[Cdk-commits] SF.net SVN: cdk:[11768] cdk/trunk/src

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

Revision: 11768
          http://cdk.svn.sourceforge.net/cdk/?rev=11768&view=rev
Author:   egonw
Date:     2008-07-26 19:23:44 +0000 (Sat, 26 Jul 2008)

Log Message:
-----------
Removed dependency of charges on nonotify

Modified Paths:
--------------
    cdk/trunk/src/META-INF/charges.cdkdepends
    cdk/trunk/src/main/org/openscience/cdk/charges/Electronegativity.java
    cdk/trunk/src/main/org/openscience/cdk/charges/PiElectronegativity.java

Modified: cdk/trunk/src/META-INF/charges.cdkdepends
===================================================================
--- cdk/trunk/src/META-INF/charges.cdkdepends	2008-07-26 18:25:18 UTC (rev 11767)
+++ cdk/trunk/src/META-INF/charges.cdkdepends	2008-07-26 19:23:44 UTC (rev 11768)
@@ -1,10 +1,9 @@
 cdk-core.jar
 cdk-data.jar
 cdk-extra.jar
-cdk-nonotify.jar
 cdk-interfaces.jar
 cdk-io.jar
 cdk-standard.jar
 cdk-reaction.jar
 cdk-standard.jar
-cdk-valencycheck.jar
\ No newline at end of file
+cdk-valencycheck.jar

Modified: cdk/trunk/src/main/org/openscience/cdk/charges/Electronegativity.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/charges/Electronegativity.java	2008-07-26 18:25:18 UTC (rev 11767)
+++ cdk/trunk/src/main/org/openscience/cdk/charges/Electronegativity.java	2008-07-26 19:23:44 UTC (rev 11768)
@@ -1,7 +1,4 @@
-/*  $RCSfile$
- *  $Author: rajarshi $
- *  $Date: 2008-02-21 19:19:31 +0100 (Thu, 21 Feb 2008) $
- *  $Revision: 10199 $
+/*  $Revision: 10199 $ $Author: rajarshi $ $Date: 2008-02-21 19:19:31 +0100 (Thu, 21 Feb 2008) $
  *
  *  Copyright (C) 2008  Miguel Rojas <mig...@ya...>
  *
@@ -27,7 +24,7 @@
 import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.nonotify.NNMolecule;
+import org.openscience.cdk.interfaces.IMolecule;
 
 /**
  * Calculation of the electronegativity of orbitals of a molecule 
@@ -48,7 +45,7 @@
     /**Number of maximum resonance structures*/
 	private int maxRS = 50;
 
-	private NNMolecule molSigma;
+	private IMolecule molSigma;
 	private IAtomContainer acOldS;
 	private double[] marsiliFactors;
 	
@@ -106,7 +103,7 @@
 
         try {
         	if(!ac.equals(acOldS)){
-        		molSigma = new NNMolecule(ac);
+        		molSigma = ac.getBuilder().newMolecule(ac);
         		peoe.setMaxGasteigerIters(maxI);
 	    		peoe.assignGasteigerMarsiliSigmaPartialCharges(molSigma, true);
 	    		marsiliFactors = peoe.assignGasteigerSigmaMarsiliFactors(molSigma);

Modified: cdk/trunk/src/main/org/openscience/cdk/charges/PiElectronegativity.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/charges/PiElectronegativity.java	2008-07-26 18:25:18 UTC (rev 11767)
+++ cdk/trunk/src/main/org/openscience/cdk/charges/PiElectronegativity.java	2008-07-26 19:23:44 UTC (rev 11768)
@@ -26,7 +26,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomContainerSet;
 import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.nonotify.NNMolecule;
+import org.openscience.cdk.interfaces.IMolecule;
 
 /**
  * Calculation of the electronegativity of orbitals of a molecule 
@@ -48,7 +48,7 @@
     /**Number of maximum resonance structures*/
 	private int maxRS = 50;
 	
-	private NNMolecule molPi;
+	private IMolecule molPi;
 	private IAtomContainer acOldP;
 	private double[][] gasteigerFactors;
 	
@@ -108,7 +108,7 @@
 
         try {
         	if(!ac.equals(acOldP)){
-        		molPi = new NNMolecule(ac);
+        		molPi = ac.getBuilder().newMolecule(ac);
         		
                 peoe = new GasteigerMarsiliPartialCharges();
 	    		peoe.assignGasteigerMarsiliSigmaPartialCharges(molPi, true);


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