org.openscience.cdk.tools.manipulator

Class MoleculeSetManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

public class MoleculeSetManipulator
extends Object

See Also:

ChemModelManipulator

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
MoleculeSetManipulator()

Method Summary

Modifier and Type	Method and Description
static List<IAtomContainer>	getAllAtomContainers(IAtomContainerSet set) Returns all the AtomContainer's of a MoleculeSet.
static List<IChemObject>	getAllChemObjects(IAtomContainerSet set)
static List<String>	getAllIDs(IAtomContainerSet set)
static int	getAtomCount(IAtomContainerSet set)
static int	getBondCount(IAtomContainerSet set)
static IAtomContainer	getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom)
static IAtomContainer	getRelevantAtomContainer(IAtomContainerSet moleculeSet, IBond bond)
static double	getTotalCharge(IAtomContainerSet set)
static double	getTotalFormalCharge(IAtomContainerSet set)
static int	getTotalHydrogenCount(IAtomContainerSet set)
static void	removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
static void	removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
static void	setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal)

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeSetManipulator

public MoleculeSetManipulator()

Method Detail

getAtomCount

public static int getAtomCount(IAtomContainerSet set)

getBondCount

public static int getBondCount(IAtomContainerSet set)

removeAtomAndConnectedElectronContainers

public static void removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
                                                            IAtom atom)

removeElectronContainer

public static void removeElectronContainer(IAtomContainerSet set,
                                           IElectronContainer electrons)

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set)

Returns all the AtomContainer's of a MoleculeSet.

Parameters:

set - The collection of IAtomContainer objects

Returns:

a list containing individual IAtomContainer's

getTotalCharge

public static double getTotalCharge(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

The total charge on the collection of molecules

See Also:

AtomContainerSetManipulator

getTotalFormalCharge

public static double getTotalFormalCharge(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

The total formal charge on the collection of molecules

See Also:

AtomContainerSetManipulator

getTotalHydrogenCount

public static int getTotalHydrogenCount(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

the total implicit hydrogen count on the collection of molecules

See Also:

AtomContainerSetManipulator

getAllIDs

public static List<String> getAllIDs(IAtomContainerSet set)

setAtomProperties

public static void setAtomProperties(IAtomContainerSet set,
                                     Object propKey,
                                     Object propVal)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet moleculeSet,
                                                      IAtom atom)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet moleculeSet,
                                                      IBond bond)

getAllChemObjects

public static List<IChemObject> getAllChemObjects(IAtomContainerSet set)