[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/app AtomTypeTable.java,1.2,1.3

[Egon W. <eg...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/app
In directory sc8-pr-cvs1:/tmp/cvs-serv25080/src/org/openscience/jmol/app

Modified Files:
	AtomTypeTable.java 
Log Message:
Removed toolbar with non-functioning buttons (add/remove) and implemented reading of user defined atom types.

Index: AtomTypeTable.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/app/AtomTypeTable.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -r1.2 -r1.3
*** AtomTypeTable.java	6 Feb 2003 17:59:02 -0000	1.2
--- AtomTypeTable.java	10 Feb 2003 19:35:45 -0000	1.3
***************
*** 28,31 ****
--- 28,33 ----
  import org.openscience.jmol.render.AtomColors;
  
+ import org.openscience.cdk.tools.AtomTypeFactory;
+ 
  import javax.swing.JTable;
  import javax.swing.DefaultCellEditor;
***************
*** 90,94 ****
  public class AtomTypeTable extends JDialog implements ActionListener {
  
!   private static String SAU = "org/openscience/jmol/Data/AtomTypes";
  
    /*
--- 92,97 ----
  public class AtomTypeTable extends JDialog implements ActionListener {
  
!   private static String SAU = "jmol_atomtypes.txt";
!     private org.openscience.cdk.tools.LoggingTool logger;
  
    /*
***************
*** 106,124 ****
  
    public AtomTypeTable(JFrame fr, File UAF) {
- 
      this(fr);
- 
      try {
!       ReadAtypes(new FileInputStream(UAF));
!     } catch (Exception e1) {
!       try {
!         URL url = this.getClass().getClassLoader().getResource(SAU);
! 
!         // URL url = ClassLoader.getSystemResource(SAU);
!         ReadAtypes(url.openStream());
!       } catch (Exception e2) {
!         System.err.println("Cannot read System AtomTypes: " + e2.toString());
!         e2.printStackTrace();
!       }
      }
    }
--- 109,121 ----
  
    public AtomTypeTable(JFrame fr, File UAF) {
      this(fr);
      try {
!         if (UAF.exists()) {
!             ReadAtypes(UAF.toString());
!         } else {
!             ReadAtypes(SAU);
!         }
!     } catch (Exception exc) {
!         System.err.println("Error while reading AtomTypes.");
      }
    }
***************
*** 130,133 ****
--- 127,132 ----
            true);
  
+     logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName());
+           
      // Create a model of the data.
      atModel = new AtomTypesModel();
***************
*** 244,248 ****
      buttonPanel.add(OK);
  
!     JToolBar toolbar = new JToolBar();
  
      JButton natb =
--- 243,247 ----
      buttonPanel.add(OK);
  
!     /** JToolBar toolbar = new JToolBar();
  
      JButton natb =
***************
*** 265,274 ****
  
      toolbar.add(natb);
!     toolbar.add(datb);
  
      JPanel container = new JPanel();
      container.setLayout(new BorderLayout());
  
!     container.add(toolbar, BorderLayout.NORTH);
      container.add(AtomTableWrapper, BorderLayout.CENTER);
      container.add(buttonPanel, BorderLayout.SOUTH);
--- 264,273 ----
  
      toolbar.add(natb);
!     toolbar.add(datb); **/
  
      JPanel container = new JPanel();
      container.setLayout(new BorderLayout());
  
!     // container.add(toolbar, BorderLayout.NORTH);
      container.add(AtomTableWrapper, BorderLayout.CENTER);
      container.add(buttonPanel, BorderLayout.SOUTH);
***************
*** 570,642 ****
  
