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 write (iout,*) "ishif1",ishif1,j
495 ! deltang = pinorm(phi(j)-phi_ref(j+ishif1))
496 deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),&
497 theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
498 if (dabs(deltang).gt.diffang_max) then
499 if (ll.gt.longest) longest = ll
504 if (ll.gt.longest) longest = ll
505 if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
506 rad2deg*phi_ref(j+ishif1),rad2deg*deltang
507 angn=angn+dabs(deltang)
510 ff = dfloat(longest)/dfloat(nend - nbeg + 4)
511 if (lprn) write (iout,*)"segment",i," longest fragment within",&
512 diffang_max*rad2deg,":",longest," fraction",ff
513 if (ff.lt.fract) fract = ff
521 if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,&
524 end subroutine angnorm
525 !-------------------------------------------------------------------------
526 subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,&
527 diffang_max,anorm,fract)
529 use geometry_data, only:nstart_sup,nend_sup,phi,theta,&
531 ! implicit real*8 (a-h,o-z)
532 ! include 'DIMENSIONS'
533 ! include 'DIMENSIONS.ZSCOPT'
534 ! include 'DIMENSIONS.COMPAR'
535 ! include 'COMMON.IOUNITS'
536 ! include 'COMMON.VAR'
537 ! include 'COMMON.COMPAR'
538 ! include 'COMMON.CHAIN'
539 ! include 'COMMON.GEO'
540 integer :: ncont,icont(2,ncont),longest
541 real(kind=8) :: anorm,diffang_max,fract
542 integer :: npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
543 real(kind=8) :: pinorm
545 integer :: jfrag,ishif1,ishif2
546 integer :: nn,nn4,nne,npart,i,j,jstart,jend,ic1,ic2,idi,iic
547 integer :: nbeg,nend,ll
548 real(kind=8) :: angn,ishifc,deltang,ff
550 if (lprn) write (iout,'(80(1h*))')
552 ! Determine the segments for which angles will be compared
555 nne = min0(nend_sup,nres)
556 if (lprn) write (iout,*) "nn4",nn4," nne",nne
557 npart=npiece(jfrag,1)
560 ! write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
561 if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or. &
562 icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
564 do while (jstart.lt.ncont .and. &
565 icont(1,jstart).lt.ifrag(1,i,jfrag))
566 ! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
567 ! & " ifrag",ifrag(1,i,jfrag)
570 ! write (iout,*) "jstart",jstart," icont",icont(1,jstart),
571 ! & " ifrag",ifrag(1,i,jfrag)
572 if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
575 ifrag_c(1,npiece_c)=icont(1,jstart)
577 do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
578 ! write (iout,*) "jend",jend," icont",icont(1,jend),
579 ! & " ifrag",ifrag(2,i,jfrag)
582 ! write (iout,*) "jend",jend," icont",icont(1,jend),
583 ! & " ifrag",ifrag(2,i,jfrag)
585 ifrag_c(2,npiece_c)=icont(1,jend)+1
586 ishift_c(npiece_c)=ishif1
587 ! write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
588 ! & " ic1",ic1," ic2",ic2,
589 ! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
591 if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
596 ! write (iout,*) "idi",idi
598 if (icont(2,1).gt.ifrag(2,i,jfrag) .or. &
599 icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
601 do while (jstart.lt.ncont .and. &
602 icont(2,jstart).lt.ifrag(1,i,jfrag))
603 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
604 ! & " ifrag",ifrag(1,i,jfrag)
607 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
608 ! & " ifrag",ifrag(1,i,jfrag)
609 if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
612 ifrag_c(2,npiece_c)=icont(2,jstart)+1
614 do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
615 ! write (iout,*) "jend",jend," icont",icont(2,jend),
616 ! & " ifrag",ifrag(2,i,jfrag)
619 ! write (iout,*) "jend",jend," icont",icont(2,jend),
620 ! & " ifrag",ifrag(2,i,jfrag)
621 else if (idi.eq.-1) then
622 if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or. &
623 icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
625 do while (jstart.gt.ncont .and. &
626 icont(2,jstart).lt.ifrag(1,i,jfrag))
627 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
628 ! & " ifrag",ifrag(1,i,jfrag)
631 ! write (iout,*) "jstart",jstart," icont",icont(2,jstart),
632 ! & " ifrag",ifrag(1,i,jfrag)
633 if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
636 ifrag_c(2,npiece_c)=icont(2,jstart)+1
638 do while (jend.lt.ncont .and. &
639 icont(2,jend).gt.ifrag(2,i,jfrag))
640 ! write (iout,*) "jend",jend," icont",icont(2,jend),
641 ! & " ifrag",ifrag(2,i,jfrag)
644 ! write (iout,*) "jend",jend," icont",icont(2,jend),
645 ! & " ifrag",ifrag(2,i,jfrag)
653 ! write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
654 ! & " jstart:",jstart," jend",jend,
655 ! & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
656 ifrag_c(1,npiece_c)=ic1
657 ifrag_c(2,npiece_c)=ic2+1
658 ishift_c(npiece_c)=ishif2
662 write (iout,*) "Before merge: npiece_c",npiece_c
664 write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
668 ! Merge overlapping segments (e.g., avoid splitting helices)
671 do while (i .lt. npiece_c)
672 if (ishift_c(i).eq.ishift_c(i+1) .and. &
673 ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
674 ifrag_c(2,i)=ifrag_c(2,i+1)
676 ishift_c(j)=ishift_c(j+1)
677 ifrag_c(1,j)=ifrag_c(1,j+1)
678 ifrag_c(2,j)=ifrag_c(2,j+1)
686 write (iout,*) "After merge: npiece_c",npiece_c
688 write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
