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: @Test
      public void test114D() throws Exception {
          String filename = "data/pdb/114D.pdb";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
  
          ISimpleChemObjectReader reader = new PDBReader(ins);
          Assert.assertNotNull(reader);
  
          IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
          Assert.assertNotNull(chemFile);
          Assert.assertEquals(1, chemFile.getChemSequenceCount());
  
          org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
          Assert.assertNotNull(seq);
          Assert.assertEquals(1, seq.getChemModelCount());
  
          IChemModel model = seq.getChemModel(0);
          Assert.assertNotNull(model);
          Assert.assertEquals(1, model.getMoleculeSet().getAtomContainerCount());
  
          IAtomContainer container = model.getMoleculeSet().getAtomContainer(0);
          Assert.assertTrue(container instanceof IBioPolymer);
          IBioPolymer polymer = (IBioPolymer) container;
  
          Assert.assertTrue("Strand A is not a PDBStrand", polymer.getStrand("A") instanceof PDBStrand);
          PDBStrand strandA = (PDBStrand) polymer.getStrand("A");
          Iterator<String> lst = strandA.getMonomerNamesInSequentialOrder().iterator();
          String monomer1 = lst.next();
          IMonomer mono1 = strandA.getMonomer(monomer1);
          Assert.assertNotNull(mono1);
          Assert.assertNotNull(mono1.getMonomerName());
          Assert.assertTrue("Monomer is not a PDBMonomer", mono1 instanceof PDBMonomer);
          PDBMonomer pdbMonomer = (PDBMonomer) mono1;
          Assert.assertEquals(pdbMonomer.getResSeq(), "1");
  
          String monomer2 = lst.next();
          IMonomer mono2 = strandA.getMonomer(monomer2);
          Assert.assertTrue("Monomer is not a PDBMonomer", mono2 instanceof PDBMonomer);
          PDBMonomer pdbMonomer2 = (PDBMonomer) mono2;
          Assert.assertEquals(pdbMonomer2.getResSeq(), "2");
  
          // chemical validation
          Assert.assertEquals(552, ChemFileManipulator.getAtomCount(chemFile));
          Assert.assertEquals(2, polymer.getStrandCount());
          Assert.assertEquals(24, polymer.getMonomerCount());
  
          Assert.assertTrue(polymer.getStrandNames().contains("A"));
          Assert.assertTrue(polymer.getStrandNames().contains("B"));
          Assert.assertFalse(polymer.getStrandNames().contains("C"));
          Assert.assertEquals(24, polymer.getMonomerCount());
  
          Assert.assertTrue(polymer instanceof PDBPolymer);
          PDBPolymer pdb = (PDBPolymer) polymer;
  
          // PDB validation
          Assert.assertEquals(0, pdb.getStructures().size());
  
      }
test_case.class_method_signature: PDBReaderTest.test114D()
test_case.full_signature: @Test public void test114D()
test_case.identifier: test114D
test_case.invocations: getResourceAsStream getClassLoader getClass assertNotNull read assertNotNull assertEquals getChemSequenceCount getChemSequence assertNotNull assertEquals getChemModelCount getChemModel assertNotNull assertEquals getAtomContainerCount getMoleculeSet getAtomContainer getMoleculeSet assertTrue assertTrue getStrand getStrand iterator getMonomerNamesInSequentialOrder next getMonomer assertNotNull assertNotNull getMonomerName assertTrue assertEquals getResSeq next getMonomer assertTrue assertEquals getResSeq assertEquals getAtomCount assertEquals getStrandCount assertEquals getMonomerCount assertTrue contains getStrandNames assertTrue contains getStrandNames assertFalse contains getStrandNames assertEquals getMonomerCount assertTrue assertEquals size getStructures
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void test114D()
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)