Re: [Cdk-devel] CDK Tutorials

[Rajarshi G. <rx...@ps...>]

On Mon, 2005-06-27 at 09:29 +0000, Michael Xu wrote:
> Hi, 
> I am currently doing a protein viewer project. I am interested in
> using cdk for my projects. However, I had difficulty using the
> classes. I needed to read in a pdb file and set it into a ChemObject
> object. From there, I want to calculate the atom's partial charge.
> I've searched for CDK tutorials but couldn't find any. Is there any
> tutorials on CDK for me to refer to? I am seriously stuck at this
> step. Could you be as kind as to give me some pointers? Thank you. 

A very good source of examples are the application programs in the CDK
distribution. 

An example of reading structures from multiple files (each of which may
contain multiple molecules) is:

static public Vector loadMoleculesSimple(String[] args, boolean withH) {
    Vector v = new Vector();
    try {
        int i = 0;
        int j = 0;

        for (i = 0; i < args.length; i++) {
            File input = new File(args[i]);
            ChemObjectReader reader = new ReaderFactory().createReader
(new FileReader(input));
            ChemFile content = (ChemFile)reader.read((ChemObject)new
ChemFile());
            AtomContainer[] c = ChemFileManipulator.getAllAtomContainers
(content);

            // we should do this loop in case we have files
            // that contain multiple molecules
            for (j = 0; j < c.length; j++) {
                v.add(c[j]);
            }
        }
    } catch (Exception e) {
        System.out.println(e.toString());
    }
    return v;
}

You supply a String[] of file names and get back a Vector of
AtonContainer's. I use it for loading HIN's and SDF's - I assume it
would work for PDB's, but I have'nt tested it on that.

HTH,

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Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
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