Cool - the absolute actually calls out to InChI which is a bit of pain.
Patch it future will update to be all Java though.
J
Regards,
John W May
john.wilkinson...@gmail.com
On 3 September 2015 at 11:42, Martin Gütlein <guetl...@posteo.de> wrote:
> Sorry my fault. The SmilesGenerator removed the stereochemistry. Just
> noticed that I have to use .absolute() instead of .unique()
>
>
> Am 03.09.2015 um 12:36 schrieb Martin Gütlein:
>
> Hi John,
>
> Awesome, thanks. SuppressHydrogens works good, but it suppresses Hs with
> stereochem-information as well. Can this be avoided?
>
> > although possible you should perhaps store and index (unique check) you
> structures separately.
>
> Thats what we try to not do, if possible.
>
> Martin
>
>
> Am 03.09.2015 um 11:32 schrieb John M:
>
> Hi Martin,
>
> By design CDK separates out standardisation (H rep, tautomers,
> protonation) from canonicalisation (ordering). You've found the method to
> "sprout" hydrogens but you actually want the opposite -
> suppressHydrogens(mol)
> <http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.html#suppressHydrogens%28org.openscience.cdk.interfaces.IAtomContainer%29>
> .
>
> I think you might be conflating two things, although possible you should
> perhaps store and index (unique check) you structures separately. For your
> example you could assign a unique tautomer but you'll be back at square one
> with your first example.
>
> O=C[CH]1Cc2[nH]cnc2CC1 -> 1,3 proton shift -> C(=O)[CH]1Cc2c(CC1)[nH]cn2
> CC(=O)N -> 1,3 proton shift -> CC(O)=N
>
> Thanks,
>
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 3 September 2015 at 09:27, Martin Gütlein <guetl...@uni-mainz.de>
> wrote:
>
>> One more thing:
>> I noticed that unique SMILES differentiate explicit and implicit
>> Hydrogens, e.g. "[H]Cl" is different form "Cl". This can be solved by
>> running AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol).
>> However, I do not like having my all Hs defined explicitly. Is there an
>> option in the CDK to convert explict Hs back to implicit, leaving only
>> thoses Hs as explict that are relevant?
>>
>> Martin
>>
>>
>> Am 03.09.2015 um 09:48 schrieb Martin Gütlein:
>>
>> Hi John,
>>
>> thanks for your reply, I tried to use unique (kekulized) SMILES instead
>> of InChIs.
>> Whats good is that the structure for (most) compounds is stored correctly
>> (i.e., I can create an IAtomContainer that is apparently equal).
>>
>> However, I found an example were the unique SMILES of two identical
>> structures is different (see below).
>>
>> Kind regards,
>> Martin
>>
>>
>> for (String smi : new String[] { "O=C[CH]1Cc2[nH]cnc2CC1",
>> "C(=O)[CH]1Cc2c(CC1)[nH]cn2" })
>> {
>> IAtomContainer mol = new
>> SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smi);
>> System.out.println(SmilesGenerator.unique().create(mol));
>> }
>>
>>
>>
>>
>>
>>
>> Am 02.09.2015 um 20:58 schrieb John M:
>>
>> Just to add on - if you really want to use InChI (don't) then you could
>> store the AuxInfo but the CDK doesn't have a conversion method that accepts
>> it when turning it back into an AtomContainer.
>>
>> I also notice you're using unique SMILES (default by old APIs), you
>> probably want isomeric that a non-canonical but store stereochemistry.
>>
>> IAtomContainer mol = SmilesGenerator.isomeric().create(container);
>>
>> John
>>
>> Regards,
>> John W May
>> john.wilkinson...@gmail.com
>>
>> On 2 September 2015 at 19:54, John M < <john.wilkinson...@gmail.com>
>> john.wilkinson...@gmail.com> wrote:
>>
>>> Hi Martin,
>>>
>>> The InChI is an identifier and not a structure representation it should
>>> never be used as such. For maximum preservation you should store compounds
>>> as Kekulé SMILES or Molfile. You can store additional data such as
>>> coordinates supplementary to the SMILES.
>>>
>>> You might find a recent presentation by Noel (O Babel) and Rajarshi
>>> (CDK) useful:
>>>
>>> <http://baoilleach.blogspot.co.uk/2015/08/the-whole-of-cheminformatics-best.html>
>>> http://baoilleach.blogspot.co.uk/2015/08/the-whole-of-cheminformatics-best.html
>>>
>>> John
>>>
>>>
>>
>>
>> --
>> Dr. Martin Gütlein
>> Phone:+49 (0)6131 39 23336 (office)+49 (0)177 623 9499 (mobile)
>> Email:guetl...@uni-mainz.de
>>
>>
>
> --
> Dr. Martin Gütlein
> Phone:+49 (0)6131 39 23336 (office)+49 (0)177 623 9499 (mobile)
> Email:guetl...@uni-mainz.de
>
>
>
> --
> Dr. Martin Gütlein
> Phone:+49 (0)6131 39 23336 (office)+49 (0)177 623 9499 (mobile)
> Email:guetl...@uni-mainz.de
>
>
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