Package org.openscience.cdk.debug

Class DebugAminoAcid

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Monomer

org.openscience.cdk.AminoAcid

org.openscience.cdk.debug.DebugAminoAcid

All Implemented Interfaces:

Serializable, Cloneable, IAminoAcid, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer

public class DebugAminoAcid
extends AminoAcid
implements IAminoAcid

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Field Summary

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

Constructor Summary

Constructors

Constructor	Description
DebugAminoAcid()

Method Summary

Modifier and Type	Method	Description
void	add(IAtomContainer atomContainer)	Adds all atoms and electronContainers of a given atomcontainer to this container.
void	addAtom(IAtom atom)	Adds an atom to this container.
void	addBond(int atom1, int atom2, IBond.Order order)	Adds a bond to this container.
void	addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo)	Adds a bond to this container.
void	addBond(IBond bond)	Adds a Bond to this AtomContainer.
void	addCTerminus(IAtom atom)	Add an Atom and makes it the C-terminus atom.
void	addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	addListener(IChemObjectListener col)	Use this to add yourself to this IChemObject as a listener.
void	addLonePair(int atomID)	Adds a LonePair to this Atom.
void	addLonePair(ILonePair ec)	Adds a lone pair to this AtomContainer.
void	addNTerminus(IAtom atom)	Add an Atom and makes it the N-terminus atom.
void	addProperties(Map<Object,Object> properties)	Sets the properties of this object.
void	addSingleElectron(int atomID)	Adds a SingleElectron to this Atom.
void	addSingleElectron(ISingleElectron ec)	Adds a single electron to this AtomContainer.
void	addStereoElement(IStereoElement parity)	Adds a stereo element to this container.
Iterable<IAtom>	atoms()	Returns an Iterable for looping over all atoms in this container.
Iterable<IBond>	bonds()	Returns an Iterable for looping over all bonds in this container.
IAminoAcid	clone()	Clones this AminoAcid object.
boolean	contains(IAtom atom)	True, if the AtomContainer contains the given atom object.
boolean	contains(IBond bond)	True, if the AtomContainer contains the given bond object.
boolean	contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	contains(ILonePair ec)	True, if the AtomContainer contains the given LonePair object.
boolean	contains(ISingleElectron ec)	True, if the AtomContainer contains the given SingleElectron object.
Iterable<IElectronContainer>	electronContainers()	Returns an Iterable for looping over all electron containers in this container.
IAtom	getAtom(int idx)	Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
int	getAtomCount()	Returns the number of Atoms in this Container.
int	getAtomNumber(IAtom atom)	Returns the position of a given atom in the atoms array.
IBond	getBond(int idx)	Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
IBond	getBond(IAtom atom1, IAtom atom2)	Returns the bond that connects the two given atoms.
int	getBondCount()	Returns the number of Bonds in this Container.
int	getBondNumber(IAtom atom1, IAtom atom2)	Returns the position of the bond between two given atoms in the electronContainers array.
int	getBondNumber(IBond bond)	Returns the position of a given bond in the electronContainers array.
double	getBondOrderSum(IAtom atom)	Returns the sum of the bond orders for a given Atom.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
int	getConnectedAtomsCount(IAtom atom)	Returns the number of connected atoms (explicit degree) to the specified atom.
List<IAtom>	getConnectedAtomsList(IAtom atom)	Returns the atoms connected connected to the specified atom by a bond.
int	getConnectedBondsCount(IAtom atom)	Returns the number of connected bonds (explicit degree) to the specified atom.
List<IBond>	getConnectedBondsList(IAtom atom)	Returns the bonds connected connected to the specified atom.
List<IElectronContainer>	getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
int	getConnectedLonePairsCount(IAtom atom)	Returns the number of lone pairs connected to the specified atom.
List<ILonePair>	getConnectedLonePairsList(IAtom atom)	Returns the lone pairs connected connected to the specified atom.
int	getConnectedSingleElectronsCount(IAtom atom)	Returns the number of single electrons connected to the specified atom.
List<ISingleElectron>	getConnectedSingleElectronsList(IAtom atom)	Returns the single electrons connected connected to the specified atom.
IAtom	getCTerminus()	Retrieves the C-terminus atom.
IElectronContainer	getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
int	getElectronContainerCount()	Returns the number of ElectronContainers in this Container.
IAtom	getFirstAtom()	Returns the atom at position 0 in the container.
boolean	getFlag(int flagType)	Returns the value of a given flag.
boolean[]	getFlags()	Returns the whole set of flags.
String	getID()	Returns the identifier (ID) of this object.
IAtom	getLastAtom()	Returns the atom at the last position in the container.
int	getListenerCount()	Returns the number of ChemObjectListeners registered with this object.
ILonePair	getLonePair(int idx)	Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
int	getLonePairCount()	Returns the number of LonePairs in this Container.
int	getLonePairNumber(ILonePair bond)	Returns the position of a given lone pair in the lone pair array.
IBond.Order	getMaximumBondOrder(IAtom atom)	Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	getMinimumBondOrder(IAtom atom)	Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
String	getMonomerName()	Retrieves the monomer name.
String	getMonomerType()	Retrieves the monomer type.
IAtom	getNTerminus()	Retrieves the N-terminus atom.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
ISingleElectron	getSingleElectron(int idx)	Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
int	getSingleElectronCount()	Returns the number of the single electrons in this container.
int	getSingleElectronNumber(ISingleElectron bond)	Returns the position of a given single electron in the single electron array.
Iterable<ILonePair>	lonePairs()	Returns an Iterable for looping over all lone pairs in this container.
void	notifyChanged()	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	notifyChanged(IChemObjectChangeEvent evt)	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	remove(IAtomContainer atomContainer)	Removes all atoms and electronContainers of a given atomcontainer from this container.
void	removeAllBonds()	Removes all Bonds from this container.
void	removeAllElectronContainers()	Removes electronContainers from this container.
void	removeAllElements()	Removes all atoms, bonds and stereo elements from this container.
void	removeAtom(IAtom atom)	Safely remove an atom from the container.
void	removeAtomOnly(int position)	Unsafely remove atom at index.
void	removeAtomOnly(IAtom atom)	Unsafely remove atom.
IBond	removeBond(int pos)	Removes the bond at the given position from the AtomContainer.
IBond	removeBond(IAtom atom1, IAtom atom2)	Removes the bond that connects the two given atoms.
void	removeBond(IBond bond)	Removes the bond from this container.
IElectronContainer	removeElectronContainer(int position)	Removes the bond at the given position from this container.
void	removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	removeListener(IChemObjectListener col)	Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
ILonePair	removeLonePair(int pos)	Removes the lone pair at the given position from the AtomContainer.
void	removeLonePair(ILonePair ec)	Removes the lone pair from the AtomContainer.
void	removeProperty(Object description)	Removes a property for a IChemObject.
ISingleElectron	removeSingleElectron(int pos)	Removes the single electron at the given position from the AtomContainer.
void	removeSingleElectron(ISingleElectron ec)	Removes the single electron from the AtomContainer.
void	setAtom(int number, IAtom atom)	Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	setAtoms(IAtom[] atoms)	Sets the array of atoms of this AtomContainer.
void	setFlag(int flagType, boolean flagValue)	Sets the value of some flag.
void	setFlags(boolean[] flagsNew)	Sets the whole set of flags.
void	setID(String identifier)	Sets the identifier (ID) of this object.
void	setMonomerName(String cMonomerName)	Sets the name of the Monomer object.
void	setMonomerType(String cMonomerType)	Sets the type of the Monomer object.
void	setProperty(Object description, Object property)	Sets a property for a IChemObject.
Iterable<ISingleElectron>	singleElectrons()	Returns an Iterable for looping over all single electrons in this container.
void	stateChanged(IChemObjectChangeEvent event)	Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
Iterable<IStereoElement>	stereoElements()	Returns the stereo elements defined for this atom container.

