On 8 September 2011 10:33, Martin Guetlein
<[email protected]>wrote:
>
>
> On Thu, Sep 8, 2011 at 9:26 AM, Egon Willighagen <
> [email protected]> wrote:
>
>> Hi Martin,
>>
>> I have not had time to answer earlier; it was on my list, but since
>> you seem stuck with it...
>>
>> On Fri, Sep 2, 2011 at 12:12 PM, Martin Guetlein
>> <[email protected]> wrote:
>> > IMHO, the problem is that the smiles writer (is there a smarts writer?)
>>
>> No. What is the data model you like to save as SMARTS?
>>
>
> You mean the java interface within CDK? At the moment I have an IMolecule.
>
>
>>
>> > has its own armaticity detection.
>>
>> Not really.
>>
>> It might be solved by using SmilesGenerator.setUseAromaticityFlag(true)...
>>
>> Can you give that a try?
>>
>
> setUseAromaticityFlag(true) is already part of the code, but has no effect
> on this example.
>
Indeed.
My guess is some other essential configuration is removed by
mcsmolecule.removeAtomAndConnectedElectronContainers(atom);
Nina
>
> Martin
>
>
>>
>> Egon
>>
>>
>> --
>> Dr E.L. Willighagen
>> Postdoctoral Researcher
>> Institutet för miljömedicin
>> Karolinska Institutet (http://ki.se/imm)
>> Homepage: http://egonw.github.com/
>> LinkedIn: http://se.linkedin.com/in/egonw
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: http://www.citeulike.org/user/egonw/tag/papers
>>
>
>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 7633 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> [email protected]
>
>
> ------------------------------------------------------------------------------
> Doing More with Less: The Next Generation Virtual Desktop
> What are the key obstacles that have prevented many mid-market businesses
> from deploying virtual desktops? How do next-generation virtual desktops
> provide companies an easier-to-deploy, easier-to-manage and more affordable
> virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops? How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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