test_class.file: storage/pdb/src/test/java/org/openscience/cdk/templates/AminoAcidsTest.java
test_class.identifier: AminoAcidsTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetHashMapBySingleCharCode() {
          Map<String, IAminoAcid> map = AminoAcids.getHashMapBySingleCharCode();
          Assert.assertNotNull(map);
          Assert.assertEquals(20, map.size());
  
          String[] aas = {"G", "A", "V", "L"};
          for (String aa1 : aas) {
              AminoAcid aa = (AminoAcid) map.get(aa1);
              Assert.assertNotNull("Did not find AA for: " + aa1, aa);
          }
      }
test_case.class_method_signature: AminoAcidsTest.testGetHashMapBySingleCharCode()
test_case.full_signature: @Test public void testGetHashMapBySingleCharCode()
test_case.identifier: testGetHashMapBySingleCharCode
test_case.invocations: getHashMapBySingleCharCode assertNotNull assertEquals size get assertNotNull
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetHashMapBySingleCharCode()
focal_class.declarator: LOGGER = LoggingToolFactory.createLoggingTool(AminoAcids.class)
focal_class.modifier: private static final
focal_class.original_string: private static final ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(AminoAcids.class);
focal_class.type: ILoggingTool
focal_class.var_name: LOGGER
focal_class.declarator: aminoAcids         = null
focal_class.modifier: private static
focal_class.original_string: private static AminoAcid[] aminoAcids         = null;
focal_class.type: AminoAcid[]
focal_class.var_name: aminoAcids
focal_class.declarator: RESIDUE_NAME       = "residueName"
focal_class.modifier: public final static
focal_class.original_string: public final static String RESIDUE_NAME       = "residueName";
focal_class.type: String
focal_class.var_name: RESIDUE_NAME
focal_class.declarator: RESIDUE_NAME_SHORT = "residueNameShort"
focal_class.modifier: public final static
focal_class.original_string: public final static String RESIDUE_NAME_SHORT = "residueNameShort";
focal_class.type: String
focal_class.var_name: RESIDUE_NAME_SHORT
focal_class.declarator: NO_ATOMS           = "noOfAtoms"
focal_class.modifier: public final static
focal_class.original_string: public final static String NO_ATOMS           = "noOfAtoms";
focal_class.type: String
focal_class.var_name: NO_ATOMS
focal_class.declarator: NO_BONDS           = "noOfBonds"
focal_class.modifier: public final static
focal_class.original_string: public final static String NO_BONDS           = "noOfBonds";
focal_class.type: String
focal_class.var_name: NO_BONDS
focal_class.declarator: ID                 = "id"
focal_class.modifier: public final static
focal_class.original_string: public final static String ID                 = "id";
focal_class.type: String
focal_class.var_name: ID
focal_class.file: storage/pdb/src/main/java/org/openscience/cdk/templates/AminoAcids.java
focal_class.identifier: AminoAcids
focal_class.class_method_signature: AminoAcids.aaBondInfo()
focal_class.full_signature: public static int[][] aaBondInfo()
focal_class.identifier: aaBondInfo
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: int[][]
focal_class.signature: int[][] aaBondInfo()
focal_class.class_method_signature: AminoAcids.createAAs()
focal_class.full_signature: public synchronized static AminoAcid[] createAAs()
focal_class.identifier: createAAs
focal_class.modifiers: public synchronized static
focal_class.parameters: ()
focal_class.return: AminoAcid[]
focal_class.signature: AminoAcid[] createAAs()
focal_class.class_method_signature: AminoAcids.getHashMapBySingleCharCode()
focal_class.full_signature: public static Map<String, IAminoAcid> getHashMapBySingleCharCode()
focal_class.identifier: getHashMapBySingleCharCode
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: Map<String, IAminoAcid>
focal_class.signature: Map<String, IAminoAcid> getHashMapBySingleCharCode()
focal_class.class_method_signature: AminoAcids.getHashMapByThreeLetterCode()
focal_class.full_signature: public static Map<String, IAminoAcid> getHashMapByThreeLetterCode()
focal_class.identifier: getHashMapByThreeLetterCode
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: Map<String, IAminoAcid>
focal_class.signature: Map<String, IAminoAcid> getHashMapByThreeLetterCode()
focal_class.class_method_signature: AminoAcids.convertThreeLetterCodeToOneLetterCode(String threeLetterCode)
focal_class.full_signature: public static String convertThreeLetterCodeToOneLetterCode(String threeLetterCode)
focal_class.identifier: convertThreeLetterCodeToOneLetterCode
focal_class.modifiers: public static
focal_class.parameters: (String threeLetterCode)
focal_class.return: String
focal_class.signature: String convertThreeLetterCodeToOneLetterCode(String threeLetterCode)
focal_class.class_method_signature: AminoAcids.convertOneLetterCodeToThreeLetterCode(String oneLetterCode)
focal_class.full_signature: public static String convertOneLetterCodeToThreeLetterCode(String oneLetterCode)
focal_class.identifier: convertOneLetterCodeToThreeLetterCode
focal_class.modifiers: public static
focal_class.parameters: (String oneLetterCode)
focal_class.return: String
focal_class.signature: String convertOneLetterCodeToThreeLetterCode(String oneLetterCode)
focal_method.body: public static Map<String, IAminoAcid> getHashMapBySingleCharCode() {
          IAminoAcid[] monomers = createAAs();
          HashMap<String, IAminoAcid> map = new HashMap<String, IAminoAcid>();
          for (int i = 0; i < monomers.length; i++) {
              map.put((String) monomers[i].getProperty(RESIDUE_NAME_SHORT), monomers[i]);
          }
          return map;
      }
focal_method.class_method_signature: AminoAcids.getHashMapBySingleCharCode()
focal_method.full_signature: public static Map<String, IAminoAcid> getHashMapBySingleCharCode()
focal_method.identifier: getHashMapBySingleCharCode
focal_method.invocations: createAAs put getProperty
focal_method.modifiers: public static
focal_method.parameters: ()
focal_method.return: Map<String, IAminoAcid>
focal_method.signature: Map<String, IAminoAcid> getHashMapBySingleCharCode()