Package org.openscience.cdk.silent
Class PseudoAtom
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IPseudoAtom
- Direct Known Subclasses:
FragmentAtom
public class PseudoAtom extends Atom implements Serializable, Cloneable, IPseudoAtom
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.
- See Also:
Atom
, Serialized Form- Source code:
- main
- Belongs to CDK module:
- silent
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
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Fields inherited from class org.openscience.cdk.silent.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
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Fields inherited from class org.openscience.cdk.silent.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
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Fields inherited from class org.openscience.cdk.silent.Isotope
exactMass, naturalAbundance
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Fields inherited from class org.openscience.cdk.silent.Element
atomicNumber
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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 Constructor Description PseudoAtom()
Constructs an empty PseudoAtom.PseudoAtom(String label)
Constructs an Atom from a String containing an element symbol.PseudoAtom(String label, javax.vecmath.Point2d point2d)
Constructs an Atom from an Element and a Point2d.PseudoAtom(String label, javax.vecmath.Point3d point3d)
Constructs an Atom from an Element and a Point3d.PseudoAtom(IElement element)
Constructs an PseudoAtom from a IAtom.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IPseudoAtom
clone()
Clones this atom object and its content.int
getAttachPointNum()
Access the attachment point number.String
getLabel()
Returns the label of this PseudoAtom.void
setAttachPointNum(int attachPoint)
Set the attachment point number.void
setLabel(String label)
Sets the label of this PseudoAtom.void
setStereoParity(Integer stereoParity)
Dummy method: the stereo parity is undefined, final.String
toString()
Returns a one line string representation of this Atom.-
Methods inherited from class org.openscience.cdk.silent.Atom
bonds, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d
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Methods inherited from class org.openscience.cdk.silent.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
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Methods inherited from class org.openscience.cdk.silent.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Methods inherited from class org.openscience.cdk.silent.Element
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
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Methods inherited from class org.openscience.cdk.silent.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
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Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Constructor Detail
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PseudoAtom
public PseudoAtom()
Constructs an empty PseudoAtom.
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PseudoAtom
public PseudoAtom(String label)
Constructs an Atom from a String containing an element symbol.- Parameters:
label
- The String describing the PseudoAtom
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PseudoAtom
public PseudoAtom(IElement element)
Constructs an PseudoAtom from a IAtom.- Parameters:
element
- IAtom from which the PseudoAtom is constructed
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PseudoAtom
public PseudoAtom(String label, javax.vecmath.Point3d point3d)
Constructs an Atom from an Element and a Point3d.- Parameters:
label
- The String describing the PseudoAtompoint3d
- The 3D coordinates of the atom
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PseudoAtom
public PseudoAtom(String label, javax.vecmath.Point2d point2d)
Constructs an Atom from an Element and a Point2d.- Parameters:
label
- The String describing the PseudoAtompoint2d
- The Point
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Method Detail
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getLabel
public String getLabel()
Returns the label of this PseudoAtom.- Specified by:
getLabel
in interfaceIPseudoAtom
- Returns:
- The label for this PseudoAtom
- See Also:
setLabel(java.lang.String)
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setLabel
public void setLabel(String label)
Sets the label of this PseudoAtom.- Specified by:
setLabel
in interfaceIPseudoAtom
- Parameters:
label
- The new label for this PseudoAtom- See Also:
getLabel()
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getAttachPointNum
public int getAttachPointNum()
Access the attachment point number. The default, 0, indicates this atom is not an attachment point.- Specified by:
getAttachPointNum
in interfaceIPseudoAtom
- Returns:
- attach point number
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setAttachPointNum
public void setAttachPointNum(int attachPoint)
Set the attachment point number.- Specified by:
setAttachPointNum
in interfaceIPseudoAtom
- Parameters:
attachPoint
- attach point number
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setStereoParity
public void setStereoParity(Integer stereoParity)
Dummy method: the stereo parity is undefined, final.- Specified by:
setStereoParity
in interfaceIAtom
- Overrides:
setStereoParity
in classAtom
- Parameters:
stereoParity
- The stereo parity for this atom- See Also:
for predefined values.
,Atom.getStereoParity()
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toString
public String toString()
Returns a one line string representation of this Atom. Methods is conform RFC #9.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classAtom
- Returns:
- The string representation of this Atom
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clone
public IPseudoAtom clone() throws CloneNotSupportedException
Description copied from class:Atom
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 classAtom
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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