test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private final static
test_class.original_string: private final static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.declarator: ifac
test_class.modifier: private
test_class.original_string: private IsotopeFactory                  ifac;
test_class.type: IsotopeFactory
test_class.var_name: ifac
test_class.file: tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
test_class.identifier: MolecularFormulaManipulatorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetDBE_IMolecularFormula() throws Exception {
          IMolecularFormula formula = new MolecularFormula();
          formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10);
          formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 22);
  
          Assert.assertEquals(0.0, MolecularFormulaManipulator.getDBE(formula), 0.01);
  
          formula = new MolecularFormula();
          formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10);
          formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 16);
  
          Assert.assertEquals(3.0, MolecularFormulaManipulator.getDBE(formula), 0.01);
  
          formula = new MolecularFormula();
          formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10);
          formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 16);
          formula.addIsotope(builder.newInstance(IIsotope.class, "O"));
  
          Assert.assertEquals(3.0, MolecularFormulaManipulator.getDBE(formula), 0.01);
  
          formula = new MolecularFormula();
          formula.addIsotope(builder.newInstance(IIsotope.class, "C"), 10);
          formula.addIsotope(builder.newInstance(IIsotope.class, "H"), 19);
          formula.addIsotope(builder.newInstance(IIsotope.class, "N"));
  
          Assert.assertEquals(2.0, MolecularFormulaManipulator.getDBE(formula), 0.01);
  
      }
test_case.class_method_signature: MolecularFormulaManipulatorTest.testGetDBE_IMolecularFormula()
test_case.full_signature: @Test public void testGetDBE_IMolecularFormula()
test_case.identifier: testGetDBE_IMolecularFormula
test_case.invocations: addIsotope newInstance addIsotope newInstance assertEquals getDBE addIsotope newInstance addIsotope newInstance assertEquals getDBE addIsotope newInstance addIsotope newInstance addIsotope newInstance assertEquals getDBE addIsotope newInstance addIsotope newInstance addIsotope newInstance assertEquals getDBE
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetDBE_IMolecularFormula()
focal_class.declarator: MolWeight                = AtomContainerManipulator.MolWeight
focal_class.modifier: public static final
focal_class.original_string: public static final int MolWeight                = AtomContainerManipulator.MolWeight;
focal_class.type: int
focal_class.var_name: MolWeight
focal_class.declarator: MolWeightIgnoreSpecified = AtomContainerManipulator.MolWeightIgnoreSpecified
focal_class.modifier: public static final
focal_class.original_string: public static final int MolWeightIgnoreSpecified = AtomContainerManipulator.MolWeightIgnoreSpecified;
focal_class.type: int
focal_class.var_name: MolWeightIgnoreSpecified
focal_class.declarator: MonoIsotopic             = AtomContainerManipulator.MonoIsotopic
focal_class.modifier: public static final
focal_class.original_string: public static final int MonoIsotopic             = AtomContainerManipulator.MonoIsotopic;
focal_class.type: int
focal_class.var_name: MonoIsotopic
focal_class.declarator: MostAbundant             = AtomContainerManipulator.MostAbundant
focal_class.modifier: public static final
focal_class.original_string: public static final int MostAbundant             = AtomContainerManipulator.MostAbundant;
focal_class.type: int
focal_class.var_name: MostAbundant
focal_class.declarator: NAT_ABUN_COMP = new Comparator<IIsotope>() {
          @Override
          public int compare(IIsotope o1, IIsotope o2) {
              return -Double.compare(o1.getNaturalAbundance(),
                                     o2.getNaturalAbundance());
          }
      }
focal_class.modifier: public static final
focal_class.original_string: public static final Comparator<IIsotope> NAT_ABUN_COMP = new Comparator<IIsotope>() {
          @Override
          public int compare(IIsotope o1, IIsotope o2) {
              return -Double.compare(o1.getNaturalAbundance(),
                                     o2.getNaturalAbundance());
          }
      };
focal_class.type: Comparator<IIsotope>
focal_class.var_name: NAT_ABUN_COMP
focal_class.declarator: HYPHEN = '-'
focal_class.modifier: private static final
focal_class.original_string: private static final char HYPHEN = '-';
focal_class.type: char
focal_class.var_name: HYPHEN
focal_class.declarator: MINUS  = '–';
focal_class.modifier: private static final
focal_class.original_string: private static final char MINUS  = '–';
focal_class.type: char
focal_class.var_name: MINUS
focal_class.declarator: HYPHEN_STR = "-"
focal_class.modifier: private static final
focal_class.original_string: private static final String HYPHEN_STR = "-";
focal_class.type: String
focal_class.var_name: HYPHEN_STR
focal_class.declarator: MINUS_STR  = "–";
focal_class.modifier: private static final