Methods inherited from class org.openscience.cdk.AminoAcid

toString

Methods inherited from class org.openscience.cdk.AtomContainer

addBond, getConnectedBondsCount, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, newAtom, newAtom, newBond, removeAtom, removeAtomAndConnectedElectronContainers, setBonds, setStereoElements, setTitle, shallowCopy

Methods inherited from class org.openscience.cdk.ChemObject

clear, compare, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties

Methods inherited from class java.lang.Object

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

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

addBond, getConnectedBondsCount, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, newAtom, newAtom, newAtom, newAtom, newBond, newBond, removeAtom, removeAtomAndConnectedElectronContainers, setBonds, setStereoElements, setTitle

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

clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, toString

Constructor Details

DebugAminoAcid

public DebugAminoAcid()

Method Details

addStereoElement

public void addStereoElement(IStereoElement parity)

Adds a stereo element to this container.

Specified by:

addStereoElement in interface IAtomContainer

Overrides:

addStereoElement in class AtomContainer

Parameters:

parity - The new IStereoElement for this container

See Also:

• IAtomContainer.stereoElements()

stereoElements

public Iterable<IStereoElement> stereoElements()

Returns the stereo elements defined for this atom container.

Specified by:

stereoElements in interface IAtomContainer

Overrides:

stereoElements in class AtomContainer

Returns:

An Iterable of IStereoElements.

See Also:

• IAtomContainer.addStereoElement(IStereoElement)

setAtoms

public void setAtoms(IAtom[] atoms)

Sets the array of atoms of this AtomContainer.

Specified by:

setAtoms in interface IAtomContainer

Overrides:

setAtoms in class AtomContainer

Parameters:

atoms - The array of atoms to be assigned to this AtomContainer

See Also:

• IAtomContainer.atoms()

setAtom

public void setAtom(int number,
 IAtom atom)

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

Specified by:

setAtom in interface IAtomContainer

Overrides:

setAtom in class AtomContainer

Parameters:

number - The index of the atom to be set.

atom - The atom to be stored at position idx

See Also:

• IAtomContainer.getAtom(int)

getAtom

public IAtom getAtom(int idx)

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

Specified by:

getAtom in interface IAtomContainer

Overrides:

getAtom in class AtomContainer

Parameters:

idx - atom index

Returns:

the atom stored at the index

See Also:

• IAtomContainer.setAtom(int, org.openscience.cdk.interfaces.IAtom)

getBond

public IBond getBond(int idx)

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

Specified by:

getBond in interface IAtomContainer

Overrides:

getBond in class AtomContainer

Parameters:

idx - bond index

Returns:

the bond stored at the index

getLonePair

public ILonePair getLonePair(int idx)

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

Specified by:

getLonePair in interface IAtomContainer

Overrides:

getLonePair in class AtomContainer

Parameters:

idx - lone pair index

Returns:

the lone pair stored at the index

getSingleElectron

public ISingleElectron getSingleElectron(int idx)

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

Specified by:

getSingleElectron in interface IAtomContainer

Overrides:

getSingleElectron in class AtomContainer

Parameters:

idx - single electron index

Returns:

the single electron stored at the index

atoms

public Iterable<IAtom> atoms()

Returns an Iterable for looping over all atoms in this container.

Specified by:

atoms in interface IAtomContainer

Overrides:

atoms in class AtomContainer

Returns:

An Iterable with the atoms in this container

bonds

public Iterable<IBond> bonds()

Returns an Iterable for looping over all bonds in this container.

Specified by:

bonds in interface IAtomContainer

Overrides:

bonds in class AtomContainer

Returns:

An Iterable with the bonds in this container

lonePairs

public Iterable<ILonePair> lonePairs()

Returns an Iterable for looping over all lone pairs in this container.

Specified by:

lonePairs in interface IAtomContainer

Overrides:

lonePairs in class AtomContainer

Returns:

An Iterable with the lone pairs in this container

singleElectrons

public Iterable<ISingleElectron> singleElectrons()

Returns an Iterable for looping over all single electrons in this container.

Specified by:

singleElectrons in interface IAtomContainer

Overrides:

singleElectrons in class AtomContainer

Returns:

An Iterable with the single electrons in this container

electronContainers

public Iterable<IElectronContainer> electronContainers()

Returns an Iterable for looping over all electron containers in this container.

Specified by:

electronContainers in interface IAtomContainer

Overrides:

electronContainers in class AtomContainer

Returns:

An Iterable with the electron containers in this container

getFirstAtom

public IAtom getFirstAtom()

Returns the atom at position 0 in the container.

Specified by:

getFirstAtom in interface IAtomContainer

Overrides:

getFirstAtom in class AtomContainer

Returns:

The atom at position 0 .

getLastAtom

public IAtom getLastAtom()

Returns the atom at the last position in the container.

Specified by:

getLastAtom in interface IAtomContainer

Overrides:

getLastAtom in class AtomContainer

Returns:

The atom at the last position

getAtomNumber

public int getAtomNumber(IAtom atom)

Returns the position of a given atom in the atoms array. It returns -1 if the atom atom does not exist.

Specified by:

getAtomNumber in interface IAtomContainer

Overrides:

getAtomNumber in class AtomContainer

Parameters:

atom - The atom to be sought

Returns:

The Position of the atom in the atoms array in [0,..].

getBondNumber

public int getBondNumber(IAtom atom1,
 IAtom atom2)

Returns the position of the bond between two given atoms in the electronContainers array. It returns -1 if the bond does not exist.

Specified by:

getBondNumber in interface IAtomContainer

Overrides:

getBondNumber in class AtomContainer

Parameters:

atom1 - The first atom

atom2 - The second atom

Returns:

The Position of the bond between a1 and a2 in the electronContainers array.

getBondNumber

public int getBondNumber(IBond bond)

Returns the position of a given bond in the electronContainers array. It returns -1 if the bond does not exist.

Specified by:

getBondNumber in interface IAtomContainer

Overrides:

getBondNumber in class AtomContainer

Parameters:

bond - The bond to be sought

Returns:

The Position of the bond in the electronContainers array in [0,..].

getLonePairNumber

public int getLonePairNumber(ILonePair bond)

Returns the position of a given lone pair in the lone pair array. It returns -1 if the lone pair does not exist.

Specified by:

getLonePairNumber in interface IAtomContainer

Overrides:

getLonePairNumber in class AtomContainer

Parameters:

bond - The lone pair to be sought

Returns:

The Position of the lone pair in the array..

getSingleElectronNumber

public int getSingleElectronNumber(ISingleElectron bond)

Returns the position of a given single electron in the single electron array. It returns -1 if the single electron does not exist.

Specified by:

getSingleElectronNumber in interface IAtomContainer

Overrides:

getSingleElectronNumber in class AtomContainer

Parameters:

bond - The single electron to be sought

Returns:

The Position of the single electron in the array.

getElectronContainer

public IElectronContainer getElectronContainer(int number)

Returns the ElectronContainer at position number in the container.

Specified by:

getElectronContainer in interface IAtomContainer

Overrides:

getElectronContainer in class AtomContainer

Parameters:

number - The position of the ElectronContainer to be returned.

Returns:

The ElectronContainer at position number.

See Also:

• IAtomContainer.addElectronContainer(IElectronContainer)

getBond

public IBond getBond(IAtom atom1,
 IAtom atom2)

Returns the bond that connects the two given atoms.

Specified by:

getBond in interface IAtomContainer

Overrides:

getBond in class AtomContainer

Parameters:

atom1 - The first atom

atom2 - The second atom

Returns:

The bond that connects the two atoms

getAtomCount

public int getAtomCount()

Returns the number of Atoms in this Container.

Specified by:

getAtomCount in interface IAtomContainer

Overrides:

getAtomCount in class AtomContainer

Returns:

The number of Atoms in this Container

getBondCount

public int getBondCount()

Returns the number of Bonds in this Container.

Specified by:

getBondCount in interface IAtomContainer

Overrides:

getBondCount in class AtomContainer

Returns:

The number of Bonds in this Container

getLonePairCount

public int getLonePairCount()

Returns the number of LonePairs in this Container.

Specified by:

getLonePairCount in interface IAtomContainer

Overrides:

getLonePairCount in class AtomContainer

Returns:

The number of LonePairs in this Container

getSingleElectronCount

public int getSingleElectronCount()

Returns the number of the single electrons in this container.

Specified by:

getSingleElectronCount in interface IAtomContainer

Overrides:

getSingleElectronCount in class AtomContainer

Returns:

The number of SingleElectron objects of this AtomContainer

getElectronContainerCount

public int getElectronContainerCount()

Returns the number of ElectronContainers in this Container.

Specified by:

getElectronContainerCount in interface IAtomContainer

Overrides:

getElectronContainerCount in class AtomContainer

Returns:

The number of ElectronContainers in this Container

getConnectedAtomsList

public List<IAtom> getConnectedAtomsList(IAtom atom)

Returns the atoms connected connected to the specified atom by a bond.

Specified by:

getConnectedAtomsList in interface IAtomContainer

Overrides:

getConnectedAtomsList in class AtomContainer

Parameters:

atom - the atom

Returns:

connected atoms

getConnectedBondsList

public List<IBond> getConnectedBondsList(IAtom atom)

Returns the bonds connected connected to the specified atom.

Specified by:

getConnectedBondsList in interface IAtomContainer

Overrides:

getConnectedBondsList in class AtomContainer

Parameters:

atom - the atom

Returns:

connected bonds

getConnectedLonePairsList

public List<ILonePair> getConnectedLonePairsList(IAtom atom)

Returns the lone pairs connected connected to the specified atom.

Specified by:

getConnectedLonePairsList in interface IAtomContainer

Overrides:

getConnectedLonePairsList in class AtomContainer

Parameters:

atom - the atom

Returns:

connected lone pairs

getConnectedSingleElectronsList

public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)

Returns the single electrons connected connected to the specified atom.

Specified by:

getConnectedSingleElectronsList in interface IAtomContainer

Overrides:

getConnectedSingleElectronsList in class AtomContainer

Parameters:

atom - the atom

Returns:

connected lone pairs

getConnectedElectronContainersList

public List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

Specified by:

getConnectedElectronContainersList in interface IAtomContainer

Overrides:

getConnectedElectronContainersList in class AtomContainer

Parameters:

atom - the atom

Returns:

connected lone pairs

getConnectedAtomsCount

public int getConnectedAtomsCount(IAtom atom)

Returns the number of connected atoms (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.

Specified by:

getConnectedAtomsCount in interface IAtomContainer

Overrides:

getConnectedAtomsCount in class AtomContainer

Parameters:

atom - the atom

Returns:

number of connected bonds

getConnectedBondsCount

public int getConnectedBondsCount(IAtom atom)

Returns the number of connected bonds (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.

Specified by:

getConnectedBondsCount in interface IAtomContainer

Overrides:

getConnectedBondsCount in class AtomContainer

Parameters:

atom - the atom

Returns:

number of connected bonds

getConnectedLonePairsCount

public int getConnectedLonePairsCount(IAtom atom)

Returns the number of lone pairs connected to the specified atom.

Specified by:

getConnectedLonePairsCount in interface IAtomContainer

Overrides:

getConnectedLonePairsCount in class AtomContainer

Parameters:

atom - the atom

Returns:

number of connected bonds

getConnectedSingleElectronsCount

public int getConnectedSingleElectronsCount(IAtom atom)

Returns the number of single electrons connected to the specified atom.

Specified by:

getConnectedSingleElectronsCount in interface IAtomContainer

Overrides:

getConnectedSingleElectronsCount in class AtomContainer

Parameters:

atom - the atom

Returns:

number of connected bonds

getBondOrderSum

public double getBondOrderSum(IAtom atom)

Returns the sum of the bond orders for a given Atom.

Specified by:

getBondOrderSum in interface IAtomContainer

Overrides:

getBondOrderSum in class AtomContainer

Parameters:

atom - The atom

Returns:

The number of bondorders for this atom

getMaximumBondOrder

public IBond.Order getMaximumBondOrder(IAtom atom)

Returns the maximum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.

Specified by:

getMaximumBondOrder in interface IAtomContainer

Overrides:

getMaximumBondOrder in class AtomContainer

Parameters:

atom - The atom

Returns:

The maximum bond order that this atom currently has

getMinimumBondOrder

public IBond.Order getMinimumBondOrder(IAtom atom)

Returns the minimum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.

Specified by:

getMinimumBondOrder in interface IAtomContainer

Overrides:

getMinimumBondOrder in class AtomContainer

Parameters:

atom - The atom

Returns:

The minimum bond order that this atom currently has

add

public void add(IAtomContainer atomContainer)

Adds all atoms and electronContainers of a given atomcontainer to this container.

Specified by:

add in interface IAtomContainer

Overrides:

add in class AtomContainer

Parameters:

atomContainer - The atomcontainer to be added

addAtom

public void addAtom(IAtom atom)

Adds an atom to this container.

Specified by:

addAtom in interface IAtomContainer

Overrides:

addAtom in class AtomContainer

Parameters:

atom - The atom to be added to this container

addBond

public void addBond(IBond bond)

Adds a Bond to this AtomContainer.

Specified by:

addBond in interface IAtomContainer

Overrides:

addBond in class AtomContainer

Parameters:

bond - The bond to added to this container

addLonePair

public void addLonePair(ILonePair ec)

Adds a lone pair to this AtomContainer.

Specified by:

addLonePair in interface IAtomContainer

Overrides:

addLonePair in class AtomContainer

Parameters:

ec - The LonePair to added to this container

addSingleElectron

public void addSingleElectron(ISingleElectron ec)

Adds a single electron to this AtomContainer.

Specified by:

addSingleElectron in interface IAtomContainer

Overrides:

addSingleElectron in class AtomContainer

Parameters:

ec - The SingleElectron to added to this container

addElectronContainer

public void addElectronContainer(IElectronContainer electronContainer)

Adds a ElectronContainer to this AtomContainer.

Specified by:

addElectronContainer in interface IAtomContainer

Overrides:

addElectronContainer in class AtomContainer

Parameters:

electronContainer - The ElectronContainer to added to this container

remove

public void remove(IAtomContainer atomContainer)

Removes all atoms and electronContainers of a given atomcontainer from this container.

Specified by:

remove in interface IAtomContainer

Overrides:

remove in class AtomContainer

Parameters:

atomContainer - The atomcontainer to be removed

removeElectronContainer

public IElectronContainer removeElectronContainer(int position)

Removes the bond at the given position from this container.

Specified by:

removeElectronContainer in interface IAtomContainer

Overrides:

removeElectronContainer in class AtomContainer

Parameters:

position - The position of the bond in the electronContainers array

Returns:

the IElectronContainer that was removed

removeElectronContainer

public void removeElectronContainer(IElectronContainer electronContainer)

Removes this ElectronContainer from this container.

Specified by:

removeElectronContainer in interface IAtomContainer

Overrides:

removeElectronContainer in class AtomContainer

Parameters:

electronContainer - The electronContainer to be removed

removeAtomOnly

public void removeAtomOnly(int position)

Unsafely remove atom at index.
Removes the atom at the given position from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removing all electronContainers to this atom from the container manually.

