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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
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1 parent 9d9b04a commit 7f7ea85795b1c4ab652bb97d0cddea0cb7c5b0ee egonw committed May 19, 2004
Showing with 11 additions and 6 deletions.
  1. +4 −0 build.xml
  2. +7 −6 src/org/openscience/cdk/io/JMEReader.java
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4 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" />
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13 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;
}

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