! Module file: setupfixed
!
! CNS module
! **********
!
! Authors: Axel Brunger
!
! copyright Yale University
!
! Function:
!
!    Sets up fixed atom selection and
!    performs various checks for 
!    1. isolated atoms
!    2. isolated di-atomic molecules
!    3. atoms at special positions
!
!    Adds isolated atoms, diatomic molecules, and/or special-position atoms to the
!    fixed atom selection.
!
! Requirements:
!    Needs to be called from cns main level

module {setupfixed}

(
  &mode;              {string}                 {"minimization", "cartesian", "torsion"}
  &atom_select;       {selection }             {input: all selected atoms for refinement}
  &atom_fixed;        {selection }             {input: explicitly fixed atoms}
  &atom_total_fixed;  {atomic property array } {output: all fixed atoms}
  &atom_multiplicity; {atomic property array } {output: multiplicity of atoms}
  &mset=$mset;        {symbol}                 {output: number of disconnected sets}
  
)

!
!MODIFICATION: set message level to on for show statements, ATB 10/18/10
!
 
 set message ? end
 evaluate ($message_old_fix=$result)
 set echo ? end
 evaluate ($echo_old_fix=$result)
 if ( $log_level = verbose ) then
   set echo=on message=normal end
 else
   set echo=off message=off end
 end if
 
 checkversion 1.3

 connectivity
    selection=( &atom_select and not &atom_fixed ) 
    nsetto=&atom_total_fixed {- stores the size of each disconnected set -}
 end
 
 evaluate (&mset=$mset) {- symbol $mset is returned by connectivity -}

 display
 display  list of isolated (non-covalently bonded) atoms:
 set message=on end
 show element ( name ) ( attribute &atom_total_fixed = 1 )
 set message=off end
 if ($select=0) then
       display  --none--
 end if

 display
 display  list of isolated (non-covalently bonded) di-atomic molecules:
 set message=on end
 show element ( name ) ( attribute &atom_total_fixed = 2 )
 set message=off end
 if ($select=0) then
       display  --none--
 end if
 
 
 {- check for special positions -}
 xray
    special
       selection=( &atom_select ) 
       to=&atom_multiplicity
    end
 end
 
 display
 display  list of atoms at special positions:
 set message=on end
 show element ( name ) ( attribute &atom_multiplicity > 1 ) 
 set message=off end
 if ($select=0) then
    display  --none--
 end if
 
 display
 display 
 {- check to make sure that none of the atoms at 
    special positions have covalent bonds -}
 set message=on end
 show elem ( name ) ( ( attribute &atom_multiplicity > 1 ) and
                      ( attribute &atom_total_fixed > 1 ) )
 set message=off end
 if ($select > 0) then
    display  The above atoms are at special positions. They have covalent bonds
    display  This is presently not allowed for refinement in CNS 
    abort
 end if
 
 display
 
 if ( &mode = "torsion" ) then
 
 {- for torsion angle dynamics fix isolated atoms, atoms at special positions
    and explicitly fixed atoms -}
    
    ident (&atom_total_fixed) ( ( attribute &atom_total_fixed = 1 ) or
                                ( attribute &atom_total_fixed = 2 ) or
                                ( attribute &atom_multiplicity > 1 ) or
                                ( not ( &atom_select ) ) or
                                ( &atom_fixed ) )
                     
    display  $select isolated atoms, atoms in di-atomic molecules, 
    display  atoms at special positions, explicitly fixed atoms, 
    display  and atoms not selected for refinement will be fixed. 
    
 elseif ( &mode = "cartesian" ) then
 
 {- for cartesian dynamics just fix the special positions
    and the explicity fixed atoms -}
    
    ident (&atom_total_fixed) ( ( attribute &atom_multiplicity > 1 ) or
                                ( not( &atom_select ) ) or
                                ( &atom_fixed ) )
                     
    display  $select atoms at special positions, 
    display  explicitly fixed atoms, and atoms not selected for 
    display  refinement will be fixed. 

 elseif ( &mode = "minimization" ) then
 
 {- for minimization just fix the special positions and
    the explicitly fixed atoms -}
    
    ident (&atom_total_fixed) ( ( attribute &atom_multiplicity > 1 ) or
                                ( not( &atom_select ) ) or
                                ( &atom_fixed ) )

    display  $select atoms at special positions, 
    display  explicitly fixed atoms, and atoms not selected for 
    display  refinement will be fixed. 

 end if
 
 display

set message=$message_old_fix echo=$echo_old_fix end