hi list, (again) some problems/ questions regarding pdb file reading and writing:
in short: i am generating pdb files with cdk with the following code: FileWriter output = new FileWriter(...) PDBWriter pdbWriter = new PDBWriter(output); Molecule molecule = new Molecule(...); pdbWriter.write(molecule); pdbWriter.close(); the result is something like: HETATM 41 C MOL 8,460 5,977 21,933 HETATM 42 C MOL 7,310 -2,963 19,960 HETATM 43 C MOL 7,885 -2,750 21,390 HETATM 44 C MOL 6,797 -2,337 22,376 TER but the problem is that i cannot read those files or at least the containing atoms with the cdk: reader.PDBReader pdbReader = new PDBReader(...); ChemFile chemFile = (ChemFile) pdbReader.read((ChemObject) new ChemFile()); I tried in fact all methods and their daughter methods of: List *Containers = ChemFileManipulator.getALL*(chemFile); (getting all moleculesets, getting all atomcontainers...). is it possible that cdk has problems reading pdb files generated by itself? maybe i oversaw the "getAllAtoms" method somewhere? btw. the files can be perfectly read and displayed with jmol / pymol. thanks, raphael ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
