subroutine conf_compar(jcon,lprn,print_class)
      implicit real*8 (a-h,o-z)
#ifdef MPI
      include "mpif.h"
#endif
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'DIMENSIONS.COMPAR'
      include 'DIMENSIONS.FREE'
      include 'COMMON.CONTROL'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      include 'COMMON.PEPTCONT'
      include 'COMMON.CONTACTS1'
      include 'COMMON.HEADER'
      include 'COMMON.FREE'
      include 'COMMON.ENERGIES'
#ifdef MPI
      include 'COMMON.MPI'
#endif
      integer ilen
      external ilen
      logical lprn,print_class
      integer ncont_frag(mmaxfrag),
     & icont_frag(2,maxcont,mmaxfrag),ncontsc,
     & icontsc(1,maxcont),nsccont_frag(mmaxfrag),
     & isccont_frag(2,maxcont,mmaxfrag)
      integer isecstr(maxres)
      integer itemp(maxfrag)
      character*4 liczba
      double precision Epot
c      print *,"Enter conf_compar",jcon
      call angnorm12(rmsang)
c Level 1: check secondary and supersecondary structure
      call elecont(lprn,ncont,icont,nnt,nct)
      if (lprn) then
        write (iout,*) "elecont finished"
        call flush(iout)
      endif
      call secondary2(lprn,.false.,ncont,icont,isecstr)
      if (lprn) then
        write (iout,*) "secondary2 finished"
        call flush(iout)
      endif
      call contact(lprn,ncontsc,icontsc,nnt,nct)
      if (lprn) then
         write(iout,*) "Assigning electrostatic contacts"
         call flush(iout)
      endif
      call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,
     &   icont_frag)
      if (lprn) then
        write(iout,*) "Assigning sidechain contacts"
        call flush(iout)
      endif
      call contacts_between_fragments(lprn,3,ncontsc,icontsc,
     &   nsccont_frag,isccont_frag)
      if (lprn) then
        write(iout,*) "--> After contacts_between_fragments"
        call flush(iout)
      endif
      do i=1,nlevel
        do j=1,isnfrag(nlevel+1)
          iclass(j,i)=0
        enddo
      enddo
      do j=1,nfrag(1)
        ind = icant(j,j)
        if (lprn) then
          write (iout,'(80(1h=))') 
          write (iout,*) "Level",1," fragment",j
          write (iout,'(80(1h=))') 
        endif
        call flush(iout)
        rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
c Compare electrostatic contacts in the current conf with that in the native
c structure.
        if (lprn) write (iout,*) 
     &    "Comparing electrostatic contact map and local structure" 
        call flush(iout)
        ncnat=ncont_frag_ref(ind)
c        write (iout,*) "before match_contact:",nc_fragm(j,1),
c     &   nc_req_setf(j,1)
c        call flush(iout)
        call match_secondary(j,isecstr,nsec_match,lprn)
        if (lprn) write (iout,*) "Fragment",j," nsec_match",
     &    nsec_match," length",len_frag(j,1)," min_len",
     &    frac_sec*len_frag(j,1)
        if (nsec_match.lt.frac_sec*len_frag(j,1)) then
          iclass(j,1)=0
          if (lprn) write (iout,*) "Fragment",j,
     &      " has incorrect secondary structure"
        else
          iclass(j,1)=1
          if (lprn) write (iout,*) "Fragment",j,
     &      " has correct secondary structure"
        endif
        if (ielecont(j,1).gt.0) then
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &      ncont_frag_ref(ind),icont_frag_ref(1,1,ind),
     &      ncont_frag(ind),icont_frag(1,1,ind),
     &      j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
     &      nc_req_setf(j,1),istruct(j),.true.,lprn)
        else if (isccont(j,1).gt.0) then
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &      nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),
     &      nsccont_frag(ind),isccont_frag(1,1,ind),
     &      j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
     &      nc_req_setf(j,1),istruct(j),.true.,lprn)
        else if (iloc(j).gt.0) then
c          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &      0,icont_frag_ref(1,1,ind),
     &      ncont_frag(ind),icont_frag(1,1,ind),
     &      j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
     &      0,istruct(j),.true.,lprn)
c          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
        else
          ishif=0
          nc_match=1
        endif
        if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
        ishif=ishif1
        qfrag(j,1)=qwolynes(1,j)
        if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
        if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
c        write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
        if (irms(j,1).gt.0) then
          if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
            iclass_rms=2
            ishifft_rms=0
          else
            ishiff=0
            rms=1.0d2
            iclass_rms=0
            do while (rms.gt.rmscutfrag(1,j,1) .and. 
