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
40 double precision, dimension (max_template,maxres) :: rescore
41 double precision, dimension (max_template,maxres) :: rescore2
42 character*24 tpl_k_rescore
43 c -----------------------------------------------------------------
44 c Reading multiple PDB ref structures and calculation of retraints
45 c not using pre-computed ones stored in files model_ki_{dist,angle}
47 c -----------------------------------------------------------------
50 c Alternative: reading from input
51 call card_concat(controlcard)
52 call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0)
53 call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0)
54 call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new
55 call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new
56 call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
57 call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
58 call readi(controlcard,"HOMOL_NSET",homol_nset,1)
59 read2sigma=(index(controlcard,'READ2SIGMA').gt.0)
60 call readi(controlcard,"IHSET",ihset,1)
61 write (iout,*) "homol_nset ",homol_nset
62 if (homol_nset.gt.1)then
63 call card_concat(controlcard)
64 read(controlcard,*) (waga_homology(i),i=1,homol_nset)
65 c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
66 c write(iout,*) "iset homology_weight "
68 c write(iout,*) i,waga_homology(i)
71 iset=mod(kolor,homol_nset)+1
76 c write(iout,*) "waga_homology(",iset,")",waga_homology(iset)
78 cd write (iout,*) "nnt",nnt," nct",nct
90 c Reading HM global scores (prob not required)
93 do k=1,constr_homology
97 c open (4,file="HMscore")
98 c do k=1,constr_homology
99 c read (4,*,end=521) hmscore_tmp
100 c hmscore(k)=hmscore_tmp ! Another transformation can be used
101 c write(*,*) "Model", k, ":", hmscore(k)
112 c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
114 if (read_homol_frag) then
115 call read_klapaucjusz
118 do k=1,constr_homology
120 read(inp,'(a)') pdbfile
121 c Next stament causes error upon compilation (?)
122 c if(me.eq.king.or. .not. out1file)
123 c write (iout,'(2a)') 'PDB data will be read from file ',
124 c & pdbfile(:ilen(pdbfile))
125 write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file',
126 & pdbfile(:ilen(pdbfile))
127 open(ipdbin,file=pdbfile,status='old',err=33)
129 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
130 & pdbfile(:ilen(pdbfile))
133 c print *,'Begin reading pdb data'
135 c Files containing res sim or local scores (former containing sigmas)
138 write(kic2,'(bz,i2.2)') k
140 tpl_k_rescore="template"//kic2//".sco"
144 call readpdb_template(k)
146 call readpdb(out_template_coord)
157 write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
158 & (crefjlee(j,i+nres),j=1,3)
160 write (iout,*) "read_constr_homology: after reading pdb file"
165 c Distance restraints
168 C Copy the coordinates from reference coordinates (?)
172 c write (iout,*) "c(",j,i,") =",c(j,i)
176 c From read_dist_constr (commented out 25/11/2014 <-> res sim)
178 c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
179 open (ientin,file=tpl_k_rescore,status='old')
180 if (nnt.gt.1) rescore(k,1)=0.0d0
181 do irec=nnt,nct ! loop for reading res sim
183 read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
186 idomain(k,i_tmp)=idomain_tmp
187 rescore(k,i_tmp)=rescore_tmp
188 rescore2(k,i_tmp)=rescore2_tmp
189 write(iout,'(a7,i5,2f10.5,i5)') "rescore",
190 & i_tmp,rescore2_tmp,rescore_tmp,
194 read (ientin,*,end=1401) rescore_tmp
196 c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
197 rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
198 c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
203 if (waga_dist.ne.0.0d0) then
211 distal=dsqrt(x12*x12+y12*y12+z12*z12)
212 c write (iout,*) k,i,j,distal,dist2_cut
214 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
215 & .and. distal.le.dist2_cut ) then
221 c write (iout,*) "k",k
222 c write (iout,*) "i",i," j",j," constr_homology",
230 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
232 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
233 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
234 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
236 if (odl(k,ii).le.dist_cut) then
237 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
240 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
241 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
243 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
244 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
248 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
258 c Theta, dihedral and SC retraints
260 if (waga_angle.gt.0.0d0) then
261 c open (ientin,file=tpl_k_sigma_dih,status='old')
262 c do irec=1,maxres-3 ! loop for reading sigma_dih
263 c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
264 c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
265 c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
266 c & sigma_dih(k,i+nnt-1)
271 if (idomain(k,i).eq.0) then
275 dih(k,i)=phiref(i) ! right?
276 c read (ientin,*) sigma_dih(k,i) ! original variant
277 c write (iout,*) "dih(",k,i,") =",dih(k,i)
278 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
279 c & "rescore(",k,i-1,") =",rescore(k,i-1),
280 c & "rescore(",k,i-2,") =",rescore(k,i-2),
281 c & "rescore(",k,i-3,") =",rescore(k,i-3)
283 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
284 & rescore(k,i-2)+rescore(k,i-3))/4.0
285 c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
286 c write (iout,*) "Raw sigmas for dihedral angle restraints"
287 c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
288 c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
289 c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
290 c Instead of res sim other local measure of b/b str reliability possible
291 if (sigma_dih(k,i).ne.0)
292 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
293 c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
298 if (waga_theta.gt.0.0d0) then
299 c open (ientin,file=tpl_k_sigma_theta,status='old')
300 c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
301 c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
302 c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
303 c & sigma_theta(k,i+nnt-1)
308 do i = nnt+2,nct ! right? without parallel.
309 c do i = i=1,nres ! alternative for bounds acc to readpdb?
310 c do i=ithet_start,ithet_end ! with FG parallel.
311 if (idomain(k,i).eq.0) then
315 thetatpl(k,i)=thetaref(i)
316 c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
317 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
318 c & "rescore(",k,i-1,") =",rescore(k,i-1),
319 c & "rescore(",k,i-2,") =",rescore(k,i-2)
320 c read (ientin,*) sigma_theta(k,i) ! 1st variant
321 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
322 & rescore(k,i-2))/3.0
323 c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
324 if (sigma_theta(k,i).ne.0)
325 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
327 c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
328 c rescore(k,i-2) ! right expression ?
329 c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
333 if (waga_d.gt.0.0d0) then
334 c open (ientin,file=tpl_k_sigma_d,status='old')
335 c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
336 c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
337 c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
338 c & sigma_d(k,i+nnt-1)
342 do i = nnt,nct ! right? without parallel.
343 c do i=2,nres-1 ! alternative for bounds acc to readpdb?
344 c do i=loc_start,loc_end ! with FG parallel.
345 if (itype(i).eq.10) cycle
346 if (idomain(k,i).eq.0 ) then
353 c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
354 c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
355 c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
356 c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
357 sigma_d(k,i)=rescore(k,i) ! right expression ?
358 if (sigma_d(k,i).ne.0)
359 & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
361 c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
362 c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
363 c read (ientin,*) sigma_d(k,i) ! 1st variant
368 c remove distance restraints not used in any model from the list
369 c shift data in all arrays
371 if (waga_dist.ne.0.0d0) then
377 if (ii_in_use(ii).eq.0.and.liiflag) then
381 if (ii_in_use(ii).ne.0.and..not.liiflag.or.
382 & .not.liiflag.and.ii.eq.lim_odl) then
383 if (ii.eq.lim_odl) then
389 do ki=iistart,lim_odl-iishift
390 ires_homo(ki)=ires_homo(ki+iishift)
391 jres_homo(ki)=jres_homo(ki+iishift)
392 ii_in_use(ki)=ii_in_use(ki+iishift)
393 do k=1,constr_homology
394 odl(k,ki)=odl(k,ki+iishift)
395 sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
396 l_homo(k,ki)=l_homo(k,ki+iishift)
400 lim_odl=lim_odl-iishift
406 endif ! .not. klapaucjusz
408 if (constr_homology.gt.0) call homology_partition
409 if (constr_homology.gt.0) call init_int_table
410 cd write (iout,*) "homology_partition: lim_theta= ",lim_theta,
411 cd & "lim_xx=",lim_xx
412 c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
413 c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
417 if (.not.lprn) return
418 cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
419 c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
420 write (iout,*) "Distance restraints from templates"
422 write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
423 & ii,ires_homo(ii),jres_homo(ii),
424 & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
425 & ki=1,constr_homology)
427 write (iout,*) "Dihedral angle restraints from templates"
429 write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
430 & (rad2deg*dih(ki,i),
431 & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
433 write (iout,*) "Virtual-bond angle restraints from templates"
435 write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
436 & (rad2deg*thetatpl(ki,i),
437 & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
439 write (iout,*) "SC restraints from templates"
441 write(iout,'(i5,100(4f8.2,4x))') i,
442 & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
443 & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
446 c -----------------------------------------------------------------
449 c----------------------------------------------------------------------
450 subroutine read_klapaucjusz
456 include 'COMMON.SETUP'
457 include 'COMMON.CONTROL'
458 include 'COMMON.HOMOLOGY'
459 include 'COMMON.CHAIN'
460 include 'COMMON.IOUNITS'
462 include 'COMMON.INTERACT'
463 include 'COMMON.NAMES'
464 include 'COMMON.HOMRESTR'
465 character*256 fragfile
466 integer ninclust(maxclust),inclust(max_template,maxclust),
467 & nresclust(maxclust),iresclust(maxres,maxclust)
470 character*24 model_ki_dist, model_ki_angle
471 character*500 controlcard
472 integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
473 integer idomain(max_template,maxres)
474 logical lprn /.true./
480 double precision rescore_tmp,x12,y12,z12,rescore2_tmp
481 double precision, dimension (max_template,maxres) :: rescore
482 double precision, dimension (max_template,maxres) :: rescore2
483 character*24 tpl_k_rescore
490 call getenv("FRAGFILE",fragfile)
491 write (iout,*) "read_klapaucjusz ",fragfile
492 open(ientin,file=fragfile,status="old",err=10)
493 read(ientin,*) constr_homology,nclust
499 do k=1,constr_homology
500 read(ientin,'(a)') pdbfile
501 write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
502 & pdbfile(:ilen(pdbfile))
503 open(ipdbin,file=pdbfile,status='old',err=33)
505 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
506 & pdbfile(:ilen(pdbfile))
510 call readpdb_template(k)
513 c chomo(j,i,k)=c(j,i)
523 read(ientin,*) ninclust(i),nresclust(i)
524 read(ientin,*) (inclust(k,i),k=1,ninclust(i))
525 read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
531 do ll = 1,ninclust(l)
539 idomain(k,iresclust(i,l)+1) = 1
541 idomain(k,iresclust(i,l)) = 1
545 c Distance restraints
548 C Copy the coordinates from reference coordinates (?)
552 c write (iout,*) "c(",j,i,") =",c(j,i)
555 call int_from_cart(.true.,.false.)
556 call sc_loc_geom(.false.)
561 if (waga_dist.ne.0.0d0) then
569 distal=dsqrt(x12*x12+y12*y12+z12*z12)
570 c write (iout,*) k,i,j,distal,dist2_cut
572 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
573 & .and. distal.le.dist2_cut ) then
579 c write (iout,*) "k",k
580 c write (iout,*) "i",i," j",j," constr_homology",
588 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
590 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
591 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
592 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
594 if (odl(k,ii).le.dist_cut) then
595 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
598 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
599 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
601 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
602 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
606 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
609 c l_homo(k,ii)=.false.
616 c Theta, dihedral and SC retraints
618 if (waga_angle.gt.0.0d0) then
620 if (idomain(k,i).eq.0) then
625 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
626 & rescore(k,i-2)+rescore(k,i-3))/4.0
627 c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
628 c & " sigma_dihed",sigma_dih(k,i)
629 if (sigma_dih(k,i).ne.0)
630 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
635 if (waga_theta.gt.0.0d0) then
637 if (idomain(k,i).eq.0) then
638 c sigma_theta(k,i)=0.0
641 thetatpl(k,i)=thetaref(i)
642 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
643 & rescore(k,i-2))/3.0
644 if (sigma_theta(k,i).ne.0)
645 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
649 if (waga_d.gt.0.0d0) then
651 if (itype(i).eq.10) cycle
652 if (idomain(k,i).eq.0 ) then
659 sigma_d(k,i)=rescore(k,i)
660 if (sigma_d(k,i).ne.0)
661 & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
662 if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
668 c remove distance restraints not used in any model from the list
669 c shift data in all arrays
671 if (waga_dist.ne.0.0d0) then
677 if (ii_in_use(ii).eq.0.and.liiflag) then
681 if (ii_in_use(ii).ne.0.and..not.liiflag.or.
682 & .not.liiflag.and.ii.eq.lim_odl) then
683 if (ii.eq.lim_odl) then
689 do ki=iistart,lim_odl-iishift
690 ires_homo(ki)=ires_homo(ki+iishift)
691 jres_homo(ki)=jres_homo(ki+iishift)
692 ii_in_use(ki)=ii_in_use(ki+iishift)
693 do k=1,constr_homology
694 odl(k,ki)=odl(k,ki+iishift)
695 sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
696 l_homo(k,ki)=l_homo(k,ki+iishift)
700 lim_odl=lim_odl-iishift
706 write (iout,*) "ires_homo and jres_homo arrays, lim_odl",lim_odl
708 write (iout,*) i,ires_homo(i),jres_homo(i)
712 10 stop "Error in fragment file"