Thanks,
Yannick
On Thu, Feb 8, 2018 at 2:41 PM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> Stereochemistry was not copied properly: https://github.com/
> cdk/cdk/commit/c05d6658dba750467db06a3f46414abe374e33a6#diff-
> 0b33035e99ab1a3283d5f24de671e111
>
> On 8 February 2018 at 20:00, Yannick .Djoumbou <y.djoum...@gmail.com>
> wrote:
>
>> Hi John,
>>
>> I have switched to CDK 2.1.1 and it works properly now. I am wondering
>> what caused this discrepancy in the older version.
>>
>> Thanks,
>>
>> On Thu, Feb 8, 2018 at 11:12 AM, Yannick .Djoumbou <y.djoum...@gmail.com>
>> wrote:
>>
>>> Hi John,
>>>
>>> I am using CDK 1.5.13. I just copy/pasted your code, and I get exactly
>>> the response as I did before: 2 different InChIKeys.
>>>
>>> Thanks,
>>>
>>> Yannick
>>>
>>> On Wed, Feb 7, 2018 at 4:20 PM, John Mayfield <
>>> john.wilkinson...@gmail.com> wrote:
>>>
>>>> Which version are you using, works okay for me on 2.2-SNAPSHOT and not
>>>> much should have changed their since a few years:
>>>>
>>>> public static void main(String[] args) throws CDKException {
>>>> String smi =
>>>> "C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C";
>>>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>>>> SmilesParser smipar = new SmilesParser(bldr);
>>>> IAtomContainer mol = smipar.parseSmiles(smi);
>>>>
>>>> System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey());
>>>> // not needed
>>>> // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
>>>>
>>>> System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchiKey());
>>>> }
>>>>
>>>> You don't need to assign the atom types, but I tried with/without the
>>>> answer was the same.
>>>>
>>>> BFPYWIDHMRZLRN-SLHNCBLASA-N
>>>> BFPYWIDHMRZLRN-SLHNCBLASA-N
>>>>
>>>> John
>>>>
>>>> On 7 February 2018 at 22:06, Yannick .Djoumbou <y.djoum...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I have been under deep debugging more for a few hours, only to find
>>>>> that there seem the InChIKey of molecules seem to change when I use the
>>>>> AtomContainerManipulator to convert implicit hydrogens into explicit ones.
>>>>>
>>>>> For instance
>>>>>
>>>>> I have the following 17-Ethinylestradiol molecule:
>>>>>
>>>>> C[C@]12CC[C@H]3[C@@H](CCC4=CC(O)=CC=C34)[C@@H]1CC[C@@]2(O)C#C
>>>>>
>>>>> PubChem CID: 5991
>>>>>
>>>>>
>>>>> If I use
>>>>>
>>>>>
>>>>> InChIGeneratorFactory inchiGenFactory = InChIGeneratorFactory.getInsta
>>>>> nce();
>>>>>
>>>>> System.out.println("INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: ") +
>>>>> inchiGenFactory.getInChIGenerator(molClone).getInchiKey());
>>>>>
>>>>>
>>>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms("
>>>>> 17-Ethinylestradiol");
>>>>>
>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens("
>>>>> 17-Ethinylestradiol");
>>>>>
>>>>>
>>>>> System.out.println("INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: ") +
>>>>> inchiGenFactory.getInChIGenerator(molClone).getInchiKey());
>>>>>
>>>>>
>>>>> I get the following output:
>>>>>
>>>>>
>>>>> INCHIKEY BEFORE ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-SLHNCBLASA-N
>>>>>
>>>>> INCHIKEY AFTER ADDING EXPLICIT HYDROGEN: BFPYWIDHMRZLRN-OQPPHWFISA-N
>>>>>
>>>>> This causes a problem down the path for me.
>>>>>
>>>>>
>>>>> An interesting point is that I used the structures generated (via
>>>>> isomeric SMILES) upon conversion of implicit hydrogen by CDK and
>>>>> visualized
>>>>> them using Marvin Sketch (Seee attached file), and the look identical to
>>>>> me. I also used the isomeric SMILES strings before and after conversion to
>>>>> search for same stereoisitopes in PubChem, and found the exact same
>>>>> structure. So I am confused as to why CDK would return different
>>>>> InChIKeys.
>>>>>
>>>>>
>>>>> Is there an explanation for this, or may be some other steps I should
>>>>> take to avoid this?
>>>>>
>>>>>
>>>>> Thank you for your consideration.
>>>>>
>>>>>
>>>>> Best,
>>>>>
>>>>>
>>>>> Yannick
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
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>>>>>
>>>>>
>>>>
>>>
>>
>
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