test_class.declarator: logger = LoggingToolFactory.createLoggingTool(SSSRFinderTest.class)
test_class.modifier: private final
test_class.original_string: private final ILoggingTool logger = LoggingToolFactory.createLoggingTool(SSSRFinderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: legacy/src/test/java/org/openscience/cdk/ringsearch/SSSRFinderTest.java
test_class.identifier: SSSRFinderTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testProblem1() throws Exception {
          IAtomContainer molecule = null;
          IRing ring = null;
          String filename = "data/mdl/figueras-test-sep3D.mol";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
          molecule = (IAtomContainer) reader.read((IChemObject) new AtomContainer());
          reader.close();
          logger.debug("Testing " + filename);
  
          IRingSet ringSet = new SSSRFinder(molecule).findSSSR();
          logger.debug("Found ring set of size: " + ringSet.getAtomContainerCount());
          Assert.assertEquals(3, ringSet.getAtomContainerCount());
          for (int f = 0; f < ringSet.getAtomContainerCount(); f++) {
              ring = (IRing) ringSet.getAtomContainer(f);
              logger.debug("ring: " + toString(ring, molecule));
          }
      }
test_case.class_method_signature: SSSRFinderTest.testProblem1()
test_case.full_signature: @Test public void testProblem1()
test_case.identifier: testProblem1
test_case.invocations: getResourceAsStream getClassLoader getClass read close debug findSSSR debug getAtomContainerCount assertEquals getAtomContainerCount getAtomContainerCount getAtomContainer debug toString
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testProblem1()
focal_class.declarator: atomContainer
focal_class.modifier: private
focal_class.original_string: private IAtomContainer atomContainer;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.declarator: cycleBasis
focal_class.modifier: private
focal_class.original_string: private CycleBasis     cycleBasis;
focal_class.type: CycleBasis
focal_class.var_name: cycleBasis
focal_class.file: legacy/src/main/java/org/openscience/cdk/ringsearch/SSSRFinder.java
focal_class.identifier: SSSRFinder
focal_class.class_method_signature: SSSRFinder.SSSRFinder(IAtomContainer container)
focal_class.full_signature: public  SSSRFinder(IAtomContainer container)
focal_class.identifier: SSSRFinder
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.signature:  SSSRFinder(IAtomContainer container)
focal_class.class_method_signature: SSSRFinder.findSSSR()
focal_class.full_signature: public IRingSet findSSSR()
focal_class.identifier: findSSSR
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IRingSet
focal_class.signature: IRingSet findSSSR()
focal_class.class_method_signature: SSSRFinder.findEssentialRings()
focal_class.full_signature: public IRingSet findEssentialRings()
focal_class.identifier: findEssentialRings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IRingSet
focal_class.signature: IRingSet findEssentialRings()
focal_class.class_method_signature: SSSRFinder.findRelevantRings()
focal_class.full_signature: public IRingSet findRelevantRings()
focal_class.identifier: findRelevantRings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IRingSet
focal_class.signature: IRingSet findRelevantRings()
focal_class.class_method_signature: SSSRFinder.findEquivalenceClasses()
focal_class.full_signature: public List findEquivalenceClasses()
focal_class.identifier: findEquivalenceClasses
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List
focal_class.signature: List findEquivalenceClasses()
focal_class.class_method_signature: SSSRFinder.getSSSRWeightVector()
focal_class.full_signature: public int[] getSSSRWeightVector()
focal_class.identifier: getSSSRWeightVector
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int[]
focal_class.signature: int[] getSSSRWeightVector()
focal_class.class_method_signature: SSSRFinder.getEquivalenceClassesSizeVector()
focal_class.full_signature: public int[] getEquivalenceClassesSizeVector()
focal_class.identifier: getEquivalenceClassesSizeVector
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int[]
focal_class.signature: int[] getEquivalenceClassesSizeVector()
focal_class.class_method_signature: SSSRFinder.cycleBasis()
focal_class.full_signature: private CycleBasis cycleBasis()
focal_class.identifier: cycleBasis
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: CycleBasis
focal_class.signature: CycleBasis cycleBasis()
focal_class.class_method_signature: SSSRFinder.toRingSet(IAtomContainer container, Collection cycles)
focal_class.full_signature: private static IRingSet toRingSet(IAtomContainer container, Collection cycles)
focal_class.identifier: toRingSet
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, Collection cycles)
focal_class.return: IRingSet
focal_class.signature: IRingSet toRingSet(IAtomContainer container, Collection cycles)
focal_method.body: public IRingSet findSSSR() {
          if (atomContainer == null) {
              return null;
          }
          IRingSet ringSet = toRingSet(atomContainer, cycleBasis().cycles());
          //		atomContainer.setProperty(CDKConstants.SMALLEST_RINGS, ringSet);
          return ringSet;
  
      }
focal_method.class_method_signature: SSSRFinder.findSSSR()
focal_method.full_signature: public IRingSet findSSSR()
focal_method.identifier: findSSSR
focal_method.invocations: toRingSet cycles cycleBasis
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: IRingSet
focal_method.signature: IRingSet findSSSR()