Uses of Interface
org.openscience.cdk.interfaces.IMolecularFormula

Packages that use IMolecularFormula

Package	Description
org.openscience.cdk.config
org.openscience.cdk.debug
org.openscience.cdk.formula
org.openscience.cdk.formula.rules
org.openscience.cdk.interfaces
org.openscience.cdk.silent
org.openscience.cdk.tools.manipulator

Uses of IMolecularFormula in org.openscience.cdk.config

Methods in org.openscience.cdk.config with parameters of type IMolecularFormula

Modifier and Type	Method	Description
static void	Isotopes.clearMajorIsotopes(IMolecularFormula formula)	Clear the isotope information from istopes that are major (e.g.

Uses of IMolecularFormula in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IMolecularFormula

Modifier and Type	Class	Description
class	DebugMolecularFormula	Debugging implementation of IMolecularFormula.

Methods in org.openscience.cdk.debug that return IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	DebugMolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
IMolecularFormula	DebugMolecularFormula.addIsotope(IIsotope isotope)	Adds an Isotope to this MolecularFormula one time.
IMolecularFormula	DebugMolecularFormula.addIsotope(IIsotope isotope, int count)	Adds an Isotope to this MolecularFormula in a number of occurrences.
IMolecularFormula	DebugAdductFormula.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.
IMolecularFormula	DebugMolecularFormulaSet.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.

Methods in org.openscience.cdk.debug that return types with arguments of type IMolecularFormula

Modifier and Type	Method	Description
Iterator<IMolecularFormula>	DebugAdductFormula.iterator()	Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
Iterator<IMolecularFormula>	DebugMolecularFormulaSet.iterator()	Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
Iterable<IMolecularFormula>	DebugAdductFormula.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
Iterable<IMolecularFormula>	DebugMolecularFormulaSet.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.

Methods in org.openscience.cdk.debug with parameters of type IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	DebugMolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
void	DebugAdductFormula.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
void	DebugMolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
boolean	DebugAdductFormula.contains(IMolecularFormula formula)	True, if the AdductFormula contains the given IMolecularFormula object.
boolean	DebugMolecularFormulaSet.contains(IMolecularFormula formula)	True, if the MolecularFormulaSet contains the given IMolecularFormula object.
void	DebugAdductFormula.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.
void	DebugMolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.

Constructors in org.openscience.cdk.debug with parameters of type IMolecularFormula

Modifier	Constructor	Description
	DebugAdductFormula(IMolecularFormula formula)
	DebugMolecularFormulaSet(IMolecularFormula formula)

Uses of IMolecularFormula in org.openscience.cdk.formula

Classes in org.openscience.cdk.formula that implement IMolecularFormula

Modifier and Type	Class	Description
class	MolecularFormula	Class defining a molecular formula object.

Methods in org.openscience.cdk.formula that return IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	MolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
IMolecularFormula	MolecularFormula.addIsotope(IIsotope isotope)	Adds an Isotope to this MolecularFormula one time.
IMolecularFormula	MolecularFormula.addIsotope(IIsotope isotope, int count)	Adds an Isotope to this MolecularFormula in a number of occurrences.
IMolecularFormula	IsotopeContainer.getFormula()	Get the IMolecularFormula object of this container.
IMolecularFormula	AdductFormula.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.
IMolecularFormula	MolecularFormulaSet.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.
IMolecularFormula	MolecularFormulaGenerator.getNextFormula()	Returns next generated formula or null in case no new formula was found (search is finished).
IMolecularFormula	MolecularFormulaChecker.isValid(IMolecularFormula formula)	Validate if a IMolecularFormula is valid.

Methods in org.openscience.cdk.formula that return types with arguments of type IMolecularFormula

Modifier and Type	Method	Description
List<IMolecularFormula>	IsotopeContainer.getFormulas()	Access the formulas of this isotope container.
Iterator<IMolecularFormula>	AdductFormula.iterator()	Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
Iterator<IMolecularFormula>	MolecularFormulaSet.iterator()	Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
Iterable<IMolecularFormula>	AdductFormula.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
Iterable<IMolecularFormula>	MolecularFormulaSet.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.

