On 9/13/07, Raphael wrote on the CDK user mailing 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?
Might be a bug. Filed it as such. A JUnit test must be written. http://sourceforge.net/tracker/index.php?func=detail&aid=1794439&group_id=20024&atid=120024 Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- 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
