Re: [Cdk-devel] [Cdk-user] Inchi to structure

[Christophe M. <chr...@ma...>]

Ok thank you very much.
I have to check with my wife. She is the brain, I'm the hands ;-)
Thanks again.

Christophe Marcourt



On Mon, Nov 11, 2013 at 4:42 PM, John May <jo...@eb...> wrote:

> Yes you need to process the structures separately. It’s not that there is
> a good but more likely there is non-covalent bonding - you can see how
> toolkits interpret - [Na+].[Cl-]<http://apps.ideaconsult.net:8080/ambit2/depict?search=%5BNa+%5D.%5BCl-%5D>
> .
>
> There might be some code in a down stream product which lays out multiple
> molecules and have CC’ed in cdk-devel list.
>
> J
>
>
> On 11 Nov 2013, at 15:26, Christophe Marcourt <chr...@ma...>
> wrote:
>
> Ok, now it seems everything is working except that sometimes I have a
> CDKException due to disconnected molecule. So I'm
> using ConnectivityChecker.partitionIntoMolecules() method but I have a set
> of IAtomContainer.
> Do I have to process all of the IAtomContainer or is there only one which
> represents the good structure ? And how to get the good one ? ;-)
> Thank you.
>
>
> Christophe Marcourt
>
>
> On Mon, Nov 11, 2013 at 3:49 PM, Christophe Marcourt <
> chr...@ma...> wrote:
>
>> Ok, I already know this, so nothing more.
>> Fair enough.
>> Thank you for your time.
>>
>>
>> Christophe Marcourt
>>
>>
>> On Mon, Nov 11, 2013 at 3:48 PM, John May <jo...@eb...> wrote:
>>
>>> The JavaDoc has some… here’s how to create an IAtomContainer from an
>>> InChI string.
>>>
>>>
>>> http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/inchi/InChIToStructure.html
>>>
>>> and here shows generating coordinates
>>>
>>>
>>> http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/layout/StructureDiagramGenerator.html
>>>
>>> Cheers,
>>> J
>>>
>>> On 11 Nov 2013, at 14:29, Christophe Marcourt <chr...@ma...>
>>> wrote:
>>>
>>> Thank you very much.
>>> Is there a documentation which describes how to get a structure from an
>>> inchi using cdk java API ?
>>>
>>>
>>> Christophe Marcourt
>>>
>>>
>>> On Mon, Nov 11, 2013 at 3:25 PM, John May <jo...@eb...> wrote:
>>>
>>>> Hi Christophe,
>>>>
>>>> The InChI stores coordinates in the AuxInfo and without that the IUPAC
>>>> binary (called by the CDK) won’t set structure coordinates. To obtain a
>>>> depiction you need to generate coordinates from scratch. The 2D coordinates
>>>> are generated using the StructureDiagramGenerator<http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/layout/StructureDiagramGenerator.html> whilst
>>>> 3D coordinates are generated with ModelBuilder3D<http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/modeling/builder3d/ModelBuilder3D.html>.
>>>> It should be noted that neither method currently respects stereochemistry
>>>> although that information is present.
>>>>
>>>> Thanks,
>>>> John
>>>>
>>>> On 11 Nov 2013, at 12:59, Christophe Marcourt <chr...@ma...>
>>>> wrote:
>>>>
>>>> Hello all,
>>>>
>>>> I'm using cdk-inchi packages to turn an Inchi code to a strcuture.
>>>> I used the written code from the InChIToStructure javadoc.
>>>> It works fine but as the javadoc said "The generated IAtomContainer
>>>> will have all 2D and 3D coordinates set to 0.0" !
>>>> When I used chemspider web services, it returns with a good structure.
>>>> So how can one use InChIToStructure to have the real structure ? And
>>>> not only with 0 in it...
>>>> Thanks.
>>>>
>>>> Christophe Marcourt
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>>>
>>>
>>
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