source/wham/conform_compar.f90

   1       module conform_compar
   2 !-----------------------------------------------------------------------------
   3       use names
   4       use io_units
   5       use geometry_data, only:nres
   6       use math, only:pinorm
   7       use geometry, only:dist
   8       use regularize_, only:fitsq
   9 !
  10       use wham_data
  11 #ifndef CLUSTER
  12       use w_compar_data
  13 #endif
  14 #ifdef MPI
  15       use MPI_data
  16 !      include "COMMON.MPI"
  17 #endif
  18       implicit none
  19 !-----------------------------------------------------------------------------
  20 !
  21 !
  22 !-----------------------------------------------------------------------------
  23       contains
  24 #ifndef CLUSTER
  25 !-----------------------------------------------------------------------------
  26 ! conf_compar.F
  27 !-----------------------------------------------------------------------------
  28       subroutine conf_compar(jcon,lprn,print_class)
  29 !      implicit real*8 (a-h,o-z)
  30       use energy_data, only:icont,ncont,nnt,nct,maxcont!,&
  31 !                      nsccont_frag_ref,isccont_frag_ref
  32 #ifdef MPI
  33       include "mpif.h"
  34 #endif
  35 !      include 'DIMENSIONS'
  36 !      include 'DIMENSIONS.ZSCOPT'
  37 !      include 'DIMENSIONS.COMPAR'
  38 !      include 'DIMENSIONS.FREE'
  39 !      include 'COMMON.CONTROL'
  40 !      include 'COMMON.IOUNITS'
  41 !      include 'COMMON.COMPAR'
  42 !      include 'COMMON.CHAIN'
  43 !      include 'COMMON.INTERACT'
  44 !      include 'COMMON.VAR'
  45 !      include 'COMMON.PEPTCONT'
  46 !      include 'COMMON.CONTACTS1'
  47 !      include 'COMMON.HEADER'
  48 !      include 'COMMON.FREE'
  49 !      include 'COMMON.ENERGIES'
  50 !#ifdef MPI
  51 !      include 'COMMON.MPI'
  52 !#endif
  53 !      integer ilen
  54 !      external ilen
  55       logical :: lprn,print_class
  56       integer :: ncont_frag(mmaxfrag),&
  57        icont_frag(2,maxcont,mmaxfrag),ncontsc,&
  58        icontsc(1,maxcont),nsccont_frag(mmaxfrag),&
  59        isccont_frag(2,maxcont,mmaxfrag)
  60       integer :: isecstr(nres)
  61       integer :: itemp(maxfrag)
  62       character(len=4) :: liczba
  63       real(kind=8) :: Epot,rms
  64       integer :: jcon,i,j,ind,ncnat,nsec_match,ishift,ishif1,ishif2,&
  65                  nc_match,ncon_match,iclass_rms,ishifft_rms,ishiff,ishif
  66       integer :: k,kk,iclass_con,iscor,ik,ishifft_con,idig,iex,im
  67 !      print *,"Enter conf_compar",jcon
  68       call angnorm12(rmsang)
  69 ! Level 1: check secondary and supersecondary structure
  70       call elecont(lprn,ncont,icont,nnt,nct)
  71       if (lprn) then
  72         write (iout,*) "elecont finished"
  73         call flush(iout)
  74       endif
  75       call secondary2(lprn,.false.,ncont,icont,isecstr)
  76       if (lprn) then
  77         write (iout,*) "secondary2 finished"
  78         call flush(iout)
  79       endif
  80       call contact(lprn,ncontsc,icontsc,nnt,nct)
  81       if (lprn) then
  82          write(iout,*) "Assigning electrostatic contacts"
  83          call flush(iout)
  84       endif
  85       call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,&
  86          icont_frag)
  87       if (lprn) then
  88         write(iout,*) "Assigning sidechain contacts"
  89         call flush(iout)
  90       endif
  91       call contacts_between_fragments(lprn,3,ncontsc,icontsc,&
  92          nsccont_frag,isccont_frag)
  93       if (lprn) then
  94         write(iout,*) "--> After contacts_between_fragments"
  95         call flush(iout)
  96       endif
  97       do i=1,nlevel
  98         do j=1,isnfrag(nlevel+1)
  99           iclass(j,i)=0
 100         enddo
 101       enddo
 102       do j=1,nfrag(1)
 103         ind = icant(j,j)
 104         if (lprn) then
 105           write (iout,'(80(1h=))')
 106           write (iout,*) "Level",1," fragment",j
 107           write (iout,'(80(1h=))')
 108         endif
 109         call flush(iout)
 110         rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
 111 ! Compare electrostatic contacts in the current conf with that in the native
 112 ! structure.
 113         if (lprn) write (iout,*) &
 114           "Comparing electrostatic contact map and local structure"
 115         call flush(iout)
 116         ncnat=ncont_frag_ref(ind)
 117 !        write (iout,*) "before match_contact:",nc_fragm(j,1),
 118 !     &   nc_req_setf(j,1)
 119 !        call flush(iout)
 120         call match_secondary(j,isecstr,nsec_match,lprn)
 121         if (lprn) write (iout,*) "Fragment",j," nsec_match",&
 122           nsec_match," length",len_frag(j,1)," min_len",&
 123           frac_sec*len_frag(j,1)
 124         if (nsec_match.lt.frac_sec*len_frag(j,1)) then
 125           iclass(j,1)=0
 126           if (lprn) write (iout,*) "Fragment",j,&
 127             " has incorrect secondary structure"
 128         else
 129           iclass(j,1)=1
 130           if (lprn) write (iout,*) "Fragment",j,&
 131             " has correct secondary structure"
 132         endif
 133         if (ielecont(j,1).gt.0) then
 134           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 135             ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 136             ncont_frag(ind),icont_frag(1,1,ind),&
 137             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 138             nc_req_setf(j,1),istruct(j),.true.,lprn)
 139         else if (isccont(j,1).gt.0) then
 140           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 141             nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 142             nsccont_frag(ind),isccont_frag(1,1,ind),&
 143             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 144             nc_req_setf(j,1),istruct(j),.true.,lprn)
 145         else if (iloc(j).gt.0) then
 146 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 147           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 148             0,icont_frag_ref(1,1,ind),&
 149             ncont_frag(ind),icont_frag(1,1,ind),&
 150             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 151             0,istruct(j),.true.,lprn)
 152 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 153         else
 154           ishif=0
 155           nc_match=1
 156         endif
 157         if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
 158         ishif=ishif1
 159         qfrag(j,1)=qwolynes(1,j)
 160         if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 161         if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
 162 !        write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
 163         if (irms(j,1).gt.0) then
 164           if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
 165             iclass_rms=2
 166             ishifft_rms=0
 167           else
 168             ishiff=0
 169             rms=1.0d2
 170             iclass_rms=0
 171             do while (rms.gt.rmscutfrag(1,j,1) .and. &
 172                ishiff.lt.n_shift(1,j,1))
 173               ishiff=ishiff+1
 174               rms=rmscalc(-ishiff,1,j,jcon,lprn)
 175 !              write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
 176 !     &          " rms",rms," rmscut",rmscutfrag(1,j,1)
 177               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 178               if (rms.gt.rmscutfrag(1,j,1)) then
 179                 rms=rmscalc(ishiff,1,j,jcon,lprn)
 180 !                write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
 181 !     &           " rms",rms
 182               endif
 183               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 184             enddo
 185 !            write (iout,*) "After loop: rms",rms,
 186 !     &        " rmscut",rmscutfrag(1,j,1)
 187 !            write (iout,*) "iclass_rms",iclass_rms
 188             if (rms.le.rmscutfrag(1,j,1)) then
 189               ishifft_rms=ishiff
 190               rmsfrag(j,1)=rms
 191               iclass_rms=1
 192             endif
 193 !            write (iout,*) "iclass_rms",iclass_rms
 194           endif
 195 !          write (iout,*) "ishif",ishif
 196           if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
 197         else
 198           iclass_rms=1
 199         endif
 200 !        write (iout,*) "ishif",ishif," iclass",iclass(j,1),
 201 !     &    " iclass_rms",iclass_rms
 202         if (nc_match.gt.0 .and. iclass_rms.gt.0) then
 203           if (ishif.eq.0) then
 204             iclass(j,1)=iclass(j,1)+6
 205           else
 206             iclass(j,1)=iclass(j,1)+2
 207           endif
 208         endif
 209         ncont_nat(1,j,1)=nc_match
 210         ncont_nat(2,j,1)=ncon_match
 211         ishifft(j,1)=ishif
 212 !        write (iout,*) "iclass",iclass(j,1)
 213       enddo
 214 ! Next levels: Check arrangements of elementary fragments.
 215       do i=2,nlevel
 216         do j=1,nfrag(i)
 217         if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
 218         if (lprn) then
 219             write (iout,'(80(1h=))')
 220             write (iout,*) "Level",i," fragment",j
 221             write (iout,'(80(1h=))')
 222         endif
 223 ! If an elementary fragment doesn't exist, don't check higher hierarchy levels.
 224         do k=1,npiece(j,i)
 225           ik=ipiece(k,j,i)
 226           if (iclass(ik,1).eq.0) then
 227             iclass(j,i)=0
 228             goto 12
 229           endif
 230         enddo
 231         if (i.eq.2 .and. ielecont(j,i).gt.0) then
 232           iclass_con=0
 233           ishifft_con=0
 234           if (lprn) write (iout,*) &
 235            "Comparing electrostatic contact map: fragments",&
 236             ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 237           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 238            ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 239            ncont_frag(ind),icont_frag(1,1,ind),&
 240            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 241            nc_req_setf(j,i),2,.false.,lprn)
 242           ishif=ishif1
 243           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 244           if (nc_match.gt.0) then
 245             if (ishif.eq.0) then
 246               iclass_con=2
 247             else
 248               iclass_con=1
 249             endif
 250           endif
 251           ncont_nat(1,j,i)=nc_match
 252           ncont_nat(2,j,i)=ncon_match
 253           ishifft_con=ishif
 254         else if (i.eq.2 .and. isccont(j,i).gt.0) then
 255           iclass_con=0
 256           ishifft_con=0
 257           if (lprn) write (iout,*) &
 258            "Comparing sidechain contact map: fragments",&
 259            ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 260           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 261            nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 262            nsccont_frag(ind),isccont_frag(1,1,ind),&
 263            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 264            nc_req_setf(j,i),2,.false.,lprn)
 265           ishif=ishif1
 266           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 267           if (nc_match.gt.0) then
 268             if (ishif.eq.0) then
 269               iclass_con=2
 270             else
 271               iclass_con=1
 272             endif
 273           endif
 274           ncont_nat(1,j,i)=nc_match
 275           ncont_nat(2,j,i)=ncon_match
 276           ishifft_con=ishif
 277         else if (i.eq.2) then
 278           iclass_con=2
 279           ishifft_con=0
 280         endif
 281         if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
 282         if (lprn) write (iout,*) &
 283           "Comparing rms: fragments",&
 284            (ipiece(k,j,i),k=1,npiece(j,i))
 285         rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
 286         if (irms(j,i).gt.0) then
 287           iclass_rms=0
 288           ishifft_rms=0
 289           if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 290 !          write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
 291 !     &     " rmscutfrag",rmscutfrag(1,j,i)
 292           if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
 293             iclass_rms=2
 294             ishifft_rms=0
 295           else
 296             ishif=0
 297             rms=1.0d2
 298             do while (rms.gt.rmscutfrag(1,j,i) .and. &
 299                ishif.lt.n_shift(1,j,i))
 300               ishif=ishif+1
 301               rms=rmscalc(-ishif,i,j,jcon,lprn)
 302 !              print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
 303               if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 304               if (rms.gt.rmscutfrag(1,j,i)) then
 305                 rms=rmscalc(ishif,i,j,jcon,lprn)
 306 !                print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
 307               endif
 308               if (lprn) write (iout,*) "rms",rms
 309             enddo
 310             if (rms.le.rmscutfrag(1,j,i)) then
 311               ishifft_rms=ishif
 312               rmsfrag(j,i)=rms
 313               iclass_rms=1
 314             endif
 315           endif
 316         endif
 317         if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. &
 318           isccont(j,i).eq.0 ) then
 319           write (iout,*) "Error: no measure of comparison specified:",&
 320             " level",i," part",j
 321           stop
 322         endif
 323         if (lprn) &
 324         write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
 325         if (i.eq.2) then
 326           iclass(j,i) = min0(iclass_con,iclass_rms)
 327           if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
 328             ishifft(j,i)=ishifft_rms
 329           else
 330             ishifft(j,i)=ishifft_con
 331           endif
 332         else if (i.gt.2) then
 333           iclass(j,i) = iclass_rms
 334           ishifft(j,i)= ishifft_rms
 335         endif
 336    12   continue
 337         enddo
 338       enddo
 339       rms_nat=rmsnat(jcon)
 340       qnat=qwolynes(0,0)
 341 ! Compute the structural class
 342       iscor=0
 343       IF (.NOT. BINARY) THEN
 344       do i=1,nlevel
 345         IF (I.EQ.1) THEN
 346         do j=1,nfrag(i)
 347           itemp(j)=iclass(j,i)
 348         enddo
 349         do kk=-1,1
 350           do j=1,nfrag(i)
 351             idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
 352             iex = 2**idig
 353             im=mod(itemp(j),2)
 354             itemp(j)=itemp(j)/2
 355 !            write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 356 !     &        " iclass",iclass(j,i)," im",im
 357             iscor=iscor+im*iex
 358           enddo
 359         enddo
 360         ELSE
 361         do j=1,nfrag(i)
 362           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
 363           iex = 2**idig
 364           if (iclass(j,i).gt.0) then
 365             im=1
 366           else
 367             im=0
 368           endif
 369 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 370 !     &      " iclass",iclass(j,i)," im",im
 371           iscor=iscor+im*iex
 372         enddo
 373         do j=1,nfrag(i)
 374           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
 375           iex = 2**idig
 376           if (iclass(j,i).gt.1) then
 377             im=1
 378           else
 379             im=0
 380           endif
 381 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 382 !     &      " iclass",iclass(j,i)," im",im
 383           iscor=iscor+im*iex
 384         enddo
 385         ENDIF
 386       enddo
 387       iscore=iscor
 388       ENDIF
 389       if (print_class) then
 390 #ifdef MPI
 391           write(istat,'(i6,$)') jcon+indstart(me)-1
 392           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 393            -entfac(jcon)
 394 #else
 395           write(istat,'(i6,$)') jcon
 396           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 397             -entfac(jcon)
 398 #endif
 399           write (istat,'(f8.3,2f6.3,$)') &
 400             rms_nat,qnat,rmsang/(nres-3)
 401           do j=1,nlevel
 402             write(istat,'(1x,$,20(i3,$))') &
 403               (ncont_nat(1,k,j),k=1,nfrag(j))
 404             if (j.lt.3) then
 405               write(istat,'(1x,$,20(f5.1,f5.2$))') &
 406                 (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
 407             else
 408               write(istat,'(1x,$,20(f5.1$))') &
 409                 (rmsfrag(k,j),k=1,nfrag(j))
 410             endif
 411             write(istat,'(1x,$,20(i1,$))') &
 412               (iclass(k,j),k=1,nfrag(j))
 413           enddo
 414           if (binary) then
 415             write (istat,'("  ",$)')
 416             do j=1,nlevel
 417               write (istat,'(100(i1,$))')(iclass(k,j),&
 418                  k=1,nfrag(j))
 419               if (j.lt.nlevel) write(iout,'(".",$)')
 420             enddo
 421             write (istat,*)
 422           else
 423             write (istat,'(i10)') iscore
 424           endif
 425       endif
 426       RETURN
 427       END subroutine conf_compar
 428 !-----------------------------------------------------------------------------
 429 ! angnorm.f
 430 !-----------------------------------------------------------------------------
 431       subroutine add_angpair(ici,icj,nang_pair,iang_pair)
 432
 433 !      implicit real*8 (a-h,o-z)
 434 !      include 'DIMENSIONS'
 435 !      include 'COMMON.IOUNITS'
 436 !      include 'COMMON.CHAIN'
 437       integer :: ici,icj,nang_pair,iang_pair(2,nres)
 438       integer :: i,ian1,ian2
 439 !      write (iout,*) "add_angpair: ici",ici," icj",icj,
 440 !     &  " nang_pair",nang_pair
 441       ian1=ici+2
 442       if (ian1.lt.4 .or. ian1.gt.nres) return
 443       ian2=icj+2
 444 !      write (iout,*) "ian1",ian1," ian2",ian2
 445       if (ian2.lt.4 .or. ian2.gt.nres) return
 446       do i=1,nang_pair
 447         if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
 448       enddo
 449       nang_pair=nang_pair+1
 450       iang_pair(1,nang_pair)=ian1
 451       iang_pair(2,nang_pair)=ian2
 452       return
 453       end subroutine add_angpair
 454 !-------------------------------------------------------------------------
 455       subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,lprn)
 456
 457       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 458                               rad2deg,dwapi
 459 !      implicit real*8 (a-h,o-z)
 460 !      include 'DIMENSIONS'
 461 !      include 'DIMENSIONS.ZSCOPT'
 462 !      include 'DIMENSIONS.COMPAR'
 463 !      include 'COMMON.IOUNITS'
 464 !      include 'COMMON.VAR'
 465 !      include 'COMMON.COMPAR'
 466 !      include 'COMMON.CHAIN'
 467 !      include 'COMMON.GEO'
 468       real(kind=8) :: pinorm,deltang
 469       logical :: lprn
 470       integer :: jfrag,ishif1,ishif2,nn,npart,nn4,nne
 471       real(kind=8) :: diffang_max,angn,fract,ff
 472       integer :: i,j,nbeg,nend,ll,longest
 473       if (lprn) write (iout,'(80(1h*))')
 474       angn=0.0d0
 475       nn = 0
 476       fract = 1.0d0
 477       npart = npiece(jfrag,1)
 478       nn4 = nstart_sup+3
 479       nne = min0(nend_sup,nres)
 480       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 481       do i=1,npart
 482         nbeg = ifrag(1,i,jfrag) + 3 - ishif1
 483         if (nbeg.lt.nn4) nbeg=nn4
 484         nend = ifrag(2,i,jfrag) + 1 - ishif2
 485         if (nend.gt.nne) nend=nne
 486         if (nend.ge.nbeg) then
 487         nn = nn + nend - nbeg + 1
 488         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 489           " nn",nn," ishift1",ishif1," ishift2",ishif2
 490         if (lprn) write (iout,*) "angles"
 491         longest=0
 492         ll = 0
 493         do j=nbeg,nend
 494 !          deltang = pinorm(phi(j)-phi_ref(j+ishif1))
 495           deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
 496             theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
 497           if (dabs(deltang).gt.diffang_max) then
 498             if (ll.gt.longest) longest = ll
 499             ll = 0
 500           else
 501             ll=ll+1
 502           endif
 503           if (ll.gt.longest) longest = ll
 504           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 505            rad2deg*phi_ref(j+ishif1),rad2deg*deltang
 506           angn=angn+dabs(deltang)
 507         enddo
 508         longest=longest+3
 509         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 510         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 511           diffang_max*rad2deg,":",longest," fraction",ff
 512         if (ff.lt.fract) fract = ff
 513         endif
 514       enddo
 515       if (nn.gt.0) then
 516         angn = angn/nn
 517       else
 518         angn = dwapi
 519       endif
 520       if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
 521         " fract",fract
 522       return
 523       end subroutine angnorm
 524 !-------------------------------------------------------------------------
 525       subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
 526         diffang_max,anorm,fract)
 527
 528       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 529                               rad2deg
 530 !      implicit real*8 (a-h,o-z)
 531 !      include 'DIMENSIONS'
 532 !      include 'DIMENSIONS.ZSCOPT'
 533 !      include 'DIMENSIONS.COMPAR'
 534 !      include 'COMMON.IOUNITS'
 535 !      include 'COMMON.VAR'
 536 !      include 'COMMON.COMPAR'
 537 !      include 'COMMON.CHAIN'
 538 !      include 'COMMON.GEO'
 539       integer :: ncont,icont(2,ncont),longest
 540       real(kind=8) :: anorm,diffang_max,fract
 541       integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
 542       real(kind=8) :: pinorm
 543       logical :: lprn
 544       integer :: jfrag,ishif1,ishif2
 545       integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
 546       integer :: nbeg,nend,ll
 547       real(kind=8) :: angn,ishifc,deltang,ff
 548
 549       if (lprn) write (iout,'(80(1h*))')
 550 !
