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org.xmlcml.cml.topology
Interface RingNucleus  

All Superinterfaces:

org.xmlcml.cml.subset.BondSet, java.lang.Cloneable, org.xmlcml.cml.subset.ToolHashSet

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public interface RingNucleus

extends org.xmlcml.cml.subset.BondSet

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

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Method Summary
void	addAtoms()           add atoms from all the rings
void	addRing(Ring ring)
int	getCount()           get number of rings
void	getRingOverlaps()           find which rings have bonds in common
java.util.Vector	getRings(org.xmlcml.cml.CMLAtom atom)           get Rings in which CMLAtom particpates
java.util.Vector	getRings(org.xmlcml.cml.CMLBond bond)           get Rings in which CMLBond particpates
java.util.Vector	getRingVector()           get vector of Rings
void	getSSSR()           "Smallest set of smallest rings".
java.lang.String	toString()

 

Methods inherited from interface org.xmlcml.cml.subset.BondSet

addBond, addSubstituent, and, calculateCoordinates, contains, containsAtom, getAtomSet, getCoord2, getSubstituentDirection, getSubstitutedAtomMap, not, or, setCoord2, substituentString, transformAndAddTo, transformBy, translateBy, xor

 

Methods inherited from interface org.xmlcml.cml.subset.ToolHashSet

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

 

Method Detail

addRing

public void addRing(Ring ring)
             throws org.xmlcml.cml.CMLException

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getCount

public int getCount()

get number of rings

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getSSSR

public void getSSSR()
             throws org.xmlcml.cml.CMLException

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

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getRingOverlaps

public void getRingOverlaps()
                     throws org.xmlcml.cml.CMLException

find which rings have bonds in common

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getRingVector

public java.util.Vector getRingVector()

get vector of Rings

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addAtoms

public void addAtoms()
              throws org.xmlcml.cml.CMLException

add atoms from all the rings

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getRings

public java.util.Vector getRings(org.xmlcml.cml.CMLAtom atom)

get Rings in which CMLAtom particpates

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getRings

public java.util.Vector getRings(org.xmlcml.cml.CMLBond bond)

get Rings in which CMLBond particpates

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toString

public java.lang.String toString()

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