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

Packages that use IElement

Package	Description
org.openscience.cdk
org.openscience.cdk.config
org.openscience.cdk.debug
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 IElement in org.openscience.cdk

Classes in org.openscience.cdk that implement IElement

Modifier and Type	Class	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	Element	Implements the idea of an element in the periodic table.
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.

Constructors in org.openscience.cdk with parameters of type IElement

Modifier	Constructor	Description
	Atom(IElement element)	Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.
	AtomType(IElement element)	Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.
	Element(IElement element)	Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
	Isotope(IElement element)	Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
	PseudoAtom(IElement element)	Constructs an PseudoAtom from a IAtom.

Uses of IElement in org.openscience.cdk.config

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

Modifier and Type	Field	Description
static final IElement	Elements.ACTINIUM
static final IElement	Elements.ALUMINIUM
static final IElement	Elements.AMERICIUM
static final IElement	Elements.ANTIMONY
static final IElement	Elements.ARGON
static final IElement	Elements.ARSENIC
static final IElement	Elements.ASTATINE
static final IElement	Elements.BARIUM
static final IElement	Elements.BERKELIUM
static final IElement	Elements.BERYLLIUM
static final IElement	Elements.BISMUTH
static final IElement	Elements.BOHRIUM
static final IElement	Elements.BORON
static final IElement	Elements.BROMINE
static final IElement	Elements.CADMIUM
static final IElement	Elements.CAESIUM
static final IElement	Elements.CALCIUM
static final IElement	Elements.CALIFORNIUM
static final IElement	Elements.CARBON
static final IElement	Elements.CERIUM
static final IElement	Elements.CHLORINE
static final IElement	Elements.CHROMIUM
static final IElement	Elements.COBALT
static final IElement	Elements.COPPER
static final IElement	Elements.CURIUM
static final IElement	Elements.DARMSTADTIUM
static final IElement	Elements.DUBNIUM
static final IElement	Elements.DUMMY	These instances are for backards compatability.
static final IElement	Elements.DYSPROSIUM
static final IElement	Elements.EINSTEINIUM
static final IElement	Elements.ERBIUM
static final IElement	Elements.EUROPIUM
static final IElement	Elements.FERMIUM
static final IElement	Elements.FLEROVIUM
static final IElement	Elements.FLUORINE
static final IElement	Elements.FRANCIUM
static final IElement	Elements.GADOLINIUM
static final IElement	Elements.GALLIUM
static final IElement	Elements.GERMANIUM
static final IElement	Elements.GOLD
static final IElement	Elements.HAFNIUM
static final IElement	Elements.HASSIUM
static final IElement	Elements.HELIUM
static final IElement	Elements.HOLMIUM
static final IElement	Elements.HYDROGEN
static final IElement	Elements.INDIUM
static final IElement	Elements.IODINE
static final IElement	Elements.IRIDIUM
static final IElement	Elements.IRON
static final IElement	Elements.KRYPTON
static final IElement	Elements.LANTHANUM
static final IElement	Elements.LAWRENCIUM
static final IElement	Elements.LEAD
static final IElement	Elements.LITHIUM
static final IElement	Elements.LIVERMORIUM
static final IElement	Elements.LUTETIUM
static final IElement	Elements.MAGNESIUM
static final IElement	Elements.MANGANESE
static final IElement	Elements.MEITNERIUM
static final IElement	Elements.MENDELEVIUM
static final IElement	Elements.MERCURY
static final IElement	Elements.MOLYBDENUM
static final IElement	Elements.NEODYMIUM
static final IElement	Elements.NEON
static final IElement	Elements.NEPTUNIUM
static final IElement	Elements.NICKEL
static final IElement	Elements.NIOBIUM
static final IElement	Elements.NITROGEN
static final IElement	Elements.NOBELIUM
static final IElement	Elements.OSMIUM
static final IElement	Elements.OXYGEN
static final IElement	Elements.PALLADIUM
static final IElement	Elements.PHOSPHORUS
static final IElement	Elements.PLATINUM
static final IElement	Elements.PLUTOMNIUM	Deprecated.
static final IElement	Elements.PLUTONIUM
static final IElement	Elements.POLONIUM
static final IElement	Elements.POTASSIUM
static final IElement	Elements.PRASEODYMIUM
static final IElement	Elements.PROMETHIUM
static final IElement	Elements.PROTACTINIUM
static final IElement	Elements.RADIUM
static final IElement	Elements.RADON
static final IElement	Elements.RHENIUM
static final IElement	Elements.RHODIUM
static final IElement	Elements.ROENTGENIUM
static final IElement	Elements.RUBIDIUM
static final IElement	Elements.RUTHENIUM
static final IElement	Elements.RUTHERFORDIUM
static final IElement	Elements.SAMARIUM
static final IElement	Elements.SCANDIUM
static final IElement	Elements.SEABORGIUM
static final IElement	Elements.SELENIUM
static final IElement	Elements.SILICON
static final IElement	Elements.SILVER
static final IElement	Elements.SODIUM
static final IElement	Elements.STRONTIUM
static final IElement	Elements.SULFUR
static final IElement	Elements.TANTALUM
static final IElement	Elements.TECHNETIUM
static final IElement	Elements.TELLURIUM
static final IElement	Elements.TERBIUM
static final IElement	Elements.THALLIUM
static final IElement	Elements.THORIUM
static final IElement	Elements.THULIUM
static final IElement	Elements.TIN
static final IElement	Elements.TITANIUM
static final IElement	Elements.TUNGSTEN
static final IElement	Elements.UNUNBIUM
static final IElement	Elements.UNUNHEXIUM
static final IElement	Elements.UNUNPENTIUM
static final IElement	Elements.UNUNQUADIUM
static final IElement	Elements.UNUNTRIUM
static final IElement	Elements.URANIUM
static final IElement	Elements.VANADIUM
static final IElement	Elements.XENON
static final IElement	Elements.YTTERBIUM
static final IElement	Elements.YTTRIUM
static final IElement	Elements.ZINC
static final IElement	Elements.ZIRCONIUM