701 nbeg = ifrag_c(1,i) + 3 - ishifc
702 if (nbeg.lt.nn4) nbeg=nn4
703 nend = ifrag_c(2,i) - ishifc + 1
704 if (nend.gt.nne) nend=nne
705 if (nend.ge.nbeg) then
706 nn = nn + nend - nbeg + 1
707 if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,&
708 " nn",nn," ishifc",ishifc
709 if (lprn) write (iout,*) "angles"
712 do j=nbeg,nend-ishifc
714 ! deltang = pinorm(phi(j)-phi_ref(j+ishifc))
715 write (iout,*) "i=",j," nn",nn," ishifc",ishifc
716 deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),&
717 theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
718 if (dabs(deltang).gt.diffang_max) then
719 if (ll.gt.longest) longest = ll
724 if (ll.gt.longest) longest = ll
725 if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),&
726 rad2deg*phi_ref(j+ishifc),rad2deg*deltang
727 angn=angn+dabs(deltang)
730 ff = dfloat(longest)/dfloat(nend - nbeg + 4)
731 if (lprn) write (iout,*)"segment",i," longest fragment within",&
732 diffang_max*rad2deg,":",longest," fraction",ff
733 if (ff.lt.fract) fract = ff
736 if (nn.gt.0) anorm = angn/nn
737 if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
739 end subroutine angnorm2
740 !-------------------------------------------------------------------------
741 real(kind=8) function angnorm1(nang_pair,iang_pair,lprn)
743 use geometry_data, only:phi,theta,rad2deg
744 ! implicit real*8 (a-h,o-z)
745 ! include 'DIMENSIONS'
746 ! include 'DIMENSIONS.ZSCOPT'
747 ! include 'DIMENSIONS.COMPAR'
748 ! include 'COMMON.IOUNITS'
749 ! include 'COMMON.VAR'
750 ! include 'COMMON.COMPAR'
751 ! include 'COMMON.CHAIN'
752 ! include 'COMMON.GEO'
754 integer :: nang_pair,iang_pair(2,nres)
755 real(kind=8) :: pinorm
757 real(kind=8) :: angn,deltang
759 if (lprn) write (iout,'(80(1h*))')
760 if (lprn) write (iout,*) "nang_pair",nang_pair
761 if (lprn) write (iout,*) "angles"
765 ! deltang = pinorm(phi(ia1)-phi_ref(ia2))
766 deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),&
767 theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
768 if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),&
769 rad2deg*phi_ref(ia2),rad2deg*deltang
770 angn=angn+dabs(deltang)
773 write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
774 angnorm1 = angn/nang_pair
776 end function angnorm1
777 !------------------------------------------------------------------------------
778 subroutine angnorm12(diff)
780 use geometry_data, only:phi,theta,nstart_sup,nend_sup
781 ! implicit real*8 (a-h,o-z)
782 ! include 'DIMENSIONS'
783 ! include 'DIMENSIONS.ZSCOPT'
784 ! include 'DIMENSIONS.COMPAR'
785 ! include 'COMMON.IOUNITS'
786 ! include 'COMMON.VAR'
787 ! include 'COMMON.COMPAR'
788 ! include 'COMMON.CHAIN'
789 ! include 'COMMON.GEO'
790 real(kind=8) :: pinorm,diff
794 nne = min0(nend_sup,nres)
796 ! diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
799 ! diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
800 diff=diff+spherang(phi_ref(j),theta_ref(j-1),&
801 theta_ref(j),phi(j),theta(j-1),theta(j))
804 end subroutine angnorm12
805 !--------------------------------------------------------------------------------
806 real(kind=8) function spherang(gam1,theta11,theta12,&
807 gam2,theta21,theta22)
809 use geometry, only:arcos
810 real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,&
811 x1,x2,xmed,f1,f2,fmed
812 real(kind=8) :: tolx=1.0d-4, tolf=1.0d-4
813 real(kind=8) :: sumcos
814 !el real(kind=8) :: pinorm,sumangp !arcos,
815 integer :: it,maxit=100
816 ! Calculate the difference of the angles of two superposed 4-redidue fragments
824 ! The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
825 ! to achieve the minimum difference between the O'-C-O and P-C-P angles;
826 ! the sum of these angles is the difference returned by the function.
829 ! If thetas match, take the difference of gamma and exit.
830 if (dabs(theta11-theta12).lt.tolx &
831 .and. dabs(theta21-theta22).lt.tolx) then
832 spherang=dabs(pinorm(gam2-gam1))
835 ! If the gammas are the same, take the difference of thetas and exit.
837 x2=0.5d0*pinorm(gam2-gam1)
838 if (dabs(x2) .lt. tolx) then
839 spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
841 else if (x2.lt.0.0d0) then
845 ! Else apply regula falsi method to compute optimum overlap of the terminal Calphas
846 f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
847 f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
849 xmed=x1-f1*(x2-x1)/(f2-f1)
850 fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
851 ! write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
852 if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx) &
853 .and. dabs(fmed).lt.tolf ) then
857 else if ( fmed*f1.lt.0.0d0 ) then
866 spherang=arcos(dcos(theta11)*dcos(theta12) &
867 +dsin(theta11)*dsin(theta12)*dcos(x1))+ &
868 arcos(dcos(theta21)*dcos(theta22)+ &
869 dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
871 end function spherang
872 !--------------------------------------------------------------------------------
873 real(kind=8) function sumangp(gam1,theta11,theta12,gam2,&
876 real(kind=8) :: gam1,theta11,theta12,gam2,theta21,theta22,fi,&
877 cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,&
879 ! derivarive of the sum of the difference of the angles of a 4-residue fragment.
880 ! real(kind=8) :: arcos
889 cosd1=cost11*cost12+sint11*sint12*dcos(fi)
890 cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
891 sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1) &
892 +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
895 !-----------------------------------------------------------------------------
897 !-----------------------------------------------------------------------------
898 subroutine contact(lprint,ncont,icont,ist,ien)
901 use geometry_data, only:c,dc,dc_norm
902 use energy_data, only:itype,maxcont,molnum
904 ! include 'DIMENSIONS'
905 ! include 'DIMENSIONS.ZSCOPT'
906 ! include 'COMMON.CONTROL'
907 ! include 'COMMON.IOUNITS'
908 ! include 'COMMON.CHAIN'
909 ! include 'COMMON.INTERACT'
910 ! include 'COMMON.FFIELD'
911 ! include 'COMMON.NAMES'
912 ! include 'COMMON.CALC'
913 ! include 'COMMON.CONTPAR'
914 ! include 'COMMON.LOCAL'
915 integer :: ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2,mnum,mnum2
916 real(kind=8) :: csc !el,dist
917 real(kind=8),dimension(maxcont) :: cscore,omt1,omt2,omt12,&
919 integer :: ncont,mhum
920 integer,dimension(2,maxcont) :: icont
921 real(kind=8) :: u,v,a(3),b(3),dla,dlb
932 write (iout,110) restyp(itype(i,mnum),mnum),i,c(1,i),c(2,i),&
933 c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),&
934 dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
937 110 format (a,'(',i3,')',9f8.3)
940 iti=iabs(itype(i,mnum))
941 if (iti.le.0 .or. iti.gt.ntyp_molec(mnum)) cycle
944 itj=iabs(itype(j,mnum2))
945 if (itj.le.0 .or. itj.gt.ntyp_molec(mnum2)) cycle
948 xj = c(1,nres+j)-c(1,nres+i)
949 yj = c(2,nres+j)-c(2,nres+i)
950 zj = c(3,nres+j)-c(3,nres+i)
951 dxi = dc_norm(1,nres+i)
952 dyi = dc_norm(2,nres+i)
953 dzi = dc_norm(3,nres+i)
954 dxj = dc_norm(1,nres+j)
955 dyj = dc_norm(2,nres+j)
956 dzj = dc_norm(3,nres+j)
961 ! write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
962 if (icomparfunc.eq.1) then
963 call contfunc(csc,iti,itj)
964 else if (icomparfunc.eq.2) then
965 call scdist(csc,iti,itj)
966 else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
967 csc = dist(nres+i,nres+j)
968 else if (icomparfunc.eq.4) then
969 call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
971 write (*,*) "Error - Unknown sidechain contact function"
972 write (iout,*) "Error - Unknown sidechain contact function"
974 if (csc.lt.sc_cutoff(iti,itj)) then
975 ! write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
976 ! & " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
977 ! & dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
978 ! & dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
980 ! write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
981 ! & sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
982 ! & chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
991 ddsc(ncont)=1.0d0/rij
998 write (iout,'(a)') 'Contact map:'
1006 if (mnum.eq.0) mnum=1
1007 print *,"CONTACT",i1,i2,mnum,it1,it2
1008 write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
1009 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2,cscore(i),&
1010 sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
1011 omt1(i),omt2(i),omt12(i)
1015 end subroutine contact
1017 !----------------------------------------------------------------------------
1018 subroutine contact(lprint,ncont,icont)
1020 use energy_data, only: nnt,nct,itype,ipot,maxcont,sigma,sigmaii,molnum
1021 ! include 'DIMENSIONS'
1022 ! include 'COMMON.IOUNITS'
1023 ! include 'COMMON.CHAIN'
1024 ! include 'COMMON.INTERACT'
1025 ! include 'COMMON.FFIELD'
1026 ! include 'COMMON.NAMES'
1027 real(kind=8) :: facont=1.569D0 ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
1028 integer :: ncont,icont(2,maxcont)
1030 integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
1031 real(kind=8) :: rcomp
1032 integer :: mnum,mnum2
1035 ! print *,'nnt=',nnt,' nct=',nct
1038 iti=iabs(itype(i,1))
1041 itj=iabs(itype(j,1))
1043 ! rcomp=sigmaii(iti,itj)+1.0D0
1044 rcomp=facont*sigmaii(iti,itj)
1046 ! rcomp=sigma(iti,itj)+1.0D0
1047 rcomp=facont*sigma(iti,itj)
1050 ! print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
1051 if (dist(nres+i,nres+j).lt.rcomp) then
1059 write (iout,'(a)') 'Contact map:'
1066 write(iout,*) "test",i1,i2,it1,it2
1067 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1068 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1072 end subroutine contact
1074 !----------------------------------------------------------------------------
1075 real(kind=8) function contact_fract(ncont,ncont_ref,&
1078 use energy_data, only:maxcont
1080 ! include 'DIMENSIONS'
1081 ! include 'COMMON.IOUNITS'
1082 integer :: i,j,nmatch
1083 integer :: ncont,ncont_ref
1084 integer,dimension(2,maxcont) :: icont,icont_ref
1086 ! print *,'ncont=',ncont,' ncont_ref=',ncont_ref
1087 ! write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
1088 ! write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
1089 ! write (iout,'(20i4)') (icont(1,i),i=1,ncont)
1090 ! write (iout,'(20i4)') (icont(2,i),i=1,ncont)
1093 if (icont(1,i).eq.icont_ref(1,j) .and. &
1094 icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
1097 ! print *,' nmatch=',nmatch
1098 ! contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
1099 contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
1101 end function contact_fract
1103 !------------------------------------------------------------------------------
1104 subroutine pept_cont(lprint,ncont,icont)
1106 use geometry_data, only:c
1107 use energy_data, only:maxcont,nnt,nct,itype,molnum
1109 ! include 'DIMENSIONS'
1110 ! include 'DIMENSIONS.ZSCOPT'
1111 ! include 'COMMON.IOUNITS'
1112 ! include 'COMMON.CHAIN'
1113 ! include 'COMMON.INTERACT'
1114 ! include 'COMMON.FFIELD'
1115 ! include 'COMMON.NAMES'
1116 integer :: ncont,icont(2,maxcont)
1117 integer :: i,j,k,kkk,i1,i2,it1,it2,mnum
1119 !el real(kind=8) :: dist
1120 real(kind=8) :: rcomp=5.5d0
1123 print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
1126 c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
1130 c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
1132 if (dist(2*nres+1,2*nres+2).lt.rcomp) then
1140 write (iout,'(a)') 'PP contact map:'
1147 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1148 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
1152 end subroutine pept_cont
1153 !-----------------------------------------------------------------------------
1155 !-----------------------------------------------------------------------------
1156 subroutine contacts_between_fragments(lprint,is,ncont,icont,&
1157 ncont_interfrag,icont_interfrag)
1159 use energy_data, only:itype,maxcont,molnum
1160 ! include 'DIMENSIONS'
1161 ! include 'DIMENSIONS.ZSCOPT'
1162 ! include 'DIMENSIONS.COMPAR'
1163 ! include 'COMMON.INTERACT'
1164 ! include 'COMMON.COMPAR'
1165 ! include 'COMMON.IOUNITS'
1166 ! include 'COMMON.CHAIN'
1167 ! include 'COMMON.NAMES'
1168 integer :: icont(2,maxcont),ncont_interfrag(mmaxfrag),&
1169 icont_interfrag(2,maxcont,mmaxfrag)
1170 logical :: OK1,OK2,lprint
1171 integer :: is,ncont,i,j,ind,nc,k,ic1,ic2,l,i1,i2,it1,it2,mnum
1172 ! Determine the contacts that occur within a fragment and between fragments.
1177 ! write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
1178 ! & ,k=1,npiece(i,1))
1179 ! write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
1180 ! & ,k=1,npiece(j,1))
1181 ! write (iout,*) "ncont",ncont
1187 do while (.not.OK1 .and. l.lt.npiece(j,1))
1189 OK1=ic1.ge.ifrag(1,l,j)-is .and. &
1190 ic1.le.ifrag(2,l,j)+is
1194 do while (.not.OK2 .and. l.lt.npiece(i,1))
1196 OK2=ic2.ge.ifrag(1,l,i)-is .and. &
1197 ic2.le.ifrag(2,l,i)+is
1199 ! write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
1201 if (OK1.and.OK2) then
1203 icont_interfrag(1,nc,ind)=ic1
1204 icont_interfrag(2,nc,ind)=ic2
1205 ! write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
1208 ncont_interfrag(ind)=nc
1209 ! do k=1,ncont_interfrag(ind)
1210 ! i1=icont_interfrag(1,k,ind)
1211 ! i2=icont_interfrag(2,k,ind)
1214 ! write (iout,'(i3,2x,a,i4,2x,a,i4)')
1215 ! & i,restyp(it1),i1,restyp(it2),i2
1220 write (iout,*) "Contacts within fragments:"
1222 write (iout,*) "Fragment",i," (",(ifrag(1,k,i),&
1223 ifrag(2,k,i),k=1,npiece(i,1)),")"
1225 do k=1,ncont_interfrag(ind)
1226 i1=icont_interfrag(1,k,ind)
1227 i2=icont_interfrag(2,k,ind)
1230 it2=itype(i2,molnum(i2))
1231 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1232 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1236 write (iout,*) "Contacts between fragments:"
1240 write (iout,*) "Fragments",i," (",(ifrag(1,k,i),&
1241 ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",&
1242 (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
1243 write (iout,*) "Number of contacts",&
1244 ncont_interfrag(ind)
1246 do k=1,ncont_interfrag(ind)
1247 i1=icont_interfrag(1,k,ind)
1248 i2=icont_interfrag(2,k,ind)
1251 it2=itype(i2,molnum(i2))
1252 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
1253 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2
1259 end subroutine contacts_between_fragments
1260 !-----------------------------------------------------------------------------
1262 !-----------------------------------------------------------------------------
1263 subroutine contfunc(cscore,itypi,itypj)
1265 ! This subroutine calculates the contact function based on
1266 ! the Gay-Berne potential of interaction.
1269 ! implicit real*8 (a-h,o-z)
1270 ! include 'DIMENSIONS'
1271 ! include 'COMMON.CONTPAR'
1272 ! include 'COMMON.CALC'
1274 integer :: itypi,itypj
1275 real(kind=8) :: cscore,sig0ij,rrij,sig,rij_shift,evdw,e2
1277 sig0ij=sig_comp(itypi,itypj)
1278 chi1=chi_comp(itypi,itypj)
1279 chi2=chi_comp(itypj,itypi)
1281 chip1=chip_comp(itypi,itypj)
1282 chip2=chip_comp(itypj,itypi)
1284 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1286 ! Calculate angle-dependent terms of the contact function
1290 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1291 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1292 om12=dxi*dxj+dyi*dyj+dzi*dzj
1294 ! print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
1296 ! & rij,rrij,om1,om2,om12
1297 ! Calculate eps1(om12)
1298 faceps1=1.0D0-om12*chiom12
1299 faceps1_inv=1.0D0/faceps1
1300 eps1=dsqrt(faceps1_inv)
1301 ! Following variable is eps1*deps1/dom12
1302 eps1_om12=faceps1_inv*chiom12
1303 ! Calculate sigma(om1,om2,om12)
1307 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1308 sigsq=1.0D0-facsig*faceps1_inv
1309 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1312 chipom12=chip12*om12
1313 facp=1.0D0-om12*chipom12
1315 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1316 ! Following variable is the square root of eps2
1317 eps2rt=1.0D0-facp1*facp_inv
1319 sig=sig0ij*dsqrt(sigsq)
1320 rij_shift=1.0D0/rij-sig+sig0ij
1321 if (rij_shift.le.0.0D0) then
1323 cscore = -dlog(evdw+1.0d-6)
1326 rij_shift=1.0D0/rij_shift
1327 e2=(rij_shift*sig0ij)**expon
1328 evdw=dabs(eps1*eps2rt**2*e2)
1329 if (evdw.gt.1.0d1) evdw = 1.0d1
1330 cscore = -dlog(evdw+1.0d-6)
1332 end subroutine contfunc
1333 !------------------------------------------------------------------------------
1334 subroutine scdist(cscore,itypi,itypj)
1336 ! This subroutine calculates the contact distance
1339 ! implicit real*8 (a-h,o-z)
1340 ! include 'DIMENSIONS'
1341 ! include 'COMMON.CONTPAR'
1342 ! include 'COMMON.CALC'
1343 integer :: itypi,itypj
1344 real(kind=8) :: cscore,rrij
1346 chi1=chi_comp(itypi,itypj)
1347 chi2=chi_comp(itypj,itypi)
1349 rrij=xj*xj+yj*yj+zj*zj
1351 ! Calculate angle-dependent terms of the contact function
1355 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1356 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1357 om12=dxi*dxj+dyi*dyj+dzi*dzj
1362 cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
1364 end subroutine scdist
1365 !------------------------------------------------------------------------------
1367 !------------------------------------------------------------------------------
1368 subroutine elecont(lprint,ncont,icont,ist,ien)
1370 use geometry_data, only:c
1371 use energy_data, only:maxcont,rpp,epp,itype,itel,vblinv,vblinv2,molnum
1373 ! include 'DIMENSIONS'
1374 ! include 'DIMENSIONS.ZSCOPT'
1375 ! include 'DIMENSIONS.COMPAR'
1376 ! include 'COMMON.IOUNITS'
1377 ! include 'COMMON.CHAIN'
1378 ! include 'COMMON.INTERACT'
1379 ! include 'COMMON.FFIELD'
1380 ! include 'COMMON.NAMES'
1381 ! include 'COMMON.LOCAL'
1383 integer :: i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
1384 real(kind=8) :: rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,&
1385 xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,&
1386 vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,&
1388 real(kind=8),dimension(2,2) :: elpp6c=reshape((/-0.2379d0,&
1389 -0.2056d0,-0.2056d0,-0.0610d0/),shape(elpp6c))
1390 real(kind=8),dimension(2,2) :: elpp3c=reshape((/ 0.0503d0,&
1391 0.0000d0, 0.0000d0, 0.0692d0/),shape(elpp3c))
1392 real(kind=8),dimension(2,2) :: ael6c,ael3c,appc,bppc
1393 real(kind=8) :: elcutoff=-0.3d0
1394 real(kind=8) :: elecutoff_14=-0.5d0
1395 integer :: ncont,icont(2,maxcont),mnum
1396 real(kind=8) :: econt(maxcont)
1398 ! Load the constants of peptide bond - peptide bond interactions.
