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,molnum
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
1027 integer :: mnum,mnum2
1030 ! print *,'nnt=',nnt,' nct=',nct
1033 iti=iabs(itype(i,1))
1036 itj=iabs(itype(j,1))
1038 ! rcomp=sigmaii(iti,itj)+1.0D0
1039 rcomp=facont*sigmaii(iti,itj)
1041 ! rcomp=sigma(iti,itj)+1.0D0
1042 rcomp=facont*sigma(iti,itj)
1045 ! print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1046 if (dist(nres+i,nres+j).lt.rcomp) then
1054 write (iout,'(a)') 'Contact map:'
1061 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1062 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1066 end subroutine contact
1068 !----------------------------------------------------------------------------
1069 real(kind=8) function contact_fract(ncont,ncont_ref,&
1072 use energy_data, only:maxcont
1074 ! include 'DIMENSIONS'
1075 ! include 'COMMON.IOUNITS'
1076 integer :: i,j,nmatch
1077 integer :: ncont,ncont_ref
1078 integer,dimension(2,maxcont) :: icont,icont_ref
1080 ! print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1081 ! write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1082 ! write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1083 ! write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1084 ! write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1087 if (icont(1,i).eq.icont_ref(1,j) .and. &
1088 icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1091 ! print *,' nmatch=',nmatch
1092 ! contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1093 contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1095 end function contact_fract
1097 !------------------------------------------------------------------------------
1098 subroutine pept_cont(lprint,ncont,icont)
1100 use geometry_data, only:c
1101 use energy_data, only:maxcont,nnt,nct,itype,molnum
1103 ! include 'DIMENSIONS'
1104 ! include 'DIMENSIONS.ZSCOPT'
1105 ! include 'COMMON.IOUNITS'
1106 ! include 'COMMON.CHAIN'
1107 ! include 'COMMON.INTERACT'
1108 ! include 'COMMON.FFIELD'
1109 ! include 'COMMON.NAMES'
1110 integer :: ncont,icont(2,maxcont)
1111 integer :: i,j,k,kkk,i1,i2,it1,it2,mnum
1113 !el real(kind=8) :: dist
1114 real(kind=8) :: rcomp=5.5d0
1117 print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1120 c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1124 c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1126 if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1134 write (iout,'(a)') 'PP contact map:'
1141 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1142 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1146 end subroutine pept_cont
1147 !-----------------------------------------------------------------------------
1149 !-----------------------------------------------------------------------------
1150 subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1151 ncont_interfrag,icont_interfrag)
1153 use energy_data, only:itype,maxcont,molnum
1154 ! include 'DIMENSIONS'
1155 ! include 'DIMENSIONS.ZSCOPT'
1156 ! include 'DIMENSIONS.COMPAR'
1157 ! include 'COMMON.INTERACT'
1158 ! include 'COMMON.COMPAR'
1159 ! include 'COMMON.IOUNITS'
1160 ! include 'COMMON.CHAIN'
1161 ! include 'COMMON.NAMES'
1162 integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1163 icont_interfrag(2,maxcont,mmaxfrag)
1164 logical :: OK1,OK2,lprint
1165 integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2,mnum
1166 ! Determine the contacts that occur within a fragment and between fragments.
1171 ! write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1172 ! & ,k=1,npiece(i,1))
1173 ! write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1174 ! & ,k=1,npiece(j,1))
1175 ! write (iout,*) "ncont",ncont
1181 do while (.not.OK1 .and. l.lt.npiece(j,1))
1183 OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1184 ic1.le.ifrag(2,l,j)+is
1188 do while (.not.OK2 .and. l.lt.npiece(i,1))
1190 OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1191 ic2.le.ifrag(2,l,i)+is
1193 ! write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1195 if (OK1.and.OK2) then
1197 icont_interfrag(1,nc,ind)=ic1
1198 icont_interfrag(2,nc,ind)=ic2
1199 ! write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1202 ncont_interfrag(ind)=nc
1203 ! do k=1,ncont_interfrag(ind)
1204 ! i1=icont_interfrag(1,k,ind)
1205 ! i2=icont_interfrag(2,k,ind)
1208 ! write (iout,'(i3,2x,a,i4,2x,a,i4)')
1209 ! & i,restyp(it1),i1,restyp(it2),i2
1214 write (iout,*) "Contacts within fragments:"
1216 write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1217 ifrag(2,k,i),k=1,npiece(i,1)),")"
1219 do k=1,ncont_interfrag(ind)
1220 i1=icont_interfrag(1,k,ind)
1221 i2=icont_interfrag(2,k,ind)
1224 it2=itype(i2,molnum(i2))
1225 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1226 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1230 write (iout,*) "Contacts between fragments:"
1234 write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1235 ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1236 (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1237 write (iout,*) "Number of contacts",&
1238 ncont_interfrag(ind)
1240 do k=1,ncont_interfrag(ind)
1241 i1=icont_interfrag(1,k,ind)
1242 i2=icont_interfrag(2,k,ind)
1245 it2=itype(i2,molnum(i2))
1246 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1247 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1253 end subroutine contacts_between_fragments
1254 !-----------------------------------------------------------------------------
1256 !-----------------------------------------------------------------------------
1257 subroutine contfunc(cscore,itypi,itypj)
1259 ! This subroutine calculates the contact function based on
1260 ! the Gay-Berne potential of interaction.
1263 ! implicit real*8 (a-h,o-z)
1264 ! include 'DIMENSIONS'
1265 ! include 'COMMON.CONTPAR'
1266 ! include 'COMMON.CALC'
1268 integer :: itypi,itypj
1269 real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1271 sig0ij=sig_comp(itypi,itypj)
1272 chi1=chi_comp(itypi,itypj)
1273 chi2=chi_comp(itypj,itypi)
1275 chip1=chip_comp(itypi,itypj)
1276 chip2=chip_comp(itypj,itypi)
1278 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1280 ! Calculate angle-dependent terms of the contact function
1284 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1285 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1286 om12=dxi*dxj+dyi*dyj+dzi*dzj
1288 ! print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1290 ! & rij,rrij,om1,om2,om12
1291 ! Calculate eps1(om12)
1292 faceps1=1.0D0-om12*chiom12
1293 faceps1_inv=1.0D0/faceps1
1294 eps1=dsqrt(faceps1_inv)
1295 ! Following variable is eps1*deps1/dom12
1296 eps1_om12=faceps1_inv*chiom12
1297 ! Calculate sigma(om1,om2,om12)
1301 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1302 sigsq=1.0D0-facsig*faceps1_inv
1303 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1306 chipom12=chip12*om12
1307 facp=1.0D0-om12*chipom12
1309 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1310 ! Following variable is the square root of eps2
1311 eps2rt=1.0D0-facp1*facp_inv
1313 sig=sig0ij*dsqrt(sigsq)
1314 rij_shift=1.0D0/rij-sig+sig0ij
1315 if (rij_shift.le.0.0D0) then
1317 cscore = -dlog(evdw+1.0d-6)
1320 rij_shift=1.0D0/rij_shift
1321 e2=(rij_shift*sig0ij)**expon
1322 evdw=dabs(eps1*eps2rt**2*e2)
1323 if (evdw.gt.1.0d1) evdw = 1.0d1
1324 cscore = -dlog(evdw+1.0d-6)
1326 end subroutine contfunc
1327 !------------------------------------------------------------------------------
1328 subroutine scdist(cscore,itypi,itypj)
1330 ! This subroutine calculates the contact distance
1333 ! implicit real*8 (a-h,o-z)
1334 ! include 'DIMENSIONS'
1335 ! include 'COMMON.CONTPAR'
1336 ! include 'COMMON.CALC'
1337 integer :: itypi,itypj
1338 real(kind=8) :: cscore,rrij
1340 chi1=chi_comp(itypi,itypj)
1341 chi2=chi_comp(itypj,itypi)
1343 rrij=xj*xj+yj*yj+zj*zj
1345 ! Calculate angle-dependent terms of the contact function
1349 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1350 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1351 om12=dxi*dxj+dyi*dyj+dzi*dzj
1356 cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1358 end subroutine scdist
1359 !------------------------------------------------------------------------------
1361 !------------------------------------------------------------------------------
1362 subroutine elecont(lprint,ncont,icont,ist,ien)
1364 use geometry_data, only:c
1365 use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2,molnum
1367 ! include 'DIMENSIONS'
1368 ! include 'DIMENSIONS.ZSCOPT'
1369 ! include 'DIMENSIONS.COMPAR'
1370 ! include 'COMMON.IOUNITS'
1371 ! include 'COMMON.CHAIN'
1372 ! include 'COMMON.INTERACT'
1373 ! include 'COMMON.FFIELD'
1374 ! include 'COMMON.NAMES'
1375 ! include 'COMMON.LOCAL'
1377 integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1378 real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1379 xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1380 vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1382 real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1383 -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1384 real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1385 0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1386 real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1387 real(kind=8) :: elcutoff=-0.3d0
1388 real(kind=8) :: elecutoff_14=-0.5d0
1389 integer :: ncont,icont(2,maxcont),mnum
1390 real(kind=8) :: econt(maxcont)
1392 ! Load the constants of peptide bond - peptide bond interactions.
