[Cdk-devel] PDBAtom

[Egon W. <e.w...@sc...>]

Hi all,

with respect to the PDB 2 CML discussion, I've started making CDK ready for 
better PDB support. I've setup a new CDK module: pdb which contains these 
classes:

org/openscience/cdk/PDBAtom.java
org/openscience/cdk/io/PDBReader.java

The PDBReader has already been updated for the new PDBAtom class. The latter
has this API:

public class PDBAtom extends Atom implements java.io.Serializable, Cloneable {

    private String record;
    private double tempFactor;
    private String resName;
    private String iCode;
    private double occupancy;
    private String name;
    private String chainID;
    private String altLoc;
    private String segID;
    private int serial; 
    private String resSeq;
    private boolean oxt;
    private boolean hetAtom;
    
    public PDBAtom(String symbol, Point3d coordinate)
}

with the common get and set methods...

This broke a new test, but hope to finish up things tonight.

My next step will be to adapt the libio-cml Convertor class to output 
reasonable CML output using a new PDB dictionary (yet to be added to CVS).
As Peter said the current output created by CDK is not good.

And when that's done, I'll try to get CDK going with Jumbo 4.6 for J1.5.

Egon