Uses of Interface
org.openscience.cdk.interfaces.IIsotope
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Uses of IIsotope in org.openscience.cdk
Classes in org.openscience.cdk that implement IIsotope Modifier and Type Class Description class
Atom
Represents the idea of an chemical atom.class
AtomRef
An atom ref, references a CDKIAtom
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 Description static IIsotope[]
IsotopeFactory. EMPTY_ISOTOPE_ARRAY
Methods in org.openscience.cdk.config that return IIsotope Modifier and Type Method 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 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 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 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 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 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 Description Iterable<IIsotope>
AdductFormula. isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.Iterable<IIsotope>
MolecularFormula. isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.Iterable<IIsotope>
MolecularFormulaRange. isotopes()
Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.Methods in org.openscience.cdk.formula with parameters of type IIsotope Modifier and Type Method 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
AdductFormula. contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not the instance.boolean
MolecularFormula. contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not the instance.boolean
MolecularFormulaRange. contains(IIsotope isotope)
True, if the MolecularFormulaExpand contains the given IIsotope.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
MolecularFormula. getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula 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
MolecularFormula. removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.void
MolecularFormulaRange. removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormulaExpand. -
Uses of IIsotope in org.openscience.cdk.interfaces
Subinterfaces of IIsotope in org.openscience.cdk.interfaces Modifier and Type Interface 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 Description Iterable<IIsotope>
IAdductFormula. isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.Iterable<IIsotope>
IMolecularFormula. isotopes()
Returns anIterable
for looping over all isotopes in this IMolecularFormula.Methods in org.openscience.cdk.interfaces with parameters of type IIsotope Modifier and Type Method 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
IAdductFormula. contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object.boolean
IMolecularFormula. contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object.int
IAdductFormula. getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.int
IMolecularFormula. getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula 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 Description interface
IQueryAtom
Defines the ability to be matched againstIAtom
's.Classes in org.openscience.cdk.isomorphism.matchers that implement IIsotope Modifier and Type Class Description class
InverseSymbolSetQueryAtom
Deprecated.class
QueryAtom
class
SymbolAndChargeQueryAtom
Deprecated.class
SymbolChargeIDQueryAtom
class
SymbolQueryAtom
Deprecated.class
SymbolSetQueryAtom
Deprecated.Usenew Expr(Element, 6).and(new Expr(Element, 8))
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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 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 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 Description class
PDBAtom
Represents the idea of an atom as used in PDB files. -
Uses of IIsotope in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IIsotope Modifier and Type Class Description class
Atom
Represents the idea of an chemical atom.class
AtomType
The base class for atom types.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
Isotope
Used to store and retrieve data of a particular isotope.class
PDBAtom
Represents the idea of an atom as used in PDB files.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Methods in org.openscience.cdk.silent that return types with arguments of type IIsotope Modifier and Type Method Description Iterable<IIsotope>
AdductFormula. isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.Iterable<IIsotope>
MolecularFormula. isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.Methods in org.openscience.cdk.silent with parameters of type IIsotope Modifier and Type Method 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
AdductFormula. contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not the instance.boolean
MolecularFormula. contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not the instance.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
MolecularFormula. getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula 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 Description static Comparator<IIsotope>
AtomContainerManipulator. NAT_ABUN_COMP
static Comparator<IIsotope>
MolecularFormulaManipulator. NAT_ABUN_COMP
Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IIsotope Modifier and Type Method 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 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 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)
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