1393 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1394 ! proline) - determined by averaging ECEPP energy.
1398 ! data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1399 ! data rpp / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1400 !el data (elpp6c) /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1401 !el data (elpp3c) / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1402 !el data (elcutoff) /-0.3d0/
1403 !el data (elecutoff_14) /-0.5d0/
1406 if (lprint) write (iout,'(a)') &
1407 "Constants of electrostatic interaction energy expression."
1411 appc(i,j)=epp(i,j)*rri*rri
1412 bppc(i,j)=-2.0*epp(i,j)*rri
1413 ael6c(i,j)=elpp6c(i,j)*4.2**6
1414 ael3c(i,j)=elpp3c(i,j)*4.2**3
1416 write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1435 if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1436 if (iteli.eq.2 .and. itelj.eq.2 &
1437 .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1438 aaa=appc(iteli,itelj)
1439 bbb=bppc(iteli,itelj)
1440 ael6i=ael6c(iteli,itelj)
1441 ael3i=ael3c(iteli,itelj)
1445 xj=c(1,j)+0.5*dxj-xmedi
1446 yj=c(2,j)+0.5*dyj-ymedi
1447 zj=c(3,j)+0.5*dzj-zmedi
1448 rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1453 cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1454 cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1455 cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1456 fac=cosa-3.0*cosb*cosg
1462 el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1465 if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1466 j.eq.i+2 .and. eesij.le.elecutoff_14) then
1477 write (iout,*) 'Total average electrostatic energy: ',ees
1478 write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1480 write (iout,*) 'Electrostatic contacts before pruning: '
1484 it1=itype(i1,molnum(i1))
1485 it2=itype(i2,molnum(i1))
1486 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1487 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i1)),i2,econt(i)
1490 ! For given residues keep only the contacts with the greatest energy.
1492 do while (i.lt.ncont)
1498 do while (j.lt.ncont)
1500 if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1501 ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1502 ! write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1503 ! & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1504 if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1505 if (ic1.eq.icont(1,j)) then
1507 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1508 .and. iabs(icont(1,k)-ic1).le.2 .and. &
1509 econt(k).lt.econt(j) ) goto 21
1511 else if (ic2.eq.icont(2,j) ) then
1513 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1514 .and. iabs(icont(2,k)-ic2).le.2 .and. &
1515 econt(k).lt.econt(j) ) goto 21
1518 ! Remove ith contact
1520 icont(1,k-1)=icont(1,k)
1521 icont(2,k-1)=icont(2,k)
1526 ! write (iout,*) "ncont",ncont
1528 ! write (iout,*) icont(1,k),icont(2,k)
1531 else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1533 if (ic1.eq.icont(1,j)) then
1535 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1536 .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1537 econt(k).lt.econt(i) ) goto 21
1539 else if (ic2.eq.icont(2,j) ) then
1541 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1542 .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1543 econt(k).lt.econt(i) ) goto 21
1546 ! Remove jth contact
1548 icont(1,k-1)=icont(1,k)
1549 icont(2,k-1)=icont(2,k)
1553 ! write (iout,*) "ncont",ncont
1555 ! write (iout,*) icont(1,k),icont(2,k)
1566 write (iout,*) 'Electrostatic contacts after pruning: '
1573 it2=itype(i2,molnum(i2))
1574 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1575 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2,econt(i)
1579 end subroutine elecont
1580 !------------------------------------------------------------------------------
1582 !------------------------------------------------------------------------------
1583 subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1584 ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1585 nc_frac,nc_req_set,istr,llocal,lprn)
1587 use energy_data, only:maxcont
1588 ! implicit real*8 (a-h,o-z)
1589 ! include 'DIMENSIONS'
1590 ! include 'COMMON.IOUNITS'
1591 integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1592 integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1593 real(kind=8) :: nc_frac
1594 logical :: llocal,lprn
1595 integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1596 nc_req_set,istr,nc_match_max
1597 integer :: i,nc_req,nc_match1,is,js
1600 nc_match_max=nc_match_max+ &
1601 min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1605 else if (nc_req_set.eq.0) then
1606 nc_req=nc_match_max*nc_frac
1608 nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1609 dfloat(nc_req_set)+1.0d-7)
1611 ! write (iout,*) "match_contact: nc_req:",nc_req
1612 ! write (iout,*) "nc_match_max",nc_match_max
1613 ! write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1614 ! & " n_shif2",n_shif2
1615 ! Match current contact map against reference contact map; exit, if at least
1616 ! half of the contacts match
1617 call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1618 ncont,icont,jfrag,llocal,lprn)
1619 nc_match1_max=nc_match1
1620 if (lprn .and. nc_match.gt.0) write (iout,*) &
1621 "Shift:",0,0," nc_match1",nc_match1,&
1622 " nc_match=",nc_match," req'd",nc_req
1623 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1624 nc_req.eq.0 .and. nc_match.eq.1) then
1629 ! If sufficient matches are not found, try to shift contact maps up to three
1631 if (n_shif1.gt.0) then
1633 ! The following four tries help to find shifted beta-sheet patterns
1634 ! Shift "left" strand backward
1635 call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1636 icont_ref,ncont,icont,jfrag,llocal,lprn)
1637 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1638 if (lprn .and. nc_match.gt.0) write (iout,*) &
1639 "Shift:",-is,0," nc_match1",nc_match1,&
1640 " nc_match=",nc_match," req'd",nc_req
1641 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1642 nc_req.eq.0 .and. nc_match.eq.1) then
1647 ! Shift "left" strand forward
1648 call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1649 icont_ref,ncont,icont,jfrag,llocal,lprn)
1650 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1651 if (lprn .and. nc_match.gt.0) write (iout,*) &
1652 "Shift:",is,0," nc_match1",nc_match1,&
1653 " nc_match=",nc_match," req'd",nc_req
1654 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1655 nc_req.eq.0 .and. nc_match.eq.1) then
1661 if (nc_req.eq.0) return
1662 ! Shift "right" strand backward
1664 call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1665 icont_ref,ncont,icont,jfrag,llocal,lprn)
1666 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1667 if (lprn .and. nc_match.gt.0) write (iout,*) &
1668 "Shift:",0,-is," nc_match1",nc_match1,&
1669 " nc_match=",nc_match," req'd",nc_req
1670 if (nc_match.ge.nc_req) then
1675 ! Shift "right" strand upward
1676 call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
1677 icont_ref,ncont,icont,jfrag,llocal,lprn)
1678 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1679 if (lprn .and. nc_match.gt.0) write (iout,*) &
1680 "Shift:",0,is," nc_match1",nc_match1,&
1681 " nc_match=",nc_match," req'd",nc_req
1682 if (nc_match.ge.nc_req) then
1688 ! Now try to shift both residues in contacts.
1692 call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1693 icont_ref,ncont,icont,jfrag,llocal,lprn)
1694 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1695 if (lprn .and. nc_match.gt.0) write (iout,*) &
1696 "Shift:",-is,-js," nc_match1",nc_match1,&
1697 " nc_match=",nc_match," req'd",nc_req
1698 if (nc_match.ge.nc_req) then
1703 call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1704 icont_ref,ncont,icont,jfrag,llocal,lprn)
1705 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1706 if (lprn .and. nc_match.gt.0) write (iout,*) &
1707 "Shift:",is,js," nc_match1",nc_match1,&
1708 " nc_match=",nc_match," req'd",nc_req
1709 if (nc_match.ge.nc_req) then
1715 call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
1716 icont_ref,ncont,icont,jfrag,llocal,lprn)
1717 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1718 if (lprn .and. nc_match.gt.0) write (iout,*) &
1719 "Shift:",-js,-is," nc_match1",nc_match1,&
1720 " nc_match=",nc_match," req'd",nc_req
1721 if (nc_match.ge.nc_req) then
1727 call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
1728 icont_ref,ncont,icont,jfrag,llocal,lprn)
1729 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1730 if (lprn .and. nc_match.gt.0) write (iout,*) &
1731 "Shift:",js,is," nc_match1",nc_match1,&
1732 " nc_match=",nc_match," req'd",nc_req
1733 if (nc_match.ge.nc_req) then
1740 if (is+js.le.n_shif1) then
1741 call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1742 icont_ref,ncont,icont,jfrag,llocal,lprn)
1743 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1744 if (lprn .and. nc_match.gt.0) write (iout,*) &
1745 "Shift:",-is,js," nc_match1",nc_match1,&
1746 " nc_match=",nc_match," req'd",nc_req
1747 if (nc_match.ge.nc_req) then
1753 call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
1754 icont_ref,ncont,icont,jfrag,llocal,lprn)
1755 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1756 if (lprn .and. nc_match.gt.0) write (iout,*) &
1757 "Shift:",js,-is," nc_match1",nc_match1,&
1758 " nc_match=",nc_match," req'd",nc_req
1759 if (nc_match.ge.nc_req) then
1770 if (n_shif2.gt.0) then
1772 call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1773 icont_ref,ncont,icont,jfrag,llocal,lprn)
1774 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1775 if (lprn .and. nc_match.gt.0) write (iout,*) &
1776 "Shift:",-is,-is," nc_match1",nc_match1,&
1777 " nc_match=",nc_match," req'd",nc_req
1778 if (nc_match.ge.nc_req) then
1783 call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1784 icont_ref,ncont,icont,jfrag,llocal,lprn)
1785 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1786 if (lprn .and. nc_match.gt.0) write (iout,*) &
1787 "Shift:",is,is," nc_match1",nc_match1,&
1788 " nc_match=",nc_match," req'd",nc_req
1789 if (nc_match.ge.nc_req) then
1796 ! If this point is reached, the contact maps are different.
1801 end subroutine match_contact
1802 !-------------------------------------------------------------------------
1803 subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1804 ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1806 use energy_data, only:nnt,nct,maxcont
1807 ! implicit real*8 (a-h,o-z)
1808 ! include 'DIMENSIONS'
1809 ! include 'DIMENSIONS.ZSCOPT'
1810 ! include 'DIMENSIONS.COMPAR'
1811 ! include 'COMMON.IOUNITS'
1812 ! include 'COMMON.INTERACT'
1813 ! include 'COMMON.GEO'
1814 ! include 'COMMON.COMPAR'
1815 logical :: llocal,lprn
1816 integer ncont_ref,ncont,ishift,ishif2,nang_pair
1817 integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1818 integer,dimension(2,nres) :: iang_pair !(2,maxres)
1819 integer :: nc_match,nc_match1,ishif1,jfrag
1820 integer :: i,j,ic1,ic2
1821 real(kind=8) :: diffang,fract,rad2deg
1823 ! Compare the contact map against the reference contact map; they're stored
1824 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1825 if (lprn) write (iout,'(80(1h*))')
1828 ! Check the local structure by comparing dihedral angles.
1829 ! write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1830 if (llocal .and. ncont_ref.eq.0) then
1831 ! If there are no contacts just compare the dihedral angles and exit.
1832 call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1834 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1835 " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1836 if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1846 ic1=icont(1,i)+ishif1
1847 ic2=icont(2,i)+ishif2
1848 ! write (iout,*) "i",i," ic1",ic1," ic2",ic2
1849 if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1851 if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1852 nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1853 nc_match1=nc_match1+1
1854 icont_match(1,nc_match1)=ic1
1855 icont_match(2,nc_match1)=ic2
1856 ! call add_angpair(icont(1,i),icont_ref(1,j),
1857 ! & nang_pair,iang_pair)
1858 ! call add_angpair(icont(2,i),icont_ref(2,j),
1859 ! & nang_pair,iang_pair)
1860 if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1861 " match",icont_ref(1,j),icont_ref(2,j),&
1862 " shifts",ishif1,ishif2
1869 write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1870 write (iout,*) "icont_match"
1872 write (iout,*) icont_match(1,i),icont_match(2,i)
1875 if (llocal .and. nc_match.gt.0) then
1876 call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1877 ang_cut1(jfrag),diffang,fract)
1878 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1879 " ang_cut:",ang_cut(jfrag)*rad2deg,&
1880 " ang_cut1",ang_cut1(jfrag)*rad2deg
1881 if (diffang.gt.ang_cut(jfrag) &
1882 .or. fract.lt.frac_min(jfrag)) nc_match=0
1884 ! if (nc_match.gt.0) then
1885 ! diffang = angnorm1(nang_pair,iang_pair,lprn)
1886 ! if (diffang.gt.ang_cut(jfrag)) nc_match=0
1888 if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1889 " diffang",rad2deg*diffang," nc_match",nc_match
1891 end subroutine ncont_match
1892 !------------------------------------------------------------------------------
1893 subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1894 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1895 ! conformation considered to that of the reference conformation.
1896 ! Returns the number of equivalent residues (nsec_match).
1897 ! implicit real*8 (a-h,o-z)
1898 ! include 'DIMENSIONS'
1899 ! include 'DIMENSIONS.ZSCOPT'
1900 ! include 'DIMENSIONS.COMPAR'
1901 ! include 'COMMON.IOUNITS'
1902 ! include 'COMMON.CHAIN'
1903 ! include 'COMMON.PEPTCONT'
1904 ! include 'COMMON.COMPAR'
1906 integer :: isecstr(nres)
1907 integer :: jfrag,nsec_match,npart,i,j
1908 npart = npiece(jfrag,1)
1911 write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1912 (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1913 write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1914 write (iout,'(80i1)') (isecstr(j),j=1,nres)
1917 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1918 ! The residue has equivalent conformational state to that of the reference
1920 ! a) the conformational states are equal or
1921 ! b) the reference state is a coil and that of the conformation considered
1923 ! c) the conformational state of the conformation considered is a strand
1924 ! and that of the reference conformation is a coil.
1925 ! 10/28/02 - case (b) deleted.
