[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools SaturationChecker.java,1.32,1.33 AtomTypeFactory.java,1.30,1.31

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools
In directory sc8-pr-cvs1:/tmp/cvs-serv4720/src/org/openscience/cdk/tools

Modified Files:
	SaturationChecker.java AtomTypeFactory.java 
Log Message:
Added extra example on new API for AtomTypeFactory.getAtomTypes() and updated classes that use that method

Index: SaturationChecker.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/SaturationChecker.java,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- SaturationChecker.java	26 Aug 2003 15:06:05 -0000	1.32
+++ SaturationChecker.java	22 Sep 2003 11:48:31 -0000	1.33
@@ -45,13 +45,13 @@
 public class SaturationChecker
 {
 
-	AtomTypeFactory atf;
+	AtomTypeFactory structgenATF;
 
 	private org.openscience.cdk.tools.LoggingTool logger;
 
 	public SaturationChecker() throws IOException, ClassNotFoundException
 	{
-		atf = AtomTypeFactory.getInstance();
+		structgenATF = AtomTypeFactory.getInstance("org/openscience/cdk/config/structgen_atomtypes.xml");
 		logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName());
 	}
 
@@ -61,7 +61,7 @@
 
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		double maxBondOrder = ac.getMaximumBondOrder(atom);
-		AtomType[] atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
 		logger.debug("*** Checking for perfect configuration ***");
 		try
 		{
@@ -109,7 +109,7 @@
 	{
 		//System.out.println("In here :-), checking atom " + atom.getSymbol());
 		
-		AtomType[] atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		double maxBondOrder = ac.getMaximumBondOrder(atom);
 		int hcount = atom.getHydrogenCount();
@@ -145,7 +145,7 @@
 	 */
 	public boolean isOverSaturated(Atom atom, AtomContainer ac)
 	{
-		AtomType[] atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		double maxBondOrder = ac.getMaximumBondOrder(atom);
 		int hcount = atom.getHydrogenCount();
@@ -180,7 +180,7 @@
 	 */
 	public double getCurrentMaxBondOrder(Atom atom, AtomContainer ac)
 	{
-		AtomType[] atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+		AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
 		double bondOrderSum = ac.getBondOrderSum(atom);
 		int hcount = atom.getHydrogenCount();
 		double max = 0;
@@ -218,7 +218,7 @@
 			{
 				atom = atomContainer.getAtomAt(f);
 				//System.out.println(atom.getSymbol());
-				atomTypes1 = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+				atomTypes1 = structgenATF.getAtomTypes(atom.getSymbol());
 				//System.out.println(atomTypes1[0]);
 				if (atomContainer.getBondCount(atom) == i)
 				{
@@ -228,7 +228,7 @@
 						{
 							partner = partners[g];
 							//System.out.println("Atom has " + partners.length + " partners");
-							atomTypes2 = atf.getAtomTypes(partner.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+							atomTypes2 = structgenATF.getAtomTypes(partner.getSymbol());
 							if (atomContainer.getBond(partner,atom).getFlag(CDKConstants.ISAROMATIC) && atomContainer.getBondOrderSum(partner) < atomTypes2[0].getMaxBondOrderSum() - partner.getHydrogenCount())
 							{
 								//System.out.println("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].getMaxBondOrderSum());
@@ -248,7 +248,7 @@
 						{
 							partner = partners[g];
 							//System.out.println("Atom has " + partners.length + " partners");
-							atomTypes2 = atf.getAtomTypes(partner.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+							atomTypes2 = structgenATF.getAtomTypes(partner.getSymbol());
 							if (atomContainer.getBondOrderSum(partner) < atomTypes2[0].getMaxBondOrderSum() - partner.getHydrogenCount())
 							{
 								//System.out.println("Partner has " + atomContainer.getBondOrderSum(partner) + ", may have: " + atomTypes2[0].getMaxBondOrderSum());
@@ -361,7 +361,7 @@
         } else {
             logger.info("Calculating number of missing hydrogen atoms");
             // get default atom
-            AtomType[] atomTypes = atf.getAtomTypes(atom.getSymbol(), atf.ATOMTYPE_ID_STRUCTGEN);
+            AtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol());
             logger.debug("Found atomtypes: " + atomTypes.length);
             if (atomTypes.length > 0) {
                 AtomType defaultAtom = atomTypes[0];

Index: AtomTypeFactory.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/AtomTypeFactory.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- AtomTypeFactory.java	22 Sep 2003 10:32:26 -0000	1.30
+++ AtomTypeFactory.java	22 Sep 2003 11:48:31 -0000	1.31
@@ -43,8 +43,14 @@
  *  <pre>
  *  AtomTypeFactory factory = AtomTypeFactory.getInstance();
  *  </pre>
+ *  For each atom type list a separate AtomTypeFactory is instantiated.
  *
- * <p>For each atom type list a separate AtomTypeFactory is instantiated.
+ *  <p>To get all the atom types of an element from a specific list, this 
+ *  code can be used:
+ *  <pre>
+ *  AtomTypeFactory factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/jmol_atomtypes.txt");
+ *  AtomType[] types = factory.getAtomTypes("C");
+ *  </pre>
  *
  * @author     steinbeck
  * @created    2001-08-29