test_class.file: descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizerTest.java
test_class.identifier: SimpleAtomCanonicalizerTest
test_case.body: @Test
      public void testCanonicalizeAtoms() throws CDKException {
  
          IAtomContainer container = TestMoleculeFactory.makeAdenine();
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
  
          Collection<IAtom> atoms = new SimpleAtomCanonicalizer().canonicalizeAtoms(container);
  
          List<IAtom> mutable = new ArrayList<IAtom>(atoms);
          for (IAtom atom : mutable.subList(0, 5)) {
              Assert.assertEquals("expect sp2 carbons in first 4 entries", "C", atom.getSymbol());
              Assert.assertEquals("expect sp2 carbons in first 4 entries", IAtomType.Hybridization.SP2,
                      atom.getHybridization());
          }
          for (IAtom atom : mutable.subList(5, 8)) {
              Assert.assertEquals("expect sp2 nitrogen at indices 5-7", "N", atom.getSymbol());
              Assert.assertEquals("expect sp2 nitrogen at indices 5-7", IAtomType.Hybridization.SP2,
                      atom.getHybridization());
          }
  
          Assert.assertEquals("expect nitrogen at indices 8", "N", mutable.get(8).getSymbol());
          Assert.assertEquals("expect sp3 nitrogen at indices 8", IAtomType.Hybridization.SP3, mutable.get(8)
                  .getHybridization());
  
          Assert.assertEquals("expect nitrogen at indices 9", "N", mutable.get(9).getSymbol());
          Assert.assertEquals("expect sp3 nitrogen at indices 9", IAtomType.Hybridization.PLANAR3, mutable.get(9)
                  .getHybridization());
  
      }
test_case.class_method_signature: SimpleAtomCanonicalizerTest.testCanonicalizeAtoms()
test_case.full_signature: @Test public void testCanonicalizeAtoms()
test_case.identifier: testCanonicalizeAtoms
test_case.invocations: makeAdenine percieveAtomTypesAndConfigureAtoms canonicalizeAtoms subList assertEquals getSymbol assertEquals getHybridization subList assertEquals getSymbol assertEquals getHybridization assertEquals getSymbol get assertEquals getHybridization get assertEquals getSymbol get assertEquals getHybridization get
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCanonicalizeAtoms()
focal_class.file: descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizer.java
focal_class.identifier: SimpleAtomCanonicalizer
focal_class.class_method_signature: SimpleAtomCanonicalizer.canonicalizeAtoms(IAtomContainer container)
focal_class.full_signature: public Collection<IAtom> canonicalizeAtoms(IAtomContainer container)
focal_class.identifier: canonicalizeAtoms
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.return: Collection<IAtom>
focal_class.signature: Collection<IAtom> canonicalizeAtoms(IAtomContainer container)
focal_method.body: public Collection<IAtom> canonicalizeAtoms(IAtomContainer container) {
  
          List<IAtom> canonicalizedVertexList = new ArrayList<IAtom>();
          for (IAtom atom : container.atoms()) {
              canonicalizedVertexList.add(atom);
          }
          Collections.sort(canonicalizedVertexList, new SimpleAtomComparator());
          return canonicalizedVertexList;
      }
focal_method.class_method_signature: SimpleAtomCanonicalizer.canonicalizeAtoms(IAtomContainer container)
focal_method.full_signature: public Collection<IAtom> canonicalizeAtoms(IAtomContainer container)
focal_method.identifier: canonicalizeAtoms
focal_method.invocations: atoms add sort
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer container)
focal_method.return: Collection<IAtom>
focal_method.signature: Collection<IAtom> canonicalizeAtoms(IAtomContainer container)