1926 if (isecstr(j).eq.isec_ref(j) .or. &
1927 ! & isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1928 isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1929 nsec_match=nsec_match+1
1933 end subroutine match_secondary
1934 !------------------------------------------------------------------------------
1936 !------------------------------------------------------------------------------
1937 subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1939 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1941 ! implicit real*8 (a-h,o-z)
1942 real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1943 real(kind=8) :: uu,vv,aa,bb,dd
1944 real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1945 !el odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1946 !el + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1947 ! print *,"r1",(r1(i),i=1,3)
1948 ! print *,"r2",(r2(i),i=1,3)
1949 ! print *,"a",(a(i),i=1,3)
1950 ! print *,"b",(b(i),i=1,3)
1951 aa = a(1)**2+a(2)**2+a(3)**2
1952 bb = b(1)**2+b(2)**2+b(3)**2
1953 ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1954 ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1955 br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1957 ! print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1958 uu = (-ar*bb+br*ab)/det
1959 vv = (br*aa-ar*ab)/det
1965 !el dd1 = odl(uu,vv)
1966 dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1967 !el dd2 = odl(0.0d0,0.0d0)
1968 dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1969 !el dd3 = odl(0.0d0,1.0d0)
1970 dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1971 !el dd4 = odl(1.0d0,0.0d0)
1972 dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1973 !el dd5 = odl(1.0d0,1.0d0)
1974 dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1975 dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1979 else if (dd.eq.dd3) then
1982 else if (dd.eq.dd4) then
1985 else if (dd.eq.dd5) then
1994 ! dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
1998 ! write (8,*) uu,vv,dd,dd1
2001 end subroutine odlodc
2002 !------------------------------------------------------------------------------
2003 real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
2005 real(kind=8),dimension(3) :: r1,r2
2006 real(kind=8) :: aa,bb,u,v,ar,br,ab
2008 odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
2009 + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
2012 !------------------------------------------------------------------------------
2014 !------------------------------------------------------------------------------
2015 subroutine proc_cont
2017 use geometry_data, only:rad2deg
2018 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2020 ! implicit real*8 (a-h,o-z)
2021 ! include 'DIMENSIONS'
2022 ! include 'DIMENSIONS.ZSCOPT'
2023 ! include 'DIMENSIONS.COMPAR'
2024 ! include 'COMMON.IOUNITS'
2025 ! include 'COMMON.TIME1'
2026 ! include 'COMMON.SBRIDGE'
2027 ! include 'COMMON.CONTROL'
2028 ! include 'COMMON.COMPAR'
2029 ! include 'COMMON.CHAIN'
2030 ! include 'COMMON.HEADER'
2031 ! include 'COMMON.CONTACTS1'
2032 ! include 'COMMON.PEPTCONT'
2033 ! include 'COMMON.GEO'
2034 integer :: i,j,k,ind,len_cut,ndigit,length_frag
2036 write (iout,*) "proc_cont: nlevel",nlevel
2037 if (nlevel.lt.0) then
2038 write (iout,*) "call define_fragments"
2039 call define_fragments
2041 write (iout,*) "call secondary2"
2042 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2045 write (iout,'(80(1h=))')
2046 write (iout,*) "Electrostatic contacts"
2047 call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2048 icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2049 write (iout,'(80(1h=))')
2050 write (iout,*) "Side chain contacts"
2051 call contacts_between_fragments(.true.,0,ncont_ref,&
2052 icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2053 if (nlevel.lt.0) then
2057 if (istruct(i).le.1) then
2058 len_cut=max0(len_frag(i,1)*4/5,3)
2059 else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2060 len_cut=max0(len_frag(i,1)*2/5,3)
2062 write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2063 ncont_frag_ref(ind)," len_cut",len_cut,&
2064 " icont_single",icont_single," iloc_single",iloc_single
2066 if (iloc(i).gt.0) write (iout,*) &
2067 "Local structure used to compare structure of fragment",i,&
2069 if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2070 .and. icont_single.gt.0 .and. &
2071 ncont_frag_ref(ind).ge.len_cut) then
2072 write (iout,*) "Electrostatic contacts used to compare",&
2073 " structure of fragment",i," to native."
2076 else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2078 write (iout,*) "Side chain contacts used to compare",&
2079 " structure of fragment",i," to native."
2083 write (iout,*) "Contacts not used to compare",&
2084 " structure of fragment",i," to native."
2089 if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2090 .and. ielecont(i,1).eq.0) then
2091 write (iout,*) "RMSD used to compare",&
2092 " structure of fragment",i," to native."
2095 write (iout,*) "RMSD not used to compare",&
2096 " structure of fragment",i," to native."
2101 if (nlevel.lt.-1) then
2104 if (nlevel.gt.3) nlevel=3
2105 if (nlevel.eq.3) then
2107 npiece(1,3)=nfrag(1)
2117 else if (nlevel.eq.-1) then
2122 isnfrag(i+1)=isnfrag(i)+nfrag(i)
2126 ndigit=ndigit+2*nfrag(i)
2128 write (iout,*) "ndigit",ndigit
2129 if (.not.binary .and. ndigit.gt.30) then
2130 write (iout,*) "Highest class too large; switching to",&
2131 " binary representation."
2134 write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2135 write(iout,*) "rmscut_base_up",rmscut_base_up,&
2136 " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2142 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2146 length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2149 len_frag(j,i)=length_frag
2150 rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2151 rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2152 if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2153 rmscutfrag(1,j,i)=rmsup_lim
2154 if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2155 rmscutfrag(1,j,i)=rmsupup_lim
2158 write (iout,*) "Level",1," number of fragments:",nfrag(1)
2160 write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2161 k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2162 rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2163 ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2164 nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2167 write (iout,*) "Level",i," number of fragments:",nfrag(i)
2169 write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2170 k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2171 rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2172 nc_fragm(j,i),nc_req_setf(j,i)
2176 end subroutine proc_cont
2177 !------------------------------------------------------------------------------
2179 !------------------------------------------------------------------------------
2180 subroutine define_pairs
2182 ! use energy_data, only:nsccont_frag_ref
2183 ! implicit real*8 (a-h,o-z)
2184 ! include 'DIMENSIONS'
2185 ! include 'DIMENSIONS.ZSCOPT'
2186 ! include 'DIMENSIONS.COMPAR'
2187 ! include 'COMMON.IOUNITS'
2188 ! include 'COMMON.TIME1'
2189 ! include 'COMMON.SBRIDGE'
2190 ! include 'COMMON.CONTROL'
2191 ! include 'COMMON.COMPAR'
2192 ! include 'COMMON.FRAG'
2193 ! include 'COMMON.CHAIN'
2194 ! include 'COMMON.HEADER'
2195 ! include 'COMMON.GEO'
2196 ! include 'COMMON.CONTACTS1'
2197 ! include 'COMMON.PEPTCONT'
2198 integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2203 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2205 len_frag(j,1)=length_frag
2206 write (iout,*) "Fragment",j," length",len_frag(j,1)
