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 isn't really set up for rendering queries.
Anyways if you want to do it just add a helper routine to sets the implicit hydrogen counts to 0, for non aromatics you can put them C1C[N]CN([H])C1 [image: image.png] The radicals there are specific to the WebApp so you would just get a plain N - I may actually make than option as I don't like it (Noel Talked me into it). Other option You can also use the old *BasicAtomGenerator* which never puts hydrogens on anything... John On Thu, 1 Aug 2019 at 18:12, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > 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 depicting a query structure) or I > don't want any hydrogens to be displayed? > > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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