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

Packages that use IIsotope

Package	Description
org.openscience.cdk
org.openscience.cdk.config
org.openscience.cdk.config.isotopes
org.openscience.cdk.debug
org.openscience.cdk.formula
org.openscience.cdk.interfaces
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.pharmacophore
org.openscience.cdk.protein.data
org.openscience.cdk.silent
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IIsotope in org.openscience.cdk

Classes in org.openscience.cdk that implement IIsotope

Modifier and Type	Class and Description
class	Atom Represents the idea of an chemical atom.
class	AtomRef An atom ref, references a CDK IAtom indirectly.
class	AtomType The base class for atom types.
class	EnzymeResidueLocator Atom that represents part of an residue in an enzyme, like Arg255.
class	FragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
class	Isotope Used to store and retrieve data of a particular isotope.
class	PseudoAtom Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.

Uses of IIsotope in org.openscience.cdk.config

Fields in org.openscience.cdk.config declared as IIsotope

Modifier and Type	Field and Description
static IIsotope[]	IsotopeFactory.EMPTY_ISOTOPE_ARRAY

Methods in org.openscience.cdk.config that return IIsotope

Modifier and Type	Method and Description
IIsotope	IsotopeFactory.getIsotope(String symbol, double exactMass, double tolerance) Get an isotope based on the element symbol and exact mass.
IIsotope	IsotopeFactory.getIsotope(String symbol, int massNumber) Get isotope based on element symbol and mass number.
IIsotope[]	IsotopeFactory.getIsotopes() Gets a array of all isotopes known to the IsotopeFactory.
IIsotope[]	IsotopeFactory.getIsotopes(double exactMass, double difference) Gets an array of all isotopes matching the searched exact mass within a certain difference.
IIsotope[]	IsotopeFactory.getIsotopes(int elem) Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
IIsotope[]	IsotopeFactory.getIsotopes(String symbol) Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
IIsotope	IsotopeFactory.getMajorIsotope(int elem) Returns the most abundant (major) isotope with a given atomic number.
IIsotope	IsotopeFactory.getMajorIsotope(String symbol) Returns the most abundant (major) isotope whose symbol equals element.

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

Modifier and Type	Method and Description
protected void	IsotopeFactory.add(IIsotope isotope) Protected methods only to be used by classes extending this class to add an IIsotope.
IAtom	IsotopeFactory.configure(IAtom atom, IIsotope isotope) Configures an atom to have all the data of the given isotope.

Uses of IIsotope in org.openscience.cdk.config.isotopes

Methods in org.openscience.cdk.config.isotopes that return types with arguments of type IIsotope

Modifier and Type	Method and Description
List<IIsotope>	IsotopeHandler.getIsotopes() Returns the isotopes read from the XML file.
List<IIsotope>	IsotopeReader.readIsotopes() Triggers the XML parsing of the data file and returns the read Isotopes.

Uses of IIsotope in org.openscience.cdk.debug

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

Modifier and Type	Class and Description
class	DebugAtom Debugging data class.
class	DebugAtomType Debugging data class.
class	DebugFragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
class	DebugIsotope Debugging data class.
class	DebugPDBAtom Debugging data class.
class	DebugPseudoAtom Debugging data class.

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

Modifier and Type	Method and Description
Iterable<IIsotope>	DebugAdductFormula.isotopes() Returns an Iterator for looping over all isotopes in this adduct formula.
Iterable<IIsotope>	DebugMolecularFormula.isotopes() Returns an Iterator for looping over all isotopes in this IMolecularFormula.

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

Modifier and Type	Method and Description
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.
boolean	DebugAdductFormula.contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object and not the instance.
boolean	DebugMolecularFormula.contains(IIsotope isotope) True, if the MolecularFormula contains the given IIsotope object and not the instance.
int	DebugAdductFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
int	DebugMolecularFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
void	DebugMolecularFormula.removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormula.

Uses of IIsotope in org.openscience.cdk.formula

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

Modifier and Type	Method and Description
Iterable<IIsotope>	MolecularFormulaRange.isotopes() Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
Iterable<IIsotope>	MolecularFormula.isotopes() Returns an Iterator for looping over all isotopes in this IMolecularFormula.
Iterable<IIsotope>	AdductFormula.isotopes() Returns an Iterator for looping over all isotopes in this adduct formula.

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

Modifier and Type	Method and Description
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.
void	MolecularFormulaRange.addIsotope(IIsotope isotope, int countMin, int countMax) Adds an Isotope to this MolecularFormulaExpand in a number of maximum and minimum occurrences allowed.
boolean	MolecularFormulaRange.contains(IIsotope isotope) True, if the MolecularFormulaExpand contains the given IIsotope.
boolean	MolecularFormula.contains(IIsotope isotope) True, if the MolecularFormula contains the given IIsotope object and not the instance.
boolean	AdductFormula.contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object and not the instance.
int	MolecularFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
int	AdductFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
int	MolecularFormulaRange.getIsotopeCountMax(IIsotope isotope) Checks a set of Nodes for the maximal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
int	MolecularFormulaRange.getIsotopeCountMin(IIsotope isotope) Checks a set of Nodes for the minimal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
protected boolean	MolecularFormula.isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) Compare to IIsotope.
void	MolecularFormulaRange.removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormulaExpand.
void	MolecularFormula.removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormula.

