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 |
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.
|
Constructor and 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.
|
Modifier and Type | Field and Description |
---|---|
static IElement |
Elements.ACTINIUM |
static IElement |
Elements.ALUMINIUM |
static IElement |
Elements.AMERICIUM |
static IElement |
Elements.ANTIMONY |
static IElement |
Elements.ARGON |
static IElement |
Elements.ARSENIC |
static IElement |
Elements.ASTATINE |
static IElement |
Elements.BARIUM |
static IElement |
Elements.BERKELIUM |
static IElement |
Elements.BERYLLIUM |
static IElement |
Elements.BISMUTH |
static IElement |
Elements.BOHRIUM |
static IElement |
Elements.BORON |
static IElement |
Elements.BROMINE |
static IElement |
Elements.CADMIUM |
static IElement |
Elements.CAESIUM |
static IElement |
Elements.CALCIUM |
static IElement |
Elements.CALIFORNIUM |
static IElement |
Elements.CARBON |
static IElement |
Elements.CERIUM |
static IElement |
Elements.CHLORINE |
static IElement |
Elements.CHROMIUM |
static IElement |
Elements.COBALT |
static IElement |
Elements.COPPER |
static IElement |
Elements.CURIUM |
static IElement |
Elements.DARMSTADTIUM |
static IElement |
Elements.DUBNIUM |
static IElement |
Elements.DUMMY
These instances are for backards compatability.
|
static IElement |
Elements.DYSPROSIUM |
static IElement |
Elements.EINSTEINIUM |
static IElement |
Elements.ERBIUM |
static IElement |
Elements.EUROPIUM |
static IElement |
Elements.FERMIUM |
static IElement |
Elements.FLEROVIUM |
static IElement |
Elements.FLUORINE |
static IElement |
Elements.FRANCIUM |
static IElement |
Elements.GADOLINIUM |
static IElement |
Elements.GALLIUM |
static IElement |
Elements.GERMANIUM |
static IElement |
Elements.GOLD |
static IElement |
Elements.HAFNIUM |
static IElement |
Elements.HASSIUM |
static IElement |
Elements.HELIUM |
static IElement |
Elements.HOLMIUM |
static IElement |
Elements.HYDROGEN |
static IElement |
Elements.INDIUM |
static IElement |
Elements.IODINE |
static IElement |
Elements.IRIDIUM |
static IElement |
Elements.IRON |
static IElement |
Elements.KRYPTON |
static IElement |
Elements.LANTHANUM |
static IElement |
Elements.LAWRENCIUM |
static IElement |
Elements.LEAD |
static IElement |
Elements.LITHIUM |
static IElement |
Elements.LIVERMORIUM |
static IElement |
Elements.LUTETIUM |
static IElement |
Elements.MAGNESIUM |
static IElement |
Elements.MANGANESE |
static IElement |
Elements.MEITNERIUM |
static IElement |
Elements.MENDELEVIUM |
static IElement |
Elements.MERCURY |
static IElement |
Elements.MOLYBDENUM |
static IElement |
Elements.NEODYMIUM |
static IElement |
Elements.NEON |
static IElement |
Elements.NEPTUNIUM |
static IElement |
Elements.NICKEL |
static IElement |
Elements.NIOBIUM |
static IElement |
Elements.NITROGEN |
static IElement |
Elements.NOBELIUM |
static IElement |
Elements.OSMIUM |
static IElement |
Elements.OXYGEN |
static IElement |
Elements.PALLADIUM |
static IElement |
Elements.PHOSPHORUS |
static IElement |
Elements.PLATINUM |
static IElement |
Elements.PLUTOMNIUM
Deprecated.
|
static IElement |
Elements.PLUTONIUM |
static IElement |
Elements.POLONIUM |
static IElement |
Elements.POTASSIUM |
static IElement |
Elements.PRASEODYMIUM |
static IElement |
Elements.PROMETHIUM |
static IElement |
Elements.PROTACTINIUM |
static IElement |
Elements.RADIUM |
static IElement |
Elements.RADON |
static IElement |
Elements.RHENIUM |
static IElement |
Elements.RHODIUM |
static IElement |
Elements.ROENTGENIUM |
static IElement |
Elements.RUBIDIUM |
static IElement |
Elements.RUTHENIUM |
static IElement |
Elements.RUTHERFORDIUM |
static IElement |
Elements.SAMARIUM |
static IElement |
Elements.SCANDIUM |
static IElement |
Elements.SEABORGIUM |
static IElement |
Elements.SELENIUM |
static IElement |
Elements.SILICON |
static IElement |
Elements.SILVER |
static IElement |
Elements.SODIUM |
static IElement |
Elements.STRONTIUM |
static IElement |
Elements.SULFUR |
static IElement |
Elements.TANTALUM |
static IElement |
Elements.TECHNETIUM |
static IElement |
Elements.TELLURIUM |
static IElement |
Elements.TERBIUM |
static IElement |
Elements.THALLIUM |
static IElement |
Elements.THORIUM |
static IElement |
Elements.THULIUM |
static IElement |
Elements.TIN |
static IElement |
Elements.TITANIUM |
static IElement |
Elements.TUNGSTEN |
static IElement |
Elements.UNUNBIUM |
static IElement |
Elements.UNUNHEXIUM |
static IElement |
Elements.UNUNPENTIUM |
static IElement |
Elements.UNUNQUADIUM |
static IElement |
Elements.UNUNTRIUM |
static IElement |
Elements.URANIUM |
static IElement |
Elements.VANADIUM |
static IElement |
Elements.XENON |
static IElement |
Elements.YTTERBIUM |
static IElement |
Elements.YTTRIUM |
static IElement |
Elements.ZINC |
static IElement |
Elements.ZIRCONIUM |
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
double |
IsotopeFactory.getNaturalMass(IElement element)
Gets the natural mass of this element, defined as average of masses of
isotopes, weighted by abundance.
|
Modifier and Type | Class and 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.
|
Constructor and Description |
---|
DebugAtom(IElement element) |
DebugAtomType(IElement element) |
DebugElement(IElement element) |
DebugIsotope(IElement element) |
DebugPDBAtom(IElement element) |
DebugPseudoAtom(IElement element) |
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 |
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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
Constructor and Description |
---|
PDBAtom(IElement element)
Constructs an IPDBAtom from a Element.
|
Constructor and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
AbstractValidator.validateElement(IElement subject) |
ValidationReport |
IValidator.validateElement(IElement subject) |
ValidationReport |
ValidatorEngine.validateElement(IElement subject) |
Copyright © 2022. All rights reserved.