     &         ishiff.lt.n_shift(1,j,1))
              ishiff=ishiff+1
              rms=rmscalc(-ishiff,1,j,jcon,lprn)
c              write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
c     &          " rms",rms," rmscut",rmscutfrag(1,j,1)
              if (lprn) write (iout,*) "rms",rmsfrag(j,1) 
              if (rms.gt.rmscutfrag(1,j,1)) then
                rms=rmscalc(ishiff,1,j,jcon,lprn)
c                write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
c     &           " rms",rms
              endif
              if (lprn) write (iout,*) "rms",rmsfrag(j,1) 
            enddo
c            write (iout,*) "After loop: rms",rms,
c     &        " rmscut",rmscutfrag(1,j,1)
c            write (iout,*) "iclass_rms",iclass_rms
            if (rms.le.rmscutfrag(1,j,1)) then
              ishifft_rms=ishiff
              rmsfrag(j,1)=rms
              iclass_rms=1
            endif
c            write (iout,*) "iclass_rms",iclass_rms
          endif
c          write (iout,*) "ishif",ishif
          if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
        else
          iclass_rms=1
        endif
c        write (iout,*) "ishif",ishif," iclass",iclass(j,1),
c     &    " iclass_rms",iclass_rms
        if (nc_match.gt.0 .and. iclass_rms.gt.0) then
          if (ishif.eq.0) then
            iclass(j,1)=iclass(j,1)+6
          else
            iclass(j,1)=iclass(j,1)+2
          endif
        endif
        ncont_nat(1,j,1)=nc_match
        ncont_nat(2,j,1)=ncon_match
        ishifft(j,1)=ishif
c        write (iout,*) "iclass",iclass(j,1)
      enddo
c Next levels: Check arrangements of elementary fragments.
      do i=2,nlevel
        do j=1,nfrag(i)
        if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
        if (lprn) then
            write (iout,'(80(1h=))') 
            write (iout,*) "Level",i," fragment",j
            write (iout,'(80(1h=))') 
        endif
c If an elementary fragment doesn't exist, don't check higher hierarchy levels.
        do k=1,npiece(j,i)
          ik=ipiece(k,j,i)
          if (iclass(ik,1).eq.0) then
            iclass(j,i)=0
            goto 12
          endif
        enddo
        if (i.eq.2 .and. ielecont(j,i).gt.0) then
          iclass_con=0
          ishifft_con=0
          if (lprn) write (iout,*) 
     &     "Comparing electrostatic contact map: fragments",
     &      ipiece(1,j,i),ipiece(2,j,i)," ind",ind
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &     ncont_frag_ref(ind),icont_frag_ref(1,1,ind),
     &     ncont_frag(ind),icont_frag(1,1,ind),
     &     j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),
     &     nc_req_setf(j,i),2,.false.,lprn)
          ishif=ishif1
          if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
          if (nc_match.gt.0) then
            if (ishif.eq.0) then
              iclass_con=2
            else
              iclass_con=1
            endif
          endif
          ncont_nat(1,j,i)=nc_match
          ncont_nat(2,j,i)=ncon_match
          ishifft_con=ishif
        else if (i.eq.2 .and. isccont(j,i).gt.0) then
          iclass_con=0
          ishifft_con=0
          if (lprn) write (iout,*) 
     &     "Comparing sidechain contact map: fragments",
     &    ipiece(1,j,i),ipiece(2,j,i)," ind",ind
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &     nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),
     &     nsccont_frag(ind),isccont_frag(1,1,ind),
     &     j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),
     &     nc_req_setf(j,i),2,.false.,lprn)
          ishif=ishif1
          if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
          if (nc_match.gt.0) then
            if (ishif.eq.0) then
              iclass_con=2
            else
              iclass_con=1
            endif
          endif
          ncont_nat(1,j,i)=nc_match
          ncont_nat(2,j,i)=ncon_match
          ishifft_con=ishif
        else if (i.eq.2) then
          iclass_con=2
          ishifft_con=0
        endif
        if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
        if (lprn) write (iout,*) 
     &    "Comparing rms: fragments",
     &     (ipiece(k,j,i),k=1,npiece(j,i))
        rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
        if (irms(j,i).gt.0) then
          iclass_rms=0
          ishifft_rms=0
          if (lprn) write (iout,*) "rms",rmsfrag(j,i)
c          write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
c     &     " rmscutfrag",rmscutfrag(1,j,i)
          if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
            iclass_rms=2
            ishifft_rms=0
          else
            ishif=0
            rms=1.0d2
            do while (rms.gt.rmscutfrag(1,j,i) .and. 
