Merge pull request #322 from cdk/findbugs

Yeah, amazing how easily one does not notice these small silly mistakes....
cdk · May 18, 2017 · 1ecebf6 · 1ecebf6
2 parents 9779b93 + d56977d
commit 1ecebf6
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Showing 12 changed files with 37 additions and 33 deletions.
diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java
@@ -154,7 +154,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {
@@ -213,7 +213,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {

diff --git a/base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java b/base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java
@@ -154,7 +154,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {
@@ -213,7 +213,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {

diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java
@@ -154,7 +154,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {
@@ -213,7 +213,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {

diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java
@@ -155,7 +155,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {
@@ -214,7 +214,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomhs.hasNext()) {

diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java
@@ -158,7 +158,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {
@@ -222,7 +222,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {

diff --git a/base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java b/base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java
@@ -158,7 +158,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {
@@ -222,7 +222,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {

diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java
@@ -158,7 +158,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {
@@ -222,7 +222,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {

diff --git a/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java b/.../reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java
@@ -158,7 +158,7 @@ public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agen
                     if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                             && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {
@@ -222,7 +222,7 @@ private void setActiveCenters(IAtomContainer reactant) throws CDKException {
                     IAtom atoml = atomls.next();
                     if (atoml != null && !atoml.getFlag(CDKConstants.ISINRING)
                             && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
-                            && !atoml.equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
+                            && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
 
                         Iterator<IAtom> atomRs = reactant.getConnectedAtomsList(atoml).iterator();
                         while (atomRs.hasNext()) {

diff --git a/legacy/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java b/legacy/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java
@@ -93,7 +93,7 @@ else if (familyOxygen(atom))
     public static double predictIP(IAtomContainer container, IBond bond) throws CDKException {
         double value = 0;
 
-        if (bond.equals(IBond.Order.SINGLE)) return value;
+        if (bond.getOrder().equals(IBond.Order.SINGLE)) return value;
 
         //if some of the atoms belongs to some of the heteroatom family than
         // it can not ionized

diff --git a/misc/extra/src/main/java/org/openscience/cdk/io/ShelXWriter.java b/misc/extra/src/main/java/org/openscience/cdk/io/ShelXWriter.java
@@ -201,7 +201,14 @@ private void writeCrystal(ICrystal crystal) {
                 write(" ");
             }
             write("     ");
-            String elemID = Integer.valueOf(asortedElements.indexOf(symbol) + 1).toString();
+            String elemID = null;
+            for (int elemidx = 0; elemidx < asortedElements.size(); elemidx++) {
+                IElement elem = asortedElements.get(elemidx);
+                if (elem.getSymbol().equals(symbol)) {
+                    elemID = Integer.toString(elemidx + 1);
+                    break;
+                }
+            }
             write(elemID);
             write("    ".substring(elemID.length()));
             write(format.reset("%7.5f").format(fracCoord.x) + "   ");

diff --git a/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HybridizationNumberAtom.java b/...rc/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HybridizationNumberAtom.java
@@ -37,8 +37,6 @@
 
 public class HybridizationNumberAtom extends SMARTSAtom {
 
-    Hybridization hybridization;
-
     /**
      * Creates a new instance
      *
@@ -48,28 +46,28 @@ public HybridizationNumberAtom(int hybridizationNumber, IChemObjectBuilder build
         super(builder);
         switch (hybridizationNumber) {
             case 1:
-                hybridization = IAtomType.Hybridization.SP1;
+                setHybridization(IAtomType.Hybridization.SP1);
                 break;
             case 2:
-                hybridization = IAtomType.Hybridization.SP2;
+                setHybridization(IAtomType.Hybridization.SP2);
                 break;
             case 3:
-                hybridization = IAtomType.Hybridization.SP3;
+                setHybridization(IAtomType.Hybridization.SP3);
                 break;
             case 4:
-                hybridization = IAtomType.Hybridization.SP3D1;
+                setHybridization(IAtomType.Hybridization.SP3D1);
                 break;
             case 5:
-                hybridization = IAtomType.Hybridization.SP3D2;
+                setHybridization(IAtomType.Hybridization.SP3D2);
                 break;
             case 6:
-                hybridization = IAtomType.Hybridization.SP3D3;
+                setHybridization(IAtomType.Hybridization.SP3D3);
                 break;
             case 7:
-                hybridization = IAtomType.Hybridization.SP3D4;
+                setHybridization(IAtomType.Hybridization.SP3D4);
                 break;
             case 8:
-                hybridization = IAtomType.Hybridization.SP3D5;
+                setHybridization(IAtomType.Hybridization.SP3D5);
                 break;
         }
     }
@@ -82,7 +80,7 @@ public HybridizationNumberAtom(int hybridizationNumber, IChemObjectBuilder build
      */
     @Override
     public boolean matches(IAtom atom) {
-        return hybridization == atom.getHybridization();
+        return getHybridization() == atom.getHybridization();
     }
 
     /*
@@ -91,7 +89,7 @@ public boolean matches(IAtom atom) {
      */
     @Override
     public String toString() {
-        return ("HybridizationNumberAtom(" + hybridization.toString() + ")");
+        return ("HybridizationNumberAtom(" + getHybridization() + ")");
     }
 
 }
diff --git a/tool/structgen/src/main/java/org/openscience/cdk/structgen/RandomGenerator.java b/tool/structgen/src/main/java/org/openscience/cdk/structgen/RandomGenerator.java
@@ -73,10 +73,9 @@ public IAtomContainer proposeStructure() {
         logger.debug("RandomGenerator->proposeStructure() Start");
         do {
             try {
-                trial = (IAtomContainer) molecule.clone();
+                trial = molecule.clone();
             } catch (CloneNotSupportedException e) {
-                logger.error("Could not clone IAtomContainer!" + e.getMessage());
-                trial = null;
+                throw new IllegalStateException("Could not clone IAtomContainer!" + e.getMessage());
             }
             mutate(trial);
             if (logger.isDebugEnabled()) {