set mol [mol new propene.xyz waitfor all]
animate delete all
mol addfile propene.dcd waitfor all
mol bondsrecalc $mol

#pbc box -center origin

# part one
# select all molecules containing hydrogen
set sel [atomselect $mol {same fragment as name "H.+"}]

# get a list of atoms
set fragdata [$sel get {index fragment name}]

# now sort list of lists by fragment id to
# have atoms in the same fragment lumped together.
set fragdata [lsort -integer -index 1 $fragdata]
# add terminal dummy atom.
lappend fragdata {-1 -2 dummy}

set oldfrag -1
set idxlist {}
set tmplist {}

# loop over atoms 
foreach atom $fragdata {
  foreach {idx frag name} $atom {}
  # new fragment?
  if {$oldfrag != $frag} {
    # this will write out all 4 atom molecules containing hydrogens
    # XXX: this part of the loop will need to be adjusted to whatever
    # logic is needed to determine the atoms
    if {[llength $tmplist] == 4} {
       puts stderr "found 4-atom fragment $oldfrag with atoms $tmplist"
       set idxlist [concat $idxlist $tmplist]
    } else {
      if {$oldfrag >= 0} {
        puts stderr "ignoring fragment $oldfrag with atoms $tmplist"
      }
    }
    set tmplist {}
    set oldfrag $frag
  }
  lappend tmplist $idx
}
# we are done with this selection
$sel delete


# part two
# select all molecules containing carbon
set sel [atomselect $mol {same fragment as name "C.+"}]

# get a list of atoms
set fragdata [$sel get {index fragment name}]

# now sort list of lists by fragment id to
# have atoms in the same fragment lumped together.
set fragdata [lsort -integer -index 1 $fragdata]
# add terminal dummy atom.
lappend fragdata {-1 -2 dummy}

set oldfrag -1
set tmplist {}

# loop over atoms 
foreach atom $fragdata {
  foreach {idx frag name} $atom {}
  # new fragment?
  if {$oldfrag != $frag} {
    # this will write out all c atom molecules containing carbons
    # XXX: this part of the loop will need to be adjusted to whatever
    # logic is needed to determine the atoms
    if {[llength $tmplist] == 3} {
       puts stderr "found 3-atom fragment $oldfrag with atoms $tmplist"
       set idxlist [concat $idxlist $tmplist]
    } else {
      if {$oldfrag >= 0} {
        puts stderr "ignoring fragment $oldfrag with atoms $tmplist"
      }
    }
    set tmplist {}
    set oldfrag $frag
  }
  lappend tmplist $idx
}

# write out as pdb
set newsel [atomselect $mol "index $idxlist"]
$newsel writepdb selectedatoms.pdb

$sel delete
$newsel delete
mol delete $mol