Revert "Add a new method atom::getBond(), that allows testing as to w…

…hether two atoms are connected outside of the AtomContainer." This reverts commit c05819d.
cdk · Feb 18, 2018 · 505a588 · 505a588
1 parent e67ed6a
commit 505a588
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Showing 8 changed files with 18 additions and 108 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/AtomRef.java b/base/core/src/main/java/org/openscience/cdk/AtomRef.java
@@ -402,14 +402,6 @@ public int getBondCount() {
         return atom.getBondCount();
     }
 
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public IBond getBond(IAtom atom) {
-        return this.atom.getBond(atom);
-    }
-
     /**
      * {@inheritDoc}
      */

diff --git a/base/data/src/main/java/org/openscience/cdk/Atom.java b/base/data/src/main/java/org/openscience/cdk/Atom.java
@@ -269,14 +269,6 @@ public int getBondCount() {
         throw new UnsupportedOperationException();
     }
 
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public IBond getBond(IAtom atom) {
-        throw new UnsupportedOperationException();
-    }
-
     /**
      *  Sets the partial charge of this atom.
      *

diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainer2.java b/base/data/src/main/java/org/openscience/cdk/AtomContainer2.java
@@ -621,8 +621,15 @@ public IElectronContainer getElectronContainer(int number) {
      */
     @Override
     public IBond getBond(IAtom beg, IAtom end) {
-        final AtomRef begref = getAtomRefUnsafe(beg);
-        return begref != null ? begref.getBond(end) : null;
+        AtomRef begref = getAtomRefUnsafe(beg);
+        AtomRef endref = getAtomRefUnsafe(end);
+        if (begref != null && endref != null) {
+            for (IBond bond : begref.bonds()) {
+                if (bond.getOther(begref) == endref)
+                    return bond;
+            }
+        }
+        return null;
     }
 
     /**
@@ -1653,16 +1660,6 @@ public final Iterable<IBond> bonds() {
             return bonds;
         }
 
-        @Override
-        public IBond getBond(IAtom atom) {
-            for (IBond bond : bonds) {
-                if (bond.getBegin().equals(atom) ||
-                    bond.getEnd().equals(atom))
-                    return bond;
-            }
-            return null;
-        }
-
         @Override
         public int hashCode() {
             return deref().hashCode();

diff --git a/base/data/src/test/java/org/openscience/cdk/AtomContainer2Test.java b/base/data/src/test/java/org/openscience/cdk/AtomContainer2Test.java
@@ -33,10 +33,6 @@
 import org.openscience.cdk.interfaces.ILonePair;
 import org.openscience.cdk.interfaces.ITestObjectBuilder;
 
-import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertThat;
-
 /**
  * Checks the functionality of the AtomContainer.
  *
@@ -115,25 +111,4 @@ public void testAtomContainer_IAtomContainer() {
         Assert.assertEquals(4, container.getAtomCount());
         Assert.assertEquals(3, container.getBondCount());
     }
-
-    @Test
-    public void testAtomGetBond() {
-        IAtomContainer mol = (IAtomContainer) newChemObject();
-        IAtom          a1 = mol.getBuilder().newAtom();
-        IAtom          a2 = mol.getBuilder().newAtom();
-        IAtom          a3 = mol.getBuilder().newAtom();
-        a1.setSymbol("CH3");
-        a2.setSymbol("CH2");
-        a3.setSymbol("OH");
-        mol.addAtom(a1);
-        mol.addAtom(a2);
-        mol.addAtom(a3);
-        mol.addBond(0, 1, IBond.Order.SINGLE);
-        mol.addBond(1, 2, IBond.Order.SINGLE);
-        assertThat(mol.getBond(0),
-                   is(mol.getAtom(0).getBond(mol.getAtom(1))));
-        assertThat(mol.getBond(1),
-                   is(mol.getAtom(1).getBond(mol.getAtom(2))));
-        assertNull(mol.getAtom(0).getBond(mol.getAtom(2)));
-    }
 }
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java
@@ -204,21 +204,8 @@ public interface IAtom extends IAtomType {
      */
     Iterable<IBond> bonds();
 
