test_class.file: descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptorTest.java
test_class.identifier: MDEDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test
      public void testMDE1() throws ClassNotFoundException, CDKException, Exception {
          String filename = "data/mdl/mdeotest.sdf";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
          ChemFile content = (ChemFile) reader.read(new ChemFile());
          List cList = ChemFileManipulator.getAllAtomContainers(content);
          IAtomContainer ac = (IAtomContainer) cList.get(0);
  
          DoubleArrayResult result = (DoubleArrayResult) descriptor.calculate(ac).getValue();
  
          Assert.assertEquals(0.0000, result.get(MDEDescriptor.MDEO11), 0.0001);
          Assert.assertEquals(1.1547, result.get(MDEDescriptor.MDEO12), 0.0001);
          Assert.assertEquals(2.9416, result.get(MDEDescriptor.MDEO22), 0.0001);
      }
test_case.class_method_signature: MDEDescriptorTest.testMDE1()
test_case.full_signature: @Test public void testMDE1()
test_case.identifier: testMDE1
test_case.invocations: getResourceAsStream getClassLoader getClass read getAllAtomContainers get getValue calculate assertEquals get assertEquals get assertEquals get
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testMDE1()
focal_class.declarator: NAMES  = {"MDEC-11", "MDEC-12", "MDEC-13", "MDEC-14", "MDEC-22", "MDEC-23",
              "MDEC-24", "MDEC-33", "MDEC-34", "MDEC-44", "MDEO-11", "MDEO-12", "MDEO-22", "MDEN-11", "MDEN-12",
              "MDEN-13", "MDEN-22", "MDEN-23", "MDEN-33"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] NAMES  = {"MDEC-11", "MDEC-12", "MDEC-13", "MDEC-14", "MDEC-22", "MDEC-23",
              "MDEC-24", "MDEC-33", "MDEC-34", "MDEC-44", "MDEO-11", "MDEO-12", "MDEO-22", "MDEN-11", "MDEN-12",
              "MDEN-13", "MDEN-22", "MDEN-23", "MDEN-33"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: MDEC11 = 0
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC11 = 0;
focal_class.type: int
focal_class.var_name: MDEC11
focal_class.declarator: MDEC12 = 1
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC12 = 1;
focal_class.type: int
focal_class.var_name: MDEC12
focal_class.declarator: MDEC13 = 2
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC13 = 2;
focal_class.type: int
focal_class.var_name: MDEC13
focal_class.declarator: MDEC14 = 3
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC14 = 3;
focal_class.type: int
focal_class.var_name: MDEC14
focal_class.declarator: MDEC22 = 4
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC22 = 4;
focal_class.type: int
focal_class.var_name: MDEC22
focal_class.declarator: MDEC23 = 5
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC23 = 5;
focal_class.type: int
focal_class.var_name: MDEC23
focal_class.declarator: MDEC24 = 6
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC24 = 6;
focal_class.type: int
focal_class.var_name: MDEC24
focal_class.declarator: MDEC33 = 7
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC33 = 7;
focal_class.type: int
focal_class.var_name: MDEC33
focal_class.declarator: MDEC34 = 8
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC34 = 8;
focal_class.type: int
focal_class.var_name: MDEC34
focal_class.declarator: MDEC44 = 9
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEC44 = 9;
focal_class.type: int
focal_class.var_name: MDEC44
focal_class.declarator: MDEO11 = 10
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEO11 = 10;
focal_class.type: int
focal_class.var_name: MDEO11
focal_class.declarator: MDEO12 = 11
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEO12 = 11;
focal_class.type: int
focal_class.var_name: MDEO12
focal_class.declarator: MDEO22 = 12
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEO22 = 12;
focal_class.type: int
focal_class.var_name: MDEO22
focal_class.declarator: MDEN11 = 13
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN11 = 13;
focal_class.type: int
focal_class.var_name: MDEN11
focal_class.declarator: MDEN12 = 14
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN12 = 14;
focal_class.type: int
focal_class.var_name: MDEN12
focal_class.declarator: MDEN13 = 15
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN13 = 15;
focal_class.type: int
focal_class.var_name: MDEN13
focal_class.declarator: MDEN22 = 16
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN22 = 16;
focal_class.type: int
focal_class.var_name: MDEN22
focal_class.declarator: MDEN23 = 17
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN23 = 17;
focal_class.type: int
focal_class.var_name: MDEN23
focal_class.declarator: MDEN33 = 18
focal_class.modifier: public static final
focal_class.original_string: public static final int       MDEN33 = 18;
focal_class.type: int
focal_class.var_name: MDEN33
focal_class.declarator: C_1    = 1
focal_class.modifier: private static final
focal_class.original_string: private static final int      C_1    = 1;
focal_class.type: int
focal_class.var_name: C_1
focal_class.declarator: C_2    = 2
focal_class.modifier: private static final
focal_class.original_string: private static final int      C_2    = 2;
focal_class.type: int
focal_class.var_name: C_2
focal_class.declarator: C_3    = 3
focal_class.modifier: private static final
focal_class.original_string: private static final int      C_3    = 3;
focal_class.type: int
focal_class.var_name: C_3
focal_class.declarator: C_4    = 4
focal_class.modifier: private static final
focal_class.original_string: private static final int      C_4    = 4;
focal_class.type: int
focal_class.var_name: C_4
focal_class.declarator: O_1    = 1
focal_class.modifier: private static final
focal_class.original_string: private static final int      O_1    = 1;
focal_class.type: int
focal_class.var_name: O_1
focal_class.declarator: O_2    = 2
focal_class.modifier: private static final
focal_class.original_string: private static final int      O_2    = 2;
focal_class.type: int
focal_class.var_name: O_2
focal_class.declarator: N_1    = 1
focal_class.modifier: private static final
focal_class.original_string: private static final int      N_1    = 1;
focal_class.type: int
focal_class.var_name: N_1
focal_class.declarator: N_2    = 2
focal_class.modifier: private static final
focal_class.original_string: private static final int      N_2    = 2;
focal_class.type: int
focal_class.var_name: N_2
focal_class.declarator: N_3    = 3
focal_class.modifier: private static final
focal_class.original_string: private static final int      N_3    = 3;
focal_class.type: int
focal_class.var_name: N_3
focal_class.file: descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptor.java
focal_class.identifier: MDEDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: MDEDescriptor.MDEDescriptor()
focal_class.full_signature: public  MDEDescriptor()
focal_class.identifier: MDEDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDEDescriptor()
focal_class.class_method_signature: MDEDescriptor.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: MDEDescriptor.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: MDEDescriptor.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: MDEDescriptor.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.class_method_signature: MDEDescriptor.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: MDEDescriptor.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: MDEDescriptor.dedge(IAtomContainer atomContainer, int which)
focal_class.full_signature: private double dedge(IAtomContainer atomContainer, int which)
focal_class.identifier: dedge
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, int which)
focal_class.return: double
focal_class.signature: double dedge(IAtomContainer atomContainer, int which)
focal_class.class_method_signature: MDEDescriptor.evalATable(IAtomContainer atomContainer, int atomicNum)
focal_class.full_signature: private int[][] evalATable(IAtomContainer atomContainer, int atomicNum)
focal_class.identifier: evalATable
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, int atomicNum)
focal_class.return: int[][]
focal_class.signature: int[][] evalATable(IAtomContainer atomContainer, int atomicNum)
focal_class.class_method_signature: MDEDescriptor.evalCValue(int[][] distmat, int[][] codemat, int type1, int type2)
focal_class.full_signature: private double evalCValue(int[][] distmat, int[][] codemat, int type1, int type2)
focal_class.identifier: evalCValue
focal_class.modifiers: private
focal_class.parameters: (int[][] distmat, int[][] codemat, int type1, int type2)
focal_class.return: double
focal_class.signature: double evalCValue(int[][] distmat, int[][] codemat, int type1, int type2)
focal_class.class_method_signature: MDEDescriptor.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: MDEDescriptor.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.superclass: extends AbstractMolecularDescriptor
focal_method.body: @Override
      public DescriptorValue calculate(IAtomContainer container) {
  
          IAtomContainer local = AtomContainerManipulator.removeHydrogens(container);
  
          DoubleArrayResult retval = new DoubleArrayResult(19);
          for (int i = 0; i < 19; i++) {
              retval.add(dedge(local, i));
          }
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval,
                  getDescriptorNames());
      }
focal_method.class_method_signature: MDEDescriptor.calculate(IAtomContainer container)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtomContainer container)
focal_method.identifier: calculate
focal_method.invocations: removeHydrogens add dedge getSpecification getParameterNames getParameters getDescriptorNames
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainer container)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtomContainer container)