Specified by:

removeAtomOnly in interface IAtomContainer

Overrides:

removeAtomOnly in class AtomContainer

Parameters:

position - The position of the atom to be removed.

removeAtomOnly

public void removeAtomOnly(IAtom atom)

Unsafely remove atom.
Removes the given atom from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removeing all electronContainers to this atom from the container.

Specified by:

removeAtomOnly in interface IAtomContainer

Overrides:

removeAtomOnly in class AtomContainer

Parameters:

atom - The atom to be removed

removeBond

public IBond removeBond(int pos)

Removes the bond at the given position from the AtomContainer.

Specified by:

removeBond in interface IAtomContainer

Overrides:

removeBond in class AtomContainer

Parameters:

pos - The position of the bond to be removed.

Returns:

the bond at the given position

removeBond

public IBond removeBond(IAtom atom1,
 IAtom atom2)

Removes the bond that connects the two given atoms.

Specified by:

removeBond in interface IAtomContainer

Overrides:

removeBond in class AtomContainer

Parameters:

atom1 - The first atom

atom2 - The second atom

Returns:

The bond that connects the two atoms

removeBond

public void removeBond(IBond bond)

Removes the bond from this container.

Specified by:

removeBond in interface IAtomContainer

Overrides:

removeBond in class AtomContainer

Parameters:

bond - The bond to be removed.

removeLonePair

public ILonePair removeLonePair(int pos)

Removes the lone pair at the given position from the AtomContainer.

Specified by:

removeLonePair in interface IAtomContainer

Overrides:

removeLonePair in class AtomContainer

Parameters:

pos - The position of the LonePair to be removed.

Returns:

The removed ILonePair.

removeLonePair

public void removeLonePair(ILonePair ec)

Removes the lone pair from the AtomContainer.

Specified by:

removeLonePair in interface IAtomContainer

Overrides:

removeLonePair in class AtomContainer

Parameters:

ec - The LonePair to be removed.

removeSingleElectron

public ISingleElectron removeSingleElectron(int pos)

Removes the single electron at the given position from the AtomContainer.

Specified by:

removeSingleElectron in interface IAtomContainer

Overrides:

removeSingleElectron in class AtomContainer

Parameters:

pos - The position of the SingleElectron to be removed.

Returns:

The removed ISingleElectron

removeSingleElectron

public void removeSingleElectron(ISingleElectron ec)

Removes the single electron from the AtomContainer.

Specified by:

removeSingleElectron in interface IAtomContainer

Overrides:

removeSingleElectron in class AtomContainer

Parameters:

ec - The SingleElectron to be removed.

removeAtom

public void removeAtom(IAtom atom)

Safely remove an atom from the container.
Removes a single atom from the container updating all internal state to be consistent. All bonds connected to the atom will be deleted as well as all stereo elements. If multiple atoms/bonds are being deleted they should be gathered into a single transaction and removed with IAtomContainer.remove(IAtomContainer).
If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.

Specified by:

removeAtom in interface IAtomContainer

Overrides:

removeAtom in class AtomContainer

Parameters:

atom - the atom to be removed

removeAllElements

public void removeAllElements()

Removes all atoms, bonds and stereo elements from this container.

Specified by:

removeAllElements in interface IAtomContainer

Overrides:

removeAllElements in class AtomContainer

removeAllElectronContainers

public void removeAllElectronContainers()

Removes electronContainers from this container.

Specified by:

removeAllElectronContainers in interface IAtomContainer

Overrides:

removeAllElectronContainers in class AtomContainer

removeAllBonds

public void removeAllBonds()

Removes all Bonds from this container.

Specified by:

removeAllBonds in interface IAtomContainer

Overrides:

removeAllBonds in class AtomContainer

addBond

public void addBond(int atom1,
 int atom2,
 IBond.Order order,
 IBond.Stereo stereo)

Adds a bond to this container.

Specified by:

addBond in interface IAtomContainer

Overrides:

addBond in class AtomContainer

Parameters:

atom1 - Id of the first atom of the Bond in [0,..]

atom2 - Id of the second atom of the Bond in [0,..]

order - Bondorder

stereo - Stereochemical orientation

addBond

public void addBond(int atom1,
 int atom2,
 IBond.Order order)

Adds a bond to this container.

Specified by:

addBond in interface IAtomContainer

Parameters:

atom1 - Id of the first atom of the Bond in [0,..]

atom2 - Id of the second atom of the Bond in [0,..]

order - Bondorder

addLonePair

public void addLonePair(int atomID)

Adds a LonePair to this Atom.

Specified by:

addLonePair in interface IAtomContainer

Overrides:

addLonePair in class AtomContainer

Parameters:

atomID - The atom number to which the LonePair is added in [0,..]

addSingleElectron

public void addSingleElectron(int atomID)

Adds a SingleElectron to this Atom.

