Updated a method based on Ninas suggestion to avoid modifiying a atom…

… container when looping over it. This avoids a concurrent modification exception. Also updated some Javadocs Change-Id: If01762c6cff615d7a25de8b8f9bcee49c41eba16 Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jun 25, 2012 · eba09ca · eba09ca
1 parent 3f3fab5
commit eba09ca
Showing 1 changed file with 30 additions and 9 deletions.
diff --git a/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -226,6 +226,9 @@ public static double getTotalNaturalAbundance(IAtomContainer atomContainer) {
     }
 
     /**
+     * Get the total formal charge on a molecule.
+     *
+     * @param atomContainer the atom container to consider
      * @return The summed formal charges of all atoms in this AtomContainer.
      */
     @TestMethod("testGetTotalFormalCharge_IAtomContainer")
@@ -236,6 +239,9 @@ public static int getTotalFormalCharge(IAtomContainer atomContainer) {
         return chargeP + chargeN;
     }
     /**
+     * Get the total formal negative charge on a molecule.
+     *
+     * @param atomContainer the atom container to consider
      * @return The summed negative formal charges of all atoms in this AtomContainer.
      */
     @TestMethod("testGetTotalNegativeFormalCharge_IAtomContainer")
@@ -249,6 +255,9 @@ public static int getTotalNegativeFormalCharge(IAtomContainer atomContainer) {
         return charge;
     }
     /**
+     * Get the total positive formal charge on a molecule.
+     *
+     * @param atomContainer the atom container to consider
      * @return The summed positive formal charges of all atoms in this AtomContainer.
      */
     @TestMethod("testGetTotalPositiveFormalCharge_IAtomContainer")
@@ -263,6 +272,9 @@ public static int getTotalPositiveFormalCharge(IAtomContainer atomContainer) {
     }
 
     /**
+     * Count the total number of hydrogens (implicit and explicit).
+     *
+     * @param atomContainer the atom container to consider
      * @return The summed implicit hydrogens of all atoms in this AtomContainer.
      */
     @TestMethod("testGetTotalHydrogenCount_IAtomContainer,testGetTotalHydrogenCount_IAtomContainer_zeroImplicit,testGetTotalHydrogenCount_IAtomContainer_nullImplicit,testGetTotalHydrogenCount_ImplicitHydrogens")
@@ -277,6 +289,9 @@ public static int getTotalHydrogenCount(IAtomContainer atomContainer) {
     }
 
     /**
+     * Count explicit hydrogens.
+     *
+     * @param atomContainer the atom container to consider
      * @return The number of explicit hydrogens on the given IAtom.
      */
     @TestMethod("testCountExplicitH")
@@ -294,29 +309,35 @@ public static int countExplicitHydrogens(IAtomContainer atomContainer, IAtom ato
      * Adds explicit hydrogens (without coordinates) to the IAtomContainer,
      * equaling the number of set implicit hydrogens.
      *
+     * @param atomContainer the atom container to consider
      * @cdk.keyword hydrogens, adding
      */
     @TestMethod("testConvertImplicitToExplicitHydrogens_IAtomContainer")
     public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContainer) {
+        List<IAtom> hydrogens = new ArrayList<IAtom>();
+        List<IBond> newBonds = new ArrayList<IBond>();
+        List<Integer> atomIndex = new ArrayList<Integer>();
+
         for (IAtom atom : atomContainer.atoms()) {
             if (!atom.getSymbol().equals("H")) {
                 Integer hCount = atom.getImplicitHydrogenCount();
                 if (hCount != null) {
                     for (int i = 0; i < hCount; i++) {
-                        IAtom hydrogen = atom.getBuilder().newInstance(IAtom.class,"H");
+
+                        IAtom hydrogen = atom.getBuilder().newInstance(IAtom.class, "H");
                         hydrogen.setAtomTypeName("H");
-                        atomContainer.addAtom(hydrogen);
-                        atomContainer.addBond(
-                                atom.getBuilder().newInstance(IBond.class,
-                                        atom, hydrogen,
-                                        CDKConstants.BONDORDER_SINGLE
-                                )
-                        );
+                        hydrogens.add(hydrogen);
+                        newBonds.add(atom.getBuilder().newInstance(IBond.class,
+                                atom, hydrogen, CDKConstants.BONDORDER_SINGLE
+                        ));
                     }
-                    atom.setImplicitHydrogenCount(0);
+                    atomIndex.add(atomContainer.getAtomNumber(atom));
                 }
             }
         }
+        for (Integer index : atomIndex) atomContainer.getAtom(index).setImplicitHydrogenCount(0);
+        for (IAtom atom : hydrogens) atomContainer.addAtom(atom);
+        for (IBond bond : newBonds) atomContainer.addBond(bond);
     }
 
     /**