Thanks for your message. The workaround works nice.
Oscar
2015-01-16 14:52 GMT+01:00 John M <john.wilkinson...@gmail.com>:
> Unfortunately it's a combination of the molfile having implicit
> stereochemistry (i.e. tools have to guess from the depiction) and the CDK
> layout. I can fix both but as a simple work around go through the bonds and
> those that are double, not in a ring, or have stereo (check
> IStereoElements) should have the stereoType set to E_OR_Z... can't remember
> the exact flag.
>
> Will fix though for next release.
>
> J
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 16 January 2015 at 10:05, Oscar Mora <oscarmorape...@gmail.com> wrote:
>
>> Hi,
>>
>> I have the following question about processing SMILES format structures +
>> 2D Generation + serialization in Mol format. I am using CDK 1.5.8.
>>
>> My goal is to process an structure in SMILES format, generate 2D
>> coordinates and save it as in Mol format. The problem where I am stuck is
>> that the input SMILES has the no stereochemistry defined, but the final mol
>> output _has_ the stereochemestry defined.
>>
>> Following I have prepared a simple example to describe my problem:
>>
>> The input structure is the following one:
>>
>> ON=CC1=CC=C(O)C=C1
>>
>> The structure is read and parsed using the following code (snippet):
>>
>> [...]
>> IAtomContainer iAtomContainer = null;
>> final SmilesParser smilesParser = new
>> SmilesParser(DefaultChemObjectBuilder.getInstance());
>> iAtomContainer = smilesParser.parseSmiles(molecule);
>>
>> [...]
>>
>> then the 2D coordinates are generated.
>>
>> [...]
>> sdg.setMolecule(iAtomContainer, true);
>> sdg.generateCoordinates();
>> iAtomContainerWCoordinates = sdg.getMolecule();
>> [...]
>>
>> and finally the 'IAtomContainer' object is serialized as 'mol' file,
>> producing the following output:
>>
>> CDK 0116150922
>>
>> 10 10 0 0 0 0 0 0 0 0999 V2000
>> 3.9132 3.7394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> 2.6112 2.9947 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>> 2.6051 1.4947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.3030 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1.3030 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0280 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.3220 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -2.6148 -1.5107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.3220 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0280 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 2 1 0 0 0 0
>> 2 3 2 0 0 0 0
>> 3 4 1 0 0 0 0
>> 4 5 2 0 0 0 0
>> 5 6 1 0 0 0 0
>> 6 7 2 0 0 0 0
>> 7 8 1 0 0 0 0
>> 7 9 1 0 0 0 0
>> 9 10 2 0 0 0 0
>> 4 10 1 0 0 0 0
>> M END
>>
>> If you render the structure before (SMILES) and after (MOL) the process,
>> it is possible to watch how initially the double bond between N and C has
>> not the stereo defined, but at the end of the process is arbitrarily
>> defined (E). I have also attached two snapshots two further describe this
>> (SMILES_before.png) and (MOL_after.png).
>>
>> Why is this happening ? Is there any way to control, and keep the flag of
>> stereochemistry not defined during the transformation from SMILES to MOL?
>> (I would like that the two depictions produce the same image)
>>
>> Thanks in advance
>>
>> Oscar
>>
>>
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>
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