[Cdk-commits] SF.net SVN: cdk: [7539] trunk/cdk/src/org/openscience/cdk/modeling/ builder3d

[<raj...@us...>]

Revision: 7539
          http://svn.sourceforge.net/cdk/?rev=7539&view=rev
Author:   rajarshi
Date:     2006-12-20 12:58:28 -0800 (Wed, 20 Dec 2006)

Log Message:
-----------
fixed some deprecated code

Modified Paths:
--------------
    trunk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
    trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java

Modified: trunk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java	2006-12-20 20:49:18 UTC (rev 7538)
+++ trunk/cdk/src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java	2006-12-20 20:58:28 UTC (rev 7539)
@@ -23,20 +23,20 @@
  */
 package org.openscience.cdk.modeling.builder3d;
 
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
 
+
 /**
  * Place aliphatic chains with Z matrix method.
  *
@@ -356,9 +356,9 @@
 	 * author:    steinbeck,cho
 	 */
 	public IAtom getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule) {
-		org.openscience.cdk.interfaces.IBond[] bonds = molecule.getBonds();
-		for (int i = 0; i < bonds.length; i++) {
-			IBond bond = bonds[i];
+        Iterator bonds = molecule.bonds();
+        while (bonds.hasNext()) {
+            IBond bond = (IBond) bonds.next();
 			if (bond.getAtom(0).getFlag(CDKConstants.ISPLACED) & !(bond.getAtom(1).getFlag(CDKConstants.ISPLACED))) {
 				if (bond.getAtom(1).getFlag(CDKConstants.ISALIPHATIC) & !bond.getAtom(1).getSymbol().equals("H")) {
 					return bond.getAtom(1);
@@ -380,9 +380,9 @@
 	 * author: steinbeck,cho
 	 */
 	public IAtom getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule) {
-		org.openscience.cdk.interfaces.IBond[] bonds = molecule.getBonds();
-		for (int i = 0; i < bonds.length; i++) {
-			IBond bond = bonds[i];
+        Iterator bonds = molecule.bonds();
+        while (bonds.hasNext()) {
+            IBond bond = (IBond) bonds.next();
 			IAtom atom0 = bond.getAtom(0);
 			IAtom atom1 = bond.getAtom(1);
 			if (atom0.getFlag(CDKConstants.ISPLACED) & !(atom1.getFlag(CDKConstants.ISPLACED))) {
@@ -405,9 +405,10 @@
 	 * @return    The nextPlacedHeavyAtomWithUnplacedRingNeighbour value
 	 */
 	public IAtom getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule) {
-		org.openscience.cdk.interfaces.IBond[] bonds = molecule.getBonds();
-		for (int i = 0; i < bonds.length; i++) {
-			IBond bond = bonds[i];
+//		IBond[] bonds = molecule.getBonds();
+        Iterator bonds = molecule.bonds();
+        while (bonds.hasNext()) {
+            IBond bond = (IBond) bonds.next();
 			IAtom atom0 = bond.getAtom(0);
 			IAtom atom1 = bond.getAtom(1);
 			if (atom0.getFlag(CDKConstants.ISPLACED) & !(atom1.getFlag(CDKConstants.ISPLACED))) {

Modified: trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java	2006-12-20 20:49:18 UTC (rev 7538)
+++ trunk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java	2006-12-20 20:58:28 UTC (rev 7539)
@@ -28,29 +28,23 @@
  */
 package org.openscience.cdk.modeling.builder3d;
 
-import java.io.InputStream;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.NoSuchAtomTypeException;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IPseudoAtom;
-import org.openscience.cdk.interfaces.IRing;
-import org.openscience.cdk.interfaces.IRingSet;
+import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.ringsearch.SSSRFinder;
 import org.openscience.cdk.tools.HOSECodeGenerator;
 import org.openscience.cdk.tools.manipulator.RingSetManipulator;
 
+import java.io.InputStream;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
+
 /**
  *  Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable
  *  Therfore it uses the class MM2BasedParamterSetReader
@@ -295,27 +289,31 @@
 			}
 		}
 		
-		IBond[] bond = molecule.getBonds();
+//		IBond[] bond = molecule.getBonds();
 		String bondType;
-		for (int i=0; i < bond.length; i++) {
+        Iterator bonds = molecule.bonds();
+        while (bonds.hasNext()) {
+            IBond bond = (IBond) bonds.next();
+
 			//System.out.println("bond[" + i + "] properties : " + molecule.getBond(i).getProperties());
 			bondType = "0";
-			if (bond[i].getOrder() == 1) {
-				if ((bond[i].getAtom(0).getAtomTypeName().equals("Csp2")) & 
-					((bond[i].getAtom(1).getAtomTypeName().equals("Csp2")) | (bond[i].getAtom(1).getAtomTypeName().equals("C=")))) {
+			if (bond.getOrder() == 1) {
+				if ((bond.getAtom(0).getAtomTypeName().equals("Csp2")) &
+					((bond.getAtom(1).getAtomTypeName().equals("Csp2")) | (bond.getAtom(1).getAtomTypeName().equals("C=")))) {
 					bondType = "1";
 				}
 					
-				if ((bond[i].getAtom(0).getAtomTypeName().equals("C=")) & 
-					((bond[i].getAtom(1).getAtomTypeName().equals("Csp2")) | (bond[i].getAtom(1).getAtomTypeName().equals("C=")))) {
+				if ((bond.getAtom(0).getAtomTypeName().equals("C=")) &
+					((bond.getAtom(1).getAtomTypeName().equals("Csp2")) | (bond.getAtom(1).getAtomTypeName().equals("C=")))) {
 					bondType = "1";}
 					
-				if ((bond[i].getAtom(0).getAtomTypeName().equals("Csp")) & 
-					(bond[i].getAtom(1).getAtomTypeName().equals("Csp"))) {
+				if ((bond.getAtom(0).getAtomTypeName().equals("Csp")) &
+					(bond.getAtom(1).getAtomTypeName().equals("Csp"))) {
 					bondType = "1";}
 			}
-			molecule.getBond(i).setProperty("MMFF94 bond type", bondType);
-			//System.out.println("bond[" + i + "] properties : " + molecule.getBond(i).getProperties());
+//			molecule.getBond(i).setProperty("MMFF94 bond type", bondType);
+            bond.setProperty("MMFF94 bond type", bondType);
+            //System.out.println("bond[" + i + "] properties : " + molecule.getBond(i).getProperties());
 		}
 
 		return ringSetMolecule;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.