I never did PDBs, but shouldn't it be enought to do ChemFile chemFile = (ChemFile) reader.read(new NNChemFile());? The chemFile should contain a chemSequence should contain a chemModel should contain a setOfMolecule should contain your molecules?
On Sunday 30 December 2007 19:31:33 Rajarshi Guha wrote: > I'm not too familiar with reading PDB's. Can anybody help out? > > Begin forwarded message: > > From: U|web <[EMAIL PROTECTED]> > > Date: December 29, 2007 8:40:57 PM EST > > To: [EMAIL PROTECTED] > > Subject: Help : University Student needs help in CDK > > > > Hello, > > > > I need some help with a project in Bioinformatics. > > > > I am new in this area and I cannot find any tutorials except from > > the ones > > in your website (CDK - Java Snippets). > > > > I am trying to read from 2 pdb files, which I have done > > > > and then construct 2 molecules, > > > > in order to take their Tanimoto coefficient ( > > > > **org.openscience.cdk.similarity.Tanimoto** > > > > ). > > > > > > My problem is how to construct the molecule from the Data collected > > by the PDBReader. > > > > > > Hope you have time to help me. > > > > Best regards, > > Keranidis Stratos > > Graduate student in > > University of Thessaly > > Greece > > ------------------------------------------------------------------- > Rajarshi Guha <[EMAIL PROTECTED]> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > A man is known by the company he organizes. > -- Ambrose Bierce > > > > ------------------------------------------------------------------------- > 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 ------------------------------------------------------------------------- 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
