Uses of Interface
org.openscience.cdk.interfaces.IMolecularFormula
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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 ofIMolecularFormula
.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 positionnumber
in the chemObject.IMolecularFormula
DebugMolecularFormulaSet. getMolecularFormula(int position)
Returns the MolecularFormula at positionnumber
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 Constructor Description DebugAdductFormula(IMolecularFormula formula)
DebugMolecularFormulaSet(IMolecularFormula formula)
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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 positionnumber
in the chemObject.IMolecularFormula
MolecularFormulaSet. getMolecularFormula(int position)
Returns the MolecularFormula at positionnumber
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 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 positionnumber
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 positionnumber
in the chemObject.IMolecularFormula
MolecularFormulaSet. getMolecularFormula(int position)
Returns the MolecularFormula at positionnumber
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 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)
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.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.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.callsMolecularFormulaManipulator.getMass(IMolecularFormula, int)
with optionMolecularFormulaManipulator.MonoIsotopic
and adjusts for charge withMolecularFormulaManipulator.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.
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