Interface ElementalAnalysis
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@PublicAPI public interface ElementalAnalysis
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Method Summary
All Methods Instance Methods Abstract 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.String
formula()
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.
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Method Detail
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atomCount
BigDecimal atomCount()
Calculates the number of atoms in the molecule.- Returns:
- number of atoms
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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
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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
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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
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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
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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
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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
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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
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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
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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
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