>
> 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
>
> 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
>
>
>
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
