subroutine conf_compar(jcon,ib,iprot,nn,iscor,sbin,lprn)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      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