test_class.file: storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java
test_class.identifier: PDBReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Category(SlowTest.class)
      @Test public void readFinalPump() throws Exception {
          IChemFile chemFile = new PDBReader(getClass().getResourceAsStream("finalPump96.09.06.pdb")).read(new ChemFile());
      }
test_case.class_method_signature: PDBReaderTest.readFinalPump()
test_case.full_signature: @Category(SlowTest.class) @Test public void readFinalPump()
test_case.identifier: readFinalPump
test_case.invocations: read getResourceAsStream getClass
test_case.modifiers: @Category(SlowTest.class) @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void readFinalPump()
focal_class.declarator: logger            = LoggingToolFactory.createLoggingTool(PDBReader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool    logger            = LoggingToolFactory.createLoggingTool(PDBReader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: _oInput
focal_class.modifier: private
focal_class.original_string: private BufferedReader         _oInput;
focal_class.type: BufferedReader
focal_class.var_name: _oInput
focal_class.declarator: useRebondTool
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting       useRebondTool;
focal_class.type: BooleanIOSetting
focal_class.var_name: useRebondTool
focal_class.declarator: readConnect
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting       readConnect;
focal_class.type: BooleanIOSetting
focal_class.var_name: readConnect
focal_class.declarator: useHetDictionary
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting       useHetDictionary;
focal_class.type: BooleanIOSetting
focal_class.var_name: useHetDictionary
focal_class.declarator: atomNumberMap
focal_class.modifier: private
focal_class.original_string: private Map<Integer, IAtom>    atomNumberMap;
focal_class.type: Map<Integer, IAtom>
focal_class.var_name: atomNumberMap
focal_class.declarator: bondsFromConnectRecords
focal_class.modifier: private
focal_class.original_string: private List<IBond>            bondsFromConnectRecords;
focal_class.type: List<IBond>
focal_class.var_name: bondsFromConnectRecords
focal_class.declarator: hetDictionary
focal_class.modifier: private
focal_class.original_string: private Map<String, String>    hetDictionary;
focal_class.type: Map<String, String>
focal_class.var_name: hetDictionary
focal_class.declarator: cdkAtomTypeFactory
focal_class.modifier: private
focal_class.original_string: private AtomTypeFactory        cdkAtomTypeFactory;
focal_class.type: AtomTypeFactory
focal_class.var_name: cdkAtomTypeFactory
focal_class.declarator: hetDictionaryPath = "type_map.txt"
focal_class.modifier: private static final
focal_class.original_string: private static final String    hetDictionaryPath = "type_map.txt";
focal_class.type: String
focal_class.var_name: hetDictionaryPath
focal_class.file: storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
focal_class.identifier: PDBReader
focal_class.class_method_signature: PDBReader.PDBReader(InputStream oIn)
focal_class.full_signature: public  PDBReader(InputStream oIn)
focal_class.identifier: PDBReader
focal_class.modifiers: public
focal_class.parameters: (InputStream oIn)
focal_class.signature:  PDBReader(InputStream oIn)
focal_class.class_method_signature: PDBReader.PDBReader(Reader oIn)
focal_class.full_signature: public  PDBReader(Reader oIn)
focal_class.identifier: PDBReader
focal_class.modifiers: public
focal_class.parameters: (Reader oIn)
focal_class.signature:  PDBReader(Reader oIn)
focal_class.class_method_signature: PDBReader.PDBReader()
focal_class.full_signature: public  PDBReader()
focal_class.identifier: PDBReader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  PDBReader()
focal_class.class_method_signature: PDBReader.getFormat()
focal_class.full_signature: @Override public IResourceFormat getFormat()
focal_class.identifier: getFormat
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IResourceFormat
focal_class.signature: IResourceFormat getFormat()
focal_class.class_method_signature: PDBReader.setReader(Reader input)
focal_class.full_signature: @Override public void setReader(Reader input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (Reader input)
focal_class.return: void
focal_class.signature: void setReader(Reader input)
focal_class.class_method_signature: PDBReader.setReader(InputStream input)
focal_class.full_signature: @Override public void setReader(InputStream input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (InputStream input)
focal_class.return: void
focal_class.signature: void setReader(InputStream input)
focal_class.class_method_signature: PDBReader.accepts(Class<? extends IChemObject> classObject)
focal_class.full_signature: @Override public boolean accepts(Class<? extends IChemObject> classObject)
focal_class.identifier: accepts
focal_class.modifiers: @Override public
focal_class.parameters: (Class<? extends IChemObject> classObject)
