Ensure no modifications whilst iterating.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Oct 21, 2013 · e367ebf · e367ebf
1 parent 0debacc
commit e367ebf
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -1013,9 +1013,7 @@ private void applyMDLValenceModel(IAtom atom, int explicitValence) {
     }
 
     private void fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory) {
-		Iterator<IAtom> atoms = molecule.atoms().iterator();
-		while (atoms.hasNext()) {
-			IAtom atom = atoms.next();
+		for (IAtom atom : AtomContainerManipulator.getAtomArray(molecule)) {
 			if (atom instanceof IPseudoAtom) {
 				IPseudoAtom pseudo = (IPseudoAtom) atom;
                 if ("D".equals(pseudo.getLabel())) {

diff --git a/src/main/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java b/src/main/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java
@@ -32,6 +32,7 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.SaturationChecker;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator;
 import org.openscience.cdk.tools.manipulator.BondManipulator;
 
@@ -83,7 +84,7 @@ public IAtomContainer generate(IAtomContainerSet atomContainers) throws CDKExcep
 			do{
 				bondFormed=false;
 				for(IAtomContainer ac : atomContainers.atomContainers()){
-					for(IAtom atom : ac.atoms()){
+					for(IAtom atom : AtomContainerManipulator.getAtomArray(ac)){
 						if (!satCheck.isSaturated(atom, ac))
 						{
 							IAtom partner = getAnotherUnsaturatedNode(atom, atomContainers);

diff --git a/src/main/org/openscience/cdk/tools/ProteinBuilderTool.java b/src/main/org/openscience/cdk/tools/ProteinBuilderTool.java
@@ -34,6 +34,7 @@
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.templates.AminoAcids;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 import java.util.Map;
 
@@ -149,8 +150,8 @@ public static BioPolymer createProtein(String sequence) throws CDKException {
     }
 
     private static BioPolymer addAminoAcid(BioPolymer protein, AminoAcid aaToAdd, Strand strand) {
-        for (IAtom atom : aaToAdd.atoms())  protein.addAtom(atom, aaToAdd, strand);
-        for (IBond bond : aaToAdd.bonds()) protein.addBond(bond);
+        for (IAtom atom : AtomContainerManipulator.getAtomArray(aaToAdd)) protein.addAtom(atom, aaToAdd, strand);
+        for (IBond bond : AtomContainerManipulator.getBondArray(aaToAdd)) protein.addBond(bond);
         return protein;
     }
 }