 551 ! Determine the segments for which angles will be compared
 552 !
 553       nn4 = nstart_sup+3
 554       nne = min0(nend_sup,nres)
 555       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 556       npart=npiece(jfrag,1)
 557       npiece_c=0
 558       do i=1,npart
 559 !        write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 560         if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
 561           icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
 562         jstart=1
 563         do while (jstart.lt.ncont .and. &
 564          icont(1,jstart).lt.ifrag(1,i,jfrag))
 565 !          write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 566 !     &     " ifrag",ifrag(1,i,jfrag)
 567           jstart=jstart+1
 568         enddo
 569 !        write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 570 !     &   " ifrag",ifrag(1,i,jfrag)
 571         if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
 572         npiece_c=npiece_c+1
 573         ic1=icont(1,jstart)
 574         ifrag_c(1,npiece_c)=icont(1,jstart)
 575         jend=ncont
 576         do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
 577 !          write (iout,*) "jend",jend," icont",icont(1,jend),
 578 !     &     " ifrag",ifrag(2,i,jfrag)
 579           jend=jend-1
 580         enddo
 581 !        write (iout,*) "jend",jend," icont",icont(1,jend),
 582 !     &   " ifrag",ifrag(2,i,jfrag)
 583         ic2=icont(1,jend)
 584         ifrag_c(2,npiece_c)=icont(1,jend)+1
 585         ishift_c(npiece_c)=ishif1
 586 !        write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
 587 !     &    " ic1",ic1," ic2",ic2,
 588 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 589    11   continue
 590         if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
 591           idi=1
 592         else
 593           idi=-1
 594         endif
 595 !        write (iout,*) "idi",idi
 596         if (idi.eq.1) then
 597           if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
 598             icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
 599           jstart=1
 600           do while (jstart.lt.ncont .and. &
 601            icont(2,jstart).lt.ifrag(1,i,jfrag))
 602 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 603 !     &     " ifrag",ifrag(1,i,jfrag)
 604             jstart=jstart+1
 605           enddo
 606 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 607 !     &     " ifrag",ifrag(1,i,jfrag)
 608           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 609           npiece_c=npiece_c+1
 610           ic1=icont(2,jstart)
 611           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 612           jend=ncont
 613           do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
 614 !            write (iout,*) "jend",jend," icont",icont(2,jend),
 615 !     &     " ifrag",ifrag(2,i,jfrag)
 616             jend=jend-1
 617           enddo
 618 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 619 !     &     " ifrag",ifrag(2,i,jfrag)
 620         else if (idi.eq.-1) then
 621           if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
 622               icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
 623           jstart=ncont
 624           do while (jstart.gt.ncont .and. &
 625            icont(2,jstart).lt.ifrag(1,i,jfrag))
 626 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 627 !     &     " ifrag",ifrag(1,i,jfrag)
 628             jstart=jstart-1
 629           enddo
 630 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 631 !     &     " ifrag",ifrag(1,i,jfrag)
 632           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 633           npiece_c=npiece_c+1
 634           ic1=icont(2,jstart)
 635           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 636           jend=1
 637           do while (jend.lt.ncont .and. &
 638              icont(2,jend).gt.ifrag(2,i,jfrag))
 639 !             write (iout,*) "jend",jend," icont",icont(2,jend),
 640 !     &         " ifrag",ifrag(2,i,jfrag)
 641             jend=jend+1
 642           enddo
 643 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 644 !     &     " ifrag",ifrag(2,i,jfrag)
 645         endif
 646         ic2=icont(2,jend)
 647         if (ic2.lt.ic1) then
 648           iic = ic1
 649           ic1 = ic2
 650           ic2 = iic
 651         endif
 652 !        write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
 653 !     &    " jstart:",jstart," jend",jend,
 654 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 655         ifrag_c(1,npiece_c)=ic1
 656         ifrag_c(2,npiece_c)=ic2+1
 657         ishift_c(npiece_c)=ishif2
 658    12   continue
 659       enddo
 660       if (lprn) then
 661         write (iout,*) "Before merge: npiece_c",npiece_c
 662         do i=1,npiece_c
 663           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 664         enddo
 665       endif
 666 !
 667 ! Merge overlapping segments (e.g., avoid splitting helices)
 668 !
 669       i=1
 670       do while (i .lt. npiece_c)
 671         if (ishift_c(i).eq.ishift_c(i+1) .and. &
 672            ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
 673            ifrag_c(2,i)=ifrag_c(2,i+1)
 674            do j=i+1,npiece_c
 675              ishift_c(j)=ishift_c(j+1)
 676              ifrag_c(1,j)=ifrag_c(1,j+1)
 677              ifrag_c(2,j)=ifrag_c(2,j+1)
 678            enddo
 679            npiece_c=npiece_c-1
 680         else
 681           i=i+1
 682         endif
 683       enddo
 684       if (lprn) then
 685         write (iout,*) "After merge: npiece_c",npiece_c
 686         do i=1,npiece_c
 687           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 688         enddo
 689       endif
 690 !
 691 ! Compare angles
 692 !
 693       angn=0.0d0
 694       anorm=0
 695       nn = 0
 696       fract = 1.0d0
 697       npart = npiece_c
 698       do i=1,npart
 699         ishifc=ishift_c(i)
 700         nbeg = ifrag_c(1,i) + 3 - ishifc
 701         if (nbeg.lt.nn4) nbeg=nn4
 702         nend = ifrag_c(2,i)  - ishifc + 1
 703         if (nend.gt.nne) nend=nne
 704         if (nend.ge.nbeg) then
 705         nn = nn + nend - nbeg + 1
 706         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 707           " nn",nn," ishifc",ishifc
 708         if (lprn) write (iout,*) "angles"
 709         longest=0
 710         ll = 0
 711         do j=nbeg,nend
 712 !          deltang = pinorm(phi(j)-phi_ref(j+ishifc))
 713           deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
 714             theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
 715           if (dabs(deltang).gt.diffang_max) then
 716             if (ll.gt.longest) longest = ll
 717             ll = 0
 718           else
 719             ll=ll+1
 720           endif
 721           if (ll.gt.longest) longest = ll
 722           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 723            rad2deg*phi_ref(j+ishifc),rad2deg*deltang
 724           angn=angn+dabs(deltang)
 725         enddo
 726         longest=longest+3
 727         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 728         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 729           diffang_max*rad2deg,":",longest," fraction",ff
 730         if (ff.lt.fract) fract = ff
 731         endif
 732       enddo
 733       if (nn.gt.0) anorm = angn/nn
 734       if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
 735       return
 736       end subroutine angnorm2
 737 !-------------------------------------------------------------------------
 738       real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
 739
 740       use geometry_data, only:phi,theta,rad2deg
 741 !      implicit real*8 (a-h,o-z)
 742 !      include 'DIMENSIONS'
 743 !      include 'DIMENSIONS.ZSCOPT'
 744 !      include 'DIMENSIONS.COMPAR'
 745 !      include 'COMMON.IOUNITS'
 746 !      include 'COMMON.VAR'
 747 !      include 'COMMON.COMPAR'
 748 !      include 'COMMON.CHAIN'
 749 !      include 'COMMON.GEO'
 750       logical :: lprn
 751       integer :: nang_pair,iang_pair(2,nres)
 752       real(kind=8) :: pinorm
 753       integer :: j,ia1,ia2
 754       real(kind=8) :: angn,deltang
 755       angn=0.0d0
 756       if (lprn) write (iout,'(80(1h*))')
 757       if (lprn) write (iout,*) "nang_pair",nang_pair
 758       if (lprn) write (iout,*) "angles"
 759       do j=1,nang_pair
 760         ia1 = iang_pair(1,j)
 761         ia2 = iang_pair(2,j)
 762 !        deltang = pinorm(phi(ia1)-phi_ref(ia2))
 763          deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
 764             theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
 765         if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
 766          rad2deg*phi_ref(ia2),rad2deg*deltang
 767         angn=angn+dabs(deltang)
 768       enddo
 769       if (lprn) &
 770       write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
 771       angnorm1 = angn/nang_pair
 772       return
 773       end function angnorm1
 774 !------------------------------------------------------------------------------
 775       subroutine angnorm12(diff)
 776
 777       use geometry_data, only:phi,theta,nstart_sup,nend_sup
 778 !      implicit real*8 (a-h,o-z)
 779 !      include 'DIMENSIONS'
 780 !      include 'DIMENSIONS.ZSCOPT'
 781 !      include 'DIMENSIONS.COMPAR'
 782 !      include 'COMMON.IOUNITS'
 783 !      include 'COMMON.VAR'
 784 !      include 'COMMON.COMPAR'
 785 !      include 'COMMON.CHAIN'
 786 !      include 'COMMON.GEO'
 787       real(kind=8) :: pinorm,diff
 788       integer :: nn4,nne,j
 789       diff=0.0d0
 790       nn4 = nstart_sup+3
 791       nne = min0(nend_sup,nres)
 792 !      do j=nn4-1,nne
 793 !        diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
 794 !      enddo
 795       do j=nn4,nne
 796 !        diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
 797          diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
 798             theta_ref(j),phi(j),theta(j-1),theta(j))
 799       enddo
 800       return
 801       end subroutine angnorm12
 802 !--------------------------------------------------------------------------------
 803       real(kind=8) function spherang(gam1,theta11,theta12,&
 804          gam2,theta21,theta22)
 805 !      implicit none
 806       use geometry, only:arcos
 807       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
 808         x1,x2,xmed,f1,f2,fmed
 809       real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
 810       real(kind=8) :: sumcos
 811 !el      real(kind=8) :: pinorm,sumangp !arcos,
 812       integer :: it,maxit=100
 813 ! Calculate the difference of the angles of two superposed 4-redidue fragments
 814 !
 815 !       O      P
 816 !        \    /
 817 !     O'--C--C
 818 !             \
 819 !              P'
 820 !
 821 ! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
 822 ! to achieve the minimum difference between the O'-C-O and P-C-P angles;
 823 ! the sum of these angles is the difference returned by the function.
 824 !
 825 ! 4/28/04 AL
 826 ! If thetas match, take the difference of gamma and exit.
 827       if (dabs(theta11-theta12).lt.tolx &
 828        .and. dabs(theta21-theta22).lt.tolx) then
 829         spherang=dabs(pinorm(gam2-gam1))
 830         return
 831       endif
 832 ! If the gammas are the same, take the difference of thetas and exit.
 833       x1=0.0d0
 834       x2=0.5d0*pinorm(gam2-gam1)
 835       if (dabs(x2) .lt. tolx) then
 836         spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
 837         return
 838       else if (x2.lt.0.0d0) then
 839         x1=x2
 840         x2=0.0d0
 841       endif
 842 ! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
 843       f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
 844       f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
 845       do it=1,maxit
 846         xmed=x1-f1*(x2-x1)/(f2-f1)
 847         fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
 848 !        write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
 849         if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
 850              .and. dabs(fmed).lt.tolf ) then
 851           x1=xmed
 852           f1=fmed
 853           goto 10
 854         else if ( fmed*f1.lt.0.0d0 ) then
 855           x2=xmed
 856           f2=fmed
 857         else
 858           x1=xmed
 859           f1=fmed
 860         endif
 861       enddo
 862    10 continue
 863       spherang=arcos(dcos(theta11)*dcos(theta12) &
 864        +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
 865        arcos(dcos(theta21)*dcos(theta22)+ &
 866        dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
 867       return
 868       end function spherang
 869 !--------------------------------------------------------------------------------
 870       real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
 871        theta21,theta22,fi)
 872 !      implicit none
 873       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
 874        cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
 875        cosd2
 876 ! derivarive of the sum of the difference of the angles of a 4-residue fragment.
