Package chemaxon.calculations

Class ElementalAnalyser

java.lang.Object
chemaxon.calculations.ElementalAnalyser
@PublicApi public class ElementalAnalyser extends Object
Calculates molecular formula, mass, MS mass and composition.

API usage example: 

    ElementalAnalyser elemanal = new ElementalAnalyser();

    // run plugin on target molecules
    MolImporter mi = new MolImporter(input.smiles);
    Molecule mol = null;
    while ((mol = mi.read()) != null) {

        // set target molecule
        elemanal.setMolecule(mol);

        double exactMass = elemanal.exactMass();
        double mass = elemanal.mass();
        int massPrecision = elemanal.massPrecision();
        int atomCount1 = elemanal.atomCount(8); // oxygen atom count
        int atomCount2 = elemanal.atomCount(8, 0); // non-isotope oxygen count
        int atomCount3 = elemanal.atomCount(8, 16); // oxygen isotope count with massno=16
        String formula = elemanal.formula();
        String isotopeFormula = elemanal.isotopeFormula();
        String composition = elemanal.composition(2); // precision=2
        String isotopeComposition = elemanal.isotopeComposition(2); // precision=2

        // now use the results...
    }

  • Constructor Summary

    Constructors
    Constructor
    Description
    ElementalAnalyser()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    atomCount()
    Calculates the number of atoms in the molecule.
    int
    atomCount(int z)
    Calculates the number of atoms of a given element in the molecule (including its isotopes).
    int
    atomCount(int z, int m)
    Calculates the number of atoms of a given element in the molecule.
    String
    composition(int precision)
    Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
    String
    dotDisconnectedFormula()
    Calculates the dot-disconnected molecular formula of a multifragment molecule.
    String
    dotDisconnectedIsotopeFormula()
    Calculates the dot-disconnected isotope formula of a multifragment molecule.
    String
    dotDisconnectedIsotopeFormula(boolean symbolD)
    Calculates the dot-disconnected isotope formula of a multifragment molecule.
    double
    exactMass()
    Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
    int
    exactMassPrecision()
    Calculates the precision of the monoisitopic weight (number of significant decimal digits).
    String
    formula()
    Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
    String
    formula(int digits)
    Calculates a fixed digit sortable molecular formula.
    Smolecule
    getSmolecule()
    Deprecated, for removal: This API element is subject to removal in a future version.
    String
    isotopeComposition(int precision)
    Gets the molecular composition (w/w%).
    String
    isotopeComposition(int precision, boolean symbolD)
    Gets the molecular composition (w/w%).
    String
    isotopeFormula()
    Calculates the molecular formula (isotopes are separated).
    String
    isotopeFormula(boolean symbolD)
    Calculates the molecular formula (isotopes are separated).
    double
    mass()
    Calculates the molecular weight of the molecule.
    int
    massPrecision()
    Calculates the precision of the molecular weight (number of decimal digits).
    void
    setMolecule(MoleculeGraph mol)
    Specifies a molecule to calculate with.
    void
    setMolecule(Smolecule mol)
    Deprecated, for removal: This API element is subject to removal in a future version.
    as of Marvin 6.0, replaced by setMolecule(MoleculeGraph mol).
    void
    setMolecule(String formula)
    Specifies a molecule to calculate with.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • ElementalAnalyser

      public ElementalAnalyser()

  • Method Details

    • getSmolecule

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2026) public Smolecule getSmolecule()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Retrieves the input molecule
      Returns:
      the molecule to calculate with

    • setMolecule

      public void setMolecule(String formula) throws IllegalArgumentException
      Specifies a molecule to calculate with.
      Parameters:
      formula - the molecular formula to calculate with (e.g. C3H10, C6H11N3.2(HCl))
      Throws:
      IllegalArgumentException - if the formula is invalid
      Since:
      Marvin 5.3.2

