Package org.openscience.cdk.interfaces
Interface IFragmentAtom
- All Superinterfaces:
Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IPseudoAtom
- All Known Implementing Classes:
DebugFragmentAtom
,FragmentAtom
,FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
like the MDL molfile
Group
concept.- Author:
- egonw
- Source code:
- main
- Belongs to CDK module:
- interfaces
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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 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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Method Summary
Modifier and TypeMethodDescriptionReturns 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
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.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, toString
Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
Methods inherited from interface org.openscience.cdk.interfaces.IPseudoAtom
clone, getAttachPointNum, getLabel, setAttachPointNum, setLabel
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Method Details
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isExpanded
boolean isExpanded()Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.- Returns:
- true, if it should be considered in expended form
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setExpanded
void setExpanded(boolean bool) Sets whether this atom is to be fully drawn and not just in the abbreviated form.- Parameters:
bool
- true if the full structure should be drawn
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getFragment
IAtomContainer getFragment()Returns the fully expended form of the IFragmentAtom.- Returns:
- the fully expanded form as an IAtomContainer object
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setFragment
Sets the fully expended form of the IFragmentAtom.- Parameters:
fragment
- The fragment
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