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org::openscience::cdk::Atom Class Reference

Inheritance diagram for org::openscience::cdk::Atom:

org::openscience::cdk::AtomType org::openscience::cdk::interfaces::IAtom org::openscience::cdk::Isotope org::openscience::cdk::interfaces::IAtomType org::openscience::cdk::interfaces::IAtomType org::openscience::cdk::Element org::openscience::cdk::interfaces::IIsotope 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::IElement org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject 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

Represents the idea of an chemical atom.

An Atom class is instantiated with at least the atom symbol:

   Atom a = new Atom("C");
 

Once instantiated all field not filled by passing parameters to the constructured are null. Atoms can be configured by using the IsotopeFactory.configure() method:

   IsotopeFactory if = IsotopeFactory.getInstance(a.getBuilder());
   if.configure(a);
 

More examples about using this class can be found in the Junit test for this class.

.module data

Author:
steinbeck .created 2000-10-02 .keyword atom
See also:
org.openscience.cdk.config.IsotopeFactory::getInstance(org.openscience.cdk.interfaces.IChemObjectBuilder)

Definition at line 61 of file Atom.java.


Public Member Functions

void addListener (IChemObjectListener col)
 Atom (IElement element)
 Atom (String elementSymbol, javax.vecmath.Point2d point2d)
 Atom (String elementSymbol, javax.vecmath.Point3d point3d)
 Atom (String elementSymbol)
 Atom ()
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
int getAtomicNumber ()
String getAtomTypeName ()
double getBondOrderSum ()
IChemObjectBuilder getBuilder ()
double getCharge ()
double getCovalentRadius ()
double getExactMass ()
boolean getFlag (int flag_type)
boolean[] getFlags ()
int getFormalCharge ()
int getFormalNeighbourCount ()
javax.vecmath.Point3d getFractionalPoint3d ()
int getHybridization ()
int getHydrogenCount ()
String getID ()
int getListenerCount ()
int getMassNumber ()
double getMaxBondOrder ()
double getNaturalAbundance ()
boolean getNotification ()
javax.vecmath.Point2d getPoint2d ()
javax.vecmath.Point3d getPoint3d ()
Hashtable getProperties ()
Object getProperty (Object description)
int getStereoParity ()
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 setCharge (double charge)
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 setFractionalPoint3d (Point3d point3d)
void setFractionalPoint3d (javax.vecmath.Point3d point3d)
void setHybridization (int hybridization)
void setHydrogenCount (int hydrogenCount)
void setID (String identifier)
void setMassNumber (int massNumber)
void setMaxBondOrder (double maxBondOrder)
void setNaturalAbundance (double naturalAbundance)
void setNotification (boolean bool)
void setPoint2d (Point2d point2d)
void setPoint2d (javax.vecmath.Point2d point2d)
void setPoint3d (Point3d point3d)
void setPoint3d (javax.vecmath.Point3d point3d)
void setProperties (Hashtable properties)
void setProperty (Object description, Object property)
void setStereoParity (int stereoParity)
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
double charge = 0.0
int electronValency
int formalCharge
int formalNeighbourCount
javax.vecmath.Point3d fractionalPoint3d
int hybridization
int hydrogenCount
javax.vecmath.Point2d point2d
javax.vecmath.Point3d point3d
int stereoParity
String symbol

Package Attributes

double bondOrderSum
double covalentRadius
double maxBondOrder
double vanderwaalsRadius

Static Private Attributes

static final long serialVersionUID = -3137373012494608794L

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

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