On 8 August 2012 11:00, <ralf@ark.in-berlin.de> wrote:
On Wed, Aug 08, 2012 at 09:58:55AM +0200, Egon Willighagen wrote:
> But, JCP should be flexible about it...

So, it should not separate the molecule?

> These are just initial comments... let's continue to explore what is
> going on... I think JCP should not throw stacktraces with that
> molecule, and I like to learn about the cause...

It's not so difficult: your code in StuctureDiagramGenerator.java:258
explicitly removes all Hs before starting a layout. So, a cleanup
unexpectedly leaves a separated molecule.

Do we have means in the data model to distinguish H bridges and usual covalent bonds?  I am guessing this is also related to my recent report on InChIs and fingerprints performance. 


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