Check for division by zero in some descriptors.

cdk · Feb 10, 2022 · ca84278 · ca84278
1 parent 5e41fcb
commit ca84278
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Showing 5 changed files with 11 additions and 3 deletions.
diff --git a/...n/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java b/...n/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java
@@ -190,6 +190,8 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
 
         atomicHardness = 2 * atomicHardness;
         atomicHardness = atomicHardness * 0.172;
+        if (atomicHardness == 0)
+            return getDummyDescriptorValue(new ArithmeticException("atomicHardness was 0 before division!"));
         atomicHardness = 1 / atomicHardness;
         return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                 atomicHardness), NAMES);

diff --git a/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java b/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java
@@ -339,8 +339,8 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
         }
 
         // relative descriptors
-        double rpcg = maxpcharge / totpcharge;
-        double rncg = maxncharge / totncharge;
+        double rpcg = totpcharge == 0d ? 0 : maxpcharge / totpcharge;
+        double rncg = totncharge == 0d ? 0 : maxncharge / totncharge;
         double rpcs = atomSurfaces[pidx] * rpcg;
         double rncs = atomSurfaces[nidx] * rncg;
 

diff --git a/...ain/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java b/...ain/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java
@@ -128,6 +128,8 @@ public DescriptorValue calculate(IAtomContainer container) {
                     nsp2++;
                 else if (atom.getHybridization() == Hybridization.SP3) nsp3++;
             }
+            if (nsp2+nsp3 == 0)
+                return getDummyDescriptorValue(new ArithmeticException("Cannot divide by 0"));
             double ratio = nsp3 / (double) (nsp2 + nsp3);
             return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
                     new DoubleResult(ratio), getDescriptorNames());

diff --git a/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java b/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java
@@ -415,6 +415,8 @@ public DescriptorValue calculate(IAtomContainer container) {
         sum = 0.0;
         for (int i = 0; i < 3; i++)
             sum += lambda[i];
+        if (sum == 0.0)
+            return getDummyDescriptorValue(new ArithmeticException("Lambda sum was 0, cannot divide by 0!"));
         for (int i = 0; i < 3; i++)
             k = (lambda[i] / sum) - (1.0 / 3.0);
         k = k / (4.0 / 3.0);

diff --git a/misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java b/misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java
@@ -159,13 +159,15 @@ private Point3d getCenterOfMass(Point3d[] p, double[] atwt) {
         double x = 0.;
         double y = 0.;
         double z = 0.;
-        double totalmass = 0.;
+        double totalmass = 0d;
         for (int i = 0; i < p.length; i++) {
             x += atwt[i] * p[i].x;
             y += atwt[i] * p[i].y;
             z += atwt[i] * p[i].z;
             totalmass += atwt[i];
         }
+        if (totalmass == 0d)
+            return new Point3d(0,0,0);
         return (new Point3d(x / totalmass, y / totalmass, z / totalmass));
     }