test_class.declarator: logger = LoggingToolFactory.createLoggingTool(Mol2ReaderTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(Mol2ReaderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/io/src/test/java/org/openscience/cdk/io/Mol2ReaderTest.java
test_class.identifier: Mol2ReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test
      public void testAccepts() {
          Mol2Reader reader = new Mol2Reader();
          Assert.assertTrue(reader.accepts(ChemFile.class));
          Assert.assertTrue(reader.accepts(ChemModel.class));
          Assert.assertTrue(reader.accepts(AtomContainer.class));
      }
test_case.class_method_signature: Mol2ReaderTest.testAccepts()
test_case.full_signature: @Test public void testAccepts()
test_case.identifier: testAccepts
test_case.invocations: assertTrue accepts assertTrue accepts assertTrue accepts
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAccepts()
focal_class.declarator: firstLineisMolecule = false
focal_class.original_string: boolean                                  firstLineisMolecule = false;
focal_class.type: boolean
focal_class.var_name: firstLineisMolecule
focal_class.declarator: input               = null
focal_class.original_string: BufferedReader                           input               = null;
focal_class.type: BufferedReader
focal_class.var_name: input
focal_class.declarator: logger              = LoggingToolFactory
                                                                           .createLoggingTool(Mol2Reader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool              logger              = LoggingToolFactory
                                                                           .createLoggingTool(Mol2Reader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: ATOM_TYPE_ALIASES   = ImmutableMap
                                                                           .<String, String> builder()
                                                                           // previously produced by Open Babel
                                                                           .put("S.o2", "S.O2")
                                                                           .put("S.o", "S.O")
                                                                           // seen in MMFF94 validation suite
                                                                           .put("CL", "Cl").put("CU", "Cu")
                                                                           .put("FE", "Fe").put("BR", "Br")
                                                                           .put("NA", "Na").put("SI", "Si")
                                                                           .put("CA", "Ca").put("ZN", "Zn")
                                                                           .put("LI", "Li").put("MG", "Mg").build()
focal_class.modifier: private static final
focal_class.original_string: private static final Map<String, String> ATOM_TYPE_ALIASES   = ImmutableMap
                                                                           .<String, String> builder()
                                                                           // previously produced by Open Babel
                                                                           .put("S.o2", "S.O2")
                                                                           .put("S.o", "S.O")
                                                                           // seen in MMFF94 validation suite
                                                                           .put("CL", "Cl").put("CU", "Cu")
                                                                           .put("FE", "Fe").put("BR", "Br")
                                                                           .put("NA", "Na").put("SI", "Si")
                                                                           .put("CA", "Ca").put("ZN", "Zn")
                                                                           .put("LI", "Li").put("MG", "Mg").build();
focal_class.type: Map<String, String>
focal_class.var_name: ATOM_TYPE_ALIASES
focal_class.file: storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java
focal_class.identifier: Mol2Reader
focal_class.class_method_signature: Mol2Reader.Mol2Reader(Reader in)
focal_class.full_signature: public  Mol2Reader(Reader in)
focal_class.identifier: Mol2Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in)
focal_class.signature:  Mol2Reader(Reader in)
focal_class.class_method_signature: Mol2Reader.Mol2Reader(InputStream input)
focal_class.full_signature: public  Mol2Reader(InputStream input)
focal_class.identifier: Mol2Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream input)
focal_class.signature:  Mol2Reader(InputStream input)
focal_class.class_method_signature: Mol2Reader.Mol2Reader()
focal_class.full_signature: public  Mol2Reader()
focal_class.identifier: Mol2Reader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Mol2Reader()
focal_class.class_method_signature: Mol2Reader.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: Mol2Reader.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: Mol2Reader.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: Mol2Reader.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: Mol2Reader.read(T object)
focal_class.full_signature: @Override public T read(T object)
focal_class.identifier: read
focal_class.modifiers: @Override public
focal_class.parameters: (T object)
focal_class.return: T
focal_class.signature: T read(T object)
focal_class.class_method_signature: Mol2Reader.readChemModel(IChemModel chemModel)
focal_class.full_signature: private IChemModel readChemModel(IChemModel chemModel)
focal_class.identifier: readChemModel
focal_class.modifiers: private
focal_class.parameters: (IChemModel chemModel)
focal_class.return: IChemModel
focal_class.signature: IChemModel readChemModel(IChemModel chemModel)
focal_class.class_method_signature: Mol2Reader.readChemFile(IChemFile chemFile)
focal_class.full_signature: private IChemFile readChemFile(IChemFile chemFile)
focal_class.identifier: readChemFile
focal_class.modifiers: private
focal_class.parameters: (IChemFile chemFile)
focal_class.return: IChemFile
focal_class.signature: IChemFile readChemFile(IChemFile chemFile)
focal_class.class_method_signature: Mol2Reader.accepts(IChemObject object)
focal_class.full_signature: public boolean accepts(IChemObject object)
focal_class.identifier: accepts
focal_class.modifiers: public
focal_class.parameters: (IChemObject object)
focal_class.return: boolean
focal_class.signature: boolean accepts(IChemObject object)
focal_class.class_method_signature: Mol2Reader.readMolecule(IAtomContainer molecule)
focal_class.full_signature: private IAtomContainer readMolecule(IAtomContainer molecule)
focal_class.identifier: readMolecule
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer readMolecule(IAtomContainer molecule)
focal_class.class_method_signature: Mol2Reader.isElementSymbol(String atomTypeStr)
focal_class.full_signature: private boolean isElementSymbol(String atomTypeStr)
focal_class.identifier: isElementSymbol
focal_class.modifiers: private
focal_class.parameters: (String atomTypeStr)
focal_class.return: boolean
focal_class.signature: boolean isElementSymbol(String atomTypeStr)
focal_class.class_method_signature: Mol2Reader.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.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public boolean accepts(Class<? extends IChemObject> classObject) {
          if (IChemFile.class.equals(classObject)) return true;
          if (IChemModel.class.equals(classObject)) return true;
          if (IAtomContainer.class.equals(classObject)) return true;
          Class<?>[] interfaces = classObject.getInterfaces();
          for (Class<?> anInterface : interfaces) {
              if (IChemModel.class.equals(anInterface)) return true;
              if (IChemFile.class.equals(anInterface)) return true;
              if (IAtomContainer.class.equals(anInterface)) return true;
          }
          Class superClass = classObject.getSuperclass();
          return superClass != null && this.accepts(superClass);
      }
focal_method.class_method_signature: Mol2Reader.accepts(Class<? extends IChemObject> classObject)
focal_method.full_signature: @Override public boolean accepts(Class<? extends IChemObject> classObject)
focal_method.identifier: accepts
focal_method.invocations: equals equals equals getInterfaces equals equals equals getSuperclass accepts
focal_method.modifiers: @Override public
focal_method.parameters: (Class<? extends IChemObject> classObject)
focal_method.return: boolean
focal_method.signature: boolean accepts(Class<? extends IChemObject> classObject)