-    /**
-     * Get the number of explicit bonds connected to this atom.
-     * @return the total bond count
-     */
     int getBondCount();
 
-    /**
-     * Returns the bond connecting 'this' atom to the provided atom. If the
-     * atoms are not bonded, null is return
-     * @param atom the other atom
-     * @return the bond connecting the atoms
-     * @throws UnsupportedOperationException thrown if the bonds are not known
-     */
-    IBond getBond(IAtom atom);
-
     /**
      * Access whether this atom has been marked as aromatic. The default
      * value is false and you must explicitly perceive aromaticity with

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java b/base/silent/src/main/java/org/openscience/cdk/silent/Atom.java
@@ -271,14 +271,6 @@ public Iterable<IBond> bonds() {
         throw new UnsupportedOperationException();
     }
 
-    /**
-     * {@inheritDoc}
-     */
-    @Override
-    public IBond getBond(IAtom atom) {
-        throw new UnsupportedOperationException();
-    }
-
     /**
      *  Sets the partial charge of this atom.
      *

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer2.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer2.java
@@ -609,8 +609,15 @@ public IElectronContainer getElectronContainer(int number) {
      */
     @Override
     public IBond getBond(IAtom beg, IAtom end) {
-        final AtomRef begref = getAtomRefUnsafe(beg);
-        return begref != null ? begref.getBond(end) : null;
+        AtomRef begref = getAtomRefUnsafe(beg);
+        AtomRef endref = getAtomRefUnsafe(end);
+        if (begref != null && endref != null) {
+            for (IBond bond : begref.bonds()) {
+                if (bond.getOther(begref) == endref)
+                    return bond;
+            }
+        }
+        return null;
     }
 
     /**
@@ -1615,16 +1622,6 @@ public final Iterable<IBond> bonds() {
             return bonds;
         }
 
-        @Override
-        public IBond getBond(IAtom atom) {
-            for (IBond bond : bonds) {
-                if (bond.getBegin().equals(atom) ||
-                    bond.getEnd().equals(atom))
-                    return bond;
-            }
-            return null;
-        }
-
         @Override
         public int hashCode() {
             return deref().hashCode();

diff --git a/base/silent/src/test/java/org/openscience/cdk/silent/AtomContainer2Test.java b/base/silent/src/test/java/org/openscience/cdk/silent/AtomContainer2Test.java
@@ -35,7 +35,6 @@
 import org.openscience.cdk.interfaces.ITestObjectBuilder;
 
 import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertThat;
 
 /**
@@ -215,25 +214,4 @@ public void testAtomAdjacencyOnClone() throws CloneNotSupportedException {
         assertThat(org.getAtom(0).getBondCount(), is(1));
         assertThat(org.getAtom(1).getBondCount(), is(1));
     }
-
-    @Test
-    public void testAtomGetBond() {
-        IAtomContainer mol = (IAtomContainer) newChemObject();
-        IAtom          a1 = mol.getBuilder().newAtom();
-        IAtom          a2 = mol.getBuilder().newAtom();
-        IAtom          a3 = mol.getBuilder().newAtom();
-        a1.setSymbol("CH3");
-        a2.setSymbol("CH2");
-        a3.setSymbol("OH");
-        mol.addAtom(a1);
-        mol.addAtom(a2);
-        mol.addAtom(a3);
-        mol.addBond(0, 1, IBond.Order.SINGLE);
-        mol.addBond(1, 2, IBond.Order.SINGLE);
-        assertThat(mol.getBond(0),
-                   is(mol.getAtom(0).getBond(mol.getAtom(1))));
-        assertThat(mol.getBond(1),
-                   is(mol.getAtom(1).getBond(mol.getAtom(2))));
-        assertNull(mol.getAtom(0).getBond(mol.getAtom(2)));
-    }
 }