Methods in org.openscience.cdk.formula with parameters of type IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	MolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
void	IsotopeContainer.addFormula(IMolecularFormula formula)	Add a formula to this isotope container.
void	AdductFormula.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
void	MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
boolean	AdductFormula.contains(IMolecularFormula formula)	True, if the AdductFormula contains the given IMolecularFormula object.
boolean	MolecularFormulaSet.contains(IMolecularFormula formula)	True, if the MolecularFormulaSet contains the given IMolecularFormula object.
IsotopePattern	IsotopePatternGenerator.getIsotopes(IMolecularFormula molFor)	Get all combinatorial chemical isotopes given a structure.
IMolecularFormula	MolecularFormulaChecker.isValid(IMolecularFormula formula)	Validate if a IMolecularFormula is valid.
Double	MolecularFormulaChecker.isValidSum(IMolecularFormula formula)	Validate if a IMolecularFormula is valid.
void	AdductFormula.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.
void	MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.
void	IsotopeContainer.setFormula(IMolecularFormula formula)	Set IMolecularFormula object of this container.

Constructors in org.openscience.cdk.formula with parameters of type IMolecularFormula

Modifier	Constructor	Description
	AdductFormula(IMolecularFormula formula)	Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).
	IsotopeContainer(IMolecularFormula formula, double intensity)	Constructor of the IsotopeContainer object setting a IMolecularFormula object and intensity value.
	MolecularFormulaSet(IMolecularFormula formula)	Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).

Uses of IMolecularFormula in org.openscience.cdk.formula.rules

Methods in org.openscience.cdk.formula.rules with parameters of type IMolecularFormula

Modifier and Type	Method	Description
List<Double>	RDBERule.getRDBEValue(IMolecularFormula formula)	Method to extract the Ring Double Bond Equivalents (RDB) value.
double	ChargeRule.validate(IMolecularFormula formula)	Validate the charge of this IMolecularFormula.
double	ElementRule.validate(IMolecularFormula formula)	Validate the occurrence of this IMolecularFormula.
double	IRule.validate(IMolecularFormula formula)	Analyze the validity for the given IMolecularFormula.
double	IsotopePatternRule.validate(IMolecularFormula formula)	Validate the isotope pattern of this IMolecularFormula.
double	MMElementRule.validate(IMolecularFormula formula)	Validate the occurrence of this IMolecularFormula.
double	NitrogenRule.validate(IMolecularFormula formula)	Validate the nitrogen rule of this IMolecularFormula.
double	RDBERule.validate(IMolecularFormula formula)	Validate the RDBRule of this IMolecularFormula.
boolean	RDBERule.validate(IMolecularFormula formula, double value)	Validate the ion state.
double	ToleranceRangeRule.validate(IMolecularFormula formula)	Validate the Tolerance Range of this IMolecularFormula.

Uses of IMolecularFormula in org.openscience.cdk.interfaces

Methods in org.openscience.cdk.interfaces that return IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	IMolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
IMolecularFormula	IMolecularFormula.addIsotope(IIsotope isotope)	Adds an Isotope to this MolecularFormula one time.
IMolecularFormula	IMolecularFormula.addIsotope(IIsotope isotope, int count)	Adds an Isotope to this MolecularFormula in a number of occurrences.
IMolecularFormula	IMolecularFormulaSet.getMolecularFormula(int position)	Returns the IMolecularFormula at position number in the chemObject.

Methods in org.openscience.cdk.interfaces that return types with arguments of type IMolecularFormula

Modifier and Type	Method	Description
Iterable<IMolecularFormula>	IMolecularFormulaSet.molecularFormulas()	Returns the array of IMolecularFormula of this chemObject.

Methods in org.openscience.cdk.interfaces with parameters of type IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	IMolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
void	IMolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)	Adds an IMolecularFormula to this chemObject.
boolean	IMolecularFormulaSet.contains(IMolecularFormula formula)	True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
void	IMolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)	Removes the given IMolecularFormula from the IMolecularFormulaSet.

Uses of IMolecularFormula in org.openscience.cdk.silent

Classes in org.openscience.cdk.silent that implement IMolecularFormula

Modifier and Type	Class	Description
class	MolecularFormula	Class defining a molecular formula object.

Methods in org.openscience.cdk.silent that return IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	MolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
IMolecularFormula	MolecularFormula.addIsotope(IIsotope isotope)	Adds an Isotope to this MolecularFormula one time.
IMolecularFormula	MolecularFormula.addIsotope(IIsotope isotope, int count)	Adds an Isotope to this MolecularFormula in a number of occurrences.
IMolecularFormula	AdductFormula.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.
IMolecularFormula	MolecularFormulaSet.getMolecularFormula(int position)	Returns the MolecularFormula at position number in the chemObject.

