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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