Hmm but then to me missing of the hydrogen to mean means this which I guess
is actually what was intended:
[image: Inline images 1]
I guess the issue is partly we don't attempt depict queries.
Best we can do is:
http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=[H][N]C1=CC=CC=C1&zoom=1.5
(or show the attachment point if you add a pseudo atom)
Regards,
John W May
john.wilkinson...@gmail.com
On 27 January 2016 at 09:19, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> So not clear what you mean by that.
> Let's say I have this as a query structure: [H]NC1=CC=CC=C1
> I've explicitly added one hydrogen to the amine to ensure I don't get
> tertiary amines when doing a SSS.
> When displayed I see the explicit and the implicit hydrogens (but
> represented differently), which is misleading:
>
> http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=%5BH%5DNC1%3DCC%3DCC%3DC1&zoom=5&annotate=none
>
> What I would want to be able to do is display just the explicit H.
>
> Tim
>
>
>
> On 26/01/2016 16:22, John M wrote:
>
> The hydrogens are implicitly there, just not displayed, so no valences are
>> being changed.
>
>
> Had an interesting debate about this in the office over coffee with no
> resolution. Really if you don't show them they are depicting different
> structures IMO... '[N]1C=CC=C1' vs 'N1C=CC=C1' but that's up for debate.
>
> So it looks like its not possible to display a terminal atom (C, N ...)
>> without the hydrogens being displayed?
>
>
> Nope sorry, but you can remove them if you really want
> (setImplicitHydrogen)
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 26 January 2016 at 15:06, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
>>
>>
>> On 26/01/2016 14:57, John M wrote:
>>
>> You can't exactly replicate that because I really think the 'none'
>> hydrogen display is completely wrong as it changes the valence of atoms.
>>
>> Not sure what you mean here. This is only for display. The hydrogens are
>> implicitly there, just not displayed, so no valences are being changed.
>> I suppose the common case for this is when displaying a query structure
>> (e.g. for SSS) when the only hydrogens you want to see are the ones
>> explicitly defined as part of the query.
>>
>>
>> However you can choose which atoms have their symbol displayed and by
>> definition hydrogens which allows you to have the 'all', 'heteroterm', and
>> 'hetero'.
>>
>> It's best explained here:
>> <https://github.com/cdk/cdk/wiki/Standard-Generator#symbol-visibility>
>> https://github.com/cdk/cdk/wiki/Standard-Generator#symbol-visibility
>>
>> Note the depiction generator has a short cut for the common case:
>> *withTerminalCarbons
>> <http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/depict/DepictionGenerator.html#withTerminalCarbons%28%29>*
>> ()
>>
>>
>> So it looks like its not possible to display a terminal atom (C, N ...)
>> without the hydrogens being displayed?
>>
>> Tim
>>
>>
>> John
>>
>>
>>
>
>
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