2212 if (istruct(i).le.1 .or. istruct(j).le.1) then
2213 if (istruct(i).le.1) then
2218 if (istruct(j).le.1) then
2223 len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2225 if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2230 if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2235 len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2237 write (iout,*) "Fragments",i,j," structure",istruct(i),&
2238 istruct(j)," # contacts",&
2239 ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2240 " lengths",len_frag(i,1),len_frag(j,1),&
2241 " ll1",ll1," ll2",ll2," len_cut",len_cut
2242 if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2243 nsccont_frag_ref(ind).ge.len_cut ) then
2244 if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2245 write (iout,*) "Adding pair of helices",i,j,&
2246 " based on SC contacts"
2248 write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2249 " based on SC contacts"
2252 if (icont_pair.gt.0) then
2253 write (iout,*) "# SC contacts will be used",&
2255 isccont(nfrag(2),2)=1
2257 if (irms_pair.gt.0) then
2258 write (iout,*) "Fragment RMSD will be used",&
2262 npiece(nfrag(2),2)=2
2263 ipiece(1,nfrag(2),2)=i
2264 ipiece(2,nfrag(2),2)=j
2265 ielecont(nfrag(2),2)=0
2266 n_shift(1,nfrag(2),2)=nshift_pair
2267 n_shift(2,nfrag(2),2)=nshift_pair
2268 nc_fragm(nfrag(2),2)=ncfrac_pair
2269 nc_req_setf(nfrag(2),2)=ncreq_pair
2270 else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2271 .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2272 .and. ncont_frag_ref(ind).ge.len_cut ) then
2274 write (iout,*) "Adding pair strands/sheets",i,j,&
2275 " based on pp contacts"
2276 if (icont_pair.gt.0) then
2277 write (iout,*) "# pp contacts will be used",&
2279 ielecont(nfrag(2),2)=1
2281 if (irms_pair.gt.0) then
2282 write (iout,*) "Fragment RMSD will be used",&
2286 npiece(nfrag(2),2)=2
2287 ipiece(1,nfrag(2),2)=i
2288 ipiece(2,nfrag(2),2)=j
2289 ielecont(nfrag(2),2)=1
2290 isccont(nfrag(2),2)=0
2291 n_shift(1,nfrag(2),2)=nshift_pair
2292 n_shift(2,nfrag(2),2)=nshift_pair
2293 nc_fragm(nfrag(2),2)=ncfrac_bet
2294 nc_req_setf(nfrag(2),2)=ncreq_bet
2298 write (iout,*) "Pairs found"
2300 write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2303 end subroutine define_pairs
2304 !------------------------------------------------------------------------------
2306 !------------------------------------------------------------------------------
2307 INTEGER FUNCTION ICANT(I,J)
2316 !------------------------------------------------------------------------------
2318 !------------------------------------------------------------------------------
2319 subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2322 integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2323 real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2324 real(kind=8) :: xxtemp
2325 integer :: i,j,k,imax
2330 if (x(1,1,j).lt.xmin) then
2364 x(j,k,imax)=x(j,k,i)
2370 end subroutine imysort
2371 !------------------------------------------------------------------------------
2373 !-------------------------------------------------------------------------------
2374 real(kind=8) function qwolynes(ilevel,jfrag)
2376 use geometry_data, only:cref,nperm
2377 use control_data, only:symetr
2378 use energy_data, only:nnt,nct,itype,molnum
2380 ! include 'DIMENSIONS'
2381 ! include 'DIMENSIONS.ZSCOPT'
2382 ! include 'DIMENSIONS.COMPAR'
2383 ! include 'COMMON.IOUNITS'
2384 ! include 'COMMON.COMPAR'
2385 ! include 'COMMON.CHAIN'
2386 ! include 'COMMON.INTERACT'
2387 ! include 'COMMON.CONTROL'
2388 integer :: ilevel,jfrag,kkk
2389 integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2391 real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2392 real(kind=8) :: maxiQ !dist,
2393 real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2394 logical :: lprn=.false.
2395 real(kind=8) :: x !el sigm
2396 !el sigm(x)=0.25d0*x
2402 ! write (iout,*) "QWolyes: " jfrag",jfrag,
2403 ! & " ilevel",ilevel
2404 allocate(tempus(nperm))
2407 if (ilevel.eq.0) then
2408 if (lprn) write (iout,*) "Q computed for whole molecule"
2419 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2420 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2421 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2423 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2424 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2427 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2428 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2429 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2430 dijCM=dist(il+nres,jl+nres)
2431 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2435 write (iout,*) "il",il," jl",jl,&
2436 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2437 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2438 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2443 if (lprn) write (iout,*) "nl",nl," qq",qq
2444 else if (ilevel.eq.1) then
2445 if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2447 ! write (iout,*) "nlist_frag",nlist_frag(jfrag)
2448 do i=2,nlist_frag(jfrag)
2450 il=list_frag(i,jfrag)
2451 jl=list_frag(j,jfrag)
2452 if (iabs(il-jl).gt.nsep) then
2460 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2461 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2462 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2464 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2465 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2468 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2469 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2470 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2471 dijCM=dist(il+nres,jl+nres)
2472 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2476 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2477 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2478 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2479 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2485 if (lprn) write (iout,*) "nl",nl," qq",qq
2486 else if (ilevel.eq.2) then
2487 np=npiece(jfrag,ilevel)
2490 ip=ipiece(i,jfrag,ilevel)
2491 do j=1,nlist_frag(ip)
2494 kp=ipiece(k,jfrag,ilevel)
2495 do l=1,nlist_frag(kp)
2497 if (iabs(kl-il).gt.nsep) then
2505 d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2506 (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2507 (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2509 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2510 if (itype(il,molnum(il)).ne.10 .or. itype(kl,molnum(kl)).ne.10) then
2513 (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2514 (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2515 (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2516 dijCM=dist(il+nres,kl+nres)
2517 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2522 write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2523 " kl",kl," itype",itype(il,molnum(il)), &
2524 itype(kl,molnum(kl))
2525 write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2526 d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2534 if (lprn) write (iout,*) "nl",nl," qq",qq
2536 write (iout,*)"Error: Q can be computed only for level 1 and 2."
2541 if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2543 qwolynes=1.0d0-maxiQ
2546 end function qwolynes
2547 !-------------------------------------------------------------------------------
2548 real(kind=8) function sigm(x)
2553 !-------------------------------------------------------------------------------
2554 subroutine fragment_list
2556 ! include 'DIMENSIONS'
2557 ! include 'DIMENSIONS.ZSCOPT'
2558 ! include 'DIMENSIONS.COMPAR'
2559 ! include 'COMMON.IOUNITS'
2560 ! include 'COMMON.COMPAR'
2561 logical :: lprn=.true.
