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org::openscience::cdk::nonotify::NNPDBAtom Class Reference

Inheritance diagram for org::openscience::cdk::nonotify::NNPDBAtom:

org::openscience::cdk::protein::data::PDBAtom org::openscience::cdk::Atom org::openscience::cdk::interfaces::IPDBAtom org::openscience::cdk::AtomType org::openscience::cdk::interfaces::IAtom org::openscience::cdk::interfaces::IAtom org::openscience::cdk::Isotope org::openscience::cdk::interfaces::IAtomType 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::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::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::interfaces::IChemObject

List of all members.


Detailed Description

.module nonotify

Definition at line 39 of file NNPDBAtom.java.


Public Member Functions

void addListener (IChemObjectListener col)
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
String getAltLoc ()
int getAtomicNumber ()
String getAtomTypeName ()
double getBondOrderSum ()
IChemObjectBuilder getBuilder ()
String getChainID ()
double getCharge ()
double getCovalentRadius ()
double getExactMass ()
boolean getFlag (int flag_type)
boolean[] getFlags ()
int getFormalCharge ()
int getFormalNeighbourCount ()
javax.vecmath.Point3d getFractionalPoint3d ()
boolean getHetAtom ()
int getHybridization ()
int getHydrogenCount ()
String getICode ()
String getID ()
int getListenerCount ()
int getMassNumber ()
double getMaxBondOrder ()
String getName ()
double getNaturalAbundance ()
boolean getNotification ()
double getOccupancy ()
boolean getOxt ()
javax.vecmath.Point2d getPoint2d ()
javax.vecmath.Point3d getPoint3d ()
Hashtable getProperties ()
Object getProperty (Object description)
String getRecord ()
String getResName ()
String getResSeq ()
String getSegID ()
int getSerial ()
int getStereoParity ()
String getSymbol ()
double getTempFactor ()
int getValency ()
double getVanderwaalsRadius ()
 NNPDBAtom (String elementSymbol, javax.vecmath.Point3d point3d)
 NNPDBAtom (String elementSymbol)
 NNPDBAtom (IElement element)
void notifyChanged (IChemObjectChangeEvent evt)
void notifyChanged ()
void removeListener (IChemObjectListener col)
void removeProperty (Object description)
void setAltLoc (String newAltLoc)
void setAtomicNumber (int atomicNumber)
void setAtomTypeName (String identifier)
void setBondOrderSum (double bondOrderSum)
void setChainID (String newChainID)
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 setHetAtom (boolean newHetAtom)
void setHybridization (int hybridization)
void setHydrogenCount (int hydrogenCount)
void setICode (String newICode)
void setID (String identifier)
void setMassNumber (int massNumber)
void setMaxBondOrder (double maxBondOrder)
void setName (String newName)
void setNaturalAbundance (double naturalAbundance)
void setNotification (boolean bool)
void setOccupancy (double newOccupancy)
void setOxt (boolean newOxt)
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 setRecord (String newRecord)
void setResName (String newResName)
void setResSeq (String newResSeq)
void setSegID (String newSegID)
void setSerial (int newSerial)
void setStereoParity (int stereoParity)
void setSymbol (String symbol)
void setTempFactor (double newTempFactor)
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 = -5917516474241733313L

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

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