source/wham/conform_compar.f90

   1       module conform_compar
   2 !-----------------------------------------------------------------------------
   3       use names
   4       use io_units
   5       use geometry_data, only:nres
   6       use math, only:pinorm
   7       use geometry, only:dist
   8       use regularize_, only:fitsq
   9 !
  10       use wham_data
  11 #ifndef CLUSTER
  12       use w_compar_data
  13 #endif
  14 #ifdef MPI
  15       use MPI_data
  16 !      include "COMMON.MPI"
  17 #endif
  18       implicit none
  19 !-----------------------------------------------------------------------------
  20 !
  21 !
  22 !-----------------------------------------------------------------------------
  23       contains
  24 #ifndef CLUSTER
  25 !-----------------------------------------------------------------------------
  26 ! conf_compar.F
  27 !-----------------------------------------------------------------------------
  28       subroutine conf_compar(jcon,lprn,print_class)
  29 !      implicit real*8 (a-h,o-z)
  30       use energy_data, only:icont,ncont,nnt,nct,maxcont!,&
  31 !                      nsccont_frag_ref,isccont_frag_ref
  32 #ifdef MPI
  33       include "mpif.h"
  34 #endif
  35 !      include 'DIMENSIONS'
  36 !      include 'DIMENSIONS.ZSCOPT'
  37 !      include 'DIMENSIONS.COMPAR'
  38 !      include 'DIMENSIONS.FREE'
  39 !      include 'COMMON.CONTROL'
  40 !      include 'COMMON.IOUNITS'
  41 !      include 'COMMON.COMPAR'
  42 !      include 'COMMON.CHAIN'
  43 !      include 'COMMON.INTERACT'
  44 !      include 'COMMON.VAR'
  45 !      include 'COMMON.PEPTCONT'
  46 !      include 'COMMON.CONTACTS1'
  47 !      include 'COMMON.HEADER'
  48 !      include 'COMMON.FREE'
  49 !      include 'COMMON.ENERGIES'
  50 !#ifdef MPI
  51 !      include 'COMMON.MPI'
  52 !#endif
  53 !      integer ilen
  54 !      external ilen
  55       logical :: lprn,print_class
  56       integer :: ncont_frag(mmaxfrag),&
  57        icont_frag(2,maxcont,mmaxfrag),ncontsc,&
  58        icontsc(1,maxcont),nsccont_frag(mmaxfrag),&
  59        isccont_frag(2,maxcont,mmaxfrag)
  60       integer :: isecstr(nres)
  61       integer :: itemp(maxfrag)
  62       character(len=4) :: liczba
  63       real(kind=8) :: Epot,rms
  64       integer :: jcon,i,j,ind,ncnat,nsec_match,ishift,ishif1,ishif2,&
  65                  nc_match,ncon_match,iclass_rms,ishifft_rms,ishiff,ishif
  66       integer :: k,kk,iclass_con,iscor,ik,ishifft_con,idig,iex,im
  67 !      print *,"Enter conf_compar",jcon
  68       call angnorm12(rmsang)
  69 ! Level 1: check secondary and supersecondary structure
  70       call elecont(lprn,ncont,icont,nnt,nct)
  71       if (lprn) then
  72         write (iout,*) "elecont finished"
  73         call flush(iout)
  74       endif
  75       call secondary2(lprn,.false.,ncont,icont,isecstr)
  76       if (lprn) then
  77         write (iout,*) "secondary2 finished"
  78         call flush(iout)
  79       endif
  80       call contact(lprn,ncontsc,icontsc,nnt,nct)
  81       if (lprn) then
  82          write(iout,*) "Assigning electrostatic contacts"
  83          call flush(iout)
  84       endif
  85       call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,&
  86          icont_frag)
  87       if (lprn) then
  88         write(iout,*) "Assigning sidechain contacts"
  89         call flush(iout)
  90       endif
  91       call contacts_between_fragments(lprn,3,ncontsc,icontsc,&
  92          nsccont_frag,isccont_frag)
  93       if (lprn) then
  94         write(iout,*) "--> After contacts_between_fragments"
  95         call flush(iout)
  96       endif
  97       do i=1,nlevel
  98         do j=1,isnfrag(nlevel+1)
  99           iclass(j,i)=0
 100         enddo
 101       enddo
 102       do j=1,nfrag(1)
 103         ind = icant(j,j)
 104         if (lprn) then
 105           write (iout,'(80(1h=))')
 106           write (iout,*) "Level",1," fragment",j
 107           write (iout,'(80(1h=))')
 108         endif
 109         call flush(iout)
 110         rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
 111 ! Compare electrostatic contacts in the current conf with that in the native
 112 ! structure.
 113         if (lprn) write (iout,*) &
 114           "Comparing electrostatic contact map and local structure"
 115         call flush(iout)
 116         ncnat=ncont_frag_ref(ind)
 117 !        write (iout,*) "before match_contact:",nc_fragm(j,1),
 118 !     &   nc_req_setf(j,1)
 119 !        call flush(iout)
 120         call match_secondary(j,isecstr,nsec_match,lprn)
 121         if (lprn) write (iout,*) "Fragment",j," nsec_match",&
 122           nsec_match," length",len_frag(j,1)," min_len",&
 123           frac_sec*len_frag(j,1)
 124         if (nsec_match.lt.frac_sec*len_frag(j,1)) then
 125           iclass(j,1)=0
 126           if (lprn) write (iout,*) "Fragment",j,&
 127             " has incorrect secondary structure"
 128         else
 129           iclass(j,1)=1
 130           if (lprn) write (iout,*) "Fragment",j,&
 131             " has correct secondary structure"
 132         endif
 133         if (ielecont(j,1).gt.0) then
 134           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 135             ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 136             ncont_frag(ind),icont_frag(1,1,ind),&
 137             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 138             nc_req_setf(j,1),istruct(j),.true.,lprn)
 139         else if (isccont(j,1).gt.0) then
 140           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 141             nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 142             nsccont_frag(ind),isccont_frag(1,1,ind),&
 143             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 144             nc_req_setf(j,1),istruct(j),.true.,lprn)
 145         else if (iloc(j).gt.0) then
 146 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 147           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 148             0,icont_frag_ref(1,1,ind),&
 149             ncont_frag(ind),icont_frag(1,1,ind),&
 150             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 151             0,istruct(j),.true.,lprn)
 152 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 153         else
 154           ishif=0
 155           nc_match=1
 156         endif
 157         if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
 158         ishif=ishif1
 159         qfrag(j,1)=qwolynes(1,j)
 160         if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 161         if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
 162 !        write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
 163         if (irms(j,1).gt.0) then
 164           if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
 165             iclass_rms=2
 166             ishifft_rms=0
 167           else
 168             ishiff=0
 169             rms=1.0d2
 170             iclass_rms=0
 171             do while (rms.gt.rmscutfrag(1,j,1) .and. &
 172                ishiff.lt.n_shift(1,j,1))
 173               ishiff=ishiff+1
 174               rms=rmscalc(-ishiff,1,j,jcon,lprn)
 175 !              write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
 176 !     &          " rms",rms," rmscut",rmscutfrag(1,j,1)
 177               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 178               if (rms.gt.rmscutfrag(1,j,1)) then
 179                 rms=rmscalc(ishiff,1,j,jcon,lprn)
 180 !                write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
 181 !     &           " rms",rms
 182               endif
 183               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 184             enddo
 185 !            write (iout,*) "After loop: rms",rms,
 186 !     &        " rmscut",rmscutfrag(1,j,1)
 187 !            write (iout,*) "iclass_rms",iclass_rms
 188             if (rms.le.rmscutfrag(1,j,1)) then
 189               ishifft_rms=ishiff
 190               rmsfrag(j,1)=rms
 191               iclass_rms=1
 192             endif
 193 !            write (iout,*) "iclass_rms",iclass_rms
 194           endif
 195 !          write (iout,*) "ishif",ishif
 196           if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
 197         else
 198           iclass_rms=1
 199         endif
 200 !        write (iout,*) "ishif",ishif," iclass",iclass(j,1),
 201 !     &    " iclass_rms",iclass_rms
 202         if (nc_match.gt.0 .and. iclass_rms.gt.0) then
 203           if (ishif.eq.0) then
 204             iclass(j,1)=iclass(j,1)+6
 205           else
 206             iclass(j,1)=iclass(j,1)+2
 207           endif
 208         endif
 209         ncont_nat(1,j,1)=nc_match
 210         ncont_nat(2,j,1)=ncon_match
 211         ishifft(j,1)=ishif
 212 !        write (iout,*) "iclass",iclass(j,1)
 213       enddo
 214 ! Next levels: Check arrangements of elementary fragments.
 215       do i=2,nlevel
 216         do j=1,nfrag(i)
 217         if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
 218         if (lprn) then
 219             write (iout,'(80(1h=))')
 220             write (iout,*) "Level",i," fragment",j
 221             write (iout,'(80(1h=))')
 222         endif
 223 ! If an elementary fragment doesn't exist, don't check higher hierarchy levels.
 224         do k=1,npiece(j,i)
 225           ik=ipiece(k,j,i)
 226           if (iclass(ik,1).eq.0) then
 227             iclass(j,i)=0
 228             goto 12
 229           endif
 230         enddo
 231         if (i.eq.2 .and. ielecont(j,i).gt.0) then
 232           iclass_con=0
 233           ishifft_con=0
 234           if (lprn) write (iout,*) &
 235            "Comparing electrostatic contact map: fragments",&
 236             ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 237           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 238            ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 239            ncont_frag(ind),icont_frag(1,1,ind),&
 240            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 241            nc_req_setf(j,i),2,.false.,lprn)
 242           ishif=ishif1
 243           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 244           if (nc_match.gt.0) then
 245             if (ishif.eq.0) then
 246               iclass_con=2
 247             else
 248               iclass_con=1
 249             endif
 250           endif
 251           ncont_nat(1,j,i)=nc_match
 252           ncont_nat(2,j,i)=ncon_match
 253           ishifft_con=ishif
 254         else if (i.eq.2 .and. isccont(j,i).gt.0) then
 255           iclass_con=0
 256           ishifft_con=0
 257           if (lprn) write (iout,*) &
 258            "Comparing sidechain contact map: fragments",&
 259            ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 260           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 261            nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 262            nsccont_frag(ind),isccont_frag(1,1,ind),&
 263            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 264            nc_req_setf(j,i),2,.false.,lprn)
 265           ishif=ishif1
 266           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 267           if (nc_match.gt.0) then
 268             if (ishif.eq.0) then
 269               iclass_con=2
 270             else
 271               iclass_con=1
 272             endif
 273           endif
 274           ncont_nat(1,j,i)=nc_match
 275           ncont_nat(2,j,i)=ncon_match
 276           ishifft_con=ishif
 277         else if (i.eq.2) then
 278           iclass_con=2
 279           ishifft_con=0
 280         endif
 281         if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
 282         if (lprn) write (iout,*) &
 283           "Comparing rms: fragments",&
 284            (ipiece(k,j,i),k=1,npiece(j,i))
 285         rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
 286         if (irms(j,i).gt.0) then
 287           iclass_rms=0
 288           ishifft_rms=0
 289           if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 290 !          write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
 291 !     &     " rmscutfrag",rmscutfrag(1,j,i)
 292           if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
 293             iclass_rms=2
 294             ishifft_rms=0
 295           else
 296             ishif=0
 297             rms=1.0d2
 298             do while (rms.gt.rmscutfrag(1,j,i) .and. &
 299                ishif.lt.n_shift(1,j,i))
 300               ishif=ishif+1
 301               rms=rmscalc(-ishif,i,j,jcon,lprn)
 302 !              print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
 303               if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 304               if (rms.gt.rmscutfrag(1,j,i)) then
 305                 rms=rmscalc(ishif,i,j,jcon,lprn)
 306 !                print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
 307               endif
 308               if (lprn) write (iout,*) "rms",rms
 309             enddo
 310             if (rms.le.rmscutfrag(1,j,i)) then
 311               ishifft_rms=ishif
 312               rmsfrag(j,i)=rms
 313               iclass_rms=1
 314             endif
 315           endif
 316         endif
 317         if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. &
 318           isccont(j,i).eq.0 ) then
 319           write (iout,*) "Error: no measure of comparison specified:",&
 320             " level",i," part",j
 321           stop
 322         endif
 323         if (lprn) &
 324         write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
 325         if (i.eq.2) then
 326           iclass(j,i) = min0(iclass_con,iclass_rms)
 327           if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
 328             ishifft(j,i)=ishifft_rms
 329           else
 330             ishifft(j,i)=ishifft_con
 331           endif
 332         else if (i.gt.2) then
 333           iclass(j,i) = iclass_rms
 334           ishifft(j,i)= ishifft_rms
 335         endif
 336    12   continue
 337         enddo
 338       enddo
 339       rms_nat=rmsnat(jcon)
 340       qnat=qwolynes(0,0)
 341 ! Compute the structural class
 342       iscor=0
 343       IF (.NOT. BINARY) THEN
 344       do i=1,nlevel
 345         IF (I.EQ.1) THEN
 346         do j=1,nfrag(i)
 347           itemp(j)=iclass(j,i)
 348         enddo
 349         do kk=-1,1
 350           do j=1,nfrag(i)
 351             idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
 352             iex = 2**idig
 353             im=mod(itemp(j),2)
 354             itemp(j)=itemp(j)/2
 355 !            write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 356 !     &        " iclass",iclass(j,i)," im",im
 357             iscor=iscor+im*iex
 358           enddo
 359         enddo
 360         ELSE
 361         do j=1,nfrag(i)
 362           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
 363           iex = 2**idig
 364           if (iclass(j,i).gt.0) then
 365             im=1
 366           else
 367             im=0
 368           endif
 369 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 370 !     &      " iclass",iclass(j,i)," im",im
 371           iscor=iscor+im*iex
 372         enddo
 373         do j=1,nfrag(i)
 374           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
 375           iex = 2**idig
 376           if (iclass(j,i).gt.1) then
 377             im=1
 378           else
 379             im=0
 380           endif
 381 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 382 !     &      " iclass",iclass(j,i)," im",im
 383           iscor=iscor+im*iex
 384         enddo
 385         ENDIF
 386       enddo
 387       iscore=iscor
 388       ENDIF
 389       if (print_class) then
 390 #ifdef MPI
 391           write(istat,'(i6,$)') jcon+indstart(me)-1
 392           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 393            -entfac(jcon)
 394 #else
 395           write(istat,'(i6,$)') jcon
 396           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 397             -entfac(jcon)
 398 #endif
 399           write (istat,'(f8.3,2f6.3,$)') &
 400             rms_nat,qnat,rmsang/(nres-3)
 401           do j=1,nlevel
 402             write(istat,'(1x,$,20(i3,$))') &
 403               (ncont_nat(1,k,j),k=1,nfrag(j))
 404             if (j.lt.3) then
 405               write(istat,'(1x,$,20(f5.1,f5.2$))') &
 406                 (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
 407             else
 408               write(istat,'(1x,$,20(f5.1$))') &
 409                 (rmsfrag(k,j),k=1,nfrag(j))
 410             endif
 411             write(istat,'(1x,$,20(i1,$))') &
 412               (iclass(k,j),k=1,nfrag(j))
 413           enddo
 414           if (binary) then
 415             write (istat,'("  ",$)')
 416             do j=1,nlevel
 417               write (istat,'(100(i1,$))')(iclass(k,j),&
 418                  k=1,nfrag(j))
 419               if (j.lt.nlevel) write(iout,'(".",$)')
 420             enddo
 421             write (istat,*)
 422           else
 423             write (istat,'(i10)') iscore
 424           endif
 425       endif
 426       RETURN
 427       END subroutine conf_compar
 428 !-----------------------------------------------------------------------------
 429 ! angnorm.f
 430 !-----------------------------------------------------------------------------
 431       subroutine add_angpair(ici,icj,nang_pair,iang_pair)
 432
 433 !      implicit real*8 (a-h,o-z)
 434 !      include 'DIMENSIONS'
 435 !      include 'COMMON.IOUNITS'
 436 !      include 'COMMON.CHAIN'
 437       integer :: ici,icj,nang_pair,iang_pair(2,nres)
 438       integer :: i,ian1,ian2
 439 !      write (iout,*) "add_angpair: ici",ici," icj",icj,
 440 !     &  " nang_pair",nang_pair
 441       ian1=ici+2
 442       if (ian1.lt.4 .or. ian1.gt.nres) return
 443       ian2=icj+2
 444 !      write (iout,*) "ian1",ian1," ian2",ian2
 445       if (ian2.lt.4 .or. ian2.gt.nres) return
 446       do i=1,nang_pair
 447         if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
 448       enddo
 449       nang_pair=nang_pair+1
 450       iang_pair(1,nang_pair)=ian1
 451       iang_pair(2,nang_pair)=ian2
 452       return
 453       end subroutine add_angpair
 454 !-------------------------------------------------------------------------
 455       subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,lprn)
 456
 457       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 458                               rad2deg,dwapi
 459 !      implicit real*8 (a-h,o-z)
 460 !      include 'DIMENSIONS'
 461 !      include 'DIMENSIONS.ZSCOPT'
 462 !      include 'DIMENSIONS.COMPAR'
 463 !      include 'COMMON.IOUNITS'
 464 !      include 'COMMON.VAR'
 465 !      include 'COMMON.COMPAR'
 466 !      include 'COMMON.CHAIN'
 467 !      include 'COMMON.GEO'
 468       real(kind=8) :: pinorm,deltang
 469       logical :: lprn
 470       integer :: jfrag,ishif1,ishif2,nn,npart,nn4,nne
 471       real(kind=8) :: diffang_max,angn,fract,ff
 472       integer :: i,j,nbeg,nend,ll,longest
 473       if (lprn) write (iout,'(80(1h*))')
 474       angn=0.0d0
 475       nn = 0
 476       fract = 1.0d0
 477       npart = npiece(jfrag,1)
 478       nn4 = nstart_sup+3
 479       nne = min0(nend_sup,nres)
 480       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 481       do i=1,npart
 482         nbeg = ifrag(1,i,jfrag) + 3 - ishif1
 483         if (nbeg.lt.nn4) nbeg=nn4
 484         nend = ifrag(2,i,jfrag) + 1 - ishif2
 485         if (nend.gt.nne) nend=nne
 486         if (nend.ge.nbeg) then
 487         nn = nn + nend - nbeg + 1
 488         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 489           " nn",nn," ishift1",ishif1," ishift2",ishif2
 490         if (lprn) write (iout,*) "angles"
 491         longest=0
 492         ll = 0
 493         do j=nbeg,nend
 494 !          deltang = pinorm(phi(j)-phi_ref(j+ishif1))
 495           deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
 496             theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
 497           if (dabs(deltang).gt.diffang_max) then
 498             if (ll.gt.longest) longest = ll
 499             ll = 0
 500           else
 501             ll=ll+1
 502           endif
 503           if (ll.gt.longest) longest = ll
 504           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 505            rad2deg*phi_ref(j+ishif1),rad2deg*deltang
 506           angn=angn+dabs(deltang)
 507         enddo
 508         longest=longest+3
 509         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 510         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 511           diffang_max*rad2deg,":",longest," fraction",ff
 512         if (ff.lt.fract) fract = ff
 513         endif
 514       enddo
 515       if (nn.gt.0) then
 516         angn = angn/nn
 517       else
 518         angn = dwapi
 519       endif
 520       if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
 521         " fract",fract
 522       return
 523       end subroutine angnorm
 524 !-------------------------------------------------------------------------
 525       subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
 526         diffang_max,anorm,fract)
 527
 528       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 529                               rad2deg
 530 !      implicit real*8 (a-h,o-z)
 531 !      include 'DIMENSIONS'
 532 !      include 'DIMENSIONS.ZSCOPT'
 533 !      include 'DIMENSIONS.COMPAR'
 534 !      include 'COMMON.IOUNITS'
 535 !      include 'COMMON.VAR'
 536 !      include 'COMMON.COMPAR'
 537 !      include 'COMMON.CHAIN'
 538 !      include 'COMMON.GEO'
 539       integer :: ncont,icont(2,ncont),longest
 540       real(kind=8) :: anorm,diffang_max,fract
 541       integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
 542       real(kind=8) :: pinorm
 543       logical :: lprn
 544       integer :: jfrag,ishif1,ishif2
 545       integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
 546       integer :: nbeg,nend,ll
 547       real(kind=8) :: angn,ishifc,deltang,ff
 548
 549       if (lprn) write (iout,'(80(1h*))')
 550 !
