test_class.file: base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAtomTest.java
test_class.identifier: DebugAtomTest
test_class.superclass: extends AbstractAtomTest
test_case.body: @Test
      public void testDebugAtom() {
          IAtom a = new DebugAtom();
          Assert.assertNotNull(a);
      }
test_case.class_method_signature: DebugAtomTest.testDebugAtom()
test_case.full_signature: @Test public void testDebugAtom()
test_case.identifier: testDebugAtom
test_case.invocations: assertNotNull
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testDebugAtom()
focal_class.declarator: serialVersionUID = 188945429187084868L
focal_class.modifier: private static final
focal_class.original_string: private static final long serialVersionUID = 188945429187084868L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(DebugAtom.class)
focal_class.modifier: private static final
focal_class.original_string: private static final ILoggingTool logger = LoggingToolFactory.createLoggingTool(DebugAtom.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java
focal_class.identifier: DebugAtom
focal_class.interfaces: implements IAtom
focal_class.class_method_signature: DebugAtom.DebugAtom()
focal_class.full_signature: public  DebugAtom()
focal_class.identifier: DebugAtom
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  DebugAtom()
focal_class.class_method_signature: DebugAtom.DebugAtom(String symbol)
focal_class.full_signature: public  DebugAtom(String symbol)
focal_class.identifier: DebugAtom
focal_class.modifiers: public
focal_class.parameters: (String symbol)
focal_class.signature:  DebugAtom(String symbol)
focal_class.class_method_signature: DebugAtom.DebugAtom(String symbol, Point2d point2d)
focal_class.full_signature: public  DebugAtom(String symbol, Point2d point2d)
focal_class.identifier: DebugAtom
focal_class.modifiers: public
focal_class.parameters: (String symbol, Point2d point2d)
focal_class.signature:  DebugAtom(String symbol, Point2d point2d)
focal_class.class_method_signature: DebugAtom.DebugAtom(String symbol, Point3d point3d)
focal_class.full_signature: public  DebugAtom(String symbol, Point3d point3d)
focal_class.identifier: DebugAtom
focal_class.modifiers: public
focal_class.parameters: (String symbol, Point3d point3d)
focal_class.signature:  DebugAtom(String symbol, Point3d point3d)
focal_class.class_method_signature: DebugAtom.DebugAtom(IElement element)
focal_class.full_signature: public  DebugAtom(IElement element)
focal_class.identifier: DebugAtom
focal_class.modifiers: public
focal_class.parameters: (IElement element)
focal_class.signature:  DebugAtom(IElement element)
focal_class.class_method_signature: DebugAtom.getContainer()
focal_class.full_signature: @Override public IAtomContainer getContainer()
focal_class.identifier: getContainer
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getContainer()
focal_class.class_method_signature: DebugAtom.getIndex()
focal_class.full_signature: @Override public int getIndex()
focal_class.identifier: getIndex
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getIndex()
focal_class.class_method_signature: DebugAtom.bonds()
focal_class.full_signature: @Override public Iterable<IBond> bonds()
focal_class.identifier: bonds
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IBond>
focal_class.signature: Iterable<IBond> bonds()
focal_class.class_method_signature: DebugAtom.setCharge(Double charge)
focal_class.full_signature: @Override public void setCharge(Double charge)
focal_class.identifier: setCharge
focal_class.modifiers: @Override public
focal_class.parameters: (Double charge)
focal_class.return: void
focal_class.signature: void setCharge(Double charge)
focal_class.class_method_signature: DebugAtom.getCharge()
focal_class.full_signature: @Override public Double getCharge()
focal_class.identifier: getCharge
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getCharge()
focal_class.class_method_signature: DebugAtom.setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.full_signature: @Override public void setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.identifier: setImplicitHydrogenCount
focal_class.modifiers: @Override public
focal_class.parameters: (Integer hydrogenCount)
focal_class.return: void
focal_class.signature: void setImplicitHydrogenCount(Integer hydrogenCount)
