test_class.declarator: descriptor
test_class.modifier: private static
test_class.original_string: private static IMolecularDescriptor descriptor;
test_class.type: IMolecularDescriptor
test_class.var_name: descriptor
test_class.file: descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptorTest.java
test_class.identifier: TaeAminoAcidDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test
      public void testTaeAminoAcidDescriptor() throws ClassNotFoundException, CDKException, Exception {
          IBioPolymer pepseq = ProteinBuilderTool.createProtein("ACDEFGH", SilentChemObjectBuilder.getInstance());
          DescriptorValue result = descriptor.calculate(pepseq);
  
          DoubleArrayResult dar = (DoubleArrayResult) result.getValue();
          Assert.assertEquals(147, dar.length());
      }
test_case.class_method_signature: TaeAminoAcidDescriptorTest.testTaeAminoAcidDescriptor()
test_case.full_signature: @Test public void testTaeAminoAcidDescriptor()
test_case.identifier: testTaeAminoAcidDescriptor
test_case.invocations: createProtein getInstance calculate getValue assertEquals length
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testTaeAminoAcidDescriptor()
focal_class.declarator: logger    = LoggingToolFactory.createLoggingTool(TaeAminoAcidDescriptor.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool          logger    = LoggingToolFactory.createLoggingTool(TaeAminoAcidDescriptor.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: taeParams = new HashMap<String, Double[]>()
focal_class.modifier: private
focal_class.original_string: private        Map<String, Double[]> taeParams = new HashMap<String, Double[]>();
focal_class.type: Map<String, Double[]>
focal_class.var_name: taeParams
focal_class.declarator: ndesc     = 147
focal_class.modifier: private
focal_class.original_string: private        int                   ndesc     = 147;
focal_class.type: int
focal_class.var_name: ndesc
focal_class.declarator: nametrans = new HashMap<String, String>()
focal_class.modifier: private
focal_class.original_string: private Map<String, String> nametrans = new HashMap<String, String>();
focal_class.type: Map<String, String>
focal_class.var_name: nametrans
focal_class.file: descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java
focal_class.identifier: TaeAminoAcidDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: TaeAminoAcidDescriptor.getMonomers(IBioPolymer iBioPolymer)
focal_class.full_signature: private List<IMonomer> getMonomers(IBioPolymer iBioPolymer)
focal_class.identifier: getMonomers
focal_class.modifiers: private
focal_class.parameters: (IBioPolymer iBioPolymer)
focal_class.return: List<IMonomer>
focal_class.signature: List<IMonomer> getMonomers(IBioPolymer iBioPolymer)
focal_class.class_method_signature: TaeAminoAcidDescriptor.loadTAEParams()
focal_class.full_signature: private void loadTAEParams()
focal_class.identifier: loadTAEParams
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void loadTAEParams()
focal_class.class_method_signature: TaeAminoAcidDescriptor.TaeAminoAcidDescriptor()
focal_class.full_signature: public  TaeAminoAcidDescriptor()
focal_class.identifier: TaeAminoAcidDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  TaeAminoAcidDescriptor()
focal_class.class_method_signature: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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: TaeAminoAcidDescriptor.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.superclass: extends AbstractMolecularDescriptor
focal_method.body: public TaeAminoAcidDescriptor() {
          nametrans.put("a", "ala");
          nametrans.put("c", "cys");
          nametrans.put("d", "asp");
          nametrans.put("e", "glu");
          nametrans.put("f", "phe");
          nametrans.put("g", "gly");
          nametrans.put("h", "his");
          nametrans.put("i", "ile");
          nametrans.put("k", "lys");
          nametrans.put("l", "leu");
          nametrans.put("m", "met");
          nametrans.put("n", "asn");
          nametrans.put("p", "pro");
          nametrans.put("q", "gln");
          nametrans.put("r", "arg");
          nametrans.put("s", "ser");
          nametrans.put("t", "thr");
          nametrans.put("v", "val");
          nametrans.put("w", "trp");
          nametrans.put("y", "tyr");
  
          loadTAEParams();
      }
focal_method.class_method_signature: TaeAminoAcidDescriptor.TaeAminoAcidDescriptor()
focal_method.full_signature: public  TaeAminoAcidDescriptor()
focal_method.identifier: TaeAminoAcidDescriptor
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  TaeAminoAcidDescriptor()