focal_class.original_string: private static final String MINUS_STR  = "–";
focal_class.type: String
focal_class.var_name: MINUS_STR
focal_class.file: tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
focal_class.identifier: MolecularFormulaManipulator
focal_class.class_method_signature: MolecularFormulaManipulator.getAtomCount(IMolecularFormula formula)
focal_class.full_signature: public static int getAtomCount(IMolecularFormula formula)
focal_class.identifier: getAtomCount
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: int
focal_class.signature: int getAtomCount(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, IElement element)
focal_class.full_signature: public static int getElementCount(IMolecularFormula formula, IElement element)
focal_class.identifier: getElementCount
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IElement element)
focal_class.return: int
focal_class.signature: int getElementCount(IMolecularFormula formula, IElement element)
focal_class.class_method_signature: MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, IIsotope isotope)
focal_class.full_signature: public static int getElementCount(IMolecularFormula formula, IIsotope isotope)
focal_class.identifier: getElementCount
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IIsotope isotope)
focal_class.return: int
focal_class.signature: int getElementCount(IMolecularFormula formula, IIsotope isotope)
focal_class.class_method_signature: MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, String symbol)
focal_class.full_signature: public static int getElementCount(IMolecularFormula formula, String symbol)
focal_class.identifier: getElementCount
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, String symbol)
focal_class.return: int
focal_class.signature: int getElementCount(IMolecularFormula formula, String symbol)
focal_class.class_method_signature: MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula, IElement element)
focal_class.full_signature: public static List<IIsotope> getIsotopes(IMolecularFormula formula, IElement element)
focal_class.identifier: getIsotopes
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IElement element)
focal_class.return: List<IIsotope>
focal_class.signature: List<IIsotope> getIsotopes(IMolecularFormula formula, IElement element)
focal_class.class_method_signature: MolecularFormulaManipulator.elements(IMolecularFormula formula)
focal_class.full_signature: public static List<IElement> elements(IMolecularFormula formula)
focal_class.identifier: elements
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: List<IElement>
focal_class.signature: List<IElement> elements(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.containsElement(IMolecularFormula formula, IElement element)
focal_class.full_signature: public static boolean containsElement(IMolecularFormula formula, IElement element)
focal_class.identifier: containsElement
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IElement element)
focal_class.return: boolean
focal_class.signature: boolean containsElement(IMolecularFormula formula, IElement element)
focal_class.class_method_signature: MolecularFormulaManipulator.removeElement(IMolecularFormula formula, IElement element)
focal_class.full_signature: public static IMolecularFormula removeElement(IMolecularFormula formula, IElement element)
focal_class.identifier: removeElement
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IElement element)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula removeElement(IMolecularFormula formula, IElement element)
focal_class.class_method_signature: MolecularFormulaManipulator.getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne)
focal_class.full_signature: public static String getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne)
focal_class.identifier: getString
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, String[] orderElements,
                                     boolean setOne)
focal_class.return: String
focal_class.signature: String getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne)
focal_class.class_method_signature: MolecularFormulaManipulator.appendElement(StringBuilder sb, Integer mass, int elem, int count)
focal_class.full_signature: private static void appendElement(StringBuilder sb, Integer mass, int elem, int count)
focal_class.identifier: appendElement
focal_class.modifiers: private static
focal_class.parameters: (StringBuilder sb, Integer mass, int elem, int count)
focal_class.return: void
focal_class.signature: void appendElement(StringBuilder sb, Integer mass, int elem, int count)
focal_class.class_method_signature: MolecularFormulaManipulator.getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne, boolean setMassNumber)
focal_class.full_signature: public static String getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne, boolean setMassNumber)
focal_class.identifier: getString
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, String[] orderElements,
                                     boolean setOne, boolean setMassNumber)
focal_class.return: String
focal_class.signature: String getString(IMolecularFormula formula, String[] orderElements,
                                     boolean setOne, boolean setMassNumber)
focal_class.class_method_signature: MolecularFormulaManipulator.getString(IMolecularFormula formula)
focal_class.full_signature: public static String getString(IMolecularFormula formula)
focal_class.identifier: getString
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: String
focal_class.signature: String getString(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getString(IMolecularFormula formula, boolean setOne)
focal_class.full_signature: public static String getString(IMolecularFormula formula, boolean setOne)
focal_class.identifier: getString
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, boolean setOne)
focal_class.return: String
focal_class.signature: String getString(IMolecularFormula formula, boolean setOne)
focal_class.class_method_signature: MolecularFormulaManipulator.getString(IMolecularFormula formula, boolean setOne, boolean setMassNumber)
focal_class.full_signature: public static String getString(IMolecularFormula formula, boolean setOne, boolean setMassNumber)
focal_class.identifier: getString
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, boolean setOne, boolean setMassNumber)
focal_class.return: String
focal_class.signature: String getString(IMolecularFormula formula, boolean setOne, boolean setMassNumber)
focal_class.class_method_signature: MolecularFormulaManipulator.putInOrder(String[] orderElements, IMolecularFormula formula)
focal_class.full_signature: public static List<IIsotope> putInOrder(String[] orderElements, IMolecularFormula formula)
focal_class.identifier: putInOrder
focal_class.modifiers: public static
focal_class.parameters: (String[] orderElements, IMolecularFormula formula)
focal_class.return: List<IIsotope>
focal_class.signature: List<IIsotope> putInOrder(String[] orderElements, IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getHillString(IMolecularFormula formula)
focal_class.full_signature: @Deprecated public static String getHillString(IMolecularFormula formula)
focal_class.identifier: getHillString
focal_class.modifiers: @Deprecated public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: String
focal_class.signature: String getHillString(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getHTML(IMolecularFormula formula)
focal_class.full_signature: public static String getHTML(IMolecularFormula formula)
focal_class.identifier: getHTML
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: String
focal_class.signature: String getHTML(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getHTML(IMolecularFormula formula, boolean chargeB, boolean isotopeB)
focal_class.full_signature: public static String getHTML(IMolecularFormula formula, boolean chargeB, boolean isotopeB)
focal_class.identifier: getHTML
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, boolean chargeB, boolean isotopeB)
focal_class.return: String
focal_class.signature: String getHTML(IMolecularFormula formula, boolean chargeB, boolean isotopeB)
focal_class.class_method_signature: MolecularFormulaManipulator.getHTML(IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes)
focal_class.full_signature: public static String getHTML(IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes)
focal_class.identifier: getHTML
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes)
focal_class.return: String
focal_class.signature: String getHTML(IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.full_signature: public static IMolecularFormula getMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (String stringMF, IChemObjectBuilder builder)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.class_method_signature: MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.full_signature: public static IMolecularFormula getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.identifier: getMajorIsotopeMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (String stringMF, IChemObjectBuilder builder)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(String stringMF, boolean assumeMajorIsotope,
              IChemObjectBuilder builder)
focal_class.full_signature: private static IMolecularFormula getMolecularFormula(String stringMF, boolean assumeMajorIsotope,
              IChemObjectBuilder builder)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: private static
focal_class.parameters: (String stringMF, boolean assumeMajorIsotope,
              IChemObjectBuilder builder)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(String stringMF, boolean assumeMajorIsotope,
              IChemObjectBuilder builder)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(String stringMF, IMolecularFormula formula)
focal_class.full_signature: public static IMolecularFormula getMolecularFormula(String stringMF, IMolecularFormula formula)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (String stringMF, IMolecularFormula formula)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(String stringMF, IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.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: MolecularFormulaManipulator.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: MolecularFormulaManipulator.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: MolecularFormulaManipulator.isSign(char c)
