java.lang.Object
- org.openscience.cdk.isomorphism.matchers.QueryChemObject
- - org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

All Implemented Interfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IQueryAtomContainer

Direct Known Subclasses:

PharmacophoreQuery
```
public class QueryAtomContainer
extends QueryChemObject
implements IQueryAtomContainer
```
Source code:
main

Belongs to CDK module:
isomorphism

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`atomCount`	Number of atoms contained by this object.
`protected IAtom[]`	`atoms`	Internal array of atoms.
`protected int`	`bondCount`	Number of bonds contained by this object.
`protected IBond[]`	`bonds`	Internal array of bonds.
`protected int`	`growArraySize`	Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
`protected int`	`lonePairCount`	Number of lone pairs contained by this object.
`protected ILonePair[]`	`lonePairs`	Internal array of lone pairs.
`protected int`	`singleElectronCount`	Number of single electrons contained by this object.
`protected ISingleElectron[]`	`singleElectrons`	Internal array of single electrons.
`protected List<IStereoElement>`	`stereoElements`	Internal list of atom parities.

Constructor Summary

Constructors
Constructor	Description
`QueryAtomContainer(int atomCount, int bondCount, int lpCount, int seCount, IChemObjectBuilder builder)`	Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
`QueryAtomContainer(IAtomContainer container, IChemObjectBuilder builder)`	Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
`QueryAtomContainer(IChemObjectBuilder builder)`	Constructs an empty AtomContainer.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
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`	`addElectronContainer(IElectronContainer electronContainer)`	Adds a ElectronContainer to this AtomContainer.
`void`	`addLonePair(int atomID)`	Adds a LonePair to this Atom.
`void`	`addLonePair(ILonePair lonePair)`	Adds a lone pair to this AtomContainer.
`void`	`addSingleElectron(int atomID)`	Adds a LonePair to this Atom.
`void`	`addSingleElectron(ISingleElectron singleElectron)`	Adds a single electron to this AtomContainer.
`void`	`addStereoElement(IStereoElement element)`	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.
`IQueryAtomContainer`	`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 lonePair)`	True, if the AtomContainer contains the given LonePair object.
`boolean`	`contains(ISingleElectron singleElectron)`	True, if the AtomContainer contains the given SingleElectron object.
`static void`	`create(IAtomContainer dst, IAtomContainer src, Expr.Type... opts)`	Populate a query from a molecule and a provided set of expressions.
`static QueryAtomContainer`	`create(IAtomContainer src, Expr.Type... opts)`	Create a query from a molecule and a provided set of expressions.
`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)`	Deprecated. Replaced by `AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)`
`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(int idx)`	Returns the number of connected atoms (degree) 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.
`IAtom`	`getLastAtom()`	Returns the atom at the last position in the container.
`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 lonePair)`	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.
`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 singleElectron)`	Returns the position of a given single electron in the single electron array.
`String`	`getTitle()`	Access the title of the record.
`int`	`indexOf(IAtom atom)`	Access the storage index of an atom.
`int`	`indexOf(IBond bond)`	Access the storage index of a bond.
`int`	`indexOf(ILonePair pair)`	Access the storage index of a long pair.
`int`	`indexOf(ISingleElectron electron)`	Access the storage index of a single electron (radical).
`boolean`	`isEmpty()`	Indicates whether this container is empty.
`Iterable<ILonePair>`	`lonePairs()`	Returns an Iterable for looping over all lone pairs in this container.
`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 and bond from this container.
`void`	`removeAtom(int pos)`	Safely remove an atom from the container.
`void`	`removeAtom(IAtom atom)`	Removes the given atom and all connected electronContainers from the AtomContainer.
`void`	`removeAtomAndConnectedElectronContainers(IAtom atom)`	Deprecated.
`void`	`removeAtomOnly(int position)`	Removes the atom at the given position from the AtomContainer.
`void`	`removeAtomOnly(IAtom atom)`	Removes the given atom from the AtomContainer.
`IBond`	`removeBond(int position)`	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 number)`	Removes the bond at the given position from this container.
`void`	`removeElectronContainer(IElectronContainer electronContainer)`	Removes this ElectronContainer from this container.
`ILonePair`	`removeLonePair(int position)`	Removes the lone pair at the given position from the AtomContainer.
`void`	`removeLonePair(ILonePair lonePair)`	Removes the lone pair from the AtomContainer.
`ISingleElectron`	`removeSingleElectron(int position)`	Removes the single electron at the given position from the AtomContainer.
`void`	`removeSingleElectron(ISingleElectron singleElectron)`	Removes the single electron from the AtomContainer.
`void`	`setAtom(int idx, 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`	`setBonds(IBond[] bonds)`	Sets the array of bonds of this AtomContainer.
`void`	`setStereoElements(List<IStereoElement> elements)`	Set the stereo elements - this will replace the existing instance with a new instance.
`void`	`setTitle(String title)`	Modify the title of the record.
`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.
`String`	`toString()`	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, matches, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