focal_class.class_method_signature: DebugAtom.getImplicitHydrogenCount()
focal_class.full_signature: @Override public Integer getImplicitHydrogenCount()
focal_class.identifier: getImplicitHydrogenCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getImplicitHydrogenCount()
focal_class.class_method_signature: DebugAtom.setPoint2d(Point2d point2d)
focal_class.full_signature: @Override public void setPoint2d(Point2d point2d)
focal_class.identifier: setPoint2d
focal_class.modifiers: @Override public
focal_class.parameters: (Point2d point2d)
focal_class.return: void
focal_class.signature: void setPoint2d(Point2d point2d)
focal_class.class_method_signature: DebugAtom.setPoint3d(Point3d point3d)
focal_class.full_signature: @Override public void setPoint3d(Point3d point3d)
focal_class.identifier: setPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: (Point3d point3d)
focal_class.return: void
focal_class.signature: void setPoint3d(Point3d point3d)
focal_class.class_method_signature: DebugAtom.setFractionalPoint3d(Point3d point3d)
focal_class.full_signature: @Override public void setFractionalPoint3d(Point3d point3d)
focal_class.identifier: setFractionalPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: (Point3d point3d)
focal_class.return: void
focal_class.signature: void setFractionalPoint3d(Point3d point3d)
focal_class.class_method_signature: DebugAtom.setStereoParity(Integer stereoParity)
focal_class.full_signature: @Override public void setStereoParity(Integer stereoParity)
focal_class.identifier: setStereoParity
focal_class.modifiers: @Override public
focal_class.parameters: (Integer stereoParity)
focal_class.return: void
focal_class.signature: void setStereoParity(Integer stereoParity)
focal_class.class_method_signature: DebugAtom.getPoint2d()
focal_class.full_signature: @Override public Point2d getPoint2d()
focal_class.identifier: getPoint2d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point2d
focal_class.signature: Point2d getPoint2d()
focal_class.class_method_signature: DebugAtom.getPoint3d()
focal_class.full_signature: @Override public Point3d getPoint3d()
focal_class.identifier: getPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point3d
focal_class.signature: Point3d getPoint3d()
focal_class.class_method_signature: DebugAtom.getFractionalPoint3d()
focal_class.full_signature: @Override public Point3d getFractionalPoint3d()
focal_class.identifier: getFractionalPoint3d
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Point3d
focal_class.signature: Point3d getFractionalPoint3d()
focal_class.class_method_signature: DebugAtom.getStereoParity()
focal_class.full_signature: @Override public Integer getStereoParity()
focal_class.identifier: getStereoParity
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getStereoParity()
focal_class.class_method_signature: DebugAtom.setAtomTypeName(String identifier)
focal_class.full_signature: @Override public void setAtomTypeName(String identifier)
focal_class.identifier: setAtomTypeName
focal_class.modifiers: @Override public
focal_class.parameters: (String identifier)
focal_class.return: void
focal_class.signature: void setAtomTypeName(String identifier)
focal_class.class_method_signature: DebugAtom.setMaxBondOrder(IBond.Order maxBondOrder)
focal_class.full_signature: @Override public void setMaxBondOrder(IBond.Order maxBondOrder)
focal_class.identifier: setMaxBondOrder
focal_class.modifiers: @Override public
focal_class.parameters: (IBond.Order maxBondOrder)
focal_class.return: void
focal_class.signature: void setMaxBondOrder(IBond.Order maxBondOrder)
focal_class.class_method_signature: DebugAtom.setBondOrderSum(Double bondOrderSum)
focal_class.full_signature: @Override public void setBondOrderSum(Double bondOrderSum)
focal_class.identifier: setBondOrderSum
focal_class.modifiers: @Override public
focal_class.parameters: (Double bondOrderSum)
focal_class.return: void
focal_class.signature: void setBondOrderSum(Double bondOrderSum)
focal_class.class_method_signature: DebugAtom.getAtomTypeName()
focal_class.full_signature: @Override public String getAtomTypeName()
focal_class.identifier: getAtomTypeName
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAtomTypeName()
focal_class.class_method_signature: DebugAtom.getMaxBondOrder()
focal_class.full_signature: @Override public IBond.Order getMaxBondOrder()
