Remove direct usage of 'AtomContainer'

cdk · Feb 28, 2018 · 8e1e3ef · 8e1e3ef
1 parent bfacfe9
commit 8e1e3ef
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Showing 6 changed files with 71 additions and 60 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java b/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java
@@ -272,11 +272,12 @@ public static void breadthFirstSearch(IAtomContainer atomContainer, List<IAtom>
             // now look at bonds
             List<IBond> bonds = atomContainer.getConnectedBondsList(atom);
             for (IBond bond : bonds) {
+                nextAtom = bond.getOther(atom);
                 if (!bond.getFlag(CDKConstants.VISITED)) {
+                    molecule.addAtom(nextAtom);
                     molecule.addBond(bond);
                     bond.setFlag(CDKConstants.VISITED, true);
                 }
-                nextAtom = bond.getOther(atom);
                 if (!nextAtom.getFlag(CDKConstants.VISITED)) {
                     //					logger.debug("wie oft???");
                     newSphere.add(nextAtom);