- Field Detail
  - atomCount
```
protected int atomCount
```
    Number of atoms contained by this object.
  - bondCount
```
protected int bondCount
```
    Number of bonds contained by this object.
  - lonePairCount
```
protected int lonePairCount
```
    Number of lone pairs contained by this object.
  - singleElectronCount
```
protected int singleElectronCount
```
    Number of single electrons contained by this object.
  - growArraySize
```
protected int growArraySize
```
    Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
  - atoms
```
protected IAtom[] atoms
```
    Internal array of atoms.
  - bonds
```
protected IBond[] bonds
```
    Internal array of bonds.
  - lonePairs
```
protected ILonePair[] lonePairs
```
    Internal array of lone pairs.
  - singleElectrons
```
protected ISingleElectron[] singleElectrons
```
    Internal array of single electrons.
  - stereoElements
```
protected final List<IStereoElement> stereoElements
```
    Internal list of atom parities.
- Constructor Detail
  - QueryAtomContainer
```
public QueryAtomContainer(IChemObjectBuilder builder)
```
    Constructs an empty AtomContainer.
  - QueryAtomContainer
```
public QueryAtomContainer(IAtomContainer container,
                          IChemObjectBuilder builder)
```
    Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
    
    Parameters:
    
    container - An AtomContainer to copy the atoms and electronContainers from
  - QueryAtomContainer
```
public QueryAtomContainer(int atomCount,
                          int bondCount,
                          int lpCount,
                          int seCount,
                          IChemObjectBuilder builder)
```
    Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers. It will set the starting array lengths to the defined values, but will not create any Atom or ElectronContainer's.
    
    Parameters:
    
    atomCount - Number of atoms to be in this container
    
    bondCount - Number of bonds to be in this container
    
    lpCount - Number of lone pairs to be in this container
    
    seCount - Number of single electrons to be in this container
- Method Detail
  - toString
```
public String toString()
```
    Description copied from interface: IChemObject
    
    Returns a one line description of this IChemObject.
    
    Specified by:
    
    toString in interface IChemObject
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a String representation of this object
  - addStereoElement
```
public void addStereoElement(IStereoElement element)
```
    Adds a stereo element to this container.
    
    Specified by:
    
    addStereoElement in interface IAtomContainer
    
    Parameters:
    
    element - 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
    
    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
    
    Parameters:
    
    atoms - The array of atoms to be assigned to this AtomContainer
    
    See Also:
    
    getAtom(int)
  - setBonds
```
public void setBonds(IBond[] bonds)
```
    Sets the array of bonds of this AtomContainer.
    
