When a depiction is created that exceeds the size of the draw area instead of the depiction being scaled to fit within the drawing area the depiction is instead cropped resulting in, for large molecules, significant sections of structure not being visible.
fitToScreen is set to true.
Manually adjusting the scaling using:
renderer.getRenderer2DModel().setScale(double) where renderer is an AtomContainerRenderer has no visible effect.
(the same call with setZoomFactor instead of setScale does work)
Can you specify which software you used for that? I. e. which download or repository checkout?
Daniel, I can confirm problems in the CDK-JChemPaint series. I will try to get this fixed in the next release. Please do let us know which version you downloaded, so that we can confirm it is this version that is affected.
The version of CDK used was 1.3.4 from the jar available from:
https://sourceforge.net/projects/cdk/files/cdk%20%28development%29/1.3.4/
JChempaint8 was used initially and then JChempaint9 with the same result in either case.
Daniel, I'm sure with John's new Depiction tool, this is no longer a case. If not, you know where to find him :)