Uses of IIsotope in org.openscience.cdk.interfaces

Subinterfaces of IIsotope in org.openscience.cdk.interfaces

Modifier and Type	Interface and Description
interface	IAtom Represents the idea of an chemical atom.
interface	IAtomType The base class for atom types.
interface	IFragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
interface	IPDBAtom A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
interface	IPseudoAtom Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.

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

Modifier and Type	Method and Description
Iterable<IIsotope>	IMolecularFormula.isotopes() Returns an Iterable for looping over all isotopes in this IMolecularFormula.
Iterable<IIsotope>	IAdductFormula.isotopes() Returns an Iterator for looping over all isotopes in this adduct formula.

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

Modifier and Type	Method and Description
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.
boolean	IMolecularFormula.contains(IIsotope isotope) True, if the MolecularFormula contains the given IIsotope object.
boolean	IAdductFormula.contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object.
int	IMolecularFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
int	IAdductFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
void	IMolecularFormula.removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormula.

Uses of IIsotope in org.openscience.cdk.isomorphism.matchers

Subinterfaces of IIsotope in org.openscience.cdk.isomorphism.matchers

Modifier and Type	Interface and Description
interface	IQueryAtom Defines the ability to be matched against IAtom's.

Classes in org.openscience.cdk.isomorphism.matchers that implement IIsotope

Modifier and Type	Class and Description
class	InverseSymbolSetQueryAtom Deprecated. @deprecated Use new Expr(Element, 6).and(new Expr(Element, 8)).negate() etc
class	QueryAtom
class	SymbolAndChargeQueryAtom Deprecated.
class	SymbolChargeIDQueryAtom
class	SymbolQueryAtom Deprecated.
class	SymbolSetQueryAtom Deprecated. Use new Expr(Element, 6).and(new Expr(Element, 8)) etc

Uses of IIsotope in org.openscience.cdk.isomorphism.matchers.smarts

Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IIsotope

Modifier and Type	Class and Description
class	AliphaticAtom Deprecated.
class	AliphaticSymbolAtom Deprecated.
class	AnyAtom Deprecated.
class	AromaticAtom Deprecated.
class	AromaticSymbolAtom Deprecated.
class	AtomicNumberAtom Deprecated.
class	ChiralityAtom Deprecated.
class	ExplicitConnectionAtom Deprecated.
class	FormalChargeAtom Deprecated.
class	HybridizationNumberAtom Deprecated.
class	HydrogenAtom Deprecated.
class	ImplicitHCountAtom Deprecated.
class	LogicalOperatorAtom Deprecated.
class	MassAtom Deprecated.
class	NonCHHeavyAtom Deprecated.
class	PeriodicGroupNumberAtom Deprecated.
class	ReactionRoleQueryAtom Deprecated.
class	RecursiveSmartsAtom Deprecated.
class	RingIdentifierAtom Deprecated.
class	RingMembershipAtom Deprecated.
class	SmallestRingAtom Deprecated.
class	SMARTSAtom Deprecated.
class	TotalConnectionAtom Deprecated.
class	TotalHCountAtom Deprecated.
class	TotalRingConnectionAtom Deprecated.
class	TotalValencyAtom Deprecated.

Uses of IIsotope in org.openscience.cdk.pharmacophore

Classes in org.openscience.cdk.pharmacophore that implement IIsotope

Modifier and Type	Class and Description
class	PharmacophoreAtom A representation of a pharmacophore group.
class	PharmacophoreQueryAtom Represents a query pharmacophore group.

Uses of IIsotope in org.openscience.cdk.protein.data

Classes in org.openscience.cdk.protein.data that implement IIsotope

Modifier and Type	Class and Description
class	PDBAtom Represents the idea of an atom as used in PDB files.

Uses of IIsotope in org.openscience.cdk.silent

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

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

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

Modifier and Type	Method and Description
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.
boolean	MolecularFormula.contains(IIsotope isotope) True, if the MolecularFormula contains the given IIsotope object and not the instance.
boolean	AdductFormula.contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object and not the instance.
int	MolecularFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
int	AdductFormula.getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
protected boolean	MolecularFormula.isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) Compare to IIsotope.
void	MolecularFormula.removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormula.

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

Fields in org.openscience.cdk.tools.manipulator with type parameters of type IIsotope

Modifier and Type	Field and Description
static Comparator<IIsotope>	MolecularFormulaManipulator.NAT_ABUN_COMP
static Comparator<IIsotope>	AtomContainerManipulator.NAT_ABUN_COMP

Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IIsotope

Modifier and Type	Method and Description
static List<IIsotope>	MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula, IElement element) Get a list of IIsotope from a given IElement which is contained molecular.
static List<IIsotope>	MolecularFormulaManipulator.putInOrder(String[] orderElements, IMolecularFormula formula)

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

Modifier and Type	Method and Description
static int	MolecularFormulaManipulator.getElementCount(IMolecularFormula formula, IIsotope isotope) Occurrences of a given element from an isotope in a molecular formula.

Uses of IIsotope in org.openscience.cdk.validate

Methods in org.openscience.cdk.validate with parameters of type IIsotope

Modifier and Type	Method and Description
ValidationReport	AbstractValidator.validateIsotope(IIsotope subject)
ValidationReport	BasicValidator.validateIsotope(IIsotope subject)
ValidationReport	IValidator.validateIsotope(IIsotope subject)
ValidationReport	ValidatorEngine.validateIsotope(IIsotope subject)
ValidationReport	BasicValidator.validateIsotopeExistence(IIsotope isotope)