    Specified by:
    
    setBonds in interface IAtomContainer
    
    Parameters:
    
    bonds - The array of bonds to be assigned to this AtomContainer
    
    See Also:
    
    getBond(int)
  - setAtom
```
public void setAtom(int idx,
                    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
    
    Parameters:
    
    idx - 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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    Parameters:
    
    bond - The bond to be sought
    
    Returns:
    
    The Position of the bond in the electronContainers array in [0,..].
  - getLonePairNumber
```
public int getLonePairNumber(ILonePair lonePair)
```
    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
    
    Parameters:
    
    lonePair - The lone pair to be sought
    
    Returns:
    
    The Position of the lone pair in the array..
  - getSingleElectronNumber
```
public int getSingleElectronNumber(ISingleElectron singleElectron)
```
    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
    
    Parameters:
    
    singleElectron - The single electron to be sought
    
    Returns:
    
    The Position of the single electron in the array.
  - indexOf
```
public int indexOf(IAtom atom)
```
    Description copied from interface: IAtomContainer
    
    Access the storage index of an atom.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Parameters:
    
    atom - atom instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(IBond bond)
```
    Description copied from interface: IAtomContainer
    
    Access the storage index of a bond.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Parameters:
    
    bond - bond instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(ISingleElectron electron)
```
    Description copied from interface: IAtomContainer
    
    Access the storage index of a single electron (radical).
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Parameters:
    
    electron - the electron
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(ILonePair pair)
```
    Description copied from interface: IAtomContainer
    
    Access the storage index of a long pair.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Parameters:
    
    pair - the long pair
    
    Returns:
    
    the index, -1 if not found
  - getElectronContainer
```
public IElectronContainer getElectronContainer(int number)
```
    Returns the ElectronContainer at position number in the container.
    
    Specified by:
    
    getElectronContainer in interface IAtomContainer
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    Parameters:
    
    atom - The atom for which to get lone pairs
    
    Returns:
    
    The array of LonePairs of this AtomContainer
    
    See Also:
    
    getElectronContainer(int), electronContainers(), 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
    
    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
    
    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
    
    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
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The number of Bonds for this atom
  - getConnectedBondsCount
```
public int getConnectedBondsCount(int idx)
```
    Returns the number of connected atoms (degree) to the given atom.
    
    Specified by:
    
    getConnectedBondsCount in interface IAtomContainer
    
    Parameters:
    
    idx - The atomnumber the degree is searched for
    
    Returns:
    
    The number of connected atoms (degree)
  - getConnectedLonePairsCount
```
public int getConnectedLonePairsCount(IAtom atom)
```
    Returns the number of LonePairs for a given Atom.
    
    Specified by:
    
    getConnectedLonePairsCount in interface IAtomContainer
    
    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
    
    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)
```
    Deprecated.
    Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
    
    Returns the sum of the bond orders for a given Atom.
    
    Specified by:
    
    getBondOrderSum in interface IAtomContainer
    
    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
    
    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
    
    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
    
    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
    
    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
    
    Parameters:
    
    bond - The bond to added to this container
  - addLonePair
```
public void addLonePair(ILonePair lonePair)
```
    Adds a lone pair to this AtomContainer.
    
    Specified by:
    
    addLonePair in interface IAtomContainer
    
    Parameters:
    
    lonePair - The LonePair to added to this container
  - addSingleElectron
```
public void addSingleElectron(ISingleElectron singleElectron)
```
    Adds a single electron to this AtomContainer.
    
    Specified by:
    
    addSingleElectron in interface IAtomContainer
    
    Parameters:
    
    singleElectron - 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
    
    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
    
    Parameters:
    
    atomContainer - The atomcontainer to be removed
  - removeAtomOnly
```
public void removeAtomOnly(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:
    
    removeAtomOnly in interface IAtomContainer
    
    Parameters:
    
