tag:blogger.com,1999:blog-17889588.post113475390563344646..comments2024-03-13T07:14:55.283+01:00Comments on chem-bla-ics: CDK Debug classes and fixing the ModelBuilder3D bugEgon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger1125tag:blogger.com,1999:blog-17889588.post-1166615696202396672006-12-20T12:54:00.000+01:002006-12-20T12:54:00.000+01:00I need a help solving problem with ModelBuilder. P...I need a help solving problem with ModelBuilder. Posibly you can help me.<BR/><BR/>When trying to build 3d molecule from smiles CDK fails to work on the molecules having As ( e.g. C[As](=O)(C)O ). Both force fields fail.<BR/>I guess many people would like to have this working.<BR/>Do you have any idea how to fix it?<BR/><BR/>Sincerely,<BR/><BR/>Pawel<BR/><BR/>Code as below<BR/>"<BR/>ModelBuilder3D mb3d = null;<BR/><BR/> try {<BR/> SmilesParser sp = new SmilesParser();<BR/> IMolecule molecule = sp.parseSmiles("C[As](=O)(C)O");<BR/> HydrogenAdder hAdder=new HydrogenAdder();<BR/> hAdder.addExplicitHydrogensToSatisfyValency(molecule);<BR/><BR/> // get 3D cooords<BR/> mb3d = new ModelBuilder3D();<BR/> mb3d.setTemplateHandler();<BR/> mb3d.setForceField("mm2");<BR/> mb3d.setMolecule(molecule, true);<BR/> mb3d.generate3DCoordinates();<BR/> } catch (Exception e) {<BR/> throw new CDKException(e.toString());<BR/> }<BR/><BR/> IMolecule newMolecule = mb3d.getMolecule();<BR/>"<BR/><BR/>Result in error message<BR/><BR/>"<BR/>Exception in thread "main" org.openscience.cdk.exception.CDKException:<BR/>java.lang.Exception: Could not final configure atom due to problems<BR/>with force field<BR/> at app.chem.test.main(test.java:37)<BR/>"onTheEdgehttps://www.blogger.com/profile/16420943370659699572noreply@blogger.com