 877 !      real(kind=8) :: arcos
 878       cost11=dcos(theta11)
 879       cost12=dcos(theta12)
 880       cost21=dcos(theta21)
 881       cost22=dcos(theta22)
 882       sint11=dsin(theta11)
 883       sint12=dsin(theta12)
 884       sint21=dsin(theta21)
 885       sint22=dsin(theta22)
 886       cosd1=cost11*cost12+sint11*sint12*dcos(fi)
 887       cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
 888       sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
 889        +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
 890       return
 891       end function sumangp
 892 !-----------------------------------------------------------------------------
 893 ! contact.f
 894 !-----------------------------------------------------------------------------
 895       subroutine contact(lprint,ncont,icont,ist,ien)
 896
 897       use calc_data
 898       use geometry_data, only:c,dc,dc_norm
 899       use energy_data, only:itype,maxcont
 900 !      implicit none
 901 !      include 'DIMENSIONS'
 902 !      include 'DIMENSIONS.ZSCOPT'
 903 !      include 'COMMON.CONTROL'
 904 !      include 'COMMON.IOUNITS'
 905 !      include 'COMMON.CHAIN'
 906 !      include 'COMMON.INTERACT'
 907 !      include 'COMMON.FFIELD'
 908 !      include 'COMMON.NAMES'
 909 !      include 'COMMON.CALC'
 910 !      include 'COMMON.CONTPAR'
 911 !      include 'COMMON.LOCAL'
 912       integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2
 913       real(kind=8) :: csc !el,dist
 914       real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
 915           ddsc,ddla,ddlb
 916       integer :: ncont
 917       integer,dimension(2,maxcont) :: icont
 918       real(kind=8) :: u,v,a(3),b(3),dla,dlb
 919       logical :: lprint
 920 !el-------
 921       dla=0.0d0
 922       dlb=0.0d0
 923 !el------
 924       ncont=0
 925       kkk=3
 926       if (lprint) then
 927       do i=1,nres
 928         mnum=molnum(i)
 929         write (iout,110) restyp(itype(i)),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         iti=iabs(itype(i))
 937         if (iti.le.0 .or. iti.gt.ntyp) cycle
 938         do j=i+kkk,ien
 939           itj=iabs(itype(j))
 940           if (itj.le.0 .or. itj.gt.ntyp) cycle
 941           itypi=iti
 942           itypj=itj
 943           xj = c(1,nres+j)-c(1,nres+i)
 944           yj = c(2,nres+j)-c(2,nres+i)
 945           zj = c(3,nres+j)-c(3,nres+i)
 946           dxi = dc_norm(1,nres+i)
 947           dyi = dc_norm(2,nres+i)
 948           dzi = dc_norm(3,nres+i)
 949           dxj = dc_norm(1,nres+j)
 950           dyj = dc_norm(2,nres+j)
 951           dzj = dc_norm(3,nres+j)
 952           do k=1,3
 953             a(k)=dc(k,nres+i)
 954             b(k)=dc(k,nres+j)
 955           enddo
 956 !          write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
 957           if (icomparfunc.eq.1) then
 958             call contfunc(csc,iti,itj)
 959           else if (icomparfunc.eq.2) then
 960             call scdist(csc,iti,itj)
 961           else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
 962             csc = dist(nres+i,nres+j)
 963           else if (icomparfunc.eq.4) then
 964             call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
 965           else
 966             write (*,*) "Error - Unknown sidechain contact function"
 967             write (iout,*) "Error - Unknown sidechain contact function"
 968           endif
 969           if (csc.lt.sc_cutoff(iti,itj)) then
 970 !            write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
 971 !     &      " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
 972 !     &      dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
 973 !     &      dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
 974 !     &      xj,yj,zj
 975 !            write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
 976 !     &       sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
 977 !     &       chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
 978 !     &       csc
 979             ncont=ncont+1
 980             cscore(ncont)=csc
 981             icont(1,ncont)=i
 982             icont(2,ncont)=j
 983             omt1(ncont)=om1
 984             omt2(ncont)=om2
 985             omt12(ncont)=om12
 986             ddsc(ncont)=1.0d0/rij
 987             ddla(ncont)=dla
 988             ddlb(ncont)=dlb
 989           endif
 990         enddo
 991       enddo
 992       if (lprint) then
 993         write (iout,'(a)') 'Contact map:'
 994         do i=1,ncont
 995           i1=icont(1,i)
 996           i2=icont(2,i)
 997           it1=itype(i1)
 998           it2=itype(i2)
 999           write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
1000            i,restyp(it1),i1,restyp(it2),i2,cscore(i),&
1001            sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1002            omt1(i),omt2(i),omt12(i)
1003         enddo
1004       endif
1005       return
1006       end subroutine contact
1007 #else
1008 !----------------------------------------------------------------------------
1009       subroutine contact(lprint,ncont,icont)
1010
1011       use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii
1012 !      include 'DIMENSIONS'
1013 !      include 'COMMON.IOUNITS'
1014 !      include 'COMMON.CHAIN'
1015 !      include 'COMMON.INTERACT'
1016 !      include 'COMMON.FFIELD'
1017 !      include 'COMMON.NAMES'
1018       real(kind=8) :: facont=1.569D0  ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1019       integer :: ncont,icont(2,maxcont)
1020       logical :: lprint
1021       integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1022       real(kind=8) :: rcomp
1023       ncont=0
1024       kkk=3
1025 !     print *,'nnt=',nnt,' nct=',nct
1026       do i=nnt+kkk,nct
1027         iti=iabs(itype(i))
1028         do j=nnt,i-kkk
1029           itj=iabs(itype(j))
1030           if (ipot.ne.4) then
1031 !           rcomp=sigmaii(iti,itj)+1.0D0
1032             rcomp=facont*sigmaii(iti,itj)
1033           else
1034 !           rcomp=sigma(iti,itj)+1.0D0
1035             rcomp=facont*sigma(iti,itj)
1036           endif
1037 !         rcomp=6.5D0
1038 !         print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1039           if (dist(nres+i,nres+j).lt.rcomp) then
1040             ncont=ncont+1
1041             icont(1,ncont)=i
1042             icont(2,ncont)=j
1043           endif
1044         enddo
1045       enddo
1046       if (lprint) then
1047         write (iout,'(a)') 'Contact map:'
1048         do i=1,ncont
1049           i1=icont(1,i)
1050           i2=icont(2,i)
1051           it1=itype(i1)
1052           it2=itype(i2)
1053           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1054            i,restyp(it1),i1,restyp(it2),i2
1055         enddo
1056       endif
1057       return
1058       end subroutine contact
1059 #endif
1060 !----------------------------------------------------------------------------
1061       real(kind=8) function contact_fract(ncont,ncont_ref,&
1062                                            icont,icont_ref)
1063
1064       use energy_data, only:maxcont
1065 !      implicit none
1066 !      include 'DIMENSIONS'
1067 !      include 'COMMON.IOUNITS'
1068       integer :: i,j,nmatch
1069       integer :: ncont,ncont_ref
1070       integer,dimension(2,maxcont) :: icont,icont_ref
1071       nmatch=0
1072 !     print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1073 !     write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1074 !     write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1075 !     write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1076 !     write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1077       do i=1,ncont
1078         do j=1,ncont_ref
1079           if (icont(1,i).eq.icont_ref(1,j) .and. &
1080               icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1081         enddo
1082       enddo
1083 !     print *,' nmatch=',nmatch
1084 !     contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1085       contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1086       return
1087       end function contact_fract
1088 #ifndef CLUSTER
1089 !------------------------------------------------------------------------------
1090       subroutine pept_cont(lprint,ncont,icont)
1091
1092       use geometry_data, only:c
1093       use energy_data, only:maxcont,nnt,nct,itype
1094 !      implicit none
1095 !      include 'DIMENSIONS'
1096 !      include 'DIMENSIONS.ZSCOPT'
1097 !      include 'COMMON.IOUNITS'
1098 !      include 'COMMON.CHAIN'
1099 !      include 'COMMON.INTERACT'
1100 !      include 'COMMON.FFIELD'
1101 !      include 'COMMON.NAMES'
1102       integer :: ncont,icont(2,maxcont)
1103       integer :: i,j,k,kkk,i1,i2,it1,it2
1104       logical :: lprint
1105 !el      real(kind=8) :: dist
1106       real(kind=8) :: rcomp=5.5d0
1107       ncont=0
1108       kkk=0
1109       print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1110       do i=nnt,nct-3
1111         do k=1,3
1112           c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1113         enddo
1114         do j=i+2,nct-1
1115           do k=1,3
1116             c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1117           enddo
1118           if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1119             ncont=ncont+1
1120             icont(1,ncont)=i
1121             icont(2,ncont)=j
1122           endif
1123         enddo
1124       enddo
1125       if (lprint) then
1126         write (iout,'(a)') 'PP contact map:'
1127         do i=1,ncont
1128           i1=icont(1,i)
1129           i2=icont(2,i)
1130           it1=itype(i1)
1131           it2=itype(i2)
1132           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1133            i,restyp(it1),i1,restyp(it2),i2
1134         enddo
1135       endif
1136       return
1137       end subroutine pept_cont
1138 !-----------------------------------------------------------------------------
1139 ! cont_frag.f
1140 !-----------------------------------------------------------------------------
1141       subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1142          ncont_interfrag,icont_interfrag)
1143
1144       use energy_data, only:itype,maxcont
1145 !      include 'DIMENSIONS'
1146 !      include 'DIMENSIONS.ZSCOPT'
1147 !      include 'DIMENSIONS.COMPAR'
1148 !      include 'COMMON.INTERACT'
1149 !      include 'COMMON.COMPAR'
1150 !      include 'COMMON.IOUNITS'
1151 !      include 'COMMON.CHAIN'
1152 !      include 'COMMON.NAMES'
1153       integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1154         icont_interfrag(2,maxcont,mmaxfrag)
1155       logical :: OK1,OK2,lprint
1156       integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2
1157 ! Determine the contacts that occur within a fragment and between fragments.
1158       do i=1,nfrag(1)
1159         do j=1,i
1160           ind = icant(i,j)
1161           nc=0
1162 !          write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1163 !     &      ,k=1,npiece(i,1))
1164 !          write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1165 !     &      ,k=1,npiece(j,1))
1166 !          write (iout,*) "ncont",ncont
1167           do k=1,ncont
1168             ic1=icont(1,k)
1169             ic2=icont(2,k)
1170             OK1=.false.
1171             l=0
1172             do while (.not.OK1 .and. l.lt.npiece(j,1))
1173               l=l+1
1174               OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1175                ic1.le.ifrag(2,l,j)+is
1176             enddo
1177             OK2=.false.
1178             l=0
1179             do while (.not.OK2 .and. l.lt.npiece(i,1))
1180               l=l+1
1181               OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1182                ic2.le.ifrag(2,l,i)+is
1183             enddo
1184 !            write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1185 !     &        " OK2",OK2
1186             if (OK1.and.OK2) then
1187               nc=nc+1
1188               icont_interfrag(1,nc,ind)=ic1
1189               icont_interfrag(2,nc,ind)=ic2
1190 !              write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1191             endif
1192           enddo
1193           ncont_interfrag(ind)=nc
1194 !          do k=1,ncont_interfrag(ind)
1195 !              i1=icont_interfrag(1,k,ind)
1196 !              i2=icont_interfrag(2,k,ind)
1197 !              it1=itype(i1)
1198 !              it2=itype(i2)
1199 !              write (iout,'(i3,2x,a,i4,2x,a,i4)')
1200 !     &          i,restyp(it1),i1,restyp(it2),i2
1201 !          enddo
1202         enddo
1203       enddo
1204       if (lprint) then
1205         write (iout,*) "Contacts within fragments:"
1206         do i=1,nfrag(1)
1207           write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1208            ifrag(2,k,i),k=1,npiece(i,1)),")"
1209           ind=icant(i,i)
1210           do k=1,ncont_interfrag(ind)
1211             i1=icont_interfrag(1,k,ind)
1212             i2=icont_interfrag(2,k,ind)
1213             it1=itype(i1)
1214             it2=itype(i2)
1215             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1216               i,restyp(it1),i1,restyp(it2),i2
1217           enddo
1218         enddo
1219         write (iout,*)
1220         write (iout,*) "Contacts between fragments:"
1221         do i=1,nfrag(1)
1222         do j=1,i-1
1223           ind = icant(i,j)
1224           write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1225            ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1226            (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1227           write (iout,*) "Number of contacts",&
1228            ncont_interfrag(ind)
1229           ind=icant(i,j)
1230           do k=1,ncont_interfrag(ind)
1231             i1=icont_interfrag(1,k,ind)
1232             i2=icont_interfrag(2,k,ind)
1233             it1=itype(i1)
1234             it2=itype(i2)
1235             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1236               i,restyp(it1),i1,restyp(it2),i2
1237           enddo
1238         enddo
1239         enddo
1240       endif
1241       return
1242       end subroutine contacts_between_fragments
1243 !-----------------------------------------------------------------------------
1244 ! contfunc.f
1245 !-----------------------------------------------------------------------------
1246       subroutine contfunc(cscore,itypi,itypj)
1247 !
1248 ! This subroutine calculates the contact function based on
1249 ! the Gay-Berne potential of interaction.
1250 !
1251       use calc_data
1252 !      implicit real*8 (a-h,o-z)
1253 !      include 'DIMENSIONS'
1254 !      include 'COMMON.CONTPAR'
1255 !      include 'COMMON.CALC'
1256       integer :: expon=6
1257       integer :: itypi,itypj
1258       real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1259 !
1260       sig0ij=sig_comp(itypi,itypj)
1261       chi1=chi_comp(itypi,itypj)
1262       chi2=chi_comp(itypj,itypi)
1263       chi12=chi1*chi2
1264       chip1=chip_comp(itypi,itypj)
1265       chip2=chip_comp(itypj,itypi)
1266       chip12=chip1*chip2
1267       rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1268       rij=dsqrt(rrij)
1269 ! Calculate angle-dependent terms of the contact function
1270       erij(1)=xj*rij
1271       erij(2)=yj*rij
1272       erij(3)=zj*rij
1273       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1274       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1275       om12=dxi*dxj+dyi*dyj+dzi*dzj
1276       chiom12=chi12*om12
1277 !      print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1278 !     &  sig0ij,
1279 !     &  rij,rrij,om1,om2,om12
1280 ! Calculate eps1(om12)
1281       faceps1=1.0D0-om12*chiom12
1282       faceps1_inv=1.0D0/faceps1
1283       eps1=dsqrt(faceps1_inv)
1284 ! Following variable is eps1*deps1/dom12
1285       eps1_om12=faceps1_inv*chiom12
1286 ! Calculate sigma(om1,om2,om12)
1287       om1om2=om1*om2
1288       chiom1=chi1*om1
1289       chiom2=chi2*om2
1290       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1291       sigsq=1.0D0-facsig*faceps1_inv
1292 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1293       chipom1=chip1*om1
1294       chipom2=chip2*om2
1295       chipom12=chip12*om12
1296       facp=1.0D0-om12*chipom12
1297       facp_inv=1.0D0/facp
1298       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1299 ! Following variable is the square root of eps2
1300       eps2rt=1.0D0-facp1*facp_inv
1301       sigsq=1.0D0/sigsq
1302       sig=sig0ij*dsqrt(sigsq)
1303       rij_shift=1.0D0/rij-sig+sig0ij
1304       if (rij_shift.le.0.0D0) then
1305         evdw=1.0D1
1306         cscore = -dlog(evdw+1.0d-6)
1307         return
1308       endif
1309       rij_shift=1.0D0/rij_shift
1310       e2=(rij_shift*sig0ij)**expon
1311       evdw=dabs(eps1*eps2rt**2*e2)
1312       if (evdw.gt.1.0d1) evdw = 1.0d1
1313       cscore = -dlog(evdw+1.0d-6)
1314       return
1315       end subroutine contfunc
1316 !------------------------------------------------------------------------------
1317       subroutine scdist(cscore,itypi,itypj)
1318 !
