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

Author:

Laszlo Antal

Method Summary

Modifier and Type	Method and Description
java.math.BigDecimal	atomCount() Calculates the number of atoms in the molecule.
java.math.BigDecimal	atomCount(int z) Calculates the number of atoms of a given element in the molecule (including its isotopes).
java.math.BigDecimal	atomCount(int z, int m) Calculates the number of atoms of a given element in the molecule.
java.util.Map<com.chemaxon.calculations.elemanal.formula.FormulaAtom,java.math.BigDecimal>	composition() Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
java.math.BigDecimal	exactMass() Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
java.lang.String	formula() Calculates the molecular formula which is a string listing all atom types and their occurrence in the molecule.
java.lang.String	formula(java.util.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.
java.util.Map<java.math.BigDecimal,java.math.BigDecimal>	isotopeDistribution() Calculates the isotopic distributions for the molecule.
java.math.BigDecimal	mass() Calculates the molecular weight of the molecule.

Method Detail

atomCount

java.math.BigDecimal atomCount()

Calculates the number of atoms in the molecule.

Returns:

number of atoms

atomCount

java.math.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

java.math.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

java.math.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

java.math.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

formula

java.lang.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

java.lang.String formula(java.util.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

isotopeDistribution

java.util.Map<java.math.BigDecimal,java.math.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:

java.lang.ArithmeticException - if the molecule contains non-integer fragment multipliers, e.g. 2Na.1.5H2O

composition

java.util.Map<com.chemaxon.calculations.elemanal.formula.FormulaAtom,java.math.BigDecimal> composition()

Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

Returns:

molecular composition