subroutine conf_compar(jcon,ib,iprot,nn,iscor,sbin,lprn)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
#ifdef MPI
      include "mpif.h"
      integer IERROR,ERRCODE,kolor,key,comm
      include "COMMON.MPI"
#endif
      include 'DIMENSIONS.COMPAR'
      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.CLASSES'
      include 'COMMON.GEO'
      include 'COMMON.ENERGIES'
      logical lprn,lprn1,lprn2,lsig_match
      integer ncont_frag(mmaxfrag),
     & icont_frag(2,maxcont,mmaxfrag),ncontsc,
     & icontsc(1,maxcont),nsccont_frag(mmaxfrag),
     & isccont_frag(2,maxcont,mmaxfrag)
      integer jcon,ib,iprot,iscor,nn,lat
      integer i,j,k,ik,kk,ind,icant,ncnat,nsec_match,nsec_nomatch,
     &  ishif1,ishif2,
     &  nc_match,ncon_match,ishif,iclass_con,ishifft_con,iclass_rms,
     &  iclass_q,ishifft_rms,ishiff,idig,iex,im
      integer isecstr(maxres)
      integer itemp(maxfrag)
      double precision rmscalc,rms,rmsnat,qwolynes
      double precision sig_frag(maxfrag)
      character*4 liczba
      character*64 sbin
      lprn1=lprn .and. print_contact
      lprn2=lprn .and. print_secondary
c      print *,"Enter conf_compar",jcon
      call angnorm12(rmsang,iprot)
      rmsang=rmsang*rad2deg
c      if (lprn) then
c        write (liczba,'(bz,i4.4)') jcon
c        open(ipdb,file=prefintin(:ilen(prefintin))//liczba//".pdb")
c        call pdbout(energy(jcon),titel)
c        write(iout,*) "Protein",iprot," conformation",jcon,
c     &    " nlevel",nlevel(iprot)
c      endif
c      if (lprn) then
c        write (iout,*) "CONF_COMPAR: Complete reference structure"
c        do i=1,nres
c          write(iout,'(i4,3f10.5)') i,(cref(j,i,iprot),j=1,3)
c        enddo
c      endif
c Level 1: check secondary and supersecondary structure
      call elecont(lprn2,ncont,icont,nnt,nct)
      call secondary2(lprn1,.false.,ncont,icont,isecstr,iprot)
      call contact(lprn2,ncontsc,icontsc,nnt,nct)
      if (lprn) write(iout,*) "Assigning electrostatic contacts"
      call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,
     &   icont_frag,mask_p(1,ib,iprot),ib,iprot)
      if (lprn) write(iout,*) "Assigning sidechain contacts"
      call contacts_between_fragments(lprn,3,ncontsc,icontsc,
     &   nsccont_frag,isccont_frag,mask_sc(1,ib,iprot),ib,iprot)
      do i=1,nlevel(iprot)
        do j=1,isnfrag(nlevel(iprot)+1,iprot)
          iclass1(j,i)=0
        enddo
      enddo
      do j=1,nfrag(1,iprot)
        ind = icant(j,j)
        if (lprn) then
          write (iout,'(80(1h=))') 
          write (iout,*) "Level",1," fragment",j
          write (iout,'(80(1h=))') 
        endif
        rmsfrag(j,1)=rmscalc(0,1,j,jcon,ib,iprot,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",
     &    " conformation",jcon," protein",iprot 
        ncnat=ncont_frag_ref(ind,ib,iprot)
c        write (iout,*) "before match_contact:",nc_fragm(j,1,ib,iprot),
c     &   nc_req_setf(j,1,ib,iprot)
        call match_secondary(j,isecstr,nsec_match,nsec_nomatch,
     &    sig_frag(j),ib,iprot,lprn)
        if (lprn) write (iout,*) "Fragment",j," nsec_match",
     &    nsec_match," nsec_nomatch",nsec_nomatch,
     &    " length",len_frag(j,1,ib,iprot)," min_len",
     &    frac_sec(ib,iprot)*len_frag(j,1,ib,iprot)," sig_frag",
     &     sig_frag(j)
        if (nsec_match.ge.frac_sec(ib,iprot)*len_frag(j,1,ib,iprot)) 
     &  then
          iclass1(j,1)=1
          if (lprn) write (iout,*) "Fragment",j,
     &      " has correct secondary structure"
        else if (nsec_nomatch.ge.
