Package org.openscience.cdk
Class FragmentAtom
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IFragmentAtom
,IIsotope
,IPseudoAtom
- Direct Known Subclasses:
DebugFragmentAtom
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:
- data
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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 TypeMethodDescriptionclone()
Clones this atom object and its content.The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.Returns the fully expended form of the IFragmentAtom.boolean
Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.void
setExactMass
(Double mass) 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
setFragment
(IAtomContainer fragment) Sets the fully expended form of the IFragmentAtom.toString()
Returns a one line string representation of this Atom.Methods inherited from class org.openscience.cdk.PseudoAtom
getAttachPointNum, getLabel, setAttachPointNum, setLabel, setStereoParity
Methods inherited from class org.openscience.cdk.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
Methods inherited from class org.openscience.cdk.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
Methods inherited from class org.openscience.cdk.Isotope
getMassNumber, getNaturalAbundance, setMassNumber, setNaturalAbundance
Methods inherited from class org.openscience.cdk.Element
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, 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, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
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
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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
Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getMassNumber, getNaturalAbundance, setMassNumber, setNaturalAbundance
Methods inherited from interface org.openscience.cdk.interfaces.IPseudoAtom
getAttachPointNum, getLabel, setAttachPointNum, setLabel
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Constructor Details
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FragmentAtom
public FragmentAtom()
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Method Details
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isExpanded
public boolean isExpanded()Description copied from interface:IFragmentAtom
Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.- Specified by:
isExpanded
in interfaceIFragmentAtom
- Returns:
- true, if it should be considered in expended form
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setExpanded
public void setExpanded(boolean bool) Description copied from interface:IFragmentAtom
Sets whether this atom is to be fully drawn and not just in the abbreviated form.- Specified by:
setExpanded
in interfaceIFragmentAtom
- Parameters:
bool
- true if the full structure should be drawn
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getFragment
Description copied from interface:IFragmentAtom
Returns the fully expended form of the IFragmentAtom.- Specified by:
getFragment
in interfaceIFragmentAtom
- Returns:
- the fully expanded form as an IAtomContainer object
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setFragment
Description copied from interface:IFragmentAtom
Sets the fully expended form of the IFragmentAtom.- Specified by:
setFragment
in interfaceIFragmentAtom
- Parameters:
fragment
- The fragment
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setExactMass
Description copied from class:Isotope
Sets the ExactMass attribute of the Isotope object.- Specified by:
setExactMass
in interfaceIIsotope
- Overrides:
setExactMass
in classIsotope
- Parameters:
mass
- The new ExactMass 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 classIsotope
- Returns:
- The ExactMass value
- See Also:
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toString
Description copied from class:PseudoAtom
Returns a one line string representation of this Atom. Methods is conform RFC #9.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classPseudoAtom
- Returns:
- The string representation of this Atom
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clone
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 classPseudoAtom
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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