Merge pull request #321 from cdk/cleanup/AtomContainer

OK, it's a large patch, but I could not spot big things. It looks like an API change to me, which is OK in a developers branch. Better now than in stable. But I'm also going to have to trust you that you explored the impact (which I'm sure you did)... that said, if it shows up trouble, we can always revert.
cdk · May 14, 2017 · f2274f2 · f2274f2
2 parents 780ee9e + abf7bd7
commit f2274f2
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Showing 73 changed files with 2,401 additions and 2,180 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
diff --git a/base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java b/base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
@@ -180,25 +180,25 @@ public void setBonds(IBond[] bonds) {}
                                                                  public void setAtom(int number, IAtom atom) {}
 
                                                                  @Override
-                                                                 public IAtom getAtom(int number) {
+                                                                 public IAtom getAtom(int idx) {
                                                                      throw new UnsupportedOperationException(
                                                                              "not supported");
                                                                  }
 
                                                                  @Override
-                                                                 public IBond getBond(int number) {
+                                                                 public IBond getBond(int idx) {
                                                                      throw new UnsupportedOperationException(
                                                                              "not supported");
                                                                  }
 
                                                                  @Override
-                                                                 public ILonePair getLonePair(int number) {
+                                                                 public ILonePair getLonePair(int idx) {
                                                                      throw new UnsupportedOperationException(
                                                                              "not supported");
                                                                  }
 
                                                                  @Override
-                                                                 public ISingleElectron getSingleElectron(int number) {
+                                                                 public ISingleElectron getSingleElectron(int idx) {
                                                                      throw new UnsupportedOperationException(
                                                                              "not supported");
                                                                  }
@@ -375,7 +375,7 @@ public int getConnectedBondsCount(IAtom atom) {
                                                                  }
 
                                                                  @Override
-                                                                 public int getConnectedBondsCount(int atomnumber) {
+                                                                 public int getConnectedBondsCount(int idx) {
                                                                      return 0;
                                                                  }
 
@@ -444,12 +444,12 @@ public void remove(IAtomContainer atomContainer) {
                                                                  }
 
                                                                  @Override
-                                                                 public void removeAtom(int position) {
+                                                                 public void removeAtomOnly(int position) {
 
                                                                  }
 
                                                                  @Override
-                                                                 public void removeAtom(IAtom atom) {
+                                                                 public void removeAtomOnly(IAtom atom) {
 
                                                                  }
 
@@ -508,11 +508,17 @@ public void removeElectronContainer(
                                                                  }
 
                                                                  @Override
-                                                                 public void removeAtomAndConnectedElectronContainers(
+                                                                 public void removeAtom(
                                                                          IAtom atom) {
 
                                                                  }
 
+                                                                 @Override
+                                                                 @Deprecated
+                                                                 public void removeAtomAndConnectedElectronContainers(IAtom atom) {
+
+                                                                 }
+
                                                                  @Override
                                                                  public void removeAllElements() {
 

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java b/base/core/src/main/java/org/openscience/cdk/graph/PathTools.java
@@ -165,7 +165,7 @@ public static boolean depthFirstTargetSearch(IAtomContainer molecule, IAtom root
                 } else {
                     if (!depthFirstTargetSearch(molecule, nextAtom, target, path)) {
                         // we did not find the target
-                        path.removeAtom(nextAtom);
+                        path.removeAtomOnly(nextAtom);
                         path.removeBond(bond);
                     } else {
                         return true;

diff --git a/base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java b/base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java
@@ -202,7 +202,7 @@ public IAtomContainer getPath(IAtomContainer spt, IAtom atom1, IAtom atom2) thro
         PathTools.resetFlags(spt);
         path.addAtom(atom1);
         PathTools.depthFirstTargetSearch(spt, atom1, atom2, path);
-        if (path.getAtomCount() == 1) path.removeAtom(atom1); // no path found: remove initial atom
+        if (path.getAtomCount() == 1) path.removeAtomOnly(atom1); // no path found: remove initial atom
         return path;
     }
 

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java b/base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java
@@ -106,11 +106,17 @@ public IDoubleBondStereochemistry map(Map<IAtom, IAtom> atoms, Map<IBond, IBond>
         if (bonds == null) throw new IllegalArgumentException("null bond mapping provided");
 
         // map the double bond and the connected ligand bonds
-        IBond doubleBond = stereoBond != null ? bonds.get(stereoBond) : null;
+        IBond doubleBond = bonds.containsKey(stereoBond) ? bonds.get(stereoBond) : stereoBond;
         IBond[] connected = new IBond[ligandBonds.length];
 
         for (int i = 0; i < connected.length; i++) {
-            if (ligandBonds[i] != null) connected[i] = bonds.get(ligandBonds[i]);
+            if (ligandBonds[i] != null) {
+                IBond bond = bonds.get(ligandBonds[i]);
+                if (bond != null)
+                    connected[i] = bond;
+                else
+                    connected[i] = ligandBonds[i];
+            }
         }
 
         return new DoubleBondStereochemistry(doubleBond, connected, stereo);

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java b/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java
@@ -194,8 +194,15 @@ public boolean contains(IAtom atom) {
      */
     @Override
     public IStereoElement map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bonds) {
-        return new ExtendedTetrahedral(atoms.get(focus), new IAtom[]{atoms.get(peripherals[0]),
-                atoms.get(peripherals[1]), atoms.get(peripherals[2]), atoms.get(peripherals[3])}, winding);
+        IAtom focus = atoms.containsKey(this.focus) ? atoms.get(this.focus) : this.focus;
+        IAtom[] carriers = new IAtom[4];
+        for (int i = 0; i < 4; i++) {
+            IAtom newAtom = atoms.get(peripherals[i]);
+            carriers[i] = newAtom != null ? newAtom : peripherals[i];
+        }
+        return new ExtendedTetrahedral(focus,
+                                       carriers,
+                                       winding);
     }
 
     /**

diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java b/base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java
@@ -133,11 +133,17 @@ public ITetrahedralChirality map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bond
         if (atoms == null) throw new IllegalArgumentException("null atom mapping provided");
 
         // convert the chiral atom and it's ligands to their equivalent
-        IAtom chiral = chiralAtom != null ? atoms.get(chiralAtom) : null;
+        IAtom chiral = atoms.containsKey(chiralAtom) ? atoms.get(chiralAtom) : chiralAtom;
         IAtom[] ligands = new IAtom[ligandAtoms.length];
 
         for (int i = 0; i < ligands.length; i++) {
-            if (ligandAtoms[i] != null) ligands[i] = atoms.get(ligandAtoms[i]);
+            if (ligandAtoms[i] != null) {
+                IAtom atom = atoms.get(ligandAtoms[i]);
+                if (atom != null)
+                    ligands[i] = atom;
+                else
+                    ligands[i] = this.ligandAtoms[i];
+            }
         }
 
         // create a new tetrahedral instance with the mapped chiral atom and ligands