focal_class.full_signature: private static boolean isSign(char c)
focal_class.identifier: isSign
focal_class.modifiers: private static
focal_class.parameters: (char c)
focal_class.return: boolean
focal_class.signature: boolean isSign(char c)
focal_class.class_method_signature: MolecularFormulaManipulator.parseIsotope(CharIter iter,
                                          IMolecularFormula mf,
                                          boolean setMajor)
focal_class.full_signature: private static boolean parseIsotope(CharIter iter,
                                          IMolecularFormula mf,
                                          boolean setMajor)
focal_class.identifier: parseIsotope
focal_class.modifiers: private static
focal_class.parameters: (CharIter iter,
                                          IMolecularFormula mf,
                                          boolean setMajor)
focal_class.return: boolean
focal_class.signature: boolean parseIsotope(CharIter iter,
                                          IMolecularFormula mf,
                                          boolean setMajor)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(String stringMF, IMolecularFormula formula,
              boolean assumeMajorIsotope)
focal_class.full_signature: private static IMolecularFormula getMolecularFormula(String stringMF, IMolecularFormula formula,
              boolean assumeMajorIsotope)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: private static
focal_class.parameters: (String stringMF, IMolecularFormula formula,
              boolean assumeMajorIsotope)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(String stringMF, IMolecularFormula formula,
              boolean assumeMajorIsotope)
focal_class.class_method_signature: MolecularFormulaManipulator.parseCharge(CharIter iter)
focal_class.full_signature: private static int parseCharge(CharIter iter)
focal_class.identifier: parseCharge
focal_class.modifiers: private static
focal_class.parameters: (CharIter iter)
focal_class.return: int
focal_class.signature: int parseCharge(CharIter iter)
focal_class.class_method_signature: MolecularFormulaManipulator.findChargePosition(String formula)
focal_class.full_signature: private static int findChargePosition(String formula)
focal_class.identifier: findChargePosition
focal_class.modifiers: private static
focal_class.parameters: (String formula)
focal_class.return: int
focal_class.signature: int findChargePosition(String formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getTotalExactMass(IMolecularFormula formula)
focal_class.full_signature: @Deprecated public static double getTotalExactMass(IMolecularFormula formula)
focal_class.identifier: getTotalExactMass
focal_class.modifiers: @Deprecated public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getTotalExactMass(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.correctMass(double mass, Integer charge)
focal_class.full_signature: private static double correctMass(double mass, Integer charge)
focal_class.identifier: correctMass
focal_class.modifiers: private static
focal_class.parameters: (double mass, Integer charge)
focal_class.return: double
focal_class.signature: double correctMass(double mass, Integer charge)
focal_class.class_method_signature: MolecularFormulaManipulator.getTotalMassNumber(IMolecularFormula formula)
focal_class.full_signature: public static double getTotalMassNumber(IMolecularFormula formula)
focal_class.identifier: getTotalMassNumber
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getTotalMassNumber(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getExactMass(IsotopeFactory isofact, IIsotope atom)
focal_class.full_signature: private static double getExactMass(IsotopeFactory isofact, IIsotope atom)
focal_class.identifier: getExactMass
focal_class.modifiers: private static
focal_class.parameters: (IsotopeFactory isofact, IIsotope atom)
focal_class.return: double
focal_class.signature: double getExactMass(IsotopeFactory isofact, IIsotope atom)
focal_class.class_method_signature: MolecularFormulaManipulator.getMassOrAvg(IsotopeFactory isofact, IIsotope atom)
focal_class.full_signature: private static double getMassOrAvg(IsotopeFactory isofact, IIsotope atom)
focal_class.identifier: getMassOrAvg
focal_class.modifiers: private static
focal_class.parameters: (IsotopeFactory isofact, IIsotope atom)
focal_class.return: double
focal_class.signature: double getMassOrAvg(IsotopeFactory isofact, IIsotope atom)
focal_class.class_method_signature: MolecularFormulaManipulator.getMass(IMolecularFormula mf, int flav)
focal_class.full_signature: public static double getMass(IMolecularFormula mf, int flav)
focal_class.identifier: getMass
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula mf, int flav)
focal_class.return: double
focal_class.signature: double getMass(IMolecularFormula mf, int flav)
focal_class.class_method_signature: MolecularFormulaManipulator.getMass(IMolecularFormula mf)
focal_class.full_signature: public static double getMass(IMolecularFormula mf)
focal_class.identifier: getMass