2562 integer :: i,ilevel,j,k,jfrag
2565 do i=1,npiece(jfrag,1)
2566 if (lprn) write (iout,*) "jfrag=",jfrag,&
2567 "i=",i," fragment",ifrag(1,i,jfrag),&
2569 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2570 do k=1,nlist_frag(jfrag)
2571 if (list_frag(k,jfrag).eq.j) goto 10
2573 nlist_frag(jfrag)=nlist_frag(jfrag)+1
2574 list_frag(nlist_frag(jfrag),jfrag)=j
2579 write (iout,*) "Fragment list"
2581 write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2585 end subroutine fragment_list
2586 !-------------------------------------------------------------------------------
2587 real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2590 use control_data, only:symetr
2591 use geometry_data, only:nperm
2592 ! implicit real*8 (a-h,o-z)
2593 ! include 'DIMENSIONS'
2594 ! include 'DIMENSIONS.ZSCOPT'
2595 ! include 'DIMENSIONS.COMPAR'
2596 ! include 'COMMON.IOUNITS'
2597 ! include 'COMMON.COMPAR'
2598 ! include 'COMMON.CHAIN'
2599 ! include 'COMMON.INTERACT'
2600 ! include 'COMMON.VAR'
2601 ! include 'COMMON.CONTROL'
2602 real(kind=8) :: przes(3),obrot(3,3)
2603 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2604 !el logical :: iadded(nres)
2605 !el integer :: inumber(2,nres)
2606 !el common /ccc/ creff,cc,iadded,inumber
2609 integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2610 real(kind=8) :: rminrms,rms
2612 write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2613 write (iout,*) "npiece",npiece(j,i)
2616 ! write (iout,*) "symetr",symetr
2622 ! write (iout,*) "nperm",nperm
2629 ! write (iout,*) "kkk",kkk
2634 write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2635 ifrag(1,k,j),ifrag(2,k,j)
2638 call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2639 ! write (iout,*) "Exit cprep"
2641 ! write (iout,*) "ii=",ii
2644 ! write (iout,*) "kk",kk," npiece",npiece(kk,1)
2647 write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2648 " l=",l," adding fragment",&
2649 ifrag(1,l,kk),ifrag(2,l,kk)
2652 call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2653 ! write (iout,*) "After cprep"
2660 write (iout,*) "tuszukaj"
2663 write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2664 inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2671 call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2673 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2675 else if (rms.lt.-1.0d-6) then
2676 print *,'Error: rms^2 = ',rms,jcon,i
2678 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2681 ! write (iout,*) "rmsmin", rminrms, "rms", rms
2682 if (rms.le.rminrms) rminrms=rms
2684 rmscalc = dsqrt(rminrms)
2685 ! write (iout, *) "analysys", rmscalc,anatemp
2687 end function rmscalc
2688 !-------------------------------------------------------------------------
2689 subroutine cprep(if1,if2,ishif,idup,kwa)
2692 use control_data, only:symetr
2693 use geometry_data, only:nperm,cref,c
2694 ! implicit real*8 (a-h,o-z)
2695 ! include 'DIMENSIONS'
2696 ! include 'DIMENSIONS.ZSCOPT'
2697 ! include 'DIMENSIONS.COMPAR'
2698 ! include 'COMMON.CONTROL'
2699 ! include 'COMMON.IOUNITS'
2700 ! include 'COMMON.COMPAR'
2701 ! include 'COMMON.CHAIN'
2702 ! include 'COMMON.INTERACT'
2703 ! include 'COMMON.VAR'
2704 real(kind=8) :: przes(3),obrot(3,3)
2705 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2706 !el logical :: iadded(nres)
2707 !el integer :: inumber(2,nres)
2708 integer :: iistrart,kwa,blar
2709 !el common /ccc/ creff,cc,iadded,inumber
2710 integer :: if1,if2,ishif,idup,kkk,l,m
2711 ! write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2716 ! write (iout,*) "nperm",nperm
2720 ! write (iout,*) "l",l," iadded",iadded(l)
2722 if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2727 inumber(2,idup)=l+ishif
2729 creff(m,idup)=cref(m,l,kkk)
2730 cc(m,idup)=c(m,l+ishif)
2735 end subroutine cprep
2736 !-------------------------------------------------------------------------
2737 real(kind=8) function rmsnat(jcon)
2739 use control_data, only:symetr
2740 use geometry_data, only:nperm,cref,c
2741 use energy_data, only:itype,molnum
2742 ! implicit real*8 (a-h,o-z)
2743 ! include 'DIMENSIONS'
2744 ! include 'DIMENSIONS.ZSCOPT'
2745 ! include 'DIMENSIONS.COMPAR'
2746 ! include 'COMMON.IOUNITS'
2747 ! include 'COMMON.COMPAR'
2748 ! include 'COMMON.CHAIN'
2749 ! include 'COMMON.INTERACT'
2750 ! include 'COMMON.VAR'
2751 ! include 'COMMON.CONTROL'
2752 real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2754 integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2755 real(kind=8) :: rminrms,rmsminsing,rms
2765 if (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
2769 ccref(j,nnsup)=cref(j,i,kkk)
2773 call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2775 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2777 else if (rms.lt.-1.0d-6) then
2778 print *,'Error: rms^2 = ',rms,jcon,i
2780 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2783 if (rms.le.rminrms) rminrms=rms
2784 ! write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2786 rmsnat = dsqrt(rminrms)
2787 ! write (iout,*) "analysys",rmsnat, anatemp
2788 ! liczenie rmsdla pojedynczego lancucha
2791 !-------------------------------------------------------------------------------
2792 subroutine define_fragments
2794 use geometry_data, only:rad2deg
2795 use energy_data, only:itype,molnum
2796 use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2797 ! implicit real*8 (a-h,o-z)
2798 ! include 'DIMENSIONS'
2799 ! include 'DIMENSIONS.ZSCOPT'
2800 ! include 'DIMENSIONS.COMPAR'
2801 ! include 'COMMON.IOUNITS'
2802 ! include 'COMMON.TIME1'
2803 ! include 'COMMON.FRAG'
2804 ! include 'COMMON.SBRIDGE'
2805 ! include 'COMMON.CONTROL'
2806 ! include 'COMMON.COMPAR'
2807 ! include 'COMMON.CHAIN'
2808 ! include 'COMMON.HEADER'
2809 ! include 'COMMON.GEO'
2810 ! include 'COMMON.CONTACTS'
2811 ! include 'COMMON.PEPTCONT'
2812 ! include 'COMMON.INTERACT'
2813 ! include 'COMMON.NAMES'
2814 integer :: nstrand,istrand(2,nres/2)
2815 integer :: nhairp,ihairp(2,nres/5),mnum
2816 character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2817 'strand','strand pair'/),shape(strstr))
2818 integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2820 write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2821 'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2822 'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2823 ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2824 write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2825 ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2826 write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2827 ' MAXANG_HEL',angcut1_hel*rad2deg
2828 write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2829 ' MAXANG_BET',angcut1_bet*rad2deg
2830 write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2831 ' MAXANG_STRAND',angcut1_strand*rad2deg
2832 write (iout,*) 'FRAC_MIN',frac_min_set
2833 ! Find secondary structure elements (helices and beta-sheets)
2834 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2836 ! Define primary fragments. First include the helices.
2840 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2841 if (merge_helices) then
2842 write (iout,*) "Before merging helices: nhfrag",nhfrag
2844 write (2,*) hfrag(1,i),hfrag(2,i)
2847 do while (i.lt.nhfrag)
2848 if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2850 hfrag(2,i)=hfrag(2,i+1)
2852 hfrag(1,j)=hfrag(1,j+1)
2853 hfrag(2,j)=hfrag(2,j+1)
2858 write (iout,*) "After merging helices: nhfrag",nhfrag
2860 write (2,*) hfrag(1,i),hfrag(2,i)
2866 ifrag(1,1,i)=hfrag(1,i)
2867 ifrag(2,1,i)=hfrag(2,i)
2869 n_shift(2,i,1)=nshift_hel
2870 ang_cut(i)=angcut_hel
2871 ang_cut1(i)=angcut1_hel
2872 frac_min(i)=frac_min_set
2873 nc_fragm(i,1)=ncfrac_hel
2874 nc_req_setf(i,1)=ncreq_hel
2877 write (iout,*) "isplit_bet",isplit_bet
2878 if (isplit_bet.gt.1) then
2879 ! Split beta-sheets into strands and store strands as primary fragments.
2880 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2884 ifrag(1,1,ii)=istrand(1,i)
2885 ifrag(2,1,ii)=istrand(2,i)
2886 n_shift(1,ii,1)=nshift_strand
2887 n_shift(2,ii,1)=nshift_strand
2888 ang_cut(ii)=angcut_strand
2889 ang_cut1(ii)=angcut1_strand
2890 frac_min(ii)=frac_min_set
2895 nfrag(1)=nfrag(1)+nstrand
2896 else if (isplit_bet.eq.1) then
2897 ! Split only far beta-sheets; does not split hairpins.
2898 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2899 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2903 ifrag(1,1,ii)=ihairp(1,i)
2904 ifrag(2,1,ii)=ihairp(2,i)
2905 n_shift(1,ii,1)=nshift_bet
2906 n_shift(2,ii,1)=nshift_bet
2907 ang_cut(ii)=angcut_bet
2908 ang_cut1(ii)=angcut1_bet
2909 frac_min(ii)=frac_min_set
2910 nc_fragm(ii,1)=ncfrac_bet
2911 nc_req_setf(ii,1)=ncreq_bet
2914 nfrag(1)=nfrag(1)+nhairp
2918 ifrag(1,1,ii)=istrand(1,i)
2919 ifrag(2,1,ii)=istrand(2,i)
2920 n_shift(1,ii,1)=nshift_strand
2921 n_shift(2,ii,1)=nshift_strand
2922 ang_cut(ii)=angcut_strand
2923 ang_cut1(ii)=angcut1_strand
2924 frac_min(ii)=frac_min_set
2929 nfrag(1)=nfrag(1)+nstrand
2931 ! Do not split beta-sheets; each pair of strands is a primary element.
2932 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2936 ifrag(1,1,ii)=ihairp(1,i)
2937 ifrag(2,1,ii)=ihairp(2,i)
2938 n_shift(1,ii,1)=nshift_bet
2939 n_shift(2,ii,1)=nshift_bet
2940 ang_cut(ii)=angcut_bet
2941 ang_cut1(ii)=angcut1_bet
2942 frac_min(ii)=frac_min_set
2943 nc_fragm(ii,1)=ncfrac_bet
2944 nc_req_setf(ii,1)=ncreq_bet
2947 nfrag(1)=nfrag(1)+nhairp
2951 ifrag(1,1,ii)=bfrag(1,i)
2952 ifrag(2,1,ii)=bfrag(2,i)
2953 if (bfrag(3,i).lt.bfrag(4,i)) then
2954 ifrag(1,2,ii)=bfrag(3,i)
2955 ifrag(2,2,ii)=bfrag(4,i)
2957 ifrag(1,2,ii)=bfrag(4,i)
2958 ifrag(2,2,ii)=bfrag(3,i)
2960 n_shift(1,ii,1)=nshift_bet
2961 n_shift(2,ii,1)=nshift_bet
2962 ang_cut(ii)=angcut_bet
2963 ang_cut1(ii)=angcut1_bet
2964 frac_min(ii)=frac_min_set
2965 nc_fragm(ii,1)=ncfrac_bet
2966 nc_req_setf(ii,1)=ncreq_bet
2969 nfrag(1)=nfrag(1)+nbfrag
2971 write (iout,*) "The following primary fragments were found:"
2972 write (iout,*) "Helices:",nhfrag
2979 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2980 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
2982 write (iout,*) "Hairpins:",nhairp
2983 do i=nhfrag+1,nhfrag+nhairp
2986 it1=itype(i1,molnum(i1))
2987 it2=itype(i2,molnum(i2))
2988 write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2989 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2
2991 write (iout,*) "Far strand pairs:",nbfrag
2992 do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
2995 it1=itype(i1,molnum(i1))
2996 it2=itype(i2,molnum(i1))
2999 it3=itype(i3,molnum(i3))
3000 it4=itype(i4,molnum(i4))
3001 write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
3002 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2,&
3003 restyp(it3,molnum(i3)),i3,restyp(it4,molnum(i4)),i4
3005 write (iout,*) "Strands:",nstrand
3006 do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
3012 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
3013 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
3015 call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3016 istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3017 nc_fragm(1,1),nc_req_setf(1,1))
3018 write (iout,*) "Fragments after sorting:"
3025 write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3026 i,restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2
3027 if (npiece(i,1).eq.1) then
3028 write (iout,'(2x,a)') strstr(istruct(i))
3034 write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3035 restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2,strstr(istruct(i))
3039 end subroutine define_fragments
3040 !------------------------------------------------------------------------------
3041 subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3042 ! implicit real*8 (a-h,o-z)
3043 ! include 'DIMENSIONS'
3044 ! include 'DIMENSIONS.ZSCOPT'
3045 ! include 'DIMENSIONS.COMPAR'
3046 ! include 'COMMON.IOUNITS'
3047 integer :: nbfrag,bfrag(4,nres/3)
3048 integer :: nhairp,ihairp(2,nres/5)
3050 write (iout,*) "Entered find_and_remove_hairpins"
3051 write (iout,*) "nbfrag",nbfrag
3053 write (iout,*) i,(bfrag(k,i),k=1,4)
3057 do while (i.le.nbfrag)
3058 write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3059 if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3061 write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3063 ihairp(1,nhairp)=bfrag(1,i)
3064 ihairp(2,nhairp)=bfrag(3,i)
3068 bfrag(k,j)=bfrag(k,j+1)
3075 write (iout,*) "After finding hairpins:"
3076 write (iout,*) "nhairp",nhairp
3078 write (iout,*) i,ihairp(1,i),ihairp(2,i)
3080 write (iout,*) "nbfrag",nbfrag
3082 write (iout,*) i,(bfrag(k,i),k=1,4)
3085 end subroutine find_and_remove_hairpins
3086 !------------------------------------------------------------------------------
3087 subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3088 ! implicit real*8 (a-h,o-z)
3089 ! include 'DIMENSIONS'
3090 ! include 'DIMENSIONS.ZSCOPT'
3091 ! include 'DIMENSIONS.COMPAR'
3092 ! include 'COMMON.IOUNITS'
3093 integer :: nbfrag,bfrag(4,nres/3)
3094 integer :: nstrand,istrand(2,nres/2)
3095 integer :: nhairp,ihairp(2,nres/5)
3098 write (iout,*) "Entered split_beta"
3099 write (iout,*) "nbfrag",nbfrag
3101 write (iout,*) i,(bfrag(k,i),k=1,4)
3105 write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3106 call add_strand(nstrand,istrand,nhairp,ihairp,&
3107 bfrag(1,i),bfrag(2,i),found)
3108 if (bfrag(3,i).lt.bfrag(4,i)) then
3109 write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3110 call add_strand(nstrand,istrand,nhairp,ihairp,&
3111 bfrag(3,i),bfrag(4,i),found)
3113 write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3114 call add_strand(nstrand,istrand,nhairp,ihairp,&
3115 bfrag(4,i),bfrag(3,i),found)
3119 write (iout,*) "Strands found:",nstrand
3121 write (iout,*) i,istrand(1,i),istrand(2,i)
3124 end subroutine split_beta
3125 !------------------------------------------------------------------------------
3126 subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3127 ! implicit real*8 (a-h,o-z)
3128 ! include 'DIMENSIONS'
3129 ! include 'DIMENSIONS.ZSCOPT'
3130 ! include 'DIMENSIONS.COMPAR'
3131 ! include 'COMMON.IOUNITS'
3132 integer :: nstrand,istrand(2,nres/2)
3133 integer :: nhairp,ihairp(2,nres/5)
3135 integer :: is1,is2,j,idelt
3138 idelt=(ihairp(2,j)-ihairp(1,j))/6
3139 if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3140 write (iout,*) "strand",is1,is2," is part of hairpin",&
3141 ihairp(1,j),ihairp(2,j)
3146 idelt=(istrand(2,j)-istrand(1,j))/3
3147 if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3149 ! The strand already exists in the array; update its ends if necessary.
3150 write (iout,*) "strand",is1,is2," found at position",j,&
3151 ":",istrand(1,j),istrand(2,j)
3152 istrand(1,j)=min0(istrand(1,j),is1)
3153 istrand(2,j)=max0(istrand(2,j),is2)
3157 ! The strand has not been found; add it to the array.
3158 write (iout,*) "strand",is1,is2," added to the array."
