Package org.openscience.cdk.debug
Class DebugFragmentAtom
java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.Element
org.openscience.cdk.Isotope
org.openscience.cdk.AtomType
org.openscience.cdk.Atom
org.openscience.cdk.PseudoAtom
org.openscience.cdk.FragmentAtom
org.openscience.cdk.debug.DebugFragmentAtom
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IFragmentAtom
,IIsotope
,IPseudoAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
like the MDL molfile
Group
concept.- Author:
- egonw
- See Also:
- Source code:
- main
- Belongs to CDK module:
- datadebug
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
Fields inherited from class org.openscience.cdk.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
Fields inherited from class org.openscience.cdk.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
Fields inherited from class org.openscience.cdk.Isotope
exactMass, naturalAbundance
Fields inherited from class org.openscience.cdk.Element
atomicNumber
Fields inherited from interface org.openscience.cdk.interfaces.IElement
Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Use this to add yourself to this IChemObject as a listener.void
addProperties
(Map<Object, Object> properties) Sets the properties of this object.clone()
Clones this atom object and its content.Returns the atomic number of this element.Gets the id attribute of the AtomType object.Gets the bondOrderSum attribute of the AtomType object.Returns aIChemObjectBuilder
for the data classes that extend this class.Returns the partial charge of this atom.Returns the covalent radius for this AtomType.The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.boolean
getFlag
(int flagType) Returns the value of a given flag.boolean[]
getFlags()
Returns the whole set of flags.Returns the formal charge of this atom.Returns the formal neighbour count of this atom.javax.vecmath.Point3d
Returns a point specifying the location of this atom in a Crystal unit cell.Returns the fully expended form of the IFragmentAtom.Returns the hybridization of this atom.getID()
Returns the identifier (ID) of this object.Returns the hydrogen count of this atom.getLabel()
Returns the label of this PseudoAtom.int
Returns the number of ChemObjectListeners registered with this object.Returns the atomic mass of this element.Gets the MaxBondOrder attribute of the AtomType object.Gets the NaturalAbundance attribute of the Isotope object.javax.vecmath.Point2d
Returns a point specifying the location of this atom in a 2D space.javax.vecmath.Point3d
Returns a point specifying the location of this atom in a 3D space.Returns a Map with the IChemObject's properties.<T> T
getProperty
(Object description) Returns a property for the IChemObject.Returns the stereo parity of this atom.Returns the element symbol of this element.Gets the the exact electron valency of the AtomType object.boolean
Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.void
This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.void
This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.void
Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.void
removeProperty
(Object description) Removes a property for a IChemObject.void
setAtomicNumber
(Integer atomicNumber) Sets the atomic number of this element.void
setAtomTypeName
(String identifier) Sets the if attribute of the AtomType object.void
setBondOrderSum
(Double bondOrderSum) Sets the the exact bond order sum attribute of the AtomType object.void
Sets the partial charge of this atom.void
setCovalentRadius
(Double radius) Sets the covalent radius for this AtomType.void
setExactMass
(Double exactMass) Sets the ExactMass attribute of the Isotope object.void
setExpanded
(boolean bool) Sets whether this atom is to be fully drawn and not just in the abbreviated form.void
setFlag
(int flagType, boolean flagValue) Sets the value of some flag.void
setFlags
(boolean[] flagsNew) Sets the whole set of flags.void
setFormalCharge
(Integer charge) Sets the formal charge of this atom.void
setFormalNeighbourCount
(Integer count) Sets the formal neighbour count of this atom.void
setFractionalPoint3d
(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in a Crystal unit cell.void
setFragment
(IAtomContainer fragment) Sets the fully expended form of the IFragmentAtom.void
setHybridization
(IAtomType.Hybridization hybridization) Sets the hybridization of this atom.void
Sets the identifier (ID) of this object.void
setImplicitHydrogenCount
(Integer hydrogenCount) Sets the number of implicit hydrogen count of this atom.void
Sets the label of this PseudoAtom.void
setMassNumber
(Integer massNumber) Sets the atomic mass of this element.void
setMaxBondOrder
(IBond.Order maxBondOrder) Sets the MaxBondOrder attribute of the AtomType object.void
setNaturalAbundance
(Double naturalAbundance) Sets the NaturalAbundance attribute of the Isotope object.void
setPoint2d
(javax.vecmath.Point2d point2d) Sets a point specifying the location of this atom in a 2D space.void
setPoint3d