1399 ! Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
1400 ! proline) - determined by averaging ECEPP energy.
1404 ! data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
1405 ! data rpp / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
1406 !el data (elpp6c) /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
1407 !el data (elpp3c) / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
1408 !el data (elcutoff) /-0.3d0/
1409 !el data (elecutoff_14) /-0.5d0/
1412 if (lprint) write (iout,'(a)') &
1413 "Constants of electrostatic interaction energy expression."
1417 appc(i,j)=epp(i,j)*rri*rri
1418 bppc(i,j)=-2.0*epp(i,j)*rri
1419 ael6c(i,j)=elpp6c(i,j)*4.2**6
1420 ael3c(i,j)=elpp3c(i,j)*4.2**3
1422 write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),&
1441 if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1442 if (iteli.eq.2 .and. itelj.eq.2 &
1443 .or.iteli.eq.0 .or.itelj.eq.0) goto 4
1444 aaa=appc(iteli,itelj)
1445 bbb=bppc(iteli,itelj)
1446 ael6i=ael6c(iteli,itelj)
1447 ael3i=ael3c(iteli,itelj)
1451 xj=c(1,j)+0.5*dxj-xmedi
1452 yj=c(2,j)+0.5*dyj-ymedi
1453 zj=c(3,j)+0.5*dzj-zmedi
1454 rrmij=1.0/(xj*xj+yj*yj+zj*zj)
1459 cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
1460 cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
1461 cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
1462 fac=cosa-3.0*cosb*cosg
1468 el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
1471 if (j.gt.i+2 .and. eesij.le.elcutoff .or. &
1472 j.eq.i+2 .and. eesij.le.elecutoff_14) then
1483 write (iout,*) 'Total average electrostatic energy: ',ees
1484 write (iout,*) 'VDW energy between peptide-group centers: ',evdw
1486 write (iout,*) 'Electrostatic contacts before pruning: '
1490 it1=itype(i1,molnum(i1))
1491 it2=itype(i2,molnum(i1))
1492 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1493 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i1)),i2,econt(i)
1496 ! For given residues keep only the contacts with the greatest energy.
1498 do while (i.lt.ncont)
1504 do while (j.lt.ncont)
1506 if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or. &
1507 ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
1508 ! write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
1509 ! & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
1510 if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
1511 if (ic1.eq.icont(1,j)) then
1513 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)&
1514 .and. iabs(icont(1,k)-ic1).le.2 .and. &
1515 econt(k).lt.econt(j) ) goto 21
1517 else if (ic2.eq.icont(2,j) ) then
1519 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)&
1520 .and. iabs(icont(2,k)-ic2).le.2 .and. &
1521 econt(k).lt.econt(j) ) goto 21
1524 ! Remove ith contact
1526 icont(1,k-1)=icont(1,k)
1527 icont(2,k-1)=icont(2,k)
1532 ! write (iout,*) "ncont",ncont
1534 ! write (iout,*) icont(1,k),icont(2,k)
1537 else if (econt(j).gt.ene .and. ic2.ne.ic1+2) &
1539 if (ic1.eq.icont(1,j)) then
1541 if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2 &
1542 .and. iabs(icont(1,k)-icont(1,j)).le.2 .and. &
1543 econt(k).lt.econt(i) ) goto 21
1545 else if (ic2.eq.icont(2,j) ) then
1547 if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1 &
1548 .and. iabs(icont(2,k)-icont(2,j)).le.2 .and. &
1549 econt(k).lt.econt(i) ) goto 21
1552 ! Remove jth contact
1554 icont(1,k-1)=icont(1,k)
1555 icont(2,k-1)=icont(2,k)
1559 ! write (iout,*) "ncont",ncont
1561 ! write (iout,*) icont(1,k),icont(2,k)
1572 write (iout,*) 'Electrostatic contacts after pruning: '
1579 it2=itype(i2,molnum(i2))
1580 write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
1581 i,restyp(it1,mnum),i1,restyp(it2,molnum(i2)),i2,econt(i)
1585 end subroutine elecont
1586 !------------------------------------------------------------------------------
1588 !------------------------------------------------------------------------------
1589 subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,&
1590 ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,&
1591 nc_frac,nc_req_set,istr,llocal,lprn)
1593 use energy_data, only:maxcont
1594 ! implicit real*8 (a-h,o-z)
1595 ! include 'DIMENSIONS'
1596 ! include 'COMMON.IOUNITS'
1597 integer :: ncont_ref,ncont,ishift,ishif2,nc_match
1598 integer,dimension(2,maxcont) :: icont_ref,icont !(2,maxcont)
1599 real(kind=8) :: nc_frac
1600 logical :: llocal,lprn
1601 integer :: ishif1,nc_match1_max,jfrag,n_shif1,n_shif2,&
1602 nc_req_set,istr,nc_match_max
1603 integer :: i,nc_req,nc_match1,is,js
1606 nc_match_max=nc_match_max+ &
1607 min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
1611 else if (nc_req_set.eq.0) then
1612 nc_req=nc_match_max*nc_frac
1614 nc_req = dmin1(nc_match_max*nc_frac+0.5d0,&
1615 dfloat(nc_req_set)+1.0d-7)
1617 ! write (iout,*) "match_contact: nc_req:",nc_req
1618 ! write (iout,*) "nc_match_max",nc_match_max
1619 ! write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
1620 ! & " n_shif2",n_shif2
1621 ! Match current contact map against reference contact map; exit, if at least
1622 ! half of the contacts match
1623 call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,&