3161 istrand(1,nstrand)=is1
3162 istrand(2,nstrand)=is2
3164 end subroutine add_strand
3165 !------------------------------------------------------------------------------
3166 subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3168 use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3169 use energy_data, only:itype,maxcont,molnum
3170 use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3171 use compare, only:freeres
3172 ! implicit real*8 (a-h,o-z)
3173 ! include 'DIMENSIONS'
3174 ! include 'DIMENSIONS.ZSCOPT'
3175 ! include 'COMMON.IOUNITS'
3176 ! include 'COMMON.FRAG'
3177 ! include 'COMMON.VAR'
3178 ! include 'COMMON.GEO'
3179 ! include 'COMMON.CHAIN'
3180 ! include 'COMMON.NAMES'
3181 ! include 'COMMON.INTERACT'
3182 integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres+1),&
3184 logical :: lprint,lprint_sec,not_done !el,freeres
3185 integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3186 integer :: nstrand,nbeta,nhelix,iii1,jjj1,mnum
3187 real(kind=8) :: p1,p2
3188 !rel external freeres
3189 character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3191 write (iout,*) "entered secondary2",ncont
3192 write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3194 write (iout,*) icont(1,i),icont(2,i)
3208 ! finding parallel beta
3209 !d write (iout,*) '------- looking for parallel beta -----------'
3215 if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3216 .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3217 !d write (iout,*) "parallel",i1,j1
3218 if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3221 !d write (iout,*) i1,j1
3227 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3228 freeres(i1,j1,nsec,isec)) goto 5
3232 !d write (iout,*) i1,j1,not_done
3236 if (i1-ii1.gt.1) then
3240 if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3244 bfrag(1,nbfrag)=ii1+1
3245 bfrag(2,nbfrag)=i1+1
3246 bfrag(3,nbfrag)=jj1+1
3247 bfrag(4,nbfrag)=min0(j1+1,nres)
3251 isec(ij,nsec(ij))=nbeta
3255 isec(ij,nsec(ij))=nbeta
3260 if (nbeta.le.9) then
3261 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3262 "DefPropRes 'strand",nstrand,&
3263 "' 'num = ",ii1-1,"..",i1-1,"'"
3265 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3266 "DefPropRes 'strand",nstrand,&
3267 "' 'num = ",ii1-1,"..",i1-1,"'"
3270 if (nbeta.le.9) then
3271 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3272 "DefPropRes 'strand",nstrand,&
3273 "' 'num = ",jj1-1,"..",j1-1,"'"
3275 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3276 "DefPropRes 'strand",nstrand,&
3277 "' 'num = ",jj1-1,"..",j1-1,"'"
3279 write(12,'(a8,4i4)') &
3280 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3284 endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3287 ! finding antiparallel beta
3288 !d write (iout,*) '--------- looking for antiparallel beta ---------'
3293 if (freeres(i1,j1,nsec,isec)) then
3296 !d write (iout,*) i1,j1
3303 if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3304 freeres(i1,j1,nsec,isec)) goto 6
3308 !d write (iout,*) i1,j1,not_done
3312 if (i1-ii1.gt.1) then
3316 bfrag(2,nbfrag)=min0(i1+1,nres)
3317 bfrag(3,nbfrag)=min0(jj1+1,nres)
3324 if (nsec(ij).le.2) then
3325 isec(ij,nsec(ij))=nbeta
3331 if (nsec(ij).le.2) then
3332 isec(ij,nsec(ij))=nbeta
3337 if (lprint_sec) then
3338 write (iout,'(a,i3,4i4)')'antiparallel beta',&
3339 nbeta,ii1-1,i1,jj1,j1-1
3341 if (nstrand.le.9) then
3342 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3343 "DefPropRes 'strand",nstrand,&
3344 "' 'num = ",ii1-2,"..",i1-1,"'"
3346 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3347 "DefPropRes 'strand",nstrand,&
3348 "' 'num = ",ii1-2,"..",i1-1,"'"
3351 if (nstrand.le.9) then
3352 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3353 "DefPropRes 'strand",nstrand,&
3354 "' 'num = ",j1-2,"..",jj1-1,"'"
3356 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3357 "DefPropRes 'strand",nstrand,&
3358 "' 'num = ",j1-2,"..",jj1-1,"'"
3360 write(12,'(a8,4i4)') &
3361 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3367 !d write (iout,*) "After beta:",nbfrag
3369 !d write (iout,*) (bfrag(j,i),j=1,4)
3372 if (nstrand.gt.0.and.lprint_sec) then
3373 write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3376 write(12,'(a9,i1,$)') " | strand",i
3378 write(12,'(a9,i2,$)') " | strand",i
3381 write(12,'(a1)') "'"
3385 ! finding alpha or 310 helix
3391 p1=phi(i1+2)*rad2deg
3393 if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3396 if (j1.eq.i1+3 .and. &
3397 ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3398 ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3399 !d if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3400 !o if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3403 if (nsec(ii1).eq.0) then
3412 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3416 p1=phi(i1+2)*rad2deg
3417 p2=phi(j1+2)*rad2deg
3418 if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3421 !d write (iout,*) i1,j1,not_done,p1,p2
3424 if (j1-ii1.gt.4) then
3426 !d write (iout,*)'helix',nhelix,ii1,j1
3435 if (lprint_sec) then
3436 write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3437 if (nhelix.le.9) then
3438 write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3439 "DefPropRes 'helix",nhelix,&
3440 "' 'num = ",ii1-1,"..",j1-2,"'"
3442 write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3443 "DefPropRes 'helix",nhelix,&
3444 "' 'num = ",ii1-1,"..",j1-2,"'"
3451 if (nhelix.gt.0.and.lprint_sec) then
3452 write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3454 if (nhelix.le.9) then
3455 write(12,'(a8,i1,$)') " | helix",i
3457 write(12,'(a8,i2,$)') " | helix",i
3460 write(12,'(a1)') "'"
3463 if (lprint_sec) then
3464 write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3465 write(12,'(a20)') "XMacStand ribbon.mac"
3470 write(iout,*) 'UNRES seq:',anatemp
3472 write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3476 write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3482 do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3485 do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3490 do k=hfrag(1,j),hfrag(2,j)
3496 write (iout,*) "Secondary structure"
3502 write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3503 write (iout,'(80a1)') (onelet(itype(k,mnum)),k=ist,ien)
3504 write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3509 end subroutine secondary2
3510 !-------------------------------------------------
3511 ! logical function freeres(i,j,nsec,isec)
3512 ! include 'DIMENSIONS'
3513 ! integer :: isec(nres,4),nsec(nres)
3514 ! integer :: i,j,k,l
3517 ! if (nsec(i).gt.1.or.nsec(j).gt.1) return
3520 ! if (isec(i,k).eq.isec(j,l)) return
3525 ! end function freeres
3526 !-------------------------------------------------
3527 subroutine alloc_compar_arrays(nfrg,nlev)
3529 use energy_data, only:maxcont
3531 integer :: nfrg,nlev
3533 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3534 !------------------------
3537 allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3538 allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3539 !------------------------
3542 allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3543 allocate(qfrag(nfrg,2)) !(maxfrag,2)
3544 allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3545 allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3546 allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3547 ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3548 ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3549 allocate(ncont_nat(2,nfrg,nlev+1))
3550 allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3551 ! allocate(nfrag(nlev)) !(maxlevel)
3552 allocate(isnfrag(nlev+2)) !(maxlevel+1)
3553 allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3554 allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3555 allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3556 allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3557 allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3558 !------------------------
3561 ! integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3562 allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3563 allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3564 ! integer,dimension(:),allocatable :: isec_ref !(maxres)
3565 !------------------------
3566 ! module w_comm_local
3568 allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3569 allocate(iadded(nres)) !(nres)
3570 allocate(inumber(2,nres)) !(2,nres)
3573 !-------------------------------------------------------------------------------
3574 end subroutine alloc_compar_arrays
3576 !-------------------------------------------------------------------------------
3577 end module conform_compar