focal_class.identifier: getMaxBondOrder
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IBond.Order
focal_class.signature: IBond.Order getMaxBondOrder()
focal_class.class_method_signature: DebugAtom.getBondOrderSum()
focal_class.full_signature: @Override public Double getBondOrderSum()
focal_class.identifier: getBondOrderSum
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getBondOrderSum()
focal_class.class_method_signature: DebugAtom.setFormalCharge(Integer charge)
focal_class.full_signature: @Override public void setFormalCharge(Integer charge)
focal_class.identifier: setFormalCharge
focal_class.modifiers: @Override public
focal_class.parameters: (Integer charge)
focal_class.return: void
focal_class.signature: void setFormalCharge(Integer charge)
focal_class.class_method_signature: DebugAtom.getFormalCharge()
focal_class.full_signature: @Override public Integer getFormalCharge()
focal_class.identifier: getFormalCharge
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getFormalCharge()
focal_class.class_method_signature: DebugAtom.setFormalNeighbourCount(Integer count)
focal_class.full_signature: @Override public void setFormalNeighbourCount(Integer count)
focal_class.identifier: setFormalNeighbourCount
focal_class.modifiers: @Override public
focal_class.parameters: (Integer count)
focal_class.return: void
focal_class.signature: void setFormalNeighbourCount(Integer count)
focal_class.class_method_signature: DebugAtom.getFormalNeighbourCount()
focal_class.full_signature: @Override public Integer getFormalNeighbourCount()
focal_class.identifier: getFormalNeighbourCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getFormalNeighbourCount()
focal_class.class_method_signature: DebugAtom.setHybridization(IAtomType.Hybridization hybridization)
focal_class.full_signature: @Override public void setHybridization(IAtomType.Hybridization hybridization)
focal_class.identifier: setHybridization
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomType.Hybridization hybridization)
focal_class.return: void
focal_class.signature: void setHybridization(IAtomType.Hybridization hybridization)
focal_class.class_method_signature: DebugAtom.getHybridization()
focal_class.full_signature: @Override public IAtomType.Hybridization getHybridization()
focal_class.identifier: getHybridization
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtomType.Hybridization
focal_class.signature: IAtomType.Hybridization getHybridization()
focal_class.class_method_signature: DebugAtom.setCovalentRadius(Double radius)
focal_class.full_signature: @Override public void setCovalentRadius(Double radius)
focal_class.identifier: setCovalentRadius
focal_class.modifiers: @Override public
focal_class.parameters: (Double radius)
focal_class.return: void
focal_class.signature: void setCovalentRadius(Double radius)
focal_class.class_method_signature: DebugAtom.getCovalentRadius()
focal_class.full_signature: @Override public Double getCovalentRadius()
focal_class.identifier: getCovalentRadius
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getCovalentRadius()
focal_class.class_method_signature: DebugAtom.setValency(Integer valency)
focal_class.full_signature: @Override public void setValency(Integer valency)
focal_class.identifier: setValency
focal_class.modifiers: @Override public
focal_class.parameters: (Integer valency)
focal_class.return: void
focal_class.signature: void setValency(Integer valency)
focal_class.class_method_signature: DebugAtom.getValency()
focal_class.full_signature: @Override public Integer getValency()
focal_class.identifier: getValency
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getValency()
focal_class.class_method_signature: DebugAtom.setNaturalAbundance(Double naturalAbundance)
focal_class.full_signature: @Override public void setNaturalAbundance(Double naturalAbundance)
focal_class.identifier: setNaturalAbundance
focal_class.modifiers: @Override public
focal_class.parameters: (Double naturalAbundance)
focal_class.return: void
focal_class.signature: void setNaturalAbundance(Double naturalAbundance)
focal_class.class_method_signature: DebugAtom.setExactMass(Double exactMass)
focal_class.full_signature: @Override public void setExactMass(Double exactMass)
focal_class.identifier: setExactMass
focal_class.modifiers: @Override public
focal_class.parameters: (Double exactMass)
