Hi Manuel, the mol file you included already contains coordinates. Thus the very nice, semi-3D view that you get in ChemDraw. You just need to use one of the SDFReaders in the CDK and then for example use the DepictionGenerator to make an image. That should then look like what you get in ChemDraw.
Hope that helps. Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 15. Oct 2021, at 10:54, Stesycki, Manuel <stesy...@mpi-muelheim.mpg.de> > wrote: > > Dear CDK-users, > > a user submitted a structure to our LC analytic department (see attached > mol-file). > With the help of the CDK (Version 2.3) we create an image of this structure > (CDK_V23.png). > But if you open the mol-file in ChemDraw (Version 20.1) it is displayed > completely different (ChemDraw_V20.png). > Is there a way to „draw“ the structure in CDK to match the ChemDraw version > (maybe some parameter tweaks?). > > Thank’s a lot. > > > Best regards, > Manuel Stesycki > > IT > 0208 / 306-2146 > Physikbau, Büro 106a > stesy...@mpi-muelheim.mpg.de > > Max-Planck-Institut für Kohlenforschung > Kaiser-Wilhelm-Platz 1 > D-45470 Mülheim an der Ruhr > http://www.kofo.mpg.de/de > > <CDK_V23.png> > <ChemDraw_V20.png> > <C120H80I2N8O8Rh2.mol>_______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
