Hi Daniel, all! The ModelBuilder3D seems to produce bad results since quite a while: http://blueobelisk.shapado.com/questions/3d-coordinates-best-options-cdk-rdkit-openbabel-anything-else I am/was using it as well without noticing.
@cdk-developers: What about annotating the ModelBuilder3D class as @Deprecated until this issue is fixed? Best regards, Martin On Mon, Mar 26, 2012 at 3:40 PM, Szisz Daniel <[email protected]> wrote: > Hi All! > > I'm writing this letter to discuss and get some advice on the > 3D structure generator in CDK. > As you might know there is the builder3d package, which has > the main functionalities for 3D structure generation. > During the last 1-2 months I decided to test this feature : > this is why I started a mini "project" on GitHub which has some > test classes NOW and a simple runnable class that performs the > 3d structure generation. > > I made some simple tests and I had serious failures. The reason > why I write is to get some hints where the problem can be: > building the structure on a series of smiles I got this result: > > WARNING: Maybe RingTemplateError! > KEYError: Unknown distance key in pSet: O=;Csp2 take default bond length: 1.5 > KEYError: Unknown distance key in pSet: Csp;Nsp2 take default bond length: 1.5 > WARNING: Maybe RingTemplateError! > > Coordinate generation finished > > KEYError: Unknown distance key in pSet: O;N take default bond length: 1.5 > KEYError: Unknown distance key in pSet: N;C= take default bond length: 1.5 > KEYError: Unknown distance key in pSet: C=;N take default bond length: 1.5 > > Coordinate generation finished > ... > > So the main problem is that is doesn't find a right MMFF94 parameters for > bonds. I'm suspecting a bug here and there and I would like to call for some > activity to check this. > > You can reach the Struc3DGenerator.java file at > > https://github.com/danielszisz/CDK_Builder3DTests > > and the other test files also. > > Thanks, Daniel > > > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user -- Dipl-Inf. Martin Gütlein Phone: +49 (0)761 203 7633 (office) +49 (0)177 623 9499 (mobile) Email: [email protected] ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