(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in 3D space.void
setProperty
(Object description, Object property) Sets a property for a IChemObject.void
setStereoParity
(Integer stereoParity) Dummy method: the stereo parity is undefined, final.void
Sets the element symbol of this element.void
setValency
(Integer valency) Sets the the exact electron valency of the AtomType object.Methods inherited from class org.openscience.cdk.FragmentAtom
toString
Methods inherited from class org.openscience.cdk.PseudoAtom
getAttachPointNum, setAttachPointNum
Methods inherited from class org.openscience.cdk.Atom
bonds, compare, equals, getBond, getBondCount, getContainer, getIndex, getMapIdx, hashCode, isAromatic, isInRing, setIsAromatic, setIsInRing, setMapIdx
Methods inherited from class org.openscience.cdk.ChemObject
getFlagValue, getNotification, getProperty, setNotification, setProperties, shallowCopy
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, getBond, getBondCount, getContainer, getIndex, getMapIdx, isAromatic, isInRing, setIsAromatic, setIsInRing, setMapIdx
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
getFlagValue, getNotification, getProperty, setNotification, setProperties
Methods inherited from interface org.openscience.cdk.interfaces.IPseudoAtom
getAttachPointNum, setAttachPointNum
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Constructor Details
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DebugFragmentAtom
public DebugFragmentAtom()
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Method Details
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isExpanded
public boolean isExpanded()Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.- Specified by:
isExpanded
in interfaceIFragmentAtom
- Overrides:
isExpanded
in classFragmentAtom
- Returns:
- true, if it should be considered in expended form
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setExpanded
public void setExpanded(boolean bool) Sets whether this atom is to be fully drawn and not just in the abbreviated form.- Specified by:
setExpanded
in interfaceIFragmentAtom
- Overrides:
setExpanded
in classFragmentAtom
- Parameters:
bool
- true if the full structure should be drawn
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getFragment
Returns the fully expended form of the IFragmentAtom.- Specified by:
getFragment
in interfaceIFragmentAtom
- Overrides:
getFragment
in classFragmentAtom
- Returns:
- the fully expanded form as an IAtomContainer object
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setFragment
Sets the fully expended form of the IFragmentAtom.- Specified by:
setFragment
in interfaceIFragmentAtom
- Overrides:
setFragment
in classFragmentAtom
- Parameters:
fragment
- The fragment
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setCharge
Sets the partial charge of this atom. -
getCharge
Returns the partial charge of this atom. If the charge has not been set the return value is Double.NaN -
setImplicitHydrogenCount
Sets the number of implicit hydrogen count of this atom.- Specified by:
setImplicitHydrogenCount
in interfaceIAtom
- Overrides:
setImplicitHydrogenCount
in classAtom
- Parameters:
hydrogenCount
- The number of hydrogen atoms bonded to this atom.- See Also:
-
getImplicitHydrogenCount
Returns the hydrogen count of this atom.- Specified by:
getImplicitHydrogenCount
in interfaceIAtom
- Overrides:
getImplicitHydrogenCount
in classAtom
- Returns:
- The hydrogen count of this atom.
- See Also:
-
setPoint2d
public void setPoint2d(javax.vecmath.Point2d point2d) Sets a point specifying the location of this atom in a 2D space.- Specified by:
setPoint2d
in interfaceIAtom
- Overrides:
setPoint2d
in classAtom
- Parameters:
point2d
- A point in a 2D plane- See Also:
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setPoint3d
public void setPoint3d(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in 3D space.- Specified by:
setPoint3d
in interfaceIAtom
- Overrides:
setPoint3d
in classAtom
- Parameters:
point3d
- A point in a 3-dimensional space- See Also:
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setFractionalPoint3d
public void setFractionalPoint3d(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in a Crystal unit cell.- Specified by:
setFractionalPoint3d
in interfaceIAtom
- Overrides:
setFractionalPoint3d
in classAtom
- Parameters:
point3d
- A point in a 3d fractional unit cell space- See Also:
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setStereoParity
Dummy method: the stereo parity is undefined, final.- Specified by:
setStereoParity
in interfaceIAtom
- Overrides:
setStereoParity
in classPseudoAtom
- Parameters:
stereoParity
- The stereo parity for this atom- See Also:
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getPoint2d
public javax.vecmath.Point2d getPoint2d()Returns a point specifying the location of this atom in a 2D space.- Specified by:
getPoint2d
in interfaceIAtom
- Overrides:
getPoint2d
in classAtom
- Returns:
- A point in a 2D plane. Null if unset.
- See Also:
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getPoint3d
public javax.vecmath.Point3d getPoint3d()Returns a point specifying the location of this atom in a 3D space.- Specified by:
getPoint3d
in interfaceIAtom
- Overrides:
getPoint3d
in classAtom
- Returns:
- A point in 3-dimensional space. Null if unset.
- See Also:
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getFractionalPoint3d
public javax.vecmath.Point3d getFractionalPoint3d()Returns a point specifying the location of this atom in a Crystal unit cell.- Specified by:
getFractionalPoint3d
in interfaceIAtom
- Overrides:
getFractionalPoint3d
in classAtom
- Returns:
- A point in 3d fractional unit cell space. Null if unset.
- See Also:
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getStereoParity
Returns the stereo parity of this atom. It uses the predefined values found in CDKConstants.- Specified by:
getStereoParity
in interfaceIAtom
- Overrides:
getStereoParity
in classAtom
- Returns:
- The stereo parity for this atom
- See Also:
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setAtomTypeName
Sets the if attribute of the AtomType object.- Specified by:
setAtomTypeName
in interfaceIAtomType
- Overrides:
setAtomTypeName
in classAtomType
- Parameters:
identifier
- The new AtomTypeID value. Null if unset.- See Also:
-
setMaxBondOrder
Sets the MaxBondOrder attribute of the AtomType object.- Specified by:
setMaxBondOrder
in interfaceIAtomType
- Overrides:
setMaxBondOrder
in classAtomType
- Parameters:
maxBondOrder
- The new MaxBondOrder value- See Also:
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setBondOrderSum
Sets the the exact bond order sum attribute of the AtomType object.- Specified by:
setBondOrderSum
in interfaceIAtomType
- Overrides:
setBondOrderSum
in classAtomType
- Parameters:
bondOrderSum
- The new bondOrderSum value- See Also:
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getAtomTypeName
Gets the id attribute of the AtomType object.- Specified by:
getAtomTypeName
in interfaceIAtomType
- Overrides:
getAtomTypeName
in classAtomType
- Returns:
- The id value
- See Also:
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getMaxBondOrder
Gets the MaxBondOrder attribute of the AtomType object.- Specified by:
getMaxBondOrder
in interfaceIAtomType
- Overrides:
getMaxBondOrder
in classAtomType
- Returns:
- The MaxBondOrder value
- See Also:
-
getBondOrderSum
Gets the bondOrderSum attribute of the AtomType object.- Specified by:
getBondOrderSum
in interfaceIAtomType
- Overrides:
getBondOrderSum
in classAtomType
- Returns:
- The bondOrderSum value
- See Also:
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setFormalCharge
Sets the formal charge of this atom.- Specified by:
setFormalCharge
in interfaceIAtomType
- Overrides:
setFormalCharge
in classAtomType
- Parameters:
charge
- The formal charge- See Also:
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getFormalCharge
Returns the formal charge of this atom.- Specified by:
getFormalCharge
in interfaceIAtomType
- Overrides:
getFormalCharge
in classAtomType
- Returns:
- the formal charge of this atom
- See Also:
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setFormalNeighbourCount
Sets the formal neighbour count of this atom.- Specified by:
setFormalNeighbourCount
in interfaceIAtomType
- Overrides:
setFormalNeighbourCount
in classAtomType
- Parameters:
count
- The neighbour count- See Also:
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getFormalNeighbourCount
Returns the formal neighbour count of this atom.- Specified by:
getFormalNeighbourCount
in interfaceIAtomType
- Overrides:
getFormalNeighbourCount
in classAtomType
- Returns:
- the formal neighbour count of this atom
- See Also:
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setHybridization
Sets the hybridization of this atom.- Specified by:
setHybridization
in interfaceIAtomType
- Overrides:
setHybridization
in classAtomType
- Parameters:
hybridization
- The hybridization- See Also:
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getHybridization
Returns the hybridization of this atom.- Specified by:
getHybridization
in interfaceIAtomType
- Overrides:
getHybridization
in classAtomType
- Returns:
- the hybridization of this atom
- See Also:
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setCovalentRadius
Sets the covalent radius for this AtomType.- Specified by:
setCovalentRadius
in interfaceIAtomType
- Overrides:
setCovalentRadius
in classAtomType
- Parameters:
radius
- The covalent radius for this AtomType- See Also:
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getCovalentRadius
Returns the covalent radius for this AtomType.- Specified by:
getCovalentRadius
in interfaceIAtomType
- Overrides:
getCovalentRadius
in classAtomType
- Returns:
- The covalent radius for this AtomType
- See Also:
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setValency
Sets the the exact electron valency of the AtomType object.- Specified by:
setValency
in interfaceIAtomType
- Overrides:
setValency
in classAtomType
- Parameters:
valency
- The new valency value- See Also:
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getValency
Gets the the exact electron valency of the AtomType object.- Specified by:
getValency
in interfaceIAtomType
- Overrides:
getValency
in classAtomType
- Returns:
- The valency value
- See Also:
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setNaturalAbundance
Sets the NaturalAbundance attribute of the Isotope object.- Specified by:
setNaturalAbundance
in interfaceIIsotope
- Overrides:
setNaturalAbundance
in classIsotope
- Parameters:
naturalAbundance
- The new NaturalAbundance value- See Also:
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setExactMass
Sets the ExactMass attribute of the Isotope object.- Specified by:
setExactMass
in interfaceIIsotope
- Overrides:
setExactMass
in classFragmentAtom
- Parameters:
exactMass
- The new ExactMass value- See Also:
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getNaturalAbundance
Gets the NaturalAbundance attribute of the Isotope object.Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:
Isotope isotope = new Isotope("C", 13); IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder()); if.configure(isotope);
- Specified by:
getNaturalAbundance
in interfaceIIsotope
- Overrides:
getNaturalAbundance
in classIsotope
- Returns:
- The NaturalAbundance value
- See Also:
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getExactMass
The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.- Specified by:
getExactMass
in interfaceIIsotope
- Overrides:
getExactMass
in classFragmentAtom
- Returns:
- The ExactMass value
- See Also:
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getMassNumber
Returns the atomic mass of this element.Once instantiated all field not filled by passing parameters to the constructor are null. Isotopes can be configured by using the IsotopeFactory.configure() method:
Isotope isotope = new Isotope("C", 13); IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder()); if.configure(isotope);
- Specified by:
getMassNumber
in interfaceIIsotope
- Overrides:
getMassNumber
in classIsotope
- Returns:
- The atomic mass of this element
- See Also:
-
setMassNumber
Sets the atomic mass of this element.- Specified by:
setMassNumber
in interfaceIIsotope
- Overrides:
setMassNumber
in classIsotope
- Parameters:
massNumber
- The atomic mass to be assigned to this element- See Also:
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getAtomicNumber
Returns the atomic number of this element.Once instantiated all field not filled by passing parameters to the constructor are null. Elements can be configured by using the IsotopeFactory.configure() method:
Element element = new Element("C"); IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder()); if.configure(element);
- Specified by:
getAtomicNumber
in interfaceIElement
- Overrides:
getAtomicNumber
in classElement
- Returns:
- The atomic number of this element
- See Also:
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setAtomicNumber
Sets the atomic number of this element.- Specified by:
setAtomicNumber
in interfaceIElement
- Overrides:
setAtomicNumber
in classElement
- Parameters:
atomicNumber
- The atomic mass to be assigned to this element- See Also:
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getSymbol
Returns the element symbol of this element. -
setSymbol
Sets the element symbol of this element. -
addListener
Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.- Specified by:
addListener
in interfaceIChemObject
- Overrides:
addListener
in classChemObject
- Parameters:
col
- the ChemObjectListener- See Also:
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getListenerCount
public int getListenerCount()Returns the number of ChemObjectListeners registered with this object.- Specified by:
getListenerCount
in interfaceIChemObject
- Overrides:
getListenerCount
in classChemObject
- Returns:
- the number of registered listeners.