     &         ishif.lt.n_shift(1,j,i))
              ishif=ishif+1
              rms=rmscalc(-ishif,i,j,jcon,lprn)
c              print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
              if (lprn) write (iout,*) "rms",rmsfrag(j,i) 
              if (rms.gt.rmscutfrag(1,j,i)) then
                rms=rmscalc(ishif,i,j,jcon,lprn)
c                print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
              endif
              if (lprn) write (iout,*) "rms",rms
            enddo
            if (rms.le.rmscutfrag(1,j,i)) then
              ishifft_rms=ishif
              rmsfrag(j,i)=rms
              iclass_rms=1
            endif
          endif
        endif
        if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. 
     &    isccont(j,i).eq.0 ) then
          write (iout,*) "Error: no measure of comparison specified:",
     &      " level",i," part",j
          stop
        endif
        if (lprn) 
     &  write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
        if (i.eq.2) then
          iclass(j,i) = min0(iclass_con,iclass_rms)
          if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
            ishifft(j,i)=ishifft_rms
          else
            ishifft(j,i)=ishifft_con
          endif
        else if (i.gt.2) then
          iclass(j,i) = iclass_rms
          ishifft(j,i)= ishifft_rms
        endif
   12   continue
        enddo
      enddo
      rms_nat=rmsnat(jcon)
      qnat=qwolynes(0,0)
C Compute the structural class
      iscor=0
      IF (.NOT. BINARY) THEN
      do i=1,nlevel
        IF (I.EQ.1) THEN
        do j=1,nfrag(i)
          itemp(j)=iclass(j,i)
        enddo
        do kk=-1,1
          do j=1,nfrag(i)
            idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
            iex = 2**idig
            im=mod(itemp(j),2)
            itemp(j)=itemp(j)/2
c            write (iout,*) "i",i," j",j," idig",idig," iex",iex,
c     &        " iclass",iclass(j,i)," im",im
            iscor=iscor+im*iex
          enddo
        enddo
        ELSE
        do j=1,nfrag(i)
          idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
          iex = 2**idig
          if (iclass(j,i).gt.0) then
            im=1
          else
            im=0
          endif
c          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
c     &      " iclass",iclass(j,i)," im",im
          iscor=iscor+im*iex
        enddo
        do j=1,nfrag(i)
          idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
          iex = 2**idig
          if (iclass(j,i).gt.1) then
            im=1
          else
            im=0
          endif
c          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
c     &      " iclass",iclass(j,i)," im",im
          iscor=iscor+im*iex
        enddo
        ENDIF
      enddo
      iscore=iscor
      ENDIF
      if (print_class) then
#ifdef MPI
          write(istat,'(i6,$)') jcon+indstart(me)-1
          write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),
     &     -entfac(jcon)
#else
          write(istat,'(i6,$)') jcon
          write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),
     &      -entfac(jcon)
#endif
          write (istat,'(f8.3,2f6.3,$)') 
     &      rms_nat,qnat,rmsang/(nres-3)
          do j=1,nlevel
            write(istat,'(1x,$,20(i3,$))')
     &        (ncont_nat(1,k,j),k=1,nfrag(j))
            if (j.lt.3) then
              write(istat,'(1x,$,20(f5.1,f5.2$))')
     &          (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
            else
              write(istat,'(1x,$,20(f5.1$))')
     &          (rmsfrag(k,j),k=1,nfrag(j))
            endif
            write(istat,'(1x,$,20(i1,$))')
     &        (iclass(k,j),k=1,nfrag(j))
          enddo
          if (binary) then
            write (istat,'("  ",$)')
            do j=1,nlevel
              write (istat,'(100(i1,$))')(iclass(k,j),
     &           k=1,nfrag(j))
              if (j.lt.nlevel) write(iout,'(".",$)')
            enddo
            write (istat,*)
          else
            write (istat,'(i10)') iscore
          endif
      endif
      RETURN
      END