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
with too many examples!
2. Carbon symbols are displayed (as if the withCarbonSymbols()
method had been called).
The "Visibility" option controls this, but the other answer is just
don't set to zero on carbons?
Is there an example of how to use this "Visibility" option? Doesn't seem
to be an option of DepictionGenerator.
Not setting to zero on carbons is not so straight forward as you would
still want this on terminal carbons.
I suppose these would be carbons with only one bond to a non-hydrogen
atom. Does this look right?
for (IAtom atom : mol.atoms()) {
if (atom.getAtomicNumber() ==6) {
// count the number of connections that are heavy atoms int numHeavy =0;
for (IBond bond : atom.bonds()) {
IAtom other = bond.getOther(atom);
if (other.getAtomicNumber() >1) {
numHeavy++;
}
}
// if only one then this is a terminal carbon so we need to leave the Hs
in place if (numHeavy <2) {
atom.setImplicitHydrogenCount(0);
}
}else {// non-carbon atoms atom.setImplicitHydrogenCount(0);
}
}
Tim
On Fri, 2 Aug 2019 at 12:09, Egon Willighagen
<egon.willigha...@gmail.com <mailto:egon.willigha...@gmail.com>> wrote:
On Fri, Aug 2, 2019 at 11:28 AM John Mayfield
<john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>>
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:
https://figshare.com/articles/Edition_1_4_1_0_of_Groovy_Cheminformatics_with_the_Chemistry_Development_Kit/2057790
Egon
--
Hi, do you like citation networks? Already 51% of all citations
are available <https://i4oc.org/> available for innovative new
uses <https://twitter.com/hashtag/acs2ioc>. Join me in asking the
American Chemical Society to join the Initiative for Open
Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.
-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
