Package com.chemaxon.calculations.elemanal

Interface ElementalAnalysis

  • @PublicAPI
public interface ElementalAnalysis
    Calculates molecular formula, mass, MS mass and composition.

    API usage example: 

         // build the analysis
     ElementalAnalysis elemanal = ...

     double exactMass = elemanal.exactMass();
     double mass = elemanal.mass();
     BigDecimal massPrecision = elemanal.massPrecision();
     BigDecimal atomCount1 = elemanal.atomCount(8); // oxygen atom count
     BigDecimal atomCount3 = elemanal.atomCount(8, 16); // oxygen isotope count with massno=16
     String formula = elemanal.formula();
     String composition = elemanal.composition(2); // precision=2

     // now use the results...
      }
    Since:
    Marvin 16.4.18

    • Method Summary

      All Methods Instance Methods Abstract Methods Default Methods 
      Modifier and Type Method Description
      BigDecimal atomCount()
      Calculates the number of atoms in the molecule.
      BigDecimal atomCount​(int z)
      Calculates the number of atoms of a given element in the molecule (including its isotopes).
      BigDecimal atomCount​(int z, int m)
      Calculates the number of atoms of a given element in the molecule.
      Map<com.chemaxon.calculations.elemanal.formula.FormulaAtom,​BigDecimal> composition()
      Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
      BigDecimal exactMass()
      Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
      BigDecimal formalCharge()
      Calculates the formal (total) charge of the molecule.
      String formula()
      Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
      default String formula​(com.chemaxon.calculations.elemanal.FormulaGenerationRule... rules)
      Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
      String formula​(Set<com.chemaxon.calculations.elemanal.FormulaGenerationRule> rules)
      Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
      Map<BigDecimal,​BigDecimal> isotopeDistribution()
      Calculates the isotopic distributions for the molecule.
      BigDecimal mass()
      Calculates the molecular weight of the molecule.
      BigDecimal nominalMass()
      Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
      BigDecimal sumOfRadicals()
      Calculates the sum of the radicals of all atoms of the molecule.

    • Method Detail

      • atomCount

        BigDecimal atomCount()
        Calculates the number of atoms in the molecule.
        Returns:
        number of atoms

      • atomCount

        BigDecimal atomCount​(int z)
        Calculates the number of atoms of a given element in the molecule (including its isotopes).
        Parameters:
        z - atomic number of the atom (protons)
        Returns:
        number of the specified atoms

      • atomCount

        BigDecimal atomCount​(int z,
                     int m)
        Calculates the number of atoms of a given element in the molecule.
        Parameters:
        z - atomic number of the atom (protons)
        m - mass number of the atom (protons + neutrons)
        Returns:
        number of the specified atoms

      • mass

        BigDecimal mass()
        Calculates the molecular weight of the molecule.

        The result is rounded according to the decimals of the lowest precision atomic mass value.

        Returns:
        molecular weight of the molecule

      • exactMass

        BigDecimal exactMass()
        Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
        Returns:
        weight of the molecule ion

      • nominalMass

        BigDecimal nominalMass()
        Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
        Returns:
        nominal mass of the molecule

      • formula

        String formula()
        Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.

        Note: Isotopes and charged elements are separated.

        Returns:
        formula representation of elements

      • formula

        String formula​(Set<com.chemaxon.calculations.elemanal.FormulaGenerationRule> rules)
        Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
        Returns:
        formula representation of elements
        See Also:
        FormulaGenerationRule

      • formula

        default String formula​(com.chemaxon.calculations.elemanal.FormulaGenerationRule... rules)
        Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
        Returns:
        formula representation of elements
        See Also:
        FormulaGenerationRule

      • formalCharge

        BigDecimal formalCharge()
        Calculates the formal (total) charge of the molecule.
        Returns:
        the formal charge of the molecule

      • sumOfRadicals

        BigDecimal sumOfRadicals()
        Calculates the sum of the radicals of all atoms of the molecule.
        Returns:
        the sum of the radicals of all atoms

      • isotopeDistribution

        Map<BigDecimal,​BigDecimal> isotopeDistribution()
        Calculates the isotopic distributions for the molecule.

        Takes charge into account. The maximum of distribution is normalized to 1.

        Returns:
        the map of masses and distributions.
        Throws:
        ArithmeticException - if the molecule contains non-integer fragment multipliers, e.g. 2Na.1.5H2O

      • composition

        Map<com.chemaxon.calculations.elemanal.formula.FormulaAtom,​BigDecimal> composition()
        Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
        Returns:
        molecular composition