focal_class.return: void
focal_class.signature: void setExactMass(Double exactMass)
focal_class.class_method_signature: DebugAtom.getNaturalAbundance()
focal_class.full_signature: @Override public Double getNaturalAbundance()
focal_class.identifier: getNaturalAbundance
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getNaturalAbundance()
focal_class.class_method_signature: DebugAtom.getExactMass()
focal_class.full_signature: @Override public Double getExactMass()
focal_class.identifier: getExactMass
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Double
focal_class.signature: Double getExactMass()
focal_class.class_method_signature: DebugAtom.getMassNumber()
focal_class.full_signature: @Override public Integer getMassNumber()
focal_class.identifier: getMassNumber
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getMassNumber()
focal_class.class_method_signature: DebugAtom.setMassNumber(Integer massNumber)
focal_class.full_signature: @Override public void setMassNumber(Integer massNumber)
focal_class.identifier: setMassNumber
focal_class.modifiers: @Override public
focal_class.parameters: (Integer massNumber)
focal_class.return: void
focal_class.signature: void setMassNumber(Integer massNumber)
focal_class.class_method_signature: DebugAtom.getAtomicNumber()
focal_class.full_signature: @Override public Integer getAtomicNumber()
focal_class.identifier: getAtomicNumber
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Integer
focal_class.signature: Integer getAtomicNumber()
focal_class.class_method_signature: DebugAtom.setAtomicNumber(Integer atomicNumber)
focal_class.full_signature: @Override public void setAtomicNumber(Integer atomicNumber)
focal_class.identifier: setAtomicNumber
focal_class.modifiers: @Override public
focal_class.parameters: (Integer atomicNumber)
focal_class.return: void
focal_class.signature: void setAtomicNumber(Integer atomicNumber)
focal_class.class_method_signature: DebugAtom.getSymbol()
focal_class.full_signature: @Override public String getSymbol()
focal_class.identifier: getSymbol
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getSymbol()
focal_class.class_method_signature: DebugAtom.setSymbol(String symbol)
focal_class.full_signature: @Override public void setSymbol(String symbol)
focal_class.identifier: setSymbol
focal_class.modifiers: @Override public
focal_class.parameters: (String symbol)
focal_class.return: void
focal_class.signature: void setSymbol(String symbol)
focal_class.class_method_signature: DebugAtom.addListener(IChemObjectListener col)
focal_class.full_signature: @Override public void addListener(IChemObjectListener col)
focal_class.identifier: addListener
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObjectListener col)
focal_class.return: void
focal_class.signature: void addListener(IChemObjectListener col)
focal_class.class_method_signature: DebugAtom.getListenerCount()
focal_class.full_signature: @Override public int getListenerCount()
focal_class.identifier: getListenerCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getListenerCount()
focal_class.class_method_signature: DebugAtom.removeListener(IChemObjectListener col)
focal_class.full_signature: @Override public void removeListener(IChemObjectListener col)
focal_class.identifier: removeListener
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObjectListener col)
focal_class.return: void
focal_class.signature: void removeListener(IChemObjectListener col)
focal_class.class_method_signature: DebugAtom.notifyChanged()
focal_class.full_signature: @Override public void notifyChanged()
focal_class.identifier: notifyChanged
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void notifyChanged()
focal_class.class_method_signature: DebugAtom.notifyChanged(IChemObjectChangeEvent evt)
focal_class.full_signature: @Override public void notifyChanged(IChemObjectChangeEvent evt)
focal_class.identifier: notifyChanged
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObjectChangeEvent evt)
focal_class.return: void
focal_class.signature: void notifyChanged(IChemObjectChangeEvent evt)
focal_class.class_method_signature: DebugAtom.setProperty(Object description, Object property)
focal_class.full_signature: @Override public void setProperty(Object description, Object property)
focal_class.identifier: setProperty
focal_class.modifiers: @Override public
focal_class.parameters: (Object description, Object property)
focal_class.return: void
focal_class.signature: void setProperty(Object description, Object property)
focal_class.class_method_signature: DebugAtom.removeProperty(Object description)
focal_class.full_signature: @Override public void removeProperty(Object description)
focal_class.identifier: removeProperty
focal_class.modifiers: @Override public
focal_class.parameters: (Object description)
focal_class.return: void
focal_class.signature: void removeProperty(Object description)
focal_class.class_method_signature: DebugAtom.getProperty(Object description)
focal_class.full_signature: @Override public T getProperty(Object description)
focal_class.identifier: getProperty
focal_class.modifiers: @Override public
focal_class.parameters: (Object description)
focal_class.return: T
focal_class.signature: T getProperty(Object description)
focal_class.class_method_signature: DebugAtom.getProperties()
focal_class.full_signature: @Override public Map<Object, Object> getProperties()
focal_class.identifier: getProperties
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<Object, Object>
focal_class.signature: Map<Object, Object> getProperties()
focal_class.class_method_signature: DebugAtom.getID()
focal_class.full_signature: @Override public String getID()
focal_class.identifier: getID
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getID()
focal_class.class_method_signature: DebugAtom.setID(String identifier)
focal_class.full_signature: @Override public void setID(String identifier)
focal_class.identifier: setID
focal_class.modifiers: @Override public
focal_class.parameters: (String identifier)
focal_class.return: void
focal_class.signature: void setID(String identifier)
focal_class.class_method_signature: DebugAtom.setFlag(int flagType, boolean flagValue)
focal_class.full_signature: @Override public void setFlag(int flagType, boolean flagValue)
focal_class.identifier: setFlag
focal_class.modifiers: @Override public
focal_class.parameters: (int flagType, boolean flagValue)
focal_class.return: void
focal_class.signature: void setFlag(int flagType, boolean flagValue)
focal_class.class_method_signature: DebugAtom.getFlag(int flagType)
focal_class.full_signature: @Override public boolean getFlag(int flagType)
focal_class.identifier: getFlag
focal_class.modifiers: @Override public
focal_class.parameters: (int flagType)
focal_class.return: boolean
focal_class.signature: boolean getFlag(int flagType)
focal_class.class_method_signature: DebugAtom.addProperties(Map<Object, Object> properties)
focal_class.full_signature: @Override public void addProperties(Map<Object, Object> properties)
focal_class.identifier: addProperties
focal_class.modifiers: @Override public
focal_class.parameters: (Map<Object, Object> properties)
focal_class.return: void
focal_class.signature: void addProperties(Map<Object, Object> properties)
focal_class.class_method_signature: DebugAtom.setFlags(boolean[] flagsNew)
focal_class.full_signature: @Override public void setFlags(boolean[] flagsNew)
focal_class.identifier: setFlags
focal_class.modifiers: @Override public
focal_class.parameters: (boolean[] flagsNew)
focal_class.return: void
focal_class.signature: void setFlags(boolean[] flagsNew)
focal_class.class_method_signature: DebugAtom.getFlags()
focal_class.full_signature: @Override public boolean[] getFlags()
focal_class.identifier: getFlags
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: boolean[]
focal_class.signature: boolean[] getFlags()
focal_class.class_method_signature: DebugAtom.clone()
focal_class.full_signature: @Override public IAtom clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtom
focal_class.signature: IAtom clone()
focal_class.class_method_signature: DebugAtom.getBuilder()
focal_class.full_signature: @Override public IChemObjectBuilder getBuilder()
focal_class.identifier: getBuilder
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IChemObjectBuilder
focal_class.signature: IChemObjectBuilder getBuilder()
focal_class.superclass: extends Atom
focal_method.body: public DebugAtom() {
          super();
      }
focal_method.class_method_signature: DebugAtom.DebugAtom()
focal_method.full_signature: public  DebugAtom()
focal_method.identifier: DebugAtom
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  DebugAtom()