2 !-----------------------------------------------------------------------------
5 use geometry_data, only:nres
7 use geometry, only:dist
8 use regularize_, only:fitsq
16 ! include "COMMON.MPI"
19 !-----------------------------------------------------------------------------
22 !-----------------------------------------------------------------------------
25 !-----------------------------------------------------------------------------
27 !-----------------------------------------------------------------------------
28 subroutine conf_compar(jcon,lprn,print_class)
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
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'
51 ! include 'COMMON.MPI'
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 call angnorm12(rmsang)
69 ! Level 1: check secondary and supersecondary structure
70 call elecont(lprn,ncont,icont,nnt,nct)
72 write (iout,*) "elecont finished"
75 call secondary2(lprn,.false.,ncont,icont,isecstr)
77 write (iout,*) "secondary2 finished"
80 call contact(lprn,ncontsc,icontsc,nnt,nct)
82 write(iout,*) "Assigning electrostatic contacts"
85 call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,&
88 write(iout,*) "Assigning sidechain contacts"
91 call contacts_between_fragments(lprn,3,ncontsc,icontsc,&
92 nsccont_frag,isccont_frag)
94 write(iout,*) "--> After contacts_between_fragments"
98 do j=1,isnfrag(nlevel+1)
105 write (iout,'(80(1h=))')
106 write (iout,*) "Level",1," fragment",j
107 write (iout,'(80(1h=))')
110 rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
111 ! Compare electrostatic contacts in the current conf with that in the native
113 if (lprn) write (iout,*) &
114 "Comparing electrostatic contact map and local structure"
116 ncnat=ncont_frag_ref(ind)
117 ! write (iout,*) "before match_contact:",nc_fragm(j,1),
120 call match_secondary(j,isecstr,nsec_match,lprn)
121 if (lprn) write (iout,*) "Fragment",j," nsec_match",&
122 nsec_match," length",len_frag(j,1)," min_len",&
123 frac_sec*len_frag(j,1)
124 if (nsec_match.lt.frac_sec*len_frag(j,1)) then
126 if (lprn) write (iout,*) "Fragment",j,&
127 " has incorrect secondary structure"
130 if (lprn) write (iout,*) "Fragment",j,&
131 " has correct secondary structure"
133 if (ielecont(j,1).gt.0) then
134 call match_contact(ishif1,ishif2,nc_match,ncon_match,&
135 ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
136 ncont_frag(ind),icont_frag(1,1,ind),&
137 j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
138 nc_req_setf(j,1),istruct(j),.true.,lprn)
139 else if (isccont(j,1).gt.0) then
140 call match_contact(ishif1,ishif2,nc_match,ncon_match,&
141 nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
142 nsccont_frag(ind),isccont_frag(1,1,ind),&
143 j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
144 nc_req_setf(j,1),istruct(j),.true.,lprn)
145 else if (iloc(j).gt.0) then
146 ! write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
147 call match_contact(ishif1,ishif2,nc_match,ncon_match,&
148 0,icont_frag_ref(1,1,ind),&
149 ncont_frag(ind),icont_frag(1,1,ind),&
150 j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),&
151 0,istruct(j),.true.,lprn)
152 ! write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
157 if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
159 qfrag(j,1)=qwolynes(1,j)
160 if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
161 if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
162 ! write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
163 if (irms(j,1).gt.0) then
164 if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
171 do while (rms.gt.rmscutfrag(1,j,1) .and. &
172 ishiff.lt.n_shift(1,j,1))
174 rms=rmscalc(-ishiff,1,j,jcon,lprn)
175 ! write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
176 ! & " rms",rms," rmscut",rmscutfrag(1,j,1)
177 if (lprn) write (iout,*) "rms",rmsfrag(j,1)
178 if (rms.gt.rmscutfrag(1,j,1)) then
179 rms=rmscalc(ishiff,1,j,jcon,lprn)
180 ! write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
183 if (lprn) write (iout,*) "rms",rmsfrag(j,1)
185 ! write (iout,*) "After loop: rms",rms,
186 ! & " rmscut",rmscutfrag(1,j,1)
187 ! write (iout,*) "iclass_rms",iclass_rms
188 if (rms.le.rmscutfrag(1,j,1)) then
193 ! write (iout,*) "iclass_rms",iclass_rms
195 ! write (iout,*) "ishif",ishif
196 if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
200 ! write (iout,*) "ishif",ishif," iclass",iclass(j,1),
201 ! & " iclass_rms",iclass_rms
202 if (nc_match.gt.0 .and. iclass_rms.gt.0) then
204 iclass(j,1)=iclass(j,1)+6
206 iclass(j,1)=iclass(j,1)+2
209 ncont_nat(1,j,1)=nc_match
210 ncont_nat(2,j,1)=ncon_match
212 ! write (iout,*) "iclass",iclass(j,1)
214 ! Next levels: Check arrangements of elementary fragments.
217 if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
219 write (iout,'(80(1h=))')
220 write (iout,*) "Level",i," fragment",j
221 write (iout,'(80(1h=))')
223 ! If an elementary fragment doesn't exist, don't check higher hierarchy levels.
226 if (iclass(ik,1).eq.0) then
231 if (i.eq.2 .and. ielecont(j,i).gt.0) then
234 if (lprn) write (iout,*) &
235 "Comparing electrostatic contact map: fragments",&
236 ipiece(1,j,i),ipiece(2,j,i)," ind",ind
237 call match_contact(ishif1,ishif2,nc_match,ncon_match,&
238 ncont_frag_ref(ind),icont_frag_ref(1,1,ind),&
239 ncont_frag(ind),icont_frag(1,1,ind),&
240 j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
241 nc_req_setf(j,i),2,.false.,lprn)
243 if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
244 if (nc_match.gt.0) then
251 ncont_nat(1,j,i)=nc_match
252 ncont_nat(2,j,i)=ncon_match
254 else if (i.eq.2 .and. isccont(j,i).gt.0) then
257 if (lprn) write (iout,*) &
258 "Comparing sidechain contact map: fragments",&
259 ipiece(1,j,i),ipiece(2,j,i)," ind",ind
260 call match_contact(ishif1,ishif2,nc_match,ncon_match,&
261 nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),&
262 nsccont_frag(ind),isccont_frag(1,1,ind),&
263 j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),&
264 nc_req_setf(j,i),2,.false.,lprn)
266 if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
267 if (nc_match.gt.0) then
274 ncont_nat(1,j,i)=nc_match
275 ncont_nat(2,j,i)=ncon_match
277 else if (i.eq.2) then
281 if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
282 if (lprn) write (iout,*) &
283 "Comparing rms: fragments",&
284 (ipiece(k,j,i),k=1,npiece(j,i))
285 rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
286 if (irms(j,i).gt.0) then
289 if (lprn) write (iout,*) "rms",rmsfrag(j,i)
290 ! write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
291 ! & " rmscutfrag",rmscutfrag(1,j,i)
292 if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
298 do while (rms.gt.rmscutfrag(1,j,i) .and. &
299 ishif.lt.n_shift(1,j,i))
301 rms=rmscalc(-ishif,i,j,jcon,lprn)
302 ! print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
303 if (lprn) write (iout,*) "rms",rmsfrag(j,i)
304 if (rms.gt.rmscutfrag(1,j,i)) then
305 rms=rmscalc(ishif,i,j,jcon,lprn)
306 ! print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
308 if (lprn) write (iout,*) "rms",rms
310 if (rms.le.rmscutfrag(1,j,i)) then
317 if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and. &
318 isccont(j,i).eq.0 ) then
319 write (iout,*) "Error: no measure of comparison specified:",&
324 write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
326 iclass(j,i) = min0(iclass_con,iclass_rms)
327 if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
328 ishifft(j,i)=ishifft_rms
330 ishifft(j,i)=ishifft_con
332 else if (i.gt.2) then
333 iclass(j,i) = iclass_rms
334 ishifft(j,i)= ishifft_rms
341 ! Compute the structural class
343 IF (.NOT. BINARY) THEN
351 idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
355 ! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
356 ! & " iclass",iclass(j,i)," im",im
362 idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
364 if (iclass(j,i).gt.0) then
369 ! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
370 ! & " iclass",iclass(j,i)," im",im
374 idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
376 if (iclass(j,i).gt.1) then
381 ! write (iout,*) "i",i," j",j," idig",idig," iex",iex,
382 ! & " iclass",iclass(j,i)," im",im
389 if (print_class) then
391 write(istat,'(i6,$)') jcon+indstart(me)-1
392 write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
395 write(istat,'(i6,$)') jcon
396 write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),&
399 write (istat,'(f8.3,2f6.3,$)') &
400 rms_nat,qnat,rmsang/(nres-3)
402 write(istat,'(1x,$,20(i3,$))') &
403 (ncont_nat(1,k,j),k=1,nfrag(j))
405 write(istat,'(1x,$,20(f5.1,f5.2$))') &
406 (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
408 write(istat,'(1x,$,20(f5.1$))') &
409 (rmsfrag(k,j),k=1,nfrag(j))
411 write(istat,'(1x,$,20(i1,$))') &
412 (iclass(k,j),k=1,nfrag(j))
415 write (istat,'(" ",$)')
417 write (istat,'(100(i1,$))')(iclass(k,j),&
419 if (j.lt.nlevel) write(iout,'(".",$)')
423 write (istat,'(i10)') iscore
427 END subroutine conf_compar
428 !-----------------------------------------------------------------------------
430 !-----------------------------------------------------------------------------
431 subroutine add_angpair(ici,icj,nang_pair,iang_pair)
433 ! implicit real*8 (a-h,o-z)
434 ! include 'DIMENSIONS'
435 ! include 'COMMON.IOUNITS'
436 ! include 'COMMON.CHAIN'
437 integer :: ici,icj,nang_pair,iang_pair(2,nres)
438 integer :: i,ian1,ian2
439 ! write (iout,*) "add_angpair: ici",ici," icj",icj,
440 ! & " nang_pair",nang_pair
442 if (ian1.lt.4 .or. ian1.gt.nres) return
444 ! write (iout,*) "ian1",ian1," ian2",ian2
445 if (ian2.lt.4 .or. ian2.gt.nres) return
447 if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
449 nang_pair=nang_pair+1
450 iang_pair(1,nang_pair)=ian1
451 iang_pair(2,nang_pair)=ian2
453 end subroutine add_angpair
454 !-------------------------------------------------------------------------
455 subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,lprn)
457 use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
459 ! implicit real*8 (a-h,o-z)
460 ! include 'DIMENSIONS'
461 ! include 'DIMENSIONS.ZSCOPT'
462 ! include 'DIMENSIONS.COMPAR'
463 ! include 'COMMON.IOUNITS'
464 ! include 'COMMON.VAR'
465 ! include 'COMMON.COMPAR'
466 ! include 'COMMON.CHAIN'
467 ! include 'COMMON.GEO'
468 real(kind=8) :: pinorm,deltang
470 integer :: jfrag,ishif1,ishif2,nn,npart,nn4,nne
471 real(kind=8) :: diffang_max,angn,fract,ff
472 integer :: i,j,nbeg,nend,ll,longest
473 if (lprn) write (iout,'(80(1h*))')
477 npart = npiece(jfrag,1)
479 nne = min0(nend_sup,nres)
480 if (lprn) write (iout,*) "nn4",nn4," nne",nne
482 nbeg = ifrag(1,i,jfrag) + 3 - ishif1
483 if (nbeg.lt.nn4) nbeg=nn4
484 nend = ifrag(2,i,jfrag) + 1 - ishif2
485 if (nend.gt.nne) nend=nne
486 if (nend.ge.nbeg) then
487 nn = nn + nend - nbeg + 1
488 if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
489 " nn",nn," ishift1",ishif1," ishift2",ishif2
490 if (lprn) write (iout,*) "angles"
494 ! deltang = pinorm(phi(j)-phi_ref(j+ishif1))
495 deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
496 theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
497 if (dabs(deltang).gt.diffang_max) then
498 if (ll.gt.longest) longest = ll
503 if (ll.gt.longest) longest = ll
504 if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
505 rad2deg*phi_ref(j+ishif1),rad2deg*deltang
506 angn=angn+dabs(deltang)
509 ff = dfloat(longest)/dfloat(nend - nbeg + 4)
510 if (lprn) write (iout,*)"segment",i," longest fragment within",&
511 diffang_max*rad2deg,":",longest," fraction",ff
512 if (ff.lt.fract) fract = ff
520 if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
523 end subroutine angnorm
524 !-------------------------------------------------------------------------
525 subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
526 diffang_max,anorm,fract)
528 use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
530 ! implicit real*8 (a-h,o-z)
531 ! include 'DIMENSIONS'
532 ! include 'DIMENSIONS.ZSCOPT'
533 ! include 'DIMENSIONS.COMPAR'
534 ! include 'COMMON.IOUNITS'
535 ! include 'COMMON.VAR'
536 ! include 'COMMON.COMPAR'
537 ! include 'COMMON.CHAIN'
538 ! include 'COMMON.GEO'
539 integer :: ncont,icont(2,ncont),longest
540 real(kind=8) :: anorm,diffang_max,fract
541 integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
542 real(kind=8) :: pinorm
544 integer :: jfrag,ishif1,ishif2
545 integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
546 integer :: nbeg,nend,ll
547 real(kind=8) :: angn,ishifc,deltang,ff
549 if (lprn) write (iout,'(80(1h*))')
551 ! Determine the segments for which angles will be compared
554 nne = min0(nend_sup,nres)
555 if (lprn) write (iout,*) "nn4",nn4," nne",nne
556 npart=npiece(jfrag,1)
559 ! write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
560 if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
561 icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
563 do while (jstart.lt.ncont .and. &
564 icont(1,jstart).lt.ifrag(1,i,jfrag))
565 ! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
566 ! & " ifrag",ifrag(1,i,jfrag)
569 ! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
570 ! & " ifrag",ifrag(1,i,jfrag)
571 if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
574 ifrag_c(1,npiece_c)=icont(1,jstart)
576 do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
577 ! write (iout,*) "jend",jend," icont",icont(1,jend),
578 ! & " ifrag",ifrag(2,i,jfrag)
581 ! write (iout,*) "jend",jend," icont",icont(1,jend),
582 ! & " ifrag",ifrag(2,i,jfrag)
584 ifrag_c(2,npiece_c)=icont(1,jend)+1
585 ishift_c(npiece_c)=ishif1
586 ! write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
587 ! & " ic1",ic1," ic2",ic2,
588 ! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
590 if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
595 ! write (iout,*) "idi",idi
597 if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
598 icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
600 do while (jstart.lt.ncont .and. &
601 icont(2,jstart).lt.ifrag(1,i,jfrag))
602 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
603 ! & " ifrag",ifrag(1,i,jfrag)
606 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
607 ! & " ifrag",ifrag(1,i,jfrag)
608 if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
611 ifrag_c(2,npiece_c)=icont(2,jstart)+1
613 do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
614 ! write (iout,*) "jend",jend," icont",icont(2,jend),
615 ! & " ifrag",ifrag(2,i,jfrag)
618 ! write (iout,*) "jend",jend," icont",icont(2,jend),
619 ! & " ifrag",ifrag(2,i,jfrag)
620 else if (idi.eq.-1) then
621 if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
622 icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
624 do while (jstart.gt.ncont .and. &
625 icont(2,jstart).lt.ifrag(1,i,jfrag))
626 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
627 ! & " ifrag",ifrag(1,i,jfrag)
630 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
631 ! & " ifrag",ifrag(1,i,jfrag)
632 if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
635 ifrag_c(2,npiece_c)=icont(2,jstart)+1
637 do while (jend.lt.ncont .and. &
638 icont(2,jend).gt.ifrag(2,i,jfrag))
639 ! write (iout,*) "jend",jend," icont",icont(2,jend),
640 ! & " ifrag",ifrag(2,i,jfrag)
643 ! write (iout,*) "jend",jend," icont",icont(2,jend),
644 ! & " ifrag",ifrag(2,i,jfrag)
652 ! write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
653 ! & " jstart:",jstart," jend",jend,
654 ! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
655 ifrag_c(1,npiece_c)=ic1
656 ifrag_c(2,npiece_c)=ic2+1
657 ishift_c(npiece_c)=ishif2
661 write (iout,*) "Before merge: npiece_c",npiece_c
663 write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
667 ! Merge overlapping segments (e.g., avoid splitting helices)
670 do while (i .lt. npiece_c)
671 if (ishift_c(i).eq.ishift_c(i+1) .and. &
672 ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
673 ifrag_c(2,i)=ifrag_c(2,i+1)
675 ishift_c(j)=ishift_c(j+1)
676 ifrag_c(1,j)=ifrag_c(1,j+1)
677 ifrag_c(2,j)=ifrag_c(2,j+1)
685 write (iout,*) "After merge: npiece_c",npiece_c
687 write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
700 nbeg = ifrag_c(1,i) + 3 - ishifc
701 if (nbeg.lt.nn4) nbeg=nn4
702 nend = ifrag_c(2,i) - ishifc + 1
703 if (nend.gt.nne) nend=nne
704 if (nend.ge.nbeg) then
705 nn = nn + nend - nbeg + 1
706 if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
707 " nn",nn," ishifc",ishifc
708 if (lprn) write (iout,*) "angles"
712 ! deltang = pinorm(phi(j)-phi_ref(j+ishifc))
713 deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
714 theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
715 if (dabs(deltang).gt.diffang_max) then
716 if (ll.gt.longest) longest = ll
721 if (ll.gt.longest) longest = ll
722 if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
723 rad2deg*phi_ref(j+ishifc),rad2deg*deltang
724 angn=angn+dabs(deltang)
727 ff = dfloat(longest)/dfloat(nend - nbeg + 4)
728 if (lprn) write (iout,*)"segment",i," longest fragment within",&
729 diffang_max*rad2deg,":",longest," fraction",ff
730 if (ff.lt.fract) fract = ff
733 if (nn.gt.0) anorm = angn/nn
734 if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
736 end subroutine angnorm2
737 !-------------------------------------------------------------------------
738 real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
740 use geometry_data, only:phi,theta,rad2deg
741 ! implicit real*8 (a-h,o-z)
742 ! include 'DIMENSIONS'
743 ! include 'DIMENSIONS.ZSCOPT'
744 ! include 'DIMENSIONS.COMPAR'
745 ! include 'COMMON.IOUNITS'
746 ! include 'COMMON.VAR'
747 ! include 'COMMON.COMPAR'
748 ! include 'COMMON.CHAIN'
749 ! include 'COMMON.GEO'
751 integer :: nang_pair,iang_pair(2,nres)
752 real(kind=8) :: pinorm
754 real(kind=8) :: angn,deltang
756 if (lprn) write (iout,'(80(1h*))')
757 if (lprn) write (iout,*) "nang_pair",nang_pair
758 if (lprn) write (iout,*) "angles"
762 ! deltang = pinorm(phi(ia1)-phi_ref(ia2))
763 deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
764 theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
765 if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
766 rad2deg*phi_ref(ia2),rad2deg*deltang
767 angn=angn+dabs(deltang)
770 write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
771 angnorm1 = angn/nang_pair
773 end function angnorm1
774 !------------------------------------------------------------------------------
775 subroutine angnorm12(diff)
777 use geometry_data, only:phi,theta,nstart_sup,nend_sup
778 ! implicit real*8 (a-h,o-z)
779 ! include 'DIMENSIONS'
780 ! include 'DIMENSIONS.ZSCOPT'
781 ! include 'DIMENSIONS.COMPAR'
782 ! include 'COMMON.IOUNITS'
783 ! include 'COMMON.VAR'
784 ! include 'COMMON.COMPAR'
785 ! include 'COMMON.CHAIN'
786 ! include 'COMMON.GEO'
787 real(kind=8) :: pinorm,diff
791 nne = min0(nend_sup,nres)
793 ! diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
796 ! diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
797 diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
798 theta_ref(j),phi(j),theta(j-1),theta(j))
801 end subroutine angnorm12
802 !--------------------------------------------------------------------------------
803 real(kind=8) function spherang(gam1,theta11,theta12,&
804 gam2,theta21,theta22)
806 use geometry, only:arcos
807 real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
808 x1,x2,xmed,f1,f2,fmed
809 real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
810 real(kind=8) :: sumcos
811 !el real(kind=8) :: pinorm,sumangp !arcos,
812 integer :: it,maxit=100
813 ! Calculate the difference of the angles of two superposed 4-redidue fragments
821 ! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
822 ! to achieve the minimum difference between the O'-C-O and P-C-P angles;
823 ! the sum of these angles is the difference returned by the function.
826 ! If thetas match, take the difference of gamma and exit.
827 if (dabs(theta11-theta12).lt.tolx &
828 .and. dabs(theta21-theta22).lt.tolx) then
829 spherang=dabs(pinorm(gam2-gam1))
832 ! If the gammas are the same, take the difference of thetas and exit.
834 x2=0.5d0*pinorm(gam2-gam1)
835 if (dabs(x2) .lt. tolx) then
836 spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
838 else if (x2.lt.0.0d0) then
842 ! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
843 f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
844 f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
846 xmed=x1-f1*(x2-x1)/(f2-f1)
847 fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
848 ! write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
849 if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
850 .and. dabs(fmed).lt.tolf ) then
854 else if ( fmed*f1.lt.0.0d0 ) then
863 spherang=arcos(dcos(theta11)*dcos(theta12) &
864 +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
865 arcos(dcos(theta21)*dcos(theta22)+ &
866 dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
868 end function spherang
869 !--------------------------------------------------------------------------------
870 real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
873 real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
874 cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
876 ! derivarive of the sum of the difference of the angles of a 4-residue fragment.
877 ! real(kind=8) :: arcos
886 cosd1=cost11*cost12+sint11*sint12*dcos(fi)
887 cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
888 sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
889 +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
892 !-----------------------------------------------------------------------------
894 !-----------------------------------------------------------------------------
895 subroutine contact(lprint,ncont,icont,ist,ien)
898 use geometry_data, only:c,dc,dc_norm
899 use energy_data, only:itype,maxcont,molnum
901 ! include 'DIMENSIONS'
902 ! include 'DIMENSIONS.ZSCOPT'
903 ! include 'COMMON.CONTROL'
904 ! include 'COMMON.IOUNITS'
905 ! include 'COMMON.CHAIN'
906 ! include 'COMMON.INTERACT'
907 ! include 'COMMON.FFIELD'
908 ! include 'COMMON.NAMES'
909 ! include 'COMMON.CALC'
910 ! include 'COMMON.CONTPAR'
911 ! include 'COMMON.LOCAL'
912 integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2,mnum,mnum2
913 real(kind=8) :: csc !el,dist
914 real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
916 integer :: ncont,mhum
917 integer,dimension(2,maxcont) :: icont
918 real(kind=8) :: u,v,a(3),b(3),dla,dlb
929 write (iout,110) restyp(itype(i,mnum),mnum),i,c(1,i),c(2,i),&
930 c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
931 dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
934 110 format (a,'(',i3,')',9f8.3)
937 iti=iabs(itype(i,mnum))
938 if (iti.le.0 .or. iti.gt.ntyp_molec(mnum)) cycle
941 itj=iabs(itype(j,mnum2))
942 if (itj.le.0 .or. itj.gt.ntyp_molec(mnum2)) cycle
945 xj = c(1,nres+j)-c(1,nres+i)
946 yj = c(2,nres+j)-c(2,nres+i)
947 zj = c(3,nres+j)-c(3,nres+i)
948 dxi = dc_norm(1,nres+i)
949 dyi = dc_norm(2,nres+i)
950 dzi = dc_norm(3,nres+i)
951 dxj = dc_norm(1,nres+j)
952 dyj = dc_norm(2,nres+j)
953 dzj = dc_norm(3,nres+j)
958 ! write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
959 if (icomparfunc.eq.1) then
960 call contfunc(csc,iti,itj)
961 else if (icomparfunc.eq.2) then
962 call scdist(csc,iti,itj)
963 else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
964 csc = dist(nres+i,nres+j)
965 else if (icomparfunc.eq.4) then
966 call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
968 write (*,*) "Error - Unknown sidechain contact function"
969 write (iout,*) "Error - Unknown sidechain contact function"
971 if (csc.lt.sc_cutoff(iti,itj)) then
972 ! write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
973 ! & " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
974 ! & dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
975 ! & dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
977 ! write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
978 ! & sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
979 ! & chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
988 ddsc(ncont)=1.0d0/rij
995 write (iout,'(a)') 'Contact map:'
1000 it1=itype(i1,molnum(i1))
1001 it2=itype(i2,molnum(i2))
1002 ! print *,"CONTACT",i1,mnum,it1,it2
1003 write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
1004 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2,cscore(i),&
1005 sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1006 omt1(i),omt2(i),omt12(i)
1010 end subroutine contact
1012 !----------------------------------------------------------------------------
1013 subroutine contact(lprint,ncont,icont)
1015 use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii
1016 ! include 'DIMENSIONS'
1017 ! include 'COMMON.IOUNITS'
1018 ! include 'COMMON.CHAIN'
1019 ! include 'COMMON.INTERACT'
1020 ! include 'COMMON.FFIELD'
1021 ! include 'COMMON.NAMES'
1022 real(kind=8) :: facont=1.569D0 ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1023 integer :: ncont,icont(2,maxcont)
1025 integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1026 real(kind=8) :: rcomp
1029 ! print *,'nnt=',nnt,' nct=',nct
1032 iti=iabs(itype(i,1))
1035 itj=iabs(itype(j,1))
1037 ! rcomp=sigmaii(iti,itj)+1.0D0
1038 rcomp=facont*sigmaii(iti,itj)
1040 ! rcomp=sigma(iti,itj)+1.0D0
1041 rcomp=facont*sigma(iti,itj)
1044 ! print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1045 if (dist(nres+i,nres+j).lt.rcomp) then
1053 write (iout,'(a)') 'Contact map:'
1060 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1061 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1065 end subroutine contact
1067 !----------------------------------------------------------------------------
1068 real(kind=8) function contact_fract(ncont,ncont_ref,&
1071 use energy_data, only:maxcont
1073 ! include 'DIMENSIONS'
1074 ! include 'COMMON.IOUNITS'
1075 integer :: i,j,nmatch
1076 integer :: ncont,ncont_ref
1077 integer,dimension(2,maxcont) :: icont,icont_ref
1079 ! print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1080 ! write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1081 ! write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1082 ! write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1083 ! write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1086 if (icont(1,i).eq.icont_ref(1,j) .and. &
1087 icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1090 ! print *,' nmatch=',nmatch
1091 ! contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1092 contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1094 end function contact_fract
1096 !------------------------------------------------------------------------------
1097 subroutine pept_cont(lprint,ncont,icont)
1099 use geometry_data, only:c
1100 use energy_data, only:maxcont,nnt,nct,itype,molnum
1102 ! include 'DIMENSIONS'
1103 ! include 'DIMENSIONS.ZSCOPT'
1104 ! include 'COMMON.IOUNITS'
1105 ! include 'COMMON.CHAIN'
1106 ! include 'COMMON.INTERACT'
1107 ! include 'COMMON.FFIELD'
1108 ! include 'COMMON.NAMES'
1109 integer :: ncont,icont(2,maxcont)
1110 integer :: i,j,k,kkk,i1,i2,it1,it2,mnum
1112 !el real(kind=8) :: dist
1113 real(kind=8) :: rcomp=5.5d0
1116 print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1119 c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1123 c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1125 if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1133 write (iout,'(a)') 'PP contact map:'
1140 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1141 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1145 end subroutine pept_cont
1146 !-----------------------------------------------------------------------------
1148 !-----------------------------------------------------------------------------
1149 subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1150 ncont_interfrag,icont_interfrag)
1152 use energy_data, only:itype,maxcont,molnum
1153 ! include 'DIMENSIONS'
1154 ! include 'DIMENSIONS.ZSCOPT'
1155 ! include 'DIMENSIONS.COMPAR'
1156 ! include 'COMMON.INTERACT'
1157 ! include 'COMMON.COMPAR'
1158 ! include 'COMMON.IOUNITS'
1159 ! include 'COMMON.CHAIN'
1160 ! include 'COMMON.NAMES'
1161 integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1162 icont_interfrag(2,maxcont,mmaxfrag)
1163 logical :: OK1,OK2,lprint
1164 integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2,mnum
1165 ! Determine the contacts that occur within a fragment and between fragments.
1170 ! write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1171 ! & ,k=1,npiece(i,1))
1172 ! write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1173 ! & ,k=1,npiece(j,1))
1174 ! write (iout,*) "ncont",ncont
1180 do while (.not.OK1 .and. l.lt.npiece(j,1))
1182 OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1183 ic1.le.ifrag(2,l,j)+is
1187 do while (.not.OK2 .and. l.lt.npiece(i,1))
1189 OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1190 ic2.le.ifrag(2,l,i)+is
1192 ! write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1194 if (OK1.and.OK2) then
1196 icont_interfrag(1,nc,ind)=ic1
1197 icont_interfrag(2,nc,ind)=ic2
1198 ! write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1201 ncont_interfrag(ind)=nc
1202 ! do k=1,ncont_interfrag(ind)
1203 ! i1=icont_interfrag(1,k,ind)
1204 ! i2=icont_interfrag(2,k,ind)
1207 ! write (iout,'(i3,2x,a,i4,2x,a,i4)')
1208 ! & i,restyp(it1),i1,restyp(it2),i2
1213 write (iout,*) "Contacts within fragments:"
1215 write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1216 ifrag(2,k,i),k=1,npiece(i,1)),")"
1218 do k=1,ncont_interfrag(ind)
1219 i1=icont_interfrag(1,k,ind)
1220 i2=icont_interfrag(2,k,ind)
1223 it2=itype(i2,molnum(i2))
1224 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1225 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1229 write (iout,*) "Contacts between fragments:"
1233 write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1234 ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1235 (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1236 write (iout,*) "Number of contacts",&
1237 ncont_interfrag(ind)
1239 do k=1,ncont_interfrag(ind)
1240 i1=icont_interfrag(1,k,ind)
1241 i2=icont_interfrag(2,k,ind)
1244 it2=itype(i2,molnum(i2))
1245 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1246 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1252 end subroutine contacts_between_fragments
1253 !-----------------------------------------------------------------------------
1255 !-----------------------------------------------------------------------------
1256 subroutine contfunc(cscore,itypi,itypj)
1258 ! This subroutine calculates the contact function based on
1259 ! the Gay-Berne potential of interaction.
1262 ! implicit real*8 (a-h,o-z)
1263 ! include 'DIMENSIONS'
1264 ! include 'COMMON.CONTPAR'
1265 ! include 'COMMON.CALC'
1267 integer :: itypi,itypj
1268 real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1270 sig0ij=sig_comp(itypi,itypj)
1271 chi1=chi_comp(itypi,itypj)
1272 chi2=chi_comp(itypj,itypi)
1274 chip1=chip_comp(itypi,itypj)
1275 chip2=chip_comp(itypj,itypi)
1277 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1279 ! Calculate angle-dependent terms of the contact function
1283 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1284 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1285 om12=dxi*dxj+dyi*dyj+dzi*dzj
1287 ! print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1289 ! & rij,rrij,om1,om2,om12
1290 ! Calculate eps1(om12)
1291 faceps1=1.0D0-om12*chiom12
1292 faceps1_inv=1.0D0/faceps1
1293 eps1=dsqrt(faceps1_inv)
1294 ! Following variable is eps1*deps1/dom12
1295 eps1_om12=faceps1_inv*chiom12
1296 ! Calculate sigma(om1,om2,om12)
1300 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1301 sigsq=1.0D0-facsig*faceps1_inv
1302 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1305 chipom12=chip12*om12
1306 facp=1.0D0-om12*chipom12
1308 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1309 ! Following variable is the square root of eps2
1310 eps2rt=1.0D0-facp1*facp_inv
1312 sig=sig0ij*dsqrt(sigsq)
1313 rij_shift=1.0D0/rij-sig+sig0ij
1314 if (rij_shift.le.0.0D0) then
1316 cscore = -dlog(evdw+1.0d-6)
1319 rij_shift=1.0D0/rij_shift
1320 e2=(rij_shift*sig0ij)**expon
1321 evdw=dabs(eps1*eps2rt**2*e2)
1322 if (evdw.gt.1.0d1) evdw = 1.0d1
1323 cscore = -dlog(evdw+1.0d-6)
1325 end subroutine contfunc
1326 !------------------------------------------------------------------------------
1327 subroutine scdist(cscore,itypi,itypj)
1329 ! This subroutine calculates the contact distance
1332 ! implicit real*8 (a-h,o-z)
1333 ! include 'DIMENSIONS'
1334 ! include 'COMMON.CONTPAR'
1335 ! include 'COMMON.CALC'
1336 integer :: itypi,itypj
1337 real(kind=8) :: cscore,rrij
1339 chi1=chi_comp(itypi,itypj)
1340 chi2=chi_comp(itypj,itypi)
1342 rrij=xj*xj+yj*yj+zj*zj
1344 ! Calculate angle-dependent terms of the contact function
1348 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1349 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1350 om12=dxi*dxj+dyi*dyj+dzi*dzj
1355 cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1357 end subroutine scdist
1358 !------------------------------------------------------------------------------
1360 !------------------------------------------------------------------------------
1361 subroutine elecont(lprint,ncont,icont,ist,ien)
1363 use geometry_data, only:c
1364 use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2,molnum
1366 ! include 'DIMENSIONS'
1367 ! include 'DIMENSIONS.ZSCOPT'
1368 ! include 'DIMENSIONS.COMPAR'
1369 ! include 'COMMON.IOUNITS'
1370 ! include 'COMMON.CHAIN'
1371 ! include 'COMMON.INTERACT'
1372 ! include 'COMMON.FFIELD'
1373 ! include 'COMMON.NAMES'
1374 ! include 'COMMON.LOCAL'
1376 integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1377 real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1378 xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1379 vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1381 real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1382 -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1383 real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1384 0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1385 real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1386 real(kind=8) :: elcutoff=-0.3d0
1387 real(kind=8) :: elecutoff_14=-0.5d0
1388 integer :: ncont,icont(2,maxcont),mnum
1389 real(kind=8) :: econt(maxcont)
1391 ! Load the constants of peptide bond - peptide bond interactions.
1392 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1393 ! proline) - determined by averaging ECEPP energy.
1397 ! data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1398 ! data rpp / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1399 !el data (elpp6c) /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1400 !el data (elpp3c) / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1401 !el data (elcutoff) /-0.3d0/
1402 !el data (elecutoff_14) /-0.5d0/
1405 if (lprint) write (iout,'(a)') &
1406 "Constants of electrostatic interaction energy expression."
1410 appc(i,j)=epp(i,j)*rri*rri
1411 bppc(i,j)=-2.0*epp(i,j)*rri
1412 ael6c(i,j)=elpp6c(i,j)*4.2**6
1413 ael3c(i,j)=elpp3c(i,j)*4.2**3
1415 write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1434 if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1435 if (iteli.eq.2 .and. itelj.eq.2 &
1436 .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1437 aaa=appc(iteli,itelj)
1438 bbb=bppc(iteli,itelj)
1439 ael6i=ael6c(iteli,itelj)
1440 ael3i=ael3c(iteli,itelj)
1444 xj=c(1,j)+0.5*dxj-xmedi
1445 yj=c(2,j)+0.5*dyj-ymedi
1446 zj=c(3,j)+0.5*dzj-zmedi
1447 rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1452 cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1453 cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1454 cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1455 fac=cosa-3.0*cosb*cosg
1461 el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1464 if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1465 j.eq.i+2 .and. eesij.le.elecutoff_14) then
1476 write (iout,*) 'Total average electrostatic energy: ',ees
1477 write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1479 write (iout,*) 'Electrostatic contacts before pruning: '
1483 it1=itype(i1,molnum(i1))
1484 it2=itype(i2,molnum(i1))
1485 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1486 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i1)),i2,econt(i)
1489 ! For given residues keep only the contacts with the greatest energy.
1491 do while (i.lt.ncont)
1497 do while (j.lt.ncont)
1499 if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1500 ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1501 ! write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1502 ! & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1503 if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1504 if (ic1.eq.icont(1,j)) then
1506 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1507 .and. iabs(icont(1,k)-ic1).le.2 .and. &
1508 econt(k).lt.econt(j) ) goto 21
1510 else if (ic2.eq.icont(2,j) ) then
1512 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1513 .and. iabs(icont(2,k)-ic2).le.2 .and. &
1514 econt(k).lt.econt(j) ) goto 21
1517 ! Remove ith contact
1519 icont(1,k-1)=icont(1,k)
1520 icont(2,k-1)=icont(2,k)
1525 ! write (iout,*) "ncont",ncont
1527 ! write (iout,*) icont(1,k),icont(2,k)
1530 else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1532 if (ic1.eq.icont(1,j)) then
1534 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1535 .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1536 econt(k).lt.econt(i) ) goto 21
1538 else if (ic2.eq.icont(2,j) ) then
1540 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1541 .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1542 econt(k).lt.econt(i) ) goto 21
1545 ! Remove jth contact
1547 icont(1,k-1)=icont(1,k)
1548 icont(2,k-1)=icont(2,k)
1552 ! write (iout,*) "ncont",ncont
1554 ! write (iout,*) icont(1,k),icont(2,k)
1565 write (iout,*) 'Electrostatic contacts after pruning: '
1572 it2=itype(i2,molnum(i2))
1573 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1574 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2,econt(i)
1578 end subroutine elecont
1579 !------------------------------------------------------------------------------
1581 !------------------------------------------------------------------------------
1582 subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1583 ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1584 nc_frac,nc_req_set,istr,llocal,lprn)
1586 use energy_data, only:maxcont
1587 ! implicit real*8 (a-h,o-z)
1588 ! include 'DIMENSIONS'
1589 ! include 'COMMON.IOUNITS'
1590 integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1591 integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1592 real(kind=8) :: nc_frac
1593 logical :: llocal,lprn
1594 integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1595 nc_req_set,istr,nc_match_max
1596 integer :: i,nc_req,nc_match1,is,js
1599 nc_match_max=nc_match_max+ &
1600 min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1604 else if (nc_req_set.eq.0) then
1605 nc_req=nc_match_max*nc_frac
1607 nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1608 dfloat(nc_req_set)+1.0d-7)
1610 ! write (iout,*) "match_contact: nc_req:",nc_req
1611 ! write (iout,*) "nc_match_max",nc_match_max
1612 ! write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1613 ! & " n_shif2",n_shif2
1614 ! Match current contact map against reference contact map; exit, if at least
1615 ! half of the contacts match
1616 call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1617 ncont,icont,jfrag,llocal,lprn)
1618 nc_match1_max=nc_match1
1619 if (lprn .and. nc_match.gt.0) write (iout,*) &
1620 "Shift:",0,0," nc_match1",nc_match1,&
1621 " nc_match=",nc_match," req'd",nc_req
1622 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1623 nc_req.eq.0 .and. nc_match.eq.1) then
1628 ! If sufficient matches are not found, try to shift contact maps up to three
1630 if (n_shif1.gt.0) then
1632 ! The following four tries help to find shifted beta-sheet patterns
1633 ! Shift "left" strand backward
1634 call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1635 icont_ref,ncont,icont,jfrag,llocal,lprn)
1636 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1637 if (lprn .and. nc_match.gt.0) write (iout,*) &
1638 "Shift:",-is,0," nc_match1",nc_match1,&
1639 " nc_match=",nc_match," req'd",nc_req
1640 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1641 nc_req.eq.0 .and. nc_match.eq.1) then
1646 ! Shift "left" strand forward
1647 call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1648 icont_ref,ncont,icont,jfrag,llocal,lprn)
1649 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1650 if (lprn .and. nc_match.gt.0) write (iout,*) &
1651 "Shift:",is,0," nc_match1",nc_match1,&
1652 " nc_match=",nc_match," req'd",nc_req
1653 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1654 nc_req.eq.0 .and. nc_match.eq.1) then
1660 if (nc_req.eq.0) return
1661 ! Shift "right" strand backward
1663 call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1664 icont_ref,ncont,icont,jfrag,llocal,lprn)
1665 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1666 if (lprn .and. nc_match.gt.0) write (iout,*) &
1667 "Shift:",0,-is," nc_match1",nc_match1,&
1668 " nc_match=",nc_match," req'd",nc_req
1669 if (nc_match.ge.nc_req) then
1674 ! Shift "right" strand upward
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
1687 ! Now try to shift both residues in contacts.
1691 call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1692 icont_ref,ncont,icont,jfrag,llocal,lprn)
1693 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1694 if (lprn .and. nc_match.gt.0) write (iout,*) &
1695 "Shift:",-is,-js," nc_match1",nc_match1,&
1696 " nc_match=",nc_match," req'd",nc_req
1697 if (nc_match.ge.nc_req) then
1702 call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1703 icont_ref,ncont,icont,jfrag,llocal,lprn)
1704 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1705 if (lprn .and. nc_match.gt.0) write (iout,*) &
1706 "Shift:",is,js," nc_match1",nc_match1,&
1707 " nc_match=",nc_match," req'd",nc_req
1708 if (nc_match.ge.nc_req) then
1714 call ncont_match(nc_match,nc_match1,-js,-is,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:",-js,-is," nc_match1",nc_match1,&
1719 " nc_match=",nc_match," req'd",nc_req
1720 if (nc_match.ge.nc_req) then
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
1739 if (is+js.le.n_shif1) then
1740 call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1741 icont_ref,ncont,icont,jfrag,llocal,lprn)
1742 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1743 if (lprn .and. nc_match.gt.0) write (iout,*) &
1744 "Shift:",-is,js," nc_match1",nc_match1,&
1745 " nc_match=",nc_match," req'd",nc_req
1746 if (nc_match.ge.nc_req) then
1752 call ncont_match(nc_match,nc_match1,js,-is,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:",js,-is," nc_match1",nc_match1,&
1757 " nc_match=",nc_match," req'd",nc_req
1758 if (nc_match.ge.nc_req) then
1769 if (n_shif2.gt.0) then
1771 call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1772 icont_ref,ncont,icont,jfrag,llocal,lprn)
1773 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1774 if (lprn .and. nc_match.gt.0) write (iout,*) &
1775 "Shift:",-is,-is," nc_match1",nc_match1,&
1776 " nc_match=",nc_match," req'd",nc_req
1777 if (nc_match.ge.nc_req) then
1782 call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1783 icont_ref,ncont,icont,jfrag,llocal,lprn)
1784 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1785 if (lprn .and. nc_match.gt.0) write (iout,*) &
1786 "Shift:",is,is," nc_match1",nc_match1,&
1787 " nc_match=",nc_match," req'd",nc_req
1788 if (nc_match.ge.nc_req) then
1795 ! If this point is reached, the contact maps are different.
1800 end subroutine match_contact
1801 !-------------------------------------------------------------------------
1802 subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1803 ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1805 use energy_data, only:nnt,nct,maxcont
1806 ! implicit real*8 (a-h,o-z)
1807 ! include 'DIMENSIONS'
1808 ! include 'DIMENSIONS.ZSCOPT'
1809 ! include 'DIMENSIONS.COMPAR'
1810 ! include 'COMMON.IOUNITS'
1811 ! include 'COMMON.INTERACT'
1812 ! include 'COMMON.GEO'
1813 ! include 'COMMON.COMPAR'
1814 logical :: llocal,lprn
1815 integer ncont_ref,ncont,ishift,ishif2,nang_pair
1816 integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1817 integer,dimension(2,nres) :: iang_pair !(2,maxres)
1818 integer :: nc_match,nc_match1,ishif1,jfrag
1819 integer :: i,j,ic1,ic2
1820 real(kind=8) :: diffang,fract,rad2deg
1822 ! Compare the contact map against the reference contact map; they're stored
1823 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1824 if (lprn) write (iout,'(80(1h*))')
1827 ! Check the local structure by comparing dihedral angles.
1828 ! write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1829 if (llocal .and. ncont_ref.eq.0) then
1830 ! If there are no contacts just compare the dihedral angles and exit.
1831 call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1833 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1834 " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1835 if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1845 ic1=icont(1,i)+ishif1
1846 ic2=icont(2,i)+ishif2
1847 ! write (iout,*) "i",i," ic1",ic1," ic2",ic2
1848 if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1850 if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1851 nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1852 nc_match1=nc_match1+1
1853 icont_match(1,nc_match1)=ic1
1854 icont_match(2,nc_match1)=ic2
1855 ! call add_angpair(icont(1,i),icont_ref(1,j),
1856 ! & nang_pair,iang_pair)
1857 ! call add_angpair(icont(2,i),icont_ref(2,j),
1858 ! & nang_pair,iang_pair)
1859 if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1860 " match",icont_ref(1,j),icont_ref(2,j),&
1861 " shifts",ishif1,ishif2
1868 write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1869 write (iout,*) "icont_match"
1871 write (iout,*) icont_match(1,i),icont_match(2,i)
1874 if (llocal .and. nc_match.gt.0) then
1875 call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1876 ang_cut1(jfrag),diffang,fract)
1877 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1878 " ang_cut:",ang_cut(jfrag)*rad2deg,&
1879 " ang_cut1",ang_cut1(jfrag)*rad2deg
1880 if (diffang.gt.ang_cut(jfrag) &
1881 .or. fract.lt.frac_min(jfrag)) nc_match=0
1883 ! if (nc_match.gt.0) then
1884 ! diffang = angnorm1(nang_pair,iang_pair,lprn)
1885 ! if (diffang.gt.ang_cut(jfrag)) nc_match=0
1887 if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1888 " diffang",rad2deg*diffang," nc_match",nc_match
1890 end subroutine ncont_match
1891 !------------------------------------------------------------------------------
1892 subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1893 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1894 ! conformation considered to that of the reference conformation.
1895 ! Returns the number of equivalent residues (nsec_match).
1896 ! implicit real*8 (a-h,o-z)
1897 ! include 'DIMENSIONS'
1898 ! include 'DIMENSIONS.ZSCOPT'
1899 ! include 'DIMENSIONS.COMPAR'
1900 ! include 'COMMON.IOUNITS'
1901 ! include 'COMMON.CHAIN'
1902 ! include 'COMMON.PEPTCONT'
1903 ! include 'COMMON.COMPAR'
1905 integer :: isecstr(nres)
1906 integer :: jfrag,nsec_match,npart,i,j
1907 npart = npiece(jfrag,1)
1910 write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1911 (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1912 write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1913 write (iout,'(80i1)') (isecstr(j),j=1,nres)
1916 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1917 ! The residue has equivalent conformational state to that of the reference
1919 ! a) the conformational states are equal or
1920 ! b) the reference state is a coil and that of the conformation considered
1922 ! c) the conformational state of the conformation considered is a strand
1923 ! and that of the reference conformation is a coil.
1924 ! 10/28/02 - case (b) deleted.
1925 if (isecstr(j).eq.isec_ref(j) .or. &
1926 ! & isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1927 isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1928 nsec_match=nsec_match+1
1932 end subroutine match_secondary
1933 !------------------------------------------------------------------------------
1935 !------------------------------------------------------------------------------
1936 subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1938 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1940 ! implicit real*8 (a-h,o-z)
1941 real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1942 real(kind=8) :: uu,vv,aa,bb,dd
1943 real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1944 !el odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1945 !el + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1946 ! print *,"r1",(r1(i),i=1,3)
1947 ! print *,"r2",(r2(i),i=1,3)
1948 ! print *,"a",(a(i),i=1,3)
1949 ! print *,"b",(b(i),i=1,3)
1950 aa = a(1)**2+a(2)**2+a(3)**2
1951 bb = b(1)**2+b(2)**2+b(3)**2
1952 ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1953 ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1954 br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1956 ! print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1957 uu = (-ar*bb+br*ab)/det
1958 vv = (br*aa-ar*ab)/det
1964 !el dd1 = odl(uu,vv)
1965 dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1966 !el dd2 = odl(0.0d0,0.0d0)
1967 dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1968 !el dd3 = odl(0.0d0,1.0d0)
1969 dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1970 !el dd4 = odl(1.0d0,0.0d0)
1971 dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1972 !el dd5 = odl(1.0d0,1.0d0)
1973 dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1974 dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1978 else if (dd.eq.dd3) then
1981 else if (dd.eq.dd4) then
1984 else if (dd.eq.dd5) then
1993 ! dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
1997 ! write (8,*) uu,vv,dd,dd1
2000 end subroutine odlodc
2001 !------------------------------------------------------------------------------
2002 real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
2004 real(kind=8),dimension(3) :: r1,r2
2005 real(kind=8) :: aa,bb,u,v,ar,br,ab
2007 odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
2008 + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
2011 !------------------------------------------------------------------------------
2013 !------------------------------------------------------------------------------
2014 subroutine proc_cont
2016 use geometry_data, only:rad2deg
2017 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2019 ! implicit real*8 (a-h,o-z)
2020 ! include 'DIMENSIONS'
2021 ! include 'DIMENSIONS.ZSCOPT'
2022 ! include 'DIMENSIONS.COMPAR'
2023 ! include 'COMMON.IOUNITS'
2024 ! include 'COMMON.TIME1'
2025 ! include 'COMMON.SBRIDGE'
2026 ! include 'COMMON.CONTROL'
2027 ! include 'COMMON.COMPAR'
2028 ! include 'COMMON.CHAIN'
2029 ! include 'COMMON.HEADER'
2030 ! include 'COMMON.CONTACTS1'
2031 ! include 'COMMON.PEPTCONT'
2032 ! include 'COMMON.GEO'
2033 integer :: i,j,k,ind,len_cut,ndigit,length_frag
2035 write (iout,*) "proc_cont: nlevel",nlevel
2036 if (nlevel.lt.0) then
2037 write (iout,*) "call define_fragments"
2038 call define_fragments
2040 write (iout,*) "call secondary2"
2041 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2044 write (iout,'(80(1h=))')
2045 write (iout,*) "Electrostatic contacts"
2046 call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2047 icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2048 write (iout,'(80(1h=))')
2049 write (iout,*) "Side chain contacts"
2050 call contacts_between_fragments(.true.,0,ncont_ref,&
2051 icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2052 if (nlevel.lt.0) then
2056 if (istruct(i).le.1) then
2057 len_cut=max0(len_frag(i,1)*4/5,3)
2058 else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2059 len_cut=max0(len_frag(i,1)*2/5,3)
2061 write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2062 ncont_frag_ref(ind)," len_cut",len_cut,&
2063 " icont_single",icont_single," iloc_single",iloc_single
2065 if (iloc(i).gt.0) write (iout,*) &
2066 "Local structure used to compare structure of fragment",i,&
2068 if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2069 .and. icont_single.gt.0 .and. &
2070 ncont_frag_ref(ind).ge.len_cut) then
2071 write (iout,*) "Electrostatic contacts used to compare",&
2072 " structure of fragment",i," to native."
2075 else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2077 write (iout,*) "Side chain contacts used to compare",&
2078 " structure of fragment",i," to native."
2082 write (iout,*) "Contacts not used to compare",&
2083 " structure of fragment",i," to native."
2088 if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2089 .and. ielecont(i,1).eq.0) then
2090 write (iout,*) "RMSD used to compare",&
2091 " structure of fragment",i," to native."
2094 write (iout,*) "RMSD not used to compare",&
2095 " structure of fragment",i," to native."
2100 if (nlevel.lt.-1) then
2103 if (nlevel.gt.3) nlevel=3
2104 if (nlevel.eq.3) then
2106 npiece(1,3)=nfrag(1)
2116 else if (nlevel.eq.-1) then
2121 isnfrag(i+1)=isnfrag(i)+nfrag(i)
2125 ndigit=ndigit+2*nfrag(i)
2127 write (iout,*) "ndigit",ndigit
2128 if (.not.binary .and. ndigit.gt.30) then
2129 write (iout,*) "Highest class too large; switching to",&
2130 " binary representation."
2133 write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2134 write(iout,*) "rmscut_base_up",rmscut_base_up,&
2135 " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2141 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2145 length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2148 len_frag(j,i)=length_frag
2149 rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2150 rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2151 if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2152 rmscutfrag(1,j,i)=rmsup_lim
2153 if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2154 rmscutfrag(1,j,i)=rmsupup_lim
2157 write (iout,*) "Level",1," number of fragments:",nfrag(1)
2159 write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2160 k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2161 rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2162 ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2163 nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2166 write (iout,*) "Level",i," number of fragments:",nfrag(i)
2168 write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2169 k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2170 rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2171 nc_fragm(j,i),nc_req_setf(j,i)
2175 end subroutine proc_cont
2176 !------------------------------------------------------------------------------
2178 !------------------------------------------------------------------------------
2179 subroutine define_pairs
2181 ! use energy_data, only:nsccont_frag_ref
2182 ! implicit real*8 (a-h,o-z)
2183 ! include 'DIMENSIONS'
2184 ! include 'DIMENSIONS.ZSCOPT'
2185 ! include 'DIMENSIONS.COMPAR'
2186 ! include 'COMMON.IOUNITS'
2187 ! include 'COMMON.TIME1'
2188 ! include 'COMMON.SBRIDGE'
2189 ! include 'COMMON.CONTROL'
2190 ! include 'COMMON.COMPAR'
2191 ! include 'COMMON.FRAG'
2192 ! include 'COMMON.CHAIN'
2193 ! include 'COMMON.HEADER'
2194 ! include 'COMMON.GEO'
2195 ! include 'COMMON.CONTACTS1'
2196 ! include 'COMMON.PEPTCONT'
2197 integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2202 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2204 len_frag(j,1)=length_frag
2205 write (iout,*) "Fragment",j," length",len_frag(j,1)
2211 if (istruct(i).le.1 .or. istruct(j).le.1) then
2212 if (istruct(i).le.1) then
2217 if (istruct(j).le.1) then
2222 len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2224 if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2229 if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2234 len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2236 write (iout,*) "Fragments",i,j," structure",istruct(i),&
2237 istruct(j)," # contacts",&
2238 ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2239 " lengths",len_frag(i,1),len_frag(j,1),&
2240 " ll1",ll1," ll2",ll2," len_cut",len_cut
2241 if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2242 nsccont_frag_ref(ind).ge.len_cut ) then
2243 if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2244 write (iout,*) "Adding pair of helices",i,j,&
2245 " based on SC contacts"
2247 write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2248 " based on SC contacts"
2251 if (icont_pair.gt.0) then
2252 write (iout,*) "# SC contacts will be used",&
2254 isccont(nfrag(2),2)=1
2256 if (irms_pair.gt.0) then
2257 write (iout,*) "Fragment RMSD will be used",&
2261 npiece(nfrag(2),2)=2
2262 ipiece(1,nfrag(2),2)=i
2263 ipiece(2,nfrag(2),2)=j
2264 ielecont(nfrag(2),2)=0
2265 n_shift(1,nfrag(2),2)=nshift_pair
2266 n_shift(2,nfrag(2),2)=nshift_pair
2267 nc_fragm(nfrag(2),2)=ncfrac_pair
2268 nc_req_setf(nfrag(2),2)=ncreq_pair
2269 else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2270 .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2271 .and. ncont_frag_ref(ind).ge.len_cut ) then
2273 write (iout,*) "Adding pair strands/sheets",i,j,&
2274 " based on pp contacts"
2275 if (icont_pair.gt.0) then
2276 write (iout,*) "# pp contacts will be used",&
2278 ielecont(nfrag(2),2)=1
2280 if (irms_pair.gt.0) then
2281 write (iout,*) "Fragment RMSD will be used",&
2285 npiece(nfrag(2),2)=2
2286 ipiece(1,nfrag(2),2)=i
2287 ipiece(2,nfrag(2),2)=j
2288 ielecont(nfrag(2),2)=1
2289 isccont(nfrag(2),2)=0
2290 n_shift(1,nfrag(2),2)=nshift_pair
2291 n_shift(2,nfrag(2),2)=nshift_pair
2292 nc_fragm(nfrag(2),2)=ncfrac_bet
2293 nc_req_setf(nfrag(2),2)=ncreq_bet
2297 write (iout,*) "Pairs found"
2299 write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2302 end subroutine define_pairs
2303 !------------------------------------------------------------------------------
2305 !------------------------------------------------------------------------------
2306 INTEGER FUNCTION ICANT(I,J)
2315 !------------------------------------------------------------------------------
2317 !------------------------------------------------------------------------------
2318 subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2321 integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2322 real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2323 real(kind=8) :: xxtemp
2324 integer :: i,j,k,imax
2329 if (x(1,1,j).lt.xmin) then
2363 x(j,k,imax)=x(j,k,i)
2369 end subroutine imysort
2370 !------------------------------------------------------------------------------
2372 !-------------------------------------------------------------------------------
2373 real(kind=8) function qwolynes(ilevel,jfrag)
2375 use geometry_data, only:cref,nperm
2376 use control_data, only:symetr
2377 use energy_data, only:nnt,nct,itype,molnum
2379 ! include 'DIMENSIONS'
2380 ! include 'DIMENSIONS.ZSCOPT'
2381 ! include 'DIMENSIONS.COMPAR'
2382 ! include 'COMMON.IOUNITS'
2383 ! include 'COMMON.COMPAR'
2384 ! include 'COMMON.CHAIN'
2385 ! include 'COMMON.INTERACT'
2386 ! include 'COMMON.CONTROL'
2387 integer :: ilevel,jfrag,kkk
2388 integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2390 real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2391 real(kind=8) :: maxiQ !dist,
2392 real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2393 logical :: lprn=.false.
2394 real(kind=8) :: x !el sigm
2395 !el sigm(x)=0.25d0*x
2401 ! write (iout,*) "QWolyes: " jfrag",jfrag,
2402 ! & " ilevel",ilevel
2403 allocate(tempus(nperm))
2406 if (ilevel.eq.0) then
2407 if (lprn) write (iout,*) "Q computed for whole molecule"
2418 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2419 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2420 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2422 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2423 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2426 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2427 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2428 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2429 dijCM=dist(il+nres,jl+nres)
2430 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2434 write (iout,*) "il",il," jl",jl,&
2435 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2436 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2437 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2442 if (lprn) write (iout,*) "nl",nl," qq",qq
2443 else if (ilevel.eq.1) then
2444 if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2446 ! write (iout,*) "nlist_frag",nlist_frag(jfrag)
2447 do i=2,nlist_frag(jfrag)
2449 il=list_frag(i,jfrag)
2450 jl=list_frag(j,jfrag)
2451 if (iabs(il-jl).gt.nsep) then
2459 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2460 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2461 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2463 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2464 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2467 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2468 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2469 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2470 dijCM=dist(il+nres,jl+nres)
2471 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2475 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2476 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2477 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2478 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2484 if (lprn) write (iout,*) "nl",nl," qq",qq
2485 else if (ilevel.eq.2) then
2486 np=npiece(jfrag,ilevel)
2489 ip=ipiece(i,jfrag,ilevel)
2490 do j=1,nlist_frag(ip)
2493 kp=ipiece(k,jfrag,ilevel)
2494 do l=1,nlist_frag(kp)
2496 if (iabs(kl-il).gt.nsep) then
2504 d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2505 (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2506 (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2508 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2509 if (itype(il,molnum(il)).ne.10 .or. itype(kl,molnum(kl)).ne.10) then
2512 (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2513 (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2514 (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2515 dijCM=dist(il+nres,kl+nres)
2516 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2521 write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2522 " kl",kl," itype",itype(il,molnum(il)), &
2523 itype(kl,molnum(kl))
2524 write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2525 d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2533 if (lprn) write (iout,*) "nl",nl," qq",qq
2535 write (iout,*)"Error: Q can be computed only for level 1 and 2."
2540 if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2542 qwolynes=1.0d0-maxiQ
2545 end function qwolynes
2546 !-------------------------------------------------------------------------------
2547 real(kind=8) function sigm(x)
2552 !-------------------------------------------------------------------------------
2553 subroutine fragment_list
2555 ! include 'DIMENSIONS'
2556 ! include 'DIMENSIONS.ZSCOPT'
2557 ! include 'DIMENSIONS.COMPAR'
2558 ! include 'COMMON.IOUNITS'
2559 ! include 'COMMON.COMPAR'
2560 logical :: lprn=.true.
2561 integer :: i,ilevel,j,k,jfrag
2564 do i=1,npiece(jfrag,1)
2565 if (lprn) write (iout,*) "jfrag=",jfrag,&
2566 "i=",i," fragment",ifrag(1,i,jfrag),&
2568 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2569 do k=1,nlist_frag(jfrag)
2570 if (list_frag(k,jfrag).eq.j) goto 10
2572 nlist_frag(jfrag)=nlist_frag(jfrag)+1
2573 list_frag(nlist_frag(jfrag),jfrag)=j
2578 write (iout,*) "Fragment list"
2580 write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2584 end subroutine fragment_list
2585 !-------------------------------------------------------------------------------
2586 real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2589 use control_data, only:symetr
2590 use geometry_data, only:nperm
2591 ! implicit real*8 (a-h,o-z)
2592 ! include 'DIMENSIONS'
2593 ! include 'DIMENSIONS.ZSCOPT'
2594 ! include 'DIMENSIONS.COMPAR'
2595 ! include 'COMMON.IOUNITS'
2596 ! include 'COMMON.COMPAR'
2597 ! include 'COMMON.CHAIN'
2598 ! include 'COMMON.INTERACT'
2599 ! include 'COMMON.VAR'
2600 ! include 'COMMON.CONTROL'
2601 real(kind=8) :: przes(3),obrot(3,3)
2602 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2603 !el logical :: iadded(nres)
2604 !el integer :: inumber(2,nres)
2605 !el common /ccc/ creff,cc,iadded,inumber
2608 integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2609 real(kind=8) :: rminrms,rms
2611 write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2612 write (iout,*) "npiece",npiece(j,i)
2615 ! write (iout,*) "symetr",symetr
2621 ! write (iout,*) "nperm",nperm
2628 ! write (iout,*) "kkk",kkk
2633 write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2634 ifrag(1,k,j),ifrag(2,k,j)
2637 call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2638 ! write (iout,*) "Exit cprep"
2640 ! write (iout,*) "ii=",ii
2643 ! write (iout,*) "kk",kk," npiece",npiece(kk,1)
2646 write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2647 " l=",l," adding fragment",&
2648 ifrag(1,l,kk),ifrag(2,l,kk)
2651 call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2652 ! write (iout,*) "After cprep"
2659 write (iout,*) "tuszukaj"
2662 write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2663 inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2670 call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2672 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2674 else if (rms.lt.-1.0d-6) then
2675 print *,'Error: rms^2 = ',rms,jcon,i
2677 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2680 ! write (iout,*) "rmsmin", rminrms, "rms", rms
2681 if (rms.le.rminrms) rminrms=rms
2683 rmscalc = dsqrt(rminrms)
2684 ! write (iout, *) "analysys", rmscalc,anatemp
2686 end function rmscalc
2687 !-------------------------------------------------------------------------
2688 subroutine cprep(if1,if2,ishif,idup,kwa)
2691 use control_data, only:symetr
2692 use geometry_data, only:nperm,cref,c
2693 ! implicit real*8 (a-h,o-z)
2694 ! include 'DIMENSIONS'
2695 ! include 'DIMENSIONS.ZSCOPT'
2696 ! include 'DIMENSIONS.COMPAR'
2697 ! include 'COMMON.CONTROL'
2698 ! include 'COMMON.IOUNITS'
2699 ! include 'COMMON.COMPAR'
2700 ! include 'COMMON.CHAIN'
2701 ! include 'COMMON.INTERACT'
2702 ! include 'COMMON.VAR'
2703 real(kind=8) :: przes(3),obrot(3,3)
2704 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2705 !el logical :: iadded(nres)
2706 !el integer :: inumber(2,nres)
2707 integer :: iistrart,kwa,blar
2708 !el common /ccc/ creff,cc,iadded,inumber
2709 integer :: if1,if2,ishif,idup,kkk,l,m
2710 ! write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2715 ! write (iout,*) "nperm",nperm
2719 ! write (iout,*) "l",l," iadded",iadded(l)
2721 if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2726 inumber(2,idup)=l+ishif
2728 creff(m,idup)=cref(m,l,kkk)
2729 cc(m,idup)=c(m,l+ishif)
2734 end subroutine cprep
2735 !-------------------------------------------------------------------------
2736 real(kind=8) function rmsnat(jcon)
2738 use control_data, only:symetr
2739 use geometry_data, only:nperm,cref,c
2740 use energy_data, only:itype,molnum
2741 ! implicit real*8 (a-h,o-z)
2742 ! include 'DIMENSIONS'
2743 ! include 'DIMENSIONS.ZSCOPT'
2744 ! include 'DIMENSIONS.COMPAR'
2745 ! include 'COMMON.IOUNITS'
2746 ! include 'COMMON.COMPAR'
2747 ! include 'COMMON.CHAIN'
2748 ! include 'COMMON.INTERACT'
2749 ! include 'COMMON.VAR'
2750 ! include 'COMMON.CONTROL'
2751 real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2753 integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2754 real(kind=8) :: rminrms,rmsminsing,rms
2764 if (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
2768 ccref(j,nnsup)=cref(j,i,kkk)
2772 call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2774 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2776 else if (rms.lt.-1.0d-6) then
2777 print *,'Error: rms^2 = ',rms,jcon,i
2779 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2782 if (rms.le.rminrms) rminrms=rms
2783 ! write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2785 rmsnat = dsqrt(rminrms)
2786 ! write (iout,*) "analysys",rmsnat, anatemp
2787 ! liczenie rmsdla pojedynczego lancucha
2790 !-------------------------------------------------------------------------------
2791 subroutine define_fragments
2793 use geometry_data, only:rad2deg
2794 use energy_data, only:itype,molnum
2795 use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2796 ! implicit real*8 (a-h,o-z)
2797 ! include 'DIMENSIONS'
2798 ! include 'DIMENSIONS.ZSCOPT'
2799 ! include 'DIMENSIONS.COMPAR'
2800 ! include 'COMMON.IOUNITS'
2801 ! include 'COMMON.TIME1'
2802 ! include 'COMMON.FRAG'
2803 ! include 'COMMON.SBRIDGE'
2804 ! include 'COMMON.CONTROL'
2805 ! include 'COMMON.COMPAR'
2806 ! include 'COMMON.CHAIN'
2807 ! include 'COMMON.HEADER'
2808 ! include 'COMMON.GEO'
2809 ! include 'COMMON.CONTACTS'
2810 ! include 'COMMON.PEPTCONT'
2811 ! include 'COMMON.INTERACT'
2812 ! include 'COMMON.NAMES'
2813 integer :: nstrand,istrand(2,nres/2)
2814 integer :: nhairp,ihairp(2,nres/5),mnum
2815 character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2816 'strand','strand pair'/),shape(strstr))
2817 integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2819 write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2820 'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2821 'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2822 ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2823 write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2824 ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2825 write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2826 ' MAXANG_HEL',angcut1_hel*rad2deg
2827 write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2828 ' MAXANG_BET',angcut1_bet*rad2deg
2829 write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2830 ' MAXANG_STRAND',angcut1_strand*rad2deg
2831 write (iout,*) 'FRAC_MIN',frac_min_set
2832 ! Find secondary structure elements (helices and beta-sheets)
2833 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2835 ! Define primary fragments. First include the helices.
2839 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2840 if (merge_helices) then
2841 write (iout,*) "Before merging helices: nhfrag",nhfrag
2843 write (2,*) hfrag(1,i),hfrag(2,i)
2846 do while (i.lt.nhfrag)
2847 if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2849 hfrag(2,i)=hfrag(2,i+1)
2851 hfrag(1,j)=hfrag(1,j+1)
2852 hfrag(2,j)=hfrag(2,j+1)
2857 write (iout,*) "After merging helices: nhfrag",nhfrag
2859 write (2,*) hfrag(1,i),hfrag(2,i)
2865 ifrag(1,1,i)=hfrag(1,i)
2866 ifrag(2,1,i)=hfrag(2,i)
2868 n_shift(2,i,1)=nshift_hel
2869 ang_cut(i)=angcut_hel
2870 ang_cut1(i)=angcut1_hel
2871 frac_min(i)=frac_min_set
2872 nc_fragm(i,1)=ncfrac_hel
2873 nc_req_setf(i,1)=ncreq_hel
2876 write (iout,*) "isplit_bet",isplit_bet
2877 if (isplit_bet.gt.1) then
2878 ! Split beta-sheets into strands and store strands as primary fragments.
2879 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2883 ifrag(1,1,ii)=istrand(1,i)
2884 ifrag(2,1,ii)=istrand(2,i)
2885 n_shift(1,ii,1)=nshift_strand
2886 n_shift(2,ii,1)=nshift_strand
2887 ang_cut(ii)=angcut_strand
2888 ang_cut1(ii)=angcut1_strand
2889 frac_min(ii)=frac_min_set
2894 nfrag(1)=nfrag(1)+nstrand
2895 else if (isplit_bet.eq.1) then
2896 ! Split only far beta-sheets; does not split hairpins.
2897 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2898 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2902 ifrag(1,1,ii)=ihairp(1,i)
2903 ifrag(2,1,ii)=ihairp(2,i)
2904 n_shift(1,ii,1)=nshift_bet
2905 n_shift(2,ii,1)=nshift_bet
2906 ang_cut(ii)=angcut_bet
2907 ang_cut1(ii)=angcut1_bet
2908 frac_min(ii)=frac_min_set
2909 nc_fragm(ii,1)=ncfrac_bet
2910 nc_req_setf(ii,1)=ncreq_bet
2913 nfrag(1)=nfrag(1)+nhairp
2917 ifrag(1,1,ii)=istrand(1,i)
2918 ifrag(2,1,ii)=istrand(2,i)
2919 n_shift(1,ii,1)=nshift_strand
2920 n_shift(2,ii,1)=nshift_strand
2921 ang_cut(ii)=angcut_strand
2922 ang_cut1(ii)=angcut1_strand
2923 frac_min(ii)=frac_min_set
2928 nfrag(1)=nfrag(1)+nstrand
2930 ! Do not split beta-sheets; each pair of strands is a primary element.
2931 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2935 ifrag(1,1,ii)=ihairp(1,i)
2936 ifrag(2,1,ii)=ihairp(2,i)
2937 n_shift(1,ii,1)=nshift_bet
2938 n_shift(2,ii,1)=nshift_bet
2939 ang_cut(ii)=angcut_bet
2940 ang_cut1(ii)=angcut1_bet
2941 frac_min(ii)=frac_min_set
2942 nc_fragm(ii,1)=ncfrac_bet
2943 nc_req_setf(ii,1)=ncreq_bet
2946 nfrag(1)=nfrag(1)+nhairp
2950 ifrag(1,1,ii)=bfrag(1,i)
2951 ifrag(2,1,ii)=bfrag(2,i)
2952 if (bfrag(3,i).lt.bfrag(4,i)) then
2953 ifrag(1,2,ii)=bfrag(3,i)
2954 ifrag(2,2,ii)=bfrag(4,i)
2956 ifrag(1,2,ii)=bfrag(4,i)
2957 ifrag(2,2,ii)=bfrag(3,i)
2959 n_shift(1,ii,1)=nshift_bet
2960 n_shift(2,ii,1)=nshift_bet
2961 ang_cut(ii)=angcut_bet
2962 ang_cut1(ii)=angcut1_bet
2963 frac_min(ii)=frac_min_set
2964 nc_fragm(ii,1)=ncfrac_bet
2965 nc_req_setf(ii,1)=ncreq_bet
2968 nfrag(1)=nfrag(1)+nbfrag
2970 write (iout,*) "The following primary fragments were found:"
2971 write (iout,*) "Helices:",nhfrag
2978 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2979 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
2981 write (iout,*) "Hairpins:",nhairp
2982 do i=nhfrag+1,nhfrag+nhairp
2985 it1=itype(i1,molnum(i1))
2986 it2=itype(i2,molnum(i2))
2987 write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2988 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2
2990 write (iout,*) "Far strand pairs:",nbfrag
2991 do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
2994 it1=itype(i1,molnum(i1))
2995 it2=itype(i2,molnum(i1))
2998 it3=itype(i3,molnum(i3))
2999 it4=itype(i4,molnum(i4))
3000 write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
3001 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2,&
3002 restyp(it3,molnum(i3)),i3,restyp(it4,molnum(i4)),i4
3004 write (iout,*) "Strands:",nstrand
3005 do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
3011 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
3012 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
3014 call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3015 istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3016 nc_fragm(1,1),nc_req_setf(1,1))
3017 write (iout,*) "Fragments after sorting:"
3024 write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3025 i,restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2
3026 if (npiece(i,1).eq.1) then
3027 write (iout,'(2x,a)') strstr(istruct(i))
3033 write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3034 restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2,strstr(istruct(i))
3038 end subroutine define_fragments
3039 !------------------------------------------------------------------------------
3040 subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3041 ! implicit real*8 (a-h,o-z)
3042 ! include 'DIMENSIONS'
3043 ! include 'DIMENSIONS.ZSCOPT'
3044 ! include 'DIMENSIONS.COMPAR'
3045 ! include 'COMMON.IOUNITS'
3046 integer :: nbfrag,bfrag(4,nres/3)
3047 integer :: nhairp,ihairp(2,nres/5)
3049 write (iout,*) "Entered find_and_remove_hairpins"
3050 write (iout,*) "nbfrag",nbfrag
3052 write (iout,*) i,(bfrag(k,i),k=1,4)
3056 do while (i.le.nbfrag)
3057 write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3058 if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3060 write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3062 ihairp(1,nhairp)=bfrag(1,i)
3063 ihairp(2,nhairp)=bfrag(3,i)
3067 bfrag(k,j)=bfrag(k,j+1)
3074 write (iout,*) "After finding hairpins:"
3075 write (iout,*) "nhairp",nhairp
3077 write (iout,*) i,ihairp(1,i),ihairp(2,i)
3079 write (iout,*) "nbfrag",nbfrag
3081 write (iout,*) i,(bfrag(k,i),k=1,4)
3084 end subroutine find_and_remove_hairpins
3085 !------------------------------------------------------------------------------
3086 subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3087 ! implicit real*8 (a-h,o-z)
3088 ! include 'DIMENSIONS'
3089 ! include 'DIMENSIONS.ZSCOPT'
3090 ! include 'DIMENSIONS.COMPAR'
3091 ! include 'COMMON.IOUNITS'
3092 integer :: nbfrag,bfrag(4,nres/3)
3093 integer :: nstrand,istrand(2,nres/2)
3094 integer :: nhairp,ihairp(2,nres/5)
3097 write (iout,*) "Entered split_beta"
3098 write (iout,*) "nbfrag",nbfrag
3100 write (iout,*) i,(bfrag(k,i),k=1,4)
3104 write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3105 call add_strand(nstrand,istrand,nhairp,ihairp,&
3106 bfrag(1,i),bfrag(2,i),found)
3107 if (bfrag(3,i).lt.bfrag(4,i)) then
3108 write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3109 call add_strand(nstrand,istrand,nhairp,ihairp,&
3110 bfrag(3,i),bfrag(4,i),found)
3112 write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3113 call add_strand(nstrand,istrand,nhairp,ihairp,&
3114 bfrag(4,i),bfrag(3,i),found)
3118 write (iout,*) "Strands found:",nstrand
3120 write (iout,*) i,istrand(1,i),istrand(2,i)
3123 end subroutine split_beta
3124 !------------------------------------------------------------------------------
3125 subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3126 ! implicit real*8 (a-h,o-z)
3127 ! include 'DIMENSIONS'
3128 ! include 'DIMENSIONS.ZSCOPT'
3129 ! include 'DIMENSIONS.COMPAR'
3130 ! include 'COMMON.IOUNITS'
3131 integer :: nstrand,istrand(2,nres/2)
3132 integer :: nhairp,ihairp(2,nres/5)
3134 integer :: is1,is2,j,idelt
3137 idelt=(ihairp(2,j)-ihairp(1,j))/6
3138 if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3139 write (iout,*) "strand",is1,is2," is part of hairpin",&
3140 ihairp(1,j),ihairp(2,j)
3145 idelt=(istrand(2,j)-istrand(1,j))/3
3146 if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3148 ! The strand already exists in the array; update its ends if necessary.
3149 write (iout,*) "strand",is1,is2," found at position",j,&
3150 ":",istrand(1,j),istrand(2,j)
3151 istrand(1,j)=min0(istrand(1,j),is1)
3152 istrand(2,j)=max0(istrand(2,j),is2)
3156 ! The strand has not been found; add it to the array.
3157 write (iout,*) "strand",is1,is2," added to the array."
3160 istrand(1,nstrand)=is1
3161 istrand(2,nstrand)=is2
3163 end subroutine add_strand
3164 !------------------------------------------------------------------------------
3165 subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3167 use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3168 use energy_data, only:itype,maxcont,molnum
3169 use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3170 use compare, only:freeres
3171 ! implicit real*8 (a-h,o-z)
3172 ! include 'DIMENSIONS'
3173 ! include 'DIMENSIONS.ZSCOPT'
3174 ! include 'COMMON.IOUNITS'
3175 ! include 'COMMON.FRAG'
3176 ! include 'COMMON.VAR'
3177 ! include 'COMMON.GEO'
3178 ! include 'COMMON.CHAIN'
3179 ! include 'COMMON.NAMES'
3180 ! include 'COMMON.INTERACT'
3181 integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres),&
3183 logical :: lprint,lprint_sec,not_done !el,freeres
3184 integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3185 integer :: nstrand,nbeta,nhelix,iii1,jjj1,mnum
3186 real(kind=8) :: p1,p2
3187 !rel external freeres
3188 character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3190 write (iout,*) "entered secondary2",ncont
3191 write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3193 write (iout,*) icont(1,i),icont(2,i)
3207 ! finding parallel beta
3208 !d write (iout,*) '------- looking for parallel beta -----------'
3214 if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3215 .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3216 !d write (iout,*) "parallel",i1,j1
3217 if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3220 !d write (iout,*) i1,j1
3226 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3227 freeres(i1,j1,nsec,isec)) goto 5
3231 !d write (iout,*) i1,j1,not_done
3235 if (i1-ii1.gt.1) then
3239 if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3243 bfrag(1,nbfrag)=ii1+1
3244 bfrag(2,nbfrag)=i1+1
3245 bfrag(3,nbfrag)=jj1+1
3246 bfrag(4,nbfrag)=min0(j1+1,nres)
3250 isec(ij,nsec(ij))=nbeta
3254 isec(ij,nsec(ij))=nbeta
3259 if (nbeta.le.9) then
3260 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3261 "DefPropRes 'strand",nstrand,&
3262 "' 'num = ",ii1-1,"..",i1-1,"'"
3264 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3265 "DefPropRes 'strand",nstrand,&
3266 "' 'num = ",ii1-1,"..",i1-1,"'"
3269 if (nbeta.le.9) then
3270 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3271 "DefPropRes 'strand",nstrand,&
3272 "' 'num = ",jj1-1,"..",j1-1,"'"
3274 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3275 "DefPropRes 'strand",nstrand,&
3276 "' 'num = ",jj1-1,"..",j1-1,"'"
3278 write(12,'(a8,4i4)') &
3279 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3283 endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3286 ! finding antiparallel beta
3287 !d write (iout,*) '--------- looking for antiparallel beta ---------'
3292 if (freeres(i1,j1,nsec,isec)) then
3295 !d write (iout,*) i1,j1
3302 if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3303 freeres(i1,j1,nsec,isec)) goto 6
3307 !d write (iout,*) i1,j1,not_done
3311 if (i1-ii1.gt.1) then
3315 bfrag(2,nbfrag)=min0(i1+1,nres)
3316 bfrag(3,nbfrag)=min0(jj1+1,nres)
3323 if (nsec(ij).le.2) then
3324 isec(ij,nsec(ij))=nbeta
3330 if (nsec(ij).le.2) then
3331 isec(ij,nsec(ij))=nbeta
3336 if (lprint_sec) then
3337 write (iout,'(a,i3,4i4)')'antiparallel beta',&
3338 nbeta,ii1-1,i1,jj1,j1-1
3340 if (nstrand.le.9) then
3341 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3342 "DefPropRes 'strand",nstrand,&
3343 "' 'num = ",ii1-2,"..",i1-1,"'"
3345 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3346 "DefPropRes 'strand",nstrand,&
3347 "' 'num = ",ii1-2,"..",i1-1,"'"
3350 if (nstrand.le.9) then
3351 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3352 "DefPropRes 'strand",nstrand,&
3353 "' 'num = ",j1-2,"..",jj1-1,"'"
3355 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3356 "DefPropRes 'strand",nstrand,&
3357 "' 'num = ",j1-2,"..",jj1-1,"'"
3359 write(12,'(a8,4i4)') &
3360 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3366 !d write (iout,*) "After beta:",nbfrag
3368 !d write (iout,*) (bfrag(j,i),j=1,4)
3371 if (nstrand.gt.0.and.lprint_sec) then
3372 write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3375 write(12,'(a9,i1,$)') " | strand",i
3377 write(12,'(a9,i2,$)') " | strand",i
3380 write(12,'(a1)') "'"
3384 ! finding alpha or 310 helix
3390 p1=phi(i1+2)*rad2deg
3392 if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3395 if (j1.eq.i1+3 .and. &
3396 ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3397 ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3398 !d if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3399 !o if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3402 if (nsec(ii1).eq.0) then
3411 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3415 p1=phi(i1+2)*rad2deg
3416 p2=phi(j1+2)*rad2deg
3417 if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3420 !d write (iout,*) i1,j1,not_done,p1,p2
3423 if (j1-ii1.gt.4) then
3425 !d write (iout,*)'helix',nhelix,ii1,j1
3434 if (lprint_sec) then
3435 write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3436 if (nhelix.le.9) then
3437 write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3438 "DefPropRes 'helix",nhelix,&
3439 "' 'num = ",ii1-1,"..",j1-2,"'"
3441 write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3442 "DefPropRes 'helix",nhelix,&
3443 "' 'num = ",ii1-1,"..",j1-2,"'"
3450 if (nhelix.gt.0.and.lprint_sec) then
3451 write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3453 if (nhelix.le.9) then
3454 write(12,'(a8,i1,$)') " | helix",i
3456 write(12,'(a8,i2,$)') " | helix",i
3459 write(12,'(a1)') "'"
3462 if (lprint_sec) then
3463 write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3464 write(12,'(a20)') "XMacStand ribbon.mac"
3469 write(iout,*) 'UNRES seq:',anatemp
3471 write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3475 write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3481 do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3484 do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3489 do k=hfrag(1,j),hfrag(2,j)
3495 write (iout,*) "Secondary structure"
3501 write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3502 write (iout,'(80a1)') (onelet(itype(k,mnum)),k=ist,ien)
3503 write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3508 end subroutine secondary2
3509 !-------------------------------------------------
3510 ! logical function freeres(i,j,nsec,isec)
3511 ! include 'DIMENSIONS'
3512 ! integer :: isec(nres,4),nsec(nres)
3513 ! integer :: i,j,k,l
3516 ! if (nsec(i).gt.1.or.nsec(j).gt.1) return
3519 ! if (isec(i,k).eq.isec(j,l)) return
3524 ! end function freeres
3525 !-------------------------------------------------
3526 subroutine alloc_compar_arrays(nfrg,nlev)
3528 use energy_data, only:maxcont
3530 integer :: nfrg,nlev
3532 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3533 !------------------------
3536 allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3537 allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3538 !------------------------
3541 allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3542 allocate(qfrag(nfrg,2)) !(maxfrag,2)
3543 allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3544 allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3545 allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3546 ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3547 ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3548 allocate(ncont_nat(2,nfrg,nlev+1))
3549 allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3550 ! allocate(nfrag(nlev)) !(maxlevel)
3551 allocate(isnfrag(nlev+2)) !(maxlevel+1)
3552 allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3553 allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3554 allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3555 allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3556 allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3557 !------------------------
3560 ! integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3561 allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3562 allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3563 ! integer,dimension(:),allocatable :: isec_ref !(maxres)
3564 !------------------------
3565 ! module w_comm_local
3567 allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3568 allocate(iadded(nres)) !(nres)
3569 allocate(inumber(2,nres)) !(2,nres)
3572 !-------------------------------------------------------------------------------
3573 end subroutine alloc_compar_arrays
3575 !-------------------------------------------------------------------------------
3576 end module conform_compar