1624 ncont,icont,jfrag,llocal,lprn)
1625 nc_match1_max=nc_match1
1626 if (lprn .and. nc_match.gt.0) write (iout,*) &
1627 "Shift:",0,0," nc_match1",nc_match1,&
1628 " nc_match=",nc_match," req'd",nc_req
1629 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1630 nc_req.eq.0 .and. nc_match.eq.1) then
1635 ! If sufficient matches are not found, try to shift contact maps up to three
1637 if (n_shif1.gt.0) then
1639 ! The following four tries help to find shifted beta-sheet patterns
1640 ! Shift "left" strand backward
1641 call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,&
1642 icont_ref,ncont,icont,jfrag,llocal,lprn)
1643 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1644 if (lprn .and. nc_match.gt.0) write (iout,*) &
1645 "Shift:",-is,0," nc_match1",nc_match1,&
1646 " nc_match=",nc_match," req'd",nc_req
1647 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1648 nc_req.eq.0 .and. nc_match.eq.1) then
1653 ! Shift "left" strand forward
1654 call ncont_match(nc_match,nc_match1,is,0,ncont_ref,&
1655 icont_ref,ncont,icont,jfrag,llocal,lprn)
1656 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1657 if (lprn .and. nc_match.gt.0) write (iout,*) &
1658 "Shift:",is,0," nc_match1",nc_match1,&
1659 " nc_match=",nc_match," req'd",nc_req
1660 if (nc_req.gt.0 .and. nc_match.ge.nc_req .or. &
1661 nc_req.eq.0 .and. nc_match.eq.1) then
1667 if (nc_req.eq.0) return
1668 ! Shift "right" strand backward
1670 call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,&
1671 icont_ref,ncont,icont,jfrag,llocal,lprn)
1672 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1673 if (lprn .and. nc_match.gt.0) write (iout,*) &
1674 "Shift:",0,-is," nc_match1",nc_match1,&
1675 " nc_match=",nc_match," req'd",nc_req
1676 if (nc_match.ge.nc_req) then
1681 ! Shift "right" strand upward
1682 call ncont_match(nc_match,nc_match1,0,is,ncont_ref,&
1683 icont_ref,ncont,icont,jfrag,llocal,lprn)
1684 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1685 if (lprn .and. nc_match.gt.0) write (iout,*) &
1686 "Shift:",0,is," nc_match1",nc_match1,&
1687 " nc_match=",nc_match," req'd",nc_req
1688 if (nc_match.ge.nc_req) then
1694 ! Now try to shift both residues in contacts.
1698 call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,&
1699 icont_ref,ncont,icont,jfrag,llocal,lprn)
1700 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1701 if (lprn .and. nc_match.gt.0) write (iout,*) &
1702 "Shift:",-is,-js," nc_match1",nc_match1,&
1703 " nc_match=",nc_match," req'd",nc_req
1704 if (nc_match.ge.nc_req) then
1709 call ncont_match(nc_match,nc_match1,is,js,ncont_ref,&
1710 icont_ref,ncont,icont,jfrag,llocal,lprn)
1711 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1712 if (lprn .and. nc_match.gt.0) write (iout,*) &
1713 "Shift:",is,js," nc_match1",nc_match1,&
1714 " nc_match=",nc_match," req'd",nc_req
1715 if (nc_match.ge.nc_req) then
1721 call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,&
1722 icont_ref,ncont,icont,jfrag,llocal,lprn)
1723 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1724 if (lprn .and. nc_match.gt.0) write (iout,*) &
1725 "Shift:",-js,-is," nc_match1",nc_match1,&
1726 " nc_match=",nc_match," req'd",nc_req
1727 if (nc_match.ge.nc_req) then
1733 call ncont_match(nc_match,nc_match1,js,is,ncont_ref,&
1734 icont_ref,ncont,icont,jfrag,llocal,lprn)
1735 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1736 if (lprn .and. nc_match.gt.0) write (iout,*) &
1737 "Shift:",js,is," nc_match1",nc_match1,&
1738 " nc_match=",nc_match," req'd",nc_req
1739 if (nc_match.ge.nc_req) then
1746 if (is+js.le.n_shif1) then
1747 call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,&
1748 icont_ref,ncont,icont,jfrag,llocal,lprn)
1749 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1750 if (lprn .and. nc_match.gt.0) write (iout,*) &
1751 "Shift:",-is,js," nc_match1",nc_match1,&
1752 " nc_match=",nc_match," req'd",nc_req
1753 if (nc_match.ge.nc_req) then
1759 call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,&
1760 icont_ref,ncont,icont,jfrag,llocal,lprn)
1761 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1762 if (lprn .and. nc_match.gt.0) write (iout,*) &
1763 "Shift:",js,-is," nc_match1",nc_match1,&
1764 " nc_match=",nc_match," req'd",nc_req
1765 if (nc_match.ge.nc_req) then
1776 if (n_shif2.gt.0) then
1778 call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,&
1779 icont_ref,ncont,icont,jfrag,llocal,lprn)
1780 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1781 if (lprn .and. nc_match.gt.0) write (iout,*) &
1782 "Shift:",-is,-is," nc_match1",nc_match1,&
1783 " nc_match=",nc_match," req'd",nc_req
1784 if (nc_match.ge.nc_req) then
1789 call ncont_match(nc_match,nc_match1,is,is,ncont_ref,&
1790 icont_ref,ncont,icont,jfrag,llocal,lprn)
1791 if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
1792 if (lprn .and. nc_match.gt.0) write (iout,*) &
1793 "Shift:",is,is," nc_match1",nc_match1,&
1794 " nc_match=",nc_match," req'd",nc_req
1795 if (nc_match.ge.nc_req) then
1802 ! If this point is reached, the contact maps are different.
1807 end subroutine match_contact
1808 !-------------------------------------------------------------------------
1809 subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,&
1810 ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
1812 use energy_data, only:nnt,nct,maxcont
1813 ! implicit real*8 (a-h,o-z)
1814 ! include 'DIMENSIONS'
1815 ! include 'DIMENSIONS.ZSCOPT'
1816 ! include 'DIMENSIONS.COMPAR'
1817 ! include 'COMMON.IOUNITS'
1818 ! include 'COMMON.INTERACT'
1819 ! include 'COMMON.GEO'
1820 ! include 'COMMON.COMPAR'
1821 logical :: llocal,lprn
1822 integer ncont_ref,ncont,ishift,ishif2,nang_pair
1823 integer,dimension(2,maxcont) :: icont_ref,icont,icont_match !(2,maxcont)
1824 integer,dimension(2,nres) :: iang_pair !(2,maxres)
1825 integer :: nc_match,nc_match1,ishif1,jfrag
1826 integer :: i,j,ic1,ic2
1827 real(kind=8) :: diffang,fract,rad2deg
1829 ! Compare the contact map against the reference contact map; they're stored
1830 ! in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
1831 if (lprn) write (iout,'(80(1h*))')
1834 ! Check the local structure by comparing dihedral angles.
1835 ! write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
1836 if (llocal .and. ncont_ref.eq.0) then
1837 ! If there are no contacts just compare the dihedral angles and exit.
1838 call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,&
1840 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1841 " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
1842 if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag)) &
1852 ic1=icont(1,i)+ishif1
1853 ic2=icont(2,i)+ishif2
1854 ! write (iout,*) "i",i," ic1",ic1," ic2",ic2
1855 if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
1857 if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
1858 nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
1859 nc_match1=nc_match1+1
1860 icont_match(1,nc_match1)=ic1
1861 icont_match(2,nc_match1)=ic2
1862 ! call add_angpair(icont(1,i),icont_ref(1,j),
1863 ! & nang_pair,iang_pair)
1864 ! call add_angpair(icont(2,i),icont_ref(2,j),
1865 ! & nang_pair,iang_pair)
1866 if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),&
1867 " match",icont_ref(1,j),icont_ref(2,j),&
1868 " shifts",ishif1,ishif2
1875 write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
1876 write (iout,*) "icont_match"
1878 write (iout,*) icont_match(1,i),icont_match(2,i)
1881 if (llocal .and. nc_match.gt.0) then
1882 call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,&
1883 ang_cut1(jfrag),diffang,fract)
1884 if (lprn) write (iout,*) "diffang:",diffang*rad2deg,&
1885 " ang_cut:",ang_cut(jfrag)*rad2deg,&
1886 " ang_cut1",ang_cut1(jfrag)*rad2deg
1887 if (diffang.gt.ang_cut(jfrag) &
1888 .or. fract.lt.frac_min(jfrag)) nc_match=0
1890 ! if (nc_match.gt.0) then
1891 ! diffang = angnorm1(nang_pair,iang_pair,lprn)
1892 ! if (diffang.gt.ang_cut(jfrag)) nc_match=0
1894 if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,&
1895 " diffang",rad2deg*diffang," nc_match",nc_match
1897 end subroutine ncont_match
1898 !------------------------------------------------------------------------------
1899 subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
1900 ! This subroutine compares the secondary structure (isecstr) of fragment jfrag
1901 ! conformation considered to that of the reference conformation.
1902 ! Returns the number of equivalent residues (nsec_match).
1903 ! implicit real*8 (a-h,o-z)
1904 ! include 'DIMENSIONS'
1905 ! include 'DIMENSIONS.ZSCOPT'
1906 ! include 'DIMENSIONS.COMPAR'
1907 ! include 'COMMON.IOUNITS'
1908 ! include 'COMMON.CHAIN'
1909 ! include 'COMMON.PEPTCONT'
1910 ! include 'COMMON.COMPAR'
1912 integer :: isecstr(nres)
1913 integer :: jfrag,nsec_match,npart,i,j
1914 npart = npiece(jfrag,1)
1917 write (iout,*) "match_secondary jfrag",jfrag," ifrag",&
1918 (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
1919 write (iout,'(80i1)') (isec_ref(j),j=1,nres)
1920 write (iout,'(80i1)') (isecstr(j),j=1,nres)
1923 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
1924 ! The residue has equivalent conformational state to that of the reference
1926 ! a) the conformational states are equal or
1927 ! b) the reference state is a coil and that of the conformation considered
1929 ! c) the conformational state of the conformation considered is a strand
1930 ! and that of the reference conformation is a coil.
1931 ! 10/28/02 - case (b) deleted.