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removeListener
Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.- Specified by:
removeListener
in interfaceIChemObject
- Overrides:
removeListener
in classChemObject
- Parameters:
col
- The ChemObjectListener to be removed- See Also:
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notifyChanged
public void notifyChanged()This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.- Specified by:
notifyChanged
in interfaceIChemObject
- Overrides:
notifyChanged
in classChemObject
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notifyChanged
This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.- Specified by:
notifyChanged
in interfaceIChemObject
- Overrides:
notifyChanged
in classChemObject
- Parameters:
evt
- A ChemObjectChangeEvent pointing to the source of where the change happened
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setProperty
Sets a property for a IChemObject.- Specified by:
setProperty
in interfaceIChemObject
- Overrides:
setProperty
in classChemObject
- Parameters:
description
- An object description of the property (most likely a unique string)property
- An object with the property itself- See Also:
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removeProperty
Removes a property for a IChemObject.- Specified by:
removeProperty
in interfaceIChemObject
- Overrides:
removeProperty
in classChemObject
- Parameters:
description
- The object description of the property (most likely a unique string)- See Also:
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getProperty
Returns a property for the IChemObject.- Specified by:
getProperty
in interfaceIChemObject
- Overrides:
getProperty
in classChemObject
- Type Parameters:
T
- generic return type- Parameters:
description
- An object description of the property (most likely a unique string)- Returns:
- The object containing the property. Returns null if propert is not set.
- See Also:
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getProperties
Returns a Map with the IChemObject's properties.- Specified by:
getProperties
in interfaceIChemObject
- Overrides:
getProperties
in classChemObject
- Returns:
- The object's properties as an Hashtable
- See Also:
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getID
Returns the identifier (ID) of this object.- Specified by:
getID
in interfaceIChemObject
- Overrides:
getID
in classChemObject
- Returns:
- a String representing the ID value
- See Also:
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setID
Sets the identifier (ID) of this object.- Specified by:
setID
in interfaceIChemObject
- Overrides:
setID
in classChemObject
- Parameters:
identifier
- a String representing the ID value- See Also:
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setFlag
public void setFlag(int flagType, boolean flagValue) Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g.CDKConstants.ISAROMATIC
orCDKConstants.VISITED
). The flags are intrinsic internal properties and should not be used to store custom values, please useIChemObject.setProperty(Object, Object)
.// set this chem object to be aromatic chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE); // ... // indicate we have visited this chem object chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
- Specified by:
setFlag
in interfaceIChemObject
- Overrides:
setFlag
in classChemObject
- Parameters:
flagType
- flag to set the value forflagValue
- value to assign to flag- See Also:
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getFlag
public boolean getFlag(int flagType) Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g.CDKConstants.ISAROMATIC
).if(chemObject.getFlag(CDKConstants.ISAROMATIC)){ // handle aromatic flag on this chem object }
- Specified by:
getFlag
in interfaceIChemObject
- Overrides:
getFlag
in classChemObject
- Parameters:
flagType
- flag to retrieve the value of- Returns:
- true if the flag
flag_type
is set - See Also:
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addProperties
Sets the properties of this object.- Specified by:
addProperties
in interfaceIChemObject
- Overrides:
addProperties
in classChemObject
- Parameters:
properties
- a Hashtable specifying the property values- See Also:
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setFlags
public void setFlags(boolean[] flagsNew) Sets the whole set of flags.- Specified by:
setFlags
in interfaceIChemObject
- Overrides:
setFlags
in classChemObject
- Parameters:
flagsNew
- the new flags.- See Also:
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getFlags
public boolean[] getFlags()Returns the whole set of flags.- Specified by:
getFlags
in interfaceIChemObject
- Overrides:
getFlags
in classChemObject
- Returns:
- the flags.
- See Also:
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clone
Clones this atom object and its content.- Specified by:
clone
in interfaceIAtom
- Specified by:
clone
in interfaceIChemObject
- Specified by:
clone
in interfaceIPseudoAtom
- Overrides:
clone
in classFragmentAtom
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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getBuilder
Returns aIChemObjectBuilder
for the data classes that extend this class.- Specified by:
getBuilder
in interfaceICDKObject
- Overrides:
getBuilder
in classChemObject
- Returns:
- The
IChemObjectBuilder
matching thisICDKObject
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getLabel
Returns the label of this PseudoAtom.- Specified by:
getLabel
in interfaceIPseudoAtom
- Overrides:
getLabel
in classPseudoAtom
- Returns:
- The label for this PseudoAtom
- See Also:
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setLabel
Sets the label of this PseudoAtom.- Specified by:
setLabel
in interfaceIPseudoAtom
- Overrides:
setLabel
in classPseudoAtom
- Parameters:
label
- The new label for this PseudoAtom- See Also:
-