Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens

2018-02-08 Thread Yannick .Djoumbou 
Thanks,

Yannick

On Thu, Feb 8, 2018 at 2:41 PM, John Mayfield 
wrote:

> Stereochemistry was not copied properly: https://github.com/
> cdk/cdk/commit/c05d6658dba750467db06a3f46414abe374e33a6#diff-
> 0b33035e99ab1a3283d5f24de671e111
>
> On 8 February 2018 at 20:00, Yannick .Djoumbou 
> 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 
>> 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 
 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
>
>
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>

>>>
>>
>
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Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens

2018-02-08 Thread Yannick .Djoumbou 
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 
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  > 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 
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>>
>>
>
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Re: [Cdk-user] InChiKey changing Upon simple conversion of implicit hydrogens

2018-02-07 Thread John Mayfield 
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  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.
> getInstance();
>
> 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
>
>
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
--
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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