Patch is now done https://github.com/cdk/cdk/pull/115.
Regards,
John W May
john.wilkinson...@gmail.com
On 17 January 2015 at 10:14, Oscar Mora <oscarmorape...@gmail.com> wrote:
> 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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