     &      frac_sec(ib,iprot)*len_frag(j,1,ib,iprot)/2) then
          iclass1(j,1)=4
          if (lprn) write (iout,*) "Fragment",j,
     &      " has wrong secondary structure"
        else
          iclass1(j,1)=0
          if (lprn) write (iout,*) "Fragment",j,
     &      " has grossly incorrect secondary structure"
        endif
        if (ielecont(j,1,ib,iprot).gt.0) then
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &     ncont_frag_ref(ind,ib,iprot),
     &     icont_frag_ref(1,1,ind,ib,iprot),
     &     ncont_frag(ind),icont_frag(1,1,ind),
     &     j,n_shift(1,j,1,ib,iprot),n_shift(2,j,1,ib,iprot),
     &     nc_fragm(j,1,ib,iprot),nc_req_setf(j,1,ib,iprot),
     &     istruct(j,ib,iprot),.true.,ib,iprot,lprn)
        else if (isccont(j,1,ib,iprot).gt.0) then
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &      nsccont_frag_ref(ind,ib,iprot),
     &      isccont_frag_ref(1,1,ind,ib,iprot),
     &      nsccont_frag(ind),isccont_frag(1,1,ind),j,
     &      n_shift(1,j,1,ib,iprot),n_shift(2,j,1,ib,iprot),
     &      nc_fragm(j,1,ib,iprot),
     &      nc_req_setf(j,1,ib,iprot),istruct(j,ib,iprot),.true.,ib,
     &      iprot,lprn)
        else if (iloc(j,ib,iprot).gt.0) then
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &      0,icont_frag_ref(1,1,ind,ib,iprot),ncont_frag(ind),
     &      icont_frag(1,1,ind),j,n_shift(1,j,1,ib,iprot),
     &      n_shift(2,j,1,ib,iprot),nc_fragm(j,1,ib,iprot),
     &      0,istruct(j,ib,iprot),.true.,ib,iprot,lprn)
        else
          ishif=0
          nc_match=1
        endif
        qfrag(j,1)=qwolynes(1,j,ib,iprot)
        if (iqwol(j,1,ib,iprot).gt.0) then
          if (qfrag(j,1).le.qcutfrag(j,1,ib,iprot)) then
            iclass_q = 2
          else
            iclass_q = 0
          endif
        else
          iclass_q = 2
        endif
        lsig_match=isig_match(j,ib,iprot).eq.0 .or. sig_frag(j).gt.0.0d0
        if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
        ishif=ishif1
        if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
        if (lprn) write (iout,*) "Ishift",ishif," nc_match",nc_match
c        write (iout,*) iprot,j," irms",irms(j,1,ib,iprot)
        if (irms(j,1,ib,iprot).gt.0) then
          if (rmsfrag(j,1).le.rmscutfrag(1,j,1,ib,iprot)) then
            iclass_rms=2
            ishifft_rms=0
          else
            ishiff=0
            rms=1.0d2
            iclass_rms=0
            do while (rms.gt.rmscutfrag(1,j,1,ib,iprot) .and.
     &         ishiff.lt.n_shift(1,j,1,ib,iprot))
              ishiff=ishiff+1
              rms=rmscalc(-ishiff,1,j,jcon,ib,iprot,lprn)
c              write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
c     &          " rms",rms," rmscut",rmscutfrag(1,j,1,ib,iprot)
              if (lprn) write (iout,*) "rms",rmsfrag(j,1)
              if (rms.gt.rmscutfrag(1,j,1,ib,iprot)) then
                rms=rmscalc(ishiff,1,j,jcon,ib,iprot,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,ib,iprot)
c            write (iout,*) "iclass_rms",iclass_rms
            if (rms.le.rmscutfrag(1,j,1,ib,iprot)) 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",iclass1(j,1),
c     &    " iclass_rms",iclass_rms
        if (iclass1(j,1).ne.4 .and. nc_match.gt.0 .and. 
     &      iclass_rms.gt.0 .and. iclass_q.gt.0 .and. lsig_match) then
          if (ishif.eq.0) then
            iclass1(j,1)=iclass1(j,1)+6
          else
            iclass1(j,1)=iclass1(j,1)+2
          endif
        endif
        ncont_nat(1,j,1)=nc_match
        ncont_nat(2,j,1)=ncon_match
        ishifft(j,1)=ishif
      enddo
c Next levels: Check arrangements of elementary fragments.
      do i=2,nlevel(iprot)
        do j=1,nfrag(i,iprot)
        if (i .eq. 2) ind = icant(ipiece(1,j,i,ib,iprot),
     &    ipiece(2,j,i,ib,iprot))
        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.
c 3/4/03 AL No, we consider the existence of a composite fragment even if
c the corresponding elementary fragments are incomplete.
