! Module file: coord_to_sdb
!
! CNS module
! **********
!
! Authors: Axel Brunger and Paul Adams
!
! copyright Yale University
!
! Function:
!    Converts internal coordinate and molecular topology 
!    information to a site database
!
! Requirements:
!    The molecular topology and coordinates must be defined
!    The selection of which sites are active must be provided
!
module {coord_to_sdb}

(
sitedb;
use_array;
fix_array;
selection=(all);
)

set message ? end
evaluate ($message_old=$result)
set echo ? end
evaluate ($echo_old=$result)
if ( $log_level = verbose ) then
  set echo=on message=normal end
else
  set echo=off message=off end
end if

set display=? end
evaluate ($curr_display=$result)

checkversion 1.3

evaluate ($counter=1)

for $id in id ( &selection ) loop coor

  show (x) ( id $id )
  evaluate (&sitedb.x_$counter=$result)
  show (y) ( id $id )
  evaluate (&sitedb.y_$counter=$result)
  show (z) ( id $id )
  evaluate (&sitedb.z_$counter=$result)
  show (b) ( id $id )
  evaluate (&sitedb.b_$counter=$result)
  show (q) ( id $id )
  evaluate (&sitedb.q_$counter=$result)
  show (chemical) ( id $id )
  evaluate (&sitedb.type_$counter=$result)

  show (segid) ( id $id )
  evaluate (&sitedb.segid_$counter=$result)
  
  show (resid) ( id $id )
  evaluate (&sitedb.g_$counter=$result)

  show sum(1) ( segid &sitedb.segid_$counter and resid &sitedb.g_$counter )

  if ( $result <= 1 ) then
    evaluate (&sitedb.g_$counter="")
  end if

  show sum(1) ( &use_array and ( id $id ) )

  if ( $result = 1 ) then

    show sum(1) ( &fix_array and ( id $id ) )

    if ( $result = 1 ) then
      evaluate (&sitedb.action_$counter="fix")
    else
      evaluate (&sitedb.action_$counter="refine")
    end if
  else
    evaluate (&sitedb.action_$counter="ignore")
  end if

  evaluate (&sitedb.counter = $counter)
  evaluate ($counter=$counter+1)

end loop coor

set message=$message_old echo=$echo_old end