test_class.declarator: hydrogenAdder
test_class.modifier: private
test_class.original_string: private CDKHydrogenAdder hydrogenAdder;
test_class.type: CDKHydrogenAdder
test_class.var_name: hydrogenAdder
test_class.file: descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java
test_class.identifier: ALOGPDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test
      public void testChloroButane() throws Exception {
          IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
          IAtom c1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "C");
          IAtom c2 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "C");
          IAtom c3 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "C");
          IAtom cl = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "Cl");
          mol.addAtom(c1);
          mol.addAtom(c2);
          mol.addAtom(c3);
          mol.addAtom(cl);
          mol.addBond(new Bond(c1, c2));
          mol.addBond(new Bond(c2, c3));
          mol.addBond(new Bond(c3, cl));
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
          CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance())
                          .addImplicitHydrogens(mol);
  
          DescriptorValue v = descriptor.calculate(mol);
          Assert.assertEquals(1.719, ((DoubleArrayResult) v.getValue()).get(0), 0.01);
          Assert.assertEquals(20.585, ((DoubleArrayResult) v.getValue()).get(2), 0.01);
      }
test_case.class_method_signature: ALOGPDescriptorTest.testChloroButane()
test_case.full_signature: @Test public void testChloroButane()
test_case.identifier: testChloroButane
test_case.invocations: newInstance getInstance newInstance getInstance newInstance getInstance newInstance getInstance newInstance getInstance addAtom addAtom addAtom addAtom addBond addBond addBond percieveAtomTypesAndConfigureAtoms addImplicitHydrogens getInstance getInstance calculate assertEquals get getValue assertEquals get getValue
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testChloroButane()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(ALOGPDescriptor.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(ALOGPDescriptor.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: atomContainer
focal_class.original_string: IAtomContainer atomContainer;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.declarator: rs
focal_class.original_string: IRingSet       rs;
focal_class.type: IRingSet
focal_class.var_name: rs
focal_class.declarator: fragment
focal_class.original_string: String[]       fragment;
focal_class.type: String[]
focal_class.var_name: fragment
focal_class.declarator: ap
focal_class.original_string: AtomicProperties ap;
focal_class.type: AtomicProperties
focal_class.var_name: ap
focal_class.declarator: frags = new int[121]
focal_class.modifier: public
focal_class.original_string: public int[] frags = new int[121];
focal_class.type: int[]
focal_class.var_name: frags
focal_class.declarator: alogpfrag
focal_class.modifier: public
focal_class.original_string: public int[] alogpfrag;
focal_class.type: int[]
focal_class.var_name: alogpfrag
focal_class.declarator: FRAGVAL = new double[121]
focal_class.modifier: final static
focal_class.original_string: final static double[] FRAGVAL = new double[121];
focal_class.type: double[]
focal_class.var_name: FRAGVAL
focal_class.declarator: REFRACVAL = new double[121]
focal_class.modifier: final static
focal_class.original_string: final static double[] REFRACVAL = new double[121];
focal_class.type: double[]
focal_class.var_name: REFRACVAL
focal_class.declarator: unassignedAtoms = ""
focal_class.original_string: String unassignedAtoms = "";
focal_class.type: String
focal_class.var_name: unassignedAtoms
focal_class.declarator: alogp  = 0.0
focal_class.original_string: double alogp  = 0.0;
focal_class.type: double
focal_class.var_name: alogp
focal_class.declarator: amr    = 0.0
focal_class.original_string: double amr    = 0.0;
focal_class.type: double
focal_class.var_name: amr
focal_class.declarator: alogp2 = 0.0
focal_class.original_string: double alogp2 = 0.0;
focal_class.type: double
focal_class.var_name: alogp2
focal_class.declarator: STRINGS = new String[]{"ALogP", "ALogp2", "AMR"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] STRINGS = new String[]{"ALogP", "ALogp2", "AMR"};
focal_class.type: String[]
focal_class.var_name: STRINGS
focal_class.file: descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
focal_class.identifier: ALOGPDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: ALOGPDescriptor.ALOGPDescriptor()
focal_class.full_signature: public  ALOGPDescriptor()
focal_class.identifier: ALOGPDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  ALOGPDescriptor()
focal_class.class_method_signature: ALOGPDescriptor.findUnassignedAtoms()
focal_class.full_signature: private void findUnassignedAtoms()
focal_class.identifier: findUnassignedAtoms
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void findUnassignedAtoms()
focal_class.class_method_signature: ALOGPDescriptor.calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_class.full_signature: private double[] calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_class.identifier: calculate
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_class.return: double[]
focal_class.signature: double[] calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_class.class_method_signature: ALOGPDescriptor.isHetero(IAtom atom)
focal_class.full_signature: private static boolean isHetero(IAtom atom)
focal_class.identifier: isHetero
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isHetero(IAtom atom)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup001_005(int i)
focal_class.full_signature: private void calcGroup001_005(int i)
focal_class.identifier: calcGroup001_005
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup001_005(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup002_006_007(int i)
