[Cdk-commits] CVS: cdk/src/org/openscience/cdk/modeling/builder3d ForceFieldConfigurator.java,1.8,1.9 ModelBuilder3D.java,1.15,1.16 TemplateHandler3D.java,1.11,1.12

[Stefan K. <sh...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22933/src/org/openscience/cdk/modeling/builder3d

Modified Files:
	ForceFieldConfigurator.java ModelBuilder3D.java 
	TemplateHandler3D.java 
Log Message:
modelbuilder3d works again


Index: ForceFieldConfigurator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- ForceFieldConfigurator.java	18 Apr 2005 12:59:24 -0000	1.8
+++ ForceFieldConfigurator.java	12 May 2005 15:10:42 -0000	1.9
@@ -181,7 +181,7 @@
 		mm2.readParameterSets();
 		parameterSet = mm2.getParamterSet();
 		atomTypes = mm2.getAtomTypes();
-	}
+  }
 	
 	public void setMMFF94Parameters() throws Exception{
 		mmff94.readParameterSets();
@@ -216,7 +216,7 @@
 	 */
 	private AtomType getAtomType(String ID) throws NoSuchAtomTypeException {
 		AtomType at = null;
-		for (int i = 0; i < atomTypes.size(); i++) {
+    for (int i = 0; i < atomTypes.size(); i++) {
 			at = (AtomType) atomTypes.get(i);
 			if (at.getID().equals(ID)) {
 				return at;

Index: ModelBuilder3D.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- ModelBuilder3D.java	11 May 2005 11:11:22 -0000	1.15
+++ ModelBuilder3D.java	12 May 2005 15:10:42 -0000	1.16
@@ -91,7 +91,9 @@
 	/**
 	 *  Constructor for the ModelBuilder3D object
 	 */
-	public ModelBuilder3D() { }
+	public ModelBuilder3D() {
+    setForceField(null);
+  }
 
 
 	/**
@@ -116,6 +118,7 @@
 	 */
 	public ModelBuilder3D(Molecule molecule) {
 		setMolecule(molecule, false);
+    setForceField(null);
 	}
 
 

Index: TemplateHandler3D.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- TemplateHandler3D.java	11 May 2005 12:31:49 -0000	1.11
+++ TemplateHandler3D.java	12 May 2005 15:10:42 -0000	1.12
@@ -34,6 +34,7 @@
 import java.util.Vector;
 import java.util.BitSet;
 import java.util.StringTokenizer;
+import java.util.zip.*;
 
 import org.openscience.cdk.SetOfMolecules;
 import org.openscience.cdk.Atom;
@@ -87,7 +88,7 @@
 			
 		try{	
 			ins = this.getClass().getClassLoader().getResourceAsStream("org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf.gz");
-			fin = new BufferedReader(new InputStreamReader(ins));
+			fin = new BufferedReader(new InputStreamReader(new GZIPInputStream(ins)));
 			imdl=new IteratingMDLReader(fin);
 		}catch (Exception exc1){
 			throw new CDKException("Problems loading file ringTemplateStructures.sdf.gz");
@@ -108,7 +109,7 @@
 		try{
 			
 			ins = this.getClass().getClassLoader().getResourceAsStream("org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt.gz");
-			fin = new BufferedReader(new InputStreamReader(ins));
+			fin = new BufferedReader(new InputStreamReader(new GZIPInputStream(ins)));
 		}catch (Exception exc3){
 			System.out.println("Could not read Fingerprints from FingerprintFile due to: "+exc3.getMessage());
 		}