Christoph Steinbeck schrieb:
In addition to Egon's answer:
Vincent Le Guilloux wrote:
First of all, the 2D depiction seems to be slightly broken: sometimes
two atoms overlap, making one of them disapearing (it can be seen when
resizing the Jtable column for example). Anyone knows about that? Is
the code bellow up to date? Should I use any other class etc. ?
The StructureDiagramGenerator can use the OverlapResolver to fix this.
Atoms should not overlap then.
Next, how does the generation of 2D coordinates works when 2D
coordinates are already set? (ie. Z = 0) There is nothing in the
documentation about that.
In principle, the existing 2D coordinates will not have any effect.
Following the CDK's working principle as a Lego-Toolkit, you can make
some use of the existing coordinates by storing them and then applying a
2D alignment between the old and the new ones using the
Kabsch-Alignment engine.
Cheers,
Chris
I might be mistaken but as far as I can see in the code the
StructureDiagramGenerator uses the OverlapResolver by default. So
Vincent's problem occures although the OverlapResolver is already
applied, right?
If I am mistaken it would be great if someone could tell how to apply
the OverlapResolver correctly as I sometimes have the same problem using
the SDG.
Thanks and best regards
Markus
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