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,molnum
 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,mnum,mnum2
 913       real(kind=8) :: csc !el,dist
 914       real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
 915           ddsc,ddla,ddlb
 916       integer :: ncont,mhum
 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         mnum=molnum(i)
 929         write (iout,110) restyp(itype(i,mnum),mnum),i,c(1,i),c(2,i),&
 930           c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
 931           dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
 932       enddo
 933       endif
 934   110 format (a,'(',i3,')',9f8.3)
 935       do i=ist,ien-kkk
 936         mnum=molnum(i)
 937         iti=iabs(itype(i,mnum))
 938         if (iti.le.0 .or. iti.gt.ntyp_molec(mnum)) cycle
 939         do j=i+kkk,ien
 940           mnum2=molnum(j)
 941           itj=iabs(itype(j,mnum2))
 942           if (itj.le.0 .or. itj.gt.ntyp_molec(mnum2)) cycle
 943           itypi=iti
 944           itypj=itj
 945           xj = c(1,nres+j)-c(1,nres+i)
 946           yj = c(2,nres+j)-c(2,nres+i)
 947           zj = c(3,nres+j)-c(3,nres+i)
 948           dxi = dc_norm(1,nres+i)
 949           dyi = dc_norm(2,nres+i)
 950           dzi = dc_norm(3,nres+i)
 951           dxj = dc_norm(1,nres+j)
 952           dyj = dc_norm(2,nres+j)
 953           dzj = dc_norm(3,nres+j)
 954           do k=1,3
 955             a(k)=dc(k,nres+i)
 956             b(k)=dc(k,nres+j)
 957           enddo
 958 !          write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
 959           if (icomparfunc.eq.1) then
 960             call contfunc(csc,iti,itj)
 961           else if (icomparfunc.eq.2) then
 962             call scdist(csc,iti,itj)
 963           else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
 964             csc = dist(nres+i,nres+j)
 965           else if (icomparfunc.eq.4) then
 966             call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
 967           else
 968             write (*,*) "Error - Unknown sidechain contact function"
 969             write (iout,*) "Error - Unknown sidechain contact function"
 970           endif
 971           if (csc.lt.sc_cutoff(iti,itj)) then
 972 !            write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
 973 !     &      " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
 974 !     &      dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
 975 !     &      dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
 976 !     &      xj,yj,zj
 977 !            write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
 978 !     &       sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
 979 !     &       chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
 980 !     &       csc
 981             ncont=ncont+1
 982             cscore(ncont)=csc
 983             icont(1,ncont)=i
 984             icont(2,ncont)=j
 985             omt1(ncont)=om1
 986             omt2(ncont)=om2
 987             omt12(ncont)=om12
 988             ddsc(ncont)=1.0d0/rij
 989             ddla(ncont)=dla
 990             ddlb(ncont)=dlb
 991           endif
 992         enddo
 993       enddo
 994       if (lprint) then
 995         write (iout,'(a)') 'Contact map:'
 996         do i=1,ncont
 997           mnum=molnum(i)
 998           i1=icont(1,i)
 999           i2=icont(2,i)
1000           it1=itype(i1,molnum(i1))
1001           it2=itype(i2,molnum(i2))
1002 !          print *,"CONTACT",i1,mnum,it1,it2
1003           write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
1004            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2,cscore(i),&
1005            sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1006            omt1(i),omt2(i),omt12(i)
1007         enddo
1008       endif
1009       return
1010       end subroutine contact
1011 #else
1012 !----------------------------------------------------------------------------
1013       subroutine contact(lprint,ncont,icont)
1014
1015       use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii
1016 !      include 'DIMENSIONS'
1017 !      include 'COMMON.IOUNITS'
1018 !      include 'COMMON.CHAIN'
1019 !      include 'COMMON.INTERACT'
1020 !      include 'COMMON.FFIELD'
1021 !      include 'COMMON.NAMES'
1022       real(kind=8) :: facont=1.569D0  ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1023       integer :: ncont,icont(2,maxcont)
1024       logical :: lprint
1025       integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1026       real(kind=8) :: rcomp
1027       ncont=0
1028       kkk=3
1029 !     print *,'nnt=',nnt,' nct=',nct
1030       do i=nnt+kkk,nct
1031         mnum=molnum(i)
1032         iti=iabs(itype(i,1))
1033         do j=nnt,i-kkk
1034           mnum2=molnum(j)
1035           itj=iabs(itype(j,1))
1036           if (ipot.ne.4) then
1037 !           rcomp=sigmaii(iti,itj)+1.0D0
1038             rcomp=facont*sigmaii(iti,itj)
1039           else
1040 !           rcomp=sigma(iti,itj)+1.0D0
1041             rcomp=facont*sigma(iti,itj)
1042           endif
1043 !         rcomp=6.5D0
1044 !         print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1045           if (dist(nres+i,nres+j).lt.rcomp) then
1046             ncont=ncont+1
1047             icont(1,ncont)=i
1048             icont(2,ncont)=j
1049           endif
1050         enddo
1051       enddo
1052       if (lprint) then
1053         write (iout,'(a)') 'Contact map:'
1054         do i=1,ncont
1055            mnum=molnum(i)
1056           i1=icont(1,i)
1057           i2=icont(2,i)
1058           it1=itype(i1,1)
1059           it2=itype(i2,1)
1060           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1061            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1062         enddo
1063       endif
1064       return
1065       end subroutine contact
1066 #endif
1067 !----------------------------------------------------------------------------
1068       real(kind=8) function contact_fract(ncont,ncont_ref,&
1069                                            icont,icont_ref)
1070
1071       use energy_data, only:maxcont
1072 !      implicit none
1073 !      include 'DIMENSIONS'
1074 !      include 'COMMON.IOUNITS'
1075       integer :: i,j,nmatch
1076       integer :: ncont,ncont_ref
1077       integer,dimension(2,maxcont) :: icont,icont_ref
1078       nmatch=0
1079 !     print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1080 !     write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1081 !     write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1082 !     write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1083 !     write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1084       do i=1,ncont
1085         do j=1,ncont_ref
1086           if (icont(1,i).eq.icont_ref(1,j) .and. &
1087               icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1088         enddo
1089       enddo
1090 !     print *,' nmatch=',nmatch
1091 !     contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1092       contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1093       return
1094       end function contact_fract
1095 #ifndef CLUSTER
1096 !------------------------------------------------------------------------------
1097       subroutine pept_cont(lprint,ncont,icont)
1098
1099       use geometry_data, only:c
1100       use energy_data, only:maxcont,nnt,nct,itype,molnum
1101 !      implicit none
1102 !      include 'DIMENSIONS'
1103 !      include 'DIMENSIONS.ZSCOPT'
1104 !      include 'COMMON.IOUNITS'
1105 !      include 'COMMON.CHAIN'
1106 !      include 'COMMON.INTERACT'
1107 !      include 'COMMON.FFIELD'
1108 !      include 'COMMON.NAMES'
1109       integer :: ncont,icont(2,maxcont)
1110       integer :: i,j,k,kkk,i1,i2,it1,it2,mnum
1111       logical :: lprint
1112 !el      real(kind=8) :: dist
1113       real(kind=8) :: rcomp=5.5d0
1114       ncont=0
1115       kkk=0
1116       print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1117       do i=nnt,nct-3
1118         do k=1,3
1119           c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1120         enddo
1121         do j=i+2,nct-1
1122           do k=1,3
1123             c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1124           enddo
1125           if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1126             ncont=ncont+1
1127             icont(1,ncont)=i
1128             icont(2,ncont)=j
1129           endif
1130         enddo
1131       enddo
1132       if (lprint) then
1133         write (iout,'(a)') 'PP contact map:'
1134         do i=1,ncont
1135           mnum=molnum(i)
1136           i1=icont(1,i)
1137           i2=icont(2,i)
1138           it1=itype(i1,mnum)
1139           it2=itype(i2,mnum)
1140           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1141            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1142         enddo
1143       endif
1144       return
1145       end subroutine pept_cont
1146 !-----------------------------------------------------------------------------
1147 ! cont_frag.f
1148 !-----------------------------------------------------------------------------
1149       subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1150          ncont_interfrag,icont_interfrag)
1151
1152       use energy_data, only:itype,maxcont,molnum
1153 !      include 'DIMENSIONS'
1154 !      include 'DIMENSIONS.ZSCOPT'
1155 !      include 'DIMENSIONS.COMPAR'
1156 !      include 'COMMON.INTERACT'
1157 !      include 'COMMON.COMPAR'
1158 !      include 'COMMON.IOUNITS'
1159 !      include 'COMMON.CHAIN'
1160 !      include 'COMMON.NAMES'
1161       integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1162         icont_interfrag(2,maxcont,mmaxfrag)
1163       logical :: OK1,OK2,lprint
1164       integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2,mnum
1165 ! Determine the contacts that occur within a fragment and between fragments.
1166       do i=1,nfrag(1)
1167         do j=1,i
1168           ind = icant(i,j)
1169           nc=0
1170 !          write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1171 !     &      ,k=1,npiece(i,1))
1172 !          write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1173 !     &      ,k=1,npiece(j,1))
1174 !          write (iout,*) "ncont",ncont
1175           do k=1,ncont
1176             ic1=icont(1,k)
1177             ic2=icont(2,k)
1178             OK1=.false.
1179             l=0
1180             do while (.not.OK1 .and. l.lt.npiece(j,1))
1181               l=l+1
1182               OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1183                ic1.le.ifrag(2,l,j)+is
1184             enddo
1185             OK2=.false.
1186             l=0
1187             do while (.not.OK2 .and. l.lt.npiece(i,1))
1188               l=l+1
1189               OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1190                ic2.le.ifrag(2,l,i)+is
1191             enddo
1192 !            write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1193 !     &        " OK2",OK2
1194             if (OK1.and.OK2) then
1195               nc=nc+1
1196               icont_interfrag(1,nc,ind)=ic1
1197               icont_interfrag(2,nc,ind)=ic2
1198 !              write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1199             endif
1200           enddo
1201           ncont_interfrag(ind)=nc
1202 !          do k=1,ncont_interfrag(ind)
1203 !              i1=icont_interfrag(1,k,ind)
1204 !              i2=icont_interfrag(2,k,ind)
1205 !              it1=itype(i1)
1206 !              it2=itype(i2)
1207 !              write (iout,'(i3,2x,a,i4,2x,a,i4)')
1208 !     &          i,restyp(it1),i1,restyp(it2),i2
1209 !          enddo
1210         enddo
1211       enddo
1212       if (lprint) then
1213         write (iout,*) "Contacts within fragments:"
1214         do i=1,nfrag(1)
1215           write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1216            ifrag(2,k,i),k=1,npiece(i,1)),")"
1217           ind=icant(i,i)
1218           do k=1,ncont_interfrag(ind)
1219             i1=icont_interfrag(1,k,ind)
1220             i2=icont_interfrag(2,k,ind)
1221             mnum=molnum(i1)
1222             it1=itype(i1,mnum)
1223             it2=itype(i2,molnum(i2))
1224             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1225               i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1226           enddo
1227         enddo
1228         write (iout,*)
1229         write (iout,*) "Contacts between fragments:"
1230         do i=1,nfrag(1)
1231         do j=1,i-1
1232           ind = icant(i,j)
1233           write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1234            ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1235            (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1236           write (iout,*) "Number of contacts",&
1237            ncont_interfrag(ind)
1238           ind=icant(i,j)
1239           do k=1,ncont_interfrag(ind)
1240             i1=icont_interfrag(1,k,ind)
1241             i2=icont_interfrag(2,k,ind)
1242             mnum=molnum(i1)
1243             it1=itype(i1,mnum)
1244             it2=itype(i2,molnum(i2))
1245             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1246               i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1247           enddo
1248         enddo
1249         enddo
1250       endif
1251       return
1252       end subroutine contacts_between_fragments
1253 !-----------------------------------------------------------------------------
1254 ! contfunc.f
1255 !-----------------------------------------------------------------------------
1256       subroutine contfunc(cscore,itypi,itypj)
1257 !
1258 ! This subroutine calculates the contact function based on
1259 ! the Gay-Berne potential of interaction.
1260 !
1261       use calc_data
1262 !      implicit real*8 (a-h,o-z)
1263 !      include 'DIMENSIONS'
1264 !      include 'COMMON.CONTPAR'
1265 !      include 'COMMON.CALC'
1266       integer :: expon=6
1267       integer :: itypi,itypj
1268       real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1269 !
1270       sig0ij=sig_comp(itypi,itypj)
1271       chi1=chi_comp(itypi,itypj)
1272       chi2=chi_comp(itypj,itypi)
1273       chi12=chi1*chi2
1274       chip1=chip_comp(itypi,itypj)
1275       chip2=chip_comp(itypj,itypi)
1276       chip12=chip1*chip2
1277       rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1278       rij=dsqrt(rrij)
1279 ! Calculate angle-dependent terms of the contact function
1280       erij(1)=xj*rij
1281       erij(2)=yj*rij
1282       erij(3)=zj*rij
1283       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1284       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1285       om12=dxi*dxj+dyi*dyj+dzi*dzj
1286       chiom12=chi12*om12
1287 !      print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1288 !     &  sig0ij,
1289 !     &  rij,rrij,om1,om2,om12
1290 ! Calculate eps1(om12)
1291       faceps1=1.0D0-om12*chiom12
1292       faceps1_inv=1.0D0/faceps1
1293       eps1=dsqrt(faceps1_inv)
1294 ! Following variable is eps1*deps1/dom12
1295       eps1_om12=faceps1_inv*chiom12
1296 ! Calculate sigma(om1,om2,om12)
1297       om1om2=om1*om2
1298       chiom1=chi1*om1
1299       chiom2=chi2*om2
1300       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1301       sigsq=1.0D0-facsig*faceps1_inv
1302 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1303       chipom1=chip1*om1
1304       chipom2=chip2*om2
1305       chipom12=chip12*om12
1306       facp=1.0D0-om12*chipom12
1307       facp_inv=1.0D0/facp
1308       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1309 ! Following variable is the square root of eps2
1310       eps2rt=1.0D0-facp1*facp_inv
1311       sigsq=1.0D0/sigsq
1312       sig=sig0ij*dsqrt(sigsq)
1313       rij_shift=1.0D0/rij-sig+sig0ij
1314       if (rij_shift.le.0.0D0) then
1315         evdw=1.0D1
1316         cscore = -dlog(evdw+1.0d-6)
1317         return
1318       endif
1319       rij_shift=1.0D0/rij_shift
1320       e2=(rij_shift*sig0ij)**expon
1321       evdw=dabs(eps1*eps2rt**2*e2)
1322       if (evdw.gt.1.0d1) evdw = 1.0d1
1323       cscore = -dlog(evdw+1.0d-6)
1324       return
1325       end subroutine contfunc
1326 !------------------------------------------------------------------------------
1327       subroutine scdist(cscore,itypi,itypj)
1328 !
1329 ! This subroutine calculates the contact distance
1330 !
1331       use calc_data
1332 !      implicit real*8 (a-h,o-z)
1333 !      include 'DIMENSIONS'
1334 !      include 'COMMON.CONTPAR'
1335 !      include 'COMMON.CALC'
1336       integer :: itypi,itypj
1337       real(kind=8) :: cscore,rrij
1338
1339       chi1=chi_comp(itypi,itypj)
1340       chi2=chi_comp(itypj,itypi)
1341       chi12=chi1*chi2
1342       rrij=xj*xj+yj*yj+zj*zj
1343       rij=dsqrt(rrij)
1344 ! Calculate angle-dependent terms of the contact function
1345       erij(1)=xj/rij
1346       erij(2)=yj/rij
1347       erij(3)=zj/rij
1348       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1349       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1350       om12=dxi*dxj+dyi*dyj+dzi*dzj
1351       chiom12=chi12*om12
1352       om1om2=om1*om2
1353       chiom1=chi1*om1
1354       chiom2=chi2*om2
1355       cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1356       return
1357       end subroutine scdist
1358 !------------------------------------------------------------------------------
1359 ! elecont.f
1360 !------------------------------------------------------------------------------
1361       subroutine elecont(lprint,ncont,icont,ist,ien)
1362
1363       use geometry_data, only:c
1364       use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2,molnum
1365 !      implicit none
1366 !      include 'DIMENSIONS'
1367 !      include 'DIMENSIONS.ZSCOPT'
1368 !      include 'DIMENSIONS.COMPAR'
1369 !      include 'COMMON.IOUNITS'
1370 !      include 'COMMON.CHAIN'
1371 !      include 'COMMON.INTERACT'
1372 !      include 'COMMON.FFIELD'
1373 !      include 'COMMON.NAMES'
1374 !      include 'COMMON.LOCAL'
1375       logical :: lprint
1376       integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1377       real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1378         xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1379         vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1380         eesij,ees,evdw,ene
1381       real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1382                        -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1383       real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1384                         0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1385       real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1386       real(kind=8) :: elcutoff=-0.3d0
1387       real(kind=8) :: elecutoff_14=-0.5d0
1388       integer :: ncont,icont(2,maxcont),mnum
1389       real(kind=8) :: econt(maxcont)
1390 !
1391 ! Load the constants of peptide bond - peptide bond interactions.
1392 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1393 ! proline) - determined by averaging ECEPP energy.
1394 !
1395 ! as of 7/06/91.
1396 !
1397 !      data epp    / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1398 !      data rpp    / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1399 !el      data (elpp6c)   /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1400 !el      data (elpp3c)   / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1401 !el      data (elcutoff) /-0.3d0/
1402 !el      data (elecutoff_14) /-0.5d0/
1403       ees=0.0d0
1404       evdw=0.0d0
1405       if (lprint) write (iout,'(a)') &
1406         "Constants of electrostatic interaction energy expression."
1407       do i=1,2
1408         do j=1,2
1409         rri=rpp(i,j)**6
1410         appc(i,j)=epp(i,j)*rri*rri
1411         bppc(i,j)=-2.0*epp(i,j)*rri
1412         ael6c(i,j)=elpp6c(i,j)*4.2**6
1413         ael3c(i,j)=elpp3c(i,j)*4.2**3
1414         if (lprint) &
1415         write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1416                                      ael3c(i,j)
1417         enddo
1418       enddo
1419       ncont=0
1420       do 1 i=ist,ien-2
1421         xi=c(1,i)
1422         yi=c(2,i)
1423         zi=c(3,i)
1424         dxi=c(1,i+1)-c(1,i)
1425         dyi=c(2,i+1)-c(2,i)
1426         dzi=c(3,i+1)-c(3,i)
1427         xmedi=xi+0.5*dxi
1428         ymedi=yi+0.5*dyi
1429         zmedi=zi+0.5*dzi
1430         do 4 j=i+2,ien-1
1431           ind=ind+1
1432           iteli=itel(i)
1433           itelj=itel(j)
1434           if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1435           if (iteli.eq.2 .and. itelj.eq.2 &
1436             .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1437           aaa=appc(iteli,itelj)
1438           bbb=bppc(iteli,itelj)
1439           ael6i=ael6c(iteli,itelj)
1440           ael3i=ael3c(iteli,itelj)
1441           dxj=c(1,j+1)-c(1,j)
1442           dyj=c(2,j+1)-c(2,j)
1443           dzj=c(3,j+1)-c(3,j)
1444           xj=c(1,j)+0.5*dxj-xmedi
1445           yj=c(2,j)+0.5*dyj-ymedi
1446           zj=c(3,j)+0.5*dzj-zmedi
1447           rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1448           rmij=sqrt(rrmij)
1449           r3ij=rrmij*rmij
1450           r6ij=r3ij*r3ij
1451           vrmij=vblinv*rmij
1452           cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1453           cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1454           cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1455           fac=cosa-3.0*cosb*cosg
1456           ev1=aaa*r6ij*r6ij
1457           ev2=bbb*r6ij
1458           fac3=ael6i*r6ij
1459           fac4=ael3i*r3ij
1460           evdwij=ev1+ev2
1461           el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1462           el2=fac4*fac
1463           eesij=el1+el2
1464           if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1465               j.eq.i+2 .and. eesij.le.elecutoff_14) then
1466              ncont=ncont+1
1467              icont(1,ncont)=i
1468              icont(2,ncont)=j
1469              econt(ncont)=eesij
1470           endif
1471           ees=ees+eesij
1472           evdw=evdw+evdwij
1473     4   continue
1474     1 continue
1475       if (lprint) then
1476         write (iout,*) 'Total average electrostatic energy: ',ees
1477         write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1478         write (iout,*)
1479         write (iout,*) 'Electrostatic contacts before pruning: '
1480         do i=1,ncont
1481           i1=icont(1,i)
1482           i2=icont(2,i)
1483           it1=itype(i1,molnum(i1))
1484           it2=itype(i2,molnum(i1))
1485           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1486            i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i1)),i2,econt(i)
1487         enddo
1488       endif
1489 ! For given residues keep only the contacts with the greatest energy.
1490       i=0
1491       do while (i.lt.ncont)
1492         i=i+1
1493         ene=econt(i)
1494         ic1=icont(1,i)
1495         ic2=icont(2,i)
1496         j=i
1497         do while (j.lt.ncont)
1498           j=j+1
1499           if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1500               ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1501 !            write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1502 !     &       " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1503             if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1504               if (ic1.eq.icont(1,j)) then
1505                 do k=1,ncont
1506                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1507                      .and. iabs(icont(1,k)-ic1).le.2 .and. &
1508                      econt(k).lt.econt(j) ) goto 21
1509                 enddo
1510               else if (ic2.eq.icont(2,j) ) then
1511                 do k=1,ncont
1512                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1513                      .and. iabs(icont(2,k)-ic2).le.2 .and. &
1514                      econt(k).lt.econt(j) ) goto 21
1515                 enddo
1516               endif
1517 ! Remove ith contact
1518               do k=i+1,ncont
1519                 icont(1,k-1)=icont(1,k)
1520                 icont(2,k-1)=icont(2,k)
1521                 econt(k-1)=econt(k)
1522               enddo
1523               i=i-1
1524               ncont=ncont-1
1525 !              write (iout,*) "ncont",ncont
1526 !              do k=1,ncont
1527 !                write (iout,*) icont(1,k),icont(2,k)
1528 !              enddo
1529               goto 20
1530             else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1531             then
1532               if (ic1.eq.icont(1,j)) then
1533                 do k=1,ncont
1534                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1535                      .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1536                      econt(k).lt.econt(i) ) goto 21
1537                 enddo
1538               else if (ic2.eq.icont(2,j) ) then
1539                 do k=1,ncont
1540                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1541                      .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1542                      econt(k).lt.econt(i) ) goto 21
1543                 enddo
1544               endif
1545 ! Remove jth contact
1546               do k=j+1,ncont
1547                 icont(1,k-1)=icont(1,k)
1548                 icont(2,k-1)=icont(2,k)
1549                 econt(k-1)=econt(k)
1550               enddo
1551               ncont=ncont-1
1552 !              write (iout,*) "ncont",ncont
1553 !              do k=1,ncont
1554 !                write (iout,*) icont(1,k),icont(2,k)
1555 !              enddo
1556               j=j-1
1557             endif
1558           endif
1559    21     continue
1560         enddo
1561    20   continue
1562       enddo
1563       if (lprint) then
1564         write (iout,*)
1565         write (iout,*) 'Electrostatic contacts after pruning: '
1566         do i=1,ncont
1567           mnum=molnum(i)
1568           i1=icont(1,i)
1569           i2=icont(2,i)
1570             mnum=molnum(i1)
1571             it1=itype(i1,mnum)
1572             it2=itype(i2,molnum(i2))
1573           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1574            i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2,econt(i)
1575         enddo
1576       endif
1577       return
1578       end subroutine elecont
1579 !------------------------------------------------------------------------------
1580 ! match_contact.f
1581 !------------------------------------------------------------------------------
1582       subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1583          ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1584          nc_frac,nc_req_set,istr,llocal,lprn)
1585
1586       use energy_data, only:maxcont
1587 !      implicit real*8 (a-h,o-z)
1588 !      include 'DIMENSIONS'
1589 !      include 'COMMON.IOUNITS'
1590       integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1591       integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1592       real(kind=8) :: nc_frac
1593       logical :: llocal,lprn
1594       integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1595                  nc_req_set,istr,nc_match_max
1596       integer :: i,nc_req,nc_match1,is,js
1597       nc_match_max=0
1598       do i=1,ncont_ref
1599         nc_match_max=nc_match_max+ &
1600          min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1601       enddo
1602       if (istr.eq.3) then
1603         nc_req=0
1604       else if (nc_req_set.eq.0) then
1605         nc_req=nc_match_max*nc_frac
1606       else
1607         nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1608           dfloat(nc_req_set)+1.0d-7)
1609       endif
1610 !      write (iout,*) "match_contact: nc_req:",nc_req
1611 !      write (iout,*) "nc_match_max",nc_match_max
1612 !      write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1613 !     &   " n_shif2",n_shif2
1614 ! Match current contact map against reference contact map; exit, if at least
1615 ! half of the contacts match
1616       call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1617           ncont,icont,jfrag,llocal,lprn)
1618       nc_match1_max=nc_match1
1619       if (lprn .and. nc_match.gt.0) write (iout,*) &
1620         "Shift:",0,0," nc_match1",nc_match1,&
1621         " nc_match=",nc_match," req'd",nc_req
1622       if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1623           nc_req.eq.0 .and. nc_match.eq.1) then
1624          ishif1=0
1625          ishif2=0
1626          return
1627       endif
1628 ! If sufficient matches are not found, try to shift contact maps up to three
1629 ! positions.
1630       if (n_shif1.gt.0) then
1631       do is=1,n_shif1
1632 ! The following four tries help to find shifted beta-sheet patterns
1633 ! Shift "left" strand backward
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 ! Shift "left" strand forward
1647         call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1648             icont_ref,ncont,icont,jfrag,llocal,lprn)
1649         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1650         if (lprn .and. nc_match.gt.0) write (iout,*) &
1651          "Shift:",is,0," nc_match1",nc_match1,&
1652          " nc_match=",nc_match," req'd",nc_req
1653         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1654            nc_req.eq.0 .and. nc_match.eq.1) then
1655           ishif1=is
1656           ishif2=0
1657           return
1658         endif
1659       enddo
1660       if (nc_req.eq.0) return
1661 ! Shift "right" strand backward
1662       do is=1,n_shif1
1663         call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1664            icont_ref,ncont,icont,jfrag,llocal,lprn)
1665         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1666         if (lprn .and. nc_match.gt.0) write (iout,*) &
1667           "Shift:",0,-is," nc_match1",nc_match1,&
1668           " nc_match=",nc_match," req'd",nc_req
1669         if (nc_match.ge.nc_req) then
1670           ishif1=0
1671           ishif2=-is
1672           return
1673         endif
1674 ! Shift "right" strand upward
1675         call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
1676           icont_ref,ncont,icont,jfrag,llocal,lprn)
1677         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1678         if (lprn .and. nc_match.gt.0) write (iout,*) &
1679           "Shift:",0,is," nc_match1",nc_match1,&
1680           " nc_match=",nc_match," req'd",nc_req
1681         if (nc_match.ge.nc_req) then
1682           ishif1=0
1683           ishif2=is
1684           return
1685         endif
1686       enddo ! is
1687 ! Now try to shift both residues in contacts.
1688       do is=1,n_shif1
1689         do js=1,is
1690           if (js.ne.is) then
1691             call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1692               icont_ref,ncont,icont,jfrag,llocal,lprn)
1693             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1694             if (lprn .and. nc_match.gt.0) write (iout,*) &
1695                "Shift:",-is,-js," nc_match1",nc_match1,&
1696                " nc_match=",nc_match," req'd",nc_req
1697             if (nc_match.ge.nc_req) then
1698               ishif1=-is
1699               ishif2=-js
1700               return
1701             endif
1702             call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1703               icont_ref,ncont,icont,jfrag,llocal,lprn)
1704             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1705             if (lprn .and. nc_match.gt.0) write (iout,*) &
1706               "Shift:",is,js," nc_match1",nc_match1,&
1707               " nc_match=",nc_match," req'd",nc_req
1708             if (nc_match.ge.nc_req) then
1709               ishif1=is
1710               ishif2=js
1711               return
1712             endif
1713 !
1714             call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
1715               icont_ref,ncont,icont,jfrag,llocal,lprn)
1716             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1717             if (lprn .and. nc_match.gt.0) write (iout,*) &
1718               "Shift:",-js,-is," nc_match1",nc_match1,&
1719               " nc_match=",nc_match," req'd",nc_req
1720             if (nc_match.ge.nc_req) then
1721               ishif1=-js
1722               ishif2=-is
1723               return
1724             endif
1725 !
1726             call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
1727               icont_ref,ncont,icont,jfrag,llocal,lprn)
1728             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1729             if (lprn .and. nc_match.gt.0) write (iout,*) &
1730               "Shift:",js,is," nc_match1",nc_match1,&
1731               " nc_match=",nc_match," req'd",nc_req
1732             if (nc_match.ge.nc_req) then
1733               ishif1=js
1734               ishif2=is
1735               return
1736             endif
1737           endif
1738 !
1739           if (is+js.le.n_shif1) then
1740           call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1741             icont_ref,ncont,icont,jfrag,llocal,lprn)
1742           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1743           if (lprn .and. nc_match.gt.0) write (iout,*) &
1744            "Shift:",-is,js," nc_match1",nc_match1,&
1745            " nc_match=",nc_match," req'd",nc_req
1746           if (nc_match.ge.nc_req) then
1747             ishif1=-is
1748             ishif2=js
1749             return
1750           endif
1751 !
1752           call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
1753             icont_ref,ncont,icont,jfrag,llocal,lprn)
1754           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1755           if (lprn .and. nc_match.gt.0) write (iout,*) &
1756            "Shift:",js,-is," nc_match1",nc_match1,&
1757            " nc_match=",nc_match," req'd",nc_req
1758           if (nc_match.ge.nc_req) then
1759             ishif1=js
1760             ishif2=-is
1761             return
1762           endif
1763           endif
1764 !
1765         enddo !js
1766       enddo !is
1767       endif
1768
1769       if (n_shif2.gt.0) then
1770       do is=1,n_shif2
1771         call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1772           icont_ref,ncont,icont,jfrag,llocal,lprn)
1773         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1774         if (lprn .and. nc_match.gt.0) write (iout,*) &
1775            "Shift:",-is,-is," nc_match1",nc_match1,&
1776            " nc_match=",nc_match," req'd",nc_req
1777         if (nc_match.ge.nc_req) then
1778           ishif1=-is
1779           ishif2=-is
1780           return
1781         endif
1782         call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1783           icont_ref,ncont,icont,jfrag,llocal,lprn)
1784         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1785         if (lprn .and. nc_match.gt.0) write (iout,*) &
1786           "Shift:",is,is," nc_match1",nc_match1,&
1787           " nc_match=",nc_match," req'd",nc_req
1788         if (nc_match.ge.nc_req) then
1789           ishif1=is
1790           ishif2=is
1791           return
1792         endif
1793       enddo
1794       endif
1795 ! If this point is reached, the contact maps are different.
1796       nc_match=0
1797       ishif1=0
1798       ishif2=0
1799       return
1800       end subroutine match_contact
1801 !-------------------------------------------------------------------------
1802       subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1803          ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1804
1805       use energy_data, only:nnt,nct,maxcont
1806 !      implicit real*8 (a-h,o-z)
1807 !      include 'DIMENSIONS'
1808 !      include 'DIMENSIONS.ZSCOPT'
1809 !      include 'DIMENSIONS.COMPAR'
1810 !      include 'COMMON.IOUNITS'
1811 !      include 'COMMON.INTERACT'
1812 !      include 'COMMON.GEO'
1813 !      include 'COMMON.COMPAR'
1814       logical :: llocal,lprn
1815       integer ncont_ref,ncont,ishift,ishif2,nang_pair
1816       integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1817       integer,dimension(2,nres) :: iang_pair !(2,maxres)
1818       integer :: nc_match,nc_match1,ishif1,jfrag
1819       integer :: i,j,ic1,ic2
1820       real(kind=8) :: diffang,fract,rad2deg
1821
1822 ! Compare the contact map against the reference contact map; they're stored
1823 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1824       if (lprn) write (iout,'(80(1h*))')
1825       nc_match=0
1826       nc_match1=0
1827 ! Check the local structure by comparing dihedral angles.
1828 !      write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1829       if (llocal .and. ncont_ref.eq.0) then
1830 ! If there are no contacts just compare the dihedral angles and exit.
1831         call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1832           lprn)
1833         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1834          " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1835         if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1836         then
1837           nc_match=1
1838         else
1839           nc_match=0
1840         endif
1841         return
1842       endif
1843       nang_pair=0
1844       do i=1,ncont
1845         ic1=icont(1,i)+ishif1
1846         ic2=icont(2,i)+ishif2
1847 !        write (iout,*) "i",i," ic1",ic1," ic2",ic2
1848         if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1849         do j=1,ncont_ref
1850           if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1851             nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1852             nc_match1=nc_match1+1
1853             icont_match(1,nc_match1)=ic1
1854             icont_match(2,nc_match1)=ic2
1855 !            call add_angpair(icont(1,i),icont_ref(1,j),
1856 !     &         nang_pair,iang_pair)
1857 !            call add_angpair(icont(2,i),icont_ref(2,j),
1858 !     &         nang_pair,iang_pair)
1859             if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1860              " match",icont_ref(1,j),icont_ref(2,j),&
1861              " shifts",ishif1,ishif2
1862             goto 10
1863           endif
1864         enddo
1865    10   continue
1866       enddo
1867       if (lprn) then
1868         write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1869         write (iout,*) "icont_match"
1870         do i=1,nc_match1
1871           write (iout,*) icont_match(1,i),icont_match(2,i)
1872         enddo
1873       endif
1874       if (llocal .and. nc_match.gt.0) then
1875         call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1876           ang_cut1(jfrag),diffang,fract)
1877         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1878          " ang_cut:",ang_cut(jfrag)*rad2deg,&
1879          " ang_cut1",ang_cut1(jfrag)*rad2deg
1880         if (diffang.gt.ang_cut(jfrag) &
1881           .or. fract.lt.frac_min(jfrag)) nc_match=0
1882       endif
1883 !      if (nc_match.gt.0) then
1884 !        diffang = angnorm1(nang_pair,iang_pair,lprn)
1885 !        if (diffang.gt.ang_cut(jfrag)) nc_match=0
1886 !      endif
1887       if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1888          " diffang",rad2deg*diffang," nc_match",nc_match
1889       return
1890       end subroutine ncont_match
1891 !------------------------------------------------------------------------------
1892       subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1893 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1894 ! conformation considered to that of the reference conformation.
1895 ! Returns the number of equivalent residues (nsec_match).
1896 !      implicit real*8 (a-h,o-z)
1897 !      include 'DIMENSIONS'
1898 !      include 'DIMENSIONS.ZSCOPT'
1899 !      include 'DIMENSIONS.COMPAR'
1900 !      include 'COMMON.IOUNITS'
1901 !      include 'COMMON.CHAIN'
1902 !      include 'COMMON.PEPTCONT'
1903 !      include 'COMMON.COMPAR'
1904       logical :: lprn
1905       integer :: isecstr(nres)
1906       integer :: jfrag,nsec_match,npart,i,j
1907       npart = npiece(jfrag,1)
1908       nsec_match=0
1909       if (lprn) then
1910         write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1911               (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1912         write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1913         write (iout,'(80i1)') (isecstr(j),j=1,nres)
1914       endif
1915       do i=1,npart
1916         do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1917 ! The residue has equivalent conformational state to that of the reference
1918 ! structure, if:
1919 !  a) the conformational states are equal or
1920 !  b) the reference state is a coil and that of the conformation considered
1921 !     is a strand or
1922 !  c) the conformational state of the conformation considered is a strand
1923 !     and that of the reference conformation is a coil.
1924 ! 10/28/02 - case (b) deleted.
1925           if (isecstr(j).eq.isec_ref(j) .or. &
1926 !     &        isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1927               isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1928             nsec_match=nsec_match+1
1929         enddo
1930       enddo
1931       return
1932       end subroutine match_secondary
1933 !------------------------------------------------------------------------------
1934 ! odlodc.f
1935 !------------------------------------------------------------------------------
1936       subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1937
1938       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1939 !                            isccont_frag_ref
1940 !      implicit real*8 (a-h,o-z)
1941       real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1942       real(kind=8) :: uu,vv,aa,bb,dd
1943       real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1944 !el      odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1945 !el       + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1946 !      print *,"r1",(r1(i),i=1,3)
1947 !      print *,"r2",(r2(i),i=1,3)
1948 !      print *,"a",(a(i),i=1,3)
1949 !      print *,"b",(b(i),i=1,3)
1950       aa = a(1)**2+a(2)**2+a(3)**2
1951       bb = b(1)**2+b(2)**2+b(3)**2
1952       ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1953       ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1954       br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1955       det = aa*bb-ab**2
1956 !      print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1957       uu = (-ar*bb+br*ab)/det
1958       vv = (br*aa-ar*ab)/det
1959 !      print *,u,v
1960       uu=dmin1(uu,1.0d0)
1961       uu=dmax1(uu,0.0d0)
1962       vv=dmin1(vv,1.0d0)
1963       vv=dmax1(vv,0.0d0)
1964 !el      dd1 = odl(uu,vv)
1965       dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1966 !el      dd2 = odl(0.0d0,0.0d0)
1967       dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1968 !el      dd3 = odl(0.0d0,1.0d0)
1969       dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1970 !el      dd4 = odl(1.0d0,0.0d0)
1971       dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1972 !el      dd5 = odl(1.0d0,1.0d0)
1973       dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1974       dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1975       if (dd.eq.dd2) then
1976         uu=0.0d0
1977         vv=0.0d0
1978       else if (dd.eq.dd3) then
1979         uu=0.0d0
1980         vv=1.0d0
1981       else if (dd.eq.dd4) then
1982         uu=1.0d0
1983         vv=0.0d0
1984       else if (dd.eq.dd5) then
1985         uu=1.0d0
1986         vv=1.0d0
1987       endif
1988 ! Control check
1989 !      do i=1,3
1990 !        x(i)=r1(i)+u*a(i)
1991 !        y(i)=r2(i)+v*b(i)
1992 !      enddo
1993 !      dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
1994 !      dd1 = dsqrt(dd1)
1995       aa = dsqrt(aa)
1996       bb = dsqrt(bb)
1997 !      write (8,*) uu,vv,dd,dd1
1998 !      print *,dd,dd1
1999       return
2000       end subroutine odlodc
2001 !------------------------------------------------------------------------------
2002       real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
2003
2004       real(kind=8),dimension(3) :: r1,r2
2005       real(kind=8) :: aa,bb,u,v,ar,br,ab
2006
2007       odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
2008        + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
2009
2010       end function odl
2011 !------------------------------------------------------------------------------
2012 ! proc_cont.f
2013 !------------------------------------------------------------------------------
2014       subroutine proc_cont
2015
2016       use geometry_data, only:rad2deg
2017       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2018 !                            isccont_frag_ref
2019 !      implicit real*8 (a-h,o-z)
2020 !      include 'DIMENSIONS'
2021 !      include 'DIMENSIONS.ZSCOPT'
2022 !      include 'DIMENSIONS.COMPAR'
2023 !      include 'COMMON.IOUNITS'
2024 !      include 'COMMON.TIME1'
2025 !      include 'COMMON.SBRIDGE'
2026 !      include 'COMMON.CONTROL'
2027 !      include 'COMMON.COMPAR'
2028 !      include 'COMMON.CHAIN'
2029 !      include 'COMMON.HEADER'
2030 !      include 'COMMON.CONTACTS1'
2031 !      include 'COMMON.PEPTCONT'
2032 !      include 'COMMON.GEO'
2033       integer :: i,j,k,ind,len_cut,ndigit,length_frag
2034
2035       write (iout,*) "proc_cont: nlevel",nlevel
2036       if (nlevel.lt.0) then
2037         write (iout,*) "call define_fragments"
2038         call define_fragments
2039       else
2040         write (iout,*) "call secondary2"
2041         call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2042            isec_ref)
2043       endif
2044       write (iout,'(80(1h=))')
2045       write (iout,*) "Electrostatic contacts"
2046       call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2047        icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2048       write (iout,'(80(1h=))')
2049       write (iout,*) "Side chain contacts"
2050       call contacts_between_fragments(.true.,0,ncont_ref,&
2051        icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2052       if (nlevel.lt.0) then
2053         do i=1,nfrag(1)
2054           ind=icant(i,i)
2055           len_cut=1000
2056           if (istruct(i).le.1) then
2057             len_cut=max0(len_frag(i,1)*4/5,3)
2058           else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2059             len_cut=max0(len_frag(i,1)*2/5,3)
2060           endif
2061           write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2062             ncont_frag_ref(ind)," len_cut",len_cut,&
2063             " icont_single",icont_single," iloc_single",iloc_single
2064           iloc(i)=iloc_single
2065           if (iloc(i).gt.0) write (iout,*) &
2066            "Local structure used to compare structure of fragment",i,&
2067            " to native."
2068           if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2069               .and. icont_single.gt.0 .and. &
2070               ncont_frag_ref(ind).ge.len_cut) then
2071             write (iout,*) "Electrostatic contacts used to compare",&
2072              " structure of fragment",i," to native."
2073             ielecont(i,1)=1
2074             isccont(i,1)=0
2075           else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2076             .ge.len_cut) then
2077             write (iout,*) "Side chain contacts used to compare",&
2078              " structure of fragment",i," to native."
2079             isccont(i,1)=1
2080             ielecont(i,1)=0
2081           else
2082             write (iout,*) "Contacts not used to compare",&
2083              " structure of fragment",i," to native."
2084             ielecont(i,1)=0
2085             isccont(i,1)=0
2086             nc_req_setf(i,1)=0
2087           endif
2088           if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2089                .and. ielecont(i,1).eq.0) then
2090             write (iout,*) "RMSD used to compare",&
2091              " structure of fragment",i," to native."
2092             irms(i,1)=1
2093           else
2094             write (iout,*) "RMSD not used to compare",&
2095              " structure of fragment",i," to native."
2096             irms(i,1)=0
2097           endif
2098         enddo
2099       endif
2100       if (nlevel.lt.-1) then
2101         call define_pairs
2102         nlevel = -nlevel
2103         if (nlevel.gt.3) nlevel=3
2104         if (nlevel.eq.3) then
2105           nfrag(3)=1
2106           npiece(1,3)=nfrag(1)
2107           do i=1,nfrag(1)
2108             ipiece(i,1,3)=i
2109           enddo
2110           ielecont(1,3)=0
2111           isccont(1,3)=0
2112           irms(1,3)=1
2113           n_shift(1,1,3)=0
2114           n_shift(2,1,3)=0
2115         endif
2116       else if (nlevel.eq.-1) then
2117         nlevel=1
2118       endif
2119       isnfrag(1)=0
2120       do i=1,nlevel
2121         isnfrag(i+1)=isnfrag(i)+nfrag(i)
2122       enddo
2123       ndigit=3*nfrag(1)
2124       do i=2,nlevel
2125         ndigit=ndigit+2*nfrag(i)
2126       enddo
2127       write (iout,*) "ndigit",ndigit
2128       if (.not.binary .and. ndigit.gt.30) then
2129         write (iout,*) "Highest class too large; switching to",&
2130           " binary representation."
2131         binary=.true.
2132       endif
2133       write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2134       write(iout,*) "rmscut_base_up",rmscut_base_up,&
2135        " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2136       do i=1,nlevel
2137         do j=1,nfrag(i)
2138           length_frag = 0
2139           if (i.eq.1) then
2140             do k=1,npiece(j,i)
2141               length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2142             enddo
2143           else
2144             do k=1,npiece(j,i)
2145               length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2146             enddo
2147           endif
2148           len_frag(j,i)=length_frag
2149           rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2150           rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2151           if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2152             rmscutfrag(1,j,i)=rmsup_lim
2153           if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2154             rmscutfrag(1,j,i)=rmsupup_lim
2155         enddo
2156       enddo
2157       write (iout,*) "Level",1," number of fragments:",nfrag(1)
2158       do j=1,nfrag(1)
2159         write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2160           k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2161           rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2162           ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2163           nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2164       enddo
2165       do i=2,nlevel
2166         write (iout,*) "Level",i," number of fragments:",nfrag(i)
2167         do j=1,nfrag(i)
2168           write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2169             k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2170             rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2171             nc_fragm(j,i),nc_req_setf(j,i)
2172         enddo
2173       enddo
2174       return
2175       end subroutine proc_cont
2176 !------------------------------------------------------------------------------
2177 ! define_pairs.f
2178 !------------------------------------------------------------------------------
2179       subroutine define_pairs
2180
2181 !      use energy_data, only:nsccont_frag_ref
2182 !      implicit real*8 (a-h,o-z)
2183 !      include 'DIMENSIONS'
2184 !      include 'DIMENSIONS.ZSCOPT'
2185 !      include 'DIMENSIONS.COMPAR'
2186 !      include 'COMMON.IOUNITS'
2187 !      include 'COMMON.TIME1'
2188 !      include 'COMMON.SBRIDGE'
2189 !      include 'COMMON.CONTROL'
2190 !      include 'COMMON.COMPAR'
2191 !      include 'COMMON.FRAG'
2192 !      include 'COMMON.CHAIN'
2193 !      include 'COMMON.HEADER'
2194 !      include 'COMMON.GEO'
2195 !      include 'COMMON.CONTACTS1'
2196 !      include 'COMMON.PEPTCONT'
2197       integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2198
2199       do j=1,nfrag(1)
2200         length_frag = 0
2201         do k=1,npiece(j,1)
2202           length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2203         enddo
2204         len_frag(j,1)=length_frag
2205         write (iout,*) "Fragment",j," length",len_frag(j,1)
2206       enddo
2207       nfrag(2)=0
2208       do i=1,nfrag(1)
2209         do j=i+1,nfrag(1)
2210           ind = icant(i,j)
2211           if (istruct(i).le.1 .or. istruct(j).le.1) then
2212             if (istruct(i).le.1) then
2213               ll1=len_frag(i,1)
2214             else
2215               ll1=len_frag(i,1)/2
2216             endif
2217             if (istruct(j).le.1) then
2218               ll2=len_frag(j,1)
2219             else
2220               ll2=len_frag(j,1)/2
2221             endif
2222             len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2223           else
2224             if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2225               ll1=len_frag(i,1)/2
2226             else
2227               ll1=len_frag(i,1)
2228             endif
2229             if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2230               ll2=len_frag(j,1)/2
2231             else
2232               ll2=len_frag(j,1)
2233             endif
2234             len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2235           endif
2236           write (iout,*) "Fragments",i,j," structure",istruct(i),&
2237              istruct(j)," # contacts",&
2238              ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2239              " lengths",len_frag(i,1),len_frag(j,1),&
2240              " ll1",ll1," ll2",ll2," len_cut",len_cut
2241           if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2242             nsccont_frag_ref(ind).ge.len_cut ) then
2243             if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2244               write (iout,*) "Adding pair of helices",i,j,&
2245               " based on SC contacts"
2246             else
2247               write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2248               " based on SC contacts"
2249             endif
2250             nfrag(2)=nfrag(2)+1
2251             if (icont_pair.gt.0) then
2252               write (iout,*)  "# SC contacts will be used",&
2253               " in comparison."
2254               isccont(nfrag(2),2)=1
2255             endif
2256             if (irms_pair.gt.0) then
2257               write (iout,*)  "Fragment RMSD will be used",&
2258               " in comparison."
2259               irms(nfrag(2),2)=1
2260             endif
2261             npiece(nfrag(2),2)=2
2262             ipiece(1,nfrag(2),2)=i
2263             ipiece(2,nfrag(2),2)=j
2264             ielecont(nfrag(2),2)=0
2265             n_shift(1,nfrag(2),2)=nshift_pair
2266             n_shift(2,nfrag(2),2)=nshift_pair
2267             nc_fragm(nfrag(2),2)=ncfrac_pair
2268             nc_req_setf(nfrag(2),2)=ncreq_pair
2269           else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2270              .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2271              .and. ncont_frag_ref(ind).ge.len_cut ) then
2272             nfrag(2)=nfrag(2)+1
2273             write (iout,*) "Adding pair strands/sheets",i,j,&
2274               " based on pp contacts"
2275             if (icont_pair.gt.0) then
2276               write (iout,*) "# pp contacts will be used",&
2277               " in comparison."
2278               ielecont(nfrag(2),2)=1
2279             endif
2280             if (irms_pair.gt.0) then
2281               write (iout,*)  "Fragment RMSD will be used",&
2282               " in comparison."
2283               irms(nfrag(2),2)=1
2284             endif
2285             npiece(nfrag(2),2)=2
2286             ipiece(1,nfrag(2),2)=i
2287             ipiece(2,nfrag(2),2)=j
2288             ielecont(nfrag(2),2)=1
2289             isccont(nfrag(2),2)=0
2290             n_shift(1,nfrag(2),2)=nshift_pair
2291             n_shift(2,nfrag(2),2)=nshift_pair
2292             nc_fragm(nfrag(2),2)=ncfrac_bet
2293             nc_req_setf(nfrag(2),2)=ncreq_bet
2294           endif
2295         enddo
2296       enddo
2297       write (iout,*) "Pairs found"
2298       do i=1,nfrag(2)
2299         write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2300       enddo
2301       return
2302       end subroutine define_pairs
2303 !------------------------------------------------------------------------------
2304 ! icant.f
2305 !------------------------------------------------------------------------------
2306       INTEGER FUNCTION ICANT(I,J)
2307       integer :: i,j
2308       IF (I.GE.J) THEN
2309         ICANT=(I*(I-1))/2+J
2310       ELSE
2311         ICANT=(J*(J-1))/2+I
2312       ENDIF
2313       RETURN
2314       END FUNCTION ICANT
2315 !------------------------------------------------------------------------------
2316 ! mysort.f
2317 !------------------------------------------------------------------------------
2318       subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2319 !      implicit none
2320       integer :: n,m,mm
2321       integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2322       real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2323       real(kind=8) :: xxtemp
2324       integer :: i,j,k,imax
2325       do i=1,n
2326         xmin=x(1,1,i)
2327         imax=i
2328         do j=i+1,n
2329           if (x(1,1,j).lt.xmin) then
2330             imax=j
2331             xmin=x(1,1,j)
2332           endif
2333         enddo
2334         xxtemp=z2(imax)
2335         z2(imax)=z2(i)
2336         z2(i)=xxtemp
2337         xxtemp=z3(imax)
2338         z3(imax)=z3(i)
2339         z3(i)=xxtemp
2340         xxtemp=z4(imax)
2341         z4(imax)=z4(i)
2342         z4(i)=xxtemp
2343         xxtemp=z5(imax)
2344         z5(imax)=z5(i)
2345         z5(i)=xxtemp
2346         xtemp=y(imax)
2347         y(imax)=y(i)
2348         y(i)=xtemp
2349         xtemp=z(imax)
2350         z(imax)=z(i)
2351         z(i)=xtemp
2352         xtemp=z6(imax)
2353         z6(imax)=z6(i)
2354         z6(i)=xtemp
2355         do j=1,2
2356           xtemp=z1(j,imax)
2357           z1(j,imax)=z1(j,i)
2358           z1(j,i)=xtemp
2359         enddo
2360         do j=1,m
2361           do k=1,mm
2362             xtemp=x(j,k,imax)
2363             x(j,k,imax)=x(j,k,i)
2364             x(j,k,i)=xtemp
2365           enddo
2366         enddo
2367       enddo
2368       return
2369       end subroutine imysort
2370 !------------------------------------------------------------------------------
2371 ! qwolynes.f
2372 !-------------------------------------------------------------------------------
2373       real(kind=8) function qwolynes(ilevel,jfrag)
2374
2375       use geometry_data, only:cref,nperm
2376       use control_data, only:symetr
2377       use energy_data, only:nnt,nct,itype,molnum
2378 !      implicit none
2379 !      include 'DIMENSIONS'
2380 !      include 'DIMENSIONS.ZSCOPT'
2381 !      include 'DIMENSIONS.COMPAR'
2382 !      include 'COMMON.IOUNITS'
2383 !      include 'COMMON.COMPAR'
2384 !      include 'COMMON.CHAIN'
2385 !      include 'COMMON.INTERACT'
2386 !      include 'COMMON.CONTROL'
2387       integer :: ilevel,jfrag,kkk
2388       integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2389       integer :: nsep=3
2390       real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2391       real(kind=8) :: maxiQ !dist,
2392       real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2393       logical :: lprn=.false.
2394       real(kind=8) :: x !el sigm
2395 !el      sigm(x)=0.25d0*x
2396       nperm=1
2397       maxiQ=0
2398       do i=1,symetr
2399       nperm=i*nperm
2400       enddo
2401 !      write (iout,*) "QWolyes: " jfrag",jfrag,
2402 !     &  " ilevel",ilevel
2403       allocate(tempus(nperm))
2404       do kkk=1,nperm
2405       qq = 0.0d0
2406       if (ilevel.eq.0) then
2407         if (lprn) write (iout,*) "Q computed for whole molecule"
2408         nl=0
2409         do il=nnt+nsep,nct
2410           do jl=nnt,il-nsep
2411             dij=0.0d0
2412             dijCM=0.0d0
2413             d0ij=0.0d0
2414             d0ijCM=0.0d0
2415             qqij=0.0d0
2416             qqijCM=0.0d0
2417             nl=nl+1
2418             d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2419                        (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2420                        (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2421             dij=dist(il,jl)
2422             qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2423             if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2424               nl=nl+1
2425               d0ijCM=dsqrt( &
2426                      (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2427                      (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2428                      (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2429               dijCM=dist(il+nres,jl+nres)
2430               qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2431             endif
2432             qq = qq+qqij+qqijCM
2433             if (lprn) then
2434               write (iout,*) "il",il," jl",jl,&
2435                " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2436               write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2437                " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2438             endif
2439           enddo
2440         enddo
2441         qq = qq/nl
2442         if (lprn) write (iout,*) "nl",nl," qq",qq
2443       else if (ilevel.eq.1) then
2444         if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2445         nl=0
2446 !        write (iout,*) "nlist_frag",nlist_frag(jfrag)
2447         do i=2,nlist_frag(jfrag)
2448           do j=1,i-1
2449             il=list_frag(i,jfrag)
2450             jl=list_frag(j,jfrag)
2451             if (iabs(il-jl).gt.nsep) then
2452               dij=0.0d0
2453               dijCM=0.0d0
2454               d0ij=0.0d0
2455               d0ijCM=0.0d0
2456               qqij=0.0d0
2457               qqijCM=0.0d0
2458               nl=nl+1
2459               d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2460                          (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2461                          (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2462               dij=dist(il,jl)
2463               qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2464               if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2465                 nl=nl+1
2466                 d0ijCM=dsqrt( &
2467                        (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2468                        (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2469                        (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2470                 dijCM=dist(il+nres,jl+nres)
2471                qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2472               endif
2473               qq = qq+qqij+qqijCM
2474               if (lprn) then
2475                 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2476                  " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2477                 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2478                  " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2479               endif
2480             endif
2481           enddo
2482         enddo
2483         qq = qq/nl
2484         if (lprn) write (iout,*) "nl",nl," qq",qq
2485       else if (ilevel.eq.2) then
2486         np=npiece(jfrag,ilevel)
2487         nl=0
2488         do i=2,np
2489           ip=ipiece(i,jfrag,ilevel)
2490           do j=1,nlist_frag(ip)
2491             il=list_frag(j,ip)
2492             do k=1,i-1
2493               kp=ipiece(k,jfrag,ilevel)
2494               do l=1,nlist_frag(kp)
2495                 kl=list_frag(l,kp)
2496                 if (iabs(kl-il).gt.nsep) then
2497                   nl=nl+1
2498                   dij=0.0d0
2499                   dijCM=0.0d0
2500                   d0ij=0.0d0
2501                   d0ijCM=0.0d0
2502                   qqij=0.0d0
2503                   qqijCM=0.0d0
2504                   d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2505                              (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2506                              (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2507                   dij=dist(il,kl)
2508                   qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2509                   if (itype(il,molnum(il)).ne.10 .or. itype(kl,molnum(kl)).ne.10) then
2510                     nl=nl+1
2511                     d0ijCM=dsqrt( &
2512                        (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2513                        (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2514                        (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2515                     dijCM=dist(il+nres,kl+nres)
2516                     qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2517                       (sigm(d0ijCM)))**2)
2518                   endif
2519                   qq = qq+qqij+qqijCM
2520                   if (lprn) then
2521                     write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2522                       " kl",kl," itype",itype(il,molnum(il)), &
2523                          itype(kl,molnum(kl))
2524                     write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2525                     d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2526                   endif
2527                 endif
2528               enddo  ! l
2529             enddo    ! k
2530           enddo      ! j
2531         enddo        ! i
2532         qq = qq/nl
2533         if (lprn) write (iout,*) "nl",nl," qq",qq
2534       else
2535         write (iout,*)"Error: Q can be computed only for level 1 and 2."
2536       endif
2537       tempus(kkk)=qq
2538       enddo
2539       do kkk=1,nperm
2540        if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2541       enddo
2542       qwolynes=1.0d0-maxiQ
2543       deallocate(tempus)
2544       return
2545       end function qwolynes
2546 !-------------------------------------------------------------------------------
2547       real(kind=8) function sigm(x)
2548       real(kind=8) :: x
2549       sigm=0.25d0*x
2550       return
2551       end function sigm
2552 !-------------------------------------------------------------------------------
2553       subroutine fragment_list
2554 !      implicit none
2555 !      include 'DIMENSIONS'
2556 !      include 'DIMENSIONS.ZSCOPT'
2557 !      include 'DIMENSIONS.COMPAR'
2558 !      include 'COMMON.IOUNITS'
2559 !      include 'COMMON.COMPAR'
2560       logical :: lprn=.true.
2561       integer :: i,ilevel,j,k,jfrag
2562       do jfrag=1,nfrag(1)
2563         nlist_frag(jfrag)=0
2564         do i=1,npiece(jfrag,1)
2565           if (lprn) write (iout,*) "jfrag=",jfrag,&
2566             "i=",i," fragment",ifrag(1,i,jfrag),&
2567             ifrag(2,i,jfrag)
2568           do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2569             do k=1,nlist_frag(jfrag)
2570               if (list_frag(k,jfrag).eq.j) goto 10
2571             enddo
2572             nlist_frag(jfrag)=nlist_frag(jfrag)+1
2573             list_frag(nlist_frag(jfrag),jfrag)=j
2574           enddo
2575   10      continue
2576         enddo
2577       enddo
2578       write (iout,*) "Fragment list"
2579       do j=1,nfrag(1)
2580         write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2581          k=1,nlist_frag(j))
2582       enddo
2583       return
2584       end subroutine fragment_list
2585 !-------------------------------------------------------------------------------
2586       real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2587
2588       use w_comm_local
2589       use control_data, only:symetr
2590       use geometry_data, only:nperm
2591 !      implicit real*8 (a-h,o-z)
2592 !      include 'DIMENSIONS'
2593 !      include 'DIMENSIONS.ZSCOPT'
2594 !      include 'DIMENSIONS.COMPAR'
2595 !      include 'COMMON.IOUNITS'
2596 !      include 'COMMON.COMPAR'
2597 !      include 'COMMON.CHAIN'
2598 !      include 'COMMON.INTERACT'
2599 !      include 'COMMON.VAR'
2600 !      include 'COMMON.CONTROL'
2601       real(kind=8) :: przes(3),obrot(3,3)
2602 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2603 !el      logical :: iadded(nres)
2604 !el      integer :: inumber(2,nres)
2605 !el      common /ccc/ creff,cc,iadded,inumber
2606       logical :: lprn
2607       logical :: non_conv
2608       integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2609       real(kind=8) :: rminrms,rms
2610       if (lprn) then
2611         write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2612         write (iout,*) "npiece",npiece(j,i)
2613         call flush(iout)
2614       endif
2615 !      write (iout,*) "symetr",symetr
2616 !      call flush(iout)
2617       nperm=1
2618       do idup=1,symetr
2619       nperm=nperm*idup
2620       enddo
2621 !      write (iout,*) "nperm",nperm
2622 !      call flush(iout)
2623       do kkk=1,nperm
2624       idup=0
2625       do l=1,nres
2626         iadded(l)=.false.
2627       enddo
2628 !      write (iout,*) "kkk",kkk
2629 !      call flush(iout)
2630       do k=1,npiece(j,i)
2631         if (i.eq.1) then
2632           if (lprn) then
2633             write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2634                ifrag(1,k,j),ifrag(2,k,j)
2635             call flush(iout)
2636           endif
2637           call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2638 !          write (iout,*) "Exit cprep"
2639 !          call flush(iout)
2640 !          write (iout,*) "ii=",ii
2641         else
2642           kk = ipiece(k,j,i)
2643 !          write (iout,*) "kk",kk," npiece",npiece(kk,1)
2644           do l=1,npiece(kk,1)
2645             if (lprn) then
2646               write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2647                 " l=",l," adding fragment",&
2648                 ifrag(1,l,kk),ifrag(2,l,kk)
2649               call flush(iout)
2650             endif
2651             call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2652 !            write (iout,*) "After cprep"
2653 !            call flush(iout)
2654           enddo
2655         endif
2656       enddo
2657       enddo
2658       if (lprn) then
2659         write (iout,*) "tuszukaj"
2660         do kkk=1,nperm
2661           do k=1,idup
2662             write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2663               inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2664           enddo
2665         enddo
2666         call flush(iout)
2667       endif
2668       rminrms=1.0d10
2669       do kkk=1,nperm
2670       call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2671       if (non_conv) then
2672         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2673         rms = 1.0d10
2674       else if (rms.lt.-1.0d-6) then
2675         print *,'Error: rms^2 = ',rms,jcon,i
2676         rms = 1.0d10
2677       else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2678         rms = 0.0d0
2679       endif
2680 !      write (iout,*) "rmsmin", rminrms, "rms", rms
2681       if (rms.le.rminrms) rminrms=rms
2682       enddo
2683       rmscalc = dsqrt(rminrms)
2684 !      write (iout, *) "analysys", rmscalc,anatemp
2685       return
2686       end function rmscalc
2687 !-------------------------------------------------------------------------
2688       subroutine cprep(if1,if2,ishif,idup,kwa)
2689
2690       use w_comm_local
2691       use control_data, only:symetr
2692       use geometry_data, only:nperm,cref,c
2693 !      implicit real*8 (a-h,o-z)
2694 !      include 'DIMENSIONS'
2695 !      include 'DIMENSIONS.ZSCOPT'
2696 !      include 'DIMENSIONS.COMPAR'
2697 !      include 'COMMON.CONTROL'
2698 !      include 'COMMON.IOUNITS'
2699 !      include 'COMMON.COMPAR'
2700 !      include 'COMMON.CHAIN'
2701 !      include 'COMMON.INTERACT'
2702 !      include 'COMMON.VAR'
2703       real(kind=8) :: przes(3),obrot(3,3)
2704 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2705 !el      logical :: iadded(nres)
2706 !el      integer :: inumber(2,nres)
2707       integer :: iistrart,kwa,blar
2708 !el      common /ccc/ creff,cc,iadded,inumber
2709       integer :: if1,if2,ishif,idup,kkk,l,m
2710 !      write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2711       nperm=1
2712       do blar=1,symetr
2713       nperm=nperm*blar
2714       enddo
2715 !      write (iout,*) "nperm",nperm
2716       kkk=kwa
2717 !      ii=0
2718       do l=if1,if2
2719 !        write (iout,*) "l",l," iadded",iadded(l)
2720 !        call flush(iout)
2721         if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2722         then
2723           idup=idup+1
2724           iadded(l)=.true.
2725           inumber(1,idup)=l
2726           inumber(2,idup)=l+ishif
2727           do m=1,3
2728             creff(m,idup)=cref(m,l,kkk)
2729             cc(m,idup)=c(m,l+ishif)
2730           enddo
2731         endif
2732       enddo
2733       return
2734       end subroutine cprep
2735 !-------------------------------------------------------------------------
2736       real(kind=8) function rmsnat(jcon)
2737
2738       use control_data, only:symetr
2739       use geometry_data, only:nperm,cref,c
2740       use energy_data, only:itype,molnum
2741 !      implicit real*8 (a-h,o-z)
2742 !      include 'DIMENSIONS'
2743 !      include 'DIMENSIONS.ZSCOPT'
2744 !      include 'DIMENSIONS.COMPAR'
2745 !      include 'COMMON.IOUNITS'
2746 !      include 'COMMON.COMPAR'
2747 !      include 'COMMON.CHAIN'
2748 !      include 'COMMON.INTERACT'
2749 !      include 'COMMON.VAR'
2750 !      include 'COMMON.CONTROL'
2751       real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2752       logical :: non_conv
2753       integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2754       real(kind=8) :: rminrms,rmsminsing,rms
2755       rminrms=10.0d10
2756       rmsminsing=10d10
2757       nperm=1
2758       do i=1,symetr
2759        nperm=nperm*i
2760       enddo
2761       do kkk=1,nperm
2762        nnsup=0
2763        do i=1,nres
2764         if (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
2765           nnsup=nnsup+1
2766           do j=1,3
2767             cc(j,nnsup)=c(j,i)
2768             ccref(j,nnsup)=cref(j,i,kkk)
2769           enddo
2770         endif
2771        enddo
2772        call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2773        if (non_conv) then
2774         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2775         rms=1.0d10
2776        else if (rms.lt.-1.0d-6) then
2777         print *,'Error: rms^2 = ',rms,jcon,i
2778         rms = 1.0d10
2779        else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2780         rms=0.0d0
2781        endif
2782        if (rms.le.rminrms) rminrms=rms
2783 !       write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2784       enddo
2785       rmsnat = dsqrt(rminrms)
2786 !      write (iout,*)  "analysys",rmsnat, anatemp
2787 !      liczenie rmsdla pojedynczego lancucha
2788       return
2789       end function rmsnat
2790 !-------------------------------------------------------------------------------
2791       subroutine define_fragments
2792
2793       use geometry_data, only:rad2deg
2794       use energy_data, only:itype,molnum
2795       use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2796 !      implicit real*8 (a-h,o-z)
2797 !      include 'DIMENSIONS'
2798 !      include 'DIMENSIONS.ZSCOPT'
2799 !      include 'DIMENSIONS.COMPAR'
2800 !      include 'COMMON.IOUNITS'
2801 !      include 'COMMON.TIME1'
2802 !      include 'COMMON.FRAG'
2803 !      include 'COMMON.SBRIDGE'
2804 !      include 'COMMON.CONTROL'
2805 !      include 'COMMON.COMPAR'
2806 !      include 'COMMON.CHAIN'
2807 !      include 'COMMON.HEADER'
2808 !      include 'COMMON.GEO'
2809 !      include 'COMMON.CONTACTS'
2810 !      include 'COMMON.PEPTCONT'
2811 !      include 'COMMON.INTERACT'
2812 !      include 'COMMON.NAMES'
2813       integer :: nstrand,istrand(2,nres/2)
2814       integer :: nhairp,ihairp(2,nres/5),mnum
2815       character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2816                           'strand','strand pair'/),shape(strstr))
2817       integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2818
2819       write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2820                      'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2821                  'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2822         ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2823       write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2824         ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2825       write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2826         ' MAXANG_HEL',angcut1_hel*rad2deg
2827       write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2828                      ' MAXANG_BET',angcut1_bet*rad2deg
2829       write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2830                      ' MAXANG_STRAND',angcut1_strand*rad2deg
2831       write (iout,*) 'FRAC_MIN',frac_min_set
2832 ! Find secondary structure elements (helices and beta-sheets)
2833       call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2834          isec_ref)
2835 ! Define primary fragments. First include the helices.
2836       nhairp=0
2837       nstrand=0
2838 ! Merge helices
2839 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2840       if (merge_helices) then
2841       write (iout,*) "Before merging helices: nhfrag",nhfrag
2842       do i=1,nhfrag
2843         write (2,*) hfrag(1,i),hfrag(2,i)
2844       enddo
2845       i=1
2846       do while (i.lt.nhfrag)
2847         if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2848           nhfrag=nhfrag-1
2849           hfrag(2,i)=hfrag(2,i+1)
2850           do j=i+1,nhfrag
2851             hfrag(1,j)=hfrag(1,j+1)
2852             hfrag(2,j)=hfrag(2,j+1)
2853           enddo
2854         endif
2855         i=i+1
2856       enddo
2857       write (iout,*) "After merging helices: nhfrag",nhfrag
2858       do i=1,nhfrag
2859         write (2,*) hfrag(1,i),hfrag(2,i)
2860       enddo
2861       endif
2862       nfrag(1)=nhfrag
2863       do i=1,nhfrag
2864         npiece(i,1)=1
2865         ifrag(1,1,i)=hfrag(1,i)
2866         ifrag(2,1,i)=hfrag(2,i)
2867         n_shift(1,i,1)=0
2868         n_shift(2,i,1)=nshift_hel
2869         ang_cut(i)=angcut_hel
2870         ang_cut1(i)=angcut1_hel
2871         frac_min(i)=frac_min_set
2872         nc_fragm(i,1)=ncfrac_hel
2873         nc_req_setf(i,1)=ncreq_hel
2874         istruct(i)=1
2875       enddo
2876       write (iout,*) "isplit_bet",isplit_bet
2877       if (isplit_bet.gt.1) then
2878 ! Split beta-sheets into strands and store strands as primary fragments.
2879         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2880         do i=1,nstrand
2881           ii=i+nfrag(1)
2882           npiece(ii,1)=1
2883           ifrag(1,1,ii)=istrand(1,i)
2884           ifrag(2,1,ii)=istrand(2,i)
2885           n_shift(1,ii,1)=nshift_strand
2886           n_shift(2,ii,1)=nshift_strand
2887           ang_cut(ii)=angcut_strand
2888           ang_cut1(ii)=angcut1_strand
2889           frac_min(ii)=frac_min_set
2890           nc_fragm(ii,1)=0
2891           nc_req_setf(ii,1)=0
2892           istruct(ii)=3
2893         enddo
2894         nfrag(1)=nfrag(1)+nstrand
2895       else if (isplit_bet.eq.1) then
2896 ! Split only far beta-sheets; does not split hairpins.
2897         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2898         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2899         do i=1,nhairp
2900           ii=i+nfrag(1)
2901           npiece(ii,1)=1
2902           ifrag(1,1,ii)=ihairp(1,i)
2903           ifrag(2,1,ii)=ihairp(2,i)
2904           n_shift(1,ii,1)=nshift_bet
2905           n_shift(2,ii,1)=nshift_bet
2906           ang_cut(ii)=angcut_bet
2907           ang_cut1(ii)=angcut1_bet
2908           frac_min(ii)=frac_min_set
2909           nc_fragm(ii,1)=ncfrac_bet
2910           nc_req_setf(ii,1)=ncreq_bet
2911           istruct(ii)=2
2912         enddo
2913         nfrag(1)=nfrag(1)+nhairp
2914         do i=1,nstrand
2915           ii=i+nfrag(1)
2916           npiece(ii,1)=1
2917           ifrag(1,1,ii)=istrand(1,i)
2918           ifrag(2,1,ii)=istrand(2,i)
2919           n_shift(1,ii,1)=nshift_strand
2920           n_shift(2,ii,1)=nshift_strand
2921           ang_cut(ii)=angcut_strand
2922           ang_cut1(ii)=angcut1_strand
2923           frac_min(ii)=frac_min_set
2924           nc_fragm(ii,1)=0
2925           nc_req_setf(ii,1)=0
2926           istruct(ii)=3
2927         enddo
2928         nfrag(1)=nfrag(1)+nstrand
2929       else
2930 ! Do not split beta-sheets; each pair of strands is a primary element.
2931         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2932         do i=1,nhairp
2933           ii=i+nfrag(1)
2934           npiece(ii,1)=1
2935           ifrag(1,1,ii)=ihairp(1,i)
2936           ifrag(2,1,ii)=ihairp(2,i)
2937           n_shift(1,ii,1)=nshift_bet
2938           n_shift(2,ii,1)=nshift_bet
2939           ang_cut(ii)=angcut_bet
2940           ang_cut1(ii)=angcut1_bet
2941           frac_min(ii)=frac_min_set
2942           nc_fragm(ii,1)=ncfrac_bet
2943           nc_req_setf(ii,1)=ncreq_bet
2944           istruct(ii)=2
2945         enddo
2946         nfrag(1)=nfrag(1)+nhairp
2947         do i=1,nbfrag
2948           ii=i+nfrag(1)
2949           npiece(ii,1)=2
2950           ifrag(1,1,ii)=bfrag(1,i)
2951           ifrag(2,1,ii)=bfrag(2,i)
2952           if (bfrag(3,i).lt.bfrag(4,i)) then
2953             ifrag(1,2,ii)=bfrag(3,i)
2954             ifrag(2,2,ii)=bfrag(4,i)
2955           else
2956             ifrag(1,2,ii)=bfrag(4,i)
2957             ifrag(2,2,ii)=bfrag(3,i)
2958           endif
2959           n_shift(1,ii,1)=nshift_bet
2960           n_shift(2,ii,1)=nshift_bet
2961           ang_cut(ii)=angcut_bet
2962           ang_cut1(ii)=angcut1_bet
2963           frac_min(ii)=frac_min_set
2964           nc_fragm(ii,1)=ncfrac_bet
2965           nc_req_setf(ii,1)=ncreq_bet
2966           istruct(ii)=4
2967         enddo
2968         nfrag(1)=nfrag(1)+nbfrag
2969       endif
2970       write (iout,*) "The following primary fragments were found:"
2971       write (iout,*) "Helices:",nhfrag
2972       do i=1,nhfrag
2973         mnum=molnum(i)
2974         i1=ifrag(1,1,i)
2975         i2=ifrag(2,1,i)
2976         it1=itype(i1,mnum)
2977         it2=itype(i2,mnum)
2978         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2979              i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
2980       enddo
2981       write (iout,*) "Hairpins:",nhairp
2982       do i=nhfrag+1,nhfrag+nhairp
2983         i1=ifrag(1,1,i)
2984         i2=ifrag(2,1,i)
2985         it1=itype(i1,molnum(i1))
2986         it2=itype(i2,molnum(i2))
2987         write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2988              i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2
2989       enddo
2990       write (iout,*) "Far strand pairs:",nbfrag
2991       do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
2992         i1=ifrag(1,1,i)
2993         i2=ifrag(2,1,i)
2994         it1=itype(i1,molnum(i1))
2995         it2=itype(i2,molnum(i1))
2996         i3=ifrag(1,2,i)
2997         i4=ifrag(2,2,i)
2998         it3=itype(i3,molnum(i3))
2999         it4=itype(i4,molnum(i4))
3000         write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
3001              i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2,&
3002                restyp(it3,molnum(i3)),i3,restyp(it4,molnum(i4)),i4
3003       enddo
3004       write (iout,*) "Strands:",nstrand
3005       do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
3006         mnum=molnum(i)
3007         i1=ifrag(1,1,i)
3008         i2=ifrag(2,1,i)
3009         it1=itype(i1,mnum)
3010         it2=itype(i2,mnum)
3011         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
3012              i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
3013       enddo
3014       call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3015         istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3016         nc_fragm(1,1),nc_req_setf(1,1))
3017       write (iout,*) "Fragments after sorting:"
3018       do i=1,nfrag(1)
3019         mnum=molnum(i)
3020         i1=ifrag(1,1,i)
3021         i2=ifrag(2,1,i)
3022         it1=itype(i1,mnum)
3023         it2=itype(i2,mnum)
3024         write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3025              i,restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2
3026         if (npiece(i,1).eq.1) then
3027           write (iout,'(2x,a)') strstr(istruct(i))
3028         else
3029           i1=ifrag(1,2,i)
3030           i2=ifrag(2,2,i)
3031           it1=itype(i1,mnum)
3032           it2=itype(i2,mnum)
3033           write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3034              restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2,strstr(istruct(i))
3035         endif
3036       enddo
3037       return
3038       end subroutine define_fragments
3039 !------------------------------------------------------------------------------
3040       subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3041 !      implicit real*8 (a-h,o-z)
3042 !      include 'DIMENSIONS'
3043 !      include 'DIMENSIONS.ZSCOPT'
3044 !      include 'DIMENSIONS.COMPAR'
3045 !      include 'COMMON.IOUNITS'
3046       integer :: nbfrag,bfrag(4,nres/3)
3047       integer :: nhairp,ihairp(2,nres/5)
3048       integer :: i,j,k
3049       write (iout,*) "Entered find_and_remove_hairpins"
3050       write (iout,*) "nbfrag",nbfrag
3051       do i=1,nbfrag
3052         write (iout,*) i,(bfrag(k,i),k=1,4)
3053       enddo
3054       nhairp=0
3055       i=1
3056       do while (i.le.nbfrag)
3057         write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3058         if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3059         then
3060           write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3061           nhairp=nhairp+1
3062           ihairp(1,nhairp)=bfrag(1,i)
3063           ihairp(2,nhairp)=bfrag(3,i)
3064           nbfrag=nbfrag-1
3065           do j=i,nbfrag
3066             do k=1,4
3067               bfrag(k,j)=bfrag(k,j+1)
3068             enddo
3069           enddo
3070         else
3071           i=i+1
3072         endif
3073       enddo
3074       write (iout,*) "After finding hairpins:"
3075       write (iout,*) "nhairp",nhairp
3076       do i=1,nhairp
3077         write (iout,*) i,ihairp(1,i),ihairp(2,i)
3078       enddo
3079       write (iout,*) "nbfrag",nbfrag
3080       do i=1,nbfrag
3081         write (iout,*) i,(bfrag(k,i),k=1,4)
3082       enddo
3083       return
3084       end subroutine find_and_remove_hairpins
3085 !------------------------------------------------------------------------------
3086       subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3087 !      implicit real*8 (a-h,o-z)
3088 !      include 'DIMENSIONS'
3089 !      include 'DIMENSIONS.ZSCOPT'
3090 !      include 'DIMENSIONS.COMPAR'
3091 !      include 'COMMON.IOUNITS'
3092       integer :: nbfrag,bfrag(4,nres/3)
3093       integer :: nstrand,istrand(2,nres/2)
3094       integer :: nhairp,ihairp(2,nres/5)
3095       logical :: found
3096       integer :: i,k
3097       write (iout,*) "Entered split_beta"
3098       write (iout,*) "nbfrag",nbfrag
3099       do i=1,nbfrag
3100         write (iout,*) i,(bfrag(k,i),k=1,4)
3101       enddo
3102       nstrand=0
3103       do i=1,nbfrag
3104         write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3105         call add_strand(nstrand,istrand,nhairp,ihairp,&
3106            bfrag(1,i),bfrag(2,i),found)
3107         if (bfrag(3,i).lt.bfrag(4,i)) then
3108           write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3109           call add_strand(nstrand,istrand,nhairp,ihairp,&
3110            bfrag(3,i),bfrag(4,i),found)
3111         else
3112           write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3113           call add_strand(nstrand,istrand,nhairp,ihairp,&
3114             bfrag(4,i),bfrag(3,i),found)
3115         endif
3116       enddo
3117       nbfrag=0
3118       write (iout,*) "Strands found:",nstrand
3119       do i=1,nstrand
3120         write (iout,*) i,istrand(1,i),istrand(2,i)
3121       enddo
3122       return
3123       end subroutine split_beta
3124 !------------------------------------------------------------------------------
3125       subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3126 !      implicit real*8 (a-h,o-z)
3127 !      include 'DIMENSIONS'
3128 !      include 'DIMENSIONS.ZSCOPT'
3129 !      include 'DIMENSIONS.COMPAR'
3130 !      include 'COMMON.IOUNITS'
3131       integer :: nstrand,istrand(2,nres/2)
3132       integer :: nhairp,ihairp(2,nres/5)
3133       logical :: found
3134       integer :: is1,is2,j,idelt
3135       found=.false.
3136       do j=1,nhairp
3137         idelt=(ihairp(2,j)-ihairp(1,j))/6
3138         if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3139           write (iout,*) "strand",is1,is2," is part of hairpin",&
3140             ihairp(1,j),ihairp(2,j)
3141           return
3142         endif
3143       enddo
3144       do j=1,nstrand
3145         idelt=(istrand(2,j)-istrand(1,j))/3
3146         if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3147         then
3148 ! The strand already exists in the array; update its ends if necessary.
3149           write (iout,*) "strand",is1,is2," found at position",j,&
3150            ":",istrand(1,j),istrand(2,j)
3151           istrand(1,j)=min0(istrand(1,j),is1)
3152           istrand(2,j)=max0(istrand(2,j),is2)
3153           return
3154         endif
3155       enddo
3156 ! The strand has not been found; add it to the array.
3157       write (iout,*) "strand",is1,is2," added to the array."
3158       found=.true.
3159       nstrand=nstrand+1
3160       istrand(1,nstrand)=is1
3161       istrand(2,nstrand)=is2
3162       return
3163       end subroutine add_strand
3164 !------------------------------------------------------------------------------
3165       subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3166
3167       use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3168       use energy_data, only:itype,maxcont,molnum
3169       use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3170       use compare, only:freeres
3171 !      implicit real*8 (a-h,o-z)
3172 !      include 'DIMENSIONS'
3173 !      include 'DIMENSIONS.ZSCOPT'
3174 !      include 'COMMON.IOUNITS'
3175 !      include 'COMMON.FRAG'
3176 !      include 'COMMON.VAR'
3177 !      include 'COMMON.GEO'
3178 !      include 'COMMON.CHAIN'
3179 !      include 'COMMON.NAMES'
3180 !      include 'COMMON.INTERACT'
3181       integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres),&
3182         isecstr(nres)
3183       logical :: lprint,lprint_sec,not_done !el,freeres
3184       integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3185       integer :: nstrand,nbeta,nhelix,iii1,jjj1,mnum
3186       real(kind=8) :: p1,p2
3187 !rel      external freeres
3188       character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3189       if (lprint) then
3190         write (iout,*) "entered secondary2",ncont
3191         write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3192         do i=1,ncont
3193           write (iout,*) icont(1,i),icont(2,i)
3194         enddo
3195       endif
3196       do i=1,nres
3197         isecstr(i)=0
3198       enddo
3199       nbfrag=0
3200       nhfrag=0
3201       do i=1,nres
3202         isec(i,1)=0
3203         isec(i,2)=0
3204         nsec(i)=0
3205       enddo
3206
3207 ! finding parallel beta
3208 !d      write (iout,*) '------- looking for parallel beta -----------'
3209       nbeta=0
3210       nstrand=0
3211       do i=1,ncont
3212         i1=icont(1,i)
3213         j1=icont(2,i)
3214         if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3215            .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3216 !d        write (iout,*) "parallel",i1,j1
3217         if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3218           ii1=i1
3219           jj1=j1
3220 !d          write (iout,*) i1,j1
3221           not_done=.true.
3222           do while (not_done)
3223            i1=i1+1
3224            j1=j1+1
3225             do j=1,ncont
3226               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3227                    freeres(i1,j1,nsec,isec)) goto 5
3228             enddo
3229             not_done=.false.
3230   5         continue
3231 !d            write (iout,*) i1,j1,not_done
3232           enddo
3233           j1=j1-1
3234           i1=i1-1
3235           if (i1-ii1.gt.1) then
3236             ii1=max0(ii1-1,1)
3237             jj1=max0(jj1-1,1)
3238             nbeta=nbeta+1
3239             if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3240                      nbeta,ii1,i1,jj1,j1
3241
3242             nbfrag=nbfrag+1
3243             bfrag(1,nbfrag)=ii1+1
3244             bfrag(2,nbfrag)=i1+1
3245             bfrag(3,nbfrag)=jj1+1
3246             bfrag(4,nbfrag)=min0(j1+1,nres)
3247
3248             do ij=ii1,i1
3249              nsec(ij)=nsec(ij)+1
3250              isec(ij,nsec(ij))=nbeta
3251             enddo
3252             do ij=jj1,j1
3253              nsec(ij)=nsec(ij)+1
3254              isec(ij,nsec(ij))=nbeta
3255             enddo
3256
3257            if(lprint_sec) then
3258             nstrand=nstrand+1
3259             if (nbeta.le.9) then
3260               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3261                 "DefPropRes 'strand",nstrand,&
3262                 "' 'num = ",ii1-1,"..",i1-1,"'"
3263             else
3264               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3265                 "DefPropRes 'strand",nstrand,&
3266                 "' 'num = ",ii1-1,"..",i1-1,"'"
3267             endif
3268             nstrand=nstrand+1
3269             if (nbeta.le.9) then
3270               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3271                 "DefPropRes 'strand",nstrand,&
3272                 "' 'num = ",jj1-1,"..",j1-1,"'"
3273             else
3274               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3275                 "DefPropRes 'strand",nstrand,&
3276                 "' 'num = ",jj1-1,"..",j1-1,"'"
3277             endif
3278               write(12,'(a8,4i4)') &
3279                 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3280            endif
3281           endif
3282         endif
3283         endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3284       enddo
3285
3286 ! finding antiparallel beta
3287 !d      write (iout,*) '--------- looking for antiparallel beta ---------'
3288
3289       do i=1,ncont
3290         i1=icont(1,i)
3291         j1=icont(2,i)
3292         if (freeres(i1,j1,nsec,isec)) then
3293           ii1=i1
3294           jj1=j1
3295 !d          write (iout,*) i1,j1
3296
3297           not_done=.true.
3298           do while (not_done)
3299            i1=i1+1
3300            j1=j1-1
3301             do j=1,ncont
3302               if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3303                    freeres(i1,j1,nsec,isec)) goto 6
3304             enddo
3305             not_done=.false.
3306   6         continue
3307 !d            write (iout,*) i1,j1,not_done
3308           enddo
3309           i1=i1-1
3310           j1=j1+1
3311           if (i1-ii1.gt.1) then
3312
3313             nbfrag=nbfrag+1
3314             bfrag(1,nbfrag)=ii1
3315             bfrag(2,nbfrag)=min0(i1+1,nres)
3316             bfrag(3,nbfrag)=min0(jj1+1,nres)
3317             bfrag(4,nbfrag)=j1
3318
3319             nbeta=nbeta+1
3320             iii1=max0(ii1-1,1)
3321             do ij=iii1,i1
3322              nsec(ij)=nsec(ij)+1
3323              if (nsec(ij).le.2) then
3324               isec(ij,nsec(ij))=nbeta
3325              endif
3326             enddo
3327             jjj1=max0(j1-1,1)
3328             do ij=jjj1,jj1
3329              nsec(ij)=nsec(ij)+1
3330              if (nsec(ij).le.2) then
3331               isec(ij,nsec(ij))=nbeta
3332              endif
3333             enddo
3334
3335
3336            if (lprint_sec) then
3337             write (iout,'(a,i3,4i4)')'antiparallel beta',&
3338                          nbeta,ii1-1,i1,jj1,j1-1
3339             nstrand=nstrand+1
3340             if (nstrand.le.9) then
3341               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3342                 "DefPropRes 'strand",nstrand,&
3343                 "' 'num = ",ii1-2,"..",i1-1,"'"
3344             else
3345               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3346                 "DefPropRes 'strand",nstrand,&
3347                 "' 'num = ",ii1-2,"..",i1-1,"'"
3348             endif
3349             nstrand=nstrand+1
3350             if (nstrand.le.9) then
3351               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3352                 "DefPropRes 'strand",nstrand,&
3353                 "' 'num = ",j1-2,"..",jj1-1,"'"
3354             else
3355               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3356                 "DefPropRes 'strand",nstrand,&
3357                 "' 'num = ",j1-2,"..",jj1-1,"'"
3358             endif
3359               write(12,'(a8,4i4)') &
3360                 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3361            endif
3362           endif
3363         endif
3364       enddo
3365
3366 !d      write (iout,*) "After beta:",nbfrag
3367 !d      do i=1,nbfrag
3368 !d        write (iout,*) (bfrag(j,i),j=1,4)
3369 !d      enddo
3370
3371       if (nstrand.gt.0.and.lprint_sec) then
3372         write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3373         do i=2,nstrand
3374          if (i.le.9) then
3375           write(12,'(a9,i1,$)') " | strand",i
3376          else
3377           write(12,'(a9,i2,$)') " | strand",i
3378          endif
3379         enddo
3380         write(12,'(a1)') "'"
3381       endif
3382
3383
3384 ! finding alpha or 310 helix
3385
3386       nhelix=0
3387       do i=1,ncont
3388         i1=icont(1,i)
3389         j1=icont(2,i)
3390         p1=phi(i1+2)*rad2deg
3391         p2=0.0
3392         if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3393
3394
3395         if (j1.eq.i1+3 .and. &
3396              ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3397              ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3398 !d          if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3399 !o          if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3400           ii1=i1
3401           jj1=j1
3402           if (nsec(ii1).eq.0) then
3403             not_done=.true.
3404           else
3405             not_done=.false.
3406           endif
3407           do while (not_done)
3408             i1=i1+1
3409             j1=j1+1
3410             do j=1,ncont
3411               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3412             enddo
3413             not_done=.false.
3414   10        continue
3415             p1=phi(i1+2)*rad2deg
3416             p2=phi(j1+2)*rad2deg
3417             if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3418                                     not_done=.false.
3419
3420 !d           write (iout,*) i1,j1,not_done,p1,p2
3421           enddo
3422           j1=j1+1
3423           if (j1-ii1.gt.4) then
3424             nhelix=nhelix+1
3425 !d            write (iout,*)'helix',nhelix,ii1,j1
3426
3427             nhfrag=nhfrag+1
3428             hfrag(1,nhfrag)=ii1
3429             hfrag(2,nhfrag)=j1
3430
3431             do ij=ii1,j1
3432              nsec(ij)=-1
3433             enddo
3434            if (lprint_sec) then
3435             write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3436             if (nhelix.le.9) then
3437               write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3438                 "DefPropRes 'helix",nhelix,&
3439                 "' 'num = ",ii1-1,"..",j1-2,"'"
3440             else
3441               write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3442                 "DefPropRes 'helix",nhelix,&
3443                 "' 'num = ",ii1-1,"..",j1-2,"'"
3444             endif
3445            endif
3446           endif
3447         endif
3448       enddo
3449
3450       if (nhelix.gt.0.and.lprint_sec) then
3451         write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3452         do i=2,nhelix
3453          if (nhelix.le.9) then
3454           write(12,'(a8,i1,$)') " | helix",i
3455          else
3456           write(12,'(a8,i2,$)') " | helix",i
3457          endif
3458         enddo
3459         write(12,'(a1)') "'"
3460       endif
3461
3462       if (lprint_sec) then
3463        write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3464        write(12,'(a20)') "XMacStand ribbon.mac"
3465       endif
3466
3467       if (lprint) then
3468
3469         write(iout,*) 'UNRES seq:',anatemp
3470         do j=1,nbfrag
3471          write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3472         enddo
3473
3474         do j=1,nhfrag
3475          write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3476         enddo
3477
3478       endif
3479
3480       do j=1,nbfrag
3481         do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3482           isecstr(k)=1
3483         enddo
3484         do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3485           isecstr(k)=1
3486         enddo
3487       enddo
3488       do j=1,nhfrag
3489         do k=hfrag(1,j),hfrag(2,j)
3490           isecstr(k)=2
3491         enddo
3492       enddo
3493       if (lprint) then
3494         write (iout,*)
3495         write (iout,*) "Secondary structure"
3496         do i=1,nres,80
3497           mnum=molnum(i)
3498           ist=i
3499           ien=min0(i+79,nres)
3500           write (iout,*)
3501           write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3502           write (iout,'(80a1)') (onelet(itype(k,mnum)),k=ist,ien)
3503           write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3504         enddo
3505         write (iout,*)
3506       endif
3507       return
3508       end subroutine secondary2
3509 !-------------------------------------------------
3510 !      logical function freeres(i,j,nsec,isec)
3511 !      include 'DIMENSIONS'
3512 !      integer :: isec(nres,4),nsec(nres)
3513 !      integer :: i,j,k,l
3514 !      freeres=.false.
3515 !
3516 !      if (nsec(i).gt.1.or.nsec(j).gt.1) return
3517 !      do k=1,nsec(i)
3518 !        do l=1,nsec(j)
3519 !          if (isec(i,k).eq.isec(j,l)) return
3520 !        enddo
3521 !      enddo
3522 !      freeres=.true.
3523 !      return
3524 !      end function freeres
3525 !-------------------------------------------------
3526        subroutine alloc_compar_arrays(nfrg,nlev)
3527
3528        use energy_data, only:maxcont
3529        use w_comm_local
3530        integer :: nfrg,nlev
3531
3532 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3533 !------------------------
3534 ! commom.contacts
3535 !      common /contacts/
3536       allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3537       allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3538 !------------------------
3539 ! COMMON.COMPAR
3540 !      common /compar/
3541       allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3542       allocate(qfrag(nfrg,2)) !(maxfrag,2)
3543       allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3544       allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3545       allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3546         ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3547         ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3548       allocate(ncont_nat(2,nfrg,nlev+1))
3549       allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3550 !      allocate(nfrag(nlev)) !(maxlevel)
3551       allocate(isnfrag(nlev+2)) !(maxlevel+1)
3552       allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3553       allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3554       allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3555       allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3556       allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3557 !------------------------
3558 ! COMMON.PEPTCONT
3559 !      common /peptcont/
3560 !      integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3561       allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3562       allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3563 !      integer,dimension(:),allocatable :: isec_ref !(maxres)
3564 !------------------------
3565 !      module w_comm_local
3566 !      common /ccc/
3567       allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3568       allocate(iadded(nres)) !(nres)
3569       allocate(inumber(2,nres)) !(2,nres)
3570
3571
3572 !-------------------------------------------------------------------------------
3573       end subroutine alloc_compar_arrays
3574 #endif
3575 !-------------------------------------------------------------------------------
3576       end module conform_compar
3577