Package chemaxon.calculations

Class 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 Detail

      • ElementalAnalyser

        public ElementalAnalyser()

    • Method Detail

      • getSmolecule

        public Smolecule getSmolecule()
        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
public void setMolecule​(Smolecule mol)
        Deprecated.
        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