IPseudoAtom (cdk 2.9 API)

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

Source code:
main

Belongs to CDK module:
interfaces

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.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

All Methods Instance Methods Abstract Methods
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, 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

- Method Detail
  - 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