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

Modifier and Type	Method	Description
IElement	IsotopeFactory.getElement(int atomicNumber)	Returns an element according to a given atomic number.
IElement	IsotopeFactory.getElement(String symbol)	Returns an Element with a given element symbol.
IElement	Elements.toIElement()	Access an IElement instance of the chemical element.

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

Modifier and Type	Method	Description
double	IsotopeFactory.getNaturalMass(IElement element)	Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.

Uses of IElement in org.openscience.cdk.debug

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

Modifier and Type	Class	Description
class	DebugAtom	Debugging data class.
class	DebugAtomType	Debugging data class.
class	DebugElement	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.

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

Modifier	Constructor	Description
	DebugAtom(IElement element)
	DebugAtomType(IElement element)
	DebugElement(IElement element)
	DebugIsotope(IElement element)
	DebugPDBAtom(IElement element)
	DebugPseudoAtom(IElement element)

Uses of IElement in org.openscience.cdk.interfaces

Subinterfaces of IElement 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	IIsotope	Used to store and retrieve data of a particular isotope.
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.

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

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

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

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

Modifier and Type	Class	Description
class	InverseSymbolSetQueryAtom	Deprecated.
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 IElement in org.openscience.cdk.isomorphism.matchers.smarts

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

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.
final 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.
final class	RecursiveSmartsAtom	Deprecated.
class	RingIdentifierAtom	Deprecated.
class	RingMembershipAtom	Deprecated.
final class	SmallestRingAtom	Deprecated.
class	SMARTSAtom	Deprecated.
final class	TotalConnectionAtom	Deprecated.
final class	TotalHCountAtom	Deprecated.
final class	TotalRingConnectionAtom	Deprecated.
final class	TotalValencyAtom	Deprecated.

Uses of IElement in org.openscience.cdk.pharmacophore

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

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

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

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

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

Constructors in org.openscience.cdk.protein.data with parameters of type IElement

Modifier	Constructor	Description
	PDBAtom(IElement element)	Constructs an IPDBAtom from a Element.

Uses of IElement in org.openscience.cdk.silent

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

Modifier and Type	Class	Description
class	Atom	Represents the idea of an chemical atom.
class	AtomType	The base class for atom types.
class	Element	Implements the idea of an element in the periodic table.
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.

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

Modifier	Constructor	Description
	Atom(IElement element)	Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.
	AtomType(IElement element)	Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.
	Element(IElement element)	Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
	Isotope(IElement element)	Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
	PDBAtom(IElement element)	Constructs an IPDBAtom from a Element.
	PseudoAtom(IElement element)	Constructs an PseudoAtom from a IAtom.

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

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

Modifier and Type	Method	Description
static List<IElement>	MolecularFormulaManipulator.elements(IMolecularFormula formula)	Get a list of all Elements which are contained molecular.
static List<IElement>	MolecularFormulaManipulator.getHeavyElements(IMolecularFormula formula)	Returns a set of nodes excluding all the hydrogens.

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

Modifier and Type	Method	Description
static boolean	MolecularFormulaManipulator.containsElement(IMolecularFormula formula, IElement element)	True, if the MolecularFormula contains the given element as IIsotope object.
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 List<IIsotope>	MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula, IElement element)	Get a list of IIsotope from a given IElement which is contained molecular.
static IMolecularFormula	MolecularFormulaManipulator.removeElement(IMolecularFormula formula, IElement element)	Removes all isotopes from a given element in the MolecularFormula.

Uses of IElement in org.openscience.cdk.validate

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

Modifier and Type	Method	Description
ValidationReport	AbstractValidator.validateElement(IElement subject)
ValidationReport	IValidator.validateElement(IElement subject)
ValidationReport	ValidatorEngine.validateElement(IElement subject)