Package org.openscience.cdk

Class PseudoAtom

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.AtomType

org.openscience.cdk.Atom

org.openscience.cdk.PseudoAtom

All Implemented Interfaces:

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

Direct Known Subclasses:

DebugPseudoAtom, EnzymeResidueLocator, FragmentAtom

public class PseudoAtom
extends Atom
implements Serializable, Cloneable, IPseudoAtom

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:

• Atom
• Serialized Form

Nested Class Summary

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

IAtomType.Hybridization

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.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

Constructor Summary

Constructors

Constructor	Description
PseudoAtom()	Constructs an empty PseudoAtom.
PseudoAtom(String label)	Constructs an Atom from a String containing an element symbol.
PseudoAtom(String label, javax.vecmath.Point2d point2d)	Constructs an Atom from an Element and a Point2d.
PseudoAtom(String label, javax.vecmath.Point3d point3d)	Constructs an Atom from an Element and a Point3d.
PseudoAtom(IElement element)	Constructs an PseudoAtom from a IAtom.

Method Summary

Modifier and Type	Method	Description
IPseudoAtom	clone()	Clones this atom object and its content.
int	getAttachPointNum()	Access the attachment point number.
String	getLabel()	Returns the label of this PseudoAtom.
void	setAttachPointNum(int attachPoint)	Set the attachment point number.
void	setLabel(String label)	Sets the label of this PseudoAtom.
void	setStereoParity(Integer stereoParity)	Dummy method: the stereo parity is undefined, final.
String	toString()	Returns a one line string representation of this Atom.

Methods inherited from class org.openscience.cdk.Atom

bonds, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, 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

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from class org.openscience.cdk.Element

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, 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, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d

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

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

Constructor Details

PseudoAtom

public PseudoAtom()

Constructs an empty PseudoAtom.

PseudoAtom

public PseudoAtom(String label)

Constructs an Atom from a String containing an element symbol.

Parameters:

label - The String describing the PseudoAtom

PseudoAtom

public PseudoAtom(IElement element)

Constructs an PseudoAtom from a IAtom.

Parameters:

element - IAtom from which the PseudoAtom is constructed

PseudoAtom

public PseudoAtom(String label,
 javax.vecmath.Point3d point3d)

Constructs an Atom from an Element and a Point3d.

Parameters:

label - The String describing the PseudoAtom

point3d - The 3D coordinates of the atom

PseudoAtom

public PseudoAtom(String label,
 javax.vecmath.Point2d point2d)

Constructs an Atom from an Element and a Point2d.

Parameters:

label - The String describing the PseudoAtom

point2d - The Point

Method Details

getLabel

public String getLabel()

Returns the label of this PseudoAtom.

Specified by:

getLabel in interface IPseudoAtom

Returns:

The label for this PseudoAtom

See Also:

• setLabel(java.lang.String)

setLabel

public void setLabel(String label)

Sets the label of this PseudoAtom.

Specified by:

setLabel in interface IPseudoAtom

Parameters:

label - The new label for this PseudoAtom

See Also:

• getLabel()

getAttachPointNum

public int getAttachPointNum()

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

Specified by:

getAttachPointNum in interface IPseudoAtom

Returns:

attach point number

setAttachPointNum

public void setAttachPointNum(int attachPoint)

Set the attachment point number.

Specified by:

setAttachPointNum in interface IPseudoAtom

Parameters:

attachPoint - attach point number

setStereoParity

public void setStereoParity(Integer stereoParity)

Dummy method: the stereo parity is undefined, final.

Specified by:

setStereoParity in interface IAtom

Overrides:

setStereoParity in class Atom

Parameters:

stereoParity - The stereo parity for this atom

See Also:

• for predefined values.
• Atom.getStereoParity()

toString

public String toString()

Returns a one line string representation of this Atom. Methods is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Atom

Returns:

The string representation of this Atom

clone

public IPseudoAtom clone()
                  throws CloneNotSupportedException

Description copied from class: Atom

Clones this atom object and its content.

Specified by:

clone in interface IAtom

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IPseudoAtom

Overrides:

clone in class Atom

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned