org.xmlcml.tools
Class AtomSetImpl

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

public class AtomSetImpl

extends ToolHashSetImpl

implements AtomSet

a set of atoms. Counts number of times an atom has been added (e.g. for bonds). An AtomSet may have coordinates associated with it which may or may not be related to the molecule. This should make calcuation of fragment geometries easier and therefore assembly less painful

See Also:

Serialized Form

Field Summary

protected java.util.HashMap

coordinate2Map

Constructor Summary

AtomSetImpl()

Method Summary

void	addAtom(Atom atom) add an atom.
void	addBond(Bond bond) adds both atoms in the bond
AtomSet	and(AtomSet atomSet) combines this with AtomSet to find common elements, else null.
void	clearCoordinate2() clear atom coordinate table
Coordinate2	getCoordinate2(Atom atom) get coordinates for atom
int	getCount(Atom atom) how many times has atom been added (0 means atom is not in set
AtomSet	not(AtomSet atomSet) combines this with AtomSet to find elements NOT in AtomSet, else null.
AtomSet	or(AtomSet atomSet) combines this with AtomSet to find all elements.
void	setCoordinate2(Atom atom, Coordinate2 c) set coordinates for atom
java.lang.String	toString()
void	transform(Transform2 t2) transform coordinates of all atoms in the set (rather inefficient)
void	translateBy(Real2 offset) translate coordinates of all atoms in the set
AtomSet	xor(AtomSet atomSet) combines this with AtomSet to find elements NOT in common, else null.

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

coordinate2Map

protected java.util.HashMap coordinate2Map

Constructor Detail

AtomSetImpl

public AtomSetImpl()

Method Detail

addAtom

public void addAtom(Atom atom)
             throws CMLException

add an atom. If atom already present, increments count

Specified by:

addAtom in interface AtomSet

addBond

public void addBond(Bond bond)
             throws CMLException

adds both atoms in the bond

Specified by:

addBond in interface AtomSet

and

public AtomSet and(AtomSet atomSet)
            throws CMLException

combines this with AtomSet to find common elements, else null.

Specified by:

and in interface AtomSet

xor

public AtomSet xor(AtomSet atomSet)
            throws CMLException

combines this with AtomSet to find elements NOT in common, else null.

Specified by:

xor in interface AtomSet

not

public AtomSet not(AtomSet atomSet)
            throws CMLException

combines this with AtomSet to find elements NOT in AtomSet, else null.

Specified by:

not in interface AtomSet

or

public AtomSet or(AtomSet atomSet)
           throws CMLException

combines this with AtomSet to find all elements.

Specified by:

or in interface AtomSet

getCount

public int getCount(Atom atom)

how many times has atom been added (0 means atom is not in set

Specified by:

getCount in interface AtomSet

clearCoordinate2

public void clearCoordinate2()

clear atom coordinate table

Specified by:

clearCoordinate2 in interface AtomSet

setCoordinate2

public void setCoordinate2(Atom atom,
                           Coordinate2 c)
                    throws CMLException

set coordinates for atom

Specified by:

setCoordinate2 in interface AtomSet

getCoordinate2

public Coordinate2 getCoordinate2(Atom atom)
                           throws CMLException

get coordinates for atom

Specified by:

getCoordinate2 in interface AtomSet

transform

public void transform(Transform2 t2)

transform coordinates of all atoms in the set (rather inefficient)

Specified by:

transform in interface AtomSet

translateBy

public void translateBy(Real2 offset)

translate coordinates of all atoms in the set

Specified by:

translateBy in interface AtomSet

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection