Package org.openscience.cdk

Class AtomType

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.AtomType

All Implemented Interfaces:

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

Direct Known Subclasses:

Atom, DebugAtomType

public class AtomType
extends Isotope
implements IAtomType, Serializable, Cloneable

The base class for atom types. Atom types are typically used to describe the behaviour of an atom of a particular element in different environment like sp³ hybridized carbon C3, etc., in some molecular modelling applications.

Author:

steinbeck

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

data

Keywords:

atom, type

Created on:

2001-08-08

Nested Class Summary

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

IAtomType.Hybridization

Field Summary

Fields

Modifier and Type	Field	Description
protected Integer	electronValency	The electron Valency of this atom with CDKConstants.UNSET as default.
protected Integer	formalCharge	The formal charge of the atom with CDKConstants.UNSET as default.
protected Integer	formalNeighbourCount	The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
protected IAtomType.Hybridization	hybridization	The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.

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, 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
AtomType(String elementSymbol)	Constructor for the AtomType object.
AtomType(String identifier, String elementSymbol)	Constructor for the AtomType object.
AtomType(IElement element)	Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.

Method Summary

Modifier and Type	Method	Description
Object	clone()	Clones this IChemObject.
boolean	compare(Object object)	Compares a atom type with this atom type.
String	getAtomTypeName()	Gets the id attribute of the AtomType object.
Double	getBondOrderSum()	Gets the bondOrderSum attribute of the AtomType object.
Double	getCovalentRadius()	Returns the covalent radius for this AtomType.
Integer	getFormalCharge()	Returns the formal charge of this atom.
Integer	getFormalNeighbourCount()	Returns the formal neighbour count of this atom.
IAtomType.Hybridization	getHybridization()	Returns the hybridization of this atom.
IBond.Order	getMaxBondOrder()	Gets the MaxBondOrder attribute of the AtomType object.
Integer	getValency()	Gets the the exact electron valency of the AtomType object.
void	setAtomTypeName(String identifier)	Sets the if attribute of the AtomType object.
void	setBondOrderSum(Double bondOrderSum)	Sets the the exact bond order sum attribute of the AtomType object.
void	setCovalentRadius(Double radius)	Sets the covalent radius for this AtomType.
void	setFormalCharge(Integer charge)	Sets the formal charge of this atom.
void	setFormalNeighbourCount(Integer count)	Sets the formal neighbour count of this atom.
void	setHybridization(IAtomType.Hybridization hybridization)	Sets the hybridization of this atom.
void	setMaxBondOrder(IBond.Order maxBondOrder)	Sets the MaxBondOrder attribute of the AtomType object.
void	setValency(Integer valency)	Sets the the exact electron valency of the AtomType object.
String	toString()	A string representation of this isotope.

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

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

Field Detail

formalCharge

protected Integer formalCharge

The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0

hybridization

protected IAtomType.Hybridization hybridization

The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.

electronValency

protected Integer electronValency

The electron Valency of this atom with CDKConstants.UNSET as default.

formalNeighbourCount

protected Integer formalNeighbourCount

The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitly connected atoms, including implicit hydrogens.

Constructor Detail

AtomType

public AtomType(String elementSymbol)

Constructor for the AtomType object. Defaults to a zero formal charge. All other fields are set to CDKConstants.UNSET.

Parameters:

elementSymbol - Symbol of the atom

AtomType

public AtomType(String identifier,
                String elementSymbol)

Constructor for the AtomType object. Defaults to a zero formal charge.

Parameters:

identifier - An id for this atom type, like C3 for sp3 carbon

elementSymbol - The element symbol identifying the element to which this atom type applies

AtomType

public AtomType(IElement element)

Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope. It does not copy the listeners and properties. If the element is an instance of IAtomType, then the maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name are copied too.

Parameters:

element - IIsotope to copy information from

Method Detail

setAtomTypeName

public void setAtomTypeName(String identifier)

Sets the if attribute of the AtomType object.

Specified by:

setAtomTypeName in interface IAtomType

Parameters:

identifier - The new AtomTypeID value. Null if unset.

See Also:

getAtomTypeName()

setMaxBondOrder

public void setMaxBondOrder(IBond.Order maxBondOrder)

Sets the MaxBondOrder attribute of the AtomType object.

