test_class.file: storage/pdb/src/test/java/org/openscience/cdk/tools/ProteinBuilderToolTest.java
test_class.identifier: ProteinBuilderToolTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testCreateProtein() throws Exception {
          IBioPolymer protein = ProteinBuilderTool.createProtein("GAGA", SilentChemObjectBuilder.getInstance());
          Assert.assertNotNull(protein);
          Assert.assertEquals(4, protein.getMonomerCount());
          Assert.assertEquals(1, protein.getStrandCount());
          Assert.assertEquals(18 + 1, protein.getAtomCount());
          // 1=terminal oxygen
          Assert.assertEquals(14 + 3 + 1, protein.getBondCount());
          // 3 = extra back bone bonds, 1=bond to terminal oxygen
      }
test_case.class_method_signature: ProteinBuilderToolTest.testCreateProtein()
test_case.full_signature: @Test public void testCreateProtein()
test_case.identifier: testCreateProtein
test_case.invocations: createProtein getInstance assertNotNull assertEquals getMonomerCount assertEquals getStrandCount assertEquals getAtomCount assertEquals getBondCount
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCreateProtein()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(ProteinBuilderTool.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(ProteinBuilderTool.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: storage/pdb/src/main/java/org/openscience/cdk/tools/ProteinBuilderTool.java
focal_class.identifier: ProteinBuilderTool
focal_class.class_method_signature: ProteinBuilderTool.addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.full_signature: public static IBioPolymer addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.identifier: addAminoAcidAtNTerminus
focal_class.modifiers: public static
focal_class.parameters: (IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.class_method_signature: ProteinBuilderTool.addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.full_signature: public static IBioPolymer addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.identifier: addAminoAcidAtCTerminus
focal_class.modifiers: public static
focal_class.parameters: (IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand,
              IAminoAcid aaToAddTo)
focal_class.class_method_signature: ProteinBuilderTool.createProtein(String sequence)
focal_class.full_signature: public static IBioPolymer createProtein(String sequence)
focal_class.identifier: createProtein
focal_class.modifiers: public static
focal_class.parameters: (String sequence)
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer createProtein(String sequence)
focal_class.class_method_signature: ProteinBuilderTool.createProtein(String sequence, IChemObjectBuilder builder)
focal_class.full_signature: public static IBioPolymer createProtein(String sequence, IChemObjectBuilder builder)
focal_class.identifier: createProtein
focal_class.modifiers: public static
focal_class.parameters: (String sequence, IChemObjectBuilder builder)
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer createProtein(String sequence, IChemObjectBuilder builder)
focal_class.class_method_signature: ProteinBuilderTool.addAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
focal_class.full_signature: private static IBioPolymer addAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
focal_class.identifier: addAminoAcid
focal_class.modifiers: private static
focal_class.parameters: (IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
focal_class.return: IBioPolymer
focal_class.signature: IBioPolymer addAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
focal_method.body: public static IBioPolymer createProtein(String sequence) throws CDKException {
          return createProtein(sequence, DefaultChemObjectBuilder.getInstance());
      }
focal_method.class_method_signature: ProteinBuilderTool.createProtein(String sequence)
focal_method.full_signature: public static IBioPolymer createProtein(String sequence)
focal_method.identifier: createProtein
focal_method.invocations: createProtein getInstance
focal_method.modifiers: public static
focal_method.parameters: (String sequence)
focal_method.return: IBioPolymer
focal_method.signature: IBioPolymer createProtein(String sequence)