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org::openscience::cdk::interfaces::IPseudoAtom Interface Reference

Inheritance diagram for org::openscience::cdk::interfaces::IPseudoAtom:

org::openscience::cdk::interfaces::IAtom org::openscience::cdk::interfaces::IAtomType org::openscience::cdk::interfaces::IIsotope org::openscience::cdk::interfaces::IElement org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::debug::DebugPseudoAtom org::openscience::cdk::PseudoAtom 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 interfaces

See also:
IAtom

Definition at line 41 of file IPseudoAtom.java.


Public Member Functions

void addListener (IChemObjectListener col)
Object clone () throws CloneNotSupportedException
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 ()
Point3d getFractionalPoint3d ()
int getHybridization ()
int getHydrogenCount ()
String getID ()
String getLabel ()
int getListenerCount ()
int getMassNumber ()
double getMaxBondOrder ()
double getNaturalAbundance ()
boolean getNotification ()
Point2d getPoint2d ()
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 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 setPoint3d (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)
String toString ()

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

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