Yep IAtomContainer, be sure to use the Silent variant/builder (i.e.
SilentChemObjectBuilder).
Looking in the code actually look looks like the random access reader could
do with an update, it read molecules as an IChemFile then unpacks the
molecule, a little odd... but I see a comment mentions this was because the
Molfile reader did set properties if only a IAtomContainer was read. Since
this is no longer the case I'll make a patch. Won't affect behaviour just a
curiosity I'd missed. Also technically an SDF can have a mix of V2000 and
V3000 which should be handled.
John
Regards,
John W May
john.wilkinson...@gmail.com
On 15 January 2016 at 16:15, "Felix Bänsch" <jonny.baen...@web.de> wrote:
> I'm using Java so I*ll try to built the code.
>
> I mean, what is the best way to read out an SDFile to e.g AtomContainers.
> Thank you so much for you help.
>
> Regards,
> Felix Bänsch
>
> *Gesendet:* Freitag, 15. Januar 2016 um 14:24 Uhr
> *Von:* "John M" <john.wilkinson...@gmail.com>
> *An:* "Felix Bänsch" <jonny.baen...@web.de>, cdkuser <
> cdk-user@lists.sourceforge.net>
> *Betreff:* Re: Re: [Cdk-user] SDFile Renderer
> Yes sorry it wasn't bundled in that release, if you're using maven you can
> include it explicitly or alternatively built the code from
> github.com/cdk/cdk.
>
>
>> And another question, which is the best reader for SDFiles?
>
>
> What do you mean?
>
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 15 January 2016 at 13:09, "Felix Bänsch" <jonny.baen...@web.de> wrote:
>>
>> Hi John,
>>
>> thanks a lot for your answer.
>> But I have another question, I git CDK 1.5.12 but there is no
>> DepictionGenerator.
>> And another question, which is the best reader for SDFiles?
>>
>> Regards,
>> Felix Bänsch
>>
>> *Gesendet:* Dienstag, 12. Januar 2016 um 11:11 Uhr
>> *Von:* "John M" <john.wilkinson...@gmail.com>
>> *An:* "Felix Bänsch" <jonny.baen...@web.de>
>> *Cc:* cdkuser <cdk-user@lists.sourceforge.net>
>> *Betreff:* Re: [Cdk-user] SDFile Renderer
>> Hi Felix,
>>
>> I've recently added a utility to make this v. easy, DepictionGenerator
>> <http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/depict/DepictionGenerator.html>.
>> Personally don't know too much about JavaFX but in Swing at least there are
>> two (good) ways. Firstly you could create a BufferedImage and put this in
>> an ImageIcon. IMO a much better is to override the ImageIcon with a custom
>> implementation, AtomContainerIcon
>> <https://github.com/johnmay/mdk/blob/a2942e2efc42639f3c4277107c01b13d90a8869b/ui/src/main/java/uk/ac/ebi/mdk/ui/render/molecule/AtomContainerIcon.java>.
>> In the later we draw direct to the screen and can resize depictions on
>> demand.
>>
>> - John
>>
>> Regards,
>> John W May
>> john.wilkinson...@gmail.com
>>
>> On 11 January 2016 at 20:02, "Felix Bänsch" <jonny.baen...@web.de>
>> wrote:
>>>
>>> Hi everyone,
>>>
>>> I'm a new to programming and I'm a total newbie at CDK.
>>> I want to write a small JavaFX program, that can read SDFiles and render
>>> the structures. I use the RandomAccessSDFReader to read the SDFile but now
>>> I have no idea how I can render the structures.
>>> Thanks a lot.
>>>
>>> Regards,
>>> Felix Bänsch
>>>
>>>
>>>
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