focal_class.full_signature: private void calcGroup002_006_007(int i)
focal_class.identifier: calcGroup002_006_007
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup002_006_007(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup003_008_009_010(int i)
focal_class.full_signature: private void calcGroup003_008_009_010(int i)
focal_class.identifier: calcGroup003_008_009_010
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup003_008_009_010(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup004_011_to_014(int i)
focal_class.full_signature: private void calcGroup004_011_to_014(int i)
focal_class.identifier: calcGroup004_011_to_014
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup004_011_to_014(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup015(int i)
focal_class.full_signature: private void calcGroup015(int i)
focal_class.identifier: calcGroup015
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup015(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup016_018_036_037(int i)
focal_class.full_signature: private void calcGroup016_018_036_037(int i)
focal_class.identifier: calcGroup016_018_036_037
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup016_018_036_037(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup017_019_020_038_to_041(int i)
focal_class.full_signature: private void calcGroup017_019_020_038_to_041(int i)
focal_class.identifier: calcGroup017_019_020_038_to_041
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup017_019_020_038_to_041(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup021_to_023_040(int i)
focal_class.full_signature: private void calcGroup021_to_023_040(int i)
focal_class.identifier: calcGroup021_to_023_040
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup021_to_023_040(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup024_027_030_033_042(int i)
focal_class.full_signature: private void calcGroup024_027_030_033_042(int i)
focal_class.identifier: calcGroup024_027_030_033_042
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup024_027_030_033_042(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup025_026_028_029_031_032_034_035_043_044(int i)
focal_class.full_signature: private void calcGroup025_026_028_029_031_032_034_035_043_044(int i)
focal_class.identifier: calcGroup025_026_028_029_031_032_034_035_043_044
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup025_026_028_029_031_032_034_035_043_044(int i)
focal_class.class_method_signature: ALOGPDescriptor.isPyrroleLikeHetero(IAtom atom)
focal_class.full_signature: private boolean isPyrroleLikeHetero(IAtom atom)
focal_class.identifier: isPyrroleLikeHetero
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isPyrroleLikeHetero(IAtom atom)
focal_class.class_method_signature: ALOGPDescriptor.getHAtomType(IAtom atom, List connectedAtoms)
focal_class.full_signature: private int getHAtomType(IAtom atom, List connectedAtoms)
focal_class.identifier: getHAtomType
focal_class.modifiers: private
focal_class.parameters: (IAtom atom, List connectedAtoms)
focal_class.return: int
focal_class.signature: int getHAtomType(IAtom atom, List connectedAtoms)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup056_57(int i)
focal_class.full_signature: private void calcGroup056_57(int i)
focal_class.identifier: calcGroup056_57
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup056_57(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup058_61(int i)
focal_class.full_signature: private void calcGroup058_61(int i)
focal_class.identifier: calcGroup058_61
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup058_61(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup059_060_063(int i)
focal_class.full_signature: private void calcGroup059_060_063(int i)
focal_class.identifier: calcGroup059_060_063
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup059_060_063(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup066_to_079(int i)
focal_class.full_signature: private void calcGroup066_to_079(int i)
focal_class.identifier: calcGroup066_to_079
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup066_to_079(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup081_to_085(int i)
focal_class.full_signature: private void calcGroup081_to_085(int i)
focal_class.identifier: calcGroup081_to_085
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup081_to_085(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup086_to_090(int i)
focal_class.full_signature: private void calcGroup086_to_090(int i)
focal_class.identifier: calcGroup086_to_090
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup086_to_090(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup091_to_095(int i)
focal_class.full_signature: private void calcGroup091_to_095(int i)
focal_class.identifier: calcGroup091_to_095
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup091_to_095(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup096_to_100(int i)
focal_class.full_signature: private void calcGroup096_to_100(int i)
focal_class.identifier: calcGroup096_to_100
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup096_to_100(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup101_to_104(int i)
focal_class.full_signature: private void calcGroup101_to_104(int i)
focal_class.identifier: calcGroup101_to_104
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup101_to_104(int i)
focal_class.class_method_signature: ALOGPDescriptor.isBondedToHydrogenOnly(IAtom ai)
focal_class.full_signature: private boolean isBondedToHydrogenOnly(IAtom ai)
focal_class.identifier: isBondedToHydrogenOnly
focal_class.modifiers: private
focal_class.parameters: (IAtom ai)
focal_class.return: boolean
focal_class.signature: boolean isBondedToHydrogenOnly(IAtom ai)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup106(int i)
focal_class.full_signature: private void calcGroup106(int i)
focal_class.identifier: calcGroup106