 551 ! Determine the segments for which angles will be compared
 552 !
 553       nn4 = nstart_sup+3
 554       nne = min0(nend_sup,nres)
 555       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 556       npart=npiece(jfrag,1)
 557       npiece_c=0
 558       do i=1,npart
 559 !        write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 560         if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
 561           icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
 562         jstart=1
 563         do while (jstart.lt.ncont .and. &
 564          icont(1,jstart).lt.ifrag(1,i,jfrag))
 565 !          write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 566 !     &     " ifrag",ifrag(1,i,jfrag)
 567           jstart=jstart+1
 568         enddo
 569 !        write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 570 !     &   " ifrag",ifrag(1,i,jfrag)
 571         if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
 572         npiece_c=npiece_c+1
 573         ic1=icont(1,jstart)
 574         ifrag_c(1,npiece_c)=icont(1,jstart)
 575         jend=ncont
 576         do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
 577 !          write (iout,*) "jend",jend," icont",icont(1,jend),
 578 !     &     " ifrag",ifrag(2,i,jfrag)
 579           jend=jend-1
 580         enddo
 581 !        write (iout,*) "jend",jend," icont",icont(1,jend),
 582 !     &   " ifrag",ifrag(2,i,jfrag)
 583         ic2=icont(1,jend)
 584         ifrag_c(2,npiece_c)=icont(1,jend)+1
 585         ishift_c(npiece_c)=ishif1
 586 !        write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
 587 !     &    " ic1",ic1," ic2",ic2,
 588 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 589    11   continue
 590         if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
 591           idi=1
 592         else
 593           idi=-1
 594         endif
 595 !        write (iout,*) "idi",idi
 596         if (idi.eq.1) then
 597           if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
 598             icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
 599           jstart=1
 600           do while (jstart.lt.ncont .and. &
 601            icont(2,jstart).lt.ifrag(1,i,jfrag))
 602 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 603 !     &     " ifrag",ifrag(1,i,jfrag)
 604             jstart=jstart+1
 605           enddo
 606 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 607 !     &     " ifrag",ifrag(1,i,jfrag)
 608           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 609           npiece_c=npiece_c+1
 610           ic1=icont(2,jstart)
 611           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 612           jend=ncont
 613           do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
 614 !            write (iout,*) "jend",jend," icont",icont(2,jend),
 615 !     &     " ifrag",ifrag(2,i,jfrag)
 616             jend=jend-1
 617           enddo
 618 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 619 !     &     " ifrag",ifrag(2,i,jfrag)
 620         else if (idi.eq.-1) then
 621           if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
 622               icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
 623           jstart=ncont
 624           do while (jstart.gt.ncont .and. &
 625            icont(2,jstart).lt.ifrag(1,i,jfrag))
 626 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 627 !     &     " ifrag",ifrag(1,i,jfrag)
 628             jstart=jstart-1
 629           enddo
 630 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 631 !     &     " ifrag",ifrag(1,i,jfrag)
 632           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 633           npiece_c=npiece_c+1
 634           ic1=icont(2,jstart)
 635           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 636           jend=1
 637           do while (jend.lt.ncont .and. &
 638              icont(2,jend).gt.ifrag(2,i,jfrag))
 639 !             write (iout,*) "jend",jend," icont",icont(2,jend),
 640 !     &         " ifrag",ifrag(2,i,jfrag)
 641             jend=jend+1
 642           enddo
 643 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 644 !     &     " ifrag",ifrag(2,i,jfrag)
 645         endif
 646         ic2=icont(2,jend)
 647         if (ic2.lt.ic1) then
 648           iic = ic1
 649           ic1 = ic2
 650           ic2 = iic
 651         endif
 652 !        write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
 653 !     &    " jstart:",jstart," jend",jend,
 654 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 655         ifrag_c(1,npiece_c)=ic1
 656         ifrag_c(2,npiece_c)=ic2+1
 657         ishift_c(npiece_c)=ishif2
 658    12   continue
 659       enddo
 660       if (lprn) then
 661         write (iout,*) "Before merge: npiece_c",npiece_c
 662         do i=1,npiece_c
 663           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 664         enddo
 665       endif
 666 !
 667 ! Merge overlapping segments (e.g., avoid splitting helices)
 668 !
 669       i=1
 670       do while (i .lt. npiece_c)
 671         if (ishift_c(i).eq.ishift_c(i+1) .and. &
 672            ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
 673            ifrag_c(2,i)=ifrag_c(2,i+1)
 674            do j=i+1,npiece_c
 675              ishift_c(j)=ishift_c(j+1)
 676              ifrag_c(1,j)=ifrag_c(1,j+1)
 677              ifrag_c(2,j)=ifrag_c(2,j+1)
 678            enddo
 679            npiece_c=npiece_c-1
 680         else
 681           i=i+1
 682         endif
 683       enddo
 684       if (lprn) then
 685         write (iout,*) "After merge: npiece_c",npiece_c
 686         do i=1,npiece_c
 687           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 688         enddo
 689       endif
 690 !
 691 ! Compare angles
 692 !
 693       angn=0.0d0
 694       anorm=0
 695       nn = 0
 696       fract = 1.0d0
 697       npart = npiece_c
 698       do i=1,npart
 699         ishifc=ishift_c(i)
 700         nbeg = ifrag_c(1,i) + 3 - ishifc
 701         if (nbeg.lt.nn4) nbeg=nn4
 702         nend = ifrag_c(2,i)  - ishifc + 1
 703         if (nend.gt.nne) nend=nne
 704         if (nend.ge.nbeg) then
 705         nn = nn + nend - nbeg + 1
 706         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 707           " nn",nn," ishifc",ishifc
 708         if (lprn) write (iout,*) "angles"
 709         longest=0
 710         ll = 0
 711         do j=nbeg,nend
 712 !          deltang = pinorm(phi(j)-phi_ref(j+ishifc))
 713           deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
 714             theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
 715           if (dabs(deltang).gt.diffang_max) then
 716             if (ll.gt.longest) longest = ll
 717             ll = 0
 718           else
 719             ll=ll+1
 720           endif
 721           if (ll.gt.longest) longest = ll
 722           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 723            rad2deg*phi_ref(j+ishifc),rad2deg*deltang
 724           angn=angn+dabs(deltang)
 725         enddo
 726         longest=longest+3
 727         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 728         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 729           diffang_max*rad2deg,":",longest," fraction",ff
 730         if (ff.lt.fract) fract = ff
 731         endif
 732       enddo
 733       if (nn.gt.0) anorm = angn/nn
 734       if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
 735       return
 736       end subroutine angnorm2
 737 !-------------------------------------------------------------------------
 738       real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
 739
 740       use geometry_data, only:phi,theta,rad2deg
 741 !      implicit real*8 (a-h,o-z)
 742 !      include 'DIMENSIONS'
 743 !      include 'DIMENSIONS.ZSCOPT'
 744 !      include 'DIMENSIONS.COMPAR'
 745 !      include 'COMMON.IOUNITS'
 746 !      include 'COMMON.VAR'
 747 !      include 'COMMON.COMPAR'
 748 !      include 'COMMON.CHAIN'
 749 !      include 'COMMON.GEO'
 750       logical :: lprn
 751       integer :: nang_pair,iang_pair(2,nres)
 752       real(kind=8) :: pinorm
 753       integer :: j,ia1,ia2
 754       real(kind=8) :: angn,deltang
 755       angn=0.0d0
 756       if (lprn) write (iout,'(80(1h*))')
 757       if (lprn) write (iout,*) "nang_pair",nang_pair
 758       if (lprn) write (iout,*) "angles"
 759       do j=1,nang_pair
 760         ia1 = iang_pair(1,j)
 761         ia2 = iang_pair(2,j)
 762 !        deltang = pinorm(phi(ia1)-phi_ref(ia2))
 763          deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
 764             theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
 765         if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
 766          rad2deg*phi_ref(ia2),rad2deg*deltang
 767         angn=angn+dabs(deltang)
 768       enddo
 769       if (lprn) &
 770       write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
 771       angnorm1 = angn/nang_pair
 772       return
 773       end function angnorm1
 774 !------------------------------------------------------------------------------
 775       subroutine angnorm12(diff)
 776
 777       use geometry_data, only:phi,theta,nstart_sup,nend_sup
 778 !      implicit real*8 (a-h,o-z)
 779 !      include 'DIMENSIONS'
 780 !      include 'DIMENSIONS.ZSCOPT'
 781 !      include 'DIMENSIONS.COMPAR'
 782 !      include 'COMMON.IOUNITS'
 783 !      include 'COMMON.VAR'
 784 !      include 'COMMON.COMPAR'
 785 !      include 'COMMON.CHAIN'
 786 !      include 'COMMON.GEO'
 787       real(kind=8) :: pinorm,diff
 788       integer :: nn4,nne,j
 789       diff=0.0d0
 790       nn4 = nstart_sup+3
 791       nne = min0(nend_sup,nres)
 792 !      do j=nn4-1,nne
 793 !        diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
 794 !      enddo
 795       do j=nn4,nne
 796 !        diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
 797          diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
 798             theta_ref(j),phi(j),theta(j-1),theta(j))
 799       enddo
 800       return
 801       end subroutine angnorm12
 802 !--------------------------------------------------------------------------------
 803       real(kind=8) function spherang(gam1,theta11,theta12,&
 804          gam2,theta21,theta22)
 805 !      implicit none
 806       use geometry, only:arcos
 807       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
 808         x1,x2,xmed,f1,f2,fmed
 809       real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
 810       real(kind=8) :: sumcos
 811 !el      real(kind=8) :: pinorm,sumangp !arcos,
 812       integer :: it,maxit=100
 813 ! Calculate the difference of the angles of two superposed 4-redidue fragments
 814 !
 815 !       O      P
 816 !        \    /
 817 !     O'--C--C
 818 !             \
 819 !              P'
 820 !
 821 ! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
 822 ! to achieve the minimum difference between the O'-C-O and P-C-P angles;
 823 ! the sum of these angles is the difference returned by the function.
 824 !
 825 ! 4/28/04 AL
 826 ! If thetas match, take the difference of gamma and exit.
 827       if (dabs(theta11-theta12).lt.tolx &
 828        .and. dabs(theta21-theta22).lt.tolx) then
 829         spherang=dabs(pinorm(gam2-gam1))
 830         return
 831       endif
 832 ! If the gammas are the same, take the difference of thetas and exit.
 833       x1=0.0d0
 834       x2=0.5d0*pinorm(gam2-gam1)
 835       if (dabs(x2) .lt. tolx) then
 836         spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
 837         return
 838       else if (x2.lt.0.0d0) then
 839         x1=x2
 840         x2=0.0d0
 841       endif
 842 ! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
 843       f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
 844       f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
 845       do it=1,maxit
 846         xmed=x1-f1*(x2-x1)/(f2-f1)
 847         fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
 848 !        write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
 849         if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
 850              .and. dabs(fmed).lt.tolf ) then
 851           x1=xmed
 852           f1=fmed
 853           goto 10
 854         else if ( fmed*f1.lt.0.0d0 ) then
 855           x2=xmed
 856           f2=fmed
 857         else
 858           x1=xmed
 859           f1=fmed
 860         endif
 861       enddo
 862    10 continue
 863       spherang=arcos(dcos(theta11)*dcos(theta12) &
 864        +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
 865        arcos(dcos(theta21)*dcos(theta22)+ &
 866        dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
 867       return
 868       end function spherang
 869 !--------------------------------------------------------------------------------
 870       real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
 871        theta21,theta22,fi)
 872 !      implicit none
 873       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
 874        cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
 875        cosd2
 876 ! derivarive of the sum of the difference of the angles of a 4-residue fragment.
 877 !      real(kind=8) :: arcos
 878       cost11=dcos(theta11)
 879       cost12=dcos(theta12)
 880       cost21=dcos(theta21)
 881       cost22=dcos(theta22)
 882       sint11=dsin(theta11)
 883       sint12=dsin(theta12)
 884       sint21=dsin(theta21)
 885       sint22=dsin(theta22)
 886       cosd1=cost11*cost12+sint11*sint12*dcos(fi)
 887       cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
 888       sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
 889        +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
 890       return
 891       end function sumangp
 892 !-----------------------------------------------------------------------------
 893 ! contact.f
 894 !-----------------------------------------------------------------------------
 895       subroutine contact(lprint,ncont,icont,ist,ien)
 896
 897       use calc_data
 898       use geometry_data, only:c,dc,dc_norm
 899       use energy_data, only:itype,maxcont
 900 !      implicit none
 901 !      include 'DIMENSIONS'
 902 !      include 'DIMENSIONS.ZSCOPT'
 903 !      include 'COMMON.CONTROL'
 904 !      include 'COMMON.IOUNITS'
 905 !      include 'COMMON.CHAIN'
 906 !      include 'COMMON.INTERACT'
 907 !      include 'COMMON.FFIELD'
 908 !      include 'COMMON.NAMES'
 909 !      include 'COMMON.CALC'
 910 !      include 'COMMON.CONTPAR'
 911 !      include 'COMMON.LOCAL'
 912       integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2
 913       real(kind=8) :: csc !el,dist
 914       real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
 915           ddsc,ddla,ddlb
 916       integer :: ncont
 917       integer,dimension(2,maxcont) :: icont
 918       real(kind=8) :: u,v,a(3),b(3),dla,dlb
 919       logical :: lprint
 920 !el-------
 921       dla=0.0d0
 922       dlb=0.0d0
 923 !el------
 924       ncont=0
 925       kkk=3
 926       if (lprint) then
 927       do i=1,nres
 928         write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),&
 929           c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
 930           dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
 931       enddo
 932       endif
 933   110 format (a,'(',i3,')',9f8.3)
 934       do i=ist,ien-kkk
 935         iti=iabs(itype(i))
 936         if (iti.le.0 .or. iti.gt.ntyp) cycle
 937         do j=i+kkk,ien
 938           itj=iabs(itype(j))
 939           if (itj.le.0 .or. itj.gt.ntyp) cycle
 940           itypi=iti
 941           itypj=itj
 942           xj = c(1,nres+j)-c(1,nres+i)
 943           yj = c(2,nres+j)-c(2,nres+i)
 944           zj = c(3,nres+j)-c(3,nres+i)
 945           dxi = dc_norm(1,nres+i)
 946           dyi = dc_norm(2,nres+i)
 947           dzi = dc_norm(3,nres+i)
 948           dxj = dc_norm(1,nres+j)
 949           dyj = dc_norm(2,nres+j)
 950           dzj = dc_norm(3,nres+j)
 951           do k=1,3
 952             a(k)=dc(k,nres+i)
 953             b(k)=dc(k,nres+j)
 954           enddo
 955 !          write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
 956           if (icomparfunc.eq.1) then
 957             call contfunc(csc,iti,itj)
 958           else if (icomparfunc.eq.2) then
 959             call scdist(csc,iti,itj)
 960           else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
 961             csc = dist(nres+i,nres+j)
 962           else if (icomparfunc.eq.4) then
 963             call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
 964           else
 965             write (*,*) "Error - Unknown sidechain contact function"
 966             write (iout,*) "Error - Unknown sidechain contact function"
 967           endif
 968           if (csc.lt.sc_cutoff(iti,itj)) then
 969 !            write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
 970 !     &      " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
 971 !     &      dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
 972 !     &      dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
 973 !     &      xj,yj,zj
 974 !            write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
 975 !     &       sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
 976 !     &       chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
 977 !     &       csc
 978             ncont=ncont+1
 979             cscore(ncont)=csc
 980             icont(1,ncont)=i
 981             icont(2,ncont)=j
 982             omt1(ncont)=om1
 983             omt2(ncont)=om2
 984             omt12(ncont)=om12
 985             ddsc(ncont)=1.0d0/rij
 986             ddla(ncont)=dla
 987             ddlb(ncont)=dlb
 988           endif
 989         enddo
 990       enddo
 991       if (lprint) then
 992         write (iout,'(a)') 'Contact map:'
 993         do i=1,ncont
 994           i1=icont(1,i)
 995           i2=icont(2,i)
 996           it1=itype(i1)
 997           it2=itype(i2)
 998           write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
 999            i,restyp(it1),i1,restyp(it2),i2,cscore(i),&
1000            sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1001            omt1(i),omt2(i),omt12(i)
1002         enddo
1003       endif
1004       return
1005       end subroutine contact
1006 #else
1007 !----------------------------------------------------------------------------
1008       subroutine contact(lprint,ncont,icont)
1009
1010       use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii
1011 !      include 'DIMENSIONS'
1012 !      include 'COMMON.IOUNITS'
1013 !      include 'COMMON.CHAIN'
1014 !      include 'COMMON.INTERACT'
1015 !      include 'COMMON.FFIELD'
1016 !      include 'COMMON.NAMES'
1017       real(kind=8) :: facont=1.569D0  ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1018       integer :: ncont,icont(2,maxcont)
1019       logical :: lprint
1020       integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1021       real(kind=8) :: rcomp
1022       ncont=0
1023       kkk=3
1024 !     print *,'nnt=',nnt,' nct=',nct
1025       do i=nnt+kkk,nct
1026         iti=iabs(itype(i))
1027         do j=nnt,i-kkk
1028           itj=iabs(itype(j))
1029           if (ipot.ne.4) then
1030 !           rcomp=sigmaii(iti,itj)+1.0D0
1031             rcomp=facont*sigmaii(iti,itj)
1032           else
1033 !           rcomp=sigma(iti,itj)+1.0D0
1034             rcomp=facont*sigma(iti,itj)
1035           endif
1036 !         rcomp=6.5D0
1037 !         print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1038           if (dist(nres+i,nres+j).lt.rcomp) then
1039             ncont=ncont+1
1040             icont(1,ncont)=i
1041             icont(2,ncont)=j
1042           endif
1043         enddo
1044       enddo
1045       if (lprint) then
1046         write (iout,'(a)') 'Contact map:'
1047         do i=1,ncont
1048           i1=icont(1,i)
1049           i2=icont(2,i)
1050           it1=itype(i1)
1051           it2=itype(i2)
1052           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1053            i,restyp(it1),i1,restyp(it2),i2
1054         enddo
1055       endif
1056       return
1057       end subroutine contact
1058 #endif
1059 !----------------------------------------------------------------------------
1060       real(kind=8) function contact_fract(ncont,ncont_ref,&
1061                                            icont,icont_ref)
1062
1063       use energy_data, only:maxcont
1064 !      implicit none
1065 !      include 'DIMENSIONS'
1066 !      include 'COMMON.IOUNITS'
1067       integer :: i,j,nmatch
1068       integer :: ncont,ncont_ref
1069       integer,dimension(2,maxcont) :: icont,icont_ref
1070       nmatch=0
1071 !     print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1072 !     write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1073 !     write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1074 !     write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1075 !     write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1076       do i=1,ncont
1077         do j=1,ncont_ref
1078           if (icont(1,i).eq.icont_ref(1,j) .and. &
1079               icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1080         enddo
1081       enddo
1082 !     print *,' nmatch=',nmatch
1083 !     contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1084       contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1085       return
1086       end function contact_fract
1087 #ifndef CLUSTER
1088 !------------------------------------------------------------------------------
1089       subroutine pept_cont(lprint,ncont,icont)
1090
1091       use geometry_data, only:c
1092       use energy_data, only:maxcont,nnt,nct,itype
1093 !      implicit none
1094 !      include 'DIMENSIONS'
1095 !      include 'DIMENSIONS.ZSCOPT'
1096 !      include 'COMMON.IOUNITS'
1097 !      include 'COMMON.CHAIN'
1098 !      include 'COMMON.INTERACT'
1099 !      include 'COMMON.FFIELD'
1100 !      include 'COMMON.NAMES'
1101       integer :: ncont,icont(2,maxcont)
1102       integer :: i,j,k,kkk,i1,i2,it1,it2
1103       logical :: lprint
1104 !el      real(kind=8) :: dist
1105       real(kind=8) :: rcomp=5.5d0
1106       ncont=0
1107       kkk=0
1108       print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1109       do i=nnt,nct-3
1110         do k=1,3
1111           c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1112         enddo
1113         do j=i+2,nct-1
1114           do k=1,3
1115             c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1116           enddo
1117           if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1118             ncont=ncont+1
1119             icont(1,ncont)=i
1120             icont(2,ncont)=j
1121           endif
1122         enddo
1123       enddo
1124       if (lprint) then
1125         write (iout,'(a)') 'PP contact map:'
1126         do i=1,ncont
1127           i1=icont(1,i)
1128           i2=icont(2,i)
1129           it1=itype(i1)
1130           it2=itype(i2)
1131           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1132            i,restyp(it1),i1,restyp(it2),i2
1133         enddo
1134       endif
1135       return
1136       end subroutine pept_cont
1137 !-----------------------------------------------------------------------------
1138 ! cont_frag.f
1139 !-----------------------------------------------------------------------------
1140       subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1141          ncont_interfrag,icont_interfrag)
1142
1143       use energy_data, only:itype,maxcont
1144 !      include 'DIMENSIONS'
1145 !      include 'DIMENSIONS.ZSCOPT'
1146 !      include 'DIMENSIONS.COMPAR'
1147 !      include 'COMMON.INTERACT'
1148 !      include 'COMMON.COMPAR'
1149 !      include 'COMMON.IOUNITS'
1150 !      include 'COMMON.CHAIN'
1151 !      include 'COMMON.NAMES'
1152       integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1153         icont_interfrag(2,maxcont,mmaxfrag)
1154       logical :: OK1,OK2,lprint
1155       integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2
1156 ! Determine the contacts that occur within a fragment and between fragments.
1157       do i=1,nfrag(1)
1158         do j=1,i
1159           ind = icant(i,j)
1160           nc=0
1161 !          write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1162 !     &      ,k=1,npiece(i,1))
1163 !          write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1164 !     &      ,k=1,npiece(j,1))
1165 !          write (iout,*) "ncont",ncont
1166           do k=1,ncont
1167             ic1=icont(1,k)
1168             ic2=icont(2,k)
1169             OK1=.false.
1170             l=0
1171             do while (.not.OK1 .and. l.lt.npiece(j,1))
1172               l=l+1
1173               OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1174                ic1.le.ifrag(2,l,j)+is
1175             enddo
1176             OK2=.false.
1177             l=0
1178             do while (.not.OK2 .and. l.lt.npiece(i,1))
1179               l=l+1
1180               OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1181                ic2.le.ifrag(2,l,i)+is
1182             enddo
1183 !            write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1184 !     &        " OK2",OK2
1185             if (OK1.and.OK2) then
1186               nc=nc+1
1187               icont_interfrag(1,nc,ind)=ic1
1188               icont_interfrag(2,nc,ind)=ic2
1189 !              write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1190             endif
1191           enddo
1192           ncont_interfrag(ind)=nc
1193 !          do k=1,ncont_interfrag(ind)
1194 !              i1=icont_interfrag(1,k,ind)
1195 !              i2=icont_interfrag(2,k,ind)
1196 !              it1=itype(i1)
1197 !              it2=itype(i2)
1198 !              write (iout,'(i3,2x,a,i4,2x,a,i4)')
1199 !     &          i,restyp(it1),i1,restyp(it2),i2
1200 !          enddo
1201         enddo
1202       enddo
1203       if (lprint) then
1204         write (iout,*) "Contacts within fragments:"
1205         do i=1,nfrag(1)
1206           write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1207            ifrag(2,k,i),k=1,npiece(i,1)),")"
1208           ind=icant(i,i)
1209           do k=1,ncont_interfrag(ind)
1210             i1=icont_interfrag(1,k,ind)
1211             i2=icont_interfrag(2,k,ind)
1212             it1=itype(i1)
1213             it2=itype(i2)
1214             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1215               i,restyp(it1),i1,restyp(it2),i2
1216           enddo
1217         enddo
1218         write (iout,*)
1219         write (iout,*) "Contacts between fragments:"
1220         do i=1,nfrag(1)
1221         do j=1,i-1
1222           ind = icant(i,j)
1223           write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1224            ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1225            (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1226           write (iout,*) "Number of contacts",&
1227            ncont_interfrag(ind)
1228           ind=icant(i,j)
1229           do k=1,ncont_interfrag(ind)
1230             i1=icont_interfrag(1,k,ind)
1231             i2=icont_interfrag(2,k,ind)
1232             it1=itype(i1)
1233             it2=itype(i2)
1234             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1235               i,restyp(it1),i1,restyp(it2),i2
1236           enddo
1237         enddo
1238         enddo
1239       endif
1240       return
1241       end subroutine contacts_between_fragments
1242 !-----------------------------------------------------------------------------
1243 ! contfunc.f
1244 !-----------------------------------------------------------------------------
1245       subroutine contfunc(cscore,itypi,itypj)
1246 !
1247 ! This subroutine calculates the contact function based on
1248 ! the Gay-Berne potential of interaction.
1249 !
1250       use calc_data
1251 !      implicit real*8 (a-h,o-z)
1252 !      include 'DIMENSIONS'
1253 !      include 'COMMON.CONTPAR'
1254 !      include 'COMMON.CALC'
1255       integer :: expon=6
1256       integer :: itypi,itypj
1257       real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1258 !
1259       sig0ij=sig_comp(itypi,itypj)
1260       chi1=chi_comp(itypi,itypj)
1261       chi2=chi_comp(itypj,itypi)
1262       chi12=chi1*chi2
1263       chip1=chip_comp(itypi,itypj)
1264       chip2=chip_comp(itypj,itypi)
1265       chip12=chip1*chip2
1266       rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1267       rij=dsqrt(rrij)
1268 ! Calculate angle-dependent terms of the contact function
1269       erij(1)=xj*rij
1270       erij(2)=yj*rij
1271       erij(3)=zj*rij
1272       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1273       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1274       om12=dxi*dxj+dyi*dyj+dzi*dzj
1275       chiom12=chi12*om12
1276 !      print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1277 !     &  sig0ij,
1278 !     &  rij,rrij,om1,om2,om12
1279 ! Calculate eps1(om12)
1280       faceps1=1.0D0-om12*chiom12
1281       faceps1_inv=1.0D0/faceps1
1282       eps1=dsqrt(faceps1_inv)
1283 ! Following variable is eps1*deps1/dom12
1284       eps1_om12=faceps1_inv*chiom12
1285 ! Calculate sigma(om1,om2,om12)
1286       om1om2=om1*om2
1287       chiom1=chi1*om1
1288       chiom2=chi2*om2
1289       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1290       sigsq=1.0D0-facsig*faceps1_inv
1291 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1292       chipom1=chip1*om1
1293       chipom2=chip2*om2
1294       chipom12=chip12*om12
1295       facp=1.0D0-om12*chipom12
1296       facp_inv=1.0D0/facp
1297       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1298 ! Following variable is the square root of eps2
1299       eps2rt=1.0D0-facp1*facp_inv
1300       sigsq=1.0D0/sigsq
1301       sig=sig0ij*dsqrt(sigsq)
1302       rij_shift=1.0D0/rij-sig+sig0ij
1303       if (rij_shift.le.0.0D0) then
1304         evdw=1.0D1
1305         cscore = -dlog(evdw+1.0d-6)
1306         return
1307       endif
1308       rij_shift=1.0D0/rij_shift
1309       e2=(rij_shift*sig0ij)**expon
1310       evdw=dabs(eps1*eps2rt**2*e2)
1311       if (evdw.gt.1.0d1) evdw = 1.0d1
1312       cscore = -dlog(evdw+1.0d-6)
1313       return
1314       end subroutine contfunc
1315 !------------------------------------------------------------------------------
1316       subroutine scdist(cscore,itypi,itypj)
1317 !
1318 ! This subroutine calculates the contact distance
1319 !
1320       use calc_data
1321 !      implicit real*8 (a-h,o-z)
1322 !      include 'DIMENSIONS'
1323 !      include 'COMMON.CONTPAR'
1324 !      include 'COMMON.CALC'
1325       integer :: itypi,itypj
1326       real(kind=8) :: cscore,rrij
1327
1328       chi1=chi_comp(itypi,itypj)
1329       chi2=chi_comp(itypj,itypi)
1330       chi12=chi1*chi2
1331       rrij=xj*xj+yj*yj+zj*zj
1332       rij=dsqrt(rrij)
1333 ! Calculate angle-dependent terms of the contact function
1334       erij(1)=xj/rij
1335       erij(2)=yj/rij
1336       erij(3)=zj/rij
1337       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1338       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1339       om12=dxi*dxj+dyi*dyj+dzi*dzj
1340       chiom12=chi12*om12
1341       om1om2=om1*om2
1342       chiom1=chi1*om1
1343       chiom2=chi2*om2
1344       cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1345       return
1346       end subroutine scdist
1347 !------------------------------------------------------------------------------
1348 ! elecont.f
1349 !------------------------------------------------------------------------------
1350       subroutine elecont(lprint,ncont,icont,ist,ien)
1351
1352       use geometry_data, only:c
1353       use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2
1354 !      implicit none
1355 !      include 'DIMENSIONS'
1356 !      include 'DIMENSIONS.ZSCOPT'
1357 !      include 'DIMENSIONS.COMPAR'
1358 !      include 'COMMON.IOUNITS'
1359 !      include 'COMMON.CHAIN'
1360 !      include 'COMMON.INTERACT'
1361 !      include 'COMMON.FFIELD'
1362 !      include 'COMMON.NAMES'
1363 !      include 'COMMON.LOCAL'
1364       logical :: lprint
1365       integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1366       real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1367         xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1368         vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1369         eesij,ees,evdw,ene
1370       real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1371                        -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1372       real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1373                         0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1374       real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1375       real(kind=8) :: elcutoff=-0.3d0
1376       real(kind=8) :: elecutoff_14=-0.5d0
1377       integer :: ncont,icont(2,maxcont)
1378       real(kind=8) :: econt(maxcont)
1379 !
1380 ! Load the constants of peptide bond - peptide bond interactions.
1381 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1382 ! proline) - determined by averaging ECEPP energy.
1383 !
1384 ! as of 7/06/91.
1385 !
1386 !      data epp    / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1387 !      data rpp    / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1388 !el      data (elpp6c)   /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1389 !el      data (elpp3c)   / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1390 !el      data (elcutoff) /-0.3d0/
1391 !el      data (elecutoff_14) /-0.5d0/
1392       ees=0.0d0
1393       evdw=0.0d0
1394       if (lprint) write (iout,'(a)') &
1395         "Constants of electrostatic interaction energy expression."
1396       do i=1,2
1397         do j=1,2
1398         rri=rpp(i,j)**6
1399         appc(i,j)=epp(i,j)*rri*rri
1400         bppc(i,j)=-2.0*epp(i,j)*rri
1401         ael6c(i,j)=elpp6c(i,j)*4.2**6
1402         ael3c(i,j)=elpp3c(i,j)*4.2**3
1403         if (lprint) &
1404         write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1405                                      ael3c(i,j)
1406         enddo
1407       enddo
1408       ncont=0
1409       do 1 i=ist,ien-2
1410         xi=c(1,i)
1411         yi=c(2,i)
1412         zi=c(3,i)
1413         dxi=c(1,i+1)-c(1,i)
1414         dyi=c(2,i+1)-c(2,i)
1415         dzi=c(3,i+1)-c(3,i)
1416         xmedi=xi+0.5*dxi
1417         ymedi=yi+0.5*dyi
1418         zmedi=zi+0.5*dzi
1419         do 4 j=i+2,ien-1
1420           ind=ind+1
1421           iteli=itel(i)
1422           itelj=itel(j)
1423           if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1424           if (iteli.eq.2 .and. itelj.eq.2 &
1425             .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1426           aaa=appc(iteli,itelj)
1427           bbb=bppc(iteli,itelj)
1428           ael6i=ael6c(iteli,itelj)
1429           ael3i=ael3c(iteli,itelj)
1430           dxj=c(1,j+1)-c(1,j)
1431           dyj=c(2,j+1)-c(2,j)
1432           dzj=c(3,j+1)-c(3,j)
1433           xj=c(1,j)+0.5*dxj-xmedi
1434           yj=c(2,j)+0.5*dyj-ymedi
1435           zj=c(3,j)+0.5*dzj-zmedi
1436           rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1437           rmij=sqrt(rrmij)
1438           r3ij=rrmij*rmij
1439           r6ij=r3ij*r3ij
1440           vrmij=vblinv*rmij
1441           cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1442           cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1443           cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1444           fac=cosa-3.0*cosb*cosg
1445           ev1=aaa*r6ij*r6ij
1446           ev2=bbb*r6ij
1447           fac3=ael6i*r6ij
1448           fac4=ael3i*r3ij
1449           evdwij=ev1+ev2
1450           el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1451           el2=fac4*fac
1452           eesij=el1+el2
1453           if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1454               j.eq.i+2 .and. eesij.le.elecutoff_14) then
1455              ncont=ncont+1
1456              icont(1,ncont)=i
1457              icont(2,ncont)=j
1458              econt(ncont)=eesij
1459           endif
1460           ees=ees+eesij
1461           evdw=evdw+evdwij
1462     4   continue
1463     1 continue
1464       if (lprint) then
1465         write (iout,*) 'Total average electrostatic energy: ',ees
1466         write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1467         write (iout,*)
1468         write (iout,*) 'Electrostatic contacts before pruning: '
1469         do i=1,ncont
1470           i1=icont(1,i)
1471           i2=icont(2,i)
1472           it1=itype(i1)
1473           it2=itype(i2)
1474           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1475            i,restyp(it1),i1,restyp(it2),i2,econt(i)
1476         enddo
1477       endif
1478 ! For given residues keep only the contacts with the greatest energy.
1479       i=0
1480       do while (i.lt.ncont)
1481         i=i+1
1482         ene=econt(i)
1483         ic1=icont(1,i)
1484         ic2=icont(2,i)
1485         j=i
1486         do while (j.lt.ncont)
1487           j=j+1
1488           if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1489               ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1490 !            write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1491 !     &       " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1492             if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1493               if (ic1.eq.icont(1,j)) then
1494                 do k=1,ncont
1495                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1496                      .and. iabs(icont(1,k)-ic1).le.2 .and. &
1497                      econt(k).lt.econt(j) ) goto 21
1498                 enddo
1499               else if (ic2.eq.icont(2,j) ) then
1500                 do k=1,ncont
1501                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1502                      .and. iabs(icont(2,k)-ic2).le.2 .and. &
1503                      econt(k).lt.econt(j) ) goto 21
1504                 enddo
1505               endif
1506 ! Remove ith contact
1507               do k=i+1,ncont
1508                 icont(1,k-1)=icont(1,k)
1509                 icont(2,k-1)=icont(2,k)
1510                 econt(k-1)=econt(k)
1511               enddo
1512               i=i-1
1513               ncont=ncont-1
1514 !              write (iout,*) "ncont",ncont
1515 !              do k=1,ncont
1516 !                write (iout,*) icont(1,k),icont(2,k)
1517 !              enddo
1518               goto 20
1519             else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1520             then
1521               if (ic1.eq.icont(1,j)) then
1522                 do k=1,ncont
1523                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1524                      .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1525                      econt(k).lt.econt(i) ) goto 21
1526                 enddo
1527               else if (ic2.eq.icont(2,j) ) then
1528                 do k=1,ncont
1529                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1530                      .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1531                      econt(k).lt.econt(i) ) goto 21
1532                 enddo
1533               endif
1534 ! Remove jth contact
1535               do k=j+1,ncont
1536                 icont(1,k-1)=icont(1,k)
1537                 icont(2,k-1)=icont(2,k)
1538                 econt(k-1)=econt(k)
1539               enddo
1540               ncont=ncont-1
1541 !              write (iout,*) "ncont",ncont
1542 !              do k=1,ncont
1543 !                write (iout,*) icont(1,k),icont(2,k)
1544 !              enddo
1545               j=j-1
1546             endif
1547           endif
1548    21     continue
1549         enddo
1550    20   continue
1551       enddo
1552       if (lprint) then
1553         write (iout,*)
1554         write (iout,*) 'Electrostatic contacts after pruning: '
1555         do i=1,ncont
1556           i1=icont(1,i)
1557           i2=icont(2,i)
1558           it1=itype(i1)
1559           it2=itype(i2)
1560           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1561            i,restyp(it1),i1,restyp(it2),i2,econt(i)
1562         enddo
1563       endif
1564       return
1565       end subroutine elecont
1566 !------------------------------------------------------------------------------
1567 ! match_contact.f
1568 !------------------------------------------------------------------------------
1569       subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1570          ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1571          nc_frac,nc_req_set,istr,llocal,lprn)
1572
1573       use energy_data, only:maxcont
1574 !      implicit real*8 (a-h,o-z)
1575 !      include 'DIMENSIONS'
1576 !      include 'COMMON.IOUNITS'
1577       integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1578       integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1579       real(kind=8) :: nc_frac
1580       logical :: llocal,lprn
1581       integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1582                  nc_req_set,istr,nc_match_max
1583       integer :: i,nc_req,nc_match1,is,js
1584       nc_match_max=0
1585       do i=1,ncont_ref
1586         nc_match_max=nc_match_max+ &
1587          min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1588       enddo
1589       if (istr.eq.3) then
1590         nc_req=0
1591       else if (nc_req_set.eq.0) then
1592         nc_req=nc_match_max*nc_frac
1593       else
1594         nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1595           dfloat(nc_req_set)+1.0d-7)
1596       endif
1597 !      write (iout,*) "match_contact: nc_req:",nc_req
1598 !      write (iout,*) "nc_match_max",nc_match_max
1599 !      write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1600 !     &   " n_shif2",n_shif2
1601 ! Match current contact map against reference contact map; exit, if at least
1602 ! half of the contacts match
1603       call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1604           ncont,icont,jfrag,llocal,lprn)
1605       nc_match1_max=nc_match1
1606       if (lprn .and. nc_match.gt.0) write (iout,*) &
1607         "Shift:",0,0," nc_match1",nc_match1,&
1608         " nc_match=",nc_match," req'd",nc_req
1609       if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1610           nc_req.eq.0 .and. nc_match.eq.1) then
1611          ishif1=0
1612          ishif2=0
1613          return
1614       endif
1615 ! If sufficient matches are not found, try to shift contact maps up to three
1616 ! positions.
1617       if (n_shif1.gt.0) then
1618       do is=1,n_shif1
1619 ! The following four tries help to find shifted beta-sheet patterns
1620 ! Shift "left" strand backward
1621         call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1622           icont_ref,ncont,icont,jfrag,llocal,lprn)
1623         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1624         if (lprn .and. nc_match.gt.0) write (iout,*) &
1625           "Shift:",-is,0," nc_match1",nc_match1,&
1626           " nc_match=",nc_match," req'd",nc_req
1627         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1628            nc_req.eq.0 .and. nc_match.eq.1) then
1629           ishif1=-is
1630           ishif2=0
1631           return
1632         endif
1633 ! Shift "left" strand forward
1634         call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1635             icont_ref,ncont,icont,jfrag,llocal,lprn)
1636         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1637         if (lprn .and. nc_match.gt.0) write (iout,*) &
1638          "Shift:",is,0," nc_match1",nc_match1,&
1639          " nc_match=",nc_match," req'd",nc_req
1640         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1641            nc_req.eq.0 .and. nc_match.eq.1) then
1642           ishif1=is
1643           ishif2=0
1644           return
1645         endif
1646       enddo
1647       if (nc_req.eq.0) return
1648 ! Shift "right" strand backward
1649       do is=1,n_shif1
1650         call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1651            icont_ref,ncont,icont,jfrag,llocal,lprn)
1652         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1653         if (lprn .and. nc_match.gt.0) write (iout,*) &
1654           "Shift:",0,-is," nc_match1",nc_match1,&
1655           " nc_match=",nc_match," req'd",nc_req
1656         if (nc_match.ge.nc_req) then
1657           ishif1=0
1658           ishif2=-is
1659           return
1660         endif
1661 ! Shift "right" strand upward
1662         call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
1663           icont_ref,ncont,icont,jfrag,llocal,lprn)
1664         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1665         if (lprn .and. nc_match.gt.0) write (iout,*) &
1666           "Shift:",0,is," nc_match1",nc_match1,&
1667           " nc_match=",nc_match," req'd",nc_req
1668         if (nc_match.ge.nc_req) then
1669           ishif1=0
1670           ishif2=is
1671           return
1672         endif
1673       enddo ! is
1674 ! Now try to shift both residues in contacts.
1675       do is=1,n_shif1
1676         do js=1,is
1677           if (js.ne.is) then
1678             call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1679               icont_ref,ncont,icont,jfrag,llocal,lprn)
1680             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1681             if (lprn .and. nc_match.gt.0) write (iout,*) &
1682                "Shift:",-is,-js," nc_match1",nc_match1,&
1683                " nc_match=",nc_match," req'd",nc_req
1684             if (nc_match.ge.nc_req) then
1685               ishif1=-is
1686               ishif2=-js
1687               return
1688             endif
1689             call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1690               icont_ref,ncont,icont,jfrag,llocal,lprn)
1691             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1692             if (lprn .and. nc_match.gt.0) write (iout,*) &
1693               "Shift:",is,js," nc_match1",nc_match1,&
1694               " nc_match=",nc_match," req'd",nc_req
1695             if (nc_match.ge.nc_req) then
1696               ishif1=is
1697               ishif2=js
1698               return
1699             endif
1700 !
1701             call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
1702               icont_ref,ncont,icont,jfrag,llocal,lprn)
1703             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1704             if (lprn .and. nc_match.gt.0) write (iout,*) &
1705               "Shift:",-js,-is," nc_match1",nc_match1,&
1706               " nc_match=",nc_match," req'd",nc_req
1707             if (nc_match.ge.nc_req) then
1708               ishif1=-js
1709               ishif2=-is
1710               return
1711             endif
1712 !
1713             call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
1714               icont_ref,ncont,icont,jfrag,llocal,lprn)
1715             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1716             if (lprn .and. nc_match.gt.0) write (iout,*) &
1717               "Shift:",js,is," nc_match1",nc_match1,&
1718               " nc_match=",nc_match," req'd",nc_req
1719             if (nc_match.ge.nc_req) then
1720               ishif1=js
1721               ishif2=is
1722               return
1723             endif
1724           endif
1725 !
1726           if (is+js.le.n_shif1) then
1727           call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1728             icont_ref,ncont,icont,jfrag,llocal,lprn)
1729           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1730           if (lprn .and. nc_match.gt.0) write (iout,*) &
1731            "Shift:",-is,js," nc_match1",nc_match1,&
1732            " nc_match=",nc_match," req'd",nc_req
1733           if (nc_match.ge.nc_req) then
1734             ishif1=-is
1735             ishif2=js
1736             return
1737           endif
1738 !
1739           call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
1740             icont_ref,ncont,icont,jfrag,llocal,lprn)
1741           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1742           if (lprn .and. nc_match.gt.0) write (iout,*) &
1743            "Shift:",js,-is," nc_match1",nc_match1,&
1744            " nc_match=",nc_match," req'd",nc_req
1745           if (nc_match.ge.nc_req) then
1746             ishif1=js
1747             ishif2=-is
1748             return
1749           endif
1750           endif
1751 !
1752         enddo !js
1753       enddo !is
1754       endif
1755
1756       if (n_shif2.gt.0) then
1757       do is=1,n_shif2
1758         call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1759           icont_ref,ncont,icont,jfrag,llocal,lprn)
1760         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1761         if (lprn .and. nc_match.gt.0) write (iout,*) &
1762            "Shift:",-is,-is," nc_match1",nc_match1,&
1763            " nc_match=",nc_match," req'd",nc_req
1764         if (nc_match.ge.nc_req) then
1765           ishif1=-is
1766           ishif2=-is
1767           return
1768         endif
1769         call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1770           icont_ref,ncont,icont,jfrag,llocal,lprn)
1771         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1772         if (lprn .and. nc_match.gt.0) write (iout,*) &
1773           "Shift:",is,is," nc_match1",nc_match1,&
1774           " nc_match=",nc_match," req'd",nc_req
1775         if (nc_match.ge.nc_req) then
1776           ishif1=is
1777           ishif2=is
1778           return
1779         endif
1780       enddo
1781       endif
1782 ! If this point is reached, the contact maps are different.
1783       nc_match=0
1784       ishif1=0
1785       ishif2=0
1786       return
1787       end subroutine match_contact
1788 !-------------------------------------------------------------------------
1789       subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1790          ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1791
1792       use energy_data, only:nnt,nct,maxcont
1793 !      implicit real*8 (a-h,o-z)
1794 !      include 'DIMENSIONS'
1795 !      include 'DIMENSIONS.ZSCOPT'
1796 !      include 'DIMENSIONS.COMPAR'
1797 !      include 'COMMON.IOUNITS'
1798 !      include 'COMMON.INTERACT'
1799 !      include 'COMMON.GEO'
1800 !      include 'COMMON.COMPAR'
1801       logical :: llocal,lprn
1802       integer ncont_ref,ncont,ishift,ishif2,nang_pair
1803       integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1804       integer,dimension(2,nres) :: iang_pair !(2,maxres)
1805       integer :: nc_match,nc_match1,ishif1,jfrag
1806       integer :: i,j,ic1,ic2
1807       real(kind=8) :: diffang,fract,rad2deg
1808
1809 ! Compare the contact map against the reference contact map; they're stored
1810 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1811       if (lprn) write (iout,'(80(1h*))')
1812       nc_match=0
1813       nc_match1=0
1814 ! Check the local structure by comparing dihedral angles.
1815 !      write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1816       if (llocal .and. ncont_ref.eq.0) then
1817 ! If there are no contacts just compare the dihedral angles and exit.
1818         call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1819           lprn)
1820         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1821          " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1822         if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1823         then
1824           nc_match=1
1825         else
1826           nc_match=0
1827         endif
1828         return
1829       endif
1830       nang_pair=0
1831       do i=1,ncont
1832         ic1=icont(1,i)+ishif1
1833         ic2=icont(2,i)+ishif2
1834 !        write (iout,*) "i",i," ic1",ic1," ic2",ic2
1835         if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1836         do j=1,ncont_ref
1837           if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1838             nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1839             nc_match1=nc_match1+1
1840             icont_match(1,nc_match1)=ic1
1841             icont_match(2,nc_match1)=ic2
1842 !            call add_angpair(icont(1,i),icont_ref(1,j),
1843 !     &         nang_pair,iang_pair)
1844 !            call add_angpair(icont(2,i),icont_ref(2,j),
1845 !     &         nang_pair,iang_pair)
1846             if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1847              " match",icont_ref(1,j),icont_ref(2,j),&
1848              " shifts",ishif1,ishif2
1849             goto 10
1850           endif
1851         enddo
1852    10   continue
1853       enddo
1854       if (lprn) then
1855         write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1856         write (iout,*) "icont_match"
1857         do i=1,nc_match1
1858           write (iout,*) icont_match(1,i),icont_match(2,i)
1859         enddo
1860       endif
1861       if (llocal .and. nc_match.gt.0) then
1862         call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1863           ang_cut1(jfrag),diffang,fract)
1864         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1865          " ang_cut:",ang_cut(jfrag)*rad2deg,&
1866          " ang_cut1",ang_cut1(jfrag)*rad2deg
1867         if (diffang.gt.ang_cut(jfrag) &
1868           .or. fract.lt.frac_min(jfrag)) nc_match=0
1869       endif
1870 !      if (nc_match.gt.0) then
1871 !        diffang = angnorm1(nang_pair,iang_pair,lprn)
1872 !        if (diffang.gt.ang_cut(jfrag)) nc_match=0
1873 !      endif
1874       if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1875          " diffang",rad2deg*diffang," nc_match",nc_match
1876       return
1877       end subroutine ncont_match
1878 !------------------------------------------------------------------------------
1879       subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1880 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1881 ! conformation considered to that of the reference conformation.
1882 ! Returns the number of equivalent residues (nsec_match).
1883 !      implicit real*8 (a-h,o-z)
1884 !      include 'DIMENSIONS'
1885 !      include 'DIMENSIONS.ZSCOPT'
1886 !      include 'DIMENSIONS.COMPAR'
1887 !      include 'COMMON.IOUNITS'
1888 !      include 'COMMON.CHAIN'
1889 !      include 'COMMON.PEPTCONT'
1890 !      include 'COMMON.COMPAR'
1891       logical :: lprn
1892       integer :: isecstr(nres)
1893       integer :: jfrag,nsec_match,npart,i,j
1894       npart = npiece(jfrag,1)
1895       nsec_match=0
1896       if (lprn) then
1897         write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1898               (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1899         write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1900         write (iout,'(80i1)') (isecstr(j),j=1,nres)
1901       endif
1902       do i=1,npart
1903         do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1904 ! The residue has equivalent conformational state to that of the reference
1905 ! structure, if:
1906 !  a) the conformational states are equal or
1907 !  b) the reference state is a coil and that of the conformation considered
1908 !     is a strand or
1909 !  c) the conformational state of the conformation considered is a strand
1910 !     and that of the reference conformation is a coil.
1911 ! 10/28/02 - case (b) deleted.
1912           if (isecstr(j).eq.isec_ref(j) .or. &
1913 !     &        isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1914               isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1915             nsec_match=nsec_match+1
1916         enddo
1917       enddo
1918       return
1919       end subroutine match_secondary
1920 !------------------------------------------------------------------------------
1921 ! odlodc.f
1922 !------------------------------------------------------------------------------
1923       subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1924
1925       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1926 !                            isccont_frag_ref
1927 !      implicit real*8 (a-h,o-z)
1928       real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1929       real(kind=8) :: uu,vv,aa,bb,dd
1930       real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1931 !el      odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1932 !el       + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1933 !      print *,"r1",(r1(i),i=1,3)
1934 !      print *,"r2",(r2(i),i=1,3)
1935 !      print *,"a",(a(i),i=1,3)
1936 !      print *,"b",(b(i),i=1,3)
1937       aa = a(1)**2+a(2)**2+a(3)**2
1938       bb = b(1)**2+b(2)**2+b(3)**2
1939       ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1940       ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1941       br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1942       det = aa*bb-ab**2
1943 !      print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1944       uu = (-ar*bb+br*ab)/det
1945       vv = (br*aa-ar*ab)/det
1946 !      print *,u,v
1947       uu=dmin1(uu,1.0d0)
1948       uu=dmax1(uu,0.0d0)
1949       vv=dmin1(vv,1.0d0)
1950       vv=dmax1(vv,0.0d0)
1951 !el      dd1 = odl(uu,vv)
1952       dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1953 !el      dd2 = odl(0.0d0,0.0d0)
1954       dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1955 !el      dd3 = odl(0.0d0,1.0d0)
1956       dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1957 !el      dd4 = odl(1.0d0,0.0d0)
1958       dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1959 !el      dd5 = odl(1.0d0,1.0d0)
1960       dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1961       dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1962       if (dd.eq.dd2) then
1963         uu=0.0d0
1964         vv=0.0d0
1965       else if (dd.eq.dd3) then
1966         uu=0.0d0
1967         vv=1.0d0
1968       else if (dd.eq.dd4) then
1969         uu=1.0d0
1970         vv=0.0d0
1971       else if (dd.eq.dd5) then
1972         uu=1.0d0
1973         vv=1.0d0
1974       endif
1975 ! Control check
1976 !      do i=1,3
1977 !        x(i)=r1(i)+u*a(i)
1978 !        y(i)=r2(i)+v*b(i)
1979 !      enddo
1980 !      dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
1981 !      dd1 = dsqrt(dd1)
1982       aa = dsqrt(aa)
1983       bb = dsqrt(bb)
1984 !      write (8,*) uu,vv,dd,dd1
1985 !      print *,dd,dd1
1986       return
1987       end subroutine odlodc
1988 !------------------------------------------------------------------------------
1989       real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
1990
1991       real(kind=8),dimension(3) :: r1,r2
1992       real(kind=8) :: aa,bb,u,v,ar,br,ab
1993
1994       odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1995        + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1996
1997       end function odl
1998 !------------------------------------------------------------------------------
1999 ! proc_cont.f
2000 !------------------------------------------------------------------------------
2001       subroutine proc_cont
2002
2003       use geometry_data, only:rad2deg
2004       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2005 !                            isccont_frag_ref
2006 !      implicit real*8 (a-h,o-z)
2007 !      include 'DIMENSIONS'
2008 !      include 'DIMENSIONS.ZSCOPT'
2009 !      include 'DIMENSIONS.COMPAR'
2010 !      include 'COMMON.IOUNITS'
2011 !      include 'COMMON.TIME1'
2012 !      include 'COMMON.SBRIDGE'
2013 !      include 'COMMON.CONTROL'
2014 !      include 'COMMON.COMPAR'
2015 !      include 'COMMON.CHAIN'
2016 !      include 'COMMON.HEADER'
2017 !      include 'COMMON.CONTACTS1'
2018 !      include 'COMMON.PEPTCONT'
2019 !      include 'COMMON.GEO'
2020       integer :: i,j,k,ind,len_cut,ndigit,length_frag
2021
2022       write (iout,*) "proc_cont: nlevel",nlevel
2023       if (nlevel.lt.0) then
2024         write (iout,*) "call define_fragments"
2025         call define_fragments
2026       else
2027         write (iout,*) "call secondary2"
2028         call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2029            isec_ref)
2030       endif
2031       write (iout,'(80(1h=))')
2032       write (iout,*) "Electrostatic contacts"
2033       call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2034        icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2035       write (iout,'(80(1h=))')
2036       write (iout,*) "Side chain contacts"
2037       call contacts_between_fragments(.true.,0,ncont_ref,&
2038        icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2039       if (nlevel.lt.0) then
2040         do i=1,nfrag(1)
2041           ind=icant(i,i)
2042           len_cut=1000
2043           if (istruct(i).le.1) then
2044             len_cut=max0(len_frag(i,1)*4/5,3)
2045           else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2046             len_cut=max0(len_frag(i,1)*2/5,3)
2047           endif
2048           write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2049             ncont_frag_ref(ind)," len_cut",len_cut,&
2050             " icont_single",icont_single," iloc_single",iloc_single
2051           iloc(i)=iloc_single
2052           if (iloc(i).gt.0) write (iout,*) &
2053            "Local structure used to compare structure of fragment",i,&
2054            " to native."
2055           if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2056               .and. icont_single.gt.0 .and. &
2057               ncont_frag_ref(ind).ge.len_cut) then
2058             write (iout,*) "Electrostatic contacts used to compare",&
2059              " structure of fragment",i," to native."
2060             ielecont(i,1)=1
2061             isccont(i,1)=0
2062           else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2063             .ge.len_cut) then
2064             write (iout,*) "Side chain contacts used to compare",&
2065              " structure of fragment",i," to native."
2066             isccont(i,1)=1
2067             ielecont(i,1)=0
2068           else
2069             write (iout,*) "Contacts not used to compare",&
2070              " structure of fragment",i," to native."
2071             ielecont(i,1)=0
2072             isccont(i,1)=0
2073             nc_req_setf(i,1)=0
2074           endif
2075           if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2076                .and. ielecont(i,1).eq.0) then
2077             write (iout,*) "RMSD used to compare",&
2078              " structure of fragment",i," to native."
2079             irms(i,1)=1
2080           else
2081             write (iout,*) "RMSD not used to compare",&
2082              " structure of fragment",i," to native."
2083             irms(i,1)=0
2084           endif
2085         enddo
2086       endif
2087       if (nlevel.lt.-1) then
2088         call define_pairs
2089         nlevel = -nlevel
2090         if (nlevel.gt.3) nlevel=3
2091         if (nlevel.eq.3) then
2092           nfrag(3)=1
2093           npiece(1,3)=nfrag(1)
2094           do i=1,nfrag(1)
2095             ipiece(i,1,3)=i
2096           enddo
2097           ielecont(1,3)=0
2098           isccont(1,3)=0
2099           irms(1,3)=1
2100           n_shift(1,1,3)=0
2101           n_shift(2,1,3)=0
2102         endif
2103       else if (nlevel.eq.-1) then
2104         nlevel=1
2105       endif
2106       isnfrag(1)=0
2107       do i=1,nlevel
2108         isnfrag(i+1)=isnfrag(i)+nfrag(i)
2109       enddo
2110       ndigit=3*nfrag(1)
2111       do i=2,nlevel
2112         ndigit=ndigit+2*nfrag(i)
2113       enddo
2114       write (iout,*) "ndigit",ndigit
2115       if (.not.binary .and. ndigit.gt.30) then
2116         write (iout,*) "Highest class too large; switching to",&
2117           " binary representation."
2118         binary=.true.
2119       endif
2120       write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2121       write(iout,*) "rmscut_base_up",rmscut_base_up,&
2122        " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2123       do i=1,nlevel
2124         do j=1,nfrag(i)
2125           length_frag = 0
2126           if (i.eq.1) then
2127             do k=1,npiece(j,i)
2128               length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2129             enddo
2130           else
2131             do k=1,npiece(j,i)
2132               length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2133             enddo
2134           endif
2135           len_frag(j,i)=length_frag
2136           rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2137           rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2138           if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2139             rmscutfrag(1,j,i)=rmsup_lim
2140           if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2141             rmscutfrag(1,j,i)=rmsupup_lim
2142         enddo
2143       enddo
2144       write (iout,*) "Level",1," number of fragments:",nfrag(1)
2145       do j=1,nfrag(1)
2146         write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2147           k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2148           rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2149           ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2150           nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2151       enddo
2152       do i=2,nlevel
2153         write (iout,*) "Level",i," number of fragments:",nfrag(i)
2154         do j=1,nfrag(i)
2155           write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2156             k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2157             rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2158             nc_fragm(j,i),nc_req_setf(j,i)
2159         enddo
2160       enddo
2161       return
2162       end subroutine proc_cont
2163 !------------------------------------------------------------------------------
2164 ! define_pairs.f
2165 !------------------------------------------------------------------------------
2166       subroutine define_pairs
2167
2168 !      use energy_data, only:nsccont_frag_ref
2169 !      implicit real*8 (a-h,o-z)
2170 !      include 'DIMENSIONS'
2171 !      include 'DIMENSIONS.ZSCOPT'
2172 !      include 'DIMENSIONS.COMPAR'
2173 !      include 'COMMON.IOUNITS'
2174 !      include 'COMMON.TIME1'
2175 !      include 'COMMON.SBRIDGE'
2176 !      include 'COMMON.CONTROL'
2177 !      include 'COMMON.COMPAR'
2178 !      include 'COMMON.FRAG'
2179 !      include 'COMMON.CHAIN'
2180 !      include 'COMMON.HEADER'
2181 !      include 'COMMON.GEO'
2182 !      include 'COMMON.CONTACTS1'
2183 !      include 'COMMON.PEPTCONT'
2184       integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2185
2186       do j=1,nfrag(1)
2187         length_frag = 0
2188         do k=1,npiece(j,1)
2189           length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2190         enddo
2191         len_frag(j,1)=length_frag
2192         write (iout,*) "Fragment",j," length",len_frag(j,1)
2193       enddo
2194       nfrag(2)=0
2195       do i=1,nfrag(1)
2196         do j=i+1,nfrag(1)
2197           ind = icant(i,j)
2198           if (istruct(i).le.1 .or. istruct(j).le.1) then
2199             if (istruct(i).le.1) then
2200               ll1=len_frag(i,1)
2201             else
2202               ll1=len_frag(i,1)/2
2203             endif
2204             if (istruct(j).le.1) then
2205               ll2=len_frag(j,1)
2206             else
2207               ll2=len_frag(j,1)/2
2208             endif
2209             len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2210           else
2211             if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2212               ll1=len_frag(i,1)/2
2213             else
2214               ll1=len_frag(i,1)
2215             endif
2216             if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2217               ll2=len_frag(j,1)/2
2218             else
2219               ll2=len_frag(j,1)
2220             endif
2221             len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2222           endif
2223           write (iout,*) "Fragments",i,j," structure",istruct(i),&
2224              istruct(j)," # contacts",&
2225              ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2226              " lengths",len_frag(i,1),len_frag(j,1),&
2227              " ll1",ll1," ll2",ll2," len_cut",len_cut
2228           if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2229             nsccont_frag_ref(ind).ge.len_cut ) then
2230             if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2231               write (iout,*) "Adding pair of helices",i,j,&
2232               " based on SC contacts"
2233             else
2234               write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2235               " based on SC contacts"
2236             endif
2237             nfrag(2)=nfrag(2)+1
2238             if (icont_pair.gt.0) then
2239               write (iout,*)  "# SC contacts will be used",&
2240               " in comparison."
2241               isccont(nfrag(2),2)=1
2242             endif
2243             if (irms_pair.gt.0) then
2244               write (iout,*)  "Fragment RMSD will be used",&
2245               " in comparison."
2246               irms(nfrag(2),2)=1
2247             endif
2248             npiece(nfrag(2),2)=2
2249             ipiece(1,nfrag(2),2)=i
2250             ipiece(2,nfrag(2),2)=j
2251             ielecont(nfrag(2),2)=0
2252             n_shift(1,nfrag(2),2)=nshift_pair
2253             n_shift(2,nfrag(2),2)=nshift_pair
2254             nc_fragm(nfrag(2),2)=ncfrac_pair
2255             nc_req_setf(nfrag(2),2)=ncreq_pair
2256           else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2257              .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2258              .and. ncont_frag_ref(ind).ge.len_cut ) then
2259             nfrag(2)=nfrag(2)+1
2260             write (iout,*) "Adding pair strands/sheets",i,j,&
2261               " based on pp contacts"
2262             if (icont_pair.gt.0) then
2263               write (iout,*) "# pp contacts will be used",&
2264               " in comparison."
2265               ielecont(nfrag(2),2)=1
2266             endif
2267             if (irms_pair.gt.0) then
2268               write (iout,*)  "Fragment RMSD will be used",&
2269               " in comparison."
2270               irms(nfrag(2),2)=1
2271             endif
2272             npiece(nfrag(2),2)=2
2273             ipiece(1,nfrag(2),2)=i
2274             ipiece(2,nfrag(2),2)=j
2275             ielecont(nfrag(2),2)=1
2276             isccont(nfrag(2),2)=0
2277             n_shift(1,nfrag(2),2)=nshift_pair
2278             n_shift(2,nfrag(2),2)=nshift_pair
2279             nc_fragm(nfrag(2),2)=ncfrac_bet
2280             nc_req_setf(nfrag(2),2)=ncreq_bet
2281           endif
2282         enddo
2283       enddo
2284       write (iout,*) "Pairs found"
2285       do i=1,nfrag(2)
2286         write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2287       enddo
2288       return
2289       end subroutine define_pairs
2290 !------------------------------------------------------------------------------
2291 ! icant.f
2292 !------------------------------------------------------------------------------
2293       INTEGER FUNCTION ICANT(I,J)
2294       integer :: i,j
2295       IF (I.GE.J) THEN
2296         ICANT=(I*(I-1))/2+J
2297       ELSE
2298         ICANT=(J*(J-1))/2+I
2299       ENDIF
2300       RETURN
2301       END FUNCTION ICANT
2302 !------------------------------------------------------------------------------
2303 ! mysort.f
2304 !------------------------------------------------------------------------------
2305       subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2306 !      implicit none
2307       integer :: n,m,mm
2308       integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2309       real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2310       real(kind=8) :: xxtemp
2311       integer :: i,j,k,imax
2312       do i=1,n
2313         xmin=x(1,1,i)
2314         imax=i
2315         do j=i+1,n
2316           if (x(1,1,j).lt.xmin) then
2317             imax=j
2318             xmin=x(1,1,j)
2319           endif
2320         enddo
2321         xxtemp=z2(imax)
2322         z2(imax)=z2(i)
2323         z2(i)=xxtemp
2324         xxtemp=z3(imax)
2325         z3(imax)=z3(i)
2326         z3(i)=xxtemp
2327         xxtemp=z4(imax)
2328         z4(imax)=z4(i)
2329         z4(i)=xxtemp
2330         xxtemp=z5(imax)
2331         z5(imax)=z5(i)
2332         z5(i)=xxtemp
2333         xtemp=y(imax)
2334         y(imax)=y(i)
2335         y(i)=xtemp
2336         xtemp=z(imax)
2337         z(imax)=z(i)
2338         z(i)=xtemp
2339         xtemp=z6(imax)
2340         z6(imax)=z6(i)
2341         z6(i)=xtemp
2342         do j=1,2
2343           xtemp=z1(j,imax)
2344           z1(j,imax)=z1(j,i)
2345           z1(j,i)=xtemp
2346         enddo
2347         do j=1,m
2348           do k=1,mm
2349             xtemp=x(j,k,imax)
2350             x(j,k,imax)=x(j,k,i)
2351             x(j,k,i)=xtemp
2352           enddo
2353         enddo
2354       enddo
2355       return
2356       end subroutine imysort
2357 !------------------------------------------------------------------------------
2358 ! qwolynes.f
2359 !-------------------------------------------------------------------------------
2360       real(kind=8) function qwolynes(ilevel,jfrag)
2361
2362       use geometry_data, only:cref,nperm
2363       use control_data, only:symetr
2364       use energy_data, only:nnt,nct,itype
2365 !      implicit none
2366 !      include 'DIMENSIONS'
2367 !      include 'DIMENSIONS.ZSCOPT'
2368 !      include 'DIMENSIONS.COMPAR'
2369 !      include 'COMMON.IOUNITS'
2370 !      include 'COMMON.COMPAR'
2371 !      include 'COMMON.CHAIN'
2372 !      include 'COMMON.INTERACT'
2373 !      include 'COMMON.CONTROL'
2374       integer :: ilevel,jfrag,kkk
2375       integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2376       integer :: nsep=3
2377       real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2378       real(kind=8) :: maxiQ !dist,
2379       real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2380       logical :: lprn=.false.
2381       real(kind=8) :: x !el sigm
2382 !el      sigm(x)=0.25d0*x
2383       nperm=1
2384       maxiQ=0
2385       do i=1,symetr
2386       nperm=i*nperm
2387       enddo
2388 !      write (iout,*) "QWolyes: " jfrag",jfrag,
2389 !     &  " ilevel",ilevel
2390       allocate(tempus(nperm))
2391       do kkk=1,nperm
2392       qq = 0.0d0
2393       if (ilevel.eq.0) then
2394         if (lprn) write (iout,*) "Q computed for whole molecule"
2395         nl=0
2396         do il=nnt+nsep,nct
2397           do jl=nnt,il-nsep
2398             dij=0.0d0
2399             dijCM=0.0d0
2400             d0ij=0.0d0
2401             d0ijCM=0.0d0
2402             qqij=0.0d0
2403             qqijCM=0.0d0
2404             nl=nl+1
2405             d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2406                        (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2407                        (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2408             dij=dist(il,jl)
2409             qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2410             if (itype(il).ne.10 .or. itype(jl).ne.10) then
2411               nl=nl+1
2412               d0ijCM=dsqrt( &
2413                      (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2414                      (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2415                      (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2416               dijCM=dist(il+nres,jl+nres)
2417               qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2418             endif
2419             qq = qq+qqij+qqijCM
2420             if (lprn) then
2421               write (iout,*) "il",il," jl",jl,&
2422                " itype",itype(il),itype(jl)
2423               write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2424                " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2425             endif
2426           enddo
2427         enddo
2428         qq = qq/nl
2429         if (lprn) write (iout,*) "nl",nl," qq",qq
2430       else if (ilevel.eq.1) then
2431         if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2432         nl=0
2433 !        write (iout,*) "nlist_frag",nlist_frag(jfrag)
2434         do i=2,nlist_frag(jfrag)
2435           do j=1,i-1
2436             il=list_frag(i,jfrag)
2437             jl=list_frag(j,jfrag)
2438             if (iabs(il-jl).gt.nsep) then
2439               dij=0.0d0
2440               dijCM=0.0d0
2441               d0ij=0.0d0
2442               d0ijCM=0.0d0
2443               qqij=0.0d0
2444               qqijCM=0.0d0
2445               nl=nl+1
2446               d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2447                          (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2448                          (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2449               dij=dist(il,jl)
2450               qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2451               if (itype(il).ne.10 .or. itype(jl).ne.10) then
2452                 nl=nl+1
2453                 d0ijCM=dsqrt( &
2454                        (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2455                        (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2456                        (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2457                 dijCM=dist(il+nres,jl+nres)
2458                qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2459               endif
2460               qq = qq+qqij+qqijCM
2461               if (lprn) then
2462                 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2463                  " itype",itype(il),itype(jl)
2464                 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2465                  " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2466               endif
2467             endif
2468           enddo
2469         enddo
2470         qq = qq/nl
2471         if (lprn) write (iout,*) "nl",nl," qq",qq
2472       else if (ilevel.eq.2) then
2473         np=npiece(jfrag,ilevel)
2474         nl=0
2475         do i=2,np
2476           ip=ipiece(i,jfrag,ilevel)
2477           do j=1,nlist_frag(ip)
2478             il=list_frag(j,ip)
2479             do k=1,i-1
2480               kp=ipiece(k,jfrag,ilevel)
2481               do l=1,nlist_frag(kp)
2482                 kl=list_frag(l,kp)
2483                 if (iabs(kl-il).gt.nsep) then
2484                   nl=nl+1
2485                   dij=0.0d0
2486                   dijCM=0.0d0
2487                   d0ij=0.0d0
2488                   d0ijCM=0.0d0
2489                   qqij=0.0d0
2490                   qqijCM=0.0d0
2491                   d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2492                              (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2493                              (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2494                   dij=dist(il,kl)
2495                   qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2496                   if (itype(il).ne.10 .or. itype(kl).ne.10) then
2497                     nl=nl+1
2498                     d0ijCM=dsqrt( &
2499                        (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2500                        (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2501                        (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2502                     dijCM=dist(il+nres,kl+nres)
2503                     qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2504                       (sigm(d0ijCM)))**2)
2505                   endif
2506                   qq = qq+qqij+qqijCM
2507                   if (lprn) then
2508                     write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2509                       " kl",kl," itype",itype(il),itype(kl)
2510                     write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2511                     d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2512                   endif
2513                 endif
2514               enddo  ! l
2515             enddo    ! k
2516           enddo      ! j
2517         enddo        ! i
2518         qq = qq/nl
2519         if (lprn) write (iout,*) "nl",nl," qq",qq
2520       else
2521         write (iout,*)"Error: Q can be computed only for level 1 and 2."
2522       endif
2523       tempus(kkk)=qq
2524       enddo
2525       do kkk=1,nperm
2526        if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2527       enddo
2528       qwolynes=1.0d0-maxiQ
2529       deallocate(tempus)
2530       return
2531       end function qwolynes
2532 !-------------------------------------------------------------------------------
2533       real(kind=8) function sigm(x)
2534       real(kind=8) :: x
2535       sigm=0.25d0*x
2536       return
2537       end function sigm
2538 !-------------------------------------------------------------------------------
2539       subroutine fragment_list
2540 !      implicit none
2541 !      include 'DIMENSIONS'
2542 !      include 'DIMENSIONS.ZSCOPT'
2543 !      include 'DIMENSIONS.COMPAR'
2544 !      include 'COMMON.IOUNITS'
2545 !      include 'COMMON.COMPAR'
2546       logical :: lprn=.true.
2547       integer :: i,ilevel,j,k,jfrag
2548       do jfrag=1,nfrag(1)
2549         nlist_frag(jfrag)=0
2550         do i=1,npiece(jfrag,1)
2551           if (lprn) write (iout,*) "jfrag=",jfrag,&
2552             "i=",i," fragment",ifrag(1,i,jfrag),&
2553             ifrag(2,i,jfrag)
2554           do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2555             do k=1,nlist_frag(jfrag)
2556               if (list_frag(k,jfrag).eq.j) goto 10
2557             enddo
2558             nlist_frag(jfrag)=nlist_frag(jfrag)+1
2559             list_frag(nlist_frag(jfrag),jfrag)=j
2560           enddo
2561   10      continue
2562         enddo
2563       enddo
2564       write (iout,*) "Fragment list"
2565       do j=1,nfrag(1)
2566         write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2567          k=1,nlist_frag(j))
2568       enddo
2569       return
2570       end subroutine fragment_list
2571 !-------------------------------------------------------------------------------
2572       real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2573
2574       use w_comm_local
2575       use control_data, only:symetr
2576       use geometry_data, only:nperm
2577 !      implicit real*8 (a-h,o-z)
2578 !      include 'DIMENSIONS'
2579 !      include 'DIMENSIONS.ZSCOPT'
2580 !      include 'DIMENSIONS.COMPAR'
2581 !      include 'COMMON.IOUNITS'
2582 !      include 'COMMON.COMPAR'
2583 !      include 'COMMON.CHAIN'
2584 !      include 'COMMON.INTERACT'
2585 !      include 'COMMON.VAR'
2586 !      include 'COMMON.CONTROL'
2587       real(kind=8) :: przes(3),obrot(3,3)
2588 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2589 !el      logical :: iadded(nres)
2590 !el      integer :: inumber(2,nres)
2591 !el      common /ccc/ creff,cc,iadded,inumber
2592       logical :: lprn
2593       logical :: non_conv
2594       integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2595       real(kind=8) :: rminrms,rms
2596       if (lprn) then
2597         write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2598         write (iout,*) "npiece",npiece(j,i)
2599         call flush(iout)
2600       endif
2601 !      write (iout,*) "symetr",symetr
2602 !      call flush(iout)
2603       nperm=1
2604       do idup=1,symetr
2605       nperm=nperm*idup
2606       enddo
2607 !      write (iout,*) "nperm",nperm
2608 !      call flush(iout)
2609       do kkk=1,nperm
2610       idup=0
2611       do l=1,nres
2612         iadded(l)=.false.
2613       enddo
2614 !      write (iout,*) "kkk",kkk
2615 !      call flush(iout)
2616       do k=1,npiece(j,i)
2617         if (i.eq.1) then
2618           if (lprn) then
2619             write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2620                ifrag(1,k,j),ifrag(2,k,j)
2621             call flush(iout)
2622           endif
2623           call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2624 !          write (iout,*) "Exit cprep"
2625 !          call flush(iout)
2626 !          write (iout,*) "ii=",ii
2627         else
2628           kk = ipiece(k,j,i)
2629 !          write (iout,*) "kk",kk," npiece",npiece(kk,1)
2630           do l=1,npiece(kk,1)
2631             if (lprn) then
2632               write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2633                 " l=",l," adding fragment",&
2634                 ifrag(1,l,kk),ifrag(2,l,kk)
2635               call flush(iout)
2636             endif
2637             call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2638 !            write (iout,*) "After cprep"
2639 !            call flush(iout)
2640           enddo
2641         endif
2642       enddo
2643       enddo
2644       if (lprn) then
2645         write (iout,*) "tuszukaj"
2646         do kkk=1,nperm
2647           do k=1,idup
2648             write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2649               inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2650           enddo
2651         enddo
2652         call flush(iout)
2653       endif
2654       rminrms=1.0d10
2655       do kkk=1,nperm
2656       call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2657       if (non_conv) then
2658         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2659         rms = 1.0d10
2660       else if (rms.lt.-1.0d-6) then
2661         print *,'Error: rms^2 = ',rms,jcon,i
2662         rms = 1.0d10
2663       else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2664         rms = 0.0d0
2665       endif
2666 !      write (iout,*) "rmsmin", rminrms, "rms", rms
2667       if (rms.le.rminrms) rminrms=rms
2668       enddo
2669       rmscalc = dsqrt(rminrms)
2670 !      write (iout, *) "analysys", rmscalc,anatemp
2671       return
2672       end function rmscalc
2673 !-------------------------------------------------------------------------
2674       subroutine cprep(if1,if2,ishif,idup,kwa)
2675
2676       use w_comm_local
2677       use control_data, only:symetr
2678       use geometry_data, only:nperm,cref,c
2679 !      implicit real*8 (a-h,o-z)
2680 !      include 'DIMENSIONS'
2681 !      include 'DIMENSIONS.ZSCOPT'
2682 !      include 'DIMENSIONS.COMPAR'
2683 !      include 'COMMON.CONTROL'
2684 !      include 'COMMON.IOUNITS'
2685 !      include 'COMMON.COMPAR'
2686 !      include 'COMMON.CHAIN'
2687 !      include 'COMMON.INTERACT'
2688 !      include 'COMMON.VAR'
2689       real(kind=8) :: przes(3),obrot(3,3)
2690 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2691 !el      logical :: iadded(nres)
2692 !el      integer :: inumber(2,nres)
2693       integer :: iistrart,kwa,blar
2694 !el      common /ccc/ creff,cc,iadded,inumber
2695       integer :: if1,if2,ishif,idup,kkk,l,m
2696 !      write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2697       nperm=1
2698       do blar=1,symetr
2699       nperm=nperm*blar
2700       enddo
2701 !      write (iout,*) "nperm",nperm
2702       kkk=kwa
2703 !      ii=0
2704       do l=if1,if2
2705 !        write (iout,*) "l",l," iadded",iadded(l)
2706 !        call flush(iout)
2707         if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2708         then
2709           idup=idup+1
2710           iadded(l)=.true.
2711           inumber(1,idup)=l
2712           inumber(2,idup)=l+ishif
2713           do m=1,3
2714             creff(m,idup)=cref(m,l,kkk)
2715             cc(m,idup)=c(m,l+ishif)
2716           enddo
2717         endif
2718       enddo
2719       return
2720       end subroutine cprep
2721 !-------------------------------------------------------------------------
2722       real(kind=8) function rmsnat(jcon)
2723
2724       use control_data, only:symetr
2725       use geometry_data, only:nperm,cref,c
2726       use energy_data, only:itype
2727 !      implicit real*8 (a-h,o-z)
2728 !      include 'DIMENSIONS'
2729 !      include 'DIMENSIONS.ZSCOPT'
2730 !      include 'DIMENSIONS.COMPAR'
2731 !      include 'COMMON.IOUNITS'
2732 !      include 'COMMON.COMPAR'
2733 !      include 'COMMON.CHAIN'
2734 !      include 'COMMON.INTERACT'
2735 !      include 'COMMON.VAR'
2736 !      include 'COMMON.CONTROL'
2737       real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2738       logical :: non_conv
2739       integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2740       real(kind=8) :: rminrms,rmsminsing,rms
2741       rminrms=10.0d10
2742       rmsminsing=10d10
2743       nperm=1
2744       do i=1,symetr
2745        nperm=nperm*i
2746       enddo
2747       do kkk=1,nperm
2748        nnsup=0
2749        do i=1,nres
2750         if (itype(i).ne.ntyp1) then
2751           nnsup=nnsup+1
2752           do j=1,3
2753             cc(j,nnsup)=c(j,i)
2754             ccref(j,nnsup)=cref(j,i,kkk)
2755           enddo
2756         endif
2757        enddo
2758        call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2759        if (non_conv) then
2760         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2761         rms=1.0d10
2762        else if (rms.lt.-1.0d-6) then
2763         print *,'Error: rms^2 = ',rms,jcon,i
2764         rms = 1.0d10
2765        else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2766         rms=0.0d0
2767        endif
2768        if (rms.le.rminrms) rminrms=rms
2769 !       write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2770       enddo
2771       rmsnat = dsqrt(rminrms)
2772 !      write (iout,*)  "analysys",rmsnat, anatemp
2773 !      liczenie rmsdla pojedynczego lancucha
2774       return
2775       end function rmsnat
2776 !-------------------------------------------------------------------------------
2777       subroutine define_fragments
2778
2779       use geometry_data, only:rad2deg
2780       use energy_data, only:itype
2781       use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2782 !      implicit real*8 (a-h,o-z)
2783 !      include 'DIMENSIONS'
2784 !      include 'DIMENSIONS.ZSCOPT'
2785 !      include 'DIMENSIONS.COMPAR'
2786 !      include 'COMMON.IOUNITS'
2787 !      include 'COMMON.TIME1'
2788 !      include 'COMMON.FRAG'
2789 !      include 'COMMON.SBRIDGE'
2790 !      include 'COMMON.CONTROL'
2791 !      include 'COMMON.COMPAR'
2792 !      include 'COMMON.CHAIN'
2793 !      include 'COMMON.HEADER'
2794 !      include 'COMMON.GEO'
2795 !      include 'COMMON.CONTACTS'
2796 !      include 'COMMON.PEPTCONT'
2797 !      include 'COMMON.INTERACT'
2798 !      include 'COMMON.NAMES'
2799       integer :: nstrand,istrand(2,nres/2)
2800       integer :: nhairp,ihairp(2,nres/5)
2801       character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2802                           'strand','strand pair'/),shape(strstr))
2803       integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2804
2805       write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2806                      'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2807                  'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2808         ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2809       write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2810         ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2811       write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2812         ' MAXANG_HEL',angcut1_hel*rad2deg
2813       write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2814                      ' MAXANG_BET',angcut1_bet*rad2deg
2815       write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2816                      ' MAXANG_STRAND',angcut1_strand*rad2deg
2817       write (iout,*) 'FRAC_MIN',frac_min_set
2818 ! Find secondary structure elements (helices and beta-sheets)
2819       call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2820          isec_ref)
2821 ! Define primary fragments. First include the helices.
2822       nhairp=0
2823       nstrand=0
2824 ! Merge helices
2825 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2826       if (merge_helices) then
2827       write (iout,*) "Before merging helices: nhfrag",nhfrag
2828       do i=1,nhfrag
2829         write (2,*) hfrag(1,i),hfrag(2,i)
2830       enddo
2831       i=1
2832       do while (i.lt.nhfrag)
2833         if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2834           nhfrag=nhfrag-1
2835           hfrag(2,i)=hfrag(2,i+1)
2836           do j=i+1,nhfrag
2837             hfrag(1,j)=hfrag(1,j+1)
2838             hfrag(2,j)=hfrag(2,j+1)
2839           enddo
2840         endif
2841         i=i+1
2842       enddo
2843       write (iout,*) "After merging helices: nhfrag",nhfrag
2844       do i=1,nhfrag
2845         write (2,*) hfrag(1,i),hfrag(2,i)
2846       enddo
2847       endif
2848       nfrag(1)=nhfrag
2849       do i=1,nhfrag
2850         npiece(i,1)=1
2851         ifrag(1,1,i)=hfrag(1,i)
2852         ifrag(2,1,i)=hfrag(2,i)
2853         n_shift(1,i,1)=0
2854         n_shift(2,i,1)=nshift_hel
2855         ang_cut(i)=angcut_hel
2856         ang_cut1(i)=angcut1_hel
2857         frac_min(i)=frac_min_set
2858         nc_fragm(i,1)=ncfrac_hel
2859         nc_req_setf(i,1)=ncreq_hel
2860         istruct(i)=1
2861       enddo
2862       write (iout,*) "isplit_bet",isplit_bet
2863       if (isplit_bet.gt.1) then
2864 ! Split beta-sheets into strands and store strands as primary fragments.
2865         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2866         do i=1,nstrand
2867           ii=i+nfrag(1)
2868           npiece(ii,1)=1
2869           ifrag(1,1,ii)=istrand(1,i)
2870           ifrag(2,1,ii)=istrand(2,i)
2871           n_shift(1,ii,1)=nshift_strand
2872           n_shift(2,ii,1)=nshift_strand
2873           ang_cut(ii)=angcut_strand
2874           ang_cut1(ii)=angcut1_strand
2875           frac_min(ii)=frac_min_set
2876           nc_fragm(ii,1)=0
2877           nc_req_setf(ii,1)=0
2878           istruct(ii)=3
2879         enddo
2880         nfrag(1)=nfrag(1)+nstrand
2881       else if (isplit_bet.eq.1) then
2882 ! Split only far beta-sheets; does not split hairpins.
2883         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2884         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2885         do i=1,nhairp
2886           ii=i+nfrag(1)
2887           npiece(ii,1)=1
2888           ifrag(1,1,ii)=ihairp(1,i)
2889           ifrag(2,1,ii)=ihairp(2,i)
2890           n_shift(1,ii,1)=nshift_bet
2891           n_shift(2,ii,1)=nshift_bet
2892           ang_cut(ii)=angcut_bet
2893           ang_cut1(ii)=angcut1_bet
2894           frac_min(ii)=frac_min_set
2895           nc_fragm(ii,1)=ncfrac_bet
2896           nc_req_setf(ii,1)=ncreq_bet
2897           istruct(ii)=2
2898         enddo
2899         nfrag(1)=nfrag(1)+nhairp
2900         do i=1,nstrand
2901           ii=i+nfrag(1)
2902           npiece(ii,1)=1
2903           ifrag(1,1,ii)=istrand(1,i)
2904           ifrag(2,1,ii)=istrand(2,i)
2905           n_shift(1,ii,1)=nshift_strand
2906           n_shift(2,ii,1)=nshift_strand
2907           ang_cut(ii)=angcut_strand
2908           ang_cut1(ii)=angcut1_strand
2909           frac_min(ii)=frac_min_set
2910           nc_fragm(ii,1)=0
2911           nc_req_setf(ii,1)=0
2912           istruct(ii)=3
2913         enddo
2914         nfrag(1)=nfrag(1)+nstrand
2915       else
2916 ! Do not split beta-sheets; each pair of strands is a primary element.
2917         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2918         do i=1,nhairp
2919           ii=i+nfrag(1)
2920           npiece(ii,1)=1
2921           ifrag(1,1,ii)=ihairp(1,i)
2922           ifrag(2,1,ii)=ihairp(2,i)
2923           n_shift(1,ii,1)=nshift_bet
2924           n_shift(2,ii,1)=nshift_bet
2925           ang_cut(ii)=angcut_bet
2926           ang_cut1(ii)=angcut1_bet
2927           frac_min(ii)=frac_min_set
2928           nc_fragm(ii,1)=ncfrac_bet
2929           nc_req_setf(ii,1)=ncreq_bet
2930           istruct(ii)=2
2931         enddo
2932         nfrag(1)=nfrag(1)+nhairp
2933         do i=1,nbfrag
2934           ii=i+nfrag(1)
2935           npiece(ii,1)=2
2936           ifrag(1,1,ii)=bfrag(1,i)
2937           ifrag(2,1,ii)=bfrag(2,i)
2938           if (bfrag(3,i).lt.bfrag(4,i)) then
2939             ifrag(1,2,ii)=bfrag(3,i)
2940             ifrag(2,2,ii)=bfrag(4,i)
2941           else
2942             ifrag(1,2,ii)=bfrag(4,i)
2943             ifrag(2,2,ii)=bfrag(3,i)
2944           endif
2945           n_shift(1,ii,1)=nshift_bet
2946           n_shift(2,ii,1)=nshift_bet
2947           ang_cut(ii)=angcut_bet
2948           ang_cut1(ii)=angcut1_bet
2949           frac_min(ii)=frac_min_set
2950           nc_fragm(ii,1)=ncfrac_bet
2951           nc_req_setf(ii,1)=ncreq_bet
2952           istruct(ii)=4
2953         enddo
2954         nfrag(1)=nfrag(1)+nbfrag
2955       endif
2956       write (iout,*) "The following primary fragments were found:"
2957       write (iout,*) "Helices:",nhfrag
2958       do i=1,nhfrag
2959         i1=ifrag(1,1,i)
2960         i2=ifrag(2,1,i)
2961         it1=itype(i1)
2962         it2=itype(i2)
2963         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2964              i,restyp(it1),i1,restyp(it2),i2
2965       enddo
2966       write (iout,*) "Hairpins:",nhairp
2967       do i=nhfrag+1,nhfrag+nhairp
2968         i1=ifrag(1,1,i)
2969         i2=ifrag(2,1,i)
2970         it1=itype(i1)
2971         it2=itype(i2)
2972         write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2973              i,restyp(it1),i1,restyp(it2),i2
2974       enddo
2975       write (iout,*) "Far strand pairs:",nbfrag
2976       do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
2977         i1=ifrag(1,1,i)
2978         i2=ifrag(2,1,i)
2979         it1=itype(i1)
2980         it2=itype(i2)
2981         i3=ifrag(1,2,i)
2982         i4=ifrag(2,2,i)
2983         it3=itype(i3)
2984         it4=itype(i4)
2985         write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
2986              i,restyp(it1),i1,restyp(it2),i2,&
2987                restyp(it3),i3,restyp(it4),i4
2988       enddo
2989       write (iout,*) "Strands:",nstrand
2990       do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
2991         i1=ifrag(1,1,i)
2992         i2=ifrag(2,1,i)
2993         it1=itype(i1)
2994         it2=itype(i2)
2995         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2996              i,restyp(it1),i1,restyp(it2),i2
2997       enddo
2998       call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
2999         istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3000         nc_fragm(1,1),nc_req_setf(1,1))
3001       write (iout,*) "Fragments after sorting:"
3002       do i=1,nfrag(1)
3003         i1=ifrag(1,1,i)
3004         i2=ifrag(2,1,i)
3005         it1=itype(i1)
3006         it2=itype(i2)
3007         write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3008              i,restyp(it1),i1,restyp(it2),i2
3009         if (npiece(i,1).eq.1) then
3010           write (iout,'(2x,a)') strstr(istruct(i))
3011         else
3012           i1=ifrag(1,2,i)
3013           i2=ifrag(2,2,i)
3014           it1=itype(i1)
3015           it2=itype(i2)
3016           write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3017              restyp(it1),i1,restyp(it2),i2,strstr(istruct(i))
3018         endif
3019       enddo
3020       return
3021       end subroutine define_fragments
3022 !------------------------------------------------------------------------------
3023       subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3024 !      implicit real*8 (a-h,o-z)
3025 !      include 'DIMENSIONS'
3026 !      include 'DIMENSIONS.ZSCOPT'
3027 !      include 'DIMENSIONS.COMPAR'
3028 !      include 'COMMON.IOUNITS'
3029       integer :: nbfrag,bfrag(4,nres/3)
3030       integer :: nhairp,ihairp(2,nres/5)
3031       integer :: i,j,k
3032       write (iout,*) "Entered find_and_remove_hairpins"
3033       write (iout,*) "nbfrag",nbfrag
3034       do i=1,nbfrag
3035         write (iout,*) i,(bfrag(k,i),k=1,4)
3036       enddo
3037       nhairp=0
3038       i=1
3039       do while (i.le.nbfrag)
3040         write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3041         if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3042         then
3043           write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3044           nhairp=nhairp+1
3045           ihairp(1,nhairp)=bfrag(1,i)
3046           ihairp(2,nhairp)=bfrag(3,i)
3047           nbfrag=nbfrag-1
3048           do j=i,nbfrag
3049             do k=1,4
3050               bfrag(k,j)=bfrag(k,j+1)
3051             enddo
3052           enddo
3053         else
3054           i=i+1
3055         endif
3056       enddo
3057       write (iout,*) "After finding hairpins:"
3058       write (iout,*) "nhairp",nhairp
3059       do i=1,nhairp
3060         write (iout,*) i,ihairp(1,i),ihairp(2,i)
3061       enddo
3062       write (iout,*) "nbfrag",nbfrag
3063       do i=1,nbfrag
3064         write (iout,*) i,(bfrag(k,i),k=1,4)
3065       enddo
3066       return
3067       end subroutine find_and_remove_hairpins
3068 !------------------------------------------------------------------------------
3069       subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3070 !      implicit real*8 (a-h,o-z)
3071 !      include 'DIMENSIONS'
3072 !      include 'DIMENSIONS.ZSCOPT'
3073 !      include 'DIMENSIONS.COMPAR'
3074 !      include 'COMMON.IOUNITS'
3075       integer :: nbfrag,bfrag(4,nres/3)
3076       integer :: nstrand,istrand(2,nres/2)
3077       integer :: nhairp,ihairp(2,nres/5)
3078       logical :: found
3079       integer :: i,k
3080       write (iout,*) "Entered split_beta"
3081       write (iout,*) "nbfrag",nbfrag
3082       do i=1,nbfrag
3083         write (iout,*) i,(bfrag(k,i),k=1,4)
3084       enddo
3085       nstrand=0
3086       do i=1,nbfrag
3087         write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3088         call add_strand(nstrand,istrand,nhairp,ihairp,&
3089            bfrag(1,i),bfrag(2,i),found)
3090         if (bfrag(3,i).lt.bfrag(4,i)) then
3091           write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3092           call add_strand(nstrand,istrand,nhairp,ihairp,&
3093            bfrag(3,i),bfrag(4,i),found)
3094         else
3095           write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3096           call add_strand(nstrand,istrand,nhairp,ihairp,&
3097             bfrag(4,i),bfrag(3,i),found)
3098         endif
3099       enddo
3100       nbfrag=0
3101       write (iout,*) "Strands found:",nstrand
3102       do i=1,nstrand
3103         write (iout,*) i,istrand(1,i),istrand(2,i)
3104       enddo
3105       return
3106       end subroutine split_beta
3107 !------------------------------------------------------------------------------
3108       subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3109 !      implicit real*8 (a-h,o-z)
3110 !      include 'DIMENSIONS'
3111 !      include 'DIMENSIONS.ZSCOPT'
3112 !      include 'DIMENSIONS.COMPAR'
3113 !      include 'COMMON.IOUNITS'
3114       integer :: nstrand,istrand(2,nres/2)
3115       integer :: nhairp,ihairp(2,nres/5)
3116       logical :: found
3117       integer :: is1,is2,j,idelt
3118       found=.false.
3119       do j=1,nhairp
3120         idelt=(ihairp(2,j)-ihairp(1,j))/6
3121         if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3122           write (iout,*) "strand",is1,is2," is part of hairpin",&
3123             ihairp(1,j),ihairp(2,j)
3124           return
3125         endif
3126       enddo
3127       do j=1,nstrand
3128         idelt=(istrand(2,j)-istrand(1,j))/3
3129         if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3130         then
3131 ! The strand already exists in the array; update its ends if necessary.
3132           write (iout,*) "strand",is1,is2," found at position",j,&
3133            ":",istrand(1,j),istrand(2,j)
3134           istrand(1,j)=min0(istrand(1,j),is1)
3135           istrand(2,j)=max0(istrand(2,j),is2)
3136           return
3137         endif
3138       enddo
3139 ! The strand has not been found; add it to the array.
3140       write (iout,*) "strand",is1,is2," added to the array."
3141       found=.true.
3142       nstrand=nstrand+1
3143       istrand(1,nstrand)=is1
3144       istrand(2,nstrand)=is2
3145       return
3146       end subroutine add_strand
3147 !------------------------------------------------------------------------------
3148       subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3149
3150       use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3151       use energy_data, only:itype,maxcont
3152       use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3153       use compare, only:freeres
3154 !      implicit real*8 (a-h,o-z)
3155 !      include 'DIMENSIONS'
3156 !      include 'DIMENSIONS.ZSCOPT'
3157 !      include 'COMMON.IOUNITS'
3158 !      include 'COMMON.FRAG'
3159 !      include 'COMMON.VAR'
3160 !      include 'COMMON.GEO'
3161 !      include 'COMMON.CHAIN'
3162 !      include 'COMMON.NAMES'
3163 !      include 'COMMON.INTERACT'
3164       integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres),&
3165         isecstr(nres)
3166       logical :: lprint,lprint_sec,not_done !el,freeres
3167       integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3168       integer :: nstrand,nbeta,nhelix,iii1,jjj1
3169       real(kind=8) :: p1,p2
3170 !rel      external freeres
3171       character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3172       if (lprint) then
3173         write (iout,*) "entered secondary2",ncont
3174         write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3175         do i=1,ncont
3176           write (iout,*) icont(1,i),icont(2,i)
3177         enddo
3178       endif
3179       do i=1,nres
3180         isecstr(i)=0
3181       enddo
3182       nbfrag=0
3183       nhfrag=0
3184       do i=1,nres
3185         isec(i,1)=0
3186         isec(i,2)=0
3187         nsec(i)=0
3188       enddo
3189
3190 ! finding parallel beta
3191 !d      write (iout,*) '------- looking for parallel beta -----------'
3192       nbeta=0
3193       nstrand=0
3194       do i=1,ncont
3195         i1=icont(1,i)
3196         j1=icont(2,i)
3197         if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3198            .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3199 !d        write (iout,*) "parallel",i1,j1
3200         if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3201           ii1=i1
3202           jj1=j1
3203 !d          write (iout,*) i1,j1
3204           not_done=.true.
3205           do while (not_done)
3206            i1=i1+1
3207            j1=j1+1
3208             do j=1,ncont
3209               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3210                    freeres(i1,j1,nsec,isec)) goto 5
3211             enddo
3212             not_done=.false.
3213   5         continue
3214 !d            write (iout,*) i1,j1,not_done
3215           enddo
3216           j1=j1-1
3217           i1=i1-1
3218           if (i1-ii1.gt.1) then
3219             ii1=max0(ii1-1,1)
3220             jj1=max0(jj1-1,1)
3221             nbeta=nbeta+1
3222             if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3223                      nbeta,ii1,i1,jj1,j1
3224
3225             nbfrag=nbfrag+1
3226             bfrag(1,nbfrag)=ii1+1
3227             bfrag(2,nbfrag)=i1+1
3228             bfrag(3,nbfrag)=jj1+1
3229             bfrag(4,nbfrag)=min0(j1+1,nres)
3230
3231             do ij=ii1,i1
3232              nsec(ij)=nsec(ij)+1
3233              isec(ij,nsec(ij))=nbeta
3234             enddo
3235             do ij=jj1,j1
3236              nsec(ij)=nsec(ij)+1
3237              isec(ij,nsec(ij))=nbeta
3238             enddo
3239
3240            if(lprint_sec) then
3241             nstrand=nstrand+1
3242             if (nbeta.le.9) then
3243               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3244                 "DefPropRes 'strand",nstrand,&
3245                 "' 'num = ",ii1-1,"..",i1-1,"'"
3246             else
3247               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3248                 "DefPropRes 'strand",nstrand,&
3249                 "' 'num = ",ii1-1,"..",i1-1,"'"
3250             endif
3251             nstrand=nstrand+1
3252             if (nbeta.le.9) then
3253               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3254                 "DefPropRes 'strand",nstrand,&
3255                 "' 'num = ",jj1-1,"..",j1-1,"'"
3256             else
3257               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3258                 "DefPropRes 'strand",nstrand,&
3259                 "' 'num = ",jj1-1,"..",j1-1,"'"
3260             endif
3261               write(12,'(a8,4i4)') &
3262                 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3263            endif
3264           endif
3265         endif
3266         endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3267       enddo
3268
3269 ! finding antiparallel beta
3270 !d      write (iout,*) '--------- looking for antiparallel beta ---------'
3271
3272       do i=1,ncont
3273         i1=icont(1,i)
3274         j1=icont(2,i)
3275         if (freeres(i1,j1,nsec,isec)) then
3276           ii1=i1
3277           jj1=j1
3278 !d          write (iout,*) i1,j1
3279
3280           not_done=.true.
3281           do while (not_done)
3282            i1=i1+1
3283            j1=j1-1
3284             do j=1,ncont
3285               if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3286                    freeres(i1,j1,nsec,isec)) goto 6
3287             enddo
3288             not_done=.false.
3289   6         continue
3290 !d            write (iout,*) i1,j1,not_done
3291           enddo
3292           i1=i1-1
3293           j1=j1+1
3294           if (i1-ii1.gt.1) then
3295
3296             nbfrag=nbfrag+1
3297             bfrag(1,nbfrag)=ii1
3298             bfrag(2,nbfrag)=min0(i1+1,nres)
3299             bfrag(3,nbfrag)=min0(jj1+1,nres)
3300             bfrag(4,nbfrag)=j1
3301
3302             nbeta=nbeta+1
3303             iii1=max0(ii1-1,1)
3304             do ij=iii1,i1
3305              nsec(ij)=nsec(ij)+1
3306              if (nsec(ij).le.2) then
3307               isec(ij,nsec(ij))=nbeta
3308              endif
3309             enddo
3310             jjj1=max0(j1-1,1)
3311             do ij=jjj1,jj1
3312              nsec(ij)=nsec(ij)+1
3313              if (nsec(ij).le.2) then
3314               isec(ij,nsec(ij))=nbeta
3315              endif
3316             enddo
3317
3318
3319            if (lprint_sec) then
3320             write (iout,'(a,i3,4i4)')'antiparallel beta',&
3321                          nbeta,ii1-1,i1,jj1,j1-1
3322             nstrand=nstrand+1
3323             if (nstrand.le.9) then
3324               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3325                 "DefPropRes 'strand",nstrand,&
3326                 "' 'num = ",ii1-2,"..",i1-1,"'"
3327             else
3328               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3329                 "DefPropRes 'strand",nstrand,&
3330                 "' 'num = ",ii1-2,"..",i1-1,"'"
3331             endif
3332             nstrand=nstrand+1
3333             if (nstrand.le.9) then
3334               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3335                 "DefPropRes 'strand",nstrand,&
3336                 "' 'num = ",j1-2,"..",jj1-1,"'"
3337             else
3338               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3339                 "DefPropRes 'strand",nstrand,&
3340                 "' 'num = ",j1-2,"..",jj1-1,"'"
3341             endif
3342               write(12,'(a8,4i4)') &
3343                 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3344            endif
3345           endif
3346         endif
3347       enddo
3348
3349 !d      write (iout,*) "After beta:",nbfrag
3350 !d      do i=1,nbfrag
3351 !d        write (iout,*) (bfrag(j,i),j=1,4)
3352 !d      enddo
3353
3354       if (nstrand.gt.0.and.lprint_sec) then
3355         write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3356         do i=2,nstrand
3357          if (i.le.9) then
3358           write(12,'(a9,i1,$)') " | strand",i
3359          else
3360           write(12,'(a9,i2,$)') " | strand",i
3361          endif
3362         enddo
3363         write(12,'(a1)') "'"
3364       endif
3365
3366
3367 ! finding alpha or 310 helix
3368
3369       nhelix=0
3370       do i=1,ncont
3371         i1=icont(1,i)
3372         j1=icont(2,i)
3373         p1=phi(i1+2)*rad2deg
3374         p2=0.0
3375         if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3376
3377
3378         if (j1.eq.i1+3 .and. &
3379              ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3380              ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3381 !d          if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3382 !o          if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3383           ii1=i1
3384           jj1=j1
3385           if (nsec(ii1).eq.0) then
3386             not_done=.true.
3387           else
3388             not_done=.false.
3389           endif
3390           do while (not_done)
3391             i1=i1+1
3392             j1=j1+1
3393             do j=1,ncont
3394               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3395             enddo
3396             not_done=.false.
3397   10        continue
3398             p1=phi(i1+2)*rad2deg
3399             p2=phi(j1+2)*rad2deg
3400             if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3401                                     not_done=.false.
3402
3403 !d           write (iout,*) i1,j1,not_done,p1,p2
3404           enddo
3405           j1=j1+1
3406           if (j1-ii1.gt.4) then
3407             nhelix=nhelix+1
3408 !d            write (iout,*)'helix',nhelix,ii1,j1
3409
3410             nhfrag=nhfrag+1
3411             hfrag(1,nhfrag)=ii1
3412             hfrag(2,nhfrag)=j1
3413
3414             do ij=ii1,j1
3415              nsec(ij)=-1
3416             enddo
3417            if (lprint_sec) then
3418             write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3419             if (nhelix.le.9) then
3420               write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3421                 "DefPropRes 'helix",nhelix,&
3422                 "' 'num = ",ii1-1,"..",j1-2,"'"
3423             else
3424               write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3425                 "DefPropRes 'helix",nhelix,&
3426                 "' 'num = ",ii1-1,"..",j1-2,"'"
3427             endif
3428            endif
3429           endif
3430         endif
3431       enddo
3432
3433       if (nhelix.gt.0.and.lprint_sec) then
3434         write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3435         do i=2,nhelix
3436          if (nhelix.le.9) then
3437           write(12,'(a8,i1,$)') " | helix",i
3438          else
3439           write(12,'(a8,i2,$)') " | helix",i
3440          endif
3441         enddo
3442         write(12,'(a1)') "'"
3443       endif
3444
3445       if (lprint_sec) then
3446        write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3447        write(12,'(a20)') "XMacStand ribbon.mac"
3448       endif
3449
3450       if (lprint) then
3451
3452         write(iout,*) 'UNRES seq:',anatemp
3453         do j=1,nbfrag
3454          write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3455         enddo
3456
3457         do j=1,nhfrag
3458          write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3459         enddo
3460
3461       endif
3462
3463       do j=1,nbfrag
3464         do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3465           isecstr(k)=1
3466         enddo
3467         do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3468           isecstr(k)=1
3469         enddo
3470       enddo
3471       do j=1,nhfrag
3472         do k=hfrag(1,j),hfrag(2,j)
3473           isecstr(k)=2
3474         enddo
3475       enddo
3476       if (lprint) then
3477         write (iout,*)
3478         write (iout,*) "Secondary structure"
3479         do i=1,nres,80
3480           ist=i
3481           ien=min0(i+79,nres)
3482           write (iout,*)
3483           write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3484           write (iout,'(80a1)') (onelet(itype(k)),k=ist,ien)
3485           write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3486         enddo
3487         write (iout,*)
3488       endif
3489       return
3490       end subroutine secondary2
3491 !-------------------------------------------------
3492 !      logical function freeres(i,j,nsec,isec)
3493 !      include 'DIMENSIONS'
3494 !      integer :: isec(nres,4),nsec(nres)
3495 !      integer :: i,j,k,l
3496 !      freeres=.false.
3497 !
3498 !      if (nsec(i).gt.1.or.nsec(j).gt.1) return
3499 !      do k=1,nsec(i)
3500 !        do l=1,nsec(j)
3501 !          if (isec(i,k).eq.isec(j,l)) return
3502 !        enddo
3503 !      enddo
3504 !      freeres=.true.
3505 !      return
3506 !      end function freeres
3507 !-------------------------------------------------
3508        subroutine alloc_compar_arrays(nfrg,nlev)
3509
3510        use energy_data, only:maxcont
3511        use w_comm_local
3512        integer :: nfrg,nlev
3513
3514 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3515 !------------------------
3516 ! commom.contacts
3517 !      common /contacts/
3518       allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3519       allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3520 !------------------------
3521 ! COMMON.COMPAR
3522 !      common /compar/
3523       allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3524       allocate(qfrag(nfrg,2)) !(maxfrag,2)
3525       allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3526       allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3527       allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3528         ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3529         ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3530       allocate(ncont_nat(2,nfrg,nlev+1))
3531       allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3532 !      allocate(nfrag(nlev)) !(maxlevel)
3533       allocate(isnfrag(nlev+2)) !(maxlevel+1)
3534       allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3535       allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3536       allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3537       allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3538       allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3539 !------------------------
3540 ! COMMON.PEPTCONT
3541 !      common /peptcont/
3542 !      integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3543       allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3544       allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3545 !      integer,dimension(:),allocatable :: isec_ref !(maxres)
3546 !------------------------
3547 !      module w_comm_local
3548 !      common /ccc/
3549       allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3550       allocate(iadded(nres)) !(nres)
3551       allocate(inumber(2,nres)) !(2,nres)
3552
3553
3554 !-------------------------------------------------------------------------------
3555       end subroutine alloc_compar_arrays
3556 #endif
3557 !-------------------------------------------------------------------------------
3558       end module conform_compar
3559