############################################################
#
#   This file contains procedures to join compounds of atoms that are
# wrapped around unit cell boundaries.
#
# $Id$
#

package provide pbctools 2.0

namespace eval ::PBCTools:: {
    namespace export pbc*
    ############################################################
    #
    # pbcjoin $compound [OPTIONS...]
    #
    #   Joins compounds of type $compound of atoms that have been
    # split due to wrapping around the unit cell boundaries, so that
    # they are not split anymore. $compound must be one of the values
    # "residue", "chain", "segment" or "bonded".
    # 
    # OPTIONS:
    #   -molid $molid|top   the molecule to use (default: top)
    #   -first $first|first|now 
    #                       the first frame to use (default: now)
    #   -last $last|last|now
    #                       the last frame to use (default: now)
    #   -all|allframes      equivalent to "-first first -last last"
    #   -now                equivalent to "-first now -last now"
    #   -sel $sel           the selection of atoms to be joined
    #                       (default: all)
    #   -noref|-ref $sel    the reference atom in the compound: 
    #
    # AUTHOR: Olaf
    #
    proc pbcjoin { compound args } {
	# loop over all frames
	#   loop over all compounds
	#     get the coordinates of all atoms in the compound
	#     get the coordinates of the reference atom in the compound
	#     wrap the coordinates of the compound into the box
	#      centered around the reference atom
    }

}