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup106(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup107(int i)
focal_class.full_signature: private void calcGroup107(int i)
focal_class.identifier: calcGroup107
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup107(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup108(int i)
focal_class.full_signature: private void calcGroup108(int i)
focal_class.identifier: calcGroup108
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup108(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup109(int i)
focal_class.full_signature: private void calcGroup109(int i)
focal_class.identifier: calcGroup109
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup109(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup110(int i)
focal_class.full_signature: private void calcGroup110(int i)
focal_class.identifier: calcGroup110
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup110(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup111(int i)
focal_class.full_signature: private void calcGroup111(int i)
focal_class.identifier: calcGroup111
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup111(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup112(int i)
focal_class.full_signature: private void calcGroup112(int i)
focal_class.identifier: calcGroup112
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup112(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup115(int i)
focal_class.full_signature: private void calcGroup115(int i)
focal_class.identifier: calcGroup115
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup115(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup116_117_120(int i)
focal_class.full_signature: private void calcGroup116_117_120(int i)
focal_class.identifier: calcGroup116_117_120
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup116_117_120(int i)
focal_class.class_method_signature: ALOGPDescriptor.calcGroup118_119(int i)
focal_class.full_signature: private void calcGroup118_119(int i)
focal_class.identifier: calcGroup118_119
focal_class.modifiers: private
focal_class.parameters: (int i)
focal_class.return: void
focal_class.signature: void calcGroup118_119(int i)
focal_class.class_method_signature: ALOGPDescriptor.inSameAromaticRing(IAtomContainer atomContainer, IAtom atom1, IAtom atom2, IRingSet rs)
focal_class.full_signature: private boolean inSameAromaticRing(IAtomContainer atomContainer, IAtom atom1, IAtom atom2, IRingSet rs)
focal_class.identifier: inSameAromaticRing
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom1, IAtom atom2, IRingSet rs)
focal_class.return: boolean
focal_class.signature: boolean inSameAromaticRing(IAtomContainer atomContainer, IAtom atom1, IAtom atom2, IRingSet rs)
focal_class.class_method_signature: ALOGPDescriptor.calculate(IAtomContainer container)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtomContainer container)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer container)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtomContainer container)
focal_class.class_method_signature: ALOGPDescriptor.getDummyDescriptorValue(Exception e)
focal_class.full_signature: private DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.identifier: getDummyDescriptorValue
focal_class.modifiers: private
focal_class.parameters: (Exception e)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.class_method_signature: ALOGPDescriptor.getDescriptorResultType()
focal_class.full_signature: @Override public IDescriptorResult getDescriptorResultType()
focal_class.identifier: getDescriptorResultType
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IDescriptorResult
focal_class.signature: IDescriptorResult getDescriptorResultType()
focal_class.class_method_signature: ALOGPDescriptor.getSpecification()
focal_class.full_signature: @Override public DescriptorSpecification getSpecification()
focal_class.identifier: getSpecification
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: DescriptorSpecification
focal_class.signature: DescriptorSpecification getSpecification()
focal_class.class_method_signature: ALOGPDescriptor.getParameterNames()
focal_class.full_signature: @Override public String[] getParameterNames()
focal_class.identifier: getParameterNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getParameterNames()
focal_class.class_method_signature: ALOGPDescriptor.getParameterType(String name)
focal_class.full_signature: @Override public Object getParameterType(String name)
focal_class.identifier: getParameterType
focal_class.modifiers: @Override public
focal_class.parameters: (String name)
focal_class.return: Object
focal_class.signature: Object getParameterType(String name)
focal_class.class_method_signature: ALOGPDescriptor.setParameters(Object[] params)
focal_class.full_signature: @Override public void setParameters(Object[] params)
focal_class.identifier: setParameters
focal_class.modifiers: @Override public
focal_class.parameters: (Object[] params)
focal_class.return: void
focal_class.signature: void setParameters(Object[] params)
focal_class.class_method_signature: ALOGPDescriptor.getParameters()
focal_class.full_signature: @Override public Object[] getParameters()
focal_class.identifier: getParameters
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Object[]
focal_class.signature: Object[] getParameters()
focal_class.class_method_signature: ALOGPDescriptor.getDescriptorNames()
focal_class.full_signature: @Override public String[] getDescriptorNames()
focal_class.identifier: getDescriptorNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getDescriptorNames()
focal_class.superclass: extends AbstractMolecularDescriptor
focal_method.body: private double[] calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs) throws CDKException {
          this.atomContainer = atomContainer;
          this.fragment = fragment;
          this.rs = rs;
          alogp = 0.0;
          amr = 0.0;
          alogp2 = 0.0;
  
