package etomica;

import etomica.atom.AtomList;

/**
 * General class for assignment of coordinates to a group of atoms.
 */
 
 /* History of changes
  * 09/01/02 (DAK) added field to flag whether total momentum should be set to
  * zero when initalizing (made in conjunction with change to Space.
  * CoordinateGroup classes, which no longer do randomizeMomentum to zero total
  * momentum). 
  * 09/04/02 (DAK) added Null inner class and NULL field
  * 01/21/04 (DAK) added initializeCoordinate(Phase) method
  */
public abstract class Conformation {

    public Conformation(Space space) {
        this.space = space;
    }

    public abstract void initializePositions(AtomList atomList);

    protected final Space space;
}//end of Configuration

@@ -117,404 +117,390 @@
 oms.
-%0A */%0A 
+  Puts
 %0A 
-/
 * 
-History of changes%0A  * 09/01/02 (DAK) added field to flag whether total momentum should be set to%0A  * zero when initalizing (made in conjunction with change to Space.%0A  * CoordinateGroup classes, which no longer do randomizeMomentum to zero total%0A  * momentum). %0A  * 09/04/02 (DAK) added Null inner class and NULL field%0A  * 01/21/04 (DAK) added initializeCoordinate(Phase) method%0A 
+a list of atoms in a standard conformation, which then can be manipulated%0A * further by a Configuration class to place the molecules in a phase, or by%0A * a super-conformation class that arranges these atoms with other ones in a %0A * molecule.%3Cbr%3E  %0A * This class is used by an AtomFactory to arrange into a standard configuration%0A * each atom group that it builds.  %0A
  */%0A
+ %0A
 publ
@@ -615,101 +615,414 @@
     
-public abstract void initializePositions(AtomList atomList);%0A%0A    protected final Space space
+/**%0A     * Defined by subclass to assign coordinates to the atoms in the given list.%0A     */%0A    public abstract void initializePositions(AtomList atomList);%0A%0A    protected final Space space;%0A    %0A    /**%0A     * Conformation that does nothing to the atom positions.%0A     */%0A    public final static Conformation NULL = new Conformation(null) %7B%0A        public void initializePositions(AtomList list) %7B%7D%0A    %7D
 ;%0A%7D/

add static NULL subclass that does nothing to conformation improve commenting