test_class.declarator: logger = LoggingToolFactory.createLoggingTool(EStateFingerprinterTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(EStateFingerprinterTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/EStateFingerprinterTest.java
test_class.identifier: EStateFingerprinterTest
test_class.superclass: extends AbstractFixedLengthFingerprinterTest
test_case.body: @Test
      @Override
      public void testBug706786() throws Exception {
  
          IAtomContainer superStructure = bug706786_1();
          IAtomContainer subStructure = bug706786_2();
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(superStructure);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(subStructure);
          addImplicitHydrogens(superStructure);
          addImplicitHydrogens(subStructure);
  
          // SMARTS is now correct and D will include H atoms, CDK had this wrong
          // for years (had it has non-H count). Whilst you can set the optional
          // SMARTS flavor CDK_LEGACY this is not correct
          AtomContainerManipulator.suppressHydrogens(superStructure);
          AtomContainerManipulator.suppressHydrogens(subStructure);
  
          IFingerprinter fpr = new EStateFingerprinter();
          IBitFingerprint superBits = fpr.getBitFingerprint(superStructure);
          IBitFingerprint subBits = fpr.getBitFingerprint(subStructure);
  
          assertThat(superBits.asBitSet(), is(asBitSet(6, 11, 12, 15, 16, 18, 33, 34, 35)));
          assertThat(subBits.asBitSet(), is(asBitSet(8, 11, 16, 35)));
      }
test_case.class_method_signature: EStateFingerprinterTest.testBug706786()
test_case.full_signature: @Test @Override public void testBug706786()
test_case.identifier: testBug706786
test_case.invocations: bug706786_1 bug706786_2 percieveAtomTypesAndConfigureAtoms percieveAtomTypesAndConfigureAtoms addImplicitHydrogens addImplicitHydrogens suppressHydrogens suppressHydrogens getBitFingerprint getBitFingerprint assertThat asBitSet is asBitSet assertThat asBitSet is asBitSet
test_case.modifiers: @Test @Override public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testBug706786()
focal_class.declarator: PATTERNS = EStateFragments.getPatterns()
focal_class.modifier: private static final
focal_class.original_string: private static final SmartsPattern[] PATTERNS = EStateFragments.getPatterns();
focal_class.type: SmartsPattern[]
focal_class.var_name: PATTERNS
focal_class.file: descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/EStateFingerprinter.java
focal_class.identifier: EStateFingerprinter
focal_class.interfaces: implements IFingerprinter
focal_class.class_method_signature: EStateFingerprinter.EStateFingerprinter()
focal_class.full_signature: public  EStateFingerprinter()
focal_class.identifier: EStateFingerprinter
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  EStateFingerprinter()
focal_class.class_method_signature: EStateFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
focal_class.full_signature: @Override public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
focal_class.identifier: getBitFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: IBitFingerprint
focal_class.signature: IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
focal_class.class_method_signature: EStateFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
focal_class.full_signature: @Override public Map<String, Integer> getRawFingerprint(IAtomContainer iAtomContainer)
focal_class.identifier: getRawFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer iAtomContainer)
focal_class.return: Map<String, Integer>
focal_class.signature: Map<String, Integer> getRawFingerprint(IAtomContainer iAtomContainer)
focal_class.class_method_signature: EStateFingerprinter.getSize()
focal_class.full_signature: @Override public int getSize()
focal_class.identifier: getSize
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getSize()
focal_class.class_method_signature: EStateFingerprinter.getCountFingerprint(IAtomContainer container)
focal_class.full_signature: @Override public ICountFingerprint getCountFingerprint(IAtomContainer container)
focal_class.identifier: getCountFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer container)
focal_class.return: ICountFingerprint
focal_class.signature: ICountFingerprint getCountFingerprint(IAtomContainer container)
focal_class.superclass: extends AbstractFingerprinter
focal_method.body: @Override
      public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) throws CDKException {
  
          int bitsetLength = PATTERNS.length;
          BitSet fingerPrint = new BitSet(bitsetLength);
  
          SmartsPattern.prepare(atomContainer);
          for (int i = 0; i < PATTERNS.length; i++) {
              if (PATTERNS[i].matches(atomContainer))
                  fingerPrint.set(i, true);
          }
          return new BitSetFingerprint(fingerPrint);
      }
focal_method.class_method_signature: EStateFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
focal_method.full_signature: @Override public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
focal_method.identifier: getBitFingerprint
focal_method.invocations: prepare matches set
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainer atomContainer)
focal_method.return: IBitFingerprint
focal_method.signature: IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)