Package org.openscience.cdk.interfaces

Interface IAtomType

All Superinterfaces:

Cloneable, ICDKObject, IChemObject, IElement, IIsotope

All Known Subinterfaces:

IAtom, IFragmentAtom, IPDBAtom, IPseudoAtom, IQueryAtom

All Known Implementing Classes:

AliphaticAtom, AliphaticSymbolAtom, AnyAtom, AromaticAtom, AromaticSymbolAtom, Atom, Atom, AtomicNumberAtom, AtomRef, AtomType, AtomType, ChiralityAtom, DebugAtom, DebugAtomType, DebugFragmentAtom, DebugPDBAtom, DebugPseudoAtom, EnzymeResidueLocator, ExplicitConnectionAtom, FormalChargeAtom, FragmentAtom, FragmentAtom, HybridizationNumberAtom, HydrogenAtom, ImplicitHCountAtom, InverseSymbolSetQueryAtom, LogicalOperatorAtom, MassAtom, NonCHHeavyAtom, PDBAtom, PDBAtom, PeriodicGroupNumberAtom, PharmacophoreAtom, PharmacophoreQueryAtom, PseudoAtom, PseudoAtom, QueryAtom, ReactionRoleQueryAtom, RecursiveSmartsAtom, RingIdentifierAtom, RingMembershipAtom, SmallestRingAtom, SMARTSAtom, SymbolAndChargeQueryAtom, SymbolChargeIDQueryAtom, SymbolQueryAtom, SymbolSetQueryAtom, TotalConnectionAtom, TotalHCountAtom, TotalRingConnectionAtom, TotalValencyAtom

public interface IAtomType
extends IIsotope

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:

egonw

Source code:

main

Belongs to CDK module:

interfaces

Keywords:

atom, type

Created on:

2005-08-24

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	IAtomType.Hybridization	An enum for the different hybridization states.

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

Modifier and Type	Method	Description
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.

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

getBuilder

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

addListener, addProperties, clone, 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

setAtomTypeName

void setAtomTypeName(String identifier)

Sets the if attribute of the AtomType object.

Parameters:

identifier - The new AtomTypeID value. Null if unset.

See Also:

getAtomTypeName()

setMaxBondOrder

void setMaxBondOrder(IBond.Order maxBondOrder)

Sets the MaxBondOrder attribute of the AtomType object.

Parameters:

maxBondOrder - The new MaxBondOrder value

See Also:

getMaxBondOrder()

setBondOrderSum

void setBondOrderSum(Double bondOrderSum)

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

Parameters:

bondOrderSum - The new bondOrderSum value

See Also:

getBondOrderSum()

getAtomTypeName

String getAtomTypeName()

Gets the id attribute of the AtomType object.

Returns:

The id value

See Also:

setAtomTypeName(java.lang.String)

getMaxBondOrder

IBond.Order getMaxBondOrder()

Gets the MaxBondOrder attribute of the AtomType object.

Returns:

The MaxBondOrder value

See Also:

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

getBondOrderSum

Double getBondOrderSum()

Gets the bondOrderSum attribute of the AtomType object.

Returns:

The bondOrderSum value

See Also:

setBondOrderSum(java.lang.Double)

setFormalCharge

void setFormalCharge(Integer charge)

Sets the formal charge of this atom.

Parameters:

charge - The formal charge

See Also:

getFormalCharge()

getFormalCharge

Integer getFormalCharge()

Returns the formal charge of this atom.

Returns:

the formal charge of this atom

See Also:

setFormalCharge(java.lang.Integer)

setFormalNeighbourCount

void setFormalNeighbourCount(Integer count)

Sets the formal neighbour count of this atom.

Parameters:

count - The neighbour count

See Also:

getFormalNeighbourCount()

getFormalNeighbourCount

Integer getFormalNeighbourCount()

Returns the formal neighbour count of this atom.

Returns:

the formal neighbour count of this atom

See Also:

setFormalNeighbourCount(java.lang.Integer)

setHybridization

void setHybridization(IAtomType.Hybridization hybridization)

Sets the hybridization of this atom.

Parameters:

hybridization - The hybridization

See Also:

getHybridization()

getHybridization

IAtomType.Hybridization getHybridization()

Returns the hybridization of this atom.

Returns:

the hybridization of this atom

See Also:

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

setCovalentRadius

void setCovalentRadius(Double radius)

Sets the covalent radius for this AtomType.

Parameters:

radius - The covalent radius for this AtomType

See Also:

getCovalentRadius()

getCovalentRadius

Double getCovalentRadius()

Returns the covalent radius for this AtomType.

Returns:

The covalent radius for this AtomType

See Also:

setCovalentRadius(java.lang.Double)

setValency

void setValency(Integer valency)

Sets the the exact electron valency of the AtomType object.

Parameters:

valency - The new valency value

See Also:

getValency()

getValency

Integer getValency()

Gets the the exact electron valency of the AtomType object.

Returns:

The valency value

See Also:

setValency(Integer)