[Cdk-commits] CVS: cdk/src/org/openscience/cdk/atomtype AtomTypeMatcher.java,1.1,1.2 HybridizationStateATMatcher.java,1.1,1.2

[Matteo F. <mf...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/atomtype
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6043/src/org/openscience/cdk/atomtype

Modified Files:
	AtomTypeMatcher.java HybridizationStateATMatcher.java 
Log Message:
added javadoc and fixed module name

Index: AtomTypeMatcher.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/atomtype/AtomTypeMatcher.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- AtomTypeMatcher.java	1 Mar 2005 14:23:19 -0000	1.1
+++ AtomTypeMatcher.java	1 Mar 2005 14:38:29 -0000	1.2
@@ -24,16 +24,18 @@
 package org.openscience.cdk.atomtype;
 
 import org.openscience.cdk.Atom;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.AtomType;
 import org.openscience.cdk.exception.CDKException;
 
 /**
  * Classes that implement this interface are atomtypes matchers.
  *
- * @cdk.module atomtype
+ * @cdk.module core
  */
 public interface AtomTypeMatcher {
-	//method that returns the atom type
+
+	/** Method that assign an atom type to a given atom. belonging to an atom container */
     public void findMatchingAtomType(AtomContainer ac, Atom atom);
 
 }

Index: HybridizationStateATMatcher.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/atomtype/HybridizationStateATMatcher.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- HybridizationStateATMatcher.java	1 Mar 2005 14:23:19 -0000	1.1
+++ HybridizationStateATMatcher.java	1 Mar 2005 14:38:29 -0000	1.2
@@ -30,14 +30,17 @@
 import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.config.AtomTypeFactory;
+import org.openscience.cdk.tools.LoggingTool;
 
 /**
  *@author         mfe4
  *@cdk.created    2004-12-02
  *@cdk.module     core
  */
+
 public class HybridizationStateATMatcher {
 
+	private LoggingTool logger;
 	double charge = 0;
 	int neighboorsCount = 0;
 
@@ -59,7 +62,9 @@
 	/**
 	 *  Constructor for the HybridizationStateATMatcher object
 	 */
-	public HybridizationStateATMatcher() { }
+	public HybridizationStateATMatcher() {
+		logger = new LoggingTool(this);
+	}
 
 
 	/**
@@ -70,6 +75,7 @@
 	 *@exception  CDKException  Description of the Exception
 	 */
 	public void findMatchingAtomType(AtomContainer ac, Atom atom) throws CDKException {
+		
 		symbol = atom.getSymbol();
 		//Hs are included?
 		Atom[] neighboors = ac.getConnectedAtoms(atom);
@@ -90,7 +96,7 @@
 				tmp_bondOrderSum = type[i].getBondOrderSum();
 				tmp_neighboorsCount = type[i].getFormalNeighbourCount();
 				tmp_charge = type[i].getFormalCharge();
-				System.out.println(i + "ATOM TYPE " + tmp_bondOrderSum + " " + tmp_maxbondOrder + " " + tmp_neighboorsCount);
+				//System.out.println(i + "ATOM TYPE " + tmp_bondOrderSum + " " + tmp_maxbondOrder + " " + tmp_neighboorsCount);
 				if (tmp_maxbondOrder == maxbondOrder && tmp_bondOrderSum == bondOrderSum) {
 					if (tmp_neighboorsCount == neighboorsCount) {
 						//System.out.println("!!!!! ATOM TYPE FOUND");
@@ -104,6 +110,7 @@
 			}
 
 		} catch (Exception ex1) {
+			logger.debug(ex1);
 			throw new CDKException("Problems with AtomTypeFactory due to " + ex1.toString());
 		}
 	}