Methods in org.openscience.cdk.silent that return types with arguments of type IMolecularFormula

Modifier and Type	Method	Description
Iterator<IMolecularFormula>	AdductFormula.iterator()	Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
Iterator<IMolecularFormula>	MolecularFormulaSet.iterator()	Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
Iterable<IMolecularFormula>	AdductFormula.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
Iterable<IMolecularFormula>	MolecularFormulaSet.molecularFormulas()	Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.

Methods in org.openscience.cdk.silent with parameters of type IMolecularFormula

Modifier and Type	Method	Description
IMolecularFormula	MolecularFormula.add(IMolecularFormula formula)	Adds an molecularFormula to this MolecularFormula.
void	AdductFormula.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
void	MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)	Adds an molecularFormula to this chemObject.
boolean	AdductFormula.contains(IMolecularFormula formula)	True, if the AdductFormula contains the given IMolecularFormula object.
boolean	MolecularFormulaSet.contains(IMolecularFormula formula)	True, if the MolecularFormulaSet contains the given IMolecularFormula object.
void	AdductFormula.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.
void	MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)	Removes an IMolecularFormula from this chemObject.

Constructors in org.openscience.cdk.silent with parameters of type IMolecularFormula

Modifier	Constructor	Description
	AdductFormula(IMolecularFormula formula)	Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).
	MolecularFormulaSet(IMolecularFormula formula)	Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).

Uses of IMolecularFormula in org.openscience.cdk.tools.manipulator

Methods in org.openscience.cdk.tools.manipulator that return IMolecularFormula

Modifier and Type	Method	Description
static IMolecularFormula	MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder)	Construct an instance of IMolecularFormula, initialized with a molecular formula string.
static IMolecularFormula	MolecularFormulaRangeManipulator.getMaximalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder)	Returns the maximal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
static IMolecularFormula	MolecularFormulaSetManipulator.getMaxOccurrenceElements(IMolecularFormulaSet mfSet)	Extract from a set of MolecularFormula the maximum occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
static IMolecularFormula	MolecularFormulaRangeManipulator.getMinimalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder)	Returns the minimal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
static IMolecularFormula	MolecularFormulaSetManipulator.getMinOccurrenceElements(IMolecularFormulaSet mfSet)	Extract from a set of MolecularFormula the minimal occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(String stringMF, IChemObjectBuilder builder)	Construct an instance of IMolecularFormula, initialized with a molecular formula string.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(String stringMF, IMolecularFormula formula)	add in a instance of IMolecularFormula the elements extracts form molecular formula string.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer)	Method that actually does the work of convert the atomContainer to IMolecularFormula.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)	Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.
static IMolecularFormula	MolecularFormulaManipulator.getMostAbundant(IAtomContainer mol)	Compute the most abundant MF.
static IMolecularFormula	MolecularFormulaManipulator.getMostAbundant(IMolecularFormula mf)	Compute the most abundant MF.
static IMolecularFormula	MolecularFormulaManipulator.removeElement(IMolecularFormula formula, IElement element)	Removes all isotopes from a given element in the MolecularFormula.

Methods in org.openscience.cdk.tools.manipulator with parameters of type IMolecularFormula

