org.openscience.cdk.interfaces
Interface IAtom

All Superinterfaces:

Cloneable, IAtomType, ICDKObject, IChemObject, IElement, IIsotope

All Known Subinterfaces:

IFragmentAtom, IPDBAtom, IPseudoAtom, IQueryAtom

All Known Implementing Classes:

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

public interface IAtom
extends IAtomType

Represents the idea of an chemical atom.

Author:

egonw

Keywords:

atom

Created on:

2005-08-24

Belongs to CDK module:

interfaces

Source code:

cdk-1.4.x

Nested Class Summary

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

IAtomType.Hybridization

Method Summary

Double	getCharge() Returns the partial charge of this atom.
javax.vecmath.Point3d	getFractionalPoint3d() Returns a point specifying the location of this atom in a Crystal unit cell.
Integer	getImplicitHydrogenCount() Returns the implicit hydrogen count of this atom.
javax.vecmath.Point2d	getPoint2d() Returns a point specifying the location of this atom in a 2D space.
javax.vecmath.Point3d	getPoint3d() Returns a point specifying the location of this atom in a 3D space.
Integer	getStereoParity() Returns the stereo parity of this atom.
void	setCharge(Double charge) Sets the partial charge of this atom.
void	setFractionalPoint3d(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in a Crystal unit cell.
void	setImplicitHydrogenCount(Integer hydrogenCount) Sets the implicit hydrogen count of this atom.
void	setPoint2d(javax.vecmath.Point2d point2d) Sets a point specifying the location of this atom in a 2D space.
void	setPoint3d(javax.vecmath.Point3d point3d) Sets a point specifying the location of this atom in 3D space.
void	setStereoParity(Integer stereoParity) Sets the stereo parity for this atom.

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.IIsotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

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

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

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

addListener, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

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

getBuilder

Method Detail

setCharge

void setCharge(Double charge)

Sets the partial charge of this atom.

Parameters:

charge - The partial charge

See Also:

getCharge()

getCharge

Double getCharge()

Returns the partial charge of this atom.

Returns:

the charge of this atom

See Also:

setCharge(java.lang.Double)

setImplicitHydrogenCount

void setImplicitHydrogenCount(Integer hydrogenCount)

Sets the implicit hydrogen count of this atom.

Parameters:

hydrogenCount - The number of hydrogen atoms bonded to this atom.

See Also:

getImplicitHydrogenCount()

getImplicitHydrogenCount

Integer getImplicitHydrogenCount()

Returns the implicit hydrogen count of this atom.

Returns:

The hydrogen count of this atom.

See Also:

setImplicitHydrogenCount(java.lang.Integer)

setPoint2d

void setPoint2d(javax.vecmath.Point2d point2d)

Sets a point specifying the location of this atom in a 2D space.

Parameters:

point2d - A point in a 2D plane

See Also:

getPoint2d()

setPoint3d

void setPoint3d(javax.vecmath.Point3d point3d)

Sets a point specifying the location of this atom in 3D space.

Parameters:

point3d - A point in a 3-dimensional space

See Also:

getPoint3d()

setFractionalPoint3d

void setFractionalPoint3d(javax.vecmath.Point3d point3d)

Sets a point specifying the location of this atom in a Crystal unit cell.

Parameters:

point3d - A point in a 3d fractional unit cell space

See Also:

getFractionalPoint3d(), Crystal

setStereoParity

void setStereoParity(Integer stereoParity)

Sets the stereo parity for this atom.

Parameters:

stereoParity - The stereo parity for this atom

See Also:

for predefined values., getStereoParity()

getPoint2d

javax.vecmath.Point2d getPoint2d()

Returns a point specifying the location of this atom in a 2D space.

Returns:

A point in a 2D plane. Null if unset.

See Also:

setPoint2d(javax.vecmath.Point2d)

getPoint3d

javax.vecmath.Point3d getPoint3d()

Returns a point specifying the location of this atom in a 3D space.

Returns:

A point in 3-dimensional space. Null if unset.

See Also:

setPoint3d(javax.vecmath.Point3d)

getFractionalPoint3d

javax.vecmath.Point3d getFractionalPoint3d()

Returns a point specifying the location of this atom in a Crystal unit cell.

Returns:

A point in 3d fractional unit cell space. Null if unset.

See Also:

setFractionalPoint3d(javax.vecmath.Point3d), for predefined values.

getStereoParity

Integer getStereoParity()

Returns the stereo parity of this atom. It uses the predefined values found in CDKConstants.

Returns:

The stereo parity for this atom

See Also:

CDKConstants, setStereoParity(java.lang.Integer)