focal_class.return: boolean
focal_class.signature: boolean accepts(Class<? extends IChemObject> classObject)
focal_class.class_method_signature: PDBReader.read(T oObj)
focal_class.full_signature: @Override public T read(T oObj)
focal_class.identifier: read
focal_class.modifiers: @Override public
focal_class.parameters: (T oObj)
focal_class.return: T
focal_class.signature: T read(T oObj)
focal_class.class_method_signature: PDBReader.readChemFile(IChemFile oFile)
focal_class.full_signature: private IChemFile readChemFile(IChemFile oFile)
focal_class.identifier: readChemFile
focal_class.modifiers: private
focal_class.parameters: (IChemFile oFile)
focal_class.return: IChemFile
focal_class.signature: IChemFile readChemFile(IChemFile oFile)
focal_class.class_method_signature: PDBReader.addBond(IAtomContainer molecule, int bondAtomNo, int bondedAtomNo)
focal_class.full_signature: private void addBond(IAtomContainer molecule, int bondAtomNo, int bondedAtomNo)
focal_class.identifier: addBond
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule, int bondAtomNo, int bondedAtomNo)
focal_class.return: void
focal_class.signature: void addBond(IAtomContainer molecule, int bondAtomNo, int bondedAtomNo)
focal_class.class_method_signature: PDBReader.createBondsWithRebondTool(IAtomContainer molecule)
focal_class.full_signature: private boolean createBondsWithRebondTool(IAtomContainer molecule)
focal_class.identifier: createBondsWithRebondTool
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: boolean
focal_class.signature: boolean createBondsWithRebondTool(IAtomContainer molecule)
focal_class.class_method_signature: PDBReader.isUpper(char c)
focal_class.full_signature: private static boolean isUpper(char c)
focal_class.identifier: isUpper
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isUpper(char c)
focal_class.class_method_signature: PDBReader.isLower(char c)
focal_class.full_signature: private static boolean isLower(char c)
focal_class.identifier: isLower
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isLower(char c)
focal_class.class_method_signature: PDBReader.isDigit(char c)
focal_class.full_signature: private static boolean isDigit(char c)
focal_class.identifier: isDigit
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isDigit(char c)
focal_class.class_method_signature: PDBReader.parseAtomSymbol(String str)
focal_class.full_signature: private String parseAtomSymbol(String str)
focal_class.identifier: parseAtomSymbol
focal_class.modifiers: private
focal_class.parameters: (String str)
focal_class.return: String
focal_class.signature: String parseAtomSymbol(String str)
focal_class.class_method_signature: PDBReader.readAtom(String cLine, int lineLength)
focal_class.full_signature: private PDBAtom readAtom(String cLine, int lineLength)
focal_class.identifier: readAtom
focal_class.modifiers: private
focal_class.parameters: (String cLine, int lineLength)
focal_class.return: PDBAtom
focal_class.signature: PDBAtom readAtom(String cLine, int lineLength)
focal_class.class_method_signature: PDBReader.typeHetatm(String resName, String atomName)
focal_class.full_signature: private String typeHetatm(String resName, String atomName)
focal_class.identifier: typeHetatm
focal_class.modifiers: private
focal_class.parameters: (String resName, String atomName)
focal_class.return: String
focal_class.signature: String typeHetatm(String resName, String atomName)
focal_class.class_method_signature: PDBReader.readHetDictionary()
focal_class.full_signature: private void readHetDictionary()
focal_class.identifier: readHetDictionary
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void readHetDictionary()
focal_class.class_method_signature: PDBReader.close()
focal_class.full_signature: @Override public void close()
focal_class.identifier: close
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void close()
focal_class.class_method_signature: PDBReader.initIOSettings()
focal_class.full_signature: private void initIOSettings()
focal_class.identifier: initIOSettings
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void initIOSettings()
focal_class.class_method_signature: PDBReader.customizeJob()
focal_class.full_signature: public void customizeJob()
focal_class.identifier: customizeJob
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void customizeJob()
focal_class.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public <T extends IChemObject> T read(T oObj) throws CDKException {
          if (oObj instanceof IChemFile) {
              return (T) readChemFile((IChemFile) oObj);
          } else {
              throw new CDKException("Only supported is reading of ChemFile objects.");
          }
      }
focal_method.class_method_signature: PDBReader.read(T oObj)
focal_method.full_signature: @Override public T read(T oObj)
focal_method.identifier: read
focal_method.invocations: readChemFile
focal_method.modifiers: @Override public
focal_method.parameters: (T oObj)
focal_method.return: T
focal_method.signature: T read(T oObj)