org.openscience.cdk.tools.manipulator

Class RingSetManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.RingSetManipulator

public class RingSetManipulator
extends Object

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
RingSetManipulator()

Method Summary

Modifier and Type	Method and Description
static List<IAtomContainer>	getAllAtomContainers(IRingSet set) Returns all the AtomContainer's in a RingSet.
static IAtomContainer	getAllInOneContainer(IRingSet ringSet) Puts all rings of a ringSet in a single atomContainer
static int	getAtomCount(IRingSet set) Return the total number of atoms over all the rings in the colllection.
static int	getBondCount(IRingSet set) Return the total number of bonds over all the rings in the colllection.
static IRing	getHeaviestRing(IRingSet ringSet, IBond bond) We define the heaviest ring as the one with the highest number of double bonds.
static IRingSet	getLargestRingSet(List<IRingSet> ringSystems) Returns the largest (number of atoms) ring set in a molecule
static IRing	getMostComplexRing(IRingSet ringSet) Returns the ring with the highest numbers of other rings attached to it.
static boolean	isSameRing(IRingSet ringSet, IAtom atom1, IAtom atom2) Checks if atom1 and atom2 share membership in the same ring or ring system.
static void	markAromaticRings(IRingSet ringset) Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.
static boolean	ringAlreadyInSet(IRing newRing, IRingSet ringSet) Checks - and returns 'true' - if a certain ring is already stored in the ringset.
static void	sort(IRingSet ringSet) Sorts the rings in the set by size.

Methods inherited from class java.lang.Object

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

Constructor Detail

RingSetManipulator

public RingSetManipulator()

Method Detail

getAtomCount

public static int getAtomCount(IRingSet set)

Return the total number of atoms over all the rings in the colllection.

Parameters:

set - The collection of rings

Returns:

The total number of atoms

getAllInOneContainer

public static IAtomContainer getAllInOneContainer(IRingSet ringSet)

Puts all rings of a ringSet in a single atomContainer

Parameters:

ringSet - The ringSet to use

Returns:

The produced atomContainer

getLargestRingSet

public static IRingSet getLargestRingSet(List<IRingSet> ringSystems)

Returns the largest (number of atoms) ring set in a molecule

Parameters:

ringSystems - RingSystems of a molecule

Returns:

The largestRingSet

getBondCount

public static int getBondCount(IRingSet set)

Return the total number of bonds over all the rings in the colllection.

Parameters:

set - The collection of rings

Returns:

The total number of bonds

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IRingSet set)

Returns all the AtomContainer's in a RingSet.

Parameters:

set - The collection of rings

Returns:

A list of IAtomContainer objects corresponding to individual rings

sort

public static void sort(IRingSet ringSet)

Sorts the rings in the set by size. The smallest ring comes first.

Parameters:

ringSet - The collection of rings

getHeaviestRing

public static IRing getHeaviestRing(IRingSet ringSet,
                                    IBond bond)

We define the heaviest ring as the one with the highest number of double bonds. Needed for example for the placement of in-ring double bonds.

Parameters:

ringSet - The collection of rings

bond - A bond which must be contained by the heaviest ring

Returns:

The ring with the higest number of double bonds connected to a given bond

getMostComplexRing

public static IRing getMostComplexRing(IRingSet ringSet)

Returns the ring with the highest numbers of other rings attached to it. If an equally complex ring is found the last one is selected allow prioritization by size with sort(IRingSet).

Parameters:

ringSet - The collection of rings

Returns:

the ring with the highest numbers of other rings attached to it.

isSameRing

public static boolean isSameRing(IRingSet ringSet,
                                 IAtom atom1,
                                 IAtom atom2)

Checks if atom1 and atom2 share membership in the same ring or ring system. Membership in the same ring is checked if the RingSet contains the SSSR of a molecule; membership in the same ring or same ring system is checked if the RingSet contains all rings of a molecule.

Important: This method only returns meaningful results if atom1 and atom2 are members of the same molecule for which the RingSet was calculated!

Parameters:

ringSet - The collection of rings

atom1 - The first atom

atom2 - The second atom

Returns:

boolean true if atom1 and atom2 share membership of at least one ring or ring system, false otherwise

ringAlreadyInSet

public static boolean ringAlreadyInSet(IRing newRing,
                                       IRingSet ringSet)

Checks - and returns 'true' - if a certain ring is already stored in the ringset. This is not a test for equality of Ring objects, but compares all Bond objects of the ring.

Parameters:

newRing - The ring to be tested if it is already stored

ringSet - The collection of rings

Returns:

true if it is already stored

markAromaticRings

public static void markAromaticRings(IRingSet ringset)

Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic. This method assumes that aromaticity perception has been done before hand.

Parameters:

ringset - The collection of rings