    • setMolecule

      public void setMolecule(MoleculeGraph mol)
      Specifies a molecule to calculate with.
      Parameters:
      mol - the molecule to calculate with

    • setMolecule

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setMolecule(Smolecule mol)
      Deprecated, for removal: This API element is subject to removal in a future version.
      as of Marvin 6.0, replaced by setMolecule(MoleculeGraph mol).
      Specifies a molecule to calculate with.
      Parameters:
      mol - the molecule to calculate with
      Since:
      Marvin 5.3, 04/29/2009

    • atomCount

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

    • atomCount

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

    • atomCount

      public int atomCount(int z, int m)
      Calculates the number of atoms of a given element in the molecule. When m is 0, number of the given element atoms is returned, but its isotopes are not included
      Parameters:
      z - atomic number of the atom (protons)
      m - mass number of the atom (protons + neutrons)
      Returns:
      number of the specified atoms

    • mass

      public double 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 weigth of the molecule

    • massPrecision

      public int massPrecision()
      Calculates the precision of the molecular weight (number of decimal digits).
      Returns:
      the number of significant digits after the decimal point

    • exactMass

      public double exactMass()
      Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
      Returns:
      weight of the molecule ion

    • exactMassPrecision

      public int exactMassPrecision()
      Calculates the precision of the monoisitopic weight (number of significant decimal digits).
      Returns:
      the number of significant digits after the decimal point

    • formula

      public String formula()
      Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule. For example the formula of benzene is C6H6.
      Returns:
      molecular formula

    • formula

      public String formula(int digits)
      Calculates a fixed digit sortable molecular formula. If the digits parameter is 4, then the formula of benzene will be "C0006H0006".
      Parameters:
      digits - number of minimum digits
      Returns:
      molecular formula

    • isotopeFormula

      public String isotopeFormula()
      Calculates the molecular formula (isotopes are separated). For example, it returns C7D5NaO2 for the deuterated sodium benzoate.
      Returns:
      isotope formula

    • isotopeFormula

      public String isotopeFormula(boolean symbolD)
      Calculates the molecular formula (isotopes are separated). For example, it returns C7[2H]5NaO2 or C7D5NaO2 for the deuterated sodium benzoate depending on symbolD parameter.
      Parameters:
      symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]
      Returns:
      isotope formula

    • dotDisconnectedFormula

      public String dotDisconnectedFormula()
      Calculates the dot-disconnected molecular formula of a multifragment molecule. For example, it returns C7H5O2.Na for sodium benzoate.
      Returns:
      the dot diconnected formula of the molecule
      Since:
      Marvin 4.0.5

    • dotDisconnectedIsotopeFormula

      public String dotDisconnectedIsotopeFormula()
      Calculates the dot-disconnected isotope formula of a multifragment molecule. For example, it returns C7D5O2.Na for the deuterated sodium benzoate.
      Returns:
      the dot diconnected isotope formula of the molecule
      Since:
      Marvin 5.0

    • dotDisconnectedIsotopeFormula

      public String dotDisconnectedIsotopeFormula(boolean symbolD)
      Calculates the dot-disconnected isotope formula of a multifragment molecule. For example, it returns C7[2H]5O2.Na or C7D5O2.Na for the deuterated sodium benzoate depending on symbolD parameter.
      Parameters:
      symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]
      Returns:
      the dot diconnected isotope formula of the molecule
      Since:
      Marvin 5.0

    • composition

      public String composition(int precision)
      Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
      Returns:
      molecular composition

    • isotopeComposition

      public String isotopeComposition(int precision)
      Gets the molecular composition (w/w%). Isotopes are separate atom types.
      Parameters:
      precision - number of decimal digits
      Returns:
      molecular composition

    • isotopeComposition

      public String isotopeComposition(int precision, boolean symbolD)
      Gets the molecular composition (w/w%). Isotopes are separate atom types.
      Parameters:
      precision - number of decimal digits
      symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]
      Returns:
      molecular composition