c
c        do k=1,npiece(j,i,ib,iprot)
c          ik=ipiece(k,j,i,ib,iprot)
c          if (iclass1(ik,1).eq.0) then
c            iclass1(j,i)=0
c            goto 12
c          endif
c        enddo
        if (i.eq.2 .and. ielecont(j,i,ib,iprot).gt.0) then
          iclass_con=0
          ishifft_con=0
          if (lprn) write (iout,*) 
     &     "Comparing electrostatic contact map: fragments",
     &      ipiece(1,j,i,ib,iprot),ipiece(2,j,i,ib,iprot)," ind",ind
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &     ncont_frag_ref(ind,ib,iprot),
     &     icont_frag_ref(1,1,ind,ib,iprot),
     &     ncont_frag(ind),icont_frag(1,1,ind),
     &     j,n_shift(1,j,i,ib,iprot),n_shift(2,j,i,ib,iprot),
     &     nc_fragm(j,i,ib,iprot),
     &     nc_req_setf(j,i,ib,iprot),2,.false.,ib,iprot,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,ib,iprot).gt.0) then
          iclass_con=0
          ishifft_con=0
          if (lprn) write (iout,*) 
     &     "Comparing sidechain contact map: fragments",
     &    ipiece(1,j,i,ib,iprot),ipiece(2,j,i,ib,iprot)," ind",ind
          call match_contact(ishif1,ishif2,nc_match,ncon_match,
     &     nsccont_frag_ref(ind,ib,iprot),
     &     isccont_frag_ref(1,1,ind,ib,iprot),
     &     nsccont_frag(ind),isccont_frag(1,1,ind),
     &     j,n_shift(1,j,i,ib,iprot),n_shift(2,j,i,ib,iprot),
     &     nc_fragm(j,i,ib,iprot),
     &     nc_req_setf(j,i,ib,iprot),2,.false.,ib,iprot,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) then
          qfrag(j,2)=qwolynes(2,j,ib,iprot)
          if (iqwol(j,i,ib,iprot).gt.0) then
            if (qfrag(j,2).le.qcutfrag(j,2,ib,iprot)) then
              iclass_q = 2
            else
              iclass_q = 0
            endif
          else
            iclass_q = 2
          endif
        else
          iclass_q = 2
        endif
        if (irms(j,i,ib,iprot).gt.0) then
          iclass_rms=0
          ishifft_rms=0
          if (lprn) write (iout,*) 
     &     "Comparing rms: fragments",
     &     (ipiece(k,j,i,ib,iprot),k=1,npiece(j,i,ib,iprot))
          rmsfrag(j,i)=rmscalc(0,i,j,jcon,ib,iprot,lprn)
          if (lprn) write (iout,*) "rms",rmsfrag(j,i),
     &      " rmscut",rmscutfrag(1,j,i,ib,iprot)
          if (rmsfrag(j,i).le.rmscutfrag(1,j,i,ib,iprot)) then
            iclass_rms=2
            ishifft_rms=0
          else
            ishif=0
            rms=1.0d2
            do while (rms.gt.rmscutfrag(1,j,i,ib,iprot) .and. 
     &         ishif.lt.n_shift(1,j,i,ib,iprot))
              ishif=ishif+1
              rms=rmscalc(-ishif,i,j,jcon,ib,iprot,lprn)
              if (lprn) write (iout,*) "rms",rms,
     &          " rmscut",rmscutfrag(1,j,i,ib,iprot)
c              print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
              if (rms.gt.rmscutfrag(1,j,i,ib,iprot)) then
                rms=rmscalc(ishif,i,j,jcon,ib,iprot,lprn)
c                print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
              endif
              if (lprn) write (iout,*) "rms",rms,
     &          " rmscut",rmscutfrag(1,j,i,ib,iprot)
            enddo
            if (rms.le.rmscutfrag(1,j,i,ib,iprot)) then
              ishifft_rms=ishif
              rmsfrag(j,i)=rms
              iclass_rms=1
            endif
          endif
        endif
        if (irms(j,i,ib,iprot).eq.0 .and. ielecont(j,i,ib,iprot).eq.0 
     &    .and. isccont(j,i,ib,iprot).eq.0 
     &    .and. iqwol(j,i,ib,iprot).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
          iclass1(j,i) = min0(iclass_con,iclass_rms,iclass_q)
          ishifft(j,i)= max0(ishifft_con,ishifft_rms)
        else if (i.gt.2) then
          iclass1(j,i) = iclass_rms
          ishifft(j,i)= ishifft_rms
        endif
   12   continue
        enddo
      enddo
      rms_nat=rmsnat(jcon,iprot)
