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 test3() {
          String formula = "(C27H33N3O8)2.2HNO3.3H2O";
          String simplifyMF = MolecularFormulaManipulator.simplifyMolecularFormula(formula);
          Assert.assertEquals("C54H74N8O25", simplifyMF);
      }
test_case.class_method_signature: MolecularFormulaManipulatorTest.test3()
test_case.full_signature: @Test public void test3()
test_case.identifier: test3
test_case.invocations: simplifyMolecularFormula assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void test3()
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 String simplifyMolecularFormula(String formula) {
          String newFormula = formula;
          char thisChar;
  
          if (formula.contains(" ")) {
              newFormula = newFormula.replace(" ", "");
          }
          if (!formula.contains(".")) return breakExtractor(formula);
  
          List<String> listMF = new ArrayList<String>();
          while (newFormula.contains(".")) {
              int pos = newFormula.indexOf('.');
              String thisFormula = newFormula.substring(0, pos);
              if (thisFormula.charAt(0) >= '0' && thisFormula.charAt(0) <= '9')
                  thisFormula = multipleExtractor(thisFormula);
  
              if (thisFormula.contains("(")) thisFormula = breakExtractor(thisFormula);
  
              listMF.add(thisFormula);
              thisFormula = newFormula.substring(pos + 1, newFormula.length());
              if (!thisFormula.contains(".")) {
  
                  if (thisFormula.charAt(0) >= '0' && thisFormula.charAt(0) <= '9')
                      thisFormula = multipleExtractor(thisFormula);
  
                  if (thisFormula.contains("(")) thisFormula = breakExtractor(thisFormula);
  
                  listMF.add(thisFormula);
              }
              newFormula = thisFormula;
          }
          if (newFormula.contains("(")) newFormula = breakExtractor(newFormula);
  
          String recentElementSymbol = "";
          String recentElementCountString = "0";
  
          List<String> eleSymb = new ArrayList<String>();
          List<Integer> eleCount = new ArrayList<Integer>();
          for (int i = 0; i < listMF.size(); i++) {
              String thisFormula = listMF.get(i);
              for (int f = 0; f < thisFormula.length(); f++) {
                  thisChar = thisFormula.charAt(f);
                  if (f < thisFormula.length()) {
                      if (thisChar >= 'A' && thisChar <= 'Z') {
                          recentElementSymbol = String.valueOf(thisChar);
                          recentElementCountString = "0";
                      }
                      if (thisChar >= 'a' && thisChar <= 'z') {
                          recentElementSymbol += thisChar;
                      }
                      if (thisChar >= '0' && thisChar <= '9') {
                          recentElementCountString += thisChar;
                      }
                  }
                  if (f == thisFormula.length() - 1
                          || (thisFormula.charAt(f + 1) >= 'A' && thisFormula.charAt(f + 1) <= 'Z')) {
                      int posit = eleSymb.indexOf(recentElementSymbol);
                      int count = Integer.valueOf(recentElementCountString);
                      if (posit == -1) {
                          eleSymb.add(recentElementSymbol);
                          eleCount.add(count);
                      } else {
                          int countP = Integer.valueOf(recentElementCountString);
                          if (countP == 0) countP = 1;
                          int countA = eleCount.get(posit);
                          if (countA == 0) countA = 1;
                          int value = countP + countA;
                          eleCount.remove(posit);
                          eleCount.add(posit, value);
                      }
  
                  }
              }
          }
          String newF = "";
          for (int i = 0; i < eleCount.size(); i++) {
              String element = eleSymb.get(i);
              int num = eleCount.get(i);
              if (num == 0)
                  newF += element;
              else
                  newF += element + num;
  
          }
          return newF;
      }
focal_method.class_method_signature: MolecularFormulaManipulator.simplifyMolecularFormula(String formula)
focal_method.full_signature: public static String simplifyMolecularFormula(String formula)
focal_method.identifier: simplifyMolecularFormula
focal_method.invocations: contains replace contains breakExtractor contains indexOf substring charAt charAt multipleExtractor contains breakExtractor add substring length contains charAt charAt multipleExtractor contains breakExtractor add contains breakExtractor size get length charAt length valueOf length charAt charAt indexOf valueOf add add valueOf get remove add size get get
focal_method.modifiers: public static
focal_method.parameters: (String formula)
focal_method.return: String
focal_method.signature: String simplifyMolecularFormula(String formula)