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 testCreateBondMatrix() {
          int[][] bonds = AminoAcids.aaBondInfo();
          Assert.assertNotNull(bonds);
      }
test_case.class_method_signature: AminoAcidsTest.testCreateBondMatrix()
test_case.full_signature: @Test public void testCreateBondMatrix()
test_case.identifier: testCreateBondMatrix
test_case.invocations: aaBondInfo assertNotNull
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCreateBondMatrix()
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 int[][] aaBondInfo() {
  
          if (aminoAcids == null) {
              createAAs();
          }
  
          int[][] info = new int[153][4];
  
          int counter = 0;
          int total = 0;
          for (int aa = 0; aa < aminoAcids.length; aa++) {
              AminoAcid acid = aminoAcids[aa];
  
              LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount());
              total += acid.getBondCount();
              LOGGER.debug("total #bonds: ", total);
  
              Iterator<IBond> bonds = acid.bonds().iterator();
              while (bonds.hasNext()) {
                  IBond bond = (IBond) bonds.next();
                  info[counter][0] = counter;
                  info[counter][1] = acid.indexOf(bond.getBegin());
                  info[counter][2] = acid.indexOf(bond.getEnd());
                  info[counter][3] = bond.getOrder().numeric();
                  counter++;
              }
          }
  
          if (counter > 153) {
              LOGGER.error("Error while creating AA info! Bond count is too large: ", counter);
              return null;
          }
  
          return info;
      }
focal_method.class_method_signature: AminoAcids.aaBondInfo()
focal_method.full_signature: public static int[][] aaBondInfo()
focal_method.identifier: aaBondInfo
focal_method.invocations: createAAs debug toString getProperty getBondCount getBondCount debug iterator bonds hasNext next indexOf getBegin indexOf getEnd numeric getOrder error
focal_method.modifiers: public static
focal_method.parameters: ()
focal_method.return: int[][]
focal_method.signature: int[][] aaBondInfo()