org.xmlcml.tools
Interface AtomSet

All Known Implementing Classes:

AtomSetImpl

public interface AtomSet

extends ToolHashSet

a set of atoms. Counts number of times an atom has been added (e.g. for bonds). Will normally be implemented by HashSet.

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
void	transform(Transform2 t2) transform coordinates of all atoms in the set (rather inefficient) Works on original molecule - probably obsolete
void	translateBy(Real2 offset) translate coordinates of all atoms in the setWorks on original molecule - probably obsolete
AtomSet	xor(AtomSet atomSet) combines this with AtomSet to find elements NOT in common, else null.

Methods inherited from interface org.xmlcml.tools.ToolHashSet

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

Method Detail

addAtom

public void addAtom(Atom atom)
             throws CMLException

add an atom. If atom already present, increments count

addBond

public void addBond(Bond bond)
             throws CMLException

adds both atoms in the bond

and

public AtomSet and(AtomSet atomSet)
            throws CMLException

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

xor

public AtomSet xor(AtomSet atomSet)
            throws CMLException

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

not

public AtomSet not(AtomSet atomSet)
            throws CMLException

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

or

public AtomSet or(AtomSet atomSet)
           throws CMLException

combines this with AtomSet to find all elements.

getCount

public int getCount(Atom atom)

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

clearCoordinate2

public void clearCoordinate2()

clear atom coordinate table

setCoordinate2

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

set coordinates for atom

getCoordinate2

public Coordinate2 getCoordinate2(Atom atom)
                           throws CMLException

get coordinates for atom

transform

public void transform(Transform2 t2)

transform coordinates of all atoms in the set (rather inefficient) Works on original molecule - probably obsolete

translateBy

public void translateBy(Real2 offset)

translate coordinates of all atoms in the setWorks on original molecule - probably obsolete