! Module file: write_sdb
!
! CNS module
! ************
!
! Authors: Axel Brunger and Paul Adams
!
! copyright Yale University
!
! Function:
!    Writes out a CNS heavy atom database file
!
! Requirements:
!    The molecular topology and coordinates must be defined

module {write_sdb}

(
&sitedb;
&sg;
&output=OUTPUT;
)

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

set display=&output end

display
display {- begin block parameter definition -} define(
display

eval($tmp_sg = """ + &sg + """)

display {============================ space group ============================}
display
display {* space group *}
display {* use International Table conventions with subscripts substituted
display    by parenthesis *}
display {===>} sg=$tmp_sg;
display

display {==================== derivative/MAD coordinates =====================}
display
display {+ list: for each site define:
display          - whether the site is to be refined, fixed or ignored
display          - derivative name (must be the same for all sites in a derivative)
display          - chemical type (note: wavelength-dependent form factors
display                                 are specified in mad_refine.inp)
display          - coordinates (x, y, z)
display          - B-value (b)
display          - occupancy (q)
display          - group name (g) +}
display
display {+ list: the optional group name (g) is a string of upto 4 characters.
display          If a group is left blank, each site is refined individually.
display          If a group is specified, all sites with the same group name
display          and the same derivative name are treated as a rigid body, and their
display          occupancies, B-values, and form factors are refined as a group. +}
display

if (&EXIST%sitedb.counter = false) then
  display module error: sitedb.counter not defined.
  abort
end if

display {+ table: rows=&sitedb.counter numbered
display           cols=9 "action" "derivative name" "chemical type"
display                  "x coordinate" "y coordinate" "z coordinate"
display                  "B-value" "occupancy" "group" +}
display

evaluate ($n=1)

while ( $n <= &sitedb.counter ) loop site

  evaluate ($tmp_action=""" + &sitedb.action_$n + """)
  evaluate ($tmp_segid=""" + &sitedb.segid_$n + """)
  evaluate ($tmp_type=""" + &sitedb.type_$n + """)
  evaluate ($tmp_group=""" + &sitedb.g_$n + """)

  display {+ choice: "refine" "fix" "ignore" +}
  display {===>} site.action_$n=$tmp_action;
  display {===>} site.segid_$n=$tmp_segid; site.type_$n=$tmp_type;
  display {===>} site.x_$n=&sitedb.x_$n; site.y_$n=&sitedb.y_$n; site.z_$n=&sitedb.z_$n;
  display {===>} site.b_$n=&sitedb.b_$n; site.q_$n=&sitedb.q_$n; site.g_$n=$tmp_group;
  display

  evaluate ($n=$n+1)

end loop site

display {* to appended new entries or merge this file with other
display    site database files use sdb_manipulate.inp *}
display
display {* to delete sites from this file either set the derivative
display    name to be blank or use delete_sites.inp *}
display
display {===========================================================================}
display {         things below this line do not normally need to be changed         }
display {===========================================================================}
display
display ) {- end block parameter definition -}
display

set display=$curr_display end

set message=$message_old echo=$echo_old end