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
