2
>> C=1C=C2C(=CC1)C=CC=C2
>> C=1C=C2C(=CC1)C=CC=C2
>> C=1C=C2C(=CC1)C=CC=C2
>>
>>
>> Kind regards,
>> J
>>
>> On Sep 26, 2014, at 2:49 PM, Martin Guetlein
>> <martin.guetl...@googlemail.com> wrote:
>>
>> Hi,
>>
>> At some point, FixBondOrdersTool apparently makes random choices and
>> this causes my SDF export to produce different results with the same
>> input on different runs.
>> Can this be circumvented somehow?
>>
>> Thanks and kind regards,
>> Martin
>>
>>
>> --
>> Dipl-Inf. Martin Gütlein
>> Phone:
>> +49 (0)761 203 8442 (office)
>> +49 (0)177 623 9499 (mobile)
>> Email:
>> guetl...@informatik.uni-freiburg.de
>>
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>>
>>
>>
>>
>> --
>> Dipl-Inf. Martin Gütlein
>> Phone:
>> +49 (0)761 203 8442 (office)
>> +49 (0)177 623 9499 (mobile)
>> Email:
>> guetl...@informatik.uni-freiburg.de
>>
>>
>>
>>
>>
>> --
>> Dipl-Inf. Martin Gütlein
>> Phone:
>> +49 (0)761 203 8442 (office)
>> +49 (0)177 623 9499 (mobile)
>> Email:
>> guetl...@informatik.uni-freiburg.de
>>
>>
>
>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 8442 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> guetl...@informatik.uni-freiburg.de
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