      qnat=qwolynes(0,0,ib,iprot)
      if (lprn) write (iout,*) "rmsnat",rms_nat," qnat",qnat
C Compute the structural class
      iscor=0
      do i=1,nlevel(iprot)
        IF (I.EQ.1) THEN
        do j=1,nfrag(i,iprot)
          itemp(j)=iclass1(j,i)
        enddo
        do kk=-1,1
          do j=1,nfrag(i,iprot)
            idig = 2*isnfrag(nlevel(iprot)+1,iprot)-2*isnfrag(i,iprot)
     &        -kk*nfrag(i,iprot)-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",iclass1(j,i)," im",im
            if (.not.binary(iprot)) iscor=iscor+im*iex
            write (sbin(nn-idig:nn-idig),'(i1)') im
          enddo
        enddo
        ELSE
        do j=1,nfrag(i,iprot)
          idig = 2*isnfrag(nlevel(iprot)+1,iprot)-2*isnfrag(i,iprot)-j
          iex = 2**idig
          if (iclass1(j,i).gt.0) then
            im=1
          else
            im=0
          endif
c          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
c     &      " iclass",iclass1(j,i)," im",im
          if (.not. binary(iprot)) iscor=iscor+im*iex
          write (sbin(nn-idig:nn-idig),'(i1)') im
        enddo
        do j=1,nfrag(i,iprot)
          idig = 2*isnfrag(nlevel(iprot)+1,iprot)-2*isnfrag(i,iprot)
     &      -nfrag(i,iprot)-j
          iex = 2**idig
          if (iclass1(j,i).gt.1) then
            im=1
          else
            im=0
          endif
c          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
c     &      " iclass",iclass1(j,i)," im",im
          write (sbin(nn-idig:nn-idig),'(i1)') im
          if (.not. binary(iprot)) iscor=iscor+im*iex
        enddo
        ENDIF
      enddo
      if (lprn) then
      write (iout,'(i5,$)') jcon
      do i=1,nlevel(iprot)
        write (iout,'(i5,$)') i
        if (i.eq.1) then
        do j=1,nfrag(i,iprot)
          write (iout,'(2i4,f6.2,i3,$)') ncont_nat(1,j,i),
     &     ncont_nat(2,j,i),rmsfrag(j,i),ishifft(j,i)
        enddo
        else
        do j=1,nfrag(i,iprot)
          write (iout,'(f6.2,i3,$)') rmsfrag(j,i),ishifft(j,i)
        enddo
        endif
        write (iout,'(" ",$)')
        do j=1,nfrag(i,iprot)
          write (iout,'(i1,$)') iclass1(j,i)
        enddo
      enddo
      if (binary(iprot)) then
        write (iout,'("  ",$)')
        do j=1,nlevel(iprot)
          write (iout,'(100(i1,$))')(iclass1(k,j),k=1,
     &      nfrag(j,iprot),iprot)
          if (j.lt.nlevel(iprot)) write(iout,'(".",$)')
        enddo
        write (iout,'(f6.2)') rms_nat
      else
        write (iout,'(i10,f6.2)') iscor,rms_nat
      endif
      endif 

      if (print_class) then
          write(istat,'(i5,2f10.2,f8.3,2f6.3,$)') 
     &      jcon,eini(jcon,iprot),entfac(jcon,iprot),
     &      rms_nat,qnat,rmsang/(nct-nnt-2)
          do j=1,nlevel(iprot)
            write(istat,'(1x,20(i3,$))')
     &        (ncont_nat(1,k,j),k=1,nfrag(j,iprot))
            if (j.eq.1) write (istat,'(1x,f4.1,$)') 
     &        (sig_frag(k),k=1,nfrag(j,iprot))
            if (j.lt.3) then
              write (istat,'(1x,20(f5.1,f5.2,$))')
     &          (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j,iprot))
            else
              write(istat,'(1x,20(f5.1,$))')
     &          (rmsfrag(k,j),k=1,nfrag(j,iprot))
            endif
            write(istat,'(1x,20(i1,$))')
     &        (iclass1(k,j),k=1,nfrag(j,iprot))
          enddo
          if (binary(iprot)) then
            write (istat,'("  ",$)')
            do j=1,nlevel(iprot)
              write (istat,'(100(i1,$))')(iclass1(k,j),
     &           k=1,nfrag(j,iprot))
              if (j.lt.nlevel(iprot)) write(istat,'(".",$)')
            enddo
            write (istat,'(i10,i3)') iscore(jcon,0,iprot),ib
          else
            write (istat,'(2i10,i3)') iscor,iscore(jcon,0,iprot),ib
          endif
      endif
      RETURN
      END