Specified by:

addSingleElectron in interface IAtomContainer

Overrides:

addSingleElectron in class AtomContainer

Parameters:

atomID - The atom number to which the SingleElectron is added in [0,..]

contains

public boolean contains(IAtom atom)

True, if the AtomContainer contains the given atom object.

Specified by:

contains in interface IAtomContainer

Overrides:

contains in class AtomContainer

Parameters:

atom - the atom this AtomContainer is searched for

Returns:

True, if the AtomContainer contains the given atom object

contains

public boolean contains(IBond bond)

True, if the AtomContainer contains the given bond object.

Specified by:

contains in interface IAtomContainer

Overrides:

contains in class AtomContainer

Parameters:

bond - the bond this AtomContainer is searched for

Returns:

True, if the AtomContainer contains the given bond object

contains

public boolean contains(ILonePair ec)

True, if the AtomContainer contains the given LonePair object.

Specified by:

contains in interface IAtomContainer

Overrides:

contains in class AtomContainer

Parameters:

ec - the LonePair this AtomContainer is searched for

Returns:

True, if the AtomContainer contains the given LonePair object

contains

public boolean contains(ISingleElectron ec)

True, if the AtomContainer contains the given SingleElectron object.

Specified by:

contains in interface IAtomContainer

Overrides:

contains in class AtomContainer

Parameters:

ec - the SingleElectron this AtomContainer is searched for

Returns:

True, if the AtomContainer contains the given SingleElectron object

contains

public boolean contains(IElectronContainer electronContainer)

True, if the AtomContainer contains the given ElectronContainer object.

Specified by:

contains in interface IAtomContainer

Overrides:

contains in class AtomContainer

Parameters:

electronContainer - ElectronContainer that is searched for

Returns:

True, if the AtomContainer contains the given bond object

addListener

public void addListener(IChemObjectListener col)

Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.

Specified by:

addListener in interface IChemObject

Overrides:

addListener in class ChemObject

Parameters:

col - the ChemObjectListener

See Also:

• ChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)

getListenerCount

public int getListenerCount()

Returns the number of ChemObjectListeners registered with this object.

Specified by:

getListenerCount in interface IChemObject

Overrides:

getListenerCount in class ChemObject

Returns:

the number of registered listeners.

removeListener

public void removeListener(IChemObjectListener col)

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.

Specified by:

removeListener in interface IChemObject

Overrides:

removeListener in class ChemObject

Parameters:

col - The ChemObjectListener to be removed

See Also:

• ChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)

notifyChanged

public void notifyChanged()

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.

Specified by:

notifyChanged in interface IChemObject

Overrides:

notifyChanged in class ChemObject

notifyChanged

public void notifyChanged(IChemObjectChangeEvent evt)

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.

Specified by:

notifyChanged in interface IChemObject

Overrides:

notifyChanged in class ChemObject

Parameters:

evt - A ChemObjectChangeEvent pointing to the source of where the change happened

setProperty

public void setProperty(Object description,
 Object property)

Sets a property for a IChemObject.

Specified by:

setProperty in interface IChemObject

Overrides:

setProperty in class ChemObject

Parameters:

description - An object description of the property (most likely a unique string)

property - An object with the property itself

See Also:

• ChemObject.getProperty(java.lang.Object)
• ChemObject.removeProperty(java.lang.Object)

removeProperty

public void removeProperty(Object description)

Removes a property for a IChemObject.

Specified by:

removeProperty in interface IChemObject

Overrides:

removeProperty in class ChemObject

Parameters:

description - The object description of the property (most likely a unique string)

See Also:

• ChemObject.setProperty(java.lang.Object, java.lang.Object)
• ChemObject.getProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description)

Returns a property for the IChemObject.

Specified by:

getProperty in interface IChemObject

Overrides:

getProperty in class ChemObject

Type Parameters:

T - generic return type

Parameters:

description - An object description of the property (most likely a unique string)

Returns:

The object containing the property. Returns null if propert is not set.

See Also:

• ChemObject.setProperty(java.lang.Object, java.lang.Object)
• ChemObject.removeProperty(java.lang.Object)

getProperties

public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Specified by:

getProperties in interface IChemObject

Overrides:

getProperties in class ChemObject

Returns:

The object's properties as an Hashtable

See Also:

• ChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)

getID

public String getID()

Returns the identifier (ID) of this object.

Specified by:

getID in interface IChemObject

Overrides:

getID in class ChemObject

Returns:

a String representing the ID value

See Also:

• ChemObject.setID(java.lang.String)

setID

public void setID(String identifier)

Sets the identifier (ID) of this object.

Specified by:

setID in interface IChemObject

Overrides:

setID in class ChemObject

Parameters:

identifier - a String representing the ID value

See Also:

• ChemObject.getID()

setFlag

public void setFlag(int flagType,
 boolean flagValue)

Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC or IChemObject.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use IChemObject.setProperty(Object, Object).

 // set this chem object to be aromatic
 chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
 // ...
 // indicate we have visited this chem object
 chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
 

Specified by:

setFlag in interface IChemObject

Overrides:

setFlag in class ChemObject

Parameters:

flagType - flag to set the value for

flagValue - value to assign to flag

See Also:

• IChemObject.getFlag(int)

getFlag

public boolean getFlag(int flagType)

Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC).

 if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
     // handle aromatic flag on this chem object
 }
 

Specified by:

getFlag in interface IChemObject

Overrides:

getFlag in class ChemObject

Parameters:

flagType - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

• IChemObject.setFlag(int, boolean)

addProperties

public void addProperties(Map<Object,Object> properties)

Sets the properties of this object.

Specified by:

addProperties in interface IChemObject

Overrides:

addProperties in class ChemObject

Parameters:

properties - a Hashtable specifying the property values

See Also:

• ChemObject.getProperties()

setFlags

public void setFlags(boolean[] flagsNew)

Sets the whole set of flags.

Specified by:

setFlags in interface IChemObject

Overrides:

setFlags in class ChemObject

Parameters:

flagsNew - the new flags.

See Also:

• ChemObject.getFlags()

getFlags

public boolean[] getFlags()

Returns the whole set of flags.

Specified by:

getFlags in interface IChemObject

Overrides:

getFlags in class ChemObject

Returns:

the flags.

See Also:

• ChemObject.setFlags(boolean[])

clone

public IAminoAcid clone()
                 throws CloneNotSupportedException

Clones this AminoAcid object.

Specified by:

clone in interface IAminoAcid

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IMonomer

Overrides:

clone in class AminoAcid

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

getBuilder

public IChemObjectBuilder getBuilder()

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Overrides:

getBuilder in class ChemObject

Returns:

The IChemObjectBuilder matching this ICDKObject

getMonomerName

public String getMonomerName()

Retrieves the monomer name.

Specified by:

getMonomerName in interface IMonomer

Overrides:

getMonomerName in class Monomer

Returns:

The name of the Monomer object

See Also:

• Monomer.setMonomerName(java.lang.String)

getMonomerType

public String getMonomerType()

Retrieves the monomer type.

Specified by:

getMonomerType in interface IMonomer

Overrides:

getMonomerType in class Monomer

Returns:

The type of the Monomer object

See Also:

• Monomer.setMonomerType(java.lang.String)

setMonomerName

public void setMonomerName(String cMonomerName)

Sets the name of the Monomer object.

Specified by:

setMonomerName in interface IMonomer

Overrides:

setMonomerName in class Monomer

Parameters:

cMonomerName - The new name for this monomer

See Also:

• Monomer.getMonomerName()

setMonomerType

public void setMonomerType(String cMonomerType)

Sets the type of the Monomer object.

Specified by:

setMonomerType in interface IMonomer

Overrides:

setMonomerType in class Monomer

Parameters:

cMonomerType - The new type for this monomer

See Also:

• Monomer.getMonomerType()

stateChanged

public void stateChanged(IChemObjectChangeEvent event)

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

Specified by:

stateChanged in interface IChemObjectListener

Overrides:

stateChanged in class AtomContainer

Parameters:

event - a ChemObjectChangeEvent object

getNTerminus

public IAtom getNTerminus()

Retrieves the N-terminus atom.

Specified by:

getNTerminus in interface IAminoAcid

Overrides:

getNTerminus in class AminoAcid

Returns:

The Atom that is the N-terminus

See Also:

• AminoAcid.addNTerminus(IAtom)

addNTerminus

public void addNTerminus(IAtom atom)

Add an Atom and makes it the N-terminus atom.

Specified by:

addNTerminus in interface IAminoAcid

Overrides:

addNTerminus in class AminoAcid

Parameters:

atom - The Atom that is the N-terminus

See Also:

• AminoAcid.getNTerminus()

getCTerminus

public IAtom getCTerminus()

Retrieves the C-terminus atom.

Specified by:

getCTerminus in interface IAminoAcid

Overrides:

getCTerminus in class AminoAcid

Returns:

The Atom that is the C-terminus

See Also:

• AminoAcid.addCTerminus(IAtom)

addCTerminus

public void addCTerminus(IAtom atom)

Add an Atom and makes it the C-terminus atom.

Specified by:

addCTerminus in interface IAminoAcid

Overrides:

addCTerminus in class AminoAcid

Parameters:

atom - The Atom that is the C-terminus

See Also:

• AminoAcid.getCTerminus()