Package org.openscience.cdk.interfaces

Interface IPseudoAtom

All Superinterfaces:

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

All Known Subinterfaces:

IFragmentAtom

All Known Implementing Classes:

DebugFragmentAtom, DebugPseudoAtom, EnzymeResidueLocator, FragmentAtom, FragmentAtom, PseudoAtom, PseudoAtom

public interface IPseudoAtom
extends IAtom

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:

• IAtom

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType

IAtomType.Hybridization

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.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 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

Method Summary

Modifier and Type	Method	Description
IPseudoAtom	clone()	Returns a deep clone of this IChemObject.
int	getAttachPointNum()	Access the attachment point number.
String	getLabel()	Returns the label of this PseudoAtom.
void	setAttachPointNum(int ap)	Set the attachment point number.
void	setLabel(String label)	Sets the label of this PseudoAtom.

Methods inherited from interface org.openscience.cdk.interfaces.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 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, 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 org.openscience.cdk.interfaces.IElement

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface org.openscience.cdk.interfaces.IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Method Details

getLabel

String getLabel()

Returns the label of this PseudoAtom.

Returns:

The label for this PseudoAtom

See Also:

• setLabel(java.lang.String)

setLabel

void setLabel(String label)

Sets the label of this PseudoAtom.

Parameters:

label - The new label for this PseudoAtom

See Also:

• getLabel()

getAttachPointNum

int getAttachPointNum()

Access the attachment point number. The default, 0, indicates this atom is not an attachment point.

Returns:

attach point number

setAttachPointNum

void setAttachPointNum(int ap)

Set the attachment point number.

Parameters:

ap - attach point number

clone

IPseudoAtom clone()
           throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtom

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned