org.xmlcml.tools
Interface RingNucleus

All Known Implementing Classes:

RingNucleusImpl

public interface RingNucleus

extends BondSet

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

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 interface org.xmlcml.tools.BondSet

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

Methods inherited from interface org.xmlcml.tools.ToolHashSet

add, addAll, and, clone, contains, debug, iterator, not, or, remove, removeAll, retainAll, size, xor

Method Detail

addRing

public void addRing(Ring ring)
             throws CMLException

getCount

public int getCount()

get number of rings

getSSSR

public void getSSSR()
             throws CMLException

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

getRingOverlaps

public void getRingOverlaps()
                     throws CMLException

find which rings have bonds in common

addAtoms

public void addAtoms()
              throws CMLException

add atoms from all the rings

calculateCoordinates

public void calculateCoordinates()

calculate coordinates for nucleus de-novo

getSubstituents

public void getSubstituents(Molecule molecule)
                     throws CMLException

get substituent atoms (recursively)

addSubstituent

public void addSubstituent(RingNucleus rn)
                    throws CMLException

add substituent(s) in RingNucleus

addSubstituent

public void addSubstituent(ChainSet ch)
                    throws CMLException

add substituent(s) in ChainSet

mergeSpiro

public void mergeSpiro(Atom atom,
                       RingNucleus otherNucleus)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object