  
!   void ReadAtypes(InputStream is) throws Exception {
!       // FIXME: this method should be removed (Egon)
!       // It is superceded by CDK's TXTBasedAtomTypeConfigurator.
! 
!     BufferedReader r = new BufferedReader(new InputStreamReader(is), 1024);
!     StringTokenizer st;
! 
!     AtomColors atomColors = AtomColors.getInstance();
! 
!     String s;
! 
!     atModel.clear();
! 
!     try {
!       while (true) {
!         s = r.readLine();
!         if (s == null) {
!           break;
!         }
!         if (!s.startsWith("#")) {
!           String name = "";
!           String rootType = "";
!           int an = 0, rl = 0, gl = 0, bl = 0;
!           double mass = 0.0, vdw = 0.0, covalent = 0.0;
!           st = new StringTokenizer(s, "\t ,;");
!           int nt = st.countTokens();
! 
!           if (nt == 9) {
!             name = st.nextToken();
!             rootType = st.nextToken();
!             String san = st.nextToken();
!             String sam = st.nextToken();
!             String svdw = st.nextToken();
!             String scov = st.nextToken();
!             String sr = st.nextToken();
!             String sg = st.nextToken();
!             String sb = st.nextToken();
! 
!             try {
!               mass = new Double(sam).doubleValue();
!               vdw = new Double(svdw).doubleValue();
!               covalent = new Double(scov).doubleValue();
!               an = new Integer(san).intValue();
!               rl = new Integer(sr).intValue();
!               gl = new Integer(sg).intValue();
!               bl = new Integer(sb).intValue();
!             } catch (NumberFormatException nfe) {
!               throw new JmolException("AtomTypeTable.ReadAtypes",
!                   "Malformed Number");
!             }
! 
!             AtomType at = new AtomType(name, rootType, an, mass, vdw, covalent);
!             // atomColors.setAtomColor(at, new Color(rl, gl, bl));
! 
!             atModel.updateAtomType(at.getBaseAtomType());
! 
!           } else {
!             throw new JmolException("AtomTypeTable.ReadAtypes",
!                 "Wrong Number of fields");
!           }
!         }
!       }    // end while
! 
!       is.close();
! 
!     }      // end Try
!         catch (IOException e) {
!     }
! 
    }
  
--- 569,584 ----
  
  
!   void ReadAtypes(String configFile) throws Exception {
!       // System.out.print("Reading config file... ");
!       AtomTypeFactory atf = new AtomTypeFactory(configFile);
!       
!       org.openscience.cdk.AtomType[] types = atf.getAllAtomTypes();
!       System.out.println("Read atom types: " + types.length);
!       for (int i=0; i<types.length; i++) {
!           // convert all AtomType's to BaseAtomType and add then
!           // to the list
!           atModel.updateAtomType(BaseAtomType.get(types[i]));
!       }
!       // System.out.println("done.");
    }
  
***************
*** 649,653 ****
    }
  
!   public synchronized Enumeration elements() {
      return atModel.elements();
    }
--- 591,628 ----
    }
  
! 	/**
! 	 *  Configures an atom. Finds the correct element type
! 	 *  by looking at the atoms atom type id (atom.getID()).
! 	 *
! 	 * @param  atom  The atom to be configured
! 	 * @return       The configured atom
! 	 */
! 	public Atom configure(Atom atom) {
!         try {
!             BaseAtomType at = get(atom.getID());
!             atom.setMaxBondOrder(at.getMaxBondOrder());
!             atom.setMaxBondOrderSum(at.getMaxBondOrderSum());
!             atom.setVanderwaalsRadius(at.getVanderwaalsRadius());
!             atom.setCovalentRadius(at.getCovalentRadius());
!             atom.setProperty("org.openscience.jmol.color", at.getColor());
!             if (at.getAtomicNumber() != 0) {
!                 atom.setAtomicNumber(at.getAtomicNumber());
!             } else {
!                 logger.debug("Did not configure atomic number: AT.an=" + at.getAtomicNumber());
!             }
!             if (at.getExactMass() > 0.0) {
!                 atom.setExactMass(at.getExactMass());
!             } else {
!                 logger.debug("Did not configure mass: AT.mass=" + at.getAtomicNumber());
!             }
!         } catch (Exception exc) {
!             logger.warn("Could not configure atom with unknown ID: " + 
!                         atom.toString() + " + (id=" + atom.getID() + ")");
!         }
!         logger.debug("Configured " + atom.toString());
! 		return atom;
! 	}
! 
!     public synchronized Enumeration elements() {
      return atModel.elements();
    }