subroutine define_pairs
      implicit real*8 (a-h,o-z)
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'DIMENSIONS.FREE'
      include 'COMMON.IOUNITS'
      include 'COMMON.TIME1'
      include 'COMMON.SBRIDGE'
      include 'COMMON.CONTROL'
      include 'COMMON.COMPAR'
      include 'COMMON.FRAG'
      include 'COMMON.CHAIN'
      include 'COMMON.HEADER'
      include 'COMMON.GEO'
      include 'COMMON.CONTACTS1'
      include 'COMMON.PEPTCONT'
      do j=1,nfrag(1)
        length_frag = 0
        do k=1,npiece(j,1)
          length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
        enddo
        len_frag(j,1)=length_frag
        write (iout,*) "Fragment",j," length",len_frag(j,1)
      enddo
      nfrag(2)=0
      do i=1,nfrag(1)
        do j=i+1,nfrag(1)
          ind = icant(i,j)
          if (istruct(i).le.1 .or. istruct(j).le.1) then
            if (istruct(i).le.1) then
              ll1=len_frag(i,1)
            else
              ll1=len_frag(i,1)/2
            endif
            if (istruct(j).le.1) then
              ll2=len_frag(j,1)
            else
              ll2=len_frag(j,1)/2
            endif
            len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
          else
            if (istruct(i).eq.2 .or. istruct(i).eq.4) then
              ll1=len_frag(i,1)/2
            else
              ll1=len_frag(i,1) 
            endif
            if (istruct(j).eq.2 .or. istruct(j).eq.4) then
              ll2=len_frag(j,1)/2
            else
              ll2=len_frag(j,1) 
            endif
            len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
          endif
          write (iout,*) "Fragments",i,j," structure",istruct(i),
     &       istruct(j)," # contacts",
     &       ncont_frag_ref(ind),nsccont_frag_ref(ind),
     &       " lengths",len_frag(i,1),len_frag(j,1),
     &       " ll1",ll1," ll2",ll2," len_cut",len_cut
          if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and.
     &      nsccont_frag_ref(ind).ge.len_cut ) then
            if (istruct(i).eq.1 .and. istruct(j).eq.1) then
              write (iout,*) "Adding pair of helices",i,j,
     &        " based on SC contacts"
            else
              write (iout,*) "Adding helix+strand/sheet pair",i,j,
     &        " based on SC contacts"
            endif
            nfrag(2)=nfrag(2)+1
            if (icont_pair.gt.0) then
              write (iout,*)  "# SC contacts will be used",
     &        " in comparison."
              isccont(nfrag(2),2)=1
            endif
            if (irms_pair.gt.0) then
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
              irms(nfrag(2),2)=1
            endif
            npiece(nfrag(2),2)=2
            ipiece(1,nfrag(2),2)=i
            ipiece(2,nfrag(2),2)=j
            ielecont(nfrag(2),2)=0
            n_shift(1,nfrag(2),2)=nshift_pair
            n_shift(2,nfrag(2),2)=nshift_pair
            nc_fragm(nfrag(2),2)=ncfrac_pair
            nc_req_setf(nfrag(2),2)=ncreq_pair
          else if ((istruct(i).ge.2 .and. istruct(i).le.4)
     &       .and. (istruct(j).ge.2 .and. istruct(i).le.4)
     &       .and. ncont_frag_ref(ind).ge.len_cut ) then
            nfrag(2)=nfrag(2)+1
            write (iout,*) "Adding pair strands/sheets",i,j,
     &        " based on pp contacts"
            if (icont_pair.gt.0) then
              write (iout,*) "# pp contacts will be used",
     &        " in comparison."
              ielecont(nfrag(2),2)=1
            endif
            if (irms_pair.gt.0) then
              write (iout,*)  "Fragment RMSD will be used",
     &        " in comparison."
              irms(nfrag(2),2)=1
            endif
            npiece(nfrag(2),2)=2
            ipiece(1,nfrag(2),2)=i
            ipiece(2,nfrag(2),2)=j
            ielecont(nfrag(2),2)=1
            isccont(nfrag(2),2)=0
            n_shift(1,nfrag(2),2)=nshift_pair
            n_shift(2,nfrag(2),2)=nshift_pair
            nc_fragm(nfrag(2),2)=ncfrac_bet
            nc_req_setf(nfrag(2),2)=ncreq_bet
          endif
        enddo
      enddo
      write (iout,*) "Pairs found"
      do i=1,nfrag(2)
        write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
      enddo
      return
      end