! Module file: coordinaterefine
!
! CNS module
! **********
!
! Authors: Piet Gros and Axel T. Brunger
!
! copyright Yale University
!
! Function:
! Refine coordinates against generalized target function
!
! Requirements:
! 0. definetarget must be called before this module. 
! 1. This module can only be called from the main level.
! 2. Target and derivative function have to be defined fully
!    see module definetarget
! 

module {coordinaterefine}
(
   &table;     {identifying text for tabulation}
   &messages;  {set verbosity "normal" | "all" | "off"}
   &tolerance; {tolerance for conjugate gradient minimizer}
   &step;      {number of steps in minimization}
   &h;         {atom selection contributing to Fcalc}  
   &hfix;      {atom subselection of &h whose parameters are not refined}
)

checkversion 1.3

{- set fixed atoms -}
fix
  selection=(not &h or &hfix)
end
do (refx=x) (&h)     {- store starting coordinates -}
do (refy=y) (&h)
do (refz=z) (&h)

show sum ( x ) ( not (tag and &h and not(&hfix)) and (&h and not(&hfix) ))
if ($select>0) then
   display TAB: &table groups present -- groups will be refined as rigid bodies.  
   minimize rigid
      for $aa in id (tag and &h and not(&hfix)) loop bref
         group=(byresidue ( id $aa ) ) 
      end loop bref 
      nstep=&step 
      drop=10.
      tolerance=&tolerance
   end
else
   display TAB: &table individual site refinement
   minimize lbfgs
      nstep=&step 
!!!      drop=10.
      tolgradient=&tolerance
   end
end if


{*fill table*}

if (&table # "") then                                {fill table with shift}
   for $1 in id (&h and not(&hfix)) loop minc_shift {parameters}
      show (x-refx) (id $1)
      evaluate ($x=$result)
      show (y-refy) (id $1)
      evaluate ($y=$result)
      show (z-refz) (id $1)
      evaluate ($z=$result)
      show element (segid ) (id $1)
      evaluate ($segid=$result)
      show element (resid ) (id $1)
      evaluate ($resid=$result)
      show element (name ) (id $1)
      evaluate ($name=$result)
display TAB: &table atom=($segid $resid $name) coord.-shift (dx,dy,dz)= $x[F9.2] $y[F9.2] $z[F9.2]
   end loop minc_shift
end if

{*update stored coordinates*}

do (refx=x) (&h)
do (refy=y) (&h)
do (refz=z) (&h)