For fun, a chiral center finder, and a couple of tests

src/main/java/signature/chemistry/ChiralCenterFinder.java

@@ -0,0 +1,37 @@
+package signature.chemistry;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class ChiralCenterFinder {
+
+    public static List<Integer> findTetrahedralChiralCenters(Molecule molecule) {
+        List<Integer> chiralCenterIndices = new ArrayList<Integer>();
+        MoleculeSignature molSig = new MoleculeSignature(molecule);
+        List<String> signatureStrings = molSig.getVertexSignatureStrings();
+        for (int i = 0; i < molecule.getAtomCount(); i++) {
+            int[] connected = molecule.getConnected(i);
+            if (connected.length < 4) {
+                continue;
+            } else {
+                String s0 = signatureStrings.get(connected[0]);
+                String s1 = signatureStrings.get(connected[1]);
+                String s2 = signatureStrings.get(connected[2]);
+                String s3 = signatureStrings.get(connected[3]);
+                if (s0.equals(s1) 
+                 || s0.equals(s2) 
+                 || s0.equals(s3)
+                 || s1.equals(s2)
+                 || s1.equals(s3)
+                 || s2.equals(s3)) {
+                    continue;
+                } else {
+                    chiralCenterIndices.add(i);
+                }
+            }
+        }
+
+        return chiralCenterIndices;
+    }
+
+}

src/main/java/signature/chemistry/Molecule.java

@@ -239,10 +239,22 @@ public void addAtom(int i, String symbol) {
         this.atoms.add(new Atom(i, symbol));
     }
 
+    public void addMultipleAtoms(int count, String symbol) {
+        for (int i = 0; i < count; i++) {
+            addAtom(symbol);
+        }
+    }
+
     public void addSingleBond(int atomNumberA, int atomNumberB) {
         this.addBond(atomNumberA, atomNumberB, 1);
     }
 
+    public void addMultipleSingleBonds(int i, int...js) {
+        for (int j : js) {
+            addSingleBond(i, j);
+        }
+    }
+
     public void addBond(int atomNumberA, int atomNumberB, int order) {
         Atom a = this.atoms.get(atomNumberA);
         Atom b = this.atoms.get(atomNumberB);

src/test/java/signature/chemistry/ChiralityTest.java

@@ -0,0 +1,78 @@
+package signature.chemistry;
+
+import java.util.List;
+
+import junit.framework.Assert;
+
+import org.junit.Test;
+
+import signature.SymmetryClass;
+
+public class ChiralityTest {
+
+    @Test
+    public void spiranTest() {
+        Molecule mol = new Molecule();
+        mol.addAtom("N");
+        mol.addMultipleAtoms(12, "C");
+        mol.addMultipleAtoms(24, "H");
+        mol.addMultipleSingleBonds(0, 1, 4, 5, 8);  // central N
+        mol.addMultipleSingleBonds(1, 2, 33, 34);   // ring 1 - CA
+        mol.addMultipleSingleBonds(2, 3, 11, 15);   // ring 1 - CB
+        mol.addMultipleSingleBonds(3, 4, 12, 16);   // ring 1 - CB
+        mol.addMultipleSingleBonds(4, 35, 36);      // ring 1 - CA
+        mol.addMultipleSingleBonds(5, 6, 29, 30);   // ring 2 - CA
+        mol.addMultipleSingleBonds(6, 7, 9, 13);    // ring 2 - CB
+        mol.addMultipleSingleBonds(7, 8, 10, 14);   // ring 2 - CB
+        mol.addMultipleSingleBonds(8, 31, 32);      // ring 2 - CA
+        mol.addMultipleSingleBonds(9, 17, 18, 19);  // CH3 A
+        mol.addMultipleSingleBonds(10, 20, 21, 22); // CH3 B
+        mol.addMultipleSingleBonds(11, 23, 24, 25); // CH3 C
+        mol.addMultipleSingleBonds(12, 26, 27, 28); // CH3 D
+
+        // 7 symmetry classes - central N, CA, CB, CH3-C, HA, HB, CH3-H 
+        MoleculeSignature molSig = new MoleculeSignature(mol);
+        List<SymmetryClass> symmetryClasses = molSig.getSymmetryClasses();
+        Assert.assertEquals(7, symmetryClasses.size());
+
+        List<Integer> tetraChiralCenters = 
+            ChiralCenterFinder.findTetrahedralChiralCenters(mol);
+        Assert.assertEquals(4, tetraChiralCenters.size());
+        Assert.assertEquals(2, (int)tetraChiralCenters.get(0));
+        Assert.assertEquals(3, (int)tetraChiralCenters.get(1));
+        Assert.assertEquals(6, (int)tetraChiralCenters.get(2));
+        Assert.assertEquals(7, (int)tetraChiralCenters.get(3));
+    }
+
+    @Test
+    public void dichlorocyclopropaneTest() {
+        Molecule mol = new Molecule();
+        mol.addAtom("C");
+        mol.addAtom("C");
+        mol.addAtom("C");
+        mol.addAtom("Cl");
+        mol.addAtom("Cl");
+        mol.addAtom("H");
+        mol.addAtom("H");
+        mol.addAtom("H");
+        mol.addAtom("H");
+        mol.addMultipleSingleBonds(0, 1, 2, 3, 5);
+        mol.addMultipleSingleBonds(1, 2, 4, 6);
+        mol.addMultipleSingleBonds(2, 7, 8);
+
+        // 5 symmetry classes - the non-chiral carbon, its hydrogens, the chiral
+        // carbons, thier hydrogens, and the chlorines.
+        MoleculeSignature molSig = new MoleculeSignature(mol);
+        List<SymmetryClass> symmetryClasses = molSig.getSymmetryClasses(); 
+//        System.out.println(symmetryClasses);
+        Assert.assertEquals(5, symmetryClasses.size());
+
+        // only two possible chiral centers
+        List<Integer> tetraChiralCenters = 
+            ChiralCenterFinder.findTetrahedralChiralCenters(mol);
+        Assert.assertEquals(2, tetraChiralCenters.size());
+        Assert.assertEquals(0, (int)tetraChiralCenters.get(0));
+        Assert.assertEquals(1, (int)tetraChiralCenters.get(1));
+    }
+
+}