source/wham/src-HCD-5D/read_constr_homology.F

   1       subroutine read_constr_homology
   2
   3       include 'DIMENSIONS'
   4       include 'DIMENSIONS.ZSCOPT'
   5       include 'DIMENSIONS.FREE'
   6 #ifdef MPI
   7       include 'mpif.h'
   8 #endif
   9       include 'COMMON.SETUP'
  10       include 'COMMON.CONTROL'
  11       include 'COMMON.CHAIN'
  12       include 'COMMON.IOUNITS'
  13       include 'COMMON.GEO'
  14       include 'COMMON.INTERACT'
  15       include 'COMMON.NAMES'
  16       include 'COMMON.HOMRESTR'
  17       include 'COMMON.HOMOLOGY'
  18 c
  19 c For new homol impl
  20 c
  21       include 'COMMON.VAR'
  22 c     include 'include_unres/COMMON.VAR'
  23 c
  24
  25 c     double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
  26 c    &                 dist_cut
  27 c     common /przechowalnia/ odl_temp(maxres,maxres,max_template),
  28 c    &    sigma_odl_temp(maxres,maxres,max_template)
  29       character*2 kic2
  30       character*24 model_ki_dist, model_ki_angle
  31       character*500 controlcard
  32       integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
  33       integer idomain(max_template,maxres)
  34       logical lprn /.true./
  35       integer ilen
  36       external ilen
  37       logical liiflag
  38 c
  39 c     FP - Nov. 2014 Temporary specifications for new vars
  40 c
  41       double precision rescore_tmp,x12,y12,z12,rescore2_tmp,
  42      &                 rescore3_tmp
  43       double precision, dimension (max_template,maxres) :: rescore
  44       double precision, dimension (max_template,maxres) :: rescore2
  45       double precision, dimension (max_template,maxres) :: rescore3
  46       character*24 tpl_k_rescore
  47 c -----------------------------------------------------------------
  48 c Reading multiple PDB ref structures and calculation of retraints
  49 c not using pre-computed ones stored in files model_ki_{dist,angle}
  50 c FP (Nov., 2014)
  51 c -----------------------------------------------------------------
  52 c
  53 c
  54 c Alternative: reading from input
  55       call card_concat(controlcard,.true.)
  56       call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
  57       call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
  58       call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
  59       call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
  60       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
  61       call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
  62       call readi(controlcard,"HOMOL_NSET",homol_nset,1)
  63       read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
  64       call readi(controlcard,"IHSET",ihset,1)
  65       if (homol_nset.gt.1)then
  66          call card_concat(controlcard,.true.)
  67          read(controlcard,*) (waga_homology(i),i=1,homol_nset)
  68 c         if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
  69 c          write(iout,*) "iset homology_weight "
  70 c         do i=1,homol_nset
  71 c          write(iout,*) i,waga_homology(i)
  72 c         enddo
  73 c         endif
  74          iset=mod(kolor,homol_nset)+1
  75       else
  76        iset=1
  77        waga_homology(1)=1.0
  78       endif
  79 c     write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
  80
  81 cd      write (iout,*) "nnt",nnt," nct",nct
  82 cd      call flush(iout)
  83
  84
  85       lim_odl=0
  86       lim_dih=0
  87 c
  88 c  New
  89 c
  90       lim_theta=0
  91       lim_xx=0
  92 c
  93 c  Reading HM global scores (prob not required)
  94 c
  95       do i = nnt,nct
  96         do k=1,constr_homology
  97          idomain(k,i)=0
  98         enddo
  99       enddo
 100 c     open (4,file="HMscore")
 101 c     do k=1,constr_homology
 102 c       read (4,*,end=521) hmscore_tmp
 103 c       hmscore(k)=hmscore_tmp ! Another transformation can be used
 104 c       write(*,*) "Model", k, ":", hmscore(k)
 105 c     enddo
 106 c521  continue
 107
 108       ii=0
 109       do i = nnt,nct-2
 110         do j=i+2,nct
 111         ii=ii+1
 112         ii_in_use(ii)=0
 113         enddo
 114       enddo
 115 c     write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
 116
 117       if (read_homol_frag) then
 118         call read_klapaucjusz
 119       else
 120
 121       do k=1,constr_homology
 122
 123         read(inp,'(a)') pdbfile
 124 c  Next stament causes error upon compilation (?)
 125 c       if(me.eq.king.or. .not. out1file)
 126 c         write (iout,'(2a)') 'PDB data will be read from file ',
 127 c    &   pdbfile(:ilen(pdbfile))
 128          write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
 129      &  pdbfile(:ilen(pdbfile))
 130         open(ipdbin,file=pdbfile,status='old',err=33)
 131         goto 34
 132   33    write (iout,'(a,5x,a)') 'Error opening PDB file',
 133      &  pdbfile(:ilen(pdbfile))
 134         stop
 135   34    continue
 136 c        print *,'Begin reading pdb data'
 137 c
 138 c Files containing res sim or local scores (former containing sigmas)
 139 c
 140
 141         write(kic2,'(bz,i2.2)') k
 142
 143         tpl_k_rescore="template"//kic2//".sco"
 144
 145         unres_pdb=.false.
 146         if (read2sigma) then
 147           call readpdb_template(k)
 148         else
 149           call readpdb
 150         endif
 151
 152 c        call readpdb
 153         do i=1,2*nres
 154           do j=1,3
 155             crefjlee(j,i)=c(j,i)
 156           enddo
 157         enddo
 158 #ifdef DEBUG
 159         do i=1,nres
 160           write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
 161      &      (crefjlee(j,i+nres),j=1,3)
 162         enddo
 163         write (iout,*) "read_constr_homology: after reading pdb file"
 164         call flush(iout)
 165 #endif
 166
 167 c
 168 c     Distance restraints
 169 c
 170 c          ... --> odl(k,ii)
 171 C Copy the coordinates from reference coordinates (?)
 172         do i=1,2*nres
 173           do j=1,3
 174             c(j,i)=cref(j,i)
 175 c           write (iout,*) "c(",j,i,") =",c(j,i)
 176           enddo
 177         enddo
 178 c
 179 c From read_dist_constr (commented out 25/11/2014 <-> res sim)
 180 c
 181 c         write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
 182           open (ientin,file=tpl_k_rescore,status='old')
 183           if (nnt.gt.1) rescore(k,1)=0.0d0
 184           do irec=nnt,nct ! loop for reading res sim
 185             if (read2sigma) then
 186              read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
 187      &                                rescore3_tmp,idomain_tmp
 188              i_tmp=i_tmp+nnt-1
 189              idomain(k,i_tmp)=idomain_tmp
 190              rescore(k,i_tmp)=rescore_tmp
 191              rescore2(k,i_tmp)=rescore2_tmp
 192              rescore3(k,i_tmp)=rescore3_tmp
 193              write(iout,'(a7,i5,3f10.5,i5)') "rescore",
 194      &                      i_tmp,rescore2_tmp,rescore_tmp,
 195      &                                rescore3_tmp,idomain_tmp
 196             else
 197              idomain(k,irec)=1
 198              read (ientin,*,end=1401) rescore_tmp
 199
 200 c           rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
 201              rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
 202 c           write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
 203             endif
 204           enddo
 205  1401   continue
 206         close (ientin)
 207         if (waga_dist.ne.0.0d0) then
 208           ii=0
 209           do i = nnt,nct-2
 210             do j=i+2,nct
 211
 212               x12=c(1,i)-c(1,j)
 213               y12=c(2,i)-c(2,j)
 214               z12=c(3,i)-c(3,j)
 215               distal=dsqrt(x12*x12+y12*y12+z12*z12)
 216 c              write (iout,*) k,i,j,distal,dist2_cut
 217
 218             if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
 219      &            .and. distal.le.dist2_cut ) then
 220
 221               ii=ii+1
 222               ii_in_use(ii)=1
 223               l_homo(k,ii)=.true.
 224
 225 c             write (iout,*) "k",k
 226 c             write (iout,*) "i",i," j",j," constr_homology",
 227 c    &                       constr_homology
 228               ires_homo(ii)=i
 229               jres_homo(ii)=j
 230               odl(k,ii)=distal
 231               if (read2sigma) then
 232                 sigma_odl(k,ii)=0
 233                 do ik=i,j
 234                  sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
 235                 enddo
 236                 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
 237                 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
 238      &        sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
 239               else
 240                 if (odl(k,ii).le.dist_cut) then
 241                  sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
 242                 else
 243 #ifdef OLDSIGMA
 244                  sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
 245      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
 246 #else
 247                  sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
 248      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
 249 #endif
 250                 endif
 251               endif
 252               sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
 253             else
 254               ii=ii+1
 255               l_homo(k,ii)=.false.
 256             endif
 257             enddo
 258           enddo
 259         lim_odl=ii
 260         endif
 261 c
 262 c     Theta, dihedral and SC retraints
 263 c
 264         if (waga_angle.gt.0.0d0) then
 265 c         open (ientin,file=tpl_k_sigma_dih,status='old')
 266 c         do irec=1,maxres-3 ! loop for reading sigma_dih
 267 c            read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
 268 c            if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
 269 c            sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
 270 c    &                            sigma_dih(k,i+nnt-1)
 271 c         enddo
 272 c1402   continue
 273 c         close (ientin)
 274           do i = nnt+3,nct
 275             if (idomain(k,i).eq.0) then
 276                sigma_dih(k,i)=0.0
 277                cycle
 278             endif
 279             dih(k,i)=phiref(i) ! right?
 280 c           read (ientin,*) sigma_dih(k,i) ! original variant
 281 c             write (iout,*) "dih(",k,i,") =",dih(k,i)
 282 c             write(iout,*) "rescore(",k,i,") =",rescore(k,i),
 283 c    &                      "rescore(",k,i-1,") =",rescore(k,i-1),
 284 c    &                      "rescore(",k,i-2,") =",rescore(k,i-2),
 285 c    &                      "rescore(",k,i-3,") =",rescore(k,i-3)
 286
 287             sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
 288      &                     rescore(k,i-2)+rescore(k,i-3))/4.0
 289 c            if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
 290 c           write (iout,*) "Raw sigmas for dihedral angle restraints"
 291 c           write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
 292 c           sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
 293 c                          rescore(k,i-2)*rescore(k,i-3)  !  right expression ?
 294 c   Instead of res sim other local measure of b/b str reliability possible
 295             if (sigma_dih(k,i).ne.0)
 296      &      sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
 297 c           sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
 298           enddo
 299           lim_dih=nct-nnt-2
 300         endif
 301
 302         if (waga_theta.gt.0.0d0) then
 303 c         open (ientin,file=tpl_k_sigma_theta,status='old')
 304 c         do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
 305 c            read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
 306 c            sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
 307 c    &                              sigma_theta(k,i+nnt-1)
 308 c         enddo
 309 c1403   continue
 310 c         close (ientin)
 311
 312           do i = nnt+2,nct ! right? without parallel.
 313 c         do i = i=1,nres ! alternative for bounds acc to readpdb?
 314 c         do i=ithet_start,ithet_end ! with FG parallel.
 315              if (idomain(k,i).eq.0) then
 316               sigma_theta(k,i)=0.0
 317               cycle
 318              endif
 319              thetatpl(k,i)=thetaref(i)
 320 c            write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
 321 c            write(iout,*)  "rescore(",k,i,") =",rescore(k,i),
 322 c    &                      "rescore(",k,i-1,") =",rescore(k,i-1),
 323 c    &                      "rescore(",k,i-2,") =",rescore(k,i-2)
 324 c            read (ientin,*) sigma_theta(k,i) ! 1st variant
 325              sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
 326      &                        rescore(k,i-2))/3.0
 327 c             if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
 328              if (sigma_theta(k,i).ne.0)
 329      &       sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
 330
 331 c            sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
 332 c                             rescore(k,i-2) !  right expression ?
 333 c            sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
 334           enddo
 335         endif
 336
 337         if (waga_d.gt.0.0d0) then
 338 c       open (ientin,file=tpl_k_sigma_d,status='old')
 339 c         do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
 340 c            read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
 341 c            sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
 342 c    &                          sigma_d(k,i+nnt-1)
 343 c         enddo
 344 c1404   continue
 345
 346           do i = nnt,nct ! right? without parallel.
 347 c         do i=2,nres-1 ! alternative for bounds acc to readpdb?
 348 c         do i=loc_start,loc_end ! with FG parallel.
 349                if (itype(i).eq.10) cycle
 350                if (idomain(k,i).eq.0 ) then
 351                   sigma_d(k,i)=0.0
 352                   cycle
 353                endif
 354                xxtpl(k,i)=xxref(i)
 355                yytpl(k,i)=yyref(i)
 356                zztpl(k,i)=zzref(i)
 357 c              write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
 358 c              write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
 359 c              write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
 360 c              write(iout,*)  "rescore(",k,i,") =",rescore(k,i)
 361                sigma_d(k,i)=rescore3(k,i) !  right expression ?
 362                if (sigma_d(k,i).ne.0)
 363      &          sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
 364
 365 c              sigma_d(k,i)=hmscore(k)*rescore(k,i) !  right expression ?
 366 c              sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
 367 c              read (ientin,*) sigma_d(k,i) ! 1st variant
 368           enddo
 369         endif
 370       enddo
 371 c
 372 c remove distance restraints not used in any model from the list
 373 c shift data in all arrays
 374 c
 375       if (waga_dist.ne.0.0d0) then
 376         ii=0
 377         liiflag=.true.
 378         do i=nnt,nct-2
 379          do j=i+2,nct
 380           ii=ii+1
 381           if (ii_in_use(ii).eq.0.and.liiflag) then
 382             liiflag=.false.
 383             iistart=ii
 384           endif
 385           if (ii_in_use(ii).ne.0.and..not.liiflag.or.
 386      &                   .not.liiflag.and.ii.eq.lim_odl) then
 387              if (ii.eq.lim_odl) then
 388               iishift=ii-iistart+1
 389              else
 390               iishift=ii-iistart
 391              endif
 392              liiflag=.true.
 393              do ki=iistart,lim_odl-iishift
 394               ires_homo(ki)=ires_homo(ki+iishift)
 395               jres_homo(ki)=jres_homo(ki+iishift)
 396               ii_in_use(ki)=ii_in_use(ki+iishift)
 397               do k=1,constr_homology
 398                odl(k,ki)=odl(k,ki+iishift)
 399                sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
 400                l_homo(k,ki)=l_homo(k,ki+iishift)
 401               enddo
 402              enddo
 403              ii=ii-iishift
 404              lim_odl=lim_odl-iishift
 405           endif
 406          enddo
 407         enddo
 408       endif
 409
 410       endif ! .not. klapaucjusz
 411
 412       if (constr_homology.gt.0) call homology_partition
 413       if (constr_homology.gt.0) call init_int_table
 414 cd      write (iout,*) "homology_partition: lim_theta= ",lim_theta,
 415 cd     & "lim_xx=",lim_xx
 416 c     write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
 417 c     write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
 418 c
 419 c Print restraints
 420 c
 421       if (.not.lprn) return
 422 cd      write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
 423 c      if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
 424        write (iout,*) "Distance restraints from templates"
 425        do ii=1,lim_odl
 426        write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
 427      &  ii,ires_homo(ii),jres_homo(ii),
 428      &  (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
 429      &  ki=1,constr_homology)
 430        enddo
 431        write (iout,*) "Dihedral angle restraints from templates"
 432        do i=nnt+3,nct
 433         write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
 434      &      (rad2deg*dih(ki,i),
 435      &      rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
 436        enddo
 437        write (iout,*) "Virtual-bond angle restraints from templates"
 438        do i=nnt+2,nct
 439         write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
 440      &      (rad2deg*thetatpl(ki,i),
 441      &      rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
 442        enddo
 443        write (iout,*) "SC restraints from templates"
 444        do i=nnt,nct
 445         write(iout,'(i5,100(4f8.2,4x))') i,
 446      &  (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
 447      &   1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
 448        enddo
 449 c      endif
 450 c -----------------------------------------------------------------
 451       return
 452       end
 453 c----------------------------------------------------------------------
 454       subroutine read_klapaucjusz
 455
 456       include 'DIMENSIONS'
 457       include 'DIMENSIONS.ZSCOPT'
 458       include 'DIMENSIONS.FREE'
 459 #ifdef MPI
 460       include 'mpif.h'
 461 #endif
 462       include 'COMMON.SETUP'
 463       include 'COMMON.CONTROL'
 464       include 'COMMON.HOMOLOGY'
 465       include 'COMMON.CHAIN'
 466       include 'COMMON.IOUNITS'
 467       include 'COMMON.GEO'
 468       include 'COMMON.INTERACT'
 469       include 'COMMON.NAMES'
 470       include 'COMMON.HOMRESTR'
 471       character*256 fragfile
 472       integer ninclust(maxclust),inclust(max_template,maxclust),
 473      &  nresclust(maxclust),iresclust(maxres,maxclust)
 474
 475       character*2 kic2
 476       character*24 model_ki_dist, model_ki_angle
 477       character*500 controlcard
 478       integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
 479       integer idomain(max_template,maxres)
 480       logical lprn /.true./
 481       integer ilen
 482       external ilen
 483       logical liiflag
 484 c
 485 c
 486       double precision rescore_tmp,x12,y12,z12,rescore2_tmp
 487       double precision, dimension (max_template,maxres) :: rescore
 488       double precision, dimension (max_template,maxres) :: rescore2
 489       character*24 tpl_k_rescore
 490
 491 c
 492 c For new homol impl
 493 c
 494       include 'COMMON.VAR'
 495 c
 496       call getenv("FRAGFILE",fragfile)
 497       open(ientin,file=fragfile,status="old",err=10)
 498       read(ientin,*) constr_homology,nclust
 499       l_homo = .false.
 500       sigma_theta=0.0
 501       sigma_d=0.0
 502       sigma_dih=0.0
 503 c Read pdb files
 504       do k=1,constr_homology
 505         read(ientin,'(a)') pdbfile
 506         write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
 507      &  pdbfile(:ilen(pdbfile))
 508         open(ipdbin,file=pdbfile,status='old',err=33)
 509         goto 34
 510   33    write (iout,'(a,5x,a)') 'Error opening PDB file',
 511      &  pdbfile(:ilen(pdbfile))
 512         stop
 513   34    continue
 514         unres_pdb=.false.
 515         call readpdb_template(k)
 516 c        do i=1,2*nres
 517 c          do j=1,3
 518 c            chomo(j,i,k)=c(j,i)
 519 c          enddo
 520 c        enddo
 521         do i=1,nres
 522           rescore(k,i)=0.2d0
 523           rescore2(k,i)=1.0d0
 524         enddo
 525       enddo
 526 c Read clusters
 527       do i=1,nclust
 528         read(ientin,*) ninclust(i),nresclust(i)
 529         read(ientin,*) (inclust(k,i),k=1,ninclust(i))
 530         read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
 531       enddo
 532 c
 533 c Loop over clusters
 534 c
 535       do l=1,nclust
 536         do ll = 1,ninclust(l)
 537
 538         k = inclust(ll,l)
 539         do i=1,nres
 540           idomain(k,i)=0
 541         enddo
 542         do i=1,nresclust(l)
 543           if (nnt.gt.1)  then
 544             idomain(k,iresclust(i,l)+1) = 1
 545           else
 546             idomain(k,iresclust(i,l)) = 1
 547           endif
 548         enddo
 549 c
 550 c     Distance restraints
 551 c
 552 c          ... --> odl(k,ii)
 553 C Copy the coordinates from reference coordinates (?)
 554         do i=1,2*nres
 555           do j=1,3
 556             c(j,i)=chomo(j,i,k)
 557 c           write (iout,*) "c(",j,i,") =",c(j,i)
 558           enddo
 559         enddo
 560         call int_from_cart(.true.,.false.)
 561         call sc_loc_geom(.false.)
 562         do i=1,nres
 563           thetaref(i)=theta(i)
 564           phiref(i)=phi(i)
 565         enddo
 566         if (waga_dist.ne.0.0d0) then
 567           ii=0
 568           do i = nnt,nct-2
 569             do j=i+2,nct
 570
 571               x12=c(1,i)-c(1,j)
 572               y12=c(2,i)-c(2,j)
 573               z12=c(3,i)-c(3,j)
 574               distal=dsqrt(x12*x12+y12*y12+z12*z12)
 575 c              write (iout,*) k,i,j,distal,dist2_cut
 576
 577             if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
 578      &            .and. distal.le.dist2_cut ) then
 579
 580               ii=ii+1
 581               ii_in_use(ii)=1
 582               l_homo(k,ii)=.true.
 583
 584 c             write (iout,*) "k",k
 585 c             write (iout,*) "i",i," j",j," constr_homology",
 586 c    &                       constr_homology
 587               ires_homo(ii)=i
 588               jres_homo(ii)=j
 589               odl(k,ii)=distal
 590               if (read2sigma) then
 591                 sigma_odl(k,ii)=0
 592                 do ik=i,j
 593                  sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
 594                 enddo
 595                 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
 596                 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
 597      &        sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
 598               else
 599                 if (odl(k,ii).le.dist_cut) then
 600                  sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
 601                 else
 602 #ifdef OLDSIGMA
 603                  sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
 604      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
 605 #else
 606                  sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
 607      &                      dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
 608 #endif
 609                 endif
 610               endif
 611               sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
 612             else
 613               ii=ii+1
 614 c              l_homo(k,ii)=.false.
 615             endif
 616             enddo
 617           enddo
 618         lim_odl=ii
 619         endif
 620 c
 621 c     Theta, dihedral and SC retraints
 622 c
 623         if (waga_angle.gt.0.0d0) then
 624           do i = nnt+3,nct
 625             if (idomain(k,i).eq.0) then
 626 c               sigma_dih(k,i)=0.0
 627                cycle
 628             endif
 629             dih(k,i)=phiref(i)
 630             sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
 631      &                     rescore(k,i-2)+rescore(k,i-3))/4.0
 632 c            write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
 633 c     &       " sigma_dihed",sigma_dih(k,i)
 634             if (sigma_dih(k,i).ne.0)
 635      &       sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
 636           enddo
 637           lim_dih=nct-nnt-2
 638         endif
 639
 640         if (waga_theta.gt.0.0d0) then
 641           do i = nnt+2,nct
 642              if (idomain(k,i).eq.0) then
 643 c              sigma_theta(k,i)=0.0
 644               cycle
 645              endif
 646              thetatpl(k,i)=thetaref(i)
 647              sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
 648      &                        rescore(k,i-2))/3.0
 649              if (sigma_theta(k,i).ne.0)
 650      &       sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
 651           enddo
 652         endif
 653
 654         if (waga_d.gt.0.0d0) then
 655           do i = nnt,nct
 656                if (itype(i).eq.10) cycle
 657                if (idomain(k,i).eq.0 ) then
 658 c                  sigma_d(k,i)=0.0
 659                   cycle
 660                endif
 661                xxtpl(k,i)=xxref(i)
 662                yytpl(k,i)=yyref(i)
 663                zztpl(k,i)=zzref(i)
 664                sigma_d(k,i)=rescore(k,i)
 665                if (sigma_d(k,i).ne.0)
 666      &          sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
 667                if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
 668           enddo
 669         endif
 670       enddo ! l
 671       enddo ! ll
 672 c
 673 c remove distance restraints not used in any model from the list
 674 c shift data in all arrays
 675 c
 676       if (waga_dist.ne.0.0d0) then
 677         ii=0
 678         liiflag=.true.
 679         do i=nnt,nct-2
 680          do j=i+2,nct
 681           ii=ii+1
 682           if (ii_in_use(ii).eq.0.and.liiflag) then
 683             liiflag=.false.
 684             iistart=ii
 685           endif
 686           if (ii_in_use(ii).ne.0.and..not.liiflag.or.
 687      &                   .not.liiflag.and.ii.eq.lim_odl) then
 688              if (ii.eq.lim_odl) then
 689               iishift=ii-iistart+1
 690              else
 691               iishift=ii-iistart
 692              endif
 693              liiflag=.true.
 694              do ki=iistart,lim_odl-iishift
 695               ires_homo(ki)=ires_homo(ki+iishift)
 696               jres_homo(ki)=jres_homo(ki+iishift)
 697               ii_in_use(ki)=ii_in_use(ki+iishift)
 698               do k=1,constr_homology
 699                odl(k,ki)=odl(k,ki+iishift)
 700                sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
 701                l_homo(k,ki)=l_homo(k,ki+iishift)
 702               enddo
 703              enddo
 704              ii=ii-iishift
 705              lim_odl=lim_odl-iishift
 706           endif
 707          enddo
 708         enddo
 709       endif
 710 #ifdef DEBUG
 711       write (iout,*) "ires_homo and jres_homo arrays, lim_odl",lim_odl
 712       do i=1,lim_odl
 713         write (iout,*) i,ires_homo(i),jres_homo(i)
 714       enddo
 715 #endif
 716       return
 717    10 stop "Error in fragment file"
 718       end