It's somewhat of a moving target. The JavaDoc is the best place to look:
http://cdk.github.io/cdk/1.5/docs/api/index.html. Many of newer methods
have small examples of how to use them (e.g. VentoFoggia
<http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/isomorphism/VentoFoggia.html>
).
We're always happy with doc contributions.
John
Regards,
John W May
john.wilkinson...@gmail.com
On 6 June 2016 at 07:05, Nikita Kozhukhov <nikita_kozhuk...@epam.com> wrote:
> Hi John,
>
>
> Thank you for the quick response, it has solved my problem.
>
>
> CDK is a really great tool, but I was having hard time trying to find
> working examples and relevant documentation.
>
> It would be great if someone could update github readme
> <https://github.com/cdk/cdk> as it contains outdated examples and
> tutorials.
>
>
> Yours sincerely,
>
> Nikita
> ------------------------------
> *От:* John M <john.wilkinson...@gmail.com>
> *Отправлено:* 3 июня 2016 г. 20:29
> *Кому:* Nikita Kozhukhov
> *Тема:* Re: [Cdk-user] DepictionGenerator - changing Visibility properties
>
> Hi Nikita,
>
> This is a common requirement and has a specialised method.
>
> DepictionGenerator dg = new DepictionGenerator();
>> dg = dg.withTerminalCarbons();
>
>
> As a side note you can still set params explicitly as you would with old
> RenderModel:
>
>
>> DepictionGenerator dg = new DepictionGenerator();
>> dg = dg.withParam(Visibility..., etc..);
>
>
> Hope that helps,
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 3 June 2016 at 17:43, Nikita Kozhukhov <nikita_kozhuk...@epam.com>
> wrote:
>
>> Hi,
>>
>>
>> Could someone provide an example of changing default properties of
>> DepictionGenerator, please? Is it really possible in 1.5.13 version of cdk?
>>
>>
>> Here is a a description of the problem I'm trying to solve.
>>
>> I created an atom container from SMILES string "[H][C@]1(C[C@]2([H])CC[C@
>> ]([H])(C1)N2C)OC(c1ccccc1)c1ccccc1".
>>
>>
>> Then I created an instance of DepictionGenerator:
>> DepictionGenerator generator = new DepictionGenerator(font);
>>
>> And finally created "depiction":
>> Depiction depiction = generator.depict(atomContainer);
>>
>> With this approach after serialization to .png or .svg, I see molecule
>> without CH3 group, which is, I guess, due to default setting
>> of SymbolVisibility.iupacRecommendationsWithoutTerminalCarbon().
>> I'd like to use SymbolVisibility.iupacRecommendations(), but it is not
>> currently possible with DepictionGenerator because of the reasons described
>> in this thread:
>> https://sourceforge.net/p/cdk/mailman/message/34796852/
>>
>> I found a workaround by using AtomContainerRenderer, but in this case I
>> don't know how to autoscale the resulting image.
>>
>> Yours sincerely,
>> Nikita
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>
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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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