org.xmlcml.tools
Class RingNucleusImpl

java.lang.Object
  |
  +--java.util.AbstractCollection
        |
        +--java.util.AbstractSet
              |
              +--java.util.HashSet
                    |
                    +--org.xmlcml.tools.ToolHashSetImpl
                          |
                          +--org.xmlcml.tools.BondSetImpl
                                |
                                +--org.xmlcml.tools.RingNucleusImpl

public class RingNucleusImpl

extends BondSetImpl

implements RingNucleus

a nucleus of rings (e.g. androstane but not biphenyl (which would be 2 separate RingNucleus)). Contains information about which rings overlap.

See Also:

Serialized Form

Field Summary

protected java.util.Vector	ringOverlapVector what RingOverlaps are there between these rings?
protected java.util.Vector	ringVector what Rings are there in this nucleus?
protected SpanningTree	spanningTree

Fields inherited from class org.xmlcml.tools.BondSetImpl

atomSet

Constructor Summary

RingNucleusImpl()

RingNucleusImpl(SpanningTree spanningTree)

Method Summary

void	addAtoms() add atoms from all the rings
void	addRing(Ring ring)
void	addSubstituent(ChainSet ch) add substituent(s) in ChainSet
void	addSubstituent(RingNucleus rn) add substituent(s) in RingNucleus
void	calculateCoordinates() calculate coordinates for nucleus de-novo
int	getCount() get number of rings
void	getRingOverlaps() find which rings have bonds in common
void	getSSSR() "Smallest set of smallest rings".
void	getSubstituents(Molecule molecule) get substituent atoms (recursively)
void	mergeSpiro(Atom atom, RingNucleus otherNucleus)
java.lang.String	toString()

Methods inherited from class org.xmlcml.tools.BondSetImpl

addBond, and, containsAtom, getAtomSet, not, or, xor

Methods inherited from class org.xmlcml.tools.ToolHashSetImpl

and, clone, debug, main, not, or, xor

Methods inherited from class java.util.HashSet

add, clear, contains, isEmpty, iterator, remove, size

Methods inherited from class java.util.AbstractSet

equals, hashCode

Methods inherited from class java.util.AbstractCollection

addAll, containsAll, removeAll, retainAll, toArray, toArray

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ringVector

protected java.util.Vector ringVector

what Rings are there in this nucleus?

ringOverlapVector

protected java.util.Vector ringOverlapVector

what RingOverlaps are there between these rings?

spanningTree

protected SpanningTree spanningTree

Constructor Detail

RingNucleusImpl

public RingNucleusImpl()

RingNucleusImpl

public RingNucleusImpl(SpanningTree spanningTree)

Method Detail

addRing

public void addRing(Ring ring)
             throws CMLException

Specified by:

addRing in interface RingNucleus

getCount

public int getCount()

Description copied from interface: RingNucleus

get number of rings

Specified by:

getCount in interface RingNucleus

getSSSR

public void getSSSR()
             throws CMLException

"Smallest set of smallest rings". Crude - not guaranteed to find minimum

Specified by:

getSSSR in interface RingNucleus

getRingOverlaps

public void getRingOverlaps()
                     throws CMLException

find which rings have bonds in common

Specified by:

getRingOverlaps in interface RingNucleus

addAtoms

public void addAtoms()
              throws CMLException

add atoms from all the rings

Specified by:

addAtoms in interface RingNucleus

calculateCoordinates

public void calculateCoordinates()

calculate coordinates for nucleus de-novo

Specified by:

calculateCoordinates in interface RingNucleus

getSubstituents

public void getSubstituents(Molecule molecule)
                     throws CMLException

get substituent atoms (recursively)

Specified by:

getSubstituents in interface RingNucleus

addSubstituent

public void addSubstituent(RingNucleus rn)
                    throws CMLException

add substituent(s) in RingNucleus

Specified by:

addSubstituent in interface RingNucleus

addSubstituent

public void addSubstituent(ChainSet ch)
                    throws CMLException

add substituent(s) in ChainSet

Specified by:

addSubstituent in interface RingNucleus

mergeSpiro

public void mergeSpiro(Atom atom,
                       RingNucleus otherNucleus)

Specified by:

mergeSpiro in interface RingNucleus

toString

public java.lang.String toString()

Specified by:

toString in interface RingNucleus

Overrides:

toString in class BondSetImpl