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)
  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        lprn=.false.
  69        print_class=.false.
  70         write (iout,*) "before anything"
  71         call flush(iout)
  72
  73 !      call angnorm12(rmsang)
  74 ! Level 1: check secondary and supersecondary structure
  75 !      call elecont(lprn,ncont,icont,nnt,nct)
  76       if (lprn) then
  77         write (iout,*) "elecont finished"
  78         call flush(iout)
  79       endif
  80       call secondary2(lprn,.false.,ncont,icont,isecstr)
  81       if (lprn) then
  82         write (iout,*) "secondary2 finished"
  83         call flush(iout)
  84       endif
  85       call contact(lprn,ncontsc,icontsc,nnt,nct)
  86       if (lprn) then
  87          write(iout,*) "Assigning electrostatic contacts"
  88          call flush(iout)
  89       endif
  90       call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,&
  91          icont_frag)
  92       if (lprn) then
  93         write(iout,*) "Assigning sidechain contacts"
  94         call flush(iout)
  95       endif
  96       call contacts_between_fragments(lprn,3,ncontsc,icontsc,&
  97          nsccont_frag,isccont_frag)
  98       if (lprn) then
  99         write(iout,*) "--> After contacts_between_fragments"
 100         call flush(iout)
 101       endif
 102       do i=1,nlevel
 103         do j=1,isnfrag(nlevel+1)
 104           iclass(j,i)=0
 105         enddo
 106       enddo
 107       do j=1,nfrag(1)
 108         ind = icant(j,j)
 109         if (lprn) then
 110           write (iout,'(80(1h=))')
 111           write (iout,*) "Level",1," fragment",j
 112           write (iout,'(80(1h=))')
 113         endif
 114         call flush(iout)
 115         rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
 116 ! Compare electrostatic contacts in the current conf with that in the native
 117 ! structure.
 118         if (lprn) write (iout,*) &
 119           "Comparing electrostatic contact map and local structure"
 120         call flush(iout)
 121         ncnat=ncont_frag_ref(ind)
 122 !        write (iout,*) "before match_contact:",nc_fragm(j,1),
 123 !     &   nc_req_setf(j,1)
 124 !        call flush(iout)
 125         call match_secondary(j,isecstr,nsec_match,lprn)
 126         if (lprn) write (iout,*) "Fragment",j," nsec_match",&
 127           nsec_match," length",len_frag(j,1)," min_len",&
 128           frac_sec*len_frag(j,1)
 129         if (nsec_match.lt.frac_sec*len_frag(j,1)) then
 130           iclass(j,1)=0
 131           if (lprn) write (iout,*) "Fragment",j,&
 132             " has incorrect secondary structure"
 133         else
 134           iclass(j,1)=1
 135           if (lprn) write (iout,*) "Fragment",j,&
 136             " has correct secondary structure"
 137         endif
 138         if (ielecont(j,1).gt.0) then
 139           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 140             ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 141             ncont_frag(ind),icont_frag(1,1,ind),&
 142             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 143             nc_req_setf(j,1),istruct(j),.true.,lprn)
 144         else if (isccont(j,1).gt.0) then
 145           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 146             nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 147             nsccont_frag(ind),isccont_frag(1,1,ind),&
 148             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 149             nc_req_setf(j,1),istruct(j),.true.,lprn)
 150         else if (iloc(j).gt.0) then
 151 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 152           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 153             0,icont_frag_ref(1,1,ind),&
 154             ncont_frag(ind),icont_frag(1,1,ind),&
 155             j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
 156             0,istruct(j),.true.,lprn)
 157 !          write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
 158         else
 159           ishif=0
 160           nc_match=1
 161         endif
 162         if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
 163         ishif=ishif1
 164         qfrag(j,1)=qwolynes(1,j)
 165         if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 166         if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
 167 !        write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
 168         if (irms(j,1).gt.0) then
 169           if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
 170             iclass_rms=2
 171             ishifft_rms=0
 172           else
 173             ishiff=0
 174             rms=1.0d2
 175             iclass_rms=0
 176             do while (rms.gt.rmscutfrag(1,j,1) .and. &
 177                ishiff.lt.n_shift(1,j,1))
 178               ishiff=ishiff+1
 179               rms=rmscalc(-ishiff,1,j,jcon,lprn)
 180 !              write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
 181 !     &          " rms",rms," rmscut",rmscutfrag(1,j,1)
 182               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 183               if (rms.gt.rmscutfrag(1,j,1)) then
 184                 rms=rmscalc(ishiff,1,j,jcon,lprn)
 185 !                write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
 186 !     &           " rms",rms
 187               endif
 188               if (lprn) write (iout,*) "rms",rmsfrag(j,1)
 189             enddo
 190 !            write (iout,*) "After loop: rms",rms,
 191 !     &        " rmscut",rmscutfrag(1,j,1)
 192 !            write (iout,*) "iclass_rms",iclass_rms
 193             if (rms.le.rmscutfrag(1,j,1)) then
 194               ishifft_rms=ishiff
 195               rmsfrag(j,1)=rms
 196               iclass_rms=1
 197             endif
 198 !            write (iout,*) "iclass_rms",iclass_rms
 199           endif
 200 !          write (iout,*) "ishif",ishif
 201           if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
 202         else
 203           iclass_rms=1
 204         endif
 205 !        write (iout,*) "ishif",ishif," iclass",iclass(j,1),
 206 !     &    " iclass_rms",iclass_rms
 207         if (nc_match.gt.0 .and. iclass_rms.gt.0) then
 208           if (ishif.eq.0) then
 209             iclass(j,1)=iclass(j,1)+6
 210           else
 211             iclass(j,1)=iclass(j,1)+2
 212           endif
 213         endif
 214         ncont_nat(1,j,1)=nc_match
 215         ncont_nat(2,j,1)=ncon_match
 216         ishifft(j,1)=ishif
 217 !        write (iout,*) "iclass",iclass(j,1)
 218       enddo
 219 ! Next levels: Check arrangements of elementary fragments.
 220       do i=2,nlevel
 221         do j=1,nfrag(i)
 222         if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
 223         if (lprn) then
 224             write (iout,'(80(1h=))')
 225             write (iout,*) "Level",i," fragment",j
 226             write (iout,'(80(1h=))')
 227         endif
 228 ! If an elementary fragment doesn't exist, don't check higher hierarchy levels.
 229         do k=1,npiece(j,i)
 230           ik=ipiece(k,j,i)
 231           if (iclass(ik,1).eq.0) then
 232             iclass(j,i)=0
 233             goto 12
 234           endif
 235         enddo
 236         if (i.eq.2 .and. ielecont(j,i).gt.0) then
 237           iclass_con=0
 238           ishifft_con=0
 239           if (lprn) write (iout,*) &
 240            "Comparing electrostatic contact map: fragments",&
 241             ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 242           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 243            ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
 244            ncont_frag(ind),icont_frag(1,1,ind),&
 245            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 246            nc_req_setf(j,i),2,.false.,lprn)
 247           ishif=ishif1
 248           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 249           if (nc_match.gt.0) then
 250             if (ishif.eq.0) then
 251               iclass_con=2
 252             else
 253               iclass_con=1
 254             endif
 255           endif
 256           ncont_nat(1,j,i)=nc_match
 257           ncont_nat(2,j,i)=ncon_match
 258           ishifft_con=ishif
 259         else if (i.eq.2 .and. isccont(j,i).gt.0) then
 260           iclass_con=0
 261           ishifft_con=0
 262           if (lprn) write (iout,*) &
 263            "Comparing sidechain contact map: fragments",&
 264            ipiece(1,j,i),ipiece(2,j,i)," ind",ind
 265           call match_contact(ishif1,ishif2,nc_match,ncon_match,&
 266            nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
 267            nsccont_frag(ind),isccont_frag(1,1,ind),&
 268            j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
 269            nc_req_setf(j,i),2,.false.,lprn)
 270           ishif=ishif1
 271           if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
 272           if (nc_match.gt.0) then
 273             if (ishif.eq.0) then
 274               iclass_con=2
 275             else
 276               iclass_con=1
 277             endif
 278           endif
 279           ncont_nat(1,j,i)=nc_match
 280           ncont_nat(2,j,i)=ncon_match
 281           ishifft_con=ishif
 282         else if (i.eq.2) then
 283           iclass_con=2
 284           ishifft_con=0
 285         endif
 286         if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
 287         if (lprn) write (iout,*) &
 288           "Comparing rms: fragments",&
 289            (ipiece(k,j,i),k=1,npiece(j,i))
 290         rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
 291         if (irms(j,i).gt.0) then
 292           iclass_rms=0
 293           ishifft_rms=0
 294           if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 295 !          write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
 296 !     &     " rmscutfrag",rmscutfrag(1,j,i)
 297           if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
 298             iclass_rms=2
 299             ishifft_rms=0
 300           else
 301             ishif=0
 302             rms=1.0d2
 303             do while (rms.gt.rmscutfrag(1,j,i) .and. &
 304                ishif.lt.n_shift(1,j,i))
 305               ishif=ishif+1
 306               rms=rmscalc(-ishif,i,j,jcon,lprn)
 307 !              print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
 308               if (lprn) write (iout,*) "rms",rmsfrag(j,i)
 309               if (rms.gt.rmscutfrag(1,j,i)) then
 310                 rms=rmscalc(ishif,i,j,jcon,lprn)
 311 !                print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
 312               endif
 313               if (lprn) write (iout,*) "rms",rms
 314             enddo
 315             if (rms.le.rmscutfrag(1,j,i)) then
 316               ishifft_rms=ishif
 317               rmsfrag(j,i)=rms
 318               iclass_rms=1
 319             endif
 320           endif
 321         endif
 322         if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. &
 323           isccont(j,i).eq.0 ) then
 324           write (iout,*) "Error: no measure of comparison specified:",&
 325             " level",i," part",j
 326           stop
 327         endif
 328         if (lprn) &
 329         write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
 330         if (i.eq.2) then
 331           iclass(j,i) = min0(iclass_con,iclass_rms)
 332           if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
 333             ishifft(j,i)=ishifft_rms
 334           else
 335             ishifft(j,i)=ishifft_con
 336           endif
 337         else if (i.gt.2) then
 338           iclass(j,i) = iclass_rms
 339           ishifft(j,i)= ishifft_rms
 340         endif
 341    12   continue
 342         enddo
 343       enddo
 344       rms_nat=rmsnat(jcon)
 345       qnat=qwolynes(0,0)
 346 ! Compute the structural class
 347       iscor=0
 348       IF (.NOT. BINARY) THEN
 349       do i=1,nlevel
 350         IF (I.EQ.1) THEN
 351         do j=1,nfrag(i)
 352           itemp(j)=iclass(j,i)
 353         enddo
 354         do kk=-1,1
 355           do j=1,nfrag(i)
 356             idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
 357             iex = 2**idig
 358             im=mod(itemp(j),2)
 359             itemp(j)=itemp(j)/2
 360 !            write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 361 !     &        " iclass",iclass(j,i)," im",im
 362             iscor=iscor+im*iex
 363           enddo
 364         enddo
 365         ELSE
 366         do j=1,nfrag(i)
 367           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
 368           iex = 2**idig
 369           if (iclass(j,i).gt.0) then
 370             im=1
 371           else
 372             im=0
 373           endif
 374 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 375 !     &      " iclass",iclass(j,i)," im",im
 376           iscor=iscor+im*iex
 377         enddo
 378         do j=1,nfrag(i)
 379           idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
 380           iex = 2**idig
 381           if (iclass(j,i).gt.1) then
 382             im=1
 383           else
 384             im=0
 385           endif
 386 !          write (iout,*) "i",i," j",j," idig",idig," iex",iex,
 387 !     &      " iclass",iclass(j,i)," im",im
 388           iscor=iscor+im*iex
 389         enddo
 390         ENDIF
 391       enddo
 392       iscore=iscor
 393       ENDIF
 394       if (print_class) then
 395 #ifdef MPI
 396           write(istat,'(i6,$)') jcon+indstart(me)-1
 397           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 398            -entfac(jcon)
 399 #else
 400           write(istat,'(i6,$)') jcon
 401           write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
 402             -entfac(jcon)
 403 #endif
 404           write (istat,'(f8.3,2f6.3,$)') &
 405             rms_nat,qnat,rmsang/(nres-3)
 406           do j=1,nlevel
 407             write(istat,'(1x,$,20(i3,$))') &
 408               (ncont_nat(1,k,j),k=1,nfrag(j))
 409             if (j.lt.3) then
 410               write(istat,'(1x,$,20(f5.1,f5.2$))') &
 411                 (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
 412             else
 413               write(istat,'(1x,$,20(f5.1$))') &
 414                 (rmsfrag(k,j),k=1,nfrag(j))
 415             endif
 416             write(istat,'(1x,$,20(i1,$))') &
 417               (iclass(k,j),k=1,nfrag(j))
 418           enddo
 419           if (binary) then
 420             write (istat,'("  ",$)')
 421             do j=1,nlevel
 422               write (istat,'(100(i1,$))')(iclass(k,j),&
 423                  k=1,nfrag(j))
 424               if (j.lt.nlevel) write(iout,'(".",$)')
 425             enddo
 426             write (istat,*)
 427           else
 428             write (istat,'(i10)') iscore
 429           endif
 430       endif
 431       RETURN
 432       END subroutine conf_compar
 433 !-----------------------------------------------------------------------------
 434 ! angnorm.f
 435 !-----------------------------------------------------------------------------
 436       subroutine add_angpair(ici,icj,nang_pair,iang_pair)
 437
 438 !      implicit real*8 (a-h,o-z)
 439 !      include 'DIMENSIONS'
 440 !      include 'COMMON.IOUNITS'
 441 !      include 'COMMON.CHAIN'
 442       integer :: ici,icj,nang_pair,iang_pair(2,nres)
 443       integer :: i,ian1,ian2
 444 !      write (iout,*) "add_angpair: ici",ici," icj",icj,
 445 !     &  " nang_pair",nang_pair
 446       ian1=ici+2
 447       if (ian1.lt.4 .or. ian1.gt.nres) return
 448       ian2=icj+2
 449 !      write (iout,*) "ian1",ian1," ian2",ian2
 450       if (ian2.lt.4 .or. ian2.gt.nres) return
 451       do i=1,nang_pair
 452         if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
 453       enddo
 454       nang_pair=nang_pair+1
 455       iang_pair(1,nang_pair)=ian1
 456       iang_pair(2,nang_pair)=ian2
 457       return
 458       end subroutine add_angpair
 459 !-------------------------------------------------------------------------
 460       subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,lprn)
 461
 462       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 463                               rad2deg,dwapi
 464 !      implicit real*8 (a-h,o-z)
 465 !      include 'DIMENSIONS'
 466 !      include 'DIMENSIONS.ZSCOPT'
 467 !      include 'DIMENSIONS.COMPAR'
 468 !      include 'COMMON.IOUNITS'
 469 !      include 'COMMON.VAR'
 470 !      include 'COMMON.COMPAR'
 471 !      include 'COMMON.CHAIN'
 472 !      include 'COMMON.GEO'
 473       real(kind=8) :: pinorm,deltang
 474       logical :: lprn
 475       integer :: jfrag,ishif1,ishif2,nn,npart,nn4,nne
 476       real(kind=8) :: diffang_max,angn,fract,ff
 477       integer :: i,j,nbeg,nend,ll,longest
 478       if (lprn) write (iout,'(80(1h*))')
 479       angn=0.0d0
 480       nn = 0
 481       fract = 1.0d0
 482       npart = npiece(jfrag,1)
 483       nn4 = nstart_sup+3
 484       nne = min0(nend_sup,nres)
 485       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 486       do i=1,npart
 487         nbeg = ifrag(1,i,jfrag) + 3 - ishif1
 488         if (nbeg.lt.nn4) nbeg=nn4
 489         nend = ifrag(2,i,jfrag) + 1 - ishif2
 490         if (nend.gt.nne) nend=nne
 491         if (nend.ge.nbeg) then
 492         nn = nn + nend - nbeg + 1
 493         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 494           " nn",nn," ishift1",ishif1," ishift2",ishif2
 495         if (lprn) write (iout,*) "angles"
 496         longest=0
 497         ll = 0
 498         do j=nbeg,nend
 499             write (iout,*) "ishif1",ishif1,j
 500 !          deltang = pinorm(phi(j)-phi_ref(j+ishif1))
 501           deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
 502             theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
 503           if (dabs(deltang).gt.diffang_max) then
 504             if (ll.gt.longest) longest = ll
 505             ll = 0
 506           else
 507             ll=ll+1
 508           endif
 509           if (ll.gt.longest) longest = ll
 510           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 511            rad2deg*phi_ref(j+ishif1),rad2deg*deltang
 512           angn=angn+dabs(deltang)
 513         enddo
 514         longest=longest+3
 515         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 516         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 517           diffang_max*rad2deg,":",longest," fraction",ff
 518         if (ff.lt.fract) fract = ff
 519         endif
 520       enddo
 521       if (nn.gt.0) then
 522         angn = angn/nn
 523       else
 524         angn = dwapi
 525       endif
 526       if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
 527         " fract",fract
 528       return
 529       end subroutine angnorm
 530 !-------------------------------------------------------------------------
 531       subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
 532         diffang_max,anorm,fract)
 533
 534       use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
 535                               rad2deg
 536 !      implicit real*8 (a-h,o-z)
 537 !      include 'DIMENSIONS'
 538 !      include 'DIMENSIONS.ZSCOPT'
 539 !      include 'DIMENSIONS.COMPAR'
 540 !      include 'COMMON.IOUNITS'
 541 !      include 'COMMON.VAR'
 542 !      include 'COMMON.COMPAR'
 543 !      include 'COMMON.CHAIN'
 544 !      include 'COMMON.GEO'
 545       integer :: ncont,icont(2,ncont),longest
 546       real(kind=8) :: anorm,diffang_max,fract
 547       integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
 548       real(kind=8) :: pinorm
 549       logical :: lprn
 550       integer :: jfrag,ishif1,ishif2
 551       integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
 552       integer :: nbeg,nend,ll
 553       real(kind=8) :: angn,ishifc,deltang,ff
 554
 555       if (lprn) write (iout,'(80(1h*))')
 556 !
 557 ! Determine the segments for which angles will be compared
 558 !
 559       nn4 = nstart_sup+3
 560       nne = min0(nend_sup,nres)
 561       if (lprn) write (iout,*) "nn4",nn4," nne",nne
 562       npart=npiece(jfrag,1)
 563       npiece_c=0
 564       do i=1,npart
 565 !        write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 566         if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
 567           icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
 568         jstart=1
 569         do while (jstart.lt.ncont .and. &
 570          icont(1,jstart).lt.ifrag(1,i,jfrag))
 571 !          write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 572 !     &     " ifrag",ifrag(1,i,jfrag)
 573           jstart=jstart+1
 574         enddo
 575 !        write (iout,*) "jstart",jstart," icont",icont(1,jstart),
 576 !     &   " ifrag",ifrag(1,i,jfrag)
 577         if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
 578         npiece_c=npiece_c+1
 579         ic1=icont(1,jstart)
 580         ifrag_c(1,npiece_c)=icont(1,jstart)
 581         jend=ncont
 582         do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
 583 !          write (iout,*) "jend",jend," icont",icont(1,jend),
 584 !     &     " ifrag",ifrag(2,i,jfrag)
 585           jend=jend-1
 586         enddo
 587 !        write (iout,*) "jend",jend," icont",icont(1,jend),
 588 !     &   " ifrag",ifrag(2,i,jfrag)
 589         ic2=icont(1,jend)
 590         ifrag_c(2,npiece_c)=icont(1,jend)+1
 591         ishift_c(npiece_c)=ishif1
 592 !        write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
 593 !     &    " ic1",ic1," ic2",ic2,
 594 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 595    11   continue
 596         if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
 597           idi=1
 598         else
 599           idi=-1
 600         endif
 601 !        write (iout,*) "idi",idi
 602         if (idi.eq.1) then
 603           if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
 604             icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
 605           jstart=1
 606           do while (jstart.lt.ncont .and. &
 607            icont(2,jstart).lt.ifrag(1,i,jfrag))
 608 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 609 !     &     " ifrag",ifrag(1,i,jfrag)
 610             jstart=jstart+1
 611           enddo
 612 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 613 !     &     " ifrag",ifrag(1,i,jfrag)
 614           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 615           npiece_c=npiece_c+1
 616           ic1=icont(2,jstart)
 617           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 618           jend=ncont
 619           do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
 620 !            write (iout,*) "jend",jend," icont",icont(2,jend),
 621 !     &     " ifrag",ifrag(2,i,jfrag)
 622             jend=jend-1
 623           enddo
 624 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 625 !     &     " ifrag",ifrag(2,i,jfrag)
 626         else if (idi.eq.-1) then
 627           if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
 628               icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
 629           jstart=ncont
 630           do while (jstart.gt.ncont .and. &
 631            icont(2,jstart).lt.ifrag(1,i,jfrag))
 632 !           write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 633 !     &     " ifrag",ifrag(1,i,jfrag)
 634             jstart=jstart-1
 635           enddo
 636 !          write (iout,*) "jstart",jstart," icont",icont(2,jstart),
 637 !     &     " ifrag",ifrag(1,i,jfrag)
 638           if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
 639           npiece_c=npiece_c+1
 640           ic1=icont(2,jstart)
 641           ifrag_c(2,npiece_c)=icont(2,jstart)+1
 642           jend=1
 643           do while (jend.lt.ncont .and. &
 644              icont(2,jend).gt.ifrag(2,i,jfrag))
 645 !             write (iout,*) "jend",jend," icont",icont(2,jend),
 646 !     &         " ifrag",ifrag(2,i,jfrag)
 647             jend=jend+1
 648           enddo
 649 !          write (iout,*) "jend",jend," icont",icont(2,jend),
 650 !     &     " ifrag",ifrag(2,i,jfrag)
 651         endif
 652         ic2=icont(2,jend)
 653         if (ic2.lt.ic1) then
 654           iic = ic1
 655           ic1 = ic2
 656           ic2 = iic
 657         endif
 658 !        write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
 659 !     &    " jstart:",jstart," jend",jend,
 660 !     &    " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
 661         ifrag_c(1,npiece_c)=ic1
 662         ifrag_c(2,npiece_c)=ic2+1
 663         ishift_c(npiece_c)=ishif2
 664    12   continue
 665       enddo
 666       if (lprn) then
 667         write (iout,*) "Before merge: npiece_c",npiece_c
 668         do i=1,npiece_c
 669           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 670         enddo
 671       endif
 672 !
 673 ! Merge overlapping segments (e.g., avoid splitting helices)
 674 !
 675       i=1
 676       do while (i .lt. npiece_c)
 677         if (ishift_c(i).eq.ishift_c(i+1) .and. &
 678            ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
 679            ifrag_c(2,i)=ifrag_c(2,i+1)
 680            do j=i+1,npiece_c
 681              ishift_c(j)=ishift_c(j+1)
 682              ifrag_c(1,j)=ifrag_c(1,j+1)
 683              ifrag_c(2,j)=ifrag_c(2,j+1)
 684            enddo
 685            npiece_c=npiece_c-1
 686         else
 687           i=i+1
 688         endif
 689       enddo
 690       if (lprn) then
 691         write (iout,*) "After merge: npiece_c",npiece_c
 692         do i=1,npiece_c
 693           write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
 694         enddo
 695       endif
 696 !
 697 ! Compare angles
 698 !
 699       angn=0.0d0
 700       anorm=0
 701       nn = 0
 702       fract = 1.0d0
 703       npart = npiece_c
 704       do i=1,npart
 705         ishifc=ishift_c(i)
 706         nbeg = ifrag_c(1,i) + 3 - ishifc
 707         if (nbeg.lt.nn4) nbeg=nn4
 708         nend = ifrag_c(2,i)  - ishifc + 1
 709         if (nend.gt.nne) nend=nne
 710         if (nend.ge.nbeg) then
 711         nn = nn + nend - nbeg + 1
 712         if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
 713           " nn",nn," ishifc",ishifc
 714         if (lprn) write (iout,*) "angles"
 715         longest=0
 716         ll = 0
 717         do j=nbeg,nend-ishifc
 718            if (j.gt.nres) cycle
 719 !          deltang = pinorm(phi(j)-phi_ref(j+ishifc))
 720            write (iout,*) "i=",j," nn",nn," ishifc",ishifc
 721           deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
 722             theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
 723           if (dabs(deltang).gt.diffang_max) then
 724             if (ll.gt.longest) longest = ll
 725             ll = 0
 726           else
 727             ll=ll+1
 728           endif
 729           if (ll.gt.longest) longest = ll
 730           if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
 731            rad2deg*phi_ref(j+ishifc),rad2deg*deltang
 732           angn=angn+dabs(deltang)
 733         enddo
 734         longest=longest+3
 735         ff = dfloat(longest)/dfloat(nend - nbeg + 4)
 736         if (lprn) write (iout,*)"segment",i," longest fragment within",&
 737           diffang_max*rad2deg,":",longest," fraction",ff
 738         if (ff.lt.fract) fract = ff
 739         endif
 740       enddo
 741       if (nn.gt.0) anorm = angn/nn
 742       if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
 743       return
 744       end subroutine angnorm2
 745 !-------------------------------------------------------------------------
 746       real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
 747
 748       use geometry_data, only:phi,theta,rad2deg
 749 !      implicit real*8 (a-h,o-z)
 750 !      include 'DIMENSIONS'
 751 !      include 'DIMENSIONS.ZSCOPT'
 752 !      include 'DIMENSIONS.COMPAR'
 753 !      include 'COMMON.IOUNITS'
 754 !      include 'COMMON.VAR'
 755 !      include 'COMMON.COMPAR'
 756 !      include 'COMMON.CHAIN'
 757 !      include 'COMMON.GEO'
 758       logical :: lprn
 759       integer :: nang_pair,iang_pair(2,nres)
 760       real(kind=8) :: pinorm
 761       integer :: j,ia1,ia2
 762       real(kind=8) :: angn,deltang
 763       angn=0.0d0
 764       if (lprn) write (iout,'(80(1h*))')
 765       if (lprn) write (iout,*) "nang_pair",nang_pair
 766       if (lprn) write (iout,*) "angles"
 767       do j=1,nang_pair
 768         ia1 = iang_pair(1,j)
 769         ia2 = iang_pair(2,j)
 770 !        deltang = pinorm(phi(ia1)-phi_ref(ia2))
 771          deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
 772             theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
 773         if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
 774          rad2deg*phi_ref(ia2),rad2deg*deltang
 775         angn=angn+dabs(deltang)
 776       enddo
 777       if (lprn) &
 778       write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
 779       angnorm1 = angn/nang_pair
 780       return
 781       end function angnorm1
 782 !------------------------------------------------------------------------------
 783       subroutine angnorm12(diff)
 784
 785       use geometry_data, only:phi,theta,nstart_sup,nend_sup
 786 !      implicit real*8 (a-h,o-z)
 787 !      include 'DIMENSIONS'
 788 !      include 'DIMENSIONS.ZSCOPT'
 789 !      include 'DIMENSIONS.COMPAR'
 790 !      include 'COMMON.IOUNITS'
 791 !      include 'COMMON.VAR'
 792 !      include 'COMMON.COMPAR'
 793 !      include 'COMMON.CHAIN'
 794 !      include 'COMMON.GEO'
 795       real(kind=8) :: pinorm,diff
 796       integer :: nn4,nne,j
 797       diff=0.0d0
 798       nn4 = nstart_sup+3
 799       nne = min0(nend_sup,nres)
 800 !      do j=nn4-1,nne
 801 !        diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
 802 !      enddo
 803       do j=nn4,nne
 804 !        diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
 805          diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
 806             theta_ref(j),phi(j),theta(j-1),theta(j))
 807       enddo
 808       return
 809       end subroutine angnorm12
 810 !--------------------------------------------------------------------------------
 811       real(kind=8) function spherang(gam1,theta11,theta12,&
 812          gam2,theta21,theta22)
 813 !      implicit none
 814       use geometry, only:arcos
 815       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
 816         x1,x2,xmed,f1,f2,fmed
 817       real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
 818       real(kind=8) :: sumcos
 819 !el      real(kind=8) :: pinorm,sumangp !arcos,
 820       integer :: it,maxit=100
 821 ! Calculate the difference of the angles of two superposed 4-redidue fragments
 822 !
 823 !       O      P
 824 !        \    /
 825 !     O'--C--C
 826 !             \
 827 !              P'
 828 !
 829 ! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
 830 ! to achieve the minimum difference between the O'-C-O and P-C-P angles;
 831 ! the sum of these angles is the difference returned by the function.
 832 !
 833 ! 4/28/04 AL
 834 ! If thetas match, take the difference of gamma and exit.
 835       if (dabs(theta11-theta12).lt.tolx &
 836        .and. dabs(theta21-theta22).lt.tolx) then
 837         spherang=dabs(pinorm(gam2-gam1))
 838         return
 839       endif
 840 ! If the gammas are the same, take the difference of thetas and exit.
 841       x1=0.0d0
 842       x2=0.5d0*pinorm(gam2-gam1)
 843       if (dabs(x2) .lt. tolx) then
 844         spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
 845         return
 846       else if (x2.lt.0.0d0) then
 847         x1=x2
 848         x2=0.0d0
 849       endif
 850 ! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
 851       f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
 852       f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
 853       do it=1,maxit
 854         xmed=x1-f1*(x2-x1)/(f2-f1)
 855         fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
 856 !        write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
 857         if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
 858              .and. dabs(fmed).lt.tolf ) then
 859           x1=xmed
 860           f1=fmed
 861           goto 10
 862         else if ( fmed*f1.lt.0.0d0 ) then
 863           x2=xmed
 864           f2=fmed
 865         else
 866           x1=xmed
 867           f1=fmed
 868         endif
 869       enddo
 870    10 continue
 871       spherang=arcos(dcos(theta11)*dcos(theta12) &
 872        +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
 873        arcos(dcos(theta21)*dcos(theta22)+ &
 874        dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
 875       return
 876       end function spherang
 877 !--------------------------------------------------------------------------------
 878       real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
 879        theta21,theta22,fi)
 880 !      implicit none
 881       real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
 882        cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
 883        cosd2
 884 ! derivarive of the sum of the difference of the angles of a 4-residue fragment.
 885 !      real(kind=8) :: arcos
 886       cost11=dcos(theta11)
 887       cost12=dcos(theta12)
 888       cost21=dcos(theta21)
 889       cost22=dcos(theta22)
 890       sint11=dsin(theta11)
 891       sint12=dsin(theta12)
 892       sint21=dsin(theta21)
 893       sint22=dsin(theta22)
 894       cosd1=cost11*cost12+sint11*sint12*dcos(fi)
 895       cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
 896       sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
 897        +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
 898       return
 899       end function sumangp
 900 !-----------------------------------------------------------------------------
 901 ! contact.f
 902 !-----------------------------------------------------------------------------
 903       subroutine contact(lprint,ncont,icont,ist,ien)
 904
 905       use calc_data
 906       use geometry_data, only:c,dc,dc_norm
 907       use energy_data, only:itype,maxcont,molnum
 908 !      implicit none
 909 !      include 'DIMENSIONS'
 910 !      include 'DIMENSIONS.ZSCOPT'
 911 !      include 'COMMON.CONTROL'
 912 !      include 'COMMON.IOUNITS'
 913 !      include 'COMMON.CHAIN'
 914 !      include 'COMMON.INTERACT'
 915 !      include 'COMMON.FFIELD'
 916 !      include 'COMMON.NAMES'
 917 !      include 'COMMON.CALC'
 918 !      include 'COMMON.CONTPAR'
 919 !      include 'COMMON.LOCAL'
 920       integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2,mnum,mnum2
 921       real(kind=8) :: csc !el,dist
 922       real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
 923           ddsc,ddla,ddlb
 924       integer :: ncont,mhum
 925       integer,dimension(2,maxcont) :: icont
 926       real(kind=8) :: u,v,a(3),b(3),dla,dlb
 927       logical :: lprint
 928 !el-------
 929       dla=0.0d0
 930       dlb=0.0d0
 931 !el------
 932       ncont=0
 933       kkk=3
 934       if (lprint) then
 935       do i=1,nres
 936         mnum=molnum(i)
 937         write (iout,110) restyp(itype(i,mnum),mnum),i,c(1,i),c(2,i),&
 938           c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
 939           dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
 940       enddo
 941       endif
 942   110 format (a,'(',i3,')',9f8.3)
 943       do i=ist,ien-kkk
 944         mnum=molnum(i)
 945         iti=iabs(itype(i,mnum))
 946         if (iti.le.0 .or. iti.gt.ntyp_molec(mnum)) cycle
 947         do j=i+kkk,ien
 948           mnum2=molnum(j)
 949           itj=iabs(itype(j,mnum2))
 950           if (itj.le.0 .or. itj.gt.ntyp_molec(mnum2)) cycle
 951           itypi=iti
 952           itypj=itj
 953           xj = c(1,nres+j)-c(1,nres+i)
 954           yj = c(2,nres+j)-c(2,nres+i)
 955           zj = c(3,nres+j)-c(3,nres+i)
 956           dxi = dc_norm(1,nres+i)
 957           dyi = dc_norm(2,nres+i)
 958           dzi = dc_norm(3,nres+i)
 959           dxj = dc_norm(1,nres+j)
 960           dyj = dc_norm(2,nres+j)
 961           dzj = dc_norm(3,nres+j)
 962           do k=1,3
 963             a(k)=dc(k,nres+i)
 964             b(k)=dc(k,nres+j)
 965           enddo
 966 !          write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
 967           if (icomparfunc.eq.1) then
 968             call contfunc(csc,iti,itj)
 969           else if (icomparfunc.eq.2) then
 970             call scdist(csc,iti,itj)
 971           else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
 972             csc = dist(nres+i,nres+j)
 973           else if (icomparfunc.eq.4) then
 974             call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
 975           else
 976             write (*,*) "Error - Unknown sidechain contact function"
 977             write (iout,*) "Error - Unknown sidechain contact function"
 978           endif
 979           if (csc.lt.sc_cutoff(iti,itj)) then
 980 !            write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
 981 !     &      " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
 982 !     &      dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
 983 !     &      dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
 984 !     &      xj,yj,zj
 985 !            write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
 986 !     &       sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
 987 !     &       chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
 988 !     &       csc
 989             ncont=ncont+1
 990             cscore(ncont)=csc
 991             icont(1,ncont)=i
 992             icont(2,ncont)=j
 993             omt1(ncont)=om1
 994             omt2(ncont)=om2
 995             omt12(ncont)=om12
 996             ddsc(ncont)=1.0d0/rij
 997             ddla(ncont)=dla
 998             ddlb(ncont)=dlb
 999           endif
1000         enddo
1001       enddo
1002       if (lprint) then
1003         write (iout,'(a)') 'Contact map:'
1004         do i=1,ncont
1005
1006           i1=icont(1,i)
1007           i2=icont(2,i)
1008 !          mnum=molnum(i1)
1009           it1=itype(i1,1)
1010           it2=itype(i2,1)
1011           if (mnum.eq.0) mnum=1
1012           print *,"CONTACT",i1,i2,mnum,it1,it2
1013           write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
1014            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2,cscore(i),&
1015            sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1016            omt1(i),omt2(i),omt12(i)
1017         enddo
1018       endif
1019       return
1020       end subroutine contact
1021 #else
1022 !----------------------------------------------------------------------------
1023       subroutine contact(lprint,ncont,icont)
1024
1025       use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii,molnum
1026 !      include 'DIMENSIONS'
1027 !      include 'COMMON.IOUNITS'
1028 !      include 'COMMON.CHAIN'
1029 !      include 'COMMON.INTERACT'
1030 !      include 'COMMON.FFIELD'
1031 !      include 'COMMON.NAMES'
1032       real(kind=8) :: facont=1.569D0  ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1033       integer :: ncont,icont(2,maxcont)
1034       logical :: lprint
1035       integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1036       real(kind=8) :: rcomp
1037       integer :: mnum,mnum2
1038       ncont=0
1039       kkk=3
1040 !     print *,'nnt=',nnt,' nct=',nct
1041       do i=nnt+kkk,nct
1042         mnum=molnum(i)
1043         iti=iabs(itype(i,1))
1044         do j=nnt,i-kkk
1045           mnum2=molnum(j)
1046           itj=iabs(itype(j,1))
1047           if (ipot.ne.4) then
1048 !           rcomp=sigmaii(iti,itj)+1.0D0
1049             rcomp=facont*sigmaii(iti,itj)
1050           else
1051 !           rcomp=sigma(iti,itj)+1.0D0
1052             rcomp=facont*sigma(iti,itj)
1053           endif
1054 !         rcomp=6.5D0
1055 !         print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1056           if (dist(nres+i,nres+j).lt.rcomp) then
1057             ncont=ncont+1
1058             icont(1,ncont)=i
1059             icont(2,ncont)=j
1060           endif
1061         enddo
1062       enddo
1063       if (lprint) then
1064         write (iout,'(a)') 'Contact map:'
1065         do i=1,ncont
1066            mnum=molnum(i)
1067           i1=icont(1,i)
1068           i2=icont(2,i)
1069           it1=itype(i1,1)
1070           it2=itype(i2,1)
1071           write(iout,*) "test",i1,i2,it1,it2
1072           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1073            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1074         enddo
1075       endif
1076       return
1077       end subroutine contact
1078 #endif
1079 !----------------------------------------------------------------------------
1080       real(kind=8) function contact_fract(ncont,ncont_ref,&
1081                                            icont,icont_ref)
1082
1083       use energy_data, only:maxcont
1084 !      implicit none
1085 !      include 'DIMENSIONS'
1086 !      include 'COMMON.IOUNITS'
1087       integer :: i,j,nmatch
1088       integer :: ncont,ncont_ref
1089       integer,dimension(2,maxcont) :: icont,icont_ref
1090       nmatch=0
1091 !     print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1092 !     write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1093 !     write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1094 !     write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1095 !     write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1096       do i=1,ncont
1097         do j=1,ncont_ref
1098           if (icont(1,i).eq.icont_ref(1,j) .and. &
1099               icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1100         enddo
1101       enddo
1102 !     print *,' nmatch=',nmatch
1103 !     contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1104       contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1105       return
1106       end function contact_fract
1107 #ifndef CLUSTER
1108 !------------------------------------------------------------------------------
1109       subroutine pept_cont(lprint,ncont,icont)
1110
1111       use geometry_data, only:c
1112       use energy_data, only:maxcont,nnt,nct,itype,molnum
1113 !      implicit none
1114 !      include 'DIMENSIONS'
1115 !      include 'DIMENSIONS.ZSCOPT'
1116 !      include 'COMMON.IOUNITS'
1117 !      include 'COMMON.CHAIN'
1118 !      include 'COMMON.INTERACT'
1119 !      include 'COMMON.FFIELD'
1120 !      include 'COMMON.NAMES'
1121       integer :: ncont,icont(2,maxcont)
1122       integer :: i,j,k,kkk,i1,i2,it1,it2,mnum
1123       logical :: lprint
1124 !el      real(kind=8) :: dist
1125       real(kind=8) :: rcomp=5.5d0
1126       ncont=0
1127       kkk=0
1128       print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1129       do i=nnt,nct-3
1130         do k=1,3
1131           c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1132         enddo
1133         do j=i+2,nct-1
1134           do k=1,3
1135             c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1136           enddo
1137           if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1138             ncont=ncont+1
1139             icont(1,ncont)=i
1140             icont(2,ncont)=j
1141           endif
1142         enddo
1143       enddo
1144       if (lprint) then
1145         write (iout,'(a)') 'PP contact map:'
1146         do i=1,ncont
1147           mnum=molnum(i)
1148           i1=icont(1,i)
1149           i2=icont(2,i)
1150           it1=itype(i1,mnum)
1151           it2=itype(i2,mnum)
1152           write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1153            i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1154         enddo
1155       endif
1156       return
1157       end subroutine pept_cont
1158 !-----------------------------------------------------------------------------
1159 ! cont_frag.f
1160 !-----------------------------------------------------------------------------
1161       subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1162          ncont_interfrag,icont_interfrag)
1163
1164       use energy_data, only:itype,maxcont,molnum
1165 !      include 'DIMENSIONS'
1166 !      include 'DIMENSIONS.ZSCOPT'
1167 !      include 'DIMENSIONS.COMPAR'
1168 !      include 'COMMON.INTERACT'
1169 !      include 'COMMON.COMPAR'
1170 !      include 'COMMON.IOUNITS'
1171 !      include 'COMMON.CHAIN'
1172 !      include 'COMMON.NAMES'
1173       integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1174         icont_interfrag(2,maxcont,mmaxfrag)
1175       logical :: OK1,OK2,lprint
1176       integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2,mnum
1177 ! Determine the contacts that occur within a fragment and between fragments.
1178       do i=1,nfrag(1)
1179         do j=1,i
1180           ind = icant(i,j)
1181           nc=0
1182 !          write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1183 !     &      ,k=1,npiece(i,1))
1184 !          write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1185 !     &      ,k=1,npiece(j,1))
1186 !          write (iout,*) "ncont",ncont
1187           do k=1,ncont
1188             ic1=icont(1,k)
1189             ic2=icont(2,k)
1190             OK1=.false.
1191             l=0
1192             do while (.not.OK1 .and. l.lt.npiece(j,1))
1193               l=l+1
1194               OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1195                ic1.le.ifrag(2,l,j)+is
1196             enddo
1197             OK2=.false.
1198             l=0
1199             do while (.not.OK2 .and. l.lt.npiece(i,1))
1200               l=l+1
1201               OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1202                ic2.le.ifrag(2,l,i)+is
1203             enddo
1204 !            write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1205 !     &        " OK2",OK2
1206             if (OK1.and.OK2) then
1207               nc=nc+1
1208               icont_interfrag(1,nc,ind)=ic1
1209               icont_interfrag(2,nc,ind)=ic2
1210 !              write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1211             endif
1212           enddo
1213           ncont_interfrag(ind)=nc
1214 !          do k=1,ncont_interfrag(ind)
1215 !              i1=icont_interfrag(1,k,ind)
1216 !              i2=icont_interfrag(2,k,ind)
1217 !              it1=itype(i1)
1218 !              it2=itype(i2)
1219 !              write (iout,'(i3,2x,a,i4,2x,a,i4)')
1220 !     &          i,restyp(it1),i1,restyp(it2),i2
1221 !          enddo
1222         enddo
1223       enddo
1224       if (lprint) then
1225         write (iout,*) "Contacts within fragments:"
1226         do i=1,nfrag(1)
1227           write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1228            ifrag(2,k,i),k=1,npiece(i,1)),")"
1229           ind=icant(i,i)
1230           do k=1,ncont_interfrag(ind)
1231             i1=icont_interfrag(1,k,ind)
1232             i2=icont_interfrag(2,k,ind)
1233             mnum=molnum(i1)
1234             it1=itype(i1,mnum)
1235             it2=itype(i2,molnum(i2))
1236             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1237               i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1238           enddo
1239         enddo
1240         write (iout,*)
1241         write (iout,*) "Contacts between fragments:"
1242         do i=1,nfrag(1)
1243         do j=1,i-1
1244           ind = icant(i,j)
1245           write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1246            ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1247            (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1248           write (iout,*) "Number of contacts",&
1249            ncont_interfrag(ind)
1250           ind=icant(i,j)
1251           do k=1,ncont_interfrag(ind)
1252             i1=icont_interfrag(1,k,ind)
1253             i2=icont_interfrag(2,k,ind)
1254             mnum=molnum(i1)
1255             it1=itype(i1,mnum)
1256             it2=itype(i2,molnum(i2))
1257             write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1258               i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1259           enddo
1260         enddo
1261         enddo
1262       endif
1263       return
1264       end subroutine contacts_between_fragments
1265 !-----------------------------------------------------------------------------
1266 ! contfunc.f
1267 !-----------------------------------------------------------------------------
1268       subroutine contfunc(cscore,itypi,itypj)
1269 !
1270 ! This subroutine calculates the contact function based on
1271 ! the Gay-Berne potential of interaction.
1272 !
1273       use calc_data
1274 !      implicit real*8 (a-h,o-z)
1275 !      include 'DIMENSIONS'
1276 !      include 'COMMON.CONTPAR'
1277 !      include 'COMMON.CALC'
1278       integer :: expon=6
1279       integer :: itypi,itypj
1280       real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1281 !
1282       sig0ij=sig_comp(itypi,itypj)
1283       chi1=chi_comp(itypi,itypj)
1284       chi2=chi_comp(itypj,itypi)
1285       chi12=chi1*chi2
1286       chip1=chip_comp(itypi,itypj)
1287       chip2=chip_comp(itypj,itypi)
1288       chip12=chip1*chip2
1289       rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1290       rij=dsqrt(rrij)
1291 ! Calculate angle-dependent terms of the contact function
1292       erij(1)=xj*rij
1293       erij(2)=yj*rij
1294       erij(3)=zj*rij
1295       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1296       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1297       om12=dxi*dxj+dyi*dyj+dzi*dzj
1298       chiom12=chi12*om12
1299 !      print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1300 !     &  sig0ij,
1301 !     &  rij,rrij,om1,om2,om12
1302 ! Calculate eps1(om12)
1303       faceps1=1.0D0-om12*chiom12
1304       faceps1_inv=1.0D0/faceps1
1305       eps1=dsqrt(faceps1_inv)
1306 ! Following variable is eps1*deps1/dom12
1307       eps1_om12=faceps1_inv*chiom12
1308 ! Calculate sigma(om1,om2,om12)
1309       om1om2=om1*om2
1310       chiom1=chi1*om1
1311       chiom2=chi2*om2
1312       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1313       sigsq=1.0D0-facsig*faceps1_inv
1314 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1315       chipom1=chip1*om1
1316       chipom2=chip2*om2
1317       chipom12=chip12*om12
1318       facp=1.0D0-om12*chipom12
1319       facp_inv=1.0D0/facp
1320       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1321 ! Following variable is the square root of eps2
1322       eps2rt=1.0D0-facp1*facp_inv
1323       sigsq=1.0D0/sigsq
1324       sig=sig0ij*dsqrt(sigsq)
1325       rij_shift=1.0D0/rij-sig+sig0ij
1326       if (rij_shift.le.0.0D0) then
1327         evdw=1.0D1
1328         cscore = -dlog(evdw+1.0d-6)
1329         return
1330       endif
1331       rij_shift=1.0D0/rij_shift
1332       e2=(rij_shift*sig0ij)**expon
1333       evdw=dabs(eps1*eps2rt**2*e2)
1334       if (evdw.gt.1.0d1) evdw = 1.0d1
1335       cscore = -dlog(evdw+1.0d-6)
1336       return
1337       end subroutine contfunc
1338 !------------------------------------------------------------------------------
1339       subroutine scdist(cscore,itypi,itypj)
1340 !
1341 ! This subroutine calculates the contact distance
1342 !
1343       use calc_data
1344 !      implicit real*8 (a-h,o-z)
1345 !      include 'DIMENSIONS'
1346 !      include 'COMMON.CONTPAR'
1347 !      include 'COMMON.CALC'
1348       integer :: itypi,itypj
1349       real(kind=8) :: cscore,rrij
1350
1351       chi1=chi_comp(itypi,itypj)
1352       chi2=chi_comp(itypj,itypi)
1353       chi12=chi1*chi2
1354       rrij=xj*xj+yj*yj+zj*zj
1355       rij=dsqrt(rrij)
1356 ! Calculate angle-dependent terms of the contact function
1357       erij(1)=xj/rij
1358       erij(2)=yj/rij
1359       erij(3)=zj/rij
1360       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1361       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1362       om12=dxi*dxj+dyi*dyj+dzi*dzj
1363       chiom12=chi12*om12
1364       om1om2=om1*om2
1365       chiom1=chi1*om1
1366       chiom2=chi2*om2
1367       cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1368       return
1369       end subroutine scdist
1370 !------------------------------------------------------------------------------
1371 ! elecont.f
1372 !------------------------------------------------------------------------------
1373       subroutine elecont(lprint,ncont,icont,ist,ien)
1374
1375       use geometry_data, only:c
1376       use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2,molnum
1377 !      implicit none
1378 !      include 'DIMENSIONS'
1379 !      include 'DIMENSIONS.ZSCOPT'
1380 !      include 'DIMENSIONS.COMPAR'
1381 !      include 'COMMON.IOUNITS'
1382 !      include 'COMMON.CHAIN'
1383 !      include 'COMMON.INTERACT'
1384 !      include 'COMMON.FFIELD'
1385 !      include 'COMMON.NAMES'
1386 !      include 'COMMON.LOCAL'
1387       logical :: lprint
1388       integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1389       real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1390         xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1391         vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1392         eesij,ees,evdw,ene
1393       real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1394                        -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1395       real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1396                         0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1397       real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1398       real(kind=8) :: elcutoff=-0.3d0
1399       real(kind=8) :: elecutoff_14=-0.5d0
1400       integer :: ncont,icont(2,maxcont),mnum
1401       real(kind=8) :: econt(maxcont)
1402 !
1403 ! Load the constants of peptide bond - peptide bond interactions.
1404 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1405 ! proline) - determined by averaging ECEPP energy.
1406 !
1407 ! as of 7/06/91.
1408 !
1409 !      data epp    / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1410 !      data rpp    / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1411 !el      data (elpp6c)   /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1412 !el      data (elpp3c)   / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1413 !el      data (elcutoff) /-0.3d0/
1414 !el      data (elecutoff_14) /-0.5d0/
1415       ees=0.0d0
1416       evdw=0.0d0
1417       if (lprint) write (iout,'(a)') &
1418         "Constants of electrostatic interaction energy expression."
1419       do i=1,2
1420         do j=1,2
1421         rri=rpp(i,j)**6
1422         appc(i,j)=epp(i,j)*rri*rri
1423         bppc(i,j)=-2.0*epp(i,j)*rri
1424         ael6c(i,j)=elpp6c(i,j)*4.2**6
1425         ael3c(i,j)=elpp3c(i,j)*4.2**3
1426         if (lprint) &
1427         write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1428                                      ael3c(i,j)
1429         enddo
1430       enddo
1431       ncont=0
1432       do 1 i=ist,ien-2
1433         xi=c(1,i)
1434         yi=c(2,i)
1435         zi=c(3,i)
1436         dxi=c(1,i+1)-c(1,i)
1437         dyi=c(2,i+1)-c(2,i)
1438         dzi=c(3,i+1)-c(3,i)
1439         xmedi=xi+0.5*dxi
1440         ymedi=yi+0.5*dyi
1441         zmedi=zi+0.5*dzi
1442         do 4 j=i+2,ien-1
1443 !          ind=ind+1
1444           iteli=itel(i)
1445           itelj=itel(j)
1446           if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1447           if (iteli.eq.2 .and. itelj.eq.2 &
1448             .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1449           aaa=appc(iteli,itelj)
1450           bbb=bppc(iteli,itelj)
1451           ael6i=ael6c(iteli,itelj)
1452           ael3i=ael3c(iteli,itelj)
1453           dxj=c(1,j+1)-c(1,j)
1454           dyj=c(2,j+1)-c(2,j)
1455           dzj=c(3,j+1)-c(3,j)
1456           xj=c(1,j)+0.5*dxj-xmedi
1457           yj=c(2,j)+0.5*dyj-ymedi
1458           zj=c(3,j)+0.5*dzj-zmedi
1459           rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1460           rmij=sqrt(rrmij)
1461           r3ij=rrmij*rmij
1462           r6ij=r3ij*r3ij
1463           vrmij=vblinv*rmij
1464           cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1465           cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1466           cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1467           fac=cosa-3.0*cosb*cosg
1468           ev1=aaa*r6ij*r6ij
1469           ev2=bbb*r6ij
1470           fac3=ael6i*r6ij
1471           fac4=ael3i*r3ij
1472           evdwij=ev1+ev2
1473           el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1474           el2=fac4*fac
1475           eesij=el1+el2
1476           if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1477               j.eq.i+2 .and. eesij.le.elecutoff_14) then
1478              ncont=ncont+1
1479              icont(1,ncont)=i
1480              icont(2,ncont)=j
1481              econt(ncont)=eesij
1482           endif
1483           ees=ees+eesij
1484           evdw=evdw+evdwij
1485     4   continue
1486     1 continue
1487       if (lprint) then
1488         write (iout,*) 'Total average electrostatic energy: ',ees
1489         write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1490         write (iout,*)
1491         write (iout,*) 'Electrostatic contacts before pruning: '
1492         do i=1,ncont
1493           i1=icont(1,i)
1494           i2=icont(2,i)
1495           it1=itype(i1,molnum(i1))
1496           it2=itype(i2,molnum(i1))
1497           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1498            i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i1)),i2,econt(i)
1499         enddo
1500       endif
1501 ! For given residues keep only the contacts with the greatest energy.
1502       i=0
1503       do while (i.lt.ncont)
1504         i=i+1
1505         ene=econt(i)
1506         ic1=icont(1,i)
1507         ic2=icont(2,i)
1508         j=i
1509         do while (j.lt.ncont)
1510           j=j+1
1511           if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1512               ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1513 !            write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1514 !     &       " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1515             if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1516               if (ic1.eq.icont(1,j)) then
1517                 do k=1,ncont
1518                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1519                      .and. iabs(icont(1,k)-ic1).le.2 .and. &
1520                      econt(k).lt.econt(j) ) goto 21
1521                 enddo
1522               else if (ic2.eq.icont(2,j) ) then
1523                 do k=1,ncont
1524                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1525                      .and. iabs(icont(2,k)-ic2).le.2 .and. &
1526                      econt(k).lt.econt(j) ) goto 21
1527                 enddo
1528               endif
1529 ! Remove ith contact
1530               do k=i+1,ncont
1531                 icont(1,k-1)=icont(1,k)
1532                 icont(2,k-1)=icont(2,k)
1533                 econt(k-1)=econt(k)
1534               enddo
1535               i=i-1
1536               ncont=ncont-1
1537 !              write (iout,*) "ncont",ncont
1538 !              do k=1,ncont
1539 !                write (iout,*) icont(1,k),icont(2,k)
1540 !              enddo
1541               goto 20
1542             else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1543             then
1544               if (ic1.eq.icont(1,j)) then
1545                 do k=1,ncont
1546                   if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1547                      .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1548                      econt(k).lt.econt(i) ) goto 21
1549                 enddo
1550               else if (ic2.eq.icont(2,j) ) then
1551                 do k=1,ncont
1552                   if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1553                      .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1554                      econt(k).lt.econt(i) ) goto 21
1555                 enddo
1556               endif
1557 ! Remove jth contact
1558               do k=j+1,ncont
1559                 icont(1,k-1)=icont(1,k)
1560                 icont(2,k-1)=icont(2,k)
1561                 econt(k-1)=econt(k)
1562               enddo
1563               ncont=ncont-1
1564 !              write (iout,*) "ncont",ncont
1565 !              do k=1,ncont
1566 !                write (iout,*) icont(1,k),icont(2,k)
1567 !              enddo
1568               j=j-1
1569             endif
1570           endif
1571    21     continue
1572         enddo
1573    20   continue
1574       enddo
1575       if (lprint) then
1576         write (iout,*)
1577         write (iout,*) 'Electrostatic contacts after pruning: '
1578         do i=1,ncont
1579 !          mnum=molnum(i)
1580           i1=icont(1,i)
1581           i2=icont(2,i)
1582             mnum=molnum(i1)
1583             it1=itype(i1,mnum)
1584             it2=itype(i2,molnum(i2))
1585           write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1586            i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2,econt(i)
1587         enddo
1588       endif
1589       return
1590       end subroutine elecont
1591 !------------------------------------------------------------------------------
1592 ! match_contact.f
1593 !------------------------------------------------------------------------------
1594       subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1595          ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1596          nc_frac,nc_req_set,istr,llocal,lprn)
1597
1598       use energy_data, only:maxcont
1599 !      implicit real*8 (a-h,o-z)
1600 !      include 'DIMENSIONS'
1601 !      include 'COMMON.IOUNITS'
1602       integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1603       integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1604       real(kind=8) :: nc_frac
1605       logical :: llocal,lprn
1606       integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1607                  nc_req_set,istr,nc_match_max
1608       integer :: i,nc_req,nc_match1,is,js
1609       nc_match_max=0
1610       do i=1,ncont_ref
1611         nc_match_max=nc_match_max+ &
1612          min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1613       enddo
1614       if (istr.eq.3) then
1615         nc_req=0
1616       else if (nc_req_set.eq.0) then
1617         nc_req=nc_match_max*nc_frac
1618       else
1619         nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1620           dfloat(nc_req_set)+1.0d-7)
1621       endif
1622 !      write (iout,*) "match_contact: nc_req:",nc_req
1623 !      write (iout,*) "nc_match_max",nc_match_max
1624 !      write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1625 !     &   " n_shif2",n_shif2
1626 ! Match current contact map against reference contact map; exit, if at least
1627 ! half of the contacts match
1628       call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1629           ncont,icont,jfrag,llocal,lprn)
1630       nc_match1_max=nc_match1
1631       if (lprn .and. nc_match.gt.0) write (iout,*) &
1632         "Shift:",0,0," nc_match1",nc_match1,&
1633         " nc_match=",nc_match," req'd",nc_req
1634       if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1635           nc_req.eq.0 .and. nc_match.eq.1) then
1636          ishif1=0
1637          ishif2=0
1638          return
1639       endif
1640 ! If sufficient matches are not found, try to shift contact maps up to three
1641 ! positions.
1642       if (n_shif1.gt.0) then
1643       do is=1,n_shif1
1644 ! The following four tries help to find shifted beta-sheet patterns
1645 ! Shift "left" strand backward
1646         call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1647           icont_ref,ncont,icont,jfrag,llocal,lprn)
1648         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1649         if (lprn .and. nc_match.gt.0) write (iout,*) &
1650           "Shift:",-is,0," nc_match1",nc_match1,&
1651           " nc_match=",nc_match," req'd",nc_req
1652         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1653            nc_req.eq.0 .and. nc_match.eq.1) then
1654           ishif1=-is
1655           ishif2=0
1656           return
1657         endif
1658 ! Shift "left" strand forward
1659         call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1660             icont_ref,ncont,icont,jfrag,llocal,lprn)
1661         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1662         if (lprn .and. nc_match.gt.0) write (iout,*) &
1663          "Shift:",is,0," nc_match1",nc_match1,&
1664          " nc_match=",nc_match," req'd",nc_req
1665         if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1666            nc_req.eq.0 .and. nc_match.eq.1) then
1667           ishif1=is
1668           ishif2=0
1669           return
1670         endif
1671       enddo
1672       if (nc_req.eq.0) return
1673 ! Shift "right" strand backward
1674       do is=1,n_shif1
1675         call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1676            icont_ref,ncont,icont,jfrag,llocal,lprn)
1677         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1678         if (lprn .and. nc_match.gt.0) write (iout,*) &
1679           "Shift:",0,-is," nc_match1",nc_match1,&
1680           " nc_match=",nc_match," req'd",nc_req
1681         if (nc_match.ge.nc_req) then
1682           ishif1=0
1683           ishif2=-is
1684           return
1685         endif
1686 ! Shift "right" strand upward
1687         call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
1688           icont_ref,ncont,icont,jfrag,llocal,lprn)
1689         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1690         if (lprn .and. nc_match.gt.0) write (iout,*) &
1691           "Shift:",0,is," nc_match1",nc_match1,&
1692           " nc_match=",nc_match," req'd",nc_req
1693         if (nc_match.ge.nc_req) then
1694           ishif1=0
1695           ishif2=is
1696           return
1697         endif
1698       enddo ! is
1699 ! Now try to shift both residues in contacts.
1700       do is=1,n_shif1
1701         do js=1,is
1702           if (js.ne.is) then
1703             call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1704               icont_ref,ncont,icont,jfrag,llocal,lprn)
1705             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1706             if (lprn .and. nc_match.gt.0) write (iout,*) &
1707                "Shift:",-is,-js," nc_match1",nc_match1,&
1708                " nc_match=",nc_match," req'd",nc_req
1709             if (nc_match.ge.nc_req) then
1710               ishif1=-is
1711               ishif2=-js
1712               return
1713             endif
1714             call ncont_match(nc_match,nc_match1,is,js,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:",is,js," nc_match1",nc_match1,&
1719               " nc_match=",nc_match," req'd",nc_req
1720             if (nc_match.ge.nc_req) then
1721               ishif1=is
1722               ishif2=js
1723               return
1724             endif
1725 !
1726             call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
1727               icont_ref,ncont,icont,jfrag,llocal,lprn)
1728             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1729             if (lprn .and. nc_match.gt.0) write (iout,*) &
1730               "Shift:",-js,-is," nc_match1",nc_match1,&
1731               " nc_match=",nc_match," req'd",nc_req
1732             if (nc_match.ge.nc_req) then
1733               ishif1=-js
1734               ishif2=-is
1735               return
1736             endif
1737 !
1738             call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
1739               icont_ref,ncont,icont,jfrag,llocal,lprn)
1740             if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1741             if (lprn .and. nc_match.gt.0) write (iout,*) &
1742               "Shift:",js,is," nc_match1",nc_match1,&
1743               " nc_match=",nc_match," req'd",nc_req
1744             if (nc_match.ge.nc_req) then
1745               ishif1=js
1746               ishif2=is
1747               return
1748             endif
1749           endif
1750 !
1751           if (is+js.le.n_shif1) then
1752           call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1753             icont_ref,ncont,icont,jfrag,llocal,lprn)
1754           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1755           if (lprn .and. nc_match.gt.0) write (iout,*) &
1756            "Shift:",-is,js," nc_match1",nc_match1,&
1757            " nc_match=",nc_match," req'd",nc_req
1758           if (nc_match.ge.nc_req) then
1759             ishif1=-is
1760             ishif2=js
1761             return
1762           endif
1763 !
1764           call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
1765             icont_ref,ncont,icont,jfrag,llocal,lprn)
1766           if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1767           if (lprn .and. nc_match.gt.0) write (iout,*) &
1768            "Shift:",js,-is," nc_match1",nc_match1,&
1769            " nc_match=",nc_match," req'd",nc_req
1770           if (nc_match.ge.nc_req) then
1771             ishif1=js
1772             ishif2=-is
1773             return
1774           endif
1775           endif
1776 !
1777         enddo !js
1778       enddo !is
1779       endif
1780
1781       if (n_shif2.gt.0) then
1782       do is=1,n_shif2
1783         call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1784           icont_ref,ncont,icont,jfrag,llocal,lprn)
1785         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1786         if (lprn .and. nc_match.gt.0) write (iout,*) &
1787            "Shift:",-is,-is," nc_match1",nc_match1,&
1788            " nc_match=",nc_match," req'd",nc_req
1789         if (nc_match.ge.nc_req) then
1790           ishif1=-is
1791           ishif2=-is
1792           return
1793         endif
1794         call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1795           icont_ref,ncont,icont,jfrag,llocal,lprn)
1796         if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1797         if (lprn .and. nc_match.gt.0) write (iout,*) &
1798           "Shift:",is,is," nc_match1",nc_match1,&
1799           " nc_match=",nc_match," req'd",nc_req
1800         if (nc_match.ge.nc_req) then
1801           ishif1=is
1802           ishif2=is
1803           return
1804         endif
1805       enddo
1806       endif
1807 ! If this point is reached, the contact maps are different.
1808       nc_match=0
1809       ishif1=0
1810       ishif2=0
1811       return
1812       end subroutine match_contact
1813 !-------------------------------------------------------------------------
1814       subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1815          ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1816
1817       use energy_data, only:nnt,nct,maxcont
1818 !      implicit real*8 (a-h,o-z)
1819 !      include 'DIMENSIONS'
1820 !      include 'DIMENSIONS.ZSCOPT'
1821 !      include 'DIMENSIONS.COMPAR'
1822 !      include 'COMMON.IOUNITS'
1823 !      include 'COMMON.INTERACT'
1824 !      include 'COMMON.GEO'
1825 !      include 'COMMON.COMPAR'
1826       logical :: llocal,lprn
1827       integer ncont_ref,ncont,ishift,ishif2,nang_pair
1828       integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1829       integer,dimension(2,nres) :: iang_pair !(2,maxres)
1830       integer :: nc_match,nc_match1,ishif1,jfrag
1831       integer :: i,j,ic1,ic2
1832       real(kind=8) :: diffang,fract,rad2deg
1833
1834 ! Compare the contact map against the reference contact map; they're stored
1835 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1836       if (lprn) write (iout,'(80(1h*))')
1837       nc_match=0
1838       nc_match1=0
1839 ! Check the local structure by comparing dihedral angles.
1840 !      write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1841       if (llocal .and. ncont_ref.eq.0) then
1842 ! If there are no contacts just compare the dihedral angles and exit.
1843         call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1844           lprn)
1845         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1846          " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1847         if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1848         then
1849           nc_match=1
1850         else
1851           nc_match=0
1852         endif
1853         return
1854       endif
1855       nang_pair=0
1856       do i=1,ncont
1857         ic1=icont(1,i)+ishif1
1858         ic2=icont(2,i)+ishif2
1859 !        write (iout,*) "i",i," ic1",ic1," ic2",ic2
1860         if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1861         do j=1,ncont_ref
1862           if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1863             nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1864             nc_match1=nc_match1+1
1865             icont_match(1,nc_match1)=ic1
1866             icont_match(2,nc_match1)=ic2
1867 !            call add_angpair(icont(1,i),icont_ref(1,j),
1868 !     &         nang_pair,iang_pair)
1869 !            call add_angpair(icont(2,i),icont_ref(2,j),
1870 !     &         nang_pair,iang_pair)
1871             if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1872              " match",icont_ref(1,j),icont_ref(2,j),&
1873              " shifts",ishif1,ishif2
1874             goto 10
1875           endif
1876         enddo
1877    10   continue
1878       enddo
1879       if (lprn) then
1880         write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1881         write (iout,*) "icont_match"
1882         do i=1,nc_match1
1883           write (iout,*) icont_match(1,i),icont_match(2,i)
1884         enddo
1885       endif
1886       if (llocal .and. nc_match.gt.0) then
1887         call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1888           ang_cut1(jfrag),diffang,fract)
1889         if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1890          " ang_cut:",ang_cut(jfrag)*rad2deg,&
1891          " ang_cut1",ang_cut1(jfrag)*rad2deg
1892         if (diffang.gt.ang_cut(jfrag) &
1893           .or. fract.lt.frac_min(jfrag)) nc_match=0
1894       endif
1895 !      if (nc_match.gt.0) then
1896 !        diffang = angnorm1(nang_pair,iang_pair,lprn)
1897 !        if (diffang.gt.ang_cut(jfrag)) nc_match=0
1898 !      endif
1899       if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1900          " diffang",rad2deg*diffang," nc_match",nc_match
1901       return
1902       end subroutine ncont_match
1903 !------------------------------------------------------------------------------
1904       subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1905 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1906 ! conformation considered to that of the reference conformation.
1907 ! Returns the number of equivalent residues (nsec_match).
1908 !      implicit real*8 (a-h,o-z)
1909 !      include 'DIMENSIONS'
1910 !      include 'DIMENSIONS.ZSCOPT'
1911 !      include 'DIMENSIONS.COMPAR'
1912 !      include 'COMMON.IOUNITS'
1913 !      include 'COMMON.CHAIN'
1914 !      include 'COMMON.PEPTCONT'
1915 !      include 'COMMON.COMPAR'
1916       logical :: lprn
1917       integer :: isecstr(nres)
1918       integer :: jfrag,nsec_match,npart,i,j
1919       npart = npiece(jfrag,1)
1920       nsec_match=0
1921       if (lprn) then
1922         write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1923               (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1924         write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1925         write (iout,'(80i1)') (isecstr(j),j=1,nres)
1926       endif
1927       do i=1,npart
1928         do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1929 ! The residue has equivalent conformational state to that of the reference
1930 ! structure, if:
1931 !  a) the conformational states are equal or
1932 !  b) the reference state is a coil and that of the conformation considered
1933 !     is a strand or
1934 !  c) the conformational state of the conformation considered is a strand
1935 !     and that of the reference conformation is a coil.
1936 ! 10/28/02 - case (b) deleted.
1937           if (isecstr(j).eq.isec_ref(j) .or. &
1938 !     &        isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1939               isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1940             nsec_match=nsec_match+1
1941         enddo
1942       enddo
1943       return
1944       end subroutine match_secondary
1945 !------------------------------------------------------------------------------
1946 ! odlodc.f
1947 !------------------------------------------------------------------------------
1948       subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1949
1950       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1951 !                            isccont_frag_ref
1952 !      implicit real*8 (a-h,o-z)
1953       real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1954       real(kind=8) :: uu,vv,aa,bb,dd
1955       real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1956 !el      odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1957 !el       + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1958 !      print *,"r1",(r1(i),i=1,3)
1959 !      print *,"r2",(r2(i),i=1,3)
1960 !      print *,"a",(a(i),i=1,3)
1961 !      print *,"b",(b(i),i=1,3)
1962       aa = a(1)**2+a(2)**2+a(3)**2
1963       bb = b(1)**2+b(2)**2+b(3)**2
1964       ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1965       ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1966       br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1967       det = aa*bb-ab**2
1968 !      print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1969       uu = (-ar*bb+br*ab)/det
1970       vv = (br*aa-ar*ab)/det
1971 !      print *,u,v
1972       uu=dmin1(uu,1.0d0)
1973       uu=dmax1(uu,0.0d0)
1974       vv=dmin1(vv,1.0d0)
1975       vv=dmax1(vv,0.0d0)
1976 !el      dd1 = odl(uu,vv)
1977       dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1978 !el      dd2 = odl(0.0d0,0.0d0)
1979       dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1980 !el      dd3 = odl(0.0d0,1.0d0)
1981       dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1982 !el      dd4 = odl(1.0d0,0.0d0)
1983       dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1984 !el      dd5 = odl(1.0d0,1.0d0)
1985       dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1986       dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1987       if (dd.eq.dd2) then
1988         uu=0.0d0
1989         vv=0.0d0
1990       else if (dd.eq.dd3) then
1991         uu=0.0d0
1992         vv=1.0d0
1993       else if (dd.eq.dd4) then
1994         uu=1.0d0
1995         vv=0.0d0
1996       else if (dd.eq.dd5) then
1997         uu=1.0d0
1998         vv=1.0d0
1999       endif
2000 ! Control check
2001 !      do i=1,3
2002 !        x(i)=r1(i)+u*a(i)
2003 !        y(i)=r2(i)+v*b(i)
2004 !      enddo
2005 !      dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
2006 !      dd1 = dsqrt(dd1)
2007       aa = dsqrt(aa)
2008       bb = dsqrt(bb)
2009 !      write (8,*) uu,vv,dd,dd1
2010 !      print *,dd,dd1
2011       return
2012       end subroutine odlodc
2013 !------------------------------------------------------------------------------
2014       real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
2015
2016       real(kind=8),dimension(3) :: r1,r2
2017       real(kind=8) :: aa,bb,u,v,ar,br,ab
2018
2019       odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
2020        + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
2021
2022       end function odl
2023 !------------------------------------------------------------------------------
2024 ! proc_cont.f
2025 !------------------------------------------------------------------------------
2026       subroutine proc_cont
2027
2028       use geometry_data, only:rad2deg
2029       use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2030 !                            isccont_frag_ref
2031 !      implicit real*8 (a-h,o-z)
2032 !      include 'DIMENSIONS'
2033 !      include 'DIMENSIONS.ZSCOPT'
2034 !      include 'DIMENSIONS.COMPAR'
2035 !      include 'COMMON.IOUNITS'
2036 !      include 'COMMON.TIME1'
2037 !      include 'COMMON.SBRIDGE'
2038 !      include 'COMMON.CONTROL'
2039 !      include 'COMMON.COMPAR'
2040 !      include 'COMMON.CHAIN'
2041 !      include 'COMMON.HEADER'
2042 !      include 'COMMON.CONTACTS1'
2043 !      include 'COMMON.PEPTCONT'
2044 !      include 'COMMON.GEO'
2045       integer :: i,j,k,ind,len_cut,ndigit,length_frag
2046
2047       write (iout,*) "proc_cont: nlevel",nlevel
2048       if (nlevel.lt.0) then
2049         write (iout,*) "call define_fragments"
2050         call define_fragments
2051       else
2052         write (iout,*) "call secondary2"
2053         call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2054            isec_ref)
2055       endif
2056       write (iout,'(80(1h=))')
2057       write (iout,*) "Electrostatic contacts"
2058       call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2059        icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2060       write (iout,'(80(1h=))')
2061       write (iout,*) "Side chain contacts"
2062       call contacts_between_fragments(.true.,0,ncont_ref,&
2063        icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2064       if (nlevel.lt.0) then
2065         do i=1,nfrag(1)
2066           ind=icant(i,i)
2067           len_cut=1000
2068           if (istruct(i).le.1) then
2069             len_cut=max0(len_frag(i,1)*4/5,3)
2070           else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2071             len_cut=max0(len_frag(i,1)*2/5,3)
2072           endif
2073           write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2074             ncont_frag_ref(ind)," len_cut",len_cut,&
2075             " icont_single",icont_single," iloc_single",iloc_single
2076           iloc(i)=iloc_single
2077           if (iloc(i).gt.0) write (iout,*) &
2078            "Local structure used to compare structure of fragment",i,&
2079            " to native."
2080           if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2081               .and. icont_single.gt.0 .and. &
2082               ncont_frag_ref(ind).ge.len_cut) then
2083             write (iout,*) "Electrostatic contacts used to compare",&
2084              " structure of fragment",i," to native."
2085             ielecont(i,1)=1
2086             isccont(i,1)=0
2087           else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2088             .ge.len_cut) then
2089             write (iout,*) "Side chain contacts used to compare",&
2090              " structure of fragment",i," to native."
2091             isccont(i,1)=1
2092             ielecont(i,1)=0
2093           else
2094             write (iout,*) "Contacts not used to compare",&
2095              " structure of fragment",i," to native."
2096             ielecont(i,1)=0
2097             isccont(i,1)=0
2098             nc_req_setf(i,1)=0
2099           endif
2100           if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2101                .and. ielecont(i,1).eq.0) then
2102             write (iout,*) "RMSD used to compare",&
2103              " structure of fragment",i," to native."
2104             irms(i,1)=1
2105           else
2106             write (iout,*) "RMSD not used to compare",&
2107              " structure of fragment",i," to native."
2108             irms(i,1)=0
2109           endif
2110         enddo
2111       endif
2112       if (nlevel.lt.-1) then
2113         call define_pairs
2114         nlevel = -nlevel
2115         if (nlevel.gt.3) nlevel=3
2116         if (nlevel.eq.3) then
2117           nfrag(3)=1
2118           npiece(1,3)=nfrag(1)
2119           do i=1,nfrag(1)
2120             ipiece(i,1,3)=i
2121           enddo
2122           ielecont(1,3)=0
2123           isccont(1,3)=0
2124           irms(1,3)=1
2125           n_shift(1,1,3)=0
2126           n_shift(2,1,3)=0
2127         endif
2128       else if (nlevel.eq.-1) then
2129         nlevel=1
2130       endif
2131       isnfrag(1)=0
2132       do i=1,nlevel
2133         isnfrag(i+1)=isnfrag(i)+nfrag(i)
2134       enddo
2135       ndigit=3*nfrag(1)
2136       do i=2,nlevel
2137         ndigit=ndigit+2*nfrag(i)
2138       enddo
2139       write (iout,*) "ndigit",ndigit
2140       if (.not.binary .and. ndigit.gt.30) then
2141         write (iout,*) "Highest class too large; switching to",&
2142           " binary representation."
2143         binary=.true.
2144       endif
2145       write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2146       write(iout,*) "rmscut_base_up",rmscut_base_up,&
2147        " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2148       do i=1,nlevel
2149         do j=1,nfrag(i)
2150           length_frag = 0
2151           if (i.eq.1) then
2152             do k=1,npiece(j,i)
2153               length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2154             enddo
2155           else
2156             do k=1,npiece(j,i)
2157               length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2158             enddo
2159           endif
2160           len_frag(j,i)=length_frag
2161           rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2162           rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2163           if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2164             rmscutfrag(1,j,i)=rmsup_lim
2165           if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2166             rmscutfrag(1,j,i)=rmsupup_lim
2167         enddo
2168       enddo
2169       write (iout,*) "Level",1," number of fragments:",nfrag(1)
2170       do j=1,nfrag(1)
2171         write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2172           k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2173           rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2174           ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2175           nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2176       enddo
2177       do i=2,nlevel
2178         write (iout,*) "Level",i," number of fragments:",nfrag(i)
2179         do j=1,nfrag(i)
2180           write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2181             k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2182             rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2183             nc_fragm(j,i),nc_req_setf(j,i)
2184         enddo
2185       enddo
2186       return
2187       end subroutine proc_cont
2188 !------------------------------------------------------------------------------
2189 ! define_pairs.f
2190 !------------------------------------------------------------------------------
2191       subroutine define_pairs
2192
2193 !      use energy_data, only:nsccont_frag_ref
2194 !      implicit real*8 (a-h,o-z)
2195 !      include 'DIMENSIONS'
2196 !      include 'DIMENSIONS.ZSCOPT'
2197 !      include 'DIMENSIONS.COMPAR'
2198 !      include 'COMMON.IOUNITS'
2199 !      include 'COMMON.TIME1'
2200 !      include 'COMMON.SBRIDGE'
2201 !      include 'COMMON.CONTROL'
2202 !      include 'COMMON.COMPAR'
2203 !      include 'COMMON.FRAG'
2204 !      include 'COMMON.CHAIN'
2205 !      include 'COMMON.HEADER'
2206 !      include 'COMMON.GEO'
2207 !      include 'COMMON.CONTACTS1'
2208 !      include 'COMMON.PEPTCONT'
2209       integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2210
2211       do j=1,nfrag(1)
2212         length_frag = 0
2213         do k=1,npiece(j,1)
2214           length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2215         enddo
2216         len_frag(j,1)=length_frag
2217         write (iout,*) "Fragment",j," length",len_frag(j,1)
2218       enddo
2219       nfrag(2)=0
2220       do i=1,nfrag(1)
2221         do j=i+1,nfrag(1)
2222           ind = icant(i,j)
2223           if (istruct(i).le.1 .or. istruct(j).le.1) then
2224             if (istruct(i).le.1) then
2225               ll1=len_frag(i,1)
2226             else
2227               ll1=len_frag(i,1)/2
2228             endif
2229             if (istruct(j).le.1) then
2230               ll2=len_frag(j,1)
2231             else
2232               ll2=len_frag(j,1)/2
2233             endif
2234             len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2235           else
2236             if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2237               ll1=len_frag(i,1)/2
2238             else
2239               ll1=len_frag(i,1)
2240             endif
2241             if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2242               ll2=len_frag(j,1)/2
2243             else
2244               ll2=len_frag(j,1)
2245             endif
2246             len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2247           endif
2248           write (iout,*) "Fragments",i,j," structure",istruct(i),&
2249              istruct(j)," # contacts",&
2250              ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2251              " lengths",len_frag(i,1),len_frag(j,1),&
2252              " ll1",ll1," ll2",ll2," len_cut",len_cut
2253           if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2254             nsccont_frag_ref(ind).ge.len_cut ) then
2255             if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2256               write (iout,*) "Adding pair of helices",i,j,&
2257               " based on SC contacts"
2258             else
2259               write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2260               " based on SC contacts"
2261             endif
2262             nfrag(2)=nfrag(2)+1
2263             if (icont_pair.gt.0) then
2264               write (iout,*)  "# SC contacts will be used",&
2265               " in comparison."
2266               isccont(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)=0
2277             n_shift(1,nfrag(2),2)=nshift_pair
2278             n_shift(2,nfrag(2),2)=nshift_pair
2279             nc_fragm(nfrag(2),2)=ncfrac_pair
2280             nc_req_setf(nfrag(2),2)=ncreq_pair
2281           else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2282              .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2283              .and. ncont_frag_ref(ind).ge.len_cut ) then
2284             nfrag(2)=nfrag(2)+1
2285             write (iout,*) "Adding pair strands/sheets",i,j,&
2286               " based on pp contacts"
2287             if (icont_pair.gt.0) then
2288               write (iout,*) "# pp contacts will be used",&
2289               " in comparison."
2290               ielecont(nfrag(2),2)=1
2291             endif
2292             if (irms_pair.gt.0) then
2293               write (iout,*)  "Fragment RMSD will be used",&
2294               " in comparison."
2295               irms(nfrag(2),2)=1
2296             endif
2297             npiece(nfrag(2),2)=2
2298             ipiece(1,nfrag(2),2)=i
2299             ipiece(2,nfrag(2),2)=j
2300             ielecont(nfrag(2),2)=1
2301             isccont(nfrag(2),2)=0
2302             n_shift(1,nfrag(2),2)=nshift_pair
2303             n_shift(2,nfrag(2),2)=nshift_pair
2304             nc_fragm(nfrag(2),2)=ncfrac_bet
2305             nc_req_setf(nfrag(2),2)=ncreq_bet
2306           endif
2307         enddo
2308       enddo
2309       write (iout,*) "Pairs found"
2310       do i=1,nfrag(2)
2311         write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2312       enddo
2313       return
2314       end subroutine define_pairs
2315 !------------------------------------------------------------------------------
2316 ! icant.f
2317 !------------------------------------------------------------------------------
2318       INTEGER FUNCTION ICANT(I,J)
2319       integer :: i,j
2320       IF (I.GE.J) THEN
2321         ICANT=(I*(I-1))/2+J
2322       ELSE
2323         ICANT=(J*(J-1))/2+I
2324       ENDIF
2325       RETURN
2326       END FUNCTION ICANT
2327 !------------------------------------------------------------------------------
2328 ! mysort.f
2329 !------------------------------------------------------------------------------
2330       subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2331 !      implicit none
2332       integer :: n,m,mm
2333       integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2334       real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2335       real(kind=8) :: xxtemp
2336       integer :: i,j,k,imax
2337       do i=1,n
2338         xmin=x(1,1,i)
2339         imax=i
2340         do j=i+1,n
2341           if (x(1,1,j).lt.xmin) then
2342             imax=j
2343             xmin=x(1,1,j)
2344           endif
2345         enddo
2346         xxtemp=z2(imax)
2347         z2(imax)=z2(i)
2348         z2(i)=xxtemp
2349         xxtemp=z3(imax)
2350         z3(imax)=z3(i)
2351         z3(i)=xxtemp
2352         xxtemp=z4(imax)
2353         z4(imax)=z4(i)
2354         z4(i)=xxtemp
2355         xxtemp=z5(imax)
2356         z5(imax)=z5(i)
2357         z5(i)=xxtemp
2358         xtemp=y(imax)
2359         y(imax)=y(i)
2360         y(i)=xtemp
2361         xtemp=z(imax)
2362         z(imax)=z(i)
2363         z(i)=xtemp
2364         xtemp=z6(imax)
2365         z6(imax)=z6(i)
2366         z6(i)=xtemp
2367         do j=1,2
2368           xtemp=z1(j,imax)
2369           z1(j,imax)=z1(j,i)
2370           z1(j,i)=xtemp
2371         enddo
2372         do j=1,m
2373           do k=1,mm
2374             xtemp=x(j,k,imax)
2375             x(j,k,imax)=x(j,k,i)
2376             x(j,k,i)=xtemp
2377           enddo
2378         enddo
2379       enddo
2380       return
2381       end subroutine imysort
2382 !------------------------------------------------------------------------------
2383 ! qwolynes.f
2384 !-------------------------------------------------------------------------------
2385       real(kind=8) function qwolynes(ilevel,jfrag)
2386
2387       use geometry_data, only:cref,nperm
2388       use control_data, only:symetr
2389       use energy_data, only:nnt,nct,itype,molnum
2390 !      implicit none
2391 !      include 'DIMENSIONS'
2392 !      include 'DIMENSIONS.ZSCOPT'
2393 !      include 'DIMENSIONS.COMPAR'
2394 !      include 'COMMON.IOUNITS'
2395 !      include 'COMMON.COMPAR'
2396 !      include 'COMMON.CHAIN'
2397 !      include 'COMMON.INTERACT'
2398 !      include 'COMMON.CONTROL'
2399       integer :: ilevel,jfrag,kkk
2400       integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2401       integer :: nsep=3
2402       real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2403       real(kind=8) :: maxiQ !dist,
2404       real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2405       logical :: lprn=.false.
2406       real(kind=8) :: x !el sigm
2407 !el      sigm(x)=0.25d0*x
2408       nperm=1
2409       maxiQ=0
2410       do i=1,symetr
2411       nperm=i*nperm
2412       enddo
2413 !      write (iout,*) "QWolyes: " jfrag",jfrag,
2414 !     &  " ilevel",ilevel
2415       allocate(tempus(nperm))
2416       do kkk=1,nperm
2417       qq = 0.0d0
2418       if (ilevel.eq.0) then
2419         if (lprn) write (iout,*) "Q computed for whole molecule"
2420         nl=0
2421         do il=nnt+nsep,nct
2422           do jl=nnt,il-nsep
2423             dij=0.0d0
2424             dijCM=0.0d0
2425             d0ij=0.0d0
2426             d0ijCM=0.0d0
2427             qqij=0.0d0
2428             qqijCM=0.0d0
2429             nl=nl+1
2430             d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2431                        (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2432                        (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2433             dij=dist(il,jl)
2434             qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2435             if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2436               nl=nl+1
2437               d0ijCM=dsqrt( &
2438                      (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2439                      (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2440                      (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2441               dijCM=dist(il+nres,jl+nres)
2442               qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2443             endif
2444             qq = qq+qqij+qqijCM
2445             if (lprn) then
2446               write (iout,*) "il",il," jl",jl,&
2447                " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2448               write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2449                " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2450             endif
2451           enddo
2452         enddo
2453         qq = qq/nl
2454         if (lprn) write (iout,*) "nl",nl," qq",qq
2455       else if (ilevel.eq.1) then
2456         if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2457         nl=0
2458 !        write (iout,*) "nlist_frag",nlist_frag(jfrag)
2459         do i=2,nlist_frag(jfrag)
2460           do j=1,i-1
2461             il=list_frag(i,jfrag)
2462             jl=list_frag(j,jfrag)
2463             if (iabs(il-jl).gt.nsep) then
2464               dij=0.0d0
2465               dijCM=0.0d0
2466               d0ij=0.0d0
2467               d0ijCM=0.0d0
2468               qqij=0.0d0
2469               qqijCM=0.0d0
2470               nl=nl+1
2471               d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2472                          (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2473                          (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2474               dij=dist(il,jl)
2475               qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2476               if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2477                 nl=nl+1
2478                 d0ijCM=dsqrt( &
2479                        (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2480                        (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2481                        (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2482                 dijCM=dist(il+nres,jl+nres)
2483                qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2484               endif
2485               qq = qq+qqij+qqijCM
2486               if (lprn) then
2487                 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2488                  " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2489                 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2490                  " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2491               endif
2492             endif
2493           enddo
2494         enddo
2495         qq = qq/nl
2496         if (lprn) write (iout,*) "nl",nl," qq",qq
2497       else if (ilevel.eq.2) then
2498         np=npiece(jfrag,ilevel)
2499         nl=0
2500         do i=2,np
2501           ip=ipiece(i,jfrag,ilevel)
2502           do j=1,nlist_frag(ip)
2503             il=list_frag(j,ip)
2504             do k=1,i-1
2505               kp=ipiece(k,jfrag,ilevel)
2506               do l=1,nlist_frag(kp)
2507                 kl=list_frag(l,kp)
2508                 if (iabs(kl-il).gt.nsep) then
2509                   nl=nl+1
2510                   dij=0.0d0
2511                   dijCM=0.0d0
2512                   d0ij=0.0d0
2513                   d0ijCM=0.0d0
2514                   qqij=0.0d0
2515                   qqijCM=0.0d0
2516                   d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2517                              (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2518                              (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2519                   dij=dist(il,kl)
2520                   qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2521                   if (itype(il,molnum(il)).ne.10 .or. itype(kl,molnum(kl)).ne.10) then
2522                     nl=nl+1
2523                     d0ijCM=dsqrt( &
2524                        (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2525                        (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2526                        (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2527                     dijCM=dist(il+nres,kl+nres)
2528                     qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2529                       (sigm(d0ijCM)))**2)
2530                   endif
2531                   qq = qq+qqij+qqijCM
2532                   if (lprn) then
2533                     write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2534                       " kl",kl," itype",itype(il,molnum(il)), &
2535                          itype(kl,molnum(kl))
2536                     write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2537                     d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2538                   endif
2539                 endif
2540               enddo  ! l
2541             enddo    ! k
2542           enddo      ! j
2543         enddo        ! i
2544         qq = qq/nl
2545         if (lprn) write (iout,*) "nl",nl," qq",qq
2546       else
2547         write (iout,*)"Error: Q can be computed only for level 1 and 2."
2548       endif
2549       tempus(kkk)=qq
2550       enddo
2551       do kkk=1,nperm
2552        if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2553       enddo
2554       qwolynes=1.0d0-maxiQ
2555       deallocate(tempus)
2556       return
2557       end function qwolynes
2558 !-------------------------------------------------------------------------------
2559       real(kind=8) function sigm(x)
2560       real(kind=8) :: x
2561       sigm=0.25d0*x
2562       return
2563       end function sigm
2564 !-------------------------------------------------------------------------------
2565       subroutine fragment_list
2566 !      implicit none
2567 !      include 'DIMENSIONS'
2568 !      include 'DIMENSIONS.ZSCOPT'
2569 !      include 'DIMENSIONS.COMPAR'
2570 !      include 'COMMON.IOUNITS'
2571 !      include 'COMMON.COMPAR'
2572       logical :: lprn=.true.
2573       integer :: i,ilevel,j,k,jfrag
2574       do jfrag=1,nfrag(1)
2575         nlist_frag(jfrag)=0
2576         do i=1,npiece(jfrag,1)
2577           if (lprn) write (iout,*) "jfrag=",jfrag,&
2578             "i=",i," fragment",ifrag(1,i,jfrag),&
2579             ifrag(2,i,jfrag)
2580           do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2581             do k=1,nlist_frag(jfrag)
2582               if (list_frag(k,jfrag).eq.j) goto 10
2583             enddo
2584             nlist_frag(jfrag)=nlist_frag(jfrag)+1
2585             list_frag(nlist_frag(jfrag),jfrag)=j
2586           enddo
2587   10      continue
2588         enddo
2589       enddo
2590       write (iout,*) "Fragment list"
2591       do j=1,nfrag(1)
2592         write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2593          k=1,nlist_frag(j))
2594       enddo
2595       return
2596       end subroutine fragment_list
2597 !-------------------------------------------------------------------------------
2598       real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2599
2600       use w_comm_local
2601       use control_data, only:symetr
2602       use geometry_data, only:nperm
2603 !      implicit real*8 (a-h,o-z)
2604 !      include 'DIMENSIONS'
2605 !      include 'DIMENSIONS.ZSCOPT'
2606 !      include 'DIMENSIONS.COMPAR'
2607 !      include 'COMMON.IOUNITS'
2608 !      include 'COMMON.COMPAR'
2609 !      include 'COMMON.CHAIN'
2610 !      include 'COMMON.INTERACT'
2611 !      include 'COMMON.VAR'
2612 !      include 'COMMON.CONTROL'
2613       real(kind=8) :: przes(3),obrot(3,3)
2614 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2615 !el      logical :: iadded(nres)
2616 !el      integer :: inumber(2,nres)
2617 !el      common /ccc/ creff,cc,iadded,inumber
2618       logical :: lprn
2619       logical :: non_conv
2620       integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2621       real(kind=8) :: rminrms,rms
2622       if (lprn) then
2623         write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2624         write (iout,*) "npiece",npiece(j,i)
2625         call flush(iout)
2626       endif
2627 !      write (iout,*) "symetr",symetr
2628 !      call flush(iout)
2629       nperm=1
2630       do idup=1,symetr
2631       nperm=nperm*idup
2632       enddo
2633 !      write (iout,*) "nperm",nperm
2634 !      call flush(iout)
2635       do kkk=1,nperm
2636       idup=0
2637       do l=1,nres
2638         iadded(l)=.false.
2639       enddo
2640 !      write (iout,*) "kkk",kkk
2641 !      call flush(iout)
2642       do k=1,npiece(j,i)
2643         if (i.eq.1) then
2644           if (lprn) then
2645             write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2646                ifrag(1,k,j),ifrag(2,k,j)
2647             call flush(iout)
2648           endif
2649           call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2650 !          write (iout,*) "Exit cprep"
2651 !          call flush(iout)
2652 !          write (iout,*) "ii=",ii
2653         else
2654           kk = ipiece(k,j,i)
2655 !          write (iout,*) "kk",kk," npiece",npiece(kk,1)
2656           do l=1,npiece(kk,1)
2657             if (lprn) then
2658               write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2659                 " l=",l," adding fragment",&
2660                 ifrag(1,l,kk),ifrag(2,l,kk)
2661               call flush(iout)
2662             endif
2663             call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2664 !            write (iout,*) "After cprep"
2665 !            call flush(iout)
2666           enddo
2667         endif
2668       enddo
2669       enddo
2670       if (lprn) then
2671         write (iout,*) "tuszukaj"
2672         do kkk=1,nperm
2673           do k=1,idup
2674             write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2675               inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2676           enddo
2677         enddo
2678         call flush(iout)
2679       endif
2680       rminrms=1.0d10
2681       do kkk=1,nperm
2682       call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2683       if (non_conv) then
2684         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2685         rms = 1.0d10
2686       else if (rms.lt.-1.0d-6) then
2687         print *,'Error: rms^2 = ',rms,jcon,i
2688         rms = 1.0d10
2689       else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2690         rms = 0.0d0
2691       endif
2692 !      write (iout,*) "rmsmin", rminrms, "rms", rms
2693       if (rms.le.rminrms) rminrms=rms
2694       enddo
2695       rmscalc = dsqrt(rminrms)
2696 !      write (iout, *) "analysys", rmscalc,anatemp
2697       return
2698       end function rmscalc
2699 !-------------------------------------------------------------------------
2700       subroutine cprep(if1,if2,ishif,idup,kwa)
2701
2702       use w_comm_local
2703       use control_data, only:symetr
2704       use geometry_data, only:nperm,cref,c
2705 !      implicit real*8 (a-h,o-z)
2706 !      include 'DIMENSIONS'
2707 !      include 'DIMENSIONS.ZSCOPT'
2708 !      include 'DIMENSIONS.COMPAR'
2709 !      include 'COMMON.CONTROL'
2710 !      include 'COMMON.IOUNITS'
2711 !      include 'COMMON.COMPAR'
2712 !      include 'COMMON.CHAIN'
2713 !      include 'COMMON.INTERACT'
2714 !      include 'COMMON.VAR'
2715       real(kind=8) :: przes(3),obrot(3,3)
2716 !el      real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2717 !el      logical :: iadded(nres)
2718 !el      integer :: inumber(2,nres)
2719       integer :: iistrart,kwa,blar
2720 !el      common /ccc/ creff,cc,iadded,inumber
2721       integer :: if1,if2,ishif,idup,kkk,l,m
2722 !      write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2723       nperm=1
2724       do blar=1,symetr
2725       nperm=nperm*blar
2726       enddo
2727 !      write (iout,*) "nperm",nperm
2728       kkk=kwa
2729 !      ii=0
2730       do l=if1,if2
2731 !        write (iout,*) "l",l," iadded",iadded(l)
2732 !        call flush(iout)
2733         if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2734         then
2735           idup=idup+1
2736           iadded(l)=.true.
2737           inumber(1,idup)=l
2738           inumber(2,idup)=l+ishif
2739           do m=1,3
2740             creff(m,idup)=cref(m,l,kkk)
2741             cc(m,idup)=c(m,l+ishif)
2742           enddo
2743         endif
2744       enddo
2745       return
2746       end subroutine cprep
2747 !-------------------------------------------------------------------------
2748       real(kind=8) function rmsnat(jcon)
2749
2750       use control_data, only:symetr
2751       use geometry_data, only:nperm,cref,c
2752       use energy_data, only:itype,molnum
2753 !      implicit real*8 (a-h,o-z)
2754 !      include 'DIMENSIONS'
2755 !      include 'DIMENSIONS.ZSCOPT'
2756 !      include 'DIMENSIONS.COMPAR'
2757 !      include 'COMMON.IOUNITS'
2758 !      include 'COMMON.COMPAR'
2759 !      include 'COMMON.CHAIN'
2760 !      include 'COMMON.INTERACT'
2761 !      include 'COMMON.VAR'
2762 !      include 'COMMON.CONTROL'
2763       real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2764       logical :: non_conv
2765       integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2766       real(kind=8) :: rminrms,rmsminsing,rms
2767       rminrms=10.0d10
2768       rmsminsing=10d10
2769       nperm=1
2770       do i=1,symetr
2771        nperm=nperm*i
2772       enddo
2773       do kkk=1,nperm
2774        nnsup=0
2775        do i=1,nres
2776         if (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
2777           nnsup=nnsup+1
2778           do j=1,3
2779             cc(j,nnsup)=c(j,i)
2780             ccref(j,nnsup)=cref(j,i,kkk)
2781           enddo
2782         endif
2783        enddo
2784        call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2785        if (non_conv) then
2786         print *,'Error: FITSQ non-convergent, jcon',jcon,i
2787         rms=1.0d10
2788        else if (rms.lt.-1.0d-6) then
2789         print *,'Error: rms^2 = ',rms,jcon,i
2790         rms = 1.0d10
2791        else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2792         rms=0.0d0
2793        endif
2794        if (rms.le.rminrms) rminrms=rms
2795 !       write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2796       enddo
2797       rmsnat = dsqrt(rminrms)
2798 !      write (iout,*)  "analysys",rmsnat, anatemp
2799 !      liczenie rmsdla pojedynczego lancucha
2800       return
2801       end function rmsnat
2802 !-------------------------------------------------------------------------------
2803       subroutine define_fragments
2804
2805       use geometry_data, only:rad2deg
2806       use energy_data, only:itype,molnum
2807       use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2808 !      implicit real*8 (a-h,o-z)
2809 !      include 'DIMENSIONS'
2810 !      include 'DIMENSIONS.ZSCOPT'
2811 !      include 'DIMENSIONS.COMPAR'
2812 !      include 'COMMON.IOUNITS'
2813 !      include 'COMMON.TIME1'
2814 !      include 'COMMON.FRAG'
2815 !      include 'COMMON.SBRIDGE'
2816 !      include 'COMMON.CONTROL'
2817 !      include 'COMMON.COMPAR'
2818 !      include 'COMMON.CHAIN'
2819 !      include 'COMMON.HEADER'
2820 !      include 'COMMON.GEO'
2821 !      include 'COMMON.CONTACTS'
2822 !      include 'COMMON.PEPTCONT'
2823 !      include 'COMMON.INTERACT'
2824 !      include 'COMMON.NAMES'
2825       integer :: nstrand,istrand(2,nres/2)
2826       integer :: nhairp,ihairp(2,nres/5),mnum
2827       character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2828                           'strand','strand pair'/),shape(strstr))
2829       integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2830
2831       write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2832                      'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2833                  'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2834         ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2835       write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2836         ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2837       write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2838         ' MAXANG_HEL',angcut1_hel*rad2deg
2839       write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2840                      ' MAXANG_BET',angcut1_bet*rad2deg
2841       write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2842                      ' MAXANG_STRAND',angcut1_strand*rad2deg
2843       write (iout,*) 'FRAC_MIN',frac_min_set
2844 ! Find secondary structure elements (helices and beta-sheets)
2845       call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2846          isec_ref)
2847 ! Define primary fragments. First include the helices.
2848       nhairp=0
2849       nstrand=0
2850 ! Merge helices
2851 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2852       if (merge_helices) then
2853       write (iout,*) "Before merging helices: nhfrag",nhfrag
2854       do i=1,nhfrag
2855         write (2,*) hfrag(1,i),hfrag(2,i)
2856       enddo
2857       i=1
2858       do while (i.lt.nhfrag)
2859         if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2860           nhfrag=nhfrag-1
2861           hfrag(2,i)=hfrag(2,i+1)
2862           do j=i+1,nhfrag
2863             hfrag(1,j)=hfrag(1,j+1)
2864             hfrag(2,j)=hfrag(2,j+1)
2865           enddo
2866         endif
2867         i=i+1
2868       enddo
2869       write (iout,*) "After merging helices: nhfrag",nhfrag
2870       do i=1,nhfrag
2871         write (2,*) hfrag(1,i),hfrag(2,i)
2872       enddo
2873       endif
2874       nfrag(1)=nhfrag
2875       do i=1,nhfrag
2876         npiece(i,1)=1
2877         ifrag(1,1,i)=hfrag(1,i)
2878         ifrag(2,1,i)=hfrag(2,i)
2879         n_shift(1,i,1)=0
2880         n_shift(2,i,1)=nshift_hel
2881         ang_cut(i)=angcut_hel
2882         ang_cut1(i)=angcut1_hel
2883         frac_min(i)=frac_min_set
2884         nc_fragm(i,1)=ncfrac_hel
2885         nc_req_setf(i,1)=ncreq_hel
2886         istruct(i)=1
2887       enddo
2888       write (iout,*) "isplit_bet",isplit_bet
2889       if (isplit_bet.gt.1) then
2890 ! Split beta-sheets into strands and store strands as primary fragments.
2891         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2892         do i=1,nstrand
2893           ii=i+nfrag(1)
2894           npiece(ii,1)=1
2895           ifrag(1,1,ii)=istrand(1,i)
2896           ifrag(2,1,ii)=istrand(2,i)
2897           n_shift(1,ii,1)=nshift_strand
2898           n_shift(2,ii,1)=nshift_strand
2899           ang_cut(ii)=angcut_strand
2900           ang_cut1(ii)=angcut1_strand
2901           frac_min(ii)=frac_min_set
2902           nc_fragm(ii,1)=0
2903           nc_req_setf(ii,1)=0
2904           istruct(ii)=3
2905         enddo
2906         nfrag(1)=nfrag(1)+nstrand
2907       else if (isplit_bet.eq.1) then
2908 ! Split only far beta-sheets; does not split hairpins.
2909         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2910         call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2911         do i=1,nhairp
2912           ii=i+nfrag(1)
2913           npiece(ii,1)=1
2914           ifrag(1,1,ii)=ihairp(1,i)
2915           ifrag(2,1,ii)=ihairp(2,i)
2916           n_shift(1,ii,1)=nshift_bet
2917           n_shift(2,ii,1)=nshift_bet
2918           ang_cut(ii)=angcut_bet
2919           ang_cut1(ii)=angcut1_bet
2920           frac_min(ii)=frac_min_set
2921           nc_fragm(ii,1)=ncfrac_bet
2922           nc_req_setf(ii,1)=ncreq_bet
2923           istruct(ii)=2
2924         enddo
2925         nfrag(1)=nfrag(1)+nhairp
2926         do i=1,nstrand
2927           ii=i+nfrag(1)
2928           npiece(ii,1)=1
2929           ifrag(1,1,ii)=istrand(1,i)
2930           ifrag(2,1,ii)=istrand(2,i)
2931           n_shift(1,ii,1)=nshift_strand
2932           n_shift(2,ii,1)=nshift_strand
2933           ang_cut(ii)=angcut_strand
2934           ang_cut1(ii)=angcut1_strand
2935           frac_min(ii)=frac_min_set
2936           nc_fragm(ii,1)=0
2937           nc_req_setf(ii,1)=0
2938           istruct(ii)=3
2939         enddo
2940         nfrag(1)=nfrag(1)+nstrand
2941       else
2942 ! Do not split beta-sheets; each pair of strands is a primary element.
2943         call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2944         do i=1,nhairp
2945           ii=i+nfrag(1)
2946           npiece(ii,1)=1
2947           ifrag(1,1,ii)=ihairp(1,i)
2948           ifrag(2,1,ii)=ihairp(2,i)
2949           n_shift(1,ii,1)=nshift_bet
2950           n_shift(2,ii,1)=nshift_bet
2951           ang_cut(ii)=angcut_bet
2952           ang_cut1(ii)=angcut1_bet
2953           frac_min(ii)=frac_min_set
2954           nc_fragm(ii,1)=ncfrac_bet
2955           nc_req_setf(ii,1)=ncreq_bet
2956           istruct(ii)=2
2957         enddo
2958         nfrag(1)=nfrag(1)+nhairp
2959         do i=1,nbfrag
2960           ii=i+nfrag(1)
2961           npiece(ii,1)=2
2962           ifrag(1,1,ii)=bfrag(1,i)
2963           ifrag(2,1,ii)=bfrag(2,i)
2964           if (bfrag(3,i).lt.bfrag(4,i)) then
2965             ifrag(1,2,ii)=bfrag(3,i)
2966             ifrag(2,2,ii)=bfrag(4,i)
2967           else
2968             ifrag(1,2,ii)=bfrag(4,i)
2969             ifrag(2,2,ii)=bfrag(3,i)
2970           endif
2971           n_shift(1,ii,1)=nshift_bet
2972           n_shift(2,ii,1)=nshift_bet
2973           ang_cut(ii)=angcut_bet
2974           ang_cut1(ii)=angcut1_bet
2975           frac_min(ii)=frac_min_set
2976           nc_fragm(ii,1)=ncfrac_bet
2977           nc_req_setf(ii,1)=ncreq_bet
2978           istruct(ii)=4
2979         enddo
2980         nfrag(1)=nfrag(1)+nbfrag
2981       endif
2982       write (iout,*) "The following primary fragments were found:"
2983       write (iout,*) "Helices:",nhfrag
2984       do i=1,nhfrag
2985         mnum=molnum(i)
2986         i1=ifrag(1,1,i)
2987         i2=ifrag(2,1,i)
2988         it1=itype(i1,mnum)
2989         it2=itype(i2,mnum)
2990         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2991              i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
2992       enddo
2993       write (iout,*) "Hairpins:",nhairp
2994       do i=nhfrag+1,nhfrag+nhairp
2995         i1=ifrag(1,1,i)
2996         i2=ifrag(2,1,i)
2997         it1=itype(i1,molnum(i1))
2998         it2=itype(i2,molnum(i2))
2999         write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
3000              i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2
3001       enddo
3002       write (iout,*) "Far strand pairs:",nbfrag
3003       do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
3004         i1=ifrag(1,1,i)
3005         i2=ifrag(2,1,i)
3006         it1=itype(i1,molnum(i1))
3007         it2=itype(i2,molnum(i1))
3008         i3=ifrag(1,2,i)
3009         i4=ifrag(2,2,i)
3010         it3=itype(i3,molnum(i3))
3011         it4=itype(i4,molnum(i4))
3012         write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
3013              i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2,&
3014                restyp(it3,molnum(i3)),i3,restyp(it4,molnum(i4)),i4
3015       enddo
3016       write (iout,*) "Strands:",nstrand
3017       do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
3018         mnum=molnum(i)
3019         i1=ifrag(1,1,i)
3020         i2=ifrag(2,1,i)
3021         it1=itype(i1,mnum)
3022         it2=itype(i2,mnum)
3023         write (iout,'(i3,2x,a,i4,2x,a,i4)') &
3024              i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
3025       enddo
3026       call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3027         istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3028         nc_fragm(1,1),nc_req_setf(1,1))
3029       write (iout,*) "Fragments after sorting:"
3030       do i=1,nfrag(1)
3031         mnum=molnum(i)
3032         i1=ifrag(1,1,i)
3033         i2=ifrag(2,1,i)
3034         it1=itype(i1,mnum)
3035         it2=itype(i2,mnum)
3036         write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3037              i,restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2
3038         if (npiece(i,1).eq.1) then
3039           write (iout,'(2x,a)') strstr(istruct(i))
3040         else
3041           i1=ifrag(1,2,i)
3042           i2=ifrag(2,2,i)
3043           it1=itype(i1,mnum)
3044           it2=itype(i2,mnum)
3045           write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3046              restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2,strstr(istruct(i))
3047         endif
3048       enddo
3049       return
3050       end subroutine define_fragments
3051 !------------------------------------------------------------------------------
3052       subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3053 !      implicit real*8 (a-h,o-z)
3054 !      include 'DIMENSIONS'
3055 !      include 'DIMENSIONS.ZSCOPT'
3056 !      include 'DIMENSIONS.COMPAR'
3057 !      include 'COMMON.IOUNITS'
3058       integer :: nbfrag,bfrag(4,nres/3)
3059       integer :: nhairp,ihairp(2,nres/5)
3060       integer :: i,j,k
3061       write (iout,*) "Entered find_and_remove_hairpins"
3062       write (iout,*) "nbfrag",nbfrag
3063       do i=1,nbfrag
3064         write (iout,*) i,(bfrag(k,i),k=1,4)
3065       enddo
3066       nhairp=0
3067       i=1
3068       do while (i.le.nbfrag)
3069         write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3070         if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3071         then
3072           write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3073           nhairp=nhairp+1
3074           ihairp(1,nhairp)=bfrag(1,i)
3075           ihairp(2,nhairp)=bfrag(3,i)
3076           nbfrag=nbfrag-1
3077           do j=i,nbfrag
3078             do k=1,4
3079               bfrag(k,j)=bfrag(k,j+1)
3080             enddo
3081           enddo
3082         else
3083           i=i+1
3084         endif
3085       enddo
3086       write (iout,*) "After finding hairpins:"
3087       write (iout,*) "nhairp",nhairp
3088       do i=1,nhairp
3089         write (iout,*) i,ihairp(1,i),ihairp(2,i)
3090       enddo
3091       write (iout,*) "nbfrag",nbfrag
3092       do i=1,nbfrag
3093         write (iout,*) i,(bfrag(k,i),k=1,4)
3094       enddo
3095       return
3096       end subroutine find_and_remove_hairpins
3097 !------------------------------------------------------------------------------
3098       subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3099 !      implicit real*8 (a-h,o-z)
3100 !      include 'DIMENSIONS'
3101 !      include 'DIMENSIONS.ZSCOPT'
3102 !      include 'DIMENSIONS.COMPAR'
3103 !      include 'COMMON.IOUNITS'
3104       integer :: nbfrag,bfrag(4,nres/3)
3105       integer :: nstrand,istrand(2,nres/2)
3106       integer :: nhairp,ihairp(2,nres/5)
3107       logical :: found
3108       integer :: i,k
3109       write (iout,*) "Entered split_beta"
3110       write (iout,*) "nbfrag",nbfrag
3111       do i=1,nbfrag
3112         write (iout,*) i,(bfrag(k,i),k=1,4)
3113       enddo
3114       nstrand=0
3115       do i=1,nbfrag
3116         write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3117         call add_strand(nstrand,istrand,nhairp,ihairp,&
3118            bfrag(1,i),bfrag(2,i),found)
3119         if (bfrag(3,i).lt.bfrag(4,i)) then
3120           write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3121           call add_strand(nstrand,istrand,nhairp,ihairp,&
3122            bfrag(3,i),bfrag(4,i),found)
3123         else
3124           write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3125           call add_strand(nstrand,istrand,nhairp,ihairp,&
3126             bfrag(4,i),bfrag(3,i),found)
3127         endif
3128       enddo
3129       nbfrag=0
3130       write (iout,*) "Strands found:",nstrand
3131       do i=1,nstrand
3132         write (iout,*) i,istrand(1,i),istrand(2,i)
3133       enddo
3134       return
3135       end subroutine split_beta
3136 !------------------------------------------------------------------------------
3137       subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3138 !      implicit real*8 (a-h,o-z)
3139 !      include 'DIMENSIONS'
3140 !      include 'DIMENSIONS.ZSCOPT'
3141 !      include 'DIMENSIONS.COMPAR'
3142 !      include 'COMMON.IOUNITS'
3143       integer :: nstrand,istrand(2,nres/2)
3144       integer :: nhairp,ihairp(2,nres/5)
3145       logical :: found
3146       integer :: is1,is2,j,idelt
3147       found=.false.
3148       do j=1,nhairp
3149         idelt=(ihairp(2,j)-ihairp(1,j))/6
3150         if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3151           write (iout,*) "strand",is1,is2," is part of hairpin",&
3152             ihairp(1,j),ihairp(2,j)
3153           return
3154         endif
3155       enddo
3156       do j=1,nstrand
3157         idelt=(istrand(2,j)-istrand(1,j))/3
3158         if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3159         then
3160 ! The strand already exists in the array; update its ends if necessary.
3161           write (iout,*) "strand",is1,is2," found at position",j,&
3162            ":",istrand(1,j),istrand(2,j)
3163           istrand(1,j)=min0(istrand(1,j),is1)
3164           istrand(2,j)=max0(istrand(2,j),is2)
3165           return
3166         endif
3167       enddo
3168 ! The strand has not been found; add it to the array.
3169       write (iout,*) "strand",is1,is2," added to the array."
3170       found=.true.
3171       nstrand=nstrand+1
3172       istrand(1,nstrand)=is1
3173       istrand(2,nstrand)=is2
3174       return
3175       end subroutine add_strand
3176 !------------------------------------------------------------------------------
3177       subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3178
3179       use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3180       use energy_data, only:itype,maxcont,molnum
3181       use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3182       use compare, only:freeres
3183 !      implicit real*8 (a-h,o-z)
3184 !      include 'DIMENSIONS'
3185 !      include 'DIMENSIONS.ZSCOPT'
3186 !      include 'COMMON.IOUNITS'
3187 !      include 'COMMON.FRAG'
3188 !      include 'COMMON.VAR'
3189 !      include 'COMMON.GEO'
3190 !      include 'COMMON.CHAIN'
3191 !      include 'COMMON.NAMES'
3192 !      include 'COMMON.INTERACT'
3193       integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres+1),&
3194         isecstr(nres+1)
3195       logical :: lprint,lprint_sec,not_done !el,freeres
3196       integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3197       integer :: nstrand,nbeta,nhelix,iii1,jjj1,mnum
3198       real(kind=8) :: p1,p2
3199 !rel      external freeres
3200       character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3201       if (lprint) then
3202         write (iout,*) "entered secondary2",ncont
3203         write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3204         do i=1,ncont
3205           write (iout,*) icont(1,i),icont(2,i)
3206         enddo
3207       endif
3208       do i=1,nres
3209         isecstr(i)=0
3210       enddo
3211       nbfrag=0
3212       nhfrag=0
3213       do i=1,nres
3214         isec(i,1)=0
3215         isec(i,2)=0
3216         nsec(i)=0
3217       enddo
3218
3219 ! finding parallel beta
3220 !d      write (iout,*) '------- looking for parallel beta -----------'
3221       nbeta=0
3222       nstrand=0
3223       do i=1,ncont
3224         i1=icont(1,i)
3225         j1=icont(2,i)
3226         if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3227            .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3228 !d        write (iout,*) "parallel",i1,j1
3229         if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3230           ii1=i1
3231           jj1=j1
3232 !d          write (iout,*) i1,j1
3233           not_done=.true.
3234           do while (not_done)
3235            i1=i1+1
3236            j1=j1+1
3237             do j=1,ncont
3238               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3239                    freeres(i1,j1,nsec,isec)) goto 5
3240             enddo
3241             not_done=.false.
3242   5         continue
3243 !d            write (iout,*) i1,j1,not_done
3244           enddo
3245           j1=j1-1
3246           i1=i1-1
3247           if (i1-ii1.gt.1) then
3248             ii1=max0(ii1-1,1)
3249             jj1=max0(jj1-1,1)
3250             nbeta=nbeta+1
3251             if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3252                      nbeta,ii1,i1,jj1,j1
3253
3254             nbfrag=nbfrag+1
3255             bfrag(1,nbfrag)=ii1+1
3256             bfrag(2,nbfrag)=i1+1
3257             bfrag(3,nbfrag)=jj1+1
3258             bfrag(4,nbfrag)=min0(j1+1,nres)
3259
3260             do ij=ii1,i1
3261              nsec(ij)=nsec(ij)+1
3262              isec(ij,nsec(ij))=nbeta
3263             enddo
3264             do ij=jj1,j1
3265              nsec(ij)=nsec(ij)+1
3266              isec(ij,nsec(ij))=nbeta
3267             enddo
3268
3269            if(lprint_sec) then
3270             nstrand=nstrand+1
3271             if (nbeta.le.9) then
3272               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3273                 "DefPropRes 'strand",nstrand,&
3274                 "' 'num = ",ii1-1,"..",i1-1,"'"
3275             else
3276               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3277                 "DefPropRes 'strand",nstrand,&
3278                 "' 'num = ",ii1-1,"..",i1-1,"'"
3279             endif
3280             nstrand=nstrand+1
3281             if (nbeta.le.9) then
3282               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3283                 "DefPropRes 'strand",nstrand,&
3284                 "' 'num = ",jj1-1,"..",j1-1,"'"
3285             else
3286               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3287                 "DefPropRes 'strand",nstrand,&
3288                 "' 'num = ",jj1-1,"..",j1-1,"'"
3289             endif
3290               write(12,'(a8,4i4)') &
3291                 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3292            endif
3293           endif
3294         endif
3295         endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3296       enddo
3297
3298 ! finding antiparallel beta
3299 !d      write (iout,*) '--------- looking for antiparallel beta ---------'
3300
3301       do i=1,ncont
3302         i1=icont(1,i)
3303         j1=icont(2,i)
3304         if (freeres(i1,j1,nsec,isec)) then
3305           ii1=i1
3306           jj1=j1
3307 !d          write (iout,*) i1,j1
3308
3309           not_done=.true.
3310           do while (not_done)
3311            i1=i1+1
3312            j1=j1-1
3313             do j=1,ncont
3314               if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3315                    freeres(i1,j1,nsec,isec)) goto 6
3316             enddo
3317             not_done=.false.
3318   6         continue
3319 !d            write (iout,*) i1,j1,not_done
3320           enddo
3321           i1=i1-1
3322           j1=j1+1
3323           if (i1-ii1.gt.1) then
3324
3325             nbfrag=nbfrag+1
3326             bfrag(1,nbfrag)=ii1
3327             bfrag(2,nbfrag)=min0(i1+1,nres)
3328             bfrag(3,nbfrag)=min0(jj1+1,nres)
3329             bfrag(4,nbfrag)=j1
3330
3331             nbeta=nbeta+1
3332             iii1=max0(ii1-1,1)
3333             do ij=iii1,i1
3334              nsec(ij)=nsec(ij)+1
3335              if (nsec(ij).le.2) then
3336               isec(ij,nsec(ij))=nbeta
3337              endif
3338             enddo
3339             jjj1=max0(j1-1,1)
3340             do ij=jjj1,jj1
3341              nsec(ij)=nsec(ij)+1
3342              if (nsec(ij).le.2) then
3343               isec(ij,nsec(ij))=nbeta
3344              endif
3345             enddo
3346
3347
3348            if (lprint_sec) then
3349             write (iout,'(a,i3,4i4)')'antiparallel beta',&
3350                          nbeta,ii1-1,i1,jj1,j1-1
3351             nstrand=nstrand+1
3352             if (nstrand.le.9) then
3353               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3354                 "DefPropRes 'strand",nstrand,&
3355                 "' 'num = ",ii1-2,"..",i1-1,"'"
3356             else
3357               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3358                 "DefPropRes 'strand",nstrand,&
3359                 "' 'num = ",ii1-2,"..",i1-1,"'"
3360             endif
3361             nstrand=nstrand+1
3362             if (nstrand.le.9) then
3363               write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3364                 "DefPropRes 'strand",nstrand,&
3365                 "' 'num = ",j1-2,"..",jj1-1,"'"
3366             else
3367               write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3368                 "DefPropRes 'strand",nstrand,&
3369                 "' 'num = ",j1-2,"..",jj1-1,"'"
3370             endif
3371               write(12,'(a8,4i4)') &
3372                 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3373            endif
3374           endif
3375         endif
3376       enddo
3377
3378 !d      write (iout,*) "After beta:",nbfrag
3379 !d      do i=1,nbfrag
3380 !d        write (iout,*) (bfrag(j,i),j=1,4)
3381 !d      enddo
3382
3383       if (nstrand.gt.0.and.lprint_sec) then
3384         write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3385         do i=2,nstrand
3386          if (i.le.9) then
3387           write(12,'(a9,i1,$)') " | strand",i
3388          else
3389           write(12,'(a9,i2,$)') " | strand",i
3390          endif
3391         enddo
3392         write(12,'(a1)') "'"
3393       endif
3394
3395
3396 ! finding alpha or 310 helix
3397
3398       nhelix=0
3399       do i=1,ncont
3400         i1=icont(1,i)
3401         j1=icont(2,i)
3402         p1=phi(i1+2)*rad2deg
3403         p2=0.0
3404         if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3405
3406
3407         if (j1.eq.i1+3 .and. &
3408              ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3409              ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3410 !d          if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3411 !o          if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3412           ii1=i1
3413           jj1=j1
3414           if (nsec(ii1).eq.0) then
3415             not_done=.true.
3416           else
3417             not_done=.false.
3418           endif
3419           do while (not_done)
3420             i1=i1+1
3421             j1=j1+1
3422             do j=1,ncont
3423               if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3424             enddo
3425             not_done=.false.
3426   10        continue
3427             p1=phi(i1+2)*rad2deg
3428             p2=phi(j1+2)*rad2deg
3429             if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3430                                     not_done=.false.
3431
3432 !d           write (iout,*) i1,j1,not_done,p1,p2
3433           enddo
3434           j1=j1+1
3435           if (j1-ii1.gt.4) then
3436             nhelix=nhelix+1
3437 !d            write (iout,*)'helix',nhelix,ii1,j1
3438
3439             nhfrag=nhfrag+1
3440             hfrag(1,nhfrag)=ii1
3441             hfrag(2,nhfrag)=j1
3442
3443             do ij=ii1,j1
3444              nsec(ij)=-1
3445             enddo
3446            if (lprint_sec) then
3447             write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3448             if (nhelix.le.9) then
3449               write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3450                 "DefPropRes 'helix",nhelix,&
3451                 "' 'num = ",ii1-1,"..",j1-2,"'"
3452             else
3453               write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3454                 "DefPropRes 'helix",nhelix,&
3455                 "' 'num = ",ii1-1,"..",j1-2,"'"
3456             endif
3457            endif
3458           endif
3459         endif
3460       enddo
3461
3462       if (nhelix.gt.0.and.lprint_sec) then
3463         write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3464         do i=2,nhelix
3465          if (nhelix.le.9) then
3466           write(12,'(a8,i1,$)') " | helix",i
3467          else
3468           write(12,'(a8,i2,$)') " | helix",i
3469          endif
3470         enddo
3471         write(12,'(a1)') "'"
3472       endif
3473
3474       if (lprint_sec) then
3475        write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3476        write(12,'(a20)') "XMacStand ribbon.mac"
3477       endif
3478
3479       if (lprint) then
3480
3481         write(iout,*) 'UNRES seq:',anatemp
3482         do j=1,nbfrag
3483          write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3484         enddo
3485
3486         do j=1,nhfrag
3487          write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3488         enddo
3489
3490       endif
3491
3492       do j=1,nbfrag
3493         do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3494           isecstr(k)=1
3495         enddo
3496         do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3497           isecstr(k)=1
3498         enddo
3499       enddo
3500       do j=1,nhfrag
3501         do k=hfrag(1,j),hfrag(2,j)
3502           isecstr(k)=2
3503         enddo
3504       enddo
3505       if (lprint) then
3506         write (iout,*)
3507         write (iout,*) "Secondary structure"
3508         do i=1,nres,80
3509           mnum=molnum(i)
3510           ist=i
3511           ien=min0(i+79,nres)
3512           write (iout,*)
3513           write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3514           write (iout,'(80a1)') (onelet(itype(k,mnum)),k=ist,ien)
3515           write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3516         enddo
3517         write (iout,*)
3518       endif
3519       return
3520       end subroutine secondary2
3521 !-------------------------------------------------
3522 !      logical function freeres(i,j,nsec,isec)
3523 !      include 'DIMENSIONS'
3524 !      integer :: isec(nres,4),nsec(nres)
3525 !      integer :: i,j,k,l
3526 !      freeres=.false.
3527 !
3528 !      if (nsec(i).gt.1.or.nsec(j).gt.1) return
3529 !      do k=1,nsec(i)
3530 !        do l=1,nsec(j)
3531 !          if (isec(i,k).eq.isec(j,l)) return
3532 !        enddo
3533 !      enddo
3534 !      freeres=.true.
3535 !      return
3536 !      end function freeres
3537 !-------------------------------------------------
3538        subroutine alloc_compar_arrays(nfrg,nlev)
3539
3540        use energy_data, only:maxcont
3541        use w_comm_local
3542        integer :: nfrg,nlev
3543
3544 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3545 !------------------------
3546 ! commom.contacts
3547 !      common /contacts/
3548       allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3549       allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3550 !------------------------
3551 ! COMMON.COMPAR
3552 !      common /compar/
3553       allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3554       allocate(qfrag(nfrg,2)) !(maxfrag,2)
3555       allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3556       allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3557       allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3558         ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3559         ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3560       allocate(ncont_nat(2,nfrg,nlev+1))
3561       allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3562 !      allocate(nfrag(nlev)) !(maxlevel)
3563       allocate(isnfrag(nlev+2)) !(maxlevel+1)
3564       allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3565       allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3566       allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3567       allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3568       allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3569 !------------------------
3570 ! COMMON.PEPTCONT
3571 !      common /peptcont/
3572 !      integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3573       allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3574       allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3575 !      integer,dimension(:),allocatable :: isec_ref !(maxres)
3576 !------------------------
3577 !      module w_comm_local
3578 !      common /ccc/
3579       allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3580       allocate(iadded(nres)) !(nres)
3581       allocate(inumber(2,nres)) !(2,nres)
3582
3583
3584 !-------------------------------------------------------------------------------
3585       end subroutine alloc_compar_arrays
3586 #endif
3587 !-------------------------------------------------------------------------------
3588       end module conform_compar
3589