DebugMonomer (cdk 1.5.15 API)

java.lang.Object
- org.openscience.cdk.ChemObject
- - org.openscience.cdk.AtomContainer
  - - org.openscience.cdk.Monomer
    - - org.openscience.cdk.debug.DebugMonomer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer
```
public class DebugMonomer
extends Monomer
implements IMonomer
```
Debugging data class.

Author:

egonw

See Also:
Serialized Form
Source code:
master

Belongs to CDK module:
datadebug

Field Summary
- Fields inherited from class org.openscience.cdk.AtomContainer
  atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors
Constructor and Description

DebugMonomer()

Constructors
Constructor and Description
`DebugMonomer()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`add(IAtomContainer atomContainer)` Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
`void`	`addAtom(IAtom atom)` Adds an atom to this container.
`void`	`addBond(IBond bond)` Adds a Bond to this AtomContainer.
`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`	`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(ILonePair ec)` Adds a lone pair to this AtomContainer.
`void`	`addLonePair(int atomID)` Adds a LonePair to this Atom.
`void`	`addProperties(Map<Object,Object> properties)` Sets the properties of this object.
`void`	`addSingleElectron(int atomID)` Adds a LonePair 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.
`IMonomer`	`clone()` Clones this AtomContainer object and its content.
`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 number)` Get the atom at position `number` in [0,..].
`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(IAtom atom1, IAtom atom2)` Returns the bond that connects the two given atoms.
`IBond`	`getBond(int number)` Get the bond at position `number` in [0,..].
`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 atoms connected to the given atom.
`List<IAtom>`	`getConnectedAtomsList(IAtom atom)` Returns an ArrayList of all atoms connected to the given atom.
`int`	`getConnectedBondsCount(IAtom atom)` Returns the number of Bonds for a given Atom.
`List<IBond>`	`getConnectedBondsList(IAtom atom)` Returns an ArrayList of all Bonds connected to the given atom.
`List<IElectronContainer>`	`getConnectedElectronContainersList(IAtom atom)` Returns an ArrayList of all electronContainers connected to the given atom.
`int`	`getConnectedLonePairsCount(IAtom atom)` Returns the number of LonePairs for a given Atom.
`List<ILonePair>`	`getConnectedLonePairsList(IAtom atom)` Returns the array of lone pairs connected to an atom.
`int`	`getConnectedSingleElectronsCount(IAtom atom)` Returns the sum of the SingleElectron for a given Atom.
`List<ISingleElectron>`	`getConnectedSingleElectronsList(IAtom atom)` Returns an array of all SingleElectron connected to the given 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 number)` Get the lone pair at position `number` in [0,..].
`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.
`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 number)` Get the single electron at position `number` in [0,..].
`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)` Removes the given atom from the AtomContainer.
`void`	`removeAtom(int position)` Removes the atom at the given position from the AtomContainer.
`void`	`removeAtomAndConnectedElectronContainers(IAtom atom)` Removes the given atom and all connected electronContainers 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.
`IBond`	`removeBond(int pos)` Removes the bond at the given position from the AtomContainer.
`void`	`removeElectronContainer(IElectronContainer electronContainer)` Removes this ElectronContainer from this container.
`IElectronContainer`	`removeElectronContainer(int position)` Removes the bond at the given position from this container.
`void`	`removeListener(IChemObjectListener col)` Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
`void`	`removeLonePair(ILonePair ec)` Removes the lone pair from the AtomContainer.
`ILonePair`	`removeLonePair(int pos)` Removes the lone pair at the given position 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)` Sets the atom at position `number` in [0,..].
`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 which this object has registered as a listener.
`Iterable<IStereoElement>`	`stereoElements()` Returns the stereo elements defined for this atom container.

Methods inherited from class org.openscience.cdk.Monomer
toString

Methods inherited from class org.openscience.cdk.AtomContainer
getConnectedBondsCount, indexOf, indexOf, indexOf, indexOf, isEmpty, setBonds, setStereoElements

Methods inherited from class org.openscience.cdk.ChemObject
compare, getFlagValue, getNotification, getProperty, setNotification, setProperties, 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.IAtomContainer
getConnectedBondsCount, indexOf, indexOf, indexOf, indexOf, isEmpty, setBonds, setStereoElements

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
getFlagValue, getNotification, getProperty, setNotification, setProperties, toString

- Constructor Detail
  - DebugMonomer
```
public DebugMonomer()
```
- Method Detail
  - 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:
    AtomContainer.getAtom(int)
  - setAtom
```
public void setAtom(int number,
           IAtom atom)
```
    Sets the atom at position number in [0,..].
    
    Specified by:
    
    setAtom in interface IAtomContainer
    
    Overrides:
    
    setAtom in class AtomContainer
    
    Parameters:
    number - The position of the atom to be set.
    atom - The atom to be stored at position number
    See Also:
    AtomContainer.getAtom(int)
  - getAtom
```
public IAtom getAtom(int number)
```
    Get the atom at position number in [0,..].
    
    Specified by:
    
    getAtom in interface IAtomContainer
    
    Overrides:
    
    getAtom in class AtomContainer
    
    Parameters:
    number - The position of the atom to be retrieved.
    
    Returns:
    The atomAt value
    See Also:
    AtomContainer.setAtom(int, org.openscience.cdk.interfaces.IAtom), AtomContainer.setAtoms(org.openscience.cdk.interfaces.IAtom[])
  - getBond
```
public IBond getBond(int number)
```
    Get the bond at position number in [0,..].
    
    Specified by:
    
    getBond in interface IAtomContainer
    
    Overrides:
    
    getBond in class AtomContainer
    
    Parameters:
    number - The position of the bond to be retrieved.
    
    Returns:
    The bondAt value
  - getLonePair
```
public ILonePair getLonePair(int number)
```
    Get the lone pair at position number in [0,..].
    
    Specified by:
    
    getLonePair in interface IAtomContainer
    
    Overrides:
    
    getLonePair in class AtomContainer
    
    Parameters:
    number - The position of the LonePair to be retrieved.
    
    Returns:
    The lone pair number
  - getSingleElectron
```
public ISingleElectron getSingleElectron(int number)
```
    Get the single electron at position number in [0,..].
    
    Specified by:
    
    getSingleElectron in interface IAtomContainer
    
    Overrides:
    
    getSingleElectron in class AtomContainer
    
    Parameters:
    number - The position of the SingleElectron to be retrieved.
    
    Returns:
    The single electron number
  - 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 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 an ArrayList of all atoms connected to the given atom.
    
    Specified by:
    
    getConnectedAtomsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedAtomsList in class AtomContainer
    
    Parameters:
    atom - The atom the bond partners are searched of.
    
    Returns:
    The ArrayList with the connected atoms
  - getConnectedBondsList
```
public List<IBond> getConnectedBondsList(IAtom atom)
```
    Returns an ArrayList of all Bonds connected to the given atom.
    
    Specified by:
    
    getConnectedBondsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedBondsList in class AtomContainer
    
    Parameters:
    atom - The atom the connected bonds are searched of
    
    Returns:
    The ArrayList with connected atoms
  - getConnectedLonePairsList
```
public List<ILonePair> getConnectedLonePairsList(IAtom atom)
```
    Returns the array of lone pairs connected to an atom.
    
    Specified by:
    
    getConnectedLonePairsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedLonePairsList in class AtomContainer
    
    Parameters:
    atom - The atom for which to get lone pairs
    
    Returns:
    The array of LonePairs of this AtomContainer
    See Also:
    AtomContainer.getElectronContainer(int), AtomContainer.electronContainers(), AtomContainer.getBond(int)
  - getConnectedSingleElectronsList
```
public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
```
    Returns an array of all SingleElectron connected to the given atom.
    
    Specified by:
    
    getConnectedSingleElectronsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedSingleElectronsList in class AtomContainer
    
    Parameters:
    atom - The atom on which the single electron is located
    
    Returns:
    The array of SingleElectron of this AtomContainer
  - getConnectedElectronContainersList
```
public List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)
```
    Returns an ArrayList of all electronContainers connected to the given atom.
    
    Specified by:
    
    getConnectedElectronContainersList in interface IAtomContainer
    
    Overrides:
    
    getConnectedElectronContainersList in class AtomContainer
    
    Parameters:
    atom - The atom the connected electronContainers are searched of
    
    Returns:
    The ArrayList with the connected atoms
  - getConnectedAtomsCount
```
public int getConnectedAtomsCount(IAtom atom)
```
    Returns the number of atoms connected to the given atom.
    
    Specified by:
    
    getConnectedAtomsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedAtomsCount in class AtomContainer
    
    Parameters:
    atom - The atom the number of bond partners are searched of.
    
    Returns:
    The the size of connected atoms
  - getConnectedBondsCount
```
public int getConnectedBondsCount(IAtom atom)
```
    Returns the number of Bonds for a given Atom.
    
    Specified by:
    
    getConnectedBondsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedBondsCount in class AtomContainer
    
    Parameters:
    atom - The atom
    
    Returns:
    The number of Bonds for this atom
  - getConnectedLonePairsCount
```
public int getConnectedLonePairsCount(IAtom atom)
```
    Returns the number of LonePairs for a given Atom.
    
    Specified by:
    
    getConnectedLonePairsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedLonePairsCount in class AtomContainer
    
    Parameters:
    atom - The atom
    
    Returns:
    The number of LonePairs for this atom
  - getConnectedSingleElectronsCount
```
public int getConnectedSingleElectronsCount(IAtom atom)
```
    Returns the sum of the SingleElectron for a given Atom.
    
    Specified by:
    
    getConnectedSingleElectronsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedSingleElectronsCount in class AtomContainer
    
    Parameters:
    atom - The atom on which the single electron is located
    
    Returns:
    The array of SingleElectron of this AtomContainer
  - 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 bond orders 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.
    
    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.
    
    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)
```
    Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
    
    Specified by:
    
    add in interface IAtomContainer
    
    Overrides:
    
    add in class AtomContainer
    
    Parameters:
    atomContainer - the other atom container
  - 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:
    Bond 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
  - removeAtom
```
public void removeAtom(int position)
```
    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:
    
    removeAtom in interface IAtomContainer
    
    Overrides:
    
    removeAtom in class AtomContainer
    
    Parameters:
    position - The position of the atom to be removed.
  - removeAtom
```
public void removeAtom(IAtom atom)
```
    Removes the given atom 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.
    
    Specified by:
    
    removeAtom in interface IAtomContainer
    
    Overrides:
    
    removeAtom 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.
  - removeAtomAndConnectedElectronContainers
```
public void removeAtomAndConnectedElectronContainers(IAtom atom)
```
    Removes the given atom and all connected electronContainers from the AtomContainer. The method will also remove any IStereoElement that the atom is contained in. If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
    
    Specified by:
    
    removeAtomAndConnectedElectronContainers in interface IAtomContainer
    
    Overrides:
    
    removeAtomAndConnectedElectronContainers 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
    
    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
  - 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 LonePair to this Atom.
    
    Specified by:
    
    addSingleElectron in interface IAtomContainer
    
    Overrides:
    
    addSingleElectron in class AtomContainer
    
    Parameters:
    atomID - The atom number to which the LonePair 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 LonePair this AtomContainer is searched for
    
    Returns:
    true if the AtomContainer contains the given LonePair 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. CDKConstants.ISAROMATIC or CDKConstants.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), CDKConstants
  - getFlag
```
public boolean getFlag(int flagType)
```
    Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC).
```
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), CDKConstants
  - 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 IMonomer clone()
               throws CloneNotSupportedException
```
    Clones this AtomContainer object and its content.
    
    Specified by:
    
    clone in interface IAtomContainer
    
    Specified by:
    
    clone in interface IChemObject
    
    Specified by:
    
    clone in interface IMonomer
    
    Overrides:
    
    clone in class Monomer
    
    Returns:
    The cloned object
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned
    See Also:
    ChemObject.shallowCopy()
  - 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 which this object has registered as a listener.
    
    Specified by:
    
    stateChanged in interface IChemObjectListener
    
    Overrides:
    
    stateChanged in class AtomContainer
    
    Parameters:
    event - A change event pointing to the source of the change

Class DebugMonomer

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainer

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.Monomer

Methods inherited from class org.openscience.cdk.AtomContainer

Methods inherited from class org.openscience.cdk.ChemObject

Methods inherited from class java.lang.Object

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

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

Constructor Detail

DebugMonomer

Method Detail

addStereoElement

stereoElements

setAtoms

setAtom

getAtom

getBond

getLonePair

getSingleElectron

atoms

bonds

lonePairs

singleElectrons

electronContainers

getFirstAtom

getLastAtom

getAtomNumber

getBondNumber

getBondNumber

getLonePairNumber

getSingleElectronNumber

getElectronContainer

getBond

getAtomCount

getBondCount

getLonePairCount

getSingleElectronCount

getElectronContainerCount

getConnectedAtomsList

getConnectedBondsList

getConnectedLonePairsList

getConnectedSingleElectronsList

getConnectedElectronContainersList

getConnectedAtomsCount

getConnectedBondsCount

getConnectedLonePairsCount

getConnectedSingleElectronsCount

getBondOrderSum

getMaximumBondOrder

getMinimumBondOrder

add

addAtom

addBond

addLonePair

addSingleElectron

addElectronContainer

remove

removeElectronContainer

removeElectronContainer

removeAtom

removeAtom

removeBond

removeBond

removeBond

removeLonePair

removeLonePair

removeSingleElectron

removeSingleElectron

removeAtomAndConnectedElectronContainers

removeAllElements

removeAllElectronContainers

removeAllBonds

addBond

addBond

addLonePair

addSingleElectron

contains