1319 ! This subroutine calculates the contact distance
1320 !
1321       use calc_data
1322 !      implicit real*8 (a-h,o-z)
1323 !      include 'DIMENSIONS'
1324 !      include 'COMMON.CONTPAR'
1325 !      include 'COMMON.CALC'
1326       integer :: itypi,itypj
1327       real(kind=8) :: cscore,rrij
1328
1329       chi1=chi_comp(itypi,itypj)
1330       chi2=chi_comp(itypj,itypi)
1331       chi12=chi1*chi2
1332       rrij=xj*xj+yj*yj+zj*zj
1333       rij=dsqrt(rrij)
1334 ! Calculate angle-dependent terms of the contact function
1335       erij(1)=xj/rij
1336       erij(2)=yj/rij
1337       erij(3)=zj/rij
1338       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1339       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1340       om12=dxi*dxj+dyi*dyj+dzi*dzj
1341       chiom12=chi12*om12
1342       om1om2=om1*om2
1343       chiom1=chi1*om1
1344       chiom2=chi2*om2
1345       cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1346       return
1347       end subroutine scdist
1348 !------------------------------------------------------------------------------
1349 ! elecont.f
1350 !------------------------------------------------------------------------------
1351       subroutine elecont(lprint,ncont,icont,ist,ien)
1352
1353       use geometry_data, only:c
1354       use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2
1355 !      implicit none
1356 !      include 'DIMENSIONS'
1357 !      include 'DIMENSIONS.ZSCOPT'
1358 !      include 'DIMENSIONS.COMPAR'
1359 !      include 'COMMON.IOUNITS'
1360 !      include 'COMMON.CHAIN'
1361 !      include 'COMMON.INTERACT'
1362 !      include 'COMMON.FFIELD'
1363 !      include 'COMMON.NAMES'
1364 !      include 'COMMON.LOCAL'
1365       logical :: lprint
1366       integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1367       real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1368         xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1369         vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1370         eesij,ees,evdw,ene
1371       real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1372                        -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1373       real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1374                         0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1375       real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1376       real(kind=8) :: elcutoff=-0.3d0
1377       real(kind=8) :: elecutoff_14=-0.5d0
1378       integer :: ncont,icont(2,maxcont)
1379       real(kind=8) :: econt(maxcont)
1380 !
1381 ! Load the constants of peptide bond - peptide bond interactions.
1382 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1383 ! proline) - determined by averaging ECEPP energy.
1384 !
1385 ! as of 7/06/91.
1386 !
1387 !      data epp    / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1388 !      data rpp    / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1389 !el      data (elpp6c)   /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1390 !el      data (elpp3c)   / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1391 !el      data (elcutoff) /-0.3d0/
1392 !el      data (elecutoff_14) /-0.5d0/
1393       ees=0.0d0
1394       evdw=0.0d0
1395       if (lprint) write (iout,'(a)') &
1396         "Constants of electrostatic interaction energy expression."
1397       do i=1,2
1398         do j=1,2
1399         rri=rpp(i,j)**6
1400         appc(i,j)=epp(i,j)*rri*rri
1401         bppc(i,j)=-2.0*epp(i,j)*rri
1402         ael6c(i,j)=elpp6c(i,j)*4.2**6
1403         ael3c(i,j)=elpp3c(i,j)*4.2**3
1404         if (lprint) &
1405         write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1406                                      ael3c(i,j)
1407         enddo
1408       enddo
1409       ncont=0
1410       do 1 i=ist,ien-2
1411         xi=c(1,i)
1412         yi=c(2,i)
1413         zi=c(3,i)
1414         dxi=c(1,i+1)-c(1,i)
1415         dyi=c(2,i+1)-c(2,i)
1416         dzi=c(3,i+1)-c(3,i)
1417         xmedi=xi+0.5*dxi
1418         ymedi=yi+0.5*dyi
1419         zmedi=zi+0.5*dzi
1420         do 4 j=i+2,ien-1
1421           ind=ind+1
1422           iteli=itel(i)
1423           itelj=itel(j)
1424           if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1425           if (iteli.eq.2 .and. itelj.eq.2 &
1426             .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1427           aaa=appc(iteli,itelj)
1428           bbb=bppc(iteli,itelj)
1429           ael6i=ael6c(iteli,itelj)
1430           ael3i=ael3c(iteli,itelj)
1431           dxj=c(1,j+1)-c(1,j)
1432           dyj=c(2,j+1)-c(2,j)
1433           dzj=c(3,j+1)-c(3,j)
1434           xj=c(1,j)+0.5*dxj-xmedi
1435           yj=c(2,j)+0.5*dyj-ymedi
1436           zj=c(3,j)+0.5*dzj-zmedi
1437           rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1438           rmij=sqrt(rrmij)
1439           r3ij=rrmij*rmij
1440           r6ij=r3ij*r3ij
1441           vrmij=vblinv*rmij
1442           cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1443           cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1444           cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1445           fac=cosa-3.0*cosb*cosg
1446           ev1=aaa*r6ij*r6ij
1447           ev2=bbb*r6ij
1448           fac3=ael6i*r6ij
1449           fac4=ael3i*r3ij
1450           evdwij=ev1+ev2
1451           el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1452           el2=fac4*fac
1453           eesij=el1+el2
1454           if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1455               j.eq.i+2 .and. eesij.le.elecutoff_14) then
1456              ncont=ncont+1
1457              icont(1,ncont)=i
1458              icont(2,ncont)=j
1459              econt(ncont)=eesij
1460           endif
1461           ees=ees+eesij
1462           evdw=evdw+evdwij
1463     4   continue
1464     1 continue
1465       if (lprint) then
1466         write (iout,*) 'Total average electrostatic energy: ',ees
1467         write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1468         write (iout,*)
1469         write (iout,*) 'Electrostatic contacts before pruning: '
1470         do i=1,ncont
1471           i1=icont(1,i)
1472           i2=icont(2,i)
1473           it1=itype(i1)
1474           it2=itype(i2)
1475           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1476            i,restyp(it1),i1,restyp(it2),i2,econt(i)
1477         enddo
1478       endif
1479 ! For given residues keep only the contacts with the greatest energy.
1480       i=0
1481       do while (i.lt.ncont)
1482         i=i+1
1483         ene=econt(i)
1484         ic1=icont(1,i)
1485         ic2=icont(2,i)
1486         j=i
1487         do while (j.lt.ncont)
1488           j=j+1
1489           if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1490               ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1491 !            write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1492 !     &       " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1493             if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1494               if (ic1.eq.icont(1,j)) then
1495                 do k=1,ncont
1496                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1497                      .and. iabs(icont(1,k)-ic1).le.2 .and. &
1498                      econt(k).lt.econt(j) ) goto 21
1499                 enddo
1500               else if (ic2.eq.icont(2,j) ) then
1501                 do k=1,ncont
1502                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1503                      .and. iabs(icont(2,k)-ic2).le.2 .and. &
1504                      econt(k).lt.econt(j) ) goto 21
1505                 enddo
1506               endif
1507 ! Remove ith contact
1508               do k=i+1,ncont
1509                 icont(1,k-1)=icont(1,k)
1510                 icont(2,k-1)=icont(2,k)
1511                 econt(k-1)=econt(k)
1512               enddo
1513               i=i-1
1514               ncont=ncont-1
1515 !              write (iout,*) "ncont",ncont
1516 !              do k=1,ncont
1517 !                write (iout,*) icont(1,k),icont(2,k)
1518 !              enddo
1519               goto 20
1520             else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1521             then
1522               if (ic1.eq.icont(1,j)) then
1523                 do k=1,ncont
1524                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1525                      .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1526                      econt(k).lt.econt(i) ) goto 21
1527                 enddo
1528               else if (ic2.eq.icont(2,j) ) then
1529                 do k=1,ncont
1530                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1531                      .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1532                      econt(k).lt.econt(i) ) goto 21
1533                 enddo
1534               endif
1535 ! Remove jth contact
1536               do k=j+1,ncont
1537                 icont(1,k-1)=icont(1,k)
1538                 icont(2,k-1)=icont(2,k)
1539                 econt(k-1)=econt(k)
1540               enddo
1541               ncont=ncont-1
1542 !              write (iout,*) "ncont",ncont
1543 !              do k=1,ncont
1544 !                write (iout,*) icont(1,k),icont(2,k)
1545 !              enddo
1546               j=j-1
1547             endif
1548           endif
1549    21     continue
1550         enddo
1551    20   continue
1552       enddo
1553       if (lprint) then
1554         write (iout,*)
1555         write (iout,*) 'Electrostatic contacts after pruning: '
1556         do i=1,ncont
1557           i1=icont(1,i)
1558           i2=icont(2,i)
1559           it1=itype(i1)
1560           it2=itype(i2)
1561           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1562            i,restyp(it1),i1,restyp(it2),i2,econt(i)
1563         enddo
1564       endif
1565       return
1566       end subroutine elecont
1567 !------------------------------------------------------------------------------
1568 ! match_contact.f
1569 !------------------------------------------------------------------------------
1570       subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1571          ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1572          nc_frac,nc_req_set,istr,llocal,lprn)
1573
1574       use energy_data, only:maxcont
1575 !      implicit real*8 (a-h,o-z)
1576 !      include 'DIMENSIONS'
1577 !      include 'COMMON.IOUNITS'
1578       integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1579       integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1580       real(kind=8) :: nc_frac
1581       logical :: llocal,lprn
1582       integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1583                  nc_req_set,istr,nc_match_max
1584       integer :: i,nc_req,nc_match1,is,js
1585       nc_match_max=0
1586       do i=1,ncont_ref
1587         nc_match_max=nc_match_max+ &
1588          min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1589       enddo
1590       if (istr.eq.3) then
1591         nc_req=0
1592       else if (nc_req_set.eq.0) then
1593         nc_req=nc_match_max*nc_frac
1594       else
1595         nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1596           dfloat(nc_req_set)+1.0d-7)
1597       endif
1598 !      write (iout,*) "match_contact: nc_req:",nc_req
1599 !      write (iout,*) "nc_match_max",nc_match_max
1600 !      write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1601 !     &   " n_shif2",n_shif2
1602 ! Match current contact map against reference contact map; exit, if at least
1603 ! half of the contacts match
1604       call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1605           ncont,icont,jfrag,llocal,lprn)
1606       nc_match1_max=nc_match1
1607       if (lprn .and. nc_match.gt.0) write (iout,*) &
1608         "Shift:",0,0," nc_match1",nc_match1,&
1609         " nc_match=",nc_match," req'd",nc_req
1610       if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1611           nc_req.eq.0 .and. nc_match.eq.1) then
1612          ishif1=0
1613          ishif2=0
1614          return
1615       endif
1616 ! If sufficient matches are not found, try to shift contact maps up to three
1617 ! positions.
1618       if (n_shif1.gt.0) then
1619       do is=1,n_shif1
1620 ! The following four tries help to find shifted beta-sheet patterns
1621 ! Shift "left" strand backward
1622         call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1623           icont_ref,ncont,icont,jfrag,llocal,lprn)
1624         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1625         if (lprn .and. nc_match.gt.0) write (iout,*) &
1626           "Shift:",-is,0," nc_match1",nc_match1,&
1627           " nc_match=",nc_match," req'd",nc_req
1628         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1629            nc_req.eq.0 .and. nc_match.eq.1) then
1630           ishif1=-is
1631           ishif2=0
1632           return
1633         endif
1634 ! Shift "left" strand forward
1635         call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1636             icont_ref,ncont,icont,jfrag,llocal,lprn)
1637         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1638         if (lprn .and. nc_match.gt.0) write (iout,*) &
1639          "Shift:",is,0," nc_match1",nc_match1,&
1640          " nc_match=",nc_match," req'd",nc_req
1641         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1642            nc_req.eq.0 .and. nc_match.eq.1) then
1643           ishif1=is
1644           ishif2=0
1645           return
1646         endif
1647       enddo
1648       if (nc_req.eq.0) return
1649 ! Shift "right" strand backward
1650       do is=1,n_shif1
1651         call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1652            icont_ref,ncont,icont,jfrag,llocal,lprn)
1653         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1654         if (lprn .and. nc_match.gt.0) write (iout,*) &
1655           "Shift:",0,-is," nc_match1",nc_match1,&
1656           " nc_match=",nc_match," req'd",nc_req
1657         if (nc_match.ge.nc_req) then
1658           ishif1=0
1659           ishif2=-is
1660           return
1661         endif
1662 ! Shift "right" strand upward
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       enddo ! is
1675 ! Now try to shift both residues in contacts.
1676       do is=1,n_shif1
1677         do js=1,is
1678           if (js.ne.is) then
1679             call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1680               icont_ref,ncont,icont,jfrag,llocal,lprn)
1681             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1682             if (lprn .and. nc_match.gt.0) write (iout,*) &
1683                "Shift:",-is,-js," nc_match1",nc_match1,&
1684                " nc_match=",nc_match," req'd",nc_req
1685             if (nc_match.ge.nc_req) then
1686               ishif1=-is
1687               ishif2=-js
1688               return
1689             endif
1690             call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1691               icont_ref,ncont,icont,jfrag,llocal,lprn)
1692             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1693             if (lprn .and. nc_match.gt.0) write (iout,*) &
1694               "Shift:",is,js," nc_match1",nc_match1,&
1695               " nc_match=",nc_match," req'd",nc_req
1696             if (nc_match.ge.nc_req) then
1697               ishif1=is
1698               ishif2=js
1699               return
1700             endif
1701 !
1702             call ncont_match(nc_match,nc_match1,-js,-is,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:",-js,-is," nc_match1",nc_match1,&
1707               " nc_match=",nc_match," req'd",nc_req
1708             if (nc_match.ge.nc_req) then
1709               ishif1=-js
1710               ishif2=-is
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           endif
1726 !
1727           if (is+js.le.n_shif1) then
1728           call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1729             icont_ref,ncont,icont,jfrag,llocal,lprn)
1730           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1731           if (lprn .and. nc_match.gt.0) write (iout,*) &
1732            "Shift:",-is,js," nc_match1",nc_match1,&
1733            " nc_match=",nc_match," req'd",nc_req
1734           if (nc_match.ge.nc_req) then
1735             ishif1=-is
1736             ishif2=js
1737             return
1738           endif
1739 !
1740           call ncont_match(nc_match,nc_match1,js,-is,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:",js,-is," nc_match1",nc_match1,&
1745            " nc_match=",nc_match," req'd",nc_req
1746           if (nc_match.ge.nc_req) then
1747             ishif1=js
1748             ishif2=-is
1749             return
1750           endif
1751           endif
1752 !
1753         enddo !js
1754       enddo !is
1755       endif
1756
1757       if (n_shif2.gt.0) then
1758       do is=1,n_shif2
1759         call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1760           icont_ref,ncont,icont,jfrag,llocal,lprn)
1761         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1762         if (lprn .and. nc_match.gt.0) write (iout,*) &
1763            "Shift:",-is,-is," nc_match1",nc_match1,&
1764            " nc_match=",nc_match," req'd",nc_req
1765         if (nc_match.ge.nc_req) then
1766           ishif1=-is
1767           ishif2=-is
1768           return
1769         endif
1770         call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1771           icont_ref,ncont,icont,jfrag,llocal,lprn)
1772         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1773         if (lprn .and. nc_match.gt.0) write (iout,*) &
1774           "Shift:",is,is," nc_match1",nc_match1,&
1775           " nc_match=",nc_match," req'd",nc_req
1776         if (nc_match.ge.nc_req) then
1777           ishif1=is
1778           ishif2=is
1779           return
1780         endif
1781       enddo
1782       endif
1783 ! If this point is reached, the contact maps are different.
