Package org.openscience.cdk.tools.manipulator

Class AtomContainerSetManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

public class AtomContainerSetManipulator
extends Object

See Also:

• ChemModelManipulator

Source code:

main

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor	Description
AtomContainerSetManipulator()

Method Summary

Modifier and Type	Method	Description
static boolean	containsByID(IAtomContainerSet atomContainerSet, String id)	Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.
static List<IAtomContainer>	getAllAtomContainers(IAtomContainerSet set)	Returns all the AtomContainer's of a MoleculeSet.
static List<IChemObject>	getAllChemObjects(IAtomContainerSet set)	Does not recursively return the contents of the AtomContainer.
static List<String>	getAllIDs(IAtomContainerSet set)
static int	getAtomCount(IAtomContainerSet set)
static int	getBondCount(IAtomContainerSet set)
static IAtomContainer	getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)
static IAtomContainer	getRelevantAtomContainer(IAtomContainerSet containerSet, 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)
static void	sort(IAtomContainerSet atomContainerSet)	Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:

Methods inherited from class java.lang.Object

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

Constructor Details

AtomContainerSetManipulator

public AtomContainerSetManipulator()

Method Details

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 of individual IAtomContainer's

getTotalCharge

public static double getTotalCharge(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

The summed charges of all atoms in this set.

getTotalFormalCharge

public static double getTotalFormalCharge(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

The summed formal charges of all atoms in this set.

getTotalHydrogenCount

public static int getTotalHydrogenCount(IAtomContainerSet set)

Parameters:

set - The collection of IAtomContainer objects

Returns:

The summed implicit hydrogens of all atoms in this set.

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 containerSet,
 IAtom atom)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet,
 IBond bond)

getAllChemObjects

public static List<IChemObject> getAllChemObjects(IAtomContainerSet set)

Does not recursively return the contents of the AtomContainer.

Parameters:

set - The collection of IAtomContainer objects

Returns:

a list of individual ChemObject's

sort

public static void sort(IAtomContainerSet atomContainerSet)

Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:

• Compare atom count
• Compare molecular weight (heavy atoms only)
• Compare bond count
• Compare sum of bond orders (heavy atoms only)

If no difference can be found with the above criteria, the IAtomContainers are considered equal.

Parameters:

atomContainerSet - The collection of IAtomContainer objects

containsByID

public static boolean containsByID(IAtomContainerSet atomContainerSet,
 String id)

Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer. Note this checks getID() for equality, not pointers.

Parameters:

id - The IAtomContainer to look for

atomContainerSet - The collection of IAtomContainer objects