Modifier and Type | Class and 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 |
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
A QueryAtom that matches all symbols but those in this container.
|
class |
QueryAtom |
class |
SymbolAndChargeQueryAtom |
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom |
class |
SymbolSetQueryAtom
A QueryAtom that matches all symbols in this container.
|
Modifier and Type | Class and Description |
---|---|
class |
AliphaticAtom
This matcher any non-aromatic atom.
|
class |
AliphaticSymbolAtom
This smarts atom matches aliphatic atom with element symbol specified.
|
class |
AnyAtom
This matcher any Atom including explicit hydrogens.
|
class |
AromaticAtom
This matcher any aromatic atom.
|
class |
AromaticSymbolAtom
This class matches aromatic atom with element symbol specified.
|
class |
AtomicNumberAtom
This matches an atom using the atomic number.
|
class |
ChiralityAtom
This matches an atom with chirality property.
|
class |
ExplicitConnectionAtom
Match an atom with the defined degree.
|
class |
FormalChargeAtom
This matcher checks the formal charge of the Atom.
|
class |
HybridizationNumberAtom
This matcher checks the hybridization state of an atom.
|
class |
HydrogenAtom
This matches Hydrogen atoms.
|
class |
ImplicitHCountAtom
This matcher checks the number of implicit hydrogens of the Atom.
|
class |
LogicalOperatorAtom
This class matches a logical operator that connects two query atoms.
|
class |
MassAtom
This class matches an atom based on the atomic mass.
|
class |
NonCHHeavyAtom
This matcher any heavy atom that is not C or H.
|
class |
PeriodicGroupNumberAtom
This matcher checks the periodic group number of an atom.
|
class |
ReactionRoleQueryAtom
Matches atoms with a particular role in a reaction.
|
class |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingIdentifierAtom
This encapsulates an atom with a ring identifier, with an optional ring
bond specified.
|
class |
RingMembershipAtom
This query is found in a specified number of ring.
|
class |
SmallestRingAtom
Match an atom in a specific size ring.
|
class |
SMARTSAtom
Abstract smarts atom.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections - referred to in
SMARTS as the connectivity.
|
class |
TotalHCountAtom
SMARTS query atom for matching the total hydrogen count.
|
class |
TotalRingConnectionAtom
This matcher checks the number of ring connections of the checked Atom with
other Atom's.
|
class |
TotalValencyAtom
This matcher checks the valence of the Atom.
|
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 |
ValidatorEngine.validateElement(IElement subject) |
ValidationReport |
IValidator.validateElement(IElement subject) |
ValidationReport |
AbstractValidator.validateElement(IElement subject) |
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