1784       nc_match=0
1785       ishif1=0
1786       ishif2=0
1787       return
1788       end subroutine match_contact
1789 !-------------------------------------------------------------------------
1790       subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1791          ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1792
1793       use energy_data, only:nnt,nct,maxcont
1794 !      implicit real*8 (a-h,o-z)
1795 !      include 'DIMENSIONS'
1796 !      include 'DIMENSIONS.ZSCOPT'
1797 !      include 'DIMENSIONS.COMPAR'
1798 !      include 'COMMON.IOUNITS'
1799 !      include 'COMMON.INTERACT'
1800 !      include 'COMMON.GEO'
1801 !      include 'COMMON.COMPAR'
1802       logical :: llocal,lprn
1803       integer ncont_ref,ncont,ishift,ishif2,nang_pair
1804       integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1805       integer,dimension(2,nres) :: iang_pair !(2,maxres)
1806       integer :: nc_match,nc_match1,ishif1,jfrag
1807       integer :: i,j,ic1,ic2
1808       real(kind=8) :: diffang,fract,rad2deg
1809
1810 ! Compare the contact map against the reference contact map; they're stored
1811 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1812       if (lprn) write (iout,'(80(1h*))')
1813       nc_match=0
1814       nc_match1=0
1815 ! Check the local structure by comparing dihedral angles.
1816 !      write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1817       if (llocal .and. ncont_ref.eq.0) then
1818 ! If there are no contacts just compare the dihedral angles and exit.
1819         call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1820           lprn)
1821         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1822          " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1823         if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1824         then
1825           nc_match=1
1826         else
1827           nc_match=0
1828         endif
1829         return
1830       endif
1831       nang_pair=0
1832       do i=1,ncont
1833         ic1=icont(1,i)+ishif1
1834         ic2=icont(2,i)+ishif2
1835 !        write (iout,*) "i",i," ic1",ic1," ic2",ic2
1836         if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1837         do j=1,ncont_ref
1838           if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1839             nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1840             nc_match1=nc_match1+1
1841             icont_match(1,nc_match1)=ic1
1842             icont_match(2,nc_match1)=ic2
1843 !            call add_angpair(icont(1,i),icont_ref(1,j),
1844 !     &         nang_pair,iang_pair)
1845 !            call add_angpair(icont(2,i),icont_ref(2,j),
1846 !     &         nang_pair,iang_pair)
1847             if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1848              " match",icont_ref(1,j),icont_ref(2,j),&
1849              " shifts",ishif1,ishif2
1850             goto 10
1851           endif
1852         enddo
1853    10   continue
1854       enddo
1855       if (lprn) then
1856         write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1857         write (iout,*) "icont_match"
1858         do i=1,nc_match1
1859           write (iout,*) icont_match(1,i),icont_match(2,i)
1860         enddo
1861       endif
1862       if (llocal .and. nc_match.gt.0) then
1863         call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1864           ang_cut1(jfrag),diffang,fract)
1865         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1866          " ang_cut:",ang_cut(jfrag)*rad2deg,&
1867          " ang_cut1",ang_cut1(jfrag)*rad2deg
1868         if (diffang.gt.ang_cut(jfrag) &
1869           .or. fract.lt.frac_min(jfrag)) nc_match=0
1870       endif
1871 !      if (nc_match.gt.0) then
1872 !        diffang = angnorm1(nang_pair,iang_pair,lprn)
1873 !        if (diffang.gt.ang_cut(jfrag)) nc_match=0
1874 !      endif
1875       if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1876          " diffang",rad2deg*diffang," nc_match",nc_match
1877       return
1878       end subroutine ncont_match
1879 !------------------------------------------------------------------------------
1880       subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1881 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1882 ! conformation considered to that of the reference conformation.
1883 ! Returns the number of equivalent residues (nsec_match).
1884 !      implicit real*8 (a-h,o-z)
1885 !      include 'DIMENSIONS'
1886 !      include 'DIMENSIONS.ZSCOPT'
1887 !      include 'DIMENSIONS.COMPAR'
1888 !      include 'COMMON.IOUNITS'
1889 !      include 'COMMON.CHAIN'
1890 !      include 'COMMON.PEPTCONT'
1891 !      include 'COMMON.COMPAR'
1892       logical :: lprn
1893       integer :: isecstr(nres)
1894       integer :: jfrag,nsec_match,npart,i,j
1895       npart = npiece(jfrag,1)
1896       nsec_match=0
1897       if (lprn) then
1898         write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1899               (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1900         write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1901         write (iout,'(80i1)') (isecstr(j),j=1,nres)
1902       endif
1903       do i=1,npart
1904         do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1905 ! The residue has equivalent conformational state to that of the reference
1906 ! structure, if:
1907 !  a) the conformational states are equal or
1908 !  b) the reference state is a coil and that of the conformation considered
1909 !     is a strand or
1910 !  c) the conformational state of the conformation considered is a strand
1911 !     and that of the reference conformation is a coil.
1912 ! 10/28/02 - case (b) deleted.
1913           if (isecstr(j).eq.isec_ref(j) .or. &
1914 !     &        isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1915               isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1916             nsec_match=nsec_match+1
1917         enddo
1918       enddo
1919       return
1920       end subroutine match_secondary
1921 !------------------------------------------------------------------------------
1922 ! odlodc.f
1923 !------------------------------------------------------------------------------
1924       subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1925
1926       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1927 !                            isccont_frag_ref
1928 !      implicit real*8 (a-h,o-z)
1929       real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1930       real(kind=8) :: uu,vv,aa,bb,dd
1931       real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1932 !el      odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1933 !el       + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1934 !      print *,"r1",(r1(i),i=1,3)
1935 !      print *,"r2",(r2(i),i=1,3)
1936 !      print *,"a",(a(i),i=1,3)
1937 !      print *,"b",(b(i),i=1,3)
1938       aa = a(1)**2+a(2)**2+a(3)**2
1939       bb = b(1)**2+b(2)**2+b(3)**2
1940       ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1941       ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1942       br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1943       det = aa*bb-ab**2
1944 !      print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1945       uu = (-ar*bb+br*ab)/det
1946       vv = (br*aa-ar*ab)/det
1947 !      print *,u,v
1948       uu=dmin1(uu,1.0d0)
1949       uu=dmax1(uu,0.0d0)
1950       vv=dmin1(vv,1.0d0)
1951       vv=dmax1(vv,0.0d0)
1952 !el      dd1 = odl(uu,vv)
1953       dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1954 !el      dd2 = odl(0.0d0,0.0d0)
1955       dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1956 !el      dd3 = odl(0.0d0,1.0d0)
1957       dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1958 !el      dd4 = odl(1.0d0,0.0d0)
1959       dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1960 !el      dd5 = odl(1.0d0,1.0d0)
1961       dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1962       dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1963       if (dd.eq.dd2) then
1964         uu=0.0d0
1965         vv=0.0d0
1966       else if (dd.eq.dd3) then
1967         uu=0.0d0
1968         vv=1.0d0
1969       else if (dd.eq.dd4) then
1970         uu=1.0d0
1971         vv=0.0d0
1972       else if (dd.eq.dd5) then
1973         uu=1.0d0
1974         vv=1.0d0
1975       endif
1976 ! Control check
1977 !      do i=1,3
1978 !        x(i)=r1(i)+u*a(i)
1979 !        y(i)=r2(i)+v*b(i)
1980 !      enddo
1981 !      dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
1982 !      dd1 = dsqrt(dd1)
1983       aa = dsqrt(aa)
1984       bb = dsqrt(bb)
1985 !      write (8,*) uu,vv,dd,dd1
1986 !      print *,dd,dd1
1987       return
1988       end subroutine odlodc
1989 !------------------------------------------------------------------------------
1990       real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
1991
1992       real(kind=8),dimension(3) :: r1,r2
1993       real(kind=8) :: aa,bb,u,v,ar,br,ab
1994
1995       odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1996        + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1997
1998       end function odl
1999 !------------------------------------------------------------------------------
2000 ! proc_cont.f
2001 !------------------------------------------------------------------------------
2002       subroutine proc_cont
2003
2004       use geometry_data, only:rad2deg
2005       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2006 !                            isccont_frag_ref
2007 !      implicit real*8 (a-h,o-z)
2008 !      include 'DIMENSIONS'
2009 !      include 'DIMENSIONS.ZSCOPT'
2010 !      include 'DIMENSIONS.COMPAR'
2011 !      include 'COMMON.IOUNITS'
2012 !      include 'COMMON.TIME1'
2013 !      include 'COMMON.SBRIDGE'
2014 !      include 'COMMON.CONTROL'
2015 !      include 'COMMON.COMPAR'
2016 !      include 'COMMON.CHAIN'
2017 !      include 'COMMON.HEADER'
2018 !      include 'COMMON.CONTACTS1'
2019 !      include 'COMMON.PEPTCONT'
2020 !      include 'COMMON.GEO'
2021       integer :: i,j,k,ind,len_cut,ndigit,length_frag
2022
2023       write (iout,*) "proc_cont: nlevel",nlevel
2024       if (nlevel.lt.0) then
2025         write (iout,*) "call define_fragments"
2026         call define_fragments
2027       else
2028         write (iout,*) "call secondary2"
2029         call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2030            isec_ref)
2031       endif
2032       write (iout,'(80(1h=))')
2033       write (iout,*) "Electrostatic contacts"
2034       call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2035        icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2036       write (iout,'(80(1h=))')
2037       write (iout,*) "Side chain contacts"
2038       call contacts_between_fragments(.true.,0,ncont_ref,&
2039        icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2040       if (nlevel.lt.0) then
2041         do i=1,nfrag(1)
2042           ind=icant(i,i)
2043           len_cut=1000
2044           if (istruct(i).le.1) then
2045             len_cut=max0(len_frag(i,1)*4/5,3)
2046           else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2047             len_cut=max0(len_frag(i,1)*2/5,3)
2048           endif
2049           write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2050             ncont_frag_ref(ind)," len_cut",len_cut,&
2051             " icont_single",icont_single," iloc_single",iloc_single
2052           iloc(i)=iloc_single
2053           if (iloc(i).gt.0) write (iout,*) &
2054            "Local structure used to compare structure of fragment",i,&
2055            " to native."
2056           if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2057               .and. icont_single.gt.0 .and. &
2058               ncont_frag_ref(ind).ge.len_cut) then
2059             write (iout,*) "Electrostatic contacts used to compare",&
2060              " structure of fragment",i," to native."
2061             ielecont(i,1)=1
2062             isccont(i,1)=0
2063           else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2064             .ge.len_cut) then
2065             write (iout,*) "Side chain contacts used to compare",&
2066              " structure of fragment",i," to native."
2067             isccont(i,1)=1
2068             ielecont(i,1)=0
2069           else
2070             write (iout,*) "Contacts not used to compare",&
2071              " structure of fragment",i," to native."
2072             ielecont(i,1)=0
2073             isccont(i,1)=0
2074             nc_req_setf(i,1)=0
2075           endif
2076           if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2077                .and. ielecont(i,1).eq.0) then
2078             write (iout,*) "RMSD used to compare",&
2079              " structure of fragment",i," to native."
2080             irms(i,1)=1
2081           else
2082             write (iout,*) "RMSD not used to compare",&
2083              " structure of fragment",i," to native."
2084             irms(i,1)=0
2085           endif
2086         enddo
2087       endif
2088       if (nlevel.lt.-1) then
2089         call define_pairs
2090         nlevel = -nlevel
2091         if (nlevel.gt.3) nlevel=3
2092         if (nlevel.eq.3) then
2093           nfrag(3)=1
2094           npiece(1,3)=nfrag(1)
2095           do i=1,nfrag(1)
2096             ipiece(i,1,3)=i
2097           enddo
2098           ielecont(1,3)=0
2099           isccont(1,3)=0
2100           irms(1,3)=1
2101           n_shift(1,1,3)=0
2102           n_shift(2,1,3)=0
2103         endif
2104       else if (nlevel.eq.-1) then
2105         nlevel=1
2106       endif
2107       isnfrag(1)=0
2108       do i=1,nlevel
2109         isnfrag(i+1)=isnfrag(i)+nfrag(i)
2110       enddo
2111       ndigit=3*nfrag(1)
2112       do i=2,nlevel
2113         ndigit=ndigit+2*nfrag(i)
2114       enddo
2115       write (iout,*) "ndigit",ndigit
2116       if (.not.binary .and. ndigit.gt.30) then
2117         write (iout,*) "Highest class too large; switching to",&
2118           " binary representation."
2119         binary=.true.
2120       endif
2121       write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2122       write(iout,*) "rmscut_base_up",rmscut_base_up,&
2123        " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2124       do i=1,nlevel
2125         do j=1,nfrag(i)
2126           length_frag = 0
2127           if (i.eq.1) then
2128             do k=1,npiece(j,i)
2129               length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2130             enddo
2131           else
2132             do k=1,npiece(j,i)
2133               length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2134             enddo
2135           endif
2136           len_frag(j,i)=length_frag
2137           rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2138           rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2139           if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2140             rmscutfrag(1,j,i)=rmsup_lim
2141           if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2142             rmscutfrag(1,j,i)=rmsupup_lim
2143         enddo
2144       enddo
2145       write (iout,*) "Level",1," number of fragments:",nfrag(1)
2146       do j=1,nfrag(1)
2147         write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2148           k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2149           rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2150           ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2151           nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2152       enddo
2153       do i=2,nlevel
2154         write (iout,*) "Level",i," number of fragments:",nfrag(i)
2155         do j=1,nfrag(i)
2156           write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2157             k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2158             rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2159             nc_fragm(j,i),nc_req_setf(j,i)
2160         enddo
2161       enddo
2162       return
2163       end subroutine proc_cont
2164 !------------------------------------------------------------------------------
2165 ! define_pairs.f
2166 !------------------------------------------------------------------------------
2167       subroutine define_pairs
2168
2169 !      use energy_data, only:nsccont_frag_ref
2170 !      implicit real*8 (a-h,o-z)
2171 !      include 'DIMENSIONS'
2172 !      include 'DIMENSIONS.ZSCOPT'
2173 !      include 'DIMENSIONS.COMPAR'
2174 !      include 'COMMON.IOUNITS'
2175 !      include 'COMMON.TIME1'
2176 !      include 'COMMON.SBRIDGE'
2177 !      include 'COMMON.CONTROL'
2178 !      include 'COMMON.COMPAR'
2179 !      include 'COMMON.FRAG'
2180 !      include 'COMMON.CHAIN'
2181 !      include 'COMMON.HEADER'
2182 !      include 'COMMON.GEO'
2183 !      include 'COMMON.CONTACTS1'
2184 !      include 'COMMON.PEPTCONT'
2185       integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2186
2187       do j=1,nfrag(1)
2188         length_frag = 0
2189         do k=1,npiece(j,1)
2190           length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2191         enddo
2192         len_frag(j,1)=length_frag
2193         write (iout,*) "Fragment",j," length",len_frag(j,1)
2194       enddo
2195       nfrag(2)=0
2196       do i=1,nfrag(1)
2197         do j=i+1,nfrag(1)
2198           ind = icant(i,j)
2199           if (istruct(i).le.1 .or. istruct(j).le.1) then
2200             if (istruct(i).le.1) then
2201               ll1=len_frag(i,1)
2202             else
2203               ll1=len_frag(i,1)/2
2204             endif
2205             if (istruct(j).le.1) then
2206               ll2=len_frag(j,1)
2207             else
2208               ll2=len_frag(j,1)/2
2209             endif
2210             len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2211           else
2212             if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2213               ll1=len_frag(i,1)/2
2214             else
2215               ll1=len_frag(i,1)
2216             endif
2217             if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2218               ll2=len_frag(j,1)/2
2219             else
2220               ll2=len_frag(j,1)
2221             endif
2222             len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2223           endif
2224           write (iout,*) "Fragments",i,j," structure",istruct(i),&
2225              istruct(j)," # contacts",&
2226              ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2227              " lengths",len_frag(i,1),len_frag(j,1),&
2228              " ll1",ll1," ll2",ll2," len_cut",len_cut
2229           if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2230             nsccont_frag_ref(ind).ge.len_cut ) then
2231             if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2232               write (iout,*) "Adding pair of helices",i,j,&
2233               " based on SC contacts"
2234             else
2235               write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2236               " based on SC contacts"
2237             endif
2238             nfrag(2)=nfrag(2)+1
2239             if (icont_pair.gt.0) then
2240               write (iout,*)  "# SC contacts will be used",&
2241               " in comparison."
2242               isccont(nfrag(2),2)=1
2243             endif
2244             if (irms_pair.gt.0) then
2245               write (iout,*)  "Fragment RMSD will be used",&
2246               " in comparison."
2247               irms(nfrag(2),2)=1
2248             endif
2249             npiece(nfrag(2),2)=2
2250             ipiece(1,nfrag(2),2)=i
2251             ipiece(2,nfrag(2),2)=j
2252             ielecont(nfrag(2),2)=0
2253             n_shift(1,nfrag(2),2)=nshift_pair
2254             n_shift(2,nfrag(2),2)=nshift_pair
2255             nc_fragm(nfrag(2),2)=ncfrac_pair
2256             nc_req_setf(nfrag(2),2)=ncreq_pair
2257           else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2258              .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2259              .and. ncont_frag_ref(ind).ge.len_cut ) then
2260             nfrag(2)=nfrag(2)+1
2261             write (iout,*) "Adding pair strands/sheets",i,j,&
2262               " based on pp contacts"
2263             if (icont_pair.gt.0) then
2264               write (iout,*) "# pp contacts will be used",&
2265               " in comparison."
2266               ielecont(nfrag(2),2)=1
2267             endif
2268             if (irms_pair.gt.0) then
2269               write (iout,*)  "Fragment RMSD will be used",&
2270               " in comparison."
2271               irms(nfrag(2),2)=1
2272             endif
2273             npiece(nfrag(2),2)=2
2274             ipiece(1,nfrag(2),2)=i
2275             ipiece(2,nfrag(2),2)=j
2276             ielecont(nfrag(2),2)=1
2277             isccont(nfrag(2),2)=0
2278             n_shift(1,nfrag(2),2)=nshift_pair
2279             n_shift(2,nfrag(2),2)=nshift_pair
2280             nc_fragm(nfrag(2),2)=ncfrac_bet
2281             nc_req_setf(nfrag(2),2)=ncreq_bet
2282           endif
2283         enddo
2284       enddo
2285       write (iout,*) "Pairs found"
2286       do i=1,nfrag(2)
2287         write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2288       enddo
2289       return
2290       end subroutine define_pairs
2291 !------------------------------------------------------------------------------
2292 ! icant.f
2293 !------------------------------------------------------------------------------
2294       INTEGER FUNCTION ICANT(I,J)
2295       integer :: i,j
2296       IF (I.GE.J) THEN
2297         ICANT=(I*(I-1))/2+J
2298       ELSE
2299         ICANT=(J*(J-1))/2+I
2300       ENDIF
2301       RETURN
2302       END FUNCTION ICANT
2303 !------------------------------------------------------------------------------
2304 ! mysort.f
2305 !------------------------------------------------------------------------------
2306       subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2307 !      implicit none
2308       integer :: n,m,mm
2309       integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2310       real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2311       real(kind=8) :: xxtemp
2312       integer :: i,j,k,imax
2313       do i=1,n
2314         xmin=x(1,1,i)
2315         imax=i
2316         do j=i+1,n
2317           if (x(1,1,j).lt.xmin) then
2318             imax=j
2319             xmin=x(1,1,j)
2320           endif
2321         enddo
2322         xxtemp=z2(imax)
2323         z2(imax)=z2(i)
2324         z2(i)=xxtemp
2325         xxtemp=z3(imax)
2326         z3(imax)=z3(i)
2327         z3(i)=xxtemp
2328         xxtemp=z4(imax)
2329         z4(imax)=z4(i)
2330         z4(i)=xxtemp
2331         xxtemp=z5(imax)
2332         z5(imax)=z5(i)
2333         z5(i)=xxtemp
2334         xtemp=y(imax)
2335         y(imax)=y(i)
2336         y(i)=xtemp
2337         xtemp=z(imax)
2338         z(imax)=z(i)
2339         z(i)=xtemp
2340         xtemp=z6(imax)
2341         z6(imax)=z6(i)
2342         z6(i)=xtemp
2343         do j=1,2
2344           xtemp=z1(j,imax)
2345           z1(j,imax)=z1(j,i)
2346           z1(j,i)=xtemp
2347         enddo
2348         do j=1,m
2349           do k=1,mm
2350             xtemp=x(j,k,imax)
2351             x(j,k,imax)=x(j,k,i)
2352             x(j,k,i)=xtemp
2353           enddo
2354         enddo
2355       enddo
2356       return
2357       end subroutine imysort
2358 !------------------------------------------------------------------------------
2359 ! qwolynes.f
2360 !-------------------------------------------------------------------------------
2361       real(kind=8) function qwolynes(ilevel,jfrag)
2362
2363       use geometry_data, only:cref,nperm
2364       use control_data, only:symetr
2365       use energy_data, only:nnt,nct,itype
2366 !      implicit none
2367 !      include 'DIMENSIONS'
2368 !      include 'DIMENSIONS.ZSCOPT'
2369 !      include 'DIMENSIONS.COMPAR'
2370 !      include 'COMMON.IOUNITS'
2371 !      include 'COMMON.COMPAR'
2372 !      include 'COMMON.CHAIN'
2373 !      include 'COMMON.INTERACT'
2374 !      include 'COMMON.CONTROL'
2375       integer :: ilevel,jfrag,kkk
2376       integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2377       integer :: nsep=3
2378       real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2379       real(kind=8) :: maxiQ !dist,
2380       real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2381       logical :: lprn=.false.
2382       real(kind=8) :: x !el sigm
2383 !el      sigm(x)=0.25d0*x
2384       nperm=1
2385       maxiQ=0
2386       do i=1,symetr
2387       nperm=i*nperm
2388       enddo
2389 !      write (iout,*) "QWolyes: " jfrag",jfrag,
2390 !     &  " ilevel",ilevel
2391       allocate(tempus(nperm))
2392       do kkk=1,nperm
2393       qq = 0.0d0
2394       if (ilevel.eq.0) then
2395         if (lprn) write (iout,*) "Q computed for whole molecule"
2396         nl=0
2397         do il=nnt+nsep,nct
2398           do jl=nnt,il-nsep
2399             dij=0.0d0
2400             dijCM=0.0d0
2401             d0ij=0.0d0
2402             d0ijCM=0.0d0
2403             qqij=0.0d0
2404             qqijCM=0.0d0
2405             nl=nl+1
2406             d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2407                        (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2408                        (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2409             dij=dist(il,jl)
2410             qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2411             if (itype(il).ne.10 .or. itype(jl).ne.10) then
2412               nl=nl+1
2413               d0ijCM=dsqrt( &
2414                      (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2415                      (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2416                      (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2417               dijCM=dist(il+nres,jl+nres)
2418               qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2419             endif
2420             qq = qq+qqij+qqijCM
2421             if (lprn) then
2422               write (iout,*) "il",il," jl",jl,&
2423                " itype",itype(il),itype(jl)
2424               write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2425                " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2426             endif
2427           enddo
2428         enddo
2429         qq = qq/nl
2430         if (lprn) write (iout,*) "nl",nl," qq",qq
2431       else if (ilevel.eq.1) then
2432         if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2433         nl=0
2434 !        write (iout,*) "nlist_frag",nlist_frag(jfrag)
2435         do i=2,nlist_frag(jfrag)
2436           do j=1,i-1
2437             il=list_frag(i,jfrag)
2438             jl=list_frag(j,jfrag)
2439             if (iabs(il-jl).gt.nsep) then
2440               dij=0.0d0
2441               dijCM=0.0d0
2442               d0ij=0.0d0
2443               d0ijCM=0.0d0
2444               qqij=0.0d0
2445               qqijCM=0.0d0
2446               nl=nl+1
2447               d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2448                          (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2449                          (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2450               dij=dist(il,jl)
2451               qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2452               if (itype(il).ne.10 .or. itype(jl).ne.10) then
2453                 nl=nl+1
2454                 d0ijCM=dsqrt( &
2455                        (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2456                        (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2457                        (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2458                 dijCM=dist(il+nres,jl+nres)
2459                qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2460               endif
2461               qq = qq+qqij+qqijCM
2462               if (lprn) then
2463                 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2464                  " itype",itype(il),itype(jl)
2465                 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2466                  " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2467               endif
2468             endif
2469           enddo
2470         enddo
2471         qq = qq/nl
2472         if (lprn) write (iout,*) "nl",nl," qq",qq
2473       else if (ilevel.eq.2) then
2474         np=npiece(jfrag,ilevel)
2475         nl=0
2476         do i=2,np
2477           ip=ipiece(i,jfrag,ilevel)
2478           do j=1,nlist_frag(ip)
2479             il=list_frag(j,ip)
2480             do k=1,i-1
2481               kp=ipiece(k,jfrag,ilevel)
2482               do l=1,nlist_frag(kp)
2483                 kl=list_frag(l,kp)
2484                 if (iabs(kl-il).gt.nsep) then
2485                   nl=nl+1
2486                   dij=0.0d0
2487                   dijCM=0.0d0
2488                   d0ij=0.0d0
2489                   d0ijCM=0.0d0
2490                   qqij=0.0d0
2491                   qqijCM=0.0d0
2492                   d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2493                              (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2494                              (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2495                   dij=dist(il,kl)
2496                   qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2497                   if (itype(il).ne.10 .or. itype(kl).ne.10) then
2498                     nl=nl+1
2499                     d0ijCM=dsqrt( &
2500                        (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2501                        (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2502                        (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2503                     dijCM=dist(il+nres,kl+nres)
2504                     qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2505                       (sigm(d0ijCM)))**2)
2506                   endif
2507                   qq = qq+qqij+qqijCM
2508                   if (lprn) then
2509                     write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2510                       " kl",kl," itype",itype(il),itype(kl)
2511                     write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2512                     d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2513                   endif
2514                 endif
2515               enddo  ! l
2516             enddo    ! k
2517           enddo      ! j
2518         enddo        ! i
2519         qq = qq/nl
2520         if (lprn) write (iout,*) "nl",nl," qq",qq
2521       else
2522         write (iout,*)"Error: Q can be computed only for level 1 and 2."
2523       endif
2524       tempus(kkk)=qq
2525       enddo
2526       do kkk=1,nperm
2527        if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2528       enddo
2529       qwolynes=1.0d0-maxiQ
2530       deallocate(tempus)
2531       return
2532       end function qwolynes
2533 !-------------------------------------------------------------------------------
2534       real(kind=8) function sigm(x)
2535       real(kind=8) :: x
2536       sigm=0.25d0*x
2537       return
2538       end function sigm
2539 !-------------------------------------------------------------------------------
2540       subroutine fragment_list
2541 !      implicit none
2542 !      include 'DIMENSIONS'
2543 !      include 'DIMENSIONS.ZSCOPT'
2544 !      include 'DIMENSIONS.COMPAR'
2545 !      include 'COMMON.IOUNITS'
2546 !      include 'COMMON.COMPAR'
2547       logical :: lprn=.true.
2548       integer :: i,ilevel,j,k,jfrag
2549       do jfrag=1,nfrag(1)
2550         nlist_frag(jfrag)=0
2551         do i=1,npiece(jfrag,1)
2552           if (lprn) write (iout,*) "jfrag=",jfrag,&
2553             "i=",i," fragment",ifrag(1,i,jfrag),&
2554             ifrag(2,i,jfrag)
2555           do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2556             do k=1,nlist_frag(jfrag)
2557               if (list_frag(k,jfrag).eq.j) goto 10
2558             enddo
2559             nlist_frag(jfrag)=nlist_frag(jfrag)+1
2560             list_frag(nlist_frag(jfrag),jfrag)=j
2561           enddo
2562   10      continue
2563         enddo
2564       enddo
2565       write (iout,*) "Fragment list"
2566       do j=1,nfrag(1)
2567         write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2568          k=1,nlist_frag(j))
2569       enddo
2570       return
2571       end subroutine fragment_list
2572 !-------------------------------------------------------------------------------
2573       real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2574
2575       use w_comm_local
2576       use control_data, only:symetr
2577       use geometry_data, only:nperm
2578 !      implicit real*8 (a-h,o-z)
2579 !      include 'DIMENSIONS'
2580 !      include 'DIMENSIONS.ZSCOPT'
2581 !      include 'DIMENSIONS.COMPAR'
2582 !      include 'COMMON.IOUNITS'
2583 !      include 'COMMON.COMPAR'
2584 !      include 'COMMON.CHAIN'
2585 !      include 'COMMON.INTERACT'
2586 !      include 'COMMON.VAR'
2587 !      include 'COMMON.CONTROL'
2588       real(kind=8) :: przes(3),obrot(3,3)
2589 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2590 !el      logical :: iadded(nres)
2591 !el      integer :: inumber(2,nres)
2592 !el      common /ccc/ creff,cc,iadded,inumber
2593       logical :: lprn
2594       logical :: non_conv
2595       integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2596       real(kind=8) :: rminrms,rms
2597       if (lprn) then
2598         write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2599         write (iout,*) "npiece",npiece(j,i)
2600         call flush(iout)
2601       endif
2602 !      write (iout,*) "symetr",symetr
2603 !      call flush(iout)
2604       nperm=1
2605       do idup=1,symetr
2606       nperm=nperm*idup
2607       enddo
2608 !      write (iout,*) "nperm",nperm
2609 !      call flush(iout)
2610       do kkk=1,nperm
2611       idup=0
2612       do l=1,nres
2613         iadded(l)=.false.
2614       enddo
2615 !      write (iout,*) "kkk",kkk
2616 !      call flush(iout)
2617       do k=1,npiece(j,i)
2618         if (i.eq.1) then
2619           if (lprn) then
2620             write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2621                ifrag(1,k,j),ifrag(2,k,j)
2622             call flush(iout)
2623           endif
2624           call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2625 !          write (iout,*) "Exit cprep"
2626 !          call flush(iout)
2627 !          write (iout,*) "ii=",ii
2628         else
2629           kk = ipiece(k,j,i)
2630 !          write (iout,*) "kk",kk," npiece",npiece(kk,1)
2631           do l=1,npiece(kk,1)
2632             if (lprn) then
2633               write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2634                 " l=",l," adding fragment",&
2635                 ifrag(1,l,kk),ifrag(2,l,kk)
2636               call flush(iout)
2637             endif
2638             call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2639 !            write (iout,*) "After cprep"
2640 !            call flush(iout)
2641           enddo
2642         endif
2643       enddo
2644       enddo
2645       if (lprn) then
2646         write (iout,*) "tuszukaj"
2647         do kkk=1,nperm
2648           do k=1,idup
2649             write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2650               inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2651           enddo
2652         enddo
2653         call flush(iout)
2654       endif
2655       rminrms=1.0d10
2656       do kkk=1,nperm
2657       call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2658       if (non_conv) then
2659         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2660         rms = 1.0d10
2661       else if (rms.lt.-1.0d-6) then
2662         print *,'Error: rms^2 = ',rms,jcon,i
2663         rms = 1.0d10
2664       else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2665         rms = 0.0d0
2666       endif
2667 !      write (iout,*) "rmsmin", rminrms, "rms", rms
2668       if (rms.le.rminrms) rminrms=rms
2669       enddo
2670       rmscalc = dsqrt(rminrms)
2671 !      write (iout, *) "analysys", rmscalc,anatemp
2672       return
2673       end function rmscalc
2674 !-------------------------------------------------------------------------
2675       subroutine cprep(if1,if2,ishif,idup,kwa)
2676
2677       use w_comm_local
2678       use control_data, only:symetr
2679       use geometry_data, only:nperm,cref,c
2680 !      implicit real*8 (a-h,o-z)
2681 !      include 'DIMENSIONS'
2682 !      include 'DIMENSIONS.ZSCOPT'
2683 !      include 'DIMENSIONS.COMPAR'
2684 !      include 'COMMON.CONTROL'
2685 !      include 'COMMON.IOUNITS'
2686 !      include 'COMMON.COMPAR'
2687 !      include 'COMMON.CHAIN'
2688 !      include 'COMMON.INTERACT'
2689 !      include 'COMMON.VAR'
2690       real(kind=8) :: przes(3),obrot(3,3)
2691 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2692 !el      logical :: iadded(nres)
2693 !el      integer :: inumber(2,nres)
2694       integer :: iistrart,kwa,blar
2695 !el      common /ccc/ creff,cc,iadded,inumber
2696       integer :: if1,if2,ishif,idup,kkk,l,m
2697 !      write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2698       nperm=1
2699       do blar=1,symetr
2700       nperm=nperm*blar
2701       enddo
2702 !      write (iout,*) "nperm",nperm
2703       kkk=kwa
2704 !      ii=0
2705       do l=if1,if2
2706 !        write (iout,*) "l",l," iadded",iadded(l)
2707 !        call flush(iout)
2708         if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2709         then
2710           idup=idup+1
2711           iadded(l)=.true.
2712           inumber(1,idup)=l
2713           inumber(2,idup)=l+ishif
2714           do m=1,3
2715             creff(m,idup)=cref(m,l,kkk)
2716             cc(m,idup)=c(m,l+ishif)
2717           enddo
2718         endif
2719       enddo
2720       return
2721       end subroutine cprep
2722 !-------------------------------------------------------------------------
2723       real(kind=8) function rmsnat(jcon)
2724
2725       use control_data, only:symetr
2726       use geometry_data, only:nperm,cref,c
2727       use energy_data, only:itype
2728 !      implicit real*8 (a-h,o-z)
2729 !      include 'DIMENSIONS'
2730 !      include 'DIMENSIONS.ZSCOPT'
2731 !      include 'DIMENSIONS.COMPAR'
2732 !      include 'COMMON.IOUNITS'
2733 !      include 'COMMON.COMPAR'
2734 !      include 'COMMON.CHAIN'
2735 !      include 'COMMON.INTERACT'
2736 !      include 'COMMON.VAR'
2737 !      include 'COMMON.CONTROL'
2738       real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2739       logical :: non_conv
2740       integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2741       real(kind=8) :: rminrms,rmsminsing,rms
2742       rminrms=10.0d10
2743       rmsminsing=10d10
2744       nperm=1
2745       do i=1,symetr
2746        nperm=nperm*i
2747       enddo
2748       do kkk=1,nperm
2749        nnsup=0
2750        do i=1,nres
2751         if (itype(i).ne.ntyp1) then
2752           nnsup=nnsup+1
2753           do j=1,3
2754             cc(j,nnsup)=c(j,i)
2755             ccref(j,nnsup)=cref(j,i,kkk)
2756           enddo
2757         endif
2758        enddo
2759        call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2760        if (non_conv) then
2761         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2762         rms=1.0d10
2763        else if (rms.lt.-1.0d-6) then
2764         print *,'Error: rms^2 = ',rms,jcon,i
2765         rms = 1.0d10
2766        else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2767         rms=0.0d0
2768        endif
2769        if (rms.le.rminrms) rminrms=rms
2770 !       write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2771       enddo
2772       rmsnat = dsqrt(rminrms)
2773 !      write (iout,*)  "analysys",rmsnat, anatemp
2774 !      liczenie rmsdla pojedynczego lancucha
2775       return
2776       end function rmsnat
2777 !-------------------------------------------------------------------------------
2778       subroutine define_fragments
2779
2780       use geometry_data, only:rad2deg
2781       use energy_data, only:itype
2782       use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2783 !      implicit real*8 (a-h,o-z)
2784 !      include 'DIMENSIONS'
2785 !      include 'DIMENSIONS.ZSCOPT'
2786 !      include 'DIMENSIONS.COMPAR'
2787 !      include 'COMMON.IOUNITS'
2788 !      include 'COMMON.TIME1'
2789 !      include 'COMMON.FRAG'
2790 !      include 'COMMON.SBRIDGE'
2791 !      include 'COMMON.CONTROL'
2792 !      include 'COMMON.COMPAR'
2793 !      include 'COMMON.CHAIN'
2794 !      include 'COMMON.HEADER'
2795 !      include 'COMMON.GEO'
2796 !      include 'COMMON.CONTACTS'
2797 !      include 'COMMON.PEPTCONT'
2798 !      include 'COMMON.INTERACT'
2799 !      include 'COMMON.NAMES'
2800       integer :: nstrand,istrand(2,nres/2)
2801       integer :: nhairp,ihairp(2,nres/5)
2802       character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2803                           'strand','strand pair'/),shape(strstr))
2804       integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2805
2806       write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2807                      'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2808                  'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2809         ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2810       write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2811         ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2812       write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2813         ' MAXANG_HEL',angcut1_hel*rad2deg
2814       write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2815                      ' MAXANG_BET',angcut1_bet*rad2deg
2816       write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2817                      ' MAXANG_STRAND',angcut1_strand*rad2deg
2818       write (iout,*) 'FRAC_MIN',frac_min_set
2819 ! Find secondary structure elements (helices and beta-sheets)
2820       call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2821          isec_ref)
2822 ! Define primary fragments. First include the helices.
2823       nhairp=0
2824       nstrand=0
2825 ! Merge helices
2826 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2827       if (merge_helices) then
2828       write (iout,*) "Before merging helices: nhfrag",nhfrag
2829       do i=1,nhfrag
2830         write (2,*) hfrag(1,i),hfrag(2,i)
2831       enddo
2832       i=1
2833       do while (i.lt.nhfrag)
2834         if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2835           nhfrag=nhfrag-1
2836           hfrag(2,i)=hfrag(2,i+1)
2837           do j=i+1,nhfrag
2838             hfrag(1,j)=hfrag(1,j+1)
2839             hfrag(2,j)=hfrag(2,j+1)
2840           enddo
2841         endif
2842         i=i+1
2843       enddo
2844       write (iout,*) "After merging helices: nhfrag",nhfrag
2845       do i=1,nhfrag
2846         write (2,*) hfrag(1,i),hfrag(2,i)
2847       enddo
2848       endif
2849       nfrag(1)=nhfrag
2850       do i=1,nhfrag
2851         npiece(i,1)=1
2852         ifrag(1,1,i)=hfrag(1,i)
2853         ifrag(2,1,i)=hfrag(2,i)
2854         n_shift(1,i,1)=0
2855         n_shift(2,i,1)=nshift_hel
2856         ang_cut(i)=angcut_hel
2857         ang_cut1(i)=angcut1_hel
2858         frac_min(i)=frac_min_set
2859         nc_fragm(i,1)=ncfrac_hel
2860         nc_req_setf(i,1)=ncreq_hel
2861         istruct(i)=1
2862       enddo
2863       write (iout,*) "isplit_bet",isplit_bet
2864       if (isplit_bet.gt.1) then
2865 ! Split beta-sheets into strands and store strands as primary fragments.
2866         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2867         do i=1,nstrand
2868           ii=i+nfrag(1)
2869           npiece(ii,1)=1
2870           ifrag(1,1,ii)=istrand(1,i)
2871           ifrag(2,1,ii)=istrand(2,i)
2872           n_shift(1,ii,1)=nshift_strand
2873           n_shift(2,ii,1)=nshift_strand
2874           ang_cut(ii)=angcut_strand
2875           ang_cut1(ii)=angcut1_strand
2876           frac_min(ii)=frac_min_set
2877           nc_fragm(ii,1)=0
2878           nc_req_setf(ii,1)=0
2879           istruct(ii)=3
2880         enddo
2881         nfrag(1)=nfrag(1)+nstrand
2882       else if (isplit_bet.eq.1) then
2883 ! Split only far beta-sheets; does not split hairpins.
2884         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2885         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2886         do i=1,nhairp
2887           ii=i+nfrag(1)
2888           npiece(ii,1)=1
2889           ifrag(1,1,ii)=ihairp(1,i)
2890           ifrag(2,1,ii)=ihairp(2,i)
2891           n_shift(1,ii,1)=nshift_bet
2892           n_shift(2,ii,1)=nshift_bet
2893           ang_cut(ii)=angcut_bet
2894           ang_cut1(ii)=angcut1_bet
2895           frac_min(ii)=frac_min_set
2896           nc_fragm(ii,1)=ncfrac_bet
2897           nc_req_setf(ii,1)=ncreq_bet
2898           istruct(ii)=2
2899         enddo
2900         nfrag(1)=nfrag(1)+nhairp
2901         do i=1,nstrand
2902           ii=i+nfrag(1)
2903           npiece(ii,1)=1
2904           ifrag(1,1,ii)=istrand(1,i)
2905           ifrag(2,1,ii)=istrand(2,i)
2906           n_shift(1,ii,1)=nshift_strand
2907           n_shift(2,ii,1)=nshift_strand
2908           ang_cut(ii)=angcut_strand
2909           ang_cut1(ii)=angcut1_strand
2910           frac_min(ii)=frac_min_set
2911           nc_fragm(ii,1)=0
2912           nc_req_setf(ii,1)=0
2913           istruct(ii)=3
2914         enddo
2915         nfrag(1)=nfrag(1)+nstrand
2916       else
2917 ! Do not split beta-sheets; each pair of strands is a primary element.
2918         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2919         do i=1,nhairp
2920           ii=i+nfrag(1)
2921           npiece(ii,1)=1
2922           ifrag(1,1,ii)=ihairp(1,i)
2923           ifrag(2,1,ii)=ihairp(2,i)
2924           n_shift(1,ii,1)=nshift_bet
2925           n_shift(2,ii,1)=nshift_bet
2926           ang_cut(ii)=angcut_bet
2927           ang_cut1(ii)=angcut1_bet
2928           frac_min(ii)=frac_min_set
2929           nc_fragm(ii,1)=ncfrac_bet
2930           nc_req_setf(ii,1)=ncreq_bet
2931           istruct(ii)=2
2932         enddo
2933         nfrag(1)=nfrag(1)+nhairp
2934         do i=1,nbfrag
2935           ii=i+nfrag(1)
2936           npiece(ii,1)=2
2937           ifrag(1,1,ii)=bfrag(1,i)
2938           ifrag(2,1,ii)=bfrag(2,i)
2939           if (bfrag(3,i).lt.bfrag(4,i)) then
2940             ifrag(1,2,ii)=bfrag(3,i)
2941             ifrag(2,2,ii)=bfrag(4,i)
2942           else
2943             ifrag(1,2,ii)=bfrag(4,i)
2944             ifrag(2,2,ii)=bfrag(3,i)
2945           endif
2946           n_shift(1,ii,1)=nshift_bet
2947           n_shift(2,ii,1)=nshift_bet
2948           ang_cut(ii)=angcut_bet
2949           ang_cut1(ii)=angcut1_bet
2950           frac_min(ii)=frac_min_set
2951           nc_fragm(ii,1)=ncfrac_bet
2952           nc_req_setf(ii,1)=ncreq_bet
2953           istruct(ii)=4
2954         enddo
2955         nfrag(1)=nfrag(1)+nbfrag
2956       endif
2957       write (iout,*) "The following primary fragments were found:"
2958       write (iout,*) "Helices:",nhfrag
2959       do i=1,nhfrag
2960         i1=ifrag(1,1,i)
2961         i2=ifrag(2,1,i)
2962         it1=itype(i1)
2963         it2=itype(i2)
2964         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2965              i,restyp(it1),i1,restyp(it2),i2
2966       enddo
2967       write (iout,*) "Hairpins:",nhairp
2968       do i=nhfrag+1,nhfrag+nhairp
2969         i1=ifrag(1,1,i)
2970         i2=ifrag(2,1,i)
2971         it1=itype(i1)
2972         it2=itype(i2)
2973         write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2974              i,restyp(it1),i1,restyp(it2),i2
2975       enddo
2976       write (iout,*) "Far strand pairs:",nbfrag
2977       do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
2978         i1=ifrag(1,1,i)
2979         i2=ifrag(2,1,i)
2980         it1=itype(i1)
2981         it2=itype(i2)
2982         i3=ifrag(1,2,i)
2983         i4=ifrag(2,2,i)
2984         it3=itype(i3)
2985         it4=itype(i4)
2986         write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
2987              i,restyp(it1),i1,restyp(it2),i2,&
2988                restyp(it3),i3,restyp(it4),i4
2989       enddo
2990       write (iout,*) "Strands:",nstrand
2991       do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
2992         i1=ifrag(1,1,i)
2993         i2=ifrag(2,1,i)
2994         it1=itype(i1)
2995         it2=itype(i2)
2996         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2997              i,restyp(it1),i1,restyp(it2),i2
2998       enddo
2999       call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3000         istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3001         nc_fragm(1,1),nc_req_setf(1,1))
3002       write (iout,*) "Fragments after sorting:"
3003       do i=1,nfrag(1)
3004         i1=ifrag(1,1,i)
3005         i2=ifrag(2,1,i)
3006         it1=itype(i1)
3007         it2=itype(i2)
3008         write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3009              i,restyp(it1),i1,restyp(it2),i2
3010         if (npiece(i,1).eq.1) then
3011           write (iout,'(2x,a)') strstr(istruct(i))
3012         else
3013           i1=ifrag(1,2,i)
3014           i2=ifrag(2,2,i)
3015           it1=itype(i1)
3016           it2=itype(i2)
3017           write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3018              restyp(it1),i1,restyp(it2),i2,strstr(istruct(i))
3019         endif
3020       enddo
3021       return
3022       end subroutine define_fragments
3023 !------------------------------------------------------------------------------
3024       subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3025 !      implicit real*8 (a-h,o-z)
3026 !      include 'DIMENSIONS'
3027 !      include 'DIMENSIONS.ZSCOPT'
3028 !      include 'DIMENSIONS.COMPAR'
3029 !      include 'COMMON.IOUNITS'
3030       integer :: nbfrag,bfrag(4,nres/3)
3031       integer :: nhairp,ihairp(2,nres/5)
3032       integer :: i,j,k
3033       write (iout,*) "Entered find_and_remove_hairpins"
3034       write (iout,*) "nbfrag",nbfrag
3035       do i=1,nbfrag
3036         write (iout,*) i,(bfrag(k,i),k=1,4)
3037       enddo
3038       nhairp=0
3039       i=1
3040       do while (i.le.nbfrag)
3041         write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3042         if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3043         then
3044           write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3045           nhairp=nhairp+1
3046           ihairp(1,nhairp)=bfrag(1,i)
3047           ihairp(2,nhairp)=bfrag(3,i)
3048           nbfrag=nbfrag-1
3049           do j=i,nbfrag
3050             do k=1,4
3051               bfrag(k,j)=bfrag(k,j+1)
3052             enddo
3053           enddo
3054         else
3055           i=i+1
3056         endif
3057       enddo
3058       write (iout,*) "After finding hairpins:"
3059       write (iout,*) "nhairp",nhairp
3060       do i=1,nhairp
3061         write (iout,*) i,ihairp(1,i),ihairp(2,i)
3062       enddo
3063       write (iout,*) "nbfrag",nbfrag
3064       do i=1,nbfrag
3065         write (iout,*) i,(bfrag(k,i),k=1,4)
3066       enddo
3067       return
3068       end subroutine find_and_remove_hairpins
3069 !------------------------------------------------------------------------------
3070       subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3071 !      implicit real*8 (a-h,o-z)
3072 !      include 'DIMENSIONS'
3073 !      include 'DIMENSIONS.ZSCOPT'
3074 !      include 'DIMENSIONS.COMPAR'
3075 !      include 'COMMON.IOUNITS'
3076       integer :: nbfrag,bfrag(4,nres/3)
3077       integer :: nstrand,istrand(2,nres/2)
3078       integer :: nhairp,ihairp(2,nres/5)
3079       logical :: found
3080       integer :: i,k
3081       write (iout,*) "Entered split_beta"
3082       write (iout,*) "nbfrag",nbfrag
3083       do i=1,nbfrag
3084         write (iout,*) i,(bfrag(k,i),k=1,4)
3085       enddo
3086       nstrand=0
3087       do i=1,nbfrag
3088         write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3089         call add_strand(nstrand,istrand,nhairp,ihairp,&
3090            bfrag(1,i),bfrag(2,i),found)
3091         if (bfrag(3,i).lt.bfrag(4,i)) then
3092           write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3093           call add_strand(nstrand,istrand,nhairp,ihairp,&
3094            bfrag(3,i),bfrag(4,i),found)
3095         else
3096           write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3097           call add_strand(nstrand,istrand,nhairp,ihairp,&
3098             bfrag(4,i),bfrag(3,i),found)
3099         endif
3100       enddo
3101       nbfrag=0
3102       write (iout,*) "Strands found:",nstrand
3103       do i=1,nstrand
3104         write (iout,*) i,istrand(1,i),istrand(2,i)
3105       enddo
3106       return
3107       end subroutine split_beta
3108 !------------------------------------------------------------------------------
3109       subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3110 !      implicit real*8 (a-h,o-z)
3111 !      include 'DIMENSIONS'
3112 !      include 'DIMENSIONS.ZSCOPT'
3113 !      include 'DIMENSIONS.COMPAR'
3114 !      include 'COMMON.IOUNITS'
3115       integer :: nstrand,istrand(2,nres/2)
3116       integer :: nhairp,ihairp(2,nres/5)
3117       logical :: found
3118       integer :: is1,is2,j,idelt
3119       found=.false.
3120       do j=1,nhairp
3121         idelt=(ihairp(2,j)-ihairp(1,j))/6
3122         if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3123           write (iout,*) "strand",is1,is2," is part of hairpin",&
3124             ihairp(1,j),ihairp(2,j)
3125           return
3126         endif
3127       enddo
3128       do j=1,nstrand
3129         idelt=(istrand(2,j)-istrand(1,j))/3
3130         if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3131         then
3132 ! The strand already exists in the array; update its ends if necessary.
3133           write (iout,*) "strand",is1,is2," found at position",j,&
3134            ":",istrand(1,j),istrand(2,j)
3135           istrand(1,j)=min0(istrand(1,j),is1)
3136           istrand(2,j)=max0(istrand(2,j),is2)
3137           return
3138         endif
3139       enddo
3140 ! The strand has not been found; add it to the array.
3141       write (iout,*) "strand",is1,is2," added to the array."
3142       found=.true.
3143       nstrand=nstrand+1
3144       istrand(1,nstrand)=is1
3145       istrand(2,nstrand)=is2
3146       return
3147       end subroutine add_strand
3148 !------------------------------------------------------------------------------
3149       subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3150
3151       use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3152       use energy_data, only:itype,maxcont
3153       use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3154       use compare, only:freeres
3155 !      implicit real*8 (a-h,o-z)
3156 !      include 'DIMENSIONS'
3157 !      include 'DIMENSIONS.ZSCOPT'
3158 !      include 'COMMON.IOUNITS'
3159 !      include 'COMMON.FRAG'
3160 !      include 'COMMON.VAR'
3161 !      include 'COMMON.GEO'
3162 !      include 'COMMON.CHAIN'
3163 !      include 'COMMON.NAMES'
3164 !      include 'COMMON.INTERACT'
3165       integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres),&
3166         isecstr(nres)
3167       logical :: lprint,lprint_sec,not_done !el,freeres
3168       integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3169       integer :: nstrand,nbeta,nhelix,iii1,jjj1
3170       real(kind=8) :: p1,p2
3171 !rel      external freeres
3172       character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3173       if (lprint) then
3174         write (iout,*) "entered secondary2",ncont
3175         write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3176         do i=1,ncont
3177           write (iout,*) icont(1,i),icont(2,i)
3178         enddo
3179       endif
3180       do i=1,nres
3181         isecstr(i)=0
3182       enddo
3183       nbfrag=0
3184       nhfrag=0
3185       do i=1,nres
3186         isec(i,1)=0
3187         isec(i,2)=0
3188         nsec(i)=0
3189       enddo
3190
3191 ! finding parallel beta
3192 !d      write (iout,*) '------- looking for parallel beta -----------'
3193       nbeta=0
3194       nstrand=0
3195       do i=1,ncont
3196         i1=icont(1,i)
3197         j1=icont(2,i)
3198         if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3199            .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3200 !d        write (iout,*) "parallel",i1,j1
3201         if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3202           ii1=i1
3203           jj1=j1
3204 !d          write (iout,*) i1,j1
3205           not_done=.true.
3206           do while (not_done)
3207            i1=i1+1
3208            j1=j1+1
3209             do j=1,ncont
3210               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3211                    freeres(i1,j1,nsec,isec)) goto 5
3212             enddo
3213             not_done=.false.
3214   5         continue
3215 !d            write (iout,*) i1,j1,not_done
3216           enddo
3217           j1=j1-1
3218           i1=i1-1
3219           if (i1-ii1.gt.1) then
3220             ii1=max0(ii1-1,1)
3221             jj1=max0(jj1-1,1)
3222             nbeta=nbeta+1
3223             if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3224                      nbeta,ii1,i1,jj1,j1
3225
3226             nbfrag=nbfrag+1
3227             bfrag(1,nbfrag)=ii1+1
3228             bfrag(2,nbfrag)=i1+1
3229             bfrag(3,nbfrag)=jj1+1
3230             bfrag(4,nbfrag)=min0(j1+1,nres)
3231
3232             do ij=ii1,i1
3233              nsec(ij)=nsec(ij)+1
3234              isec(ij,nsec(ij))=nbeta
3235             enddo
3236             do ij=jj1,j1
3237              nsec(ij)=nsec(ij)+1
3238              isec(ij,nsec(ij))=nbeta
3239             enddo
3240
3241            if(lprint_sec) then
3242             nstrand=nstrand+1
3243             if (nbeta.le.9) then
3244               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3245                 "DefPropRes 'strand",nstrand,&
3246                 "' 'num = ",ii1-1,"..",i1-1,"'"
3247             else
3248               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3249                 "DefPropRes 'strand",nstrand,&
3250                 "' 'num = ",ii1-1,"..",i1-1,"'"
3251             endif
3252             nstrand=nstrand+1
3253             if (nbeta.le.9) then
3254               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3255                 "DefPropRes 'strand",nstrand,&
3256                 "' 'num = ",jj1-1,"..",j1-1,"'"
3257             else
3258               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3259                 "DefPropRes 'strand",nstrand,&
3260                 "' 'num = ",jj1-1,"..",j1-1,"'"
3261             endif
3262               write(12,'(a8,4i4)') &
3263                 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3264            endif
3265           endif
3266         endif
3267         endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3268       enddo
3269
3270 ! finding antiparallel beta
3271 !d      write (iout,*) '--------- looking for antiparallel beta ---------'
3272
3273       do i=1,ncont
3274         i1=icont(1,i)
3275         j1=icont(2,i)
3276         if (freeres(i1,j1,nsec,isec)) then
3277           ii1=i1
3278           jj1=j1
3279 !d          write (iout,*) i1,j1
3280
3281           not_done=.true.
3282           do while (not_done)
3283            i1=i1+1
3284            j1=j1-1
3285             do j=1,ncont
3286               if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3287                    freeres(i1,j1,nsec,isec)) goto 6
3288             enddo
3289             not_done=.false.
3290   6         continue
3291 !d            write (iout,*) i1,j1,not_done
3292           enddo
3293           i1=i1-1
3294           j1=j1+1
3295           if (i1-ii1.gt.1) then
3296
3297             nbfrag=nbfrag+1
3298             bfrag(1,nbfrag)=ii1
3299             bfrag(2,nbfrag)=min0(i1+1,nres)
3300             bfrag(3,nbfrag)=min0(jj1+1,nres)
3301             bfrag(4,nbfrag)=j1
3302
3303             nbeta=nbeta+1
3304             iii1=max0(ii1-1,1)
3305             do ij=iii1,i1
3306              nsec(ij)=nsec(ij)+1
3307              if (nsec(ij).le.2) then
3308               isec(ij,nsec(ij))=nbeta
3309              endif
3310             enddo
3311             jjj1=max0(j1-1,1)
3312             do ij=jjj1,jj1
3313              nsec(ij)=nsec(ij)+1
3314              if (nsec(ij).le.2) then
3315               isec(ij,nsec(ij))=nbeta
3316              endif
3317             enddo
3318
3319
3320            if (lprint_sec) then
3321             write (iout,'(a,i3,4i4)')'antiparallel beta',&
3322                          nbeta,ii1-1,i1,jj1,j1-1
3323             nstrand=nstrand+1
3324             if (nstrand.le.9) then
3325               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3326                 "DefPropRes 'strand",nstrand,&
3327                 "' 'num = ",ii1-2,"..",i1-1,"'"
3328             else
3329               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3330                 "DefPropRes 'strand",nstrand,&
3331                 "' 'num = ",ii1-2,"..",i1-1,"'"
3332             endif
3333             nstrand=nstrand+1
3334             if (nstrand.le.9) then
3335               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3336                 "DefPropRes 'strand",nstrand,&
3337                 "' 'num = ",j1-2,"..",jj1-1,"'"
3338             else
3339               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3340                 "DefPropRes 'strand",nstrand,&
3341                 "' 'num = ",j1-2,"..",jj1-1,"'"
3342             endif
3343               write(12,'(a8,4i4)') &
3344                 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3345            endif
3346           endif
3347         endif
3348       enddo
3349
3350 !d      write (iout,*) "After beta:",nbfrag
3351 !d      do i=1,nbfrag
3352 !d        write (iout,*) (bfrag(j,i),j=1,4)
3353 !d      enddo
3354
3355       if (nstrand.gt.0.and.lprint_sec) then
3356         write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3357         do i=2,nstrand
3358          if (i.le.9) then
3359           write(12,'(a9,i1,$)') " | strand",i
3360          else
3361           write(12,'(a9,i2,$)') " | strand",i
3362          endif
3363         enddo
3364         write(12,'(a1)') "'"
3365       endif
3366
3367
3368 ! finding alpha or 310 helix
3369
3370       nhelix=0
3371       do i=1,ncont
3372         i1=icont(1,i)
3373         j1=icont(2,i)
3374         p1=phi(i1+2)*rad2deg
3375         p2=0.0
3376         if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3377
3378
3379         if (j1.eq.i1+3 .and. &
3380              ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3381              ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3382 !d          if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3383 !o          if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3384           ii1=i1
3385           jj1=j1
3386           if (nsec(ii1).eq.0) then
3387             not_done=.true.
3388           else
3389             not_done=.false.
3390           endif
3391           do while (not_done)
3392             i1=i1+1
3393             j1=j1+1
3394             do j=1,ncont
3395               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3396             enddo
3397             not_done=.false.
3398   10        continue
3399             p1=phi(i1+2)*rad2deg
3400             p2=phi(j1+2)*rad2deg
3401             if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3402                                     not_done=.false.
3403
3404 !d           write (iout,*) i1,j1,not_done,p1,p2
3405           enddo
3406           j1=j1+1
3407           if (j1-ii1.gt.4) then
3408             nhelix=nhelix+1
3409 !d            write (iout,*)'helix',nhelix,ii1,j1
3410
3411             nhfrag=nhfrag+1
3412             hfrag(1,nhfrag)=ii1
3413             hfrag(2,nhfrag)=j1
3414
3415             do ij=ii1,j1
3416              nsec(ij)=-1
3417             enddo
3418            if (lprint_sec) then
3419             write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3420             if (nhelix.le.9) then
3421               write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3422                 "DefPropRes 'helix",nhelix,&
3423                 "' 'num = ",ii1-1,"..",j1-2,"'"
3424             else
3425               write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3426                 "DefPropRes 'helix",nhelix,&
3427                 "' 'num = ",ii1-1,"..",j1-2,"'"
3428             endif
3429            endif
3430           endif
3431         endif
3432       enddo
3433
3434       if (nhelix.gt.0.and.lprint_sec) then
3435         write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3436         do i=2,nhelix
3437          if (nhelix.le.9) then
3438           write(12,'(a8,i1,$)') " | helix",i
3439          else
3440           write(12,'(a8,i2,$)') " | helix",i
3441          endif
3442         enddo
3443         write(12,'(a1)') "'"
3444       endif
3445
3446       if (lprint_sec) then
3447        write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3448        write(12,'(a20)') "XMacStand ribbon.mac"
3449       endif
3450
3451       if (lprint) then
3452
3453         write(iout,*) 'UNRES seq:',anatemp
3454         do j=1,nbfrag
3455          write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3456         enddo
3457
3458         do j=1,nhfrag
3459          write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3460         enddo
3461
3462       endif
3463
3464       do j=1,nbfrag
3465         do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3466           isecstr(k)=1
3467         enddo
3468         do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3469           isecstr(k)=1
3470         enddo
3471       enddo
3472       do j=1,nhfrag
3473         do k=hfrag(1,j),hfrag(2,j)
3474           isecstr(k)=2
3475         enddo
3476       enddo
3477       if (lprint) then
3478         write (iout,*)
3479         write (iout,*) "Secondary structure"
3480         do i=1,nres,80
3481           ist=i
3482           ien=min0(i+79,nres)
3483           write (iout,*)
3484           write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3485           write (iout,'(80a1)') (onelet(itype(k)),k=ist,ien)
3486           write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3487         enddo
3488         write (iout,*)
3489       endif
3490       return
3491       end subroutine secondary2
3492 !-------------------------------------------------
3493 !      logical function freeres(i,j,nsec,isec)
3494 !      include 'DIMENSIONS'
3495 !      integer :: isec(nres,4),nsec(nres)
3496 !      integer :: i,j,k,l
3497 !      freeres=.false.
3498 !
3499 !      if (nsec(i).gt.1.or.nsec(j).gt.1) return
3500 !      do k=1,nsec(i)
3501 !        do l=1,nsec(j)
3502 !          if (isec(i,k).eq.isec(j,l)) return
3503 !        enddo
3504 !      enddo
3505 !      freeres=.true.
3506 !      return
3507 !      end function freeres
3508 !-------------------------------------------------
3509        subroutine alloc_compar_arrays(nfrg,nlev)
3510
3511        use energy_data, only:maxcont
3512        use w_comm_local
3513        integer :: nfrg,nlev
3514
3515 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3516 !------------------------
3517 ! commom.contacts
3518 !      common /contacts/
3519       allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3520       allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3521 !------------------------
3522 ! COMMON.COMPAR
3523 !      common /compar/
3524       allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3525       allocate(qfrag(nfrg,2)) !(maxfrag,2)
3526       allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3527       allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3528       allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3529         ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3530         ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3531       allocate(ncont_nat(2,nfrg,nlev+1))
3532       allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3533 !      allocate(nfrag(nlev)) !(maxlevel)
3534       allocate(isnfrag(nlev+2)) !(maxlevel+1)
3535       allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3536       allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3537       allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3538       allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3539       allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3540 !------------------------
3541 ! COMMON.PEPTCONT
3542 !      common /peptcont/
3543 !      integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3544       allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3545       allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3546 !      integer,dimension(:),allocatable :: isec_ref !(maxres)
3547 !------------------------
3548 !      module w_comm_local
3549 !      common /ccc/
3550       allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3551       allocate(iadded(nres)) !(nres)
3552       allocate(inumber(2,nres)) !(2,nres)
3553
3554
3555 !-------------------------------------------------------------------------------
3556       end subroutine alloc_compar_arrays
3557 #endif
3558 !-------------------------------------------------------------------------------
3559       end module conform_compar
3560