Atoms are not added to IQueryAtomContainer causing an index out of bo…

…unds exception downstream. Adding the atoms fixes the issue. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Feb 6, 2014 · 1a3f3d3 · 1a3f3d3
1 parent 0eefcdc
commit 1a3f3d3
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
@@ -945,6 +945,12 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
         atom3.setSymbol("O");
         SymbolQueryAtom atom4=new SymbolQueryAtom(atomContainer.getBuilder());
         atom4.setSymbol("O");
+
+        orthopair.addAtom(atom1);
+        orthopair.addAtom(atom2);
+        orthopair.addAtom(atom3);
+        orthopair.addAtom(atom4);
+
         orthopair.addBond(new AromaticQueryBond(atom1,atom2,IBond.Order.SINGLE, atomContainer.getBuilder()));
         orthopair.addBond(new OrderQueryBond(atom1,atom3,IBond.Order.SINGLE, atomContainer.getBuilder()));
         orthopair.addBond(new OrderQueryBond(atom2,atom4,IBond.Order.SINGLE, atomContainer.getBuilder()));