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:

Atom, Atom, AtomRef, DebugAtom, DebugFragmentAtom, DebugPDBAtom, DebugPseudoAtom, EnzymeResidueLocator, FragmentAtom, FragmentAtom, PDBAtom, PDBAtom, PharmacophoreAtom, PharmacophoreQueryAtom, PseudoAtom, PseudoAtom, QueryAtom, SymbolChargeIDQueryAtom

public interface IAtom
extends IAtomType

Represents the idea of an chemical atom.

Author:

egonw

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

atom

Created on:

2005-08-24

Nested Class Summary

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

IAtomType.Hybridization

Method Summary

Modifier and Type	Method and Description
Iterable<IBond>	bonds() Returns the bonds connected to this atom.
IAtom	clone() Returns a deep clone of this IChemObject.
IBond	getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
int	getBondCount() Get the number of explicit bonds connected to this atom.
Double	getCharge() Returns the partial charge of this atom.
IAtomContainer	getContainer() Access the IAtomContainer of which this atom is a member of.
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.
int	getIndex() Acces the index of an atom in the context of an IAtomContainer.
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() Deprecated. use IStereoElements for storing stereochemistry
boolean	isAromatic() Access whether this atom has been marked as aromatic.
boolean	isInRing() Access whether this atom has been flagged as in a ring.
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	setIsAromatic(boolean arom) Mark this atom as being aromatic.
void	setIsInRing(boolean ring) Mark this atom as being in a ring.
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) Deprecated. use IStereoElements for storing stereochemistry

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, 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.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

@Deprecated
void setStereoParity(Integer stereoParity)

Deprecated. use IStereoElements for storing stereochemistry

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

@Deprecated
Integer getStereoParity()

Deprecated. use IStereoElements for storing stereochemistry

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)

getContainer

IAtomContainer getContainer()

Access the IAtomContainer of which this atom is a member of. Because atoms can be in multiple molecules this method will only work if the atom has been accessed in the context of an IAtomContainer, for example:

 IAtomContainer mol  = new AtomContainer();
 IAtom          atom = new Atom(6);

 atom.getContainer(); // null
 mol.add(atom);
 atom.getContainer(); // still null
 mol.getAtom(0).getContainer(); // not-null, returns 'mol'
 

Returns:

the atom container or null if not accessed in the context of a container

getIndex

int getIndex()

Acces the index of an atom in the context of an IAtomContainer. If the index is not known, < 0 is returned.

Returns:

atom index or < 0 if the index is not known

bonds

Iterable<IBond> bonds()

Returns the bonds connected to this atom. If the bonds are not known an exception is thrown. This method will only throw an exception if getIndex() returns < 0 or getContainer() returns null.

 IAtom atom = ...;

 if (atom.getIndex() >= 0) {
   for (IBond bond : atom.bonds()) {

   }
 }

 if (atom.getContainer() != null) {
   for (IBond bond : atom.bonds()) {

   }
 }

 IAtomContainer mol = ...;
 // guaranteed not throw an exception
 for (IBond bond : mol.getAtom(i).bonds()) {

 }
 

Returns:

iterable of bonds

Throws:

UnsupportedOperationException - thrown if the bonds are not known

getBondCount

int getBondCount()

Get the number of explicit bonds connected to this atom.

Returns:

the total bond count

getBond

IBond getBond(IAtom atom)

Returns the bond connecting 'this' atom to the provided atom. If the atoms are not bonded, null is returned.

Parameters:

atom - the other atom

Returns:

the bond connecting the atoms

Throws:

UnsupportedOperationException - thrown if the bonds are not known

isAromatic

boolean isAromatic()

Access whether this atom has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.

Returns:

aromatic status

See Also:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

void setIsAromatic(boolean arom)

Mark this atom as being aromatic.

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

isInRing

boolean isInRing()

Access whether this atom has been flagged as in a ring. The default value is false and you must explicitly find rings first.

Returns:

ring status

See Also:

IChemObject.getFlag(int), RingSearch

setIsInRing

void setIsInRing(boolean ring)

Mark this atom as being in a ring.

Parameters:

ring - ring status

See Also:

IChemObject.setFlag(int, boolean)

clone

IAtom clone()
     throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned