1 subroutine read_constr_homology
8 include 'COMMON.CONTROL'
10 include 'COMMON.IOUNITS'
12 include 'COMMON.INTERACT'
13 include 'COMMON.NAMES'
14 include 'COMMON.HOMRESTR'
15 include 'COMMON.HOMOLOGY'
20 c include 'include_unres/COMMON.VAR'
23 c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
25 c common /przechowalnia/ odl_temp(maxres,maxres,max_template),
26 c & sigma_odl_temp(maxres,maxres,max_template)
28 character*24 model_ki_dist, model_ki_angle
29 character*500 controlcard
30 integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
31 integer idomain(max_template,maxres)
37 c FP - Nov. 2014 Temporary specifications for new vars
39 double precision rescore_tmp,x12,y12,z12,rescore2_tmp
41 double precision, dimension (max_template,maxres) :: rescore
42 double precision, dimension (max_template,maxres) :: rescore2
43 double precision, dimension (max_template,maxres) :: rescore3
44 character*24 tpl_k_rescore
45 c -----------------------------------------------------------------
46 c Reading multiple PDB ref structures and calculation of retraints
47 c not using pre-computed ones stored in files model_ki_{dist,angle}
49 c -----------------------------------------------------------------
52 c Alternative: reading from input
53 call card_concat(controlcard)
54 call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
55 call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
56 call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
57 call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
58 call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
59 call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
60 call readi(controlcard,"HOMOL_NSET",homol_nset,1)
61 read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
62 call readi(controlcard,"IHSET",ihset,1)
63 write (iout,*) "homol_nset ",homol_nset
64 if (homol_nset.gt.1)then
65 call card_concat(controlcard)
66 read(controlcard,*) (waga_homology(i),i=1,homol_nset)
67 c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
68 c write(iout,*) "iset homology_weight "
70 c write(iout,*) i,waga_homology(i)
73 iset=mod(kolor,homol_nset)+1
78 c write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
80 cd write (iout,*) "nnt",nnt," nct",nct
92 c Reading HM global scores (prob not required)
95 do k=1,constr_homology
99 c open (4,file="HMscore")
100 c do k=1,constr_homology
101 c read (4,*,end=521) hmscore_tmp
102 c hmscore(k)=hmscore_tmp ! Another transformation can be used
103 c write(*,*) "Model", k, ":", hmscore(k)
114 c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
116 if (read_homol_frag) then
117 call read_klapaucjusz
120 do k=1,constr_homology
122 read(inp,'(a)') pdbfile
123 c Next stament causes error upon compilation (?)
124 c if(me.eq.king.or. .not. out1file)
125 c write (iout,'(2a)') 'PDB data will be read from file ',
126 c & pdbfile(:ilen(pdbfile))
127 write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
128 & pdbfile(:ilen(pdbfile))
129 open(ipdbin,file=pdbfile,status='old',err=33)
131 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
132 & pdbfile(:ilen(pdbfile))
135 c print *,'Begin reading pdb data'
137 c Files containing res sim or local scores (former containing sigmas)
140 write(kic2,'(bz,i2.2)') k
142 tpl_k_rescore="template"//kic2//".sco"
146 call readpdb_template(k)
148 call readpdb(out_template_coord)
159 write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
160 & (crefjlee(j,i+nres),j=1,3)
162 write (iout,*) "read_constr_homology: after reading pdb file"
167 c Distance restraints
170 C Copy the coordinates from reference coordinates (?)
174 c write (iout,*) "c(",j,i,") =",c(j,i)
178 c From read_dist_constr (commented out 25/11/2014 <-> res sim)
180 c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
181 open (ientin,file=tpl_k_rescore,status='old')
182 if (nnt.gt.1) rescore(k,1)=0.0d0
183 do irec=nnt,nct ! loop for reading res sim
185 read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
186 & rescore3_tmp,idomain_tmp
188 idomain(k,i_tmp)=idomain_tmp
189 rescore(k,i_tmp)=rescore_tmp
190 rescore2(k,i_tmp)=rescore2_tmp
191 rescore3(k,i_tmp)=rescore3_tmp
192 write(iout,'(a7,i5,3f10.5,i5)') "rescore",
193 & i_tmp,rescore2_tmp,rescore_tmp,
194 & rescore3_tmp,idomain_tmp
197 read (ientin,*,end=1401) rescore_tmp
199 c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
200 rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
201 c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
206 if (waga_dist.ne.0.0d0) then
214 distal=dsqrt(x12*x12+y12*y12+z12*z12)
215 c write (iout,*) k,i,j,distal,dist2_cut
217 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
218 & .and. distal.le.dist2_cut ) then
224 c write (iout,*) "k",k
225 c write (iout,*) "i",i," j",j," constr_homology",
233 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
235 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
236 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
237 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
239 if (odl(k,ii).le.dist_cut) then
240 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
243 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
244 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
246 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
247 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
251 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
261 c Theta, dihedral and SC retraints
263 if (waga_angle.gt.0.0d0) then
264 c open (ientin,file=tpl_k_sigma_dih,status='old')
265 c do irec=1,maxres-3 ! loop for reading sigma_dih
266 c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
267 c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
268 c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
269 c & sigma_dih(k,i+nnt-1)
274 if (idomain(k,i).eq.0) then
278 dih(k,i)=phiref(i) ! right?
279 c read (ientin,*) sigma_dih(k,i) ! original variant
280 c write (iout,*) "dih(",k,i,") =",dih(k,i)
281 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
282 c & "rescore(",k,i-1,") =",rescore(k,i-1),
283 c & "rescore(",k,i-2,") =",rescore(k,i-2),
284 c & "rescore(",k,i-3,") =",rescore(k,i-3)
286 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
287 & rescore(k,i-2)+rescore(k,i-3))/4.0
288 c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
289 c write (iout,*) "Raw sigmas for dihedral angle restraints"
290 c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
291 c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
292 c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
293 c Instead of res sim other local measure of b/b str reliability possible
294 if (sigma_dih(k,i).ne.0)
295 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
296 c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
301 if (waga_theta.gt.0.0d0) then
302 c open (ientin,file=tpl_k_sigma_theta,status='old')
303 c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
304 c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
305 c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
306 c & sigma_theta(k,i+nnt-1)
311 do i = nnt+2,nct ! right? without parallel.
312 c do i = i=1,nres ! alternative for bounds acc to readpdb?
313 c do i=ithet_start,ithet_end ! with FG parallel.
314 if (idomain(k,i).eq.0) then
318 thetatpl(k,i)=thetaref(i)
319 c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
320 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
321 c & "rescore(",k,i-1,") =",rescore(k,i-1),
322 c & "rescore(",k,i-2,") =",rescore(k,i-2)
323 c read (ientin,*) sigma_theta(k,i) ! 1st variant
324 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
325 & rescore(k,i-2))/3.0
326 c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
327 if (sigma_theta(k,i).ne.0)
328 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
330 c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
331 c rescore(k,i-2) ! right expression ?
332 c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
336 if (waga_d.gt.0.0d0) then
337 c open (ientin,file=tpl_k_sigma_d,status='old')
338 c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
339 c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
340 c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
341 c & sigma_d(k,i+nnt-1)
345 do i = nnt,nct ! right? without parallel.
346 c do i=2,nres-1 ! alternative for bounds acc to readpdb?
347 c do i=loc_start,loc_end ! with FG parallel.
348 if (itype(i).eq.10) cycle
349 if (idomain(k,i).eq.0 ) then
356 c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
357 c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
358 c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
359 c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
360 c sigma_d(k,i)=rescore(k,i) ! right expression ?
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))
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
372 c remove distance restraints not used in any model from the list
373 c shift data in all arrays
375 if (waga_dist.ne.0.0d0) then
381 if (ii_in_use(ii).eq.0.and.liiflag) then
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
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)
404 lim_odl=lim_odl-iishift
410 endif ! .not. klapaucjusz
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
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"
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)
431 write (iout,*) "Dihedral angle restraints from templates"
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)
437 write (iout,*) "Virtual-bond angle restraints from templates"
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)
443 write (iout,*) "SC restraints from templates"
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)
450 c -----------------------------------------------------------------
453 c----------------------------------------------------------------------
454 subroutine read_klapaucjusz
460 include 'COMMON.SETUP'
461 include 'COMMON.CONTROL'
462 include 'COMMON.HOMOLOGY'
463 include 'COMMON.CHAIN'
464 include 'COMMON.IOUNITS'
466 include 'COMMON.INTERACT'
467 include 'COMMON.NAMES'
468 include 'COMMON.HOMRESTR'
469 character*256 fragfile
470 integer ninclust(maxclust),inclust(max_template,maxclust),
471 & nresclust(maxclust),iresclust(maxres,maxclust)
474 character*24 model_ki_dist, model_ki_angle
475 character*500 controlcard
476 integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
477 integer idomain(max_template,maxres)
478 logical lprn /.true./
484 double precision rescore_tmp,x12,y12,z12,rescore2_tmp
485 double precision, dimension (max_template,maxres) :: rescore
486 double precision, dimension (max_template,maxres) :: rescore2
487 character*24 tpl_k_rescore
494 call getenv("FRAGFILE",fragfile)
495 write (iout,*) "read_klapaucjusz ",fragfile
496 open(ientin,file=fragfile,status="old",err=10)
497 read(ientin,*) constr_homology,nclust
503 do k=1,constr_homology
504 read(ientin,'(a)') pdbfile
505 write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
506 & pdbfile(:ilen(pdbfile))
507 open(ipdbin,file=pdbfile,status='old',err=33)
509 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
510 & pdbfile(:ilen(pdbfile))
514 call readpdb_template(k)
517 c chomo(j,i,k)=c(j,i)
527 read(ientin,*) ninclust(i),nresclust(i)
528 read(ientin,*) (inclust(k,i),k=1,ninclust(i))
529 read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
535 do ll = 1,ninclust(l)
543 idomain(k,iresclust(i,l)+1) = 1
545 idomain(k,iresclust(i,l)) = 1
549 c Distance restraints
552 C Copy the coordinates from reference coordinates (?)
556 c write (iout,*) "c(",j,i,") =",c(j,i)
559 call int_from_cart(.true.,.false.)
560 call sc_loc_geom(.false.)
565 if (waga_dist.ne.0.0d0) then
573 distal=dsqrt(x12*x12+y12*y12+z12*z12)
574 c write (iout,*) k,i,j,distal,dist2_cut
576 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
577 & .and. distal.le.dist2_cut ) then
583 c write (iout,*) "k",k
584 c write (iout,*) "i",i," j",j," constr_homology",
592 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
594 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
595 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
596 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
598 if (odl(k,ii).le.dist_cut) then
599 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
602 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
603 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
605 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
606 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
610 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
613 c l_homo(k,ii)=.false.
620 c Theta, dihedral and SC retraints
622 if (waga_angle.gt.0.0d0) then
624 if (idomain(k,i).eq.0) then
629 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
630 & rescore(k,i-2)+rescore(k,i-3))/4.0
631 c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
632 c & " sigma_dihed",sigma_dih(k,i)
633 if (sigma_dih(k,i).ne.0)
634 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
639 if (waga_theta.gt.0.0d0) then
641 if (idomain(k,i).eq.0) then
642 c sigma_theta(k,i)=0.0
645 thetatpl(k,i)=thetaref(i)
646 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
647 & rescore(k,i-2))/3.0
648 if (sigma_theta(k,i).ne.0)
649 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
653 if (waga_d.gt.0.0d0) then
655 if (itype(i).eq.10) cycle
656 if (idomain(k,i).eq.0 ) then
663 sigma_d(k,i)=rescore(k,i)
664 if (sigma_d(k,i).ne.0)
665 & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
666 if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
672 c remove distance restraints not used in any model from the list
673 c shift data in all arrays
675 if (waga_dist.ne.0.0d0) then
681 if (ii_in_use(ii).eq.0.and.liiflag) then
685 if (ii_in_use(ii).ne.0.and..not.liiflag.or.
686 & .not.liiflag.and.ii.eq.lim_odl) then
687 if (ii.eq.lim_odl) then
693 do ki=iistart,lim_odl-iishift
694 ires_homo(ki)=ires_homo(ki+iishift)
695 jres_homo(ki)=jres_homo(ki+iishift)
696 ii_in_use(ki)=ii_in_use(ki+iishift)
697 do k=1,constr_homology
698 odl(k,ki)=odl(k,ki+iishift)
699 sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
700 l_homo(k,ki)=l_homo(k,ki+iishift)
704 lim_odl=lim_odl-iishift
710 write (iout,*) "ires_homo and jres_homo arrays, lim_odl",lim_odl
712 write (iout,*) i,ires_homo(i),jres_homo(i)
716 10 stop "Error in fragment file"