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org::openscience::cdk::AtomType Class Reference

Inheritance diagram for org::openscience::cdk::AtomType:

org::openscience::cdk::Isotope org::openscience::cdk::interfaces::IAtomType org::openscience::cdk::Element org::openscience::cdk::interfaces::IIsotope org::openscience::cdk::interfaces::IIsotope org::openscience::cdk::ChemObject org::openscience::cdk::interfaces::IElement org::openscience::cdk::interfaces::IElement org::openscience::cdk::interfaces::IElement org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::Atom org::openscience::cdk::debug::DebugAtomType org::openscience::cdk::nonotify::NNAtomType org::openscience::cdk::debug::DebugAtom org::openscience::cdk::isomorphism::matchers::SymbolAndChargeQueryAtom org::openscience::cdk::isomorphism::matchers::SymbolChargeIDQueryAtom org::openscience::cdk::isomorphism::matchers::SymbolQueryAtom org::openscience::cdk::nonotify::NNAtom org::openscience::cdk::protein::data::PDBAtom org::openscience::cdk::PseudoAtom org::openscience::cdk::debug::DebugPDBAtom org::openscience::cdk::nonotify::NNPDBAtom org::openscience::cdk::debug::DebugPseudoAtom org::openscience::cdk::EnzymeResidueLocator org::openscience::cdk::FragmentAtom org::openscience::cdk::isomorphism::matchers::InverseSymbolSetQueryAtom org::openscience::cdk::isomorphism::matchers::smarts::SMARTSAtom org::openscience::cdk::isomorphism::matchers::SymbolSetQueryAtom org::openscience::cdk::nonotify::NNPseudoAtom

List of all members.


Detailed Description

The base class for atom types. Atom types are typically used to describe the behaviour of an atom of a particular element in different environment like sp3 hybridized carbon C3, etc., in some molecular modelling applications.

Author:
steinbeck .created 2001-08-08 .module data .keyword atom, type

Definition at line 47 of file AtomType.java.


Public Member Functions

void addListener (IChemObjectListener col)
 AtomType (IElement element)
 AtomType (String identifier, String elementSymbol)
 AtomType (String elementSymbol)
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
int getAtomicNumber ()
String getAtomTypeName ()
double getBondOrderSum ()
IChemObjectBuilder getBuilder ()
double getCovalentRadius ()
double getExactMass ()
boolean getFlag (int flag_type)
boolean[] getFlags ()
int getFormalCharge ()
int getFormalNeighbourCount ()
int getHybridization ()
String getID ()
int getListenerCount ()
int getMassNumber ()
double getMaxBondOrder ()
double getNaturalAbundance ()
boolean getNotification ()
Hashtable getProperties ()
Object getProperty (Object description)
String getSymbol ()
int getValency ()
double getVanderwaalsRadius ()
void notifyChanged (IChemObjectChangeEvent evt)
void notifyChanged ()
void removeListener (IChemObjectListener col)
void removeProperty (Object description)
void setAtomicNumber (int atomicNumber)
void setAtomTypeName (String identifier)
void setBondOrderSum (double bondOrderSum)
void setCovalentRadius (double radius)
void setExactMass (double exactMass)
void setFlag (int flag_type, boolean flag_value)
void setFlags (boolean[] flagsNew)
void setFormalCharge (int charge)
void setFormalNeighbourCount (int count)
void setHybridization (int hybridization)
void setID (String identifier)
void setMassNumber (int massNumber)
void setMaxBondOrder (double maxBondOrder)
void setNaturalAbundance (double naturalAbundance)
void setNotification (boolean bool)
void setProperties (Hashtable properties)
void setProperty (Object description, Object property)
void setSymbol (String symbol)
void setValency (int valency)
void setVanderwaalsRadius (double radius)
Object shallowCopy ()
String toString ()

Public Attributes

double exactMass = (double) -1
double naturalAbundance = (double) -1

Protected Attributes

int atomicNumber = 0
int electronValency
int formalCharge
int formalNeighbourCount
int hybridization
String symbol

Package Attributes

double bondOrderSum
double covalentRadius
double maxBondOrder
double vanderwaalsRadius

Private Attributes

String identifier

Static Private Attributes

static final long serialVersionUID = -7950397716808229972L

The documentation for this class was generated from the following file:

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