select a subset of atoms

An atom selection consists of selection string and list of
corresponding atoms. The object emulates a Python sequence, so that
the selected <m atom>.Atoms can be accessed through the [] operator.
The selection language is the <l http://nmr.cit.nih.gov/xplor-nih/xplorMan/node38.html#SECTION003151000000000000000 
XPLOR atom selection language>. 
Note, however, that the outer parentheses are not necessary in AtomSel 
contruction. 



Constructor:

  AtomSel(string,simulation)
    string is a selection string in the XPLOR selection language.
    simulation is an optional <m simulation>.Simulation specification. 
    It defaults to the current Simulation.

    If there is an error in the selection string, an exception is raised.


methods:
	string()      return the selection string associated with this AtomSel.

	simulation()  return the simulation associated with the selection

	indices()     return list of atom indices associated with the selection

	setIndices(list)
		      manually set the list of atom indices.

	apply(apply_instance): 
                      invoke apply_instance's run() function on 
		      each atom in the selection. apply_instance is either 
		      an instance of a class defined in the <m atomSelAction>
    		      module, or a user-defined class which derives from the 
		      <m atomSelAction>.PyAtomSelAction class. Please see 
		      the documentation for the <m atomSelAction> module for
		      more information.

	reevaluate()  some selections depend on mutable properties 
		      like coordinates. This member reevaluates such a 
		      selection.

	containsIndex(index)
		     returns true if the selection includes the atom with the
		     specified index.

	containsAtom(atom)
		     returns true if the selection includes the specified atom.

functions:
   intersect(atomSel1,atomSel2)
       evaluates whether two AtomSels select one or more of the same atoms

   monomericallyEqual(atomSel1,atomSel2)
       evaluate whether two AtomSels select atoms with the same resid, 
       resname, and atom names, ignoring any difference in segid.

   minResidDiff(atomSel1,atomSel2)
       returns minimum number of residues between atoms in two AtomSels

   intersection(atomSel1,atomSel2)
       returns an AtomSel whose indices() consists of the intersection of 
       those of atomSel1 and atomSel2. This AtomSel cannot be reevaluated.

   union(atomSel1,atomSel2)
       returns an AtomSel whose indices() consists of the union of 
       those of atomSel1 and atomSel2. This AtomSel cannot be reevaluated.

   notSelection(sel)
       returns an AtomSel whose indices() consists of all those argument sel's 
       Simulation but, not in its indices().

Example

  print out positions of alpha carbons in residues 40-43, inclusive.

sel = AtomSel("name CA and resid 40:43")
for atom in sel:
  print sel.pos()