# Copyright (c) 2002-08 Peter Guntert. All rights reserved.
## 7MACROS: dinucleotide - CYANA macro
##
## Parameters: range=<integer range>          (default: <all residues>)
##             tfcut=<real>                   (default: 0.0)
##             continue
##
## Performs grid searches for all dinucleotide fragments in the given range.
## If the cutoff value for the local, fragment-based target function, fmax,
## is positive, then all conformations with a local target function value
## below fmax will be considered as allowed. Otherwise, i.e. if fmax = 0.0, a
## conformation will be allowed if no single restraint violation exceeds the
## corresponding cutoff value defined by the variables soft_upl, soft_lol,
## etc. Unless the continue option is set, the allowed ranges of dihedral
## angles will be initialized to allow all possible angle values before the
## grid searches are started.
## The results include dihedral angle restraints and, if possible,
## stereospecific assignments for the diastereotopic groups in the fragment.

var echo info aas ires n rnu1 rnu2 rna1 rna2

syntax $macro:range=@ii=$rnum(1)..$rnum(nr) tfcut=@r=0.0 continue

echo:=off; info:=none
aas:='ADE THY GUA CYT RADE RGUA RCYT URA'

print
if (.not.continue) grid memory A=.true. selection=*
do ires 1 nr-1
  rnu1=rnum(ires); rnu2=rnum(ires+1)
  rna1=rnam(ires); rna2=rnam(ires+1)
  if (rnu1.ge.range(1) .and. rnu2.le.range(2) .and. \
      index(aas,rna1).gt.0 .and. index(aas,rna2).gt.0) then
    print "    $rna1 $rnu1 - $rna2 $rnu2:"
    grid fragment "DELTA NU2 NU1 CHI EPSI $rnu1"
    sugarring
    info:=normal
    stereoassign tfcut=$tfcut
    info:=none
    grid fragment "BETA GAMMA DELTA NU2 NU1 CHI $rnu2"
    sugarring
    info:=normal
    stereoassign tfcut=$tfcut
    info:=none
    grid fragment "DELTA NU2 NU1 EPSI $rnu1 + ZETA \
                  ALPHA BETA GAMMA DELTA NU2 NU1 $rnu2"
    sugarring $rnu1 $rnu2
    info:=normal
    stereoassign tfcut=$tfcut conformations=n
    info:=none
    if (n.gt.0) then
      grid fragment "DELTA NU2 NU1 CHI EPSI $rnu1 + ZETA \
                    ALPHA BETA GAMMA DELTA NU2 NU1 CHI $rnu2"
      sugarring $rnu1 $rnu2
      info:=normal
      stereoassign tfcut=$tfcut
      info:=none
    end if
  end if
end do
grid aco multiple