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula mf)
focal_class.return: double
focal_class.signature: double getMass(IMolecularFormula mf)
focal_class.class_method_signature: MolecularFormulaManipulator.getNaturalExactMass(IMolecularFormula formula)
focal_class.full_signature: @Deprecated public static double getNaturalExactMass(IMolecularFormula formula)
focal_class.identifier: getNaturalExactMass
focal_class.modifiers: @Deprecated public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getNaturalExactMass(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getMajorIsotopeMass(IMolecularFormula formula)
focal_class.full_signature: @Deprecated public static double getMajorIsotopeMass(IMolecularFormula formula)
focal_class.identifier: getMajorIsotopeMass
focal_class.modifiers: @Deprecated public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getMajorIsotopeMass(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getTotalNaturalAbundance(IMolecularFormula formula)
focal_class.full_signature: public static double getTotalNaturalAbundance(IMolecularFormula formula)
focal_class.identifier: getTotalNaturalAbundance
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getTotalNaturalAbundance(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getDBE(IMolecularFormula formula)
focal_class.full_signature: public static double getDBE(IMolecularFormula formula)
focal_class.identifier: getDBE
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: double
focal_class.signature: double getDBE(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer)
focal_class.full_signature: public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(IAtomContainer atomContainer)
focal_class.class_method_signature: MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)
focal_class.full_signature: public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)
focal_class.identifier: getMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer, IMolecularFormula formula)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula)
focal_class.full_signature: public static IAtomContainer getAtomContainer(IMolecularFormula formula)
focal_class.identifier: getAtomContainer
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAtomContainer(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)
focal_class.full_signature: public static IAtomContainer getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)
focal_class.identifier: getAtomContainer
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula, IAtomContainer atomContainer)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)
focal_class.class_method_signature: MolecularFormulaManipulator.getAtomContainer(String formulaString, IChemObjectBuilder builder)
focal_class.full_signature: public static IAtomContainer getAtomContainer(String formulaString, IChemObjectBuilder builder)
focal_class.identifier: getAtomContainer
focal_class.modifiers: public static
focal_class.parameters: (String formulaString, IChemObjectBuilder builder)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAtomContainer(String formulaString, IChemObjectBuilder builder)
focal_class.class_method_signature: MolecularFormulaManipulator.generateOrderEle()
focal_class.full_signature: public static String[] generateOrderEle()
focal_class.identifier: generateOrderEle
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] generateOrderEle()
focal_class.class_method_signature: MolecularFormulaManipulator.generateOrderEle_Hill_NoCarbons()
focal_class.full_signature: private static String[] generateOrderEle_Hill_NoCarbons()
focal_class.identifier: generateOrderEle_Hill_NoCarbons
focal_class.modifiers: private static
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] generateOrderEle_Hill_NoCarbons()
focal_class.class_method_signature: MolecularFormulaManipulator.generateOrderEle_Hill_WithCarbons()
focal_class.full_signature: private static String[] generateOrderEle_Hill_WithCarbons()
focal_class.identifier: generateOrderEle_Hill_WithCarbons
focal_class.modifiers: private static
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] generateOrderEle_Hill_WithCarbons()
focal_class.class_method_signature: MolecularFormulaManipulator.compare(IMolecularFormula formula1, IMolecularFormula formula2)
focal_class.full_signature: public static boolean compare(IMolecularFormula formula1, IMolecularFormula formula2)
focal_class.identifier: compare
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula1, IMolecularFormula formula2)
focal_class.return: boolean
focal_class.signature: boolean compare(IMolecularFormula formula1, IMolecularFormula formula2)
focal_class.class_method_signature: MolecularFormulaManipulator.getHeavyElements(IMolecularFormula formula)
focal_class.full_signature: public static List<IElement> getHeavyElements(IMolecularFormula formula)
focal_class.identifier: getHeavyElements
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula formula)
focal_class.return: List<IElement>
focal_class.signature: List<IElement> getHeavyElements(IMolecularFormula formula)
focal_class.class_method_signature: MolecularFormulaManipulator.simplifyMolecularFormula(String formula)
focal_class.full_signature: public static String simplifyMolecularFormula(String formula)
focal_class.identifier: simplifyMolecularFormula
focal_class.modifiers: public static
focal_class.parameters: (String formula)
focal_class.return: String
focal_class.signature: String simplifyMolecularFormula(String formula)
focal_class.class_method_signature: MolecularFormulaManipulator.breakExtractor(String formula)
focal_class.full_signature: private static String breakExtractor(String formula)
focal_class.identifier: breakExtractor
focal_class.modifiers: private static
focal_class.parameters: (String formula)
focal_class.return: String
focal_class.signature: String breakExtractor(String formula)
focal_class.class_method_signature: MolecularFormulaManipulator.multipleExtractor(String formula)
focal_class.full_signature: private static String multipleExtractor(String formula)
focal_class.identifier: multipleExtractor
focal_class.modifiers: private static
focal_class.parameters: (String formula)
focal_class.return: String
focal_class.signature: String multipleExtractor(String formula)
focal_class.class_method_signature: MolecularFormulaManipulator.muliplier(String formula, int factor)
focal_class.full_signature: private static String muliplier(String formula, int factor)
focal_class.identifier: muliplier
focal_class.modifiers: private static
focal_class.parameters: (String formula, int factor)
focal_class.return: String
focal_class.signature: String muliplier(String formula, int factor)
focal_class.class_method_signature: MolecularFormulaManipulator.adjustProtonation(IMolecularFormula mf, int hcnt)
focal_class.full_signature: public static boolean adjustProtonation(IMolecularFormula mf, int hcnt)
focal_class.identifier: adjustProtonation
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula mf, int hcnt)
focal_class.return: boolean
focal_class.signature: boolean adjustProtonation(IMolecularFormula mf, int hcnt)
focal_class.class_method_signature: MolecularFormulaManipulator.addIsotopeDist(IMolecularFormula mf,
                                            IIsotope[] isotopes,
                                            int idx, int count)
focal_class.full_signature: private static boolean addIsotopeDist(IMolecularFormula mf,
                                            IIsotope[] isotopes,
                                            int idx, int count)
focal_class.identifier: addIsotopeDist
focal_class.modifiers: private static
focal_class.parameters: (IMolecularFormula mf,
                                            IIsotope[] isotopes,
                                            int idx, int count)
focal_class.return: boolean
focal_class.signature: boolean addIsotopeDist(IMolecularFormula mf,
                                            IIsotope[] isotopes,
                                            int idx, int count)
focal_class.class_method_signature: MolecularFormulaManipulator.getMostAbundant(IMolecularFormula mf)
focal_class.full_signature: public static IMolecularFormula getMostAbundant(IMolecularFormula mf)
focal_class.identifier: getMostAbundant
focal_class.modifiers: public static
focal_class.parameters: (IMolecularFormula mf)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMostAbundant(IMolecularFormula mf)
focal_class.class_method_signature: MolecularFormulaManipulator.getMostAbundant(IAtomContainer mol)
focal_class.full_signature: public static IMolecularFormula getMostAbundant(IAtomContainer mol)
focal_class.identifier: getMostAbundant
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer mol)
focal_class.return: IMolecularFormula
focal_class.signature: IMolecularFormula getMostAbundant(IAtomContainer mol)
focal_method.body: public static double getDBE(IMolecularFormula formula) throws CDKException {
          int valencies[] = new int[5];
          IAtomContainer ac = getAtomContainer(formula);
          AtomTypeFactory factory = AtomTypeFactory.getInstance(
                  "org/openscience/cdk/config/data/structgen_atomtypes.xml", ac.getBuilder());
  
          for (int f = 0; f < ac.getAtomCount(); f++) {
              IAtomType[] types = factory.getAtomTypes(ac.getAtom(f).getSymbol());
              if (types.length == 0)
                  throw new CDKException(
                          "Calculation of double bond equivalents not possible due to problems with element "
                                  + ac.getAtom(f).getSymbol());
              //			valencies[(int) (types[0].getBondOrderSum() + ac.getAtom(f).getFormalCharge())]++;
              valencies[types[0].getBondOrderSum().intValue()]++;
          }
          return 1 + (valencies[4]) + (valencies[3] / 2) - (valencies[1] / 2);
      }
focal_method.class_method_signature: MolecularFormulaManipulator.getDBE(IMolecularFormula formula)
focal_method.full_signature: public static double getDBE(IMolecularFormula formula)
focal_method.identifier: getDBE
focal_method.invocations: getAtomContainer getInstance getBuilder getAtomCount getAtomTypes getSymbol getAtom getSymbol getAtom intValue getBondOrderSum
focal_method.modifiers: public static
focal_method.parameters: (IMolecularFormula formula)
focal_method.return: double
focal_method.signature: double getDBE(IMolecularFormula formula)