Descriptors that need a clone to avoid modifying the input.

cdk · Jan 3, 2018 · 3e2beea · 3e2beea
1 parent 7ea64b4
commit 3e2beea
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Showing 7 changed files with 21 additions and 2 deletions.
diff --git a/descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractMolecularDescriptor.java b/descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractMolecularDescriptor.java
@@ -23,6 +23,8 @@
 
 package org.openscience.cdk.qsar;
 
+import org.openscience.cdk.interfaces.IAtomContainer;
+
 /**
  * A super class for molecular descriptors allowing default implementations for
  * interface methods.
@@ -33,4 +35,12 @@
  */
 public abstract class AbstractMolecularDescriptor extends AbstractDescriptor implements IMolecularDescriptor {
 
+    protected static IAtomContainer clone(IAtomContainer mol) {
+        try {
+            return mol.clone();
+        } catch (CloneNotSupportedException e) {
+            throw new IllegalStateException("Could not clone AtomContainer!");
+        }
+    }
+
 }
diff --git a/.../main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java b/.../main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java
@@ -114,6 +114,8 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
             throw new IllegalStateException("descriptor is not initalised, invoke 'initalise' first");
         }
 
+        atomContainer = clone(atomContainer); // don't mod original
+
         // do aromaticity detection
         if (this.checkAromaticity) {
             try {

diff --git a/...c/main/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java b/...c/main/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java
@@ -97,6 +97,8 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
             throw new IllegalStateException("descriptor is not initalised, invoke 'initalise' first");
         }
 
+        atomContainer = clone(atomContainer);
+
         try {
             int count = 0;
             for (SMARTSQueryTool tool : tools) {

diff --git a/...molecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptor.java b/...molecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptor.java
@@ -65,6 +65,9 @@ public FMFDescriptor() {}
      */
     @Override
     public DescriptorValue calculate(IAtomContainer container) {
+
+        container = clone(container); // don't mod original
+
         MurckoFragmenter fragmenter = new MurckoFragmenter(true, 3);
         DoubleResult result;
         try {

diff --git a/...in/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java b/...in/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
@@ -140,6 +140,7 @@ public String[] getDescriptorNames() {
      */
     @Override
     public DescriptorValue calculate(IAtomContainer ac) {
+        ac = clone(ac); // don't mod original
         int rotatableBondsCount = 0;
         int degree0;
         int degree1;

diff --git a/...ar/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java b/...ar/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java
@@ -142,7 +142,7 @@ public String[] getDescriptorNames() {
      */
     @Override
     public DescriptorValue calculate(IAtomContainer mol) {
-
+        mol = clone(mol); // don't mod original
         int lipinskifailures = 0;
 
         IMolecularDescriptor xlogP = new XLogPDescriptor();

diff --git a/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VABCDescriptor.java b/...olecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VABCDescriptor.java
@@ -85,7 +85,8 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
     public DescriptorValue calculate(IAtomContainer atomContainer) {
         double volume;
         try {
-            volume = VABCVolume.calculate(atomContainer);
+            // clone: don't mod original
+            volume = VABCVolume.calculate(clone(atomContainer));
         } catch (CDKException exception) {
             return getDummyDescriptorValue(exception);
         }