I think you probably want this:
new DepictionGenerator().withParam(StandardGenerator.Visibility.class,
new SymbolVisibility() {
@Override
public boolean visible(IAtom
atom, List
On 02/08/2019 15:42, John Mayfield wrote:
1. explicit hydrogens are also not rendered
Er... I showed the example with the explicit hydrogens being rendered.
Let's clarify, what does "explicit hydrogen" mean to you?
Sorry, my mistake. The explicit H is displayed. I was getting mixed up
>
> 1. explicit hydrogens are also not rendered
Er... I showed the example with the explicit hydrogens being rendered.
Let's clarify, what does "explicit hydrogen" mean to you?
> 2. Carbon symbols are displayed (as if the withCarbonSymbols() method had
> been called).
The "Visibility" option
On Fri, Aug 2, 2019 at 11:28 AM John Mayfield
wrote:
> Other option You can also use the old *BasicAtomGenerator* which never
> puts hydrogens on anything...
>
Documentation on the old generator stack can be found in this copy of the
Groovy CDK book, "Depiction" chapter:
Hi John,
Iterating the atoms and setting the implicit H count to zero does hide
the implicit hydrogens but results in two nasty side effects:
1. explicit hydrogens are also not rendered
2. Carbon symbols are displayed (as if the withCarbonSymbols() method
had been called).
Tim
On
It's not an option - and I would hesitant to add it as it's "at best
ambiguous" (quoting Brecher's IUPAC :-)). Symyx/Accelrys/BioVia Draw like
to hide the hydrogens by default which is where I think the acceptability
crept in from. You right that for queries there's a use-case, but the
depiction
Can someone point to examples of how to control the display of hydrogens
when depicting using DepictionGenerator?
It looks like implicit hydrogens are displayed on terminal and hetero
atoms which is not unreasonable, but what if I ONLY want explicit
hydrogens to be displayed (e.g. when
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