If bonds are needed they can be created with help of the org.openscience.cdk.graph.rebond.RebondTool.
And the org.openscience.cdk.tools.manipulator.ChemFileManipulator provides convenience methods for ChemFiles. --Andreas Stefan Kuhn wrote: > 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 > ------------------------------------------------------------------------- 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
