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org::openscience::cdk::PseudoAtom Class Reference

Inheritance diagram for org::openscience::cdk::PseudoAtom:

org::openscience::cdk::Atom org::openscience::cdk::interfaces::IPseudoAtom 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 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 org::openscience::cdk::isomorphism::matchers::smarts::AliphaticAtom org::openscience::cdk::isomorphism::matchers::smarts::AliphaticSymbolAtom org::openscience::cdk::isomorphism::matchers::smarts::AnyAtom org::openscience::cdk::isomorphism::matchers::smarts::AromaticAtom org::openscience::cdk::isomorphism::matchers::smarts::AromaticSymbolAtom org::openscience::cdk::isomorphism::matchers::smarts::AtomicNumberAtom org::openscience::cdk::isomorphism::matchers::smarts::BracketAtom org::openscience::cdk::isomorphism::matchers::smarts::ChiralityAtom org::openscience::cdk::isomorphism::matchers::smarts::ColumnAtom org::openscience::cdk::isomorphism::matchers::smarts::ConnectionCountAtom org::openscience::cdk::isomorphism::matchers::smarts::DegreeAtom org::openscience::cdk::isomorphism::matchers::smarts::ExplicitConnectionAtom org::openscience::cdk::isomorphism::matchers::smarts::FormalChargeAtom org::openscience::cdk::isomorphism::matchers::smarts::HydrogenAtom org::openscience::cdk::isomorphism::matchers::smarts::ImplicitHCountAtom org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorAtom org::openscience::cdk::isomorphism::matchers::smarts::MassAtom org::openscience::cdk::isomorphism::matchers::smarts::RecurseAtom org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom org::openscience::cdk::isomorphism::matchers::smarts::RingAtom org::openscience::cdk::isomorphism::matchers::smarts::RingIdentifierAtom org::openscience::cdk::isomorphism::matchers::smarts::RingMembershipAtom org::openscience::cdk::isomorphism::matchers::smarts::SmallestRingAtom org::openscience::cdk::isomorphism::matchers::smarts::SMARTSOperatorAtom org::openscience::cdk::isomorphism::matchers::smarts::TotalConnectionAtom org::openscience::cdk::isomorphism::matchers::smarts::TotalHCountAtom org::openscience::cdk::isomorphism::matchers::smarts::TotalRingConnectionAtom org::openscience::cdk::isomorphism::matchers::smarts::TotalValencyAtom

List of all members.


Detailed Description

Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.

This should be replaced by the mechanism explained in RFC #8.

.module data

See also:
Atom

Definition at line 44 of file PseudoAtom.java.


Public Member Functions

void addListener (IChemObjectListener col)
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 ()
String getLabel ()
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 ()
 PseudoAtom (String label, javax.vecmath.Point2d point2d)
 PseudoAtom (String label, javax.vecmath.Point3d point3d)
 PseudoAtom (IElement element)
 PseudoAtom (String label)
 PseudoAtom ()
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 mass)
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 setLabel (String label)
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

Private Attributes

String label

Static Private Attributes

static final long serialVersionUID = 1L

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

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