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)
149 call readpdb(out_template_coord)
161 write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
162 & (crefjlee(j,i+nres),j=1,3)
164 write (iout,*) "read_constr_homology: after reading pdb file"
169 c Distance restraints
172 C Copy the coordinates from reference coordinates (?)
176 c write (iout,*) "c(",j,i,") =",c(j,i)
180 c From read_dist_constr (commented out 25/11/2014 <-> res sim)
182 c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore
183 open (ientin,file=tpl_k_rescore,status='old')
184 if (nnt.gt.1) rescore(k,1)=0.0d0
185 do irec=nnt,nct ! loop for reading res sim
187 read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
188 & rescore3_tmp,idomain_tmp
190 idomain(k,i_tmp)=idomain_tmp
191 rescore(k,i_tmp)=rescore_tmp
192 rescore2(k,i_tmp)=rescore2_tmp
193 rescore3(k,i_tmp)=rescore3_tmp
194 write(iout,'(a7,i5,3f10.5,i5)') "rescore",
195 & i_tmp,rescore2_tmp,rescore_tmp,
196 & rescore3_tmp,idomain_tmp
199 read (ientin,*,end=1401) rescore_tmp
201 c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values
202 rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores
203 c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
208 if (waga_dist.ne.0.0d0) then
216 distal=dsqrt(x12*x12+y12*y12+z12*z12)
217 c write (iout,*) k,i,j,distal,dist2_cut
219 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
220 & .and. distal.le.dist2_cut ) then
226 c write (iout,*) "k",k
227 c write (iout,*) "i",i," j",j," constr_homology",
235 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
237 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
238 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
239 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
241 if (odl(k,ii).le.dist_cut) then
242 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
245 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
246 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
248 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
249 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
253 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
263 c Theta, dihedral and SC retraints
265 if (waga_angle.gt.0.0d0) then
266 c open (ientin,file=tpl_k_sigma_dih,status='old')
267 c do irec=1,maxres-3 ! loop for reading sigma_dih
268 c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
269 c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
270 c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
271 c & sigma_dih(k,i+nnt-1)
276 if (idomain(k,i).eq.0) then
280 dih(k,i)=phiref(i) ! right?
281 c read (ientin,*) sigma_dih(k,i) ! original variant
282 c write (iout,*) "dih(",k,i,") =",dih(k,i)
283 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
284 c & "rescore(",k,i-1,") =",rescore(k,i-1),
285 c & "rescore(",k,i-2,") =",rescore(k,i-2),
286 c & "rescore(",k,i-3,") =",rescore(k,i-3)
288 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
289 & rescore(k,i-2)+rescore(k,i-3))/4.0
290 c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
291 c write (iout,*) "Raw sigmas for dihedral angle restraints"
292 c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
293 c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
294 c rescore(k,i-2)*rescore(k,i-3) ! right expression ?
295 c Instead of res sim other local measure of b/b str reliability possible
296 if (sigma_dih(k,i).ne.0)
297 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
298 c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
303 if (waga_theta.gt.0.0d0) then
304 c open (ientin,file=tpl_k_sigma_theta,status='old')
305 c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
306 c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
307 c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
308 c & sigma_theta(k,i+nnt-1)
313 do i = nnt+2,nct ! right? without parallel.
314 c do i = i=1,nres ! alternative for bounds acc to readpdb?
315 c do i=ithet_start,ithet_end ! with FG parallel.
316 if (idomain(k,i).eq.0) then
320 thetatpl(k,i)=thetaref(i)
321 c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
322 c write(iout,*) "rescore(",k,i,") =",rescore(k,i),
323 c & "rescore(",k,i-1,") =",rescore(k,i-1),
324 c & "rescore(",k,i-2,") =",rescore(k,i-2)
325 c read (ientin,*) sigma_theta(k,i) ! 1st variant
326 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
327 & rescore(k,i-2))/3.0
328 c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
329 if (sigma_theta(k,i).ne.0)
330 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
332 c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
333 c rescore(k,i-2) ! right expression ?
334 c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
338 if (waga_d.gt.0.0d0) then
339 c open (ientin,file=tpl_k_sigma_d,status='old')
340 c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
341 c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
342 c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
343 c & sigma_d(k,i+nnt-1)
347 do i = nnt,nct ! right? without parallel.
348 c do i=2,nres-1 ! alternative for bounds acc to readpdb?
349 c do i=loc_start,loc_end ! with FG parallel.
350 if (itype(i).eq.10) cycle
351 if (idomain(k,i).eq.0 ) then
358 c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
359 c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
360 c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
361 c write(iout,*) "rescore(",k,i,") =",rescore(k,i)
362 c sigma_d(k,i)=rescore(k,i) ! right expression ?
363 sigma_d(k,i)=rescore3(k,i) ! right expression ?
364 if (sigma_d(k,i).ne.0)
365 & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
367 c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
368 c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
369 c read (ientin,*) sigma_d(k,i) ! 1st variant
374 c remove distance restraints not used in any model from the list
375 c shift data in all arrays
377 if (waga_dist.ne.0.0d0) then
383 if (ii_in_use(ii).eq.0.and.liiflag) then
387 if (ii_in_use(ii).ne.0.and..not.liiflag.or.
388 & .not.liiflag.and.ii.eq.lim_odl) then
389 if (ii.eq.lim_odl) then
395 do ki=iistart,lim_odl-iishift
396 ires_homo(ki)=ires_homo(ki+iishift)
397 jres_homo(ki)=jres_homo(ki+iishift)
398 ii_in_use(ki)=ii_in_use(ki+iishift)
399 do k=1,constr_homology
400 odl(k,ki)=odl(k,ki+iishift)
401 sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
402 l_homo(k,ki)=l_homo(k,ki+iishift)
406 lim_odl=lim_odl-iishift
412 endif ! .not. klapaucjusz
414 if (constr_homology.gt.0) call homology_partition
415 if (constr_homology.gt.0) call init_int_table
416 cd write (iout,*) "homology_partition: lim_theta= ",lim_theta,
417 cd & "lim_xx=",lim_xx
418 c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
419 c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
423 if (.not.lprn) return
424 cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
425 c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
426 write (iout,*) "Distance restraints from templates"
428 write(iout,'(3i5,100(2f8.2,1x,l1,4x))')
429 & ii,ires_homo(ii),jres_homo(ii),
430 & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii),
431 & ki=1,constr_homology)
433 write (iout,*) "Dihedral angle restraints from templates"
435 write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
436 & (rad2deg*dih(ki,i),
437 & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology)
439 write (iout,*) "Virtual-bond angle restraints from templates"
441 write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)),
442 & (rad2deg*thetatpl(ki,i),
443 & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology)
445 write (iout,*) "SC restraints from templates"
447 write(iout,'(i5,100(4f8.2,4x))') i,
448 & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
449 & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
452 c -----------------------------------------------------------------
455 c----------------------------------------------------------------------
456 subroutine read_klapaucjusz
462 include 'COMMON.SETUP'
463 include 'COMMON.CONTROL'
464 include 'COMMON.HOMOLOGY'
465 include 'COMMON.CHAIN'
466 include 'COMMON.IOUNITS'
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)
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./
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
496 call getenv("FRAGFILE",fragfile)
497 write (iout,*) "read_klapaucjusz ",fragfile
498 open(ientin,file=fragfile,status="old",err=10)
499 read(ientin,*) constr_homology,nclust
505 do k=1,constr_homology
506 read(ientin,'(a)') pdbfile
507 write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
508 & pdbfile(:ilen(pdbfile))
509 open(ipdbin,file=pdbfile,status='old',err=33)
511 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
512 & pdbfile(:ilen(pdbfile))
516 call readpdb_template(k)
519 c chomo(j,i,k)=c(j,i)
529 read(ientin,*) ninclust(i),nresclust(i)
530 read(ientin,*) (inclust(k,i),k=1,ninclust(i))
531 read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
537 do ll = 1,ninclust(l)
545 idomain(k,iresclust(i,l)+1) = 1
547 idomain(k,iresclust(i,l)) = 1
551 c Distance restraints
554 C Copy the coordinates from reference coordinates (?)
558 c write (iout,*) "c(",j,i,") =",c(j,i)
561 call int_from_cart(.true.,.false.)
562 call sc_loc_geom(.false.)
567 if (waga_dist.ne.0.0d0) then
575 distal=dsqrt(x12*x12+y12*y12+z12*z12)
576 c write (iout,*) k,i,j,distal,dist2_cut
578 if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
579 & .and. distal.le.dist2_cut ) then
585 c write (iout,*) "k",k
586 c write (iout,*) "i",i," j",j," constr_homology",
594 sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik)
596 sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1)
597 if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) =
598 & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
600 if (odl(k,ii).le.dist_cut) then
601 sigma_odl(k,ii)=rescore(k,i)+rescore(k,j)
604 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
605 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
607 sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
608 & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
612 sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii))
615 c l_homo(k,ii)=.false.
622 c Theta, dihedral and SC retraints
624 if (waga_angle.gt.0.0d0) then
626 if (idomain(k,i).eq.0) then
631 sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
632 & rescore(k,i-2)+rescore(k,i-3))/4.0
633 c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
634 c & " sigma_dihed",sigma_dih(k,i)
635 if (sigma_dih(k,i).ne.0)
636 & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
641 if (waga_theta.gt.0.0d0) then
643 if (idomain(k,i).eq.0) then
644 c sigma_theta(k,i)=0.0
647 thetatpl(k,i)=thetaref(i)
648 sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
649 & rescore(k,i-2))/3.0
650 if (sigma_theta(k,i).ne.0)
651 & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i))
655 if (waga_d.gt.0.0d0) then
657 if (itype(i).eq.10) cycle
658 if (idomain(k,i).eq.0 ) then
665 sigma_d(k,i)=rescore(k,i)
666 if (sigma_d(k,i).ne.0)
667 & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i))
668 if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
674 c remove distance restraints not used in any model from the list
675 c shift data in all arrays
677 if (waga_dist.ne.0.0d0) then
683 if (ii_in_use(ii).eq.0.and.liiflag) then
687 if (ii_in_use(ii).ne.0.and..not.liiflag.or.
688 & .not.liiflag.and.ii.eq.lim_odl) then
689 if (ii.eq.lim_odl) then
695 do ki=iistart,lim_odl-iishift
696 ires_homo(ki)=ires_homo(ki+iishift)
697 jres_homo(ki)=jres_homo(ki+iishift)
698 ii_in_use(ki)=ii_in_use(ki+iishift)
699 do k=1,constr_homology
700 odl(k,ki)=odl(k,ki+iishift)
701 sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
702 l_homo(k,ki)=l_homo(k,ki+iishift)
706 lim_odl=lim_odl-iishift
712 write (iout,*) "ires_homo and jres_homo arrays, lim_odl",lim_odl
714 write (iout,*) i,ires_homo(i),jres_homo(i)
718 10 stop "Error in fragment file"