# Copyright (c) 2002-20 Peter Guentert. All rights reserved.
## 7MACROS: cyclicbond - CYANA macro
##
## Parameters: first=<integer>                (default: first residue)
##             second=<integer>               (default: last residue)
##
## Creates upper and lower limit distance restraints to constrain a
## cyclic peptide bond between the <first> and <second> amino acid
## residue.

var info echo i j res res1 res2

syntax name=*=cyclic first=*=$rnum(1) second=*=$rnum(nr) weight=@r=5.0

info:=none; echo:=off

tmp:=c$getpid
#aas:='LEU GLY ALA VAL ILE PRO SER THR GLU ASP GLN ASN LYS ARG HIS PHE TYR TRP MET CYS'
aas:='LEU GLY ALA VAL ILE PRO SER THR GLU ASP GLN ASN LYS ARG HIS PHE TYR TRP MET CYS AIB SAR ORN ACE BPY'
in=iatom('NE $first')
if (in.le.0) error "No atom NE in residue $first."
ic=iatom('C $second')
if (ic.le.0) error "No atom C in residue $second."
rn1=rnam(iar(in))
rn2=rnam(iar(ic))


write seq demo.seq
print >>demo.seq
print "link NE $first C $second" >>.

#print "$first $rn1 NE  $second $rn2 C   1.33 $weight" >>link.upl
#print "$first $rn1 QE $second $rn2 C   2.00 $weight" >>link.upl
#print "$first $rn1 CA  $second $rn2 C   2.43 $weight" >>link.upl
#print "$first $rn1 NE  $second $rn2 CA  2.53 $weight" >>link.upl
#print "$first $rn1 NE  $second $rn2 O   2.25 $weight" >>link.upl

print "$second $rn2 C   $first  $rn1 NE  1.33 $weight" >>link.upl
print "$second $rn2 C   $first  $rn1 QE  2.00 $weight" >>link.upl
print "$second $rn2 C   $first  $rn1 CD  2.43 $weight" >>link.upl
print "$second $rn2 CA  $first  $rn1 NE  2.42 $weight" >>link.upl
print "$second $rn2 CA  $first  $rn1 QE  2.53 $weight" >>link.upl
print "$second $rn2 O   $first  $rn1 NE  2.25 $weight" >>link.upl
print "$second $rn2 O   $first  $rn1 QE  3.11 $weight" >>link.upl



print >>.
remove $tmp.seq
read seq demo.seq
read upl link.upl
write upl link.upl
read lol link.upl
write lol link.lol

unset info
print "    Restraints for cyclic peptide bond between residues $first and $second added."