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 -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