          alogpfrag = new int[atomContainer.getAtomCount()];
  
          for (int i = 1; i <= 120; i++) {
              frags[i] = 0;
          }
  
          for (int i = 0; i < atomContainer.getAtomCount(); i++) {
              // alogpfrag[i] = 0; // not needed (new array initalized above)
              try {
                  if (fragment[i] != null) {
                      calcGroup001_005(i);
                      calcGroup002_006_007(i);
                      calcGroup003_008_009_010(i);
                      calcGroup004_011_to_014(i);
                      calcGroup015(i);
                      calcGroup016_018_036_037(i);
                      calcGroup017_019_020_038_to_041(i);
                      calcGroup021_to_023_040(i);
                      calcGroup024_027_030_033_042(i);
                      calcGroup025_026_028_029_031_032_034_035_043_044(i);
                      calcGroup056_57(i);
                      calcGroup058_61(i);
                      calcGroup059_060_063(i);
                      calcGroup066_to_079(i);
                      calcGroup081_to_085(i);
                      calcGroup086_to_090(i);
                      calcGroup091_to_095(i);
                      calcGroup096_to_100(i);
                      calcGroup101_to_104(i);
                      calcGroup106(i);
                      calcGroup107(i);
                      calcGroup108(i);
                      calcGroup109(i);
                      calcGroup110(i);
                      calcGroup111(i);
                      calcGroup112(i);
                      calcGroup115(i);
                      calcGroup116_117_120(i);
                      calcGroup118_119(i);
                  }
              } catch (Exception e) {
                  throw new CDKException(e.toString(), e);
              }
          } // end i atom loop
  
          logger.debug("\nFound fragments and frequencies ");
  
          for (int i = 1; i <= 120; i++) {
              alogp += FRAGVAL[i] * frags[i];
              amr += REFRACVAL[i] * frags[i];
              if (frags[i] > 0) {
                  logger.debug("frag " + i + "  --> " + frags[i]);
              }
          }
          alogp2 = alogp * alogp;
  
          this.findUnassignedAtoms();
  
          return new double[]{alogp, alogp2, amr};
  
      }
focal_method.class_method_signature: ALOGPDescriptor.calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_method.full_signature: private double[] calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_method.identifier: calculate
focal_method.invocations: getAtomCount getAtomCount calcGroup001_005 calcGroup002_006_007 calcGroup003_008_009_010 calcGroup004_011_to_014 calcGroup015 calcGroup016_018_036_037 calcGroup017_019_020_038_to_041 calcGroup021_to_023_040 calcGroup024_027_030_033_042 calcGroup025_026_028_029_031_032_034_035_043_044 calcGroup056_57 calcGroup058_61 calcGroup059_060_063 calcGroup066_to_079 calcGroup081_to_085 calcGroup086_to_090 calcGroup091_to_095 calcGroup096_to_100 calcGroup101_to_104 calcGroup106 calcGroup107 calcGroup108 calcGroup109 calcGroup110 calcGroup111 calcGroup112 calcGroup115 calcGroup116_117_120 calcGroup118_119 toString debug debug findUnassignedAtoms
focal_method.modifiers: private
focal_method.parameters: (IAtomContainer atomContainer, String[] fragment, IRingSet rs)
focal_method.return: double[]
focal_method.signature: double[] calculate(IAtomContainer atomContainer, String[] fragment, IRingSet rs)