    position - The position of the atom to be removed.
  - removeAtomOnly
```
public void removeAtomOnly(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:
    
    removeAtomOnly in interface IAtomContainer
    
    Parameters:
    
    atom - The atom to be removed
  - removeBond
```
public IBond removeBond(int position)
```
    Removes the bond at the given position from the AtomContainer.
    
    Specified by:
    
    removeBond in interface IAtomContainer
    
    Parameters:
    
    position - 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
    
    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
    
    Parameters:
    
    bond - The bond to be removed.
  - removeLonePair
```
public ILonePair removeLonePair(int position)
```
    Removes the lone pair at the given position from the AtomContainer.
    
    Specified by:
    
    removeLonePair in interface IAtomContainer
    
    Parameters:
    
    position - The position of the LonePair to be removed.
    
    Returns:
    
    The removed ILonePair.
  - removeLonePair
```
public void removeLonePair(ILonePair lonePair)
```
    Removes the lone pair from the AtomContainer.
    
    Specified by:
    
    removeLonePair in interface IAtomContainer
    
    Parameters:
    
    lonePair - The LonePair to be removed.
  - removeSingleElectron
```
public ISingleElectron removeSingleElectron(int position)
```
    Removes the single electron at the given position from the AtomContainer.
    
    Specified by:
    
    removeSingleElectron in interface IAtomContainer
    
    Parameters:
    
    position - The position of the SingleElectron to be removed.
    
    Returns:
    
    The removed ISingleElectron
  - removeSingleElectron
```
public void removeSingleElectron(ISingleElectron singleElectron)
```
    Removes the single electron from the AtomContainer.
    
    Specified by:
    
    removeSingleElectron in interface IAtomContainer
    
    Parameters:
    
    singleElectron - The SingleElectron to be removed.
  - removeElectronContainer
```
public IElectronContainer removeElectronContainer(int number)
```
    Removes the bond at the given position from this container.
    
    Specified by:
    
    removeElectronContainer in interface IAtomContainer
    
    Parameters:
    
    number - 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
    
    Parameters:
    
    electronContainer - The electronContainer to be removed
  - removeAtomAndConnectedElectronContainers
```
@Deprecated
public void removeAtomAndConnectedElectronContainers(IAtom atom)
```
    Deprecated.
    
    Safely remove an atom from the container.
    
    Specified by:
    
    removeAtomAndConnectedElectronContainers in interface IAtomContainer
    
    See Also:
    
    IAtomContainer.removeAtom(IAtom)
  - removeAtom
```
public void removeAtom(IAtom atom)
```
    Removes the given atom and all connected electronContainers from the AtomContainer.
    
    Specified by:
    
    removeAtom in interface IAtomContainer
    
    Parameters:
    
    atom - The atom to be removed
  - removeAtom
```
public void removeAtom(int pos)
```
    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
    
    Parameters:
    
    pos - the position of the atom to be removed
  - removeAllElements
```
public void removeAllElements()
```
    Removes all atoms and bond from this container.
    
    Specified by:
    
    removeAllElements in interface IAtomContainer
  - removeAllElectronContainers
```
public void removeAllElectronContainers()
```
    Removes electronContainers from this container.
    
    Specified by:
    
    removeAllElectronContainers in interface IAtomContainer
  - removeAllBonds
```
public void removeAllBonds()
```
    Removes all Bonds from this container.
    
    Specified by:
    
    removeAllBonds in interface IAtomContainer
  - 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
    
    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
    
    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
    
    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
    
    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
    
    Parameters:
    
    bond - the bond this AtomContainer is searched for
    
    Returns:
    
    true if the AtomContainer contains the given bond object
