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
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