Modifier and Type	Method	Description
static boolean	MolecularFormulaManipulator.adjustProtonation(IMolecularFormula mf, int hcnt)	Adjust the protonation of a molecular formula.
static boolean	MolecularFormulaManipulator.compare(IMolecularFormula formula1, IMolecularFormula formula2)	Compare two IMolecularFormula looking at type and number of IIsotope and charge of the formula.
static boolean	MolecularFormulaSetManipulator.contains(IMolecularFormulaSet formulaSet, IMolecularFormula formula)	True, if the IMolecularFormulaSet contains the given IMolecularFormula but not as object.
static boolean	MolecularFormulaManipulator.containsElement(IMolecularFormula formula, IElement element)	True, if the MolecularFormula contains the given element as IIsotope object.
static List<IElement>	MolecularFormulaManipulator.elements(IMolecularFormula formula)	Get a list of all Elements which are contained molecular.
static IAtomContainer	MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula)	Method that actually does the work of convert the IMolecularFormula to IAtomContainer.
static IAtomContainer	MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)	Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.
static int	MolecularFormulaManipulator.getAtomCount(IMolecularFormula formula)	Checks a set of Nodes for the occurrence of each isotopes instance in the molecular formula.
static double	MolecularFormulaManipulator.getDBE(IMolecularFormula formula)	Returns the number of double bond equivalents in this molecule.
static int	MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, String symbol)	Occurrences of a given element in a molecular formula.
static int	MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, IElement element)	Checks a set of Nodes for the occurrence of the isotopes in the molecular formula from a particular IElement.
static int	MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, IIsotope isotope)	Occurrences of a given element from an isotope in a molecular formula.
static List<IElement>	MolecularFormulaManipulator.getHeavyElements(IMolecularFormula formula)	Returns a set of nodes excluding all the hydrogens.
static String	MolecularFormulaManipulator.getHillString(IMolecularFormula formula)	Deprecated. Use MolecularFormulaManipulator.getString(org.openscience.cdk.interfaces.IMolecularFormula)
static String	MolecularFormulaManipulator.getHTML(IMolecularFormula formula)	Returns the string representation of the molecular formula based on Hill System with numbers wrapped in <sub></sub> tags.
static String	MolecularFormulaManipulator.getHTML(IMolecularFormula formula, boolean chargeB, boolean isotopeB)	Returns the string representation of the molecular formula based on Hill System with numbers wrapped in <sub></sub> tags and the isotope of each Element in <sup></sup> tags and the total charge of IMolecularFormula in <sup></sup> tags.
static String	MolecularFormulaManipulator.getHTML(IMolecularFormula formula, String[] orderElements, boolean showCharge, boolean showIsotopes)	Returns the string representation of the molecular formula with numbers wrapped in <sub></sub> tags and the isotope of each Element in <sup></sup> tags and the total showCharge of IMolecularFormula in <sup></sup> tags.
static List<IIsotope>	MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula, IElement element)	Get a list of IIsotope from a given IElement which is contained molecular.
static double	MolecularFormulaManipulator.getMajorIsotopeMass(IMolecularFormula formula)	Deprecated. use MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MonoIsotopic.
static double	MolecularFormulaManipulator.getMass(IMolecularFormula mf)	Calculate the mass of a formula, this function takes an optional 'mass flavour' that switches the computation type.
static double	MolecularFormulaManipulator.getMass(IMolecularFormula mf, int flav)	Calculate the mass of a formula, this function takes an optional 'mass flavour' that switches the computation type.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(String stringMF, IMolecularFormula formula)	add in a instance of IMolecularFormula the elements extracts form molecular formula string.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)	Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.
static IMolecularFormula	MolecularFormulaManipulator.getMostAbundant(IMolecularFormula mf)	Compute the most abundant MF.
static double	MolecularFormulaManipulator.getNaturalExactMass(IMolecularFormula formula)	Deprecated. use MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MolWeightIgnoreSpecified.
static String	MolecularFormulaManipulator.getString(IMolecularFormula formula)	Returns the string representation of the molecular formula.
static String	MolecularFormulaManipulator.getString(IMolecularFormula formula, boolean setOne)	Returns the string representation of the molecular formula.
static String	MolecularFormulaManipulator.getString(IMolecularFormula formula, boolean setOne, boolean setMassNumber)	Returns the string representation of the molecular formula.
static String	MolecularFormulaManipulator.getString(IMolecularFormula formula, String[] orderElements, boolean setOne)	Returns the string representation of the molecular formula.
static String	MolecularFormulaManipulator.getString(IMolecularFormula formula, String[] orderElements, boolean setOne, boolean setMassNumber)	Returns the string representation of the molecular formula.
static double	MolecularFormulaManipulator.getTotalExactMass(IMolecularFormula formula)	Deprecated. calls MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MonoIsotopic and adjusts for charge with MolecularFormulaManipulator.correctMass(double, Integer).
static double	MolecularFormulaManipulator.getTotalMassNumber(IMolecularFormula formula)	Get the summed mass number of all isotopes from an MolecularFormula.
static double	MolecularFormulaManipulator.getTotalNaturalAbundance(IMolecularFormula formula)	Get the summed natural abundance of all isotopes from an MolecularFormula.
static List<IIsotope>	MolecularFormulaManipulator.putInOrder(String[] orderElements, IMolecularFormula formula)
static IMolecularFormulaSet	MolecularFormulaSetManipulator.remove(IMolecularFormulaSet formulaSet, IMolecularFormula formulaMin, IMolecularFormula formulaMax)	Remove all those IMolecularFormula which are not fit theirs IElement occurrence into a limits.
static IMolecularFormula	MolecularFormulaManipulator.removeElement(IMolecularFormula formula, IElement element)	Removes all isotopes from a given element in the MolecularFormula.