  - contains
```
public boolean contains(ILonePair lonePair)
```
    True, if the AtomContainer contains the given LonePair object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Parameters:
    
    lonePair - the LonePair this AtomContainer is searched for
    
    Returns:
    
    true if the AtomContainer contains the given LonePair object
  - contains
```
public boolean contains(ISingleElectron singleElectron)
```
    True, if the AtomContainer contains the given SingleElectron object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Parameters:
    
    singleElectron - 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
    
    Parameters:
    
    electronContainer - ElectronContainer that is searched for
    
    Returns:
    
    true if the AtomContainer contains the given bond object
  - clone
```
public IQueryAtomContainer clone()
                          throws CloneNotSupportedException
```
    Clones this AtomContainer object and its content.
    
    Specified by:
    
    clone in interface IAtomContainer
    
    Specified by:
    
    clone in interface IChemObject
    
    Overrides:
    
    clone in class QueryChemObject
    
    Returns:
    
    The cloned object
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned
    
    See Also:
    
    QueryAtomContainer(org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObjectBuilder)
  - stateChanged
```
public void stateChanged(IChemObjectChangeEvent event)
```
    Called by objects to which this object has registered as a listener.
    
    Specified by:
    
    stateChanged in interface IChemObjectListener
    
    Parameters:
    
    event - A change event pointing to the source of the change
  - isEmpty
```
public boolean isEmpty()
```
    Indicates whether this container is empty. The container is considered empty if there are no atoms. Bonds are not checked as a graph with no vertexes can not have edges.
    
    Specified by:
    
    isEmpty in interface IAtomContainer
    
    Returns:
    
    whether the container is empty
  - getTitle
```
public String getTitle()
```
    Access the title of the record.
    
    Specified by:
    
    getTitle in interface IAtomContainer
    
    Returns:
    
    the title
  - setTitle
```
public void setTitle(String title)
```
    Modify the title of the record.
    
    Specified by:
    
    setTitle in interface IAtomContainer
    
    Parameters:
    
    title - the title
  - setStereoElements
```
public void setStereoElements(List<IStereoElement> elements)
```
    Description copied from interface: IAtomContainer
    
    Set the stereo elements - this will replace the existing instance with a new instance.
    
    Specified by:
    
    setStereoElements in interface IAtomContainer
    
    Parameters:
    
    elements - the new stereo elements
  - create
```
public static void create(IAtomContainer dst,
                          IAtomContainer src,
                          Expr.Type... opts)
```
    Populate a query from a molecule and a provided set of expressions. The molecule is converted and any features specified in the opts will be matched.
    
    A good starting point is the following options:
    // [nH]1ccc(=O)cc1 => n1:c:c:c(=O):c:c:1 QueryAtomContainer.create(qry, mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER, STEREOCHEMISTRY);
    
    Specifying Expr.Type.DEGREE (or Expr.Type.TOTAL_DEGREE + Expr.Type.IMPL_H_COUNT) means the molecule will not match as a substructure.
    
    // [nH]1ccc(=O)cc1 => [nD2]1:[cD2]:[cD2]:[cD2](=[OD1]):[cD2]:[cD2]:1 QueryAtomContainer.create(qry, mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, DEGREE, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    
    The Expr.Type.RING_BOND_COUNT property is useful for locking in ring systems. Specifying the ring bond count on benzene means it will not match larger ring systems (e.g. naphthalenee) but can still be substituted.
    
    // [nH]1ccc(=O)cc1 => // [nx2+0]1:[cx2+0]:[cx2+0]:[cx2+0](=[O&x0+0]):[cx2+0]:[cx2+0]:1 // IMPORTANT! use Cycles.markRingAtomsAndBonds(mol) to set ring status QueryAtomContainer.create(qry, mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, FORMAL_CHARGE, ISOTOPE, RING_BOND_COUNT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    
