Have the experimental JME reader actually compile

git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@2860 eb4e18e3-b210-0410-a6ab-dec725e4b171

build.xml

@@ -61,6 +61,8 @@
                         <include name="cmlAll.jar" />
                         <include name="base.jar" />
                         <include name="pmrlib.jar" />
+                        <include name="jmolApis.jar" />
+                        <include name="jmolIO.jar" />
                 </fileset>
                 <fileset dir="${pathtojava3d}">
                         <include name="*.jar" />
@@ -691,6 +693,7 @@
 
         <target id="test-experimental" name="test-experimental" depends="noJunit"
                 description="Performs a full JUnit test for the CDK, including experimental classes.">
+                <mkdir dir="${reports.tests}"/>
                 <junit printsummary="yes" haltonfailure="yes" fork="yes">
                     <classpath>
                         <pathelement location="${dist}/jar/cdk-core.jar" />
@@ -724,6 +727,7 @@
 
         <target id="test" name="test" depends="dist-test, noJunit"
                 description="Performs a full JUnit test for the CDK." if="junit.present">
+                <mkdir dir="${reports.tests}"/>
                 <junit printsummary="yes" haltonfailure="yes" fork="yes">
                     <classpath>
                         <pathelement location="${dist}/jar/cdk-core.jar" />

src/org/openscience/cdk/io/JMEReader.java

@@ -42,6 +42,7 @@
 import org.jmol.adapter.smarter.SmarterModelAdapter;
 import org.jmol.api.ModelAdapter;
 import org.jmol.api.ModelAdapter.AtomIterator;
+import org.jmol.api.ModelAdapter.BondIterator;
 
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.Bond;
@@ -132,23 +133,23 @@ private Molecule readMolecule(Molecule molecule) throws CDKException {
         AtomIterator atomIterator = adapter.getAtomIterator(model);
         while (atomIterator.hasNext()) {
             Atom atom = new Atom(atomIterator.getElementSymbol());
-            atom.setX3d(atomIterator.x);
+            /* atom.setX3d(atomIterator.x);
             atom.setY3d(atomIterator.y);
-            atom.setZ3d(atomIterator.z);
+            atom.setZ3d(atomIterator.z); */
             molecule.addAtom(atom);
         }
         BondIterator bondIterator = adapter.getBondIterator(model);
         while (bondIterator.hasNext()) {
-            Object atom1 = bondIterator.getgetAtomUid1();
-            Object atom2 = bondIterator.getgetAtomUid2();
-            if (atom1 instanceof org.jmol.adapter.smarter.Atom) {
+            Object atom1 = bondIterator.getAtomUid1();
+            Object atom2 = bondIterator.getAtomUid2();
+            /* if (atom1 instanceof org.jmol.adapter.smarter.Atom) {
                 org.jmol.adapter.smarter.Atom atomOne =
                     (org.jmol.adapter.smarter.Atom)atom1;
                 org.jmol.adapter.smarter.Atom atomTwo =
                     (org.jmol.adapter.smarter.Atom)atom2;
                 // now I'm stuck... no idea which atoms this bond
                 // connects... consulting Miguel
-            }
+            } */
         }
 		return molecule;
 	}