org.xmlcml.tools
Class RingImpl

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

public class RingImpl

extends BondSetImpl

implements Ring

See Also:

Serialized Form

Field Summary

protected CyclicVector	cyclicAtomVector ordered list of atoms - each element is an Atom as we traverse the Ring cyclicly.
protected CyclicVector	cyclicBondVector ordered list of bonds - each element is a Bond and links to the next bond in the ring cyclicly
protected java.lang.String	id each ring has a unique ID
protected java.util.Vector	ringOverlapVector what rings does this overlap with (FUSED or BRIDGED)? Vector stores RingOverlaps

Fields inherited from class org.xmlcml.tools.BondSetImpl

atomSet

Constructor Summary

RingImpl()

RingImpl(Molecule molecule)

Method Summary

void	addBond(Bond bond) add a bond, checking for nullity and duplicates
void	addRingOverlap(RingOverlap ringOverlap) stores knowledge of what rings are neighbours
BondSet	and(Ring ring) create a new ring as the AND of this and ring (i.e.
void	calculateCoordinates(Real2 repelPoint) calculate coordinates of a ring through two points.
void	calculateCoordinates(Ring overlapRing) stores knowledge of what rings are neighbours ?????
Real2	getCentroid()
java.util.Vector	getCyclicAtomVector() returns an ordered list of atoms corresponding to traversal of the ring
java.util.Vector	getCyclicBondVector() ordered cycle of bonds (e.g.
java.lang.String	getId()
java.util.Vector	getRingOverlapVector()
static void	main(java.lang.String[] args)
java.lang.String	toString() a String representation (mainly for diagnostics)
Ring	xor(Ring ring) create a new ring as the XOR of this and ring (i.e.

Methods inherited from class org.xmlcml.tools.BondSetImpl

and, containsAtom, getAtomSet, not, or, xor

Methods inherited from class org.xmlcml.tools.ToolHashSetImpl

and, clone, debug, 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

cyclicAtomVector

protected CyclicVector cyclicAtomVector

ordered list of atoms - each element is an Atom as we traverse the Ring cyclicly.

cyclicBondVector

protected CyclicVector cyclicBondVector

ordered list of bonds - each element is a Bond and links to the next bond in the ring cyclicly

ringOverlapVector

protected java.util.Vector ringOverlapVector

what rings does this overlap with (FUSED or BRIDGED)? Vector stores RingOverlaps

id

protected java.lang.String id

each ring has a unique ID

Constructor Detail

RingImpl

public RingImpl()

RingImpl

public RingImpl(Molecule molecule)

Method Detail

addBond

public void addBond(Bond bond)
             throws CMLException

Description copied from interface: BondSet

add a bond, checking for nullity and duplicates

Specified by:

addBond in interface Ring

Overrides:

addBond in class BondSetImpl

getRingOverlapVector

public java.util.Vector getRingOverlapVector()

Specified by:

getRingOverlapVector in interface Ring

getId

public java.lang.String getId()

Specified by:

getId in interface Ring

xor

public Ring xor(Ring ring)

create a new ring as the XOR of this and ring (i.e. formed from bonds NOT in common)

Specified by:

xor in interface Ring

and

public BondSet and(Ring ring)

create a new ring as the AND of this and ring (i.e. formed from bonds in common)

Specified by:

and in interface Ring

getCyclicBondVector

public java.util.Vector getCyclicBondVector()

ordered cycle of bonds (e.g. for creating Polygon). Starts at bond, if bond is part of ring, else arbitrary point. The second bond contains bond.atom2 and so on.

Specified by:

getCyclicBondVector in interface Ring

getCyclicAtomVector

public java.util.Vector getCyclicAtomVector()

returns an ordered list of atoms corresponding to traversal of the ring

Specified by:

getCyclicAtomVector in interface Ring

addRingOverlap

public void addRingOverlap(RingOverlap ringOverlap)

stores knowledge of what rings are neighbours

Specified by:

addRingOverlap in interface Ring

calculateCoordinates

public void calculateCoordinates(Ring overlapRing)

Description copied from interface: Ring

stores knowledge of what rings are neighbours ?????

Specified by:

calculateCoordinates in interface Ring

calculateCoordinates

public void calculateCoordinates(Real2 repelPoint)

calculate coordinates of a ring through two points. If offset = 0 or 1 these points are assumed to be adjacent, else the separation is by offset number of atoms (e.g. offset = 2 implies point[0] and point[2]). The result is an arrary of Points which is NOT applied to the coordinate table.

Specified by:

calculateCoordinates in interface Ring

getCentroid

public Real2 getCentroid()

Specified by:

getCentroid in interface Ring

toString

public java.lang.String toString()

a String representation (mainly for diagnostics)

Overrides:

toString in class BondSetImpl

main

public static void main(java.lang.String[] args)