Interface IFragmentAtom

All Superinterfaces:

Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IPseudoAtom

All Known Implementing Classes:

DebugFragmentAtom, FragmentAtom, FragmentAtom

public interface IFragmentAtom
extends IPseudoAtom

Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much like the MDL molfile Group concept.

Author:

egonw

Nested Class Summary

Nested classes/interfaces inherited from interface IAtomType

IAtomType.Hybridization

Field Summary

Fields inherited from interface IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Fields inherited from interface 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

Method Summary

Modifier and Type	Method	Description
IAtomContainer	getFragment()	Returns the fully expended form of the IFragmentAtom.
boolean	isExpanded()	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 IAtom

bonds, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity

Methods inherited from interface IAtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from interface ICDKObject

getBuilder

Methods inherited from interface IChemObject

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Methods inherited from interface IElement

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from interface IPseudoAtom

clone, getAttachPointNum, getLabel, setAttachPointNum, setLabel

Method Details

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

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

getFragment

IAtomContainer getFragment()

Returns the fully expended form of the IFragmentAtom.

Returns:

the fully expanded form as an IAtomContainer object

setFragment

void setFragment(IAtomContainer fragment)

Sets the fully expended form of the IFragmentAtom.

Parameters:

fragment - The fragment