Specified by:

setMaxBondOrder in interface IAtomType

Parameters:

maxBondOrder - The new MaxBondOrder value

See Also:

getMaxBondOrder()

setBondOrderSum

public void setBondOrderSum(Double bondOrderSum)

Sets the the exact bond order sum attribute of the AtomType object.

Specified by:

setBondOrderSum in interface IAtomType

Parameters:

bondOrderSum - The new bondOrderSum value

See Also:

getBondOrderSum()

getAtomTypeName

public String getAtomTypeName()

Gets the id attribute of the AtomType object.

Specified by:

getAtomTypeName in interface IAtomType

Returns:

The id value

See Also:

setAtomTypeName(java.lang.String)

getMaxBondOrder

public IBond.Order getMaxBondOrder()

Gets the MaxBondOrder attribute of the AtomType object.

Specified by:

getMaxBondOrder in interface IAtomType

Returns:

The MaxBondOrder value

See Also:

setMaxBondOrder(org.openscience.cdk.interfaces.IBond.Order)

getBondOrderSum

public Double getBondOrderSum()

Gets the bondOrderSum attribute of the AtomType object.

Specified by:

getBondOrderSum in interface IAtomType

Returns:

The bondOrderSum value

See Also:

setBondOrderSum(java.lang.Double)

setFormalCharge

public void setFormalCharge(Integer charge)

Sets the formal charge of this atom.

Specified by:

setFormalCharge in interface IAtomType

Parameters:

charge - The formal charge

See Also:

getFormalCharge()

getFormalCharge

public Integer getFormalCharge()

Returns the formal charge of this atom.

Specified by:

getFormalCharge in interface IAtomType

Returns:

the formal charge of this atom

See Also:

setFormalCharge(java.lang.Integer)

setFormalNeighbourCount

public void setFormalNeighbourCount(Integer count)

Sets the formal neighbour count of this atom.

Specified by:

setFormalNeighbourCount in interface IAtomType

Parameters:

count - The neighbour count

See Also:

getFormalNeighbourCount()

getFormalNeighbourCount

public Integer getFormalNeighbourCount()

Returns the formal neighbour count of this atom.

Specified by:

getFormalNeighbourCount in interface IAtomType

Returns:

the formal neighbour count of this atom

See Also:

setFormalNeighbourCount(java.lang.Integer)

setHybridization

public void setHybridization(IAtomType.Hybridization hybridization)

Sets the hybridization of this atom.

Specified by:

setHybridization in interface IAtomType

Parameters:

hybridization - The hybridization

See Also:

getHybridization()

getHybridization

public IAtomType.Hybridization getHybridization()

Returns the hybridization of this atom.

Specified by:

getHybridization in interface IAtomType

Returns:

the hybridization of this atom

See Also:

setHybridization(org.openscience.cdk.interfaces.IAtomType.Hybridization)

compare

public boolean compare(Object object)

Compares a atom type with this atom type.

Overrides:

compare in class Isotope

Parameters:

object - Object of type AtomType

Returns:

true if the atom types are equal

setCovalentRadius

public void setCovalentRadius(Double radius)

Sets the covalent radius for this AtomType.

Specified by:

setCovalentRadius in interface IAtomType

Parameters:

radius - The covalent radius for this AtomType

See Also:

getCovalentRadius()

getCovalentRadius

public Double getCovalentRadius()

Returns the covalent radius for this AtomType.

Specified by:

getCovalentRadius in interface IAtomType

Returns:

The covalent radius for this AtomType

See Also:

setCovalentRadius(java.lang.Double)

setValency

public void setValency(Integer valency)

Sets the the exact electron valency of the AtomType object.

Specified by:

setValency in interface IAtomType

Parameters:

valency - The new valency value

See Also:

getValency()

getValency

public Integer getValency()

Gets the the exact electron valency of the AtomType object.

Specified by:

getValency in interface IAtomType

Returns:

The valency value

See Also:

setValency(java.lang.Integer)

clone

public Object clone()
             throws CloneNotSupportedException

Description copied from class: ChemObject

Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.

Specified by:

clone in interface IChemObject

Overrides:

clone in class Isotope

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Description copied from class: Isotope

A string representation of this isotope.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Isotope

Returns:

A string representation of this isotope