    Note that Expr.Type.FORMAL_CHARGE, Expr.Type.IMPL_H_COUNT, and Expr.Type.ISOTOPE are ignored if null. Explicitly setting these to zero (only required for Isotope from SMILES) forces their inclusion.
    
    // [nH]1ccc(=O)cc1 => // [0n+0]1:[0c+0]:[0c+0]:[0c+0](=[O+0]):[0c+0]:[0c+0]:1 QueryAtomContainer.create(qry, mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, FORMAL_CHARGE, ISOTOPE, RING_BOND_COUNT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    Please note not all Expr.Types are currently supported, if you require a specific type that you think is useful please open an issue.
    Parameters:
    
    dst - the output destination
    
    src - the input molecule
    
    opts - set of the expr types to match
  - create
```
public static QueryAtomContainer create(IAtomContainer src,
                                        Expr.Type... opts)
```
    Create a query from a molecule and a provided set of expressions. The molecule is converted and any features specified in the opts will be matched.
    
    A good starting point is the following options:
    // [nH]1ccc(=O)cc1 => n1:c:c:c(=O):c:c:1 QueryAtomContainer.create(mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER, STEREOCHEMISTRY);
    
    Specifying Expr.Type.DEGREE (or Expr.Type.TOTAL_DEGREE + Expr.Type.IMPL_H_COUNT) means the molecule will not match as a substructure.
    
    // [nH]1ccc(=O)cc1 => [nD2]1:[cD2]:[cD2]:[cD2](=[OD1]):[cD2]:[cD2]:1 QueryAtomContainer.create(mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, DEGREE, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    
    The Expr.Type.RING_BOND_COUNT property is useful for locking in ring systems. Specifying the ring bond count on benzene means it will not match larger ring systems (e.g. naphthalenee) but can still be substituted.
    
    // [nH]1ccc(=O)cc1 => // [nx2+0]1:[cx2+0]:[cx2+0]:[cx2+0](=[O&x0+0]):[cx2+0]:[cx2+0]:1 // IMPORTANT! use Cycles.markRingAtomsAndBonds(mol) to set ring status QueryAtomContainer.create(mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, FORMAL_CHARGE, ISOTOPE, RING_BOND_COUNT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    
    Note that Expr.Type.FORMAL_CHARGE, Expr.Type.IMPL_H_COUNT, and Expr.Type.ISOTOPE are ignored if null. Explicitly setting these to zero (only required for Isotope from SMILES) forces their inclusion.
    
    // [nH]1ccc(=O)cc1 => // [0n+0]1:[0c+0]:[0c+0]:[0c+0](=[O+0]):[0c+0]:[0c+0]:1 QueryAtomContainer.create(mol, ALIPHATIC_ELEMENT, AROMATIC_ELEMENT, FORMAL_CHARGE, ISOTOPE, RING_BOND_COUNT, SINGLE_OR_AROMATIC, ALIPHATIC_ORDER);
    Please note not all Expr.Types are currently supported, if you require a specific type that you think is useful please open an issue.
    Parameters:
    
    src - the input molecule
    
    opts - set of the expr types to match
    
    Returns:
    
    the query container

Class QueryAtomContainer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Methods inherited from class java.lang.Object

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

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

Field Detail

atomCount

bondCount

lonePairCount

singleElectronCount

growArraySize

atoms

bonds

lonePairs

singleElectrons

stereoElements

Constructor Detail

QueryAtomContainer

QueryAtomContainer

QueryAtomContainer

Method Detail

toString

addStereoElement

stereoElements

setAtoms

setBonds

setAtom

getAtom

getBond

getLonePair

getSingleElectron

atoms

bonds

lonePairs

singleElectrons

electronContainers

getFirstAtom

getLastAtom

getAtomNumber

getBondNumber

getBondNumber

getLonePairNumber

getSingleElectronNumber

indexOf

indexOf

indexOf

indexOf

getElectronContainer

getBond

getAtomCount

getBondCount

getLonePairCount

getSingleElectronCount

getElectronContainerCount

getConnectedAtomsList

getConnectedBondsList

getConnectedLonePairsList

getConnectedSingleElectronsList

getConnectedElectronContainersList

getConnectedAtomsCount

getConnectedBondsCount

getConnectedBondsCount

getConnectedLonePairsCount

getConnectedSingleElectronsCount

getBondOrderSum

getMaximumBondOrder

getMinimumBondOrder

add

addAtom

addBond

addLonePair

addSingleElectron

addElectronContainer

remove

removeAtomOnly

removeAtomOnly

removeBond