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 <mailto:john.wilkinson...@gmail.com>
On 26 January 2016 at 15:06, Tim Dudgeon <tdudgeon...@gmail.com
<mailto: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
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