You should just be able to replace BasicAtomGenerator and
BasicBondGenerator with StandardGenerator in your existing code and keep
your highlighting.
It's minimal effort to add a new highlight style, but even with the high
level API you can get pretty close. Code:
https://gist.github.com/johnmay/9d144ccf047457012222614a15909abb
[image: Inline images 1]
Also not sure I like your crop option - it's misleading maybe do something
like this:
[image: Inline images 2]
John
On 3 January 2017 at 12:27, Martin Gütlein <guetl...@posteo.de> wrote:
> Hi John,
>
> The depiction I am using includes some custom highlighting of matched atom
> neighborhoods and cropping around the matches. E.g. here:
> http://coffer.informatik.uni-mainz.de/depictMatch?smiles=
> C1%5BC%40H%5D%28%5BC%40%40H%5D%28OC2%3DCC%28%3DCC%28%
> 3DC21%29O%29O%29C3%3DCC%28%3DC%28C%3DC3%29O%29O%29O&size=
> 150&atoms=3,4,5,9&highlightOutgoingBonds=true&crop=true&activating=true
>
> This is why I did not use the new DepictionGenerator yet, because I
> thought it might require some effort to change the code. But I will keep
> this in mind.
>
> Martin
>
>
> Am 03.01.2017 um 13:13 schrieb John M:
>
> For comparison:
> [image: Inline images 1]
>
> On 3 January 2017 at 12:13, John M <john.wilkinson...@gmail.com> wrote:
>
>> Looks cool. Any chance of updating the depictions?
>>
>> [image: Inline images 3]
>> That's the old code and the renderer that didn't but hydrogens on the
>> atoms by default.
>>
>> John
>>
>> On 3 January 2017 at 12:08, Martin Gütlein < <guetl...@posteo.de>
>> guetl...@posteo.de> wrote:
>>
>>> Hi,
>>>
>>> Based on the awesome CDK, we built a free QSAR web-service to predict
>>> chemical compounds:
>>> http://coffer.informatik.uni-mainz.de
>>>
>>> Please give it a try if you like.
>>>
>>> Kind regards (and sorry for the shameless ad),
>>> Martin Gütlein
>>>
>>> P.S.: The corresponding paper can be found here:
>>> http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0173-z
>>>
>>> --
>>>
>>> Dr. Martin Gütlein
>>> Phone:
>>> +49 (0)6131 39 23336 <%2B49%20%280%296131%2039%2023336> (office)
>>> +49 (0)177 623 9499 <%2B49%20%280%29177%20623%209499> (mobile)
>>> Email:
>>> guetl...@uni-mainz.de
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
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>>
>>
>
>
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