[Joelib-help] JOEAtom

[Thijs B. <th...@me...>]

Hi,

I am trying to modify the JOEAtom class to contain a field for the atom 
name,

e.g by reading the second token of a sybylmol2 atom line with

             atom.setAtomName(atom_name) in the SybylMol2 class

and the methods in JOEAtom.

     public void setAtomName(String atomname)
     {
         _atomname = new String(atomname);
     }

     public String getAtomName()
     {
         return (_atomname);
     }

I can't retrieve the stored names however when i iterate over the atoms 
from a JOEMol:

       for(int i=1;i<=mol.numAtoms();i++){
             JOEAtom atom = mol.getAtom(i);
             System.out.println(atom.getAtomName());
	}

all the names are null.

Any suggestions?

Thanks.


---
Thijs Beuming
Harel Weinstein Lab
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021
Tel: (212) 7466539
Fax: (212) 746-6361
th...@me...