1932 if (isecstr(j).eq.isec_ref(j) .or. &
1933 ! & isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
1934 isec_ref(j).eq.0 .and. isecstr(j).eq.1) &
1935 nsec_match=nsec_match+1
1939 end subroutine match_secondary
1940 !------------------------------------------------------------------------------
1942 !------------------------------------------------------------------------------
1943 subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
1945 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
1947 ! implicit real*8 (a-h,o-z)
1948 real(kind=8),dimension(3) :: r1,r2,a,b,x,y
1949 real(kind=8) :: uu,vv,aa,bb,dd
1950 real(kind=8) :: ab,ar,br,det,dd1,dd2,dd3,dd4,dd5
1951 !el odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
1952 !el + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
1953 ! print *,"r1",(r1(i),i=1,3)
1954 ! print *,"r2",(r2(i),i=1,3)
1955 ! print *,"a",(a(i),i=1,3)
1956 ! print *,"b",(b(i),i=1,3)
1957 aa = a(1)**2+a(2)**2+a(3)**2
1958 bb = b(1)**2+b(2)**2+b(3)**2
1959 ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
1960 ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
1961 br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
1963 ! print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
1964 uu = (-ar*bb+br*ab)/det
1965 vv = (br*aa-ar*ab)/det
1971 !el dd1 = odl(uu,vv)
1972 dd1 = odl(uu,vv,r1,r2,ar,br,ab,aa,bb)
1973 !el dd2 = odl(0.0d0,0.0d0)
1974 dd2 = odl(0.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1975 !el dd3 = odl(0.0d0,1.0d0)
1976 dd3 = odl(0.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1977 !el dd4 = odl(1.0d0,0.0d0)
1978 dd4 = odl(1.0d0,0.0d0,r1,r2,ar,br,ab,aa,bb)
1979 !el dd5 = odl(1.0d0,1.0d0)
1980 dd5 = odl(1.0d0,1.0d0,r1,r2,ar,br,ab,aa,bb)
1981 dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
1985 else if (dd.eq.dd3) then
1988 else if (dd.eq.dd4) then
1991 else if (dd.eq.dd5) then
2000 ! dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
2004 ! write (8,*) uu,vv,dd,dd1
2007 end subroutine odlodc
2008 !------------------------------------------------------------------------------
2009 real(kind=8) function odl(u,v,r1,r2,ar,br,ab,aa,bb)
2011 real(kind=8),dimension(3) :: r1,r2
2012 real(kind=8) :: aa,bb,u,v,ar,br,ab
2014 odl = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2 &
2015 + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
2018 !------------------------------------------------------------------------------
2020 !------------------------------------------------------------------------------
2021 subroutine proc_cont
2023 use geometry_data, only:rad2deg
2024 use energy_data, only:ncont_ref,icont_ref!,nsccont_frag_ref,&
2026 ! implicit real*8 (a-h,o-z)
2027 ! include 'DIMENSIONS'
2028 ! include 'DIMENSIONS.ZSCOPT'
2029 ! include 'DIMENSIONS.COMPAR'
2030 ! include 'COMMON.IOUNITS'
2031 ! include 'COMMON.TIME1'
2032 ! include 'COMMON.SBRIDGE'
2033 ! include 'COMMON.CONTROL'
2034 ! include 'COMMON.COMPAR'
2035 ! include 'COMMON.CHAIN'
2036 ! include 'COMMON.HEADER'
2037 ! include 'COMMON.CONTACTS1'
2038 ! include 'COMMON.PEPTCONT'
2039 ! include 'COMMON.GEO'
2040 integer :: i,j,k,ind,len_cut,ndigit,length_frag
2042 write (iout,*) "proc_cont: nlevel",nlevel
2043 if (nlevel.lt.0) then
2044 write (iout,*) "call define_fragments"
2045 call define_fragments
2047 write (iout,*) "call secondary2"
2048 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2051 write (iout,'(80(1h=))')
2052 write (iout,*) "Electrostatic contacts"
2053 call contacts_between_fragments(.true.,0,ncont_pept_ref,&
2054 icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
2055 write (iout,'(80(1h=))')
2056 write (iout,*) "Side chain contacts"
2057 call contacts_between_fragments(.true.,0,ncont_ref,&
2058 icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
2059 if (nlevel.lt.0) then
2063 if (istruct(i).le.1) then
2064 len_cut=max0(len_frag(i,1)*4/5,3)
2065 else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2066 len_cut=max0(len_frag(i,1)*2/5,3)
2068 write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",&
2069 ncont_frag_ref(ind)," len_cut",len_cut,&
2070 " icont_single",icont_single," iloc_single",iloc_single
2072 if (iloc(i).gt.0) write (iout,*) &
2073 "Local structure used to compare structure of fragment",i,&
2075 if (istruct(i).ne.3 .and. istruct(i).ne.0 &
2076 .and. icont_single.gt.0 .and. &
2077 ncont_frag_ref(ind).ge.len_cut) then
2078 write (iout,*) "Electrostatic contacts used to compare",&
2079 " structure of fragment",i," to native."
2082 else if (icont_single.gt.0 .and. nsccont_frag_ref(ind) &
2084 write (iout,*) "Side chain contacts used to compare",&
2085 " structure of fragment",i," to native."
2089 write (iout,*) "Contacts not used to compare",&
2090 " structure of fragment",i," to native."
2095 if (irms_single.gt.0 .or. isccont(i,1).eq.0 &
2096 .and. ielecont(i,1).eq.0) then
2097 write (iout,*) "RMSD used to compare",&
2098 " structure of fragment",i," to native."
2101 write (iout,*) "RMSD not used to compare",&
2102 " structure of fragment",i," to native."
2107 if (nlevel.lt.-1) then
2110 if (nlevel.gt.3) nlevel=3
2111 if (nlevel.eq.3) then
2113 npiece(1,3)=nfrag(1)
2123 else if (nlevel.eq.-1) then
2128 isnfrag(i+1)=isnfrag(i)+nfrag(i)
2132 ndigit=ndigit+2*nfrag(i)
2134 write (iout,*) "ndigit",ndigit
2135 if (.not.binary .and. ndigit.gt.30) then
2136 write (iout,*) "Highest class too large; switching to",&
2137 " binary representation."
2140 write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
2141 write(iout,*) "rmscut_base_up",rmscut_base_up,&
2142 " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
2148 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2152 length_frag=length_frag+len_frag(ipiece(k,j,i),1)
2155 len_frag(j,i)=length_frag
2156 rmscutfrag(1,j,i)=rmscut_base_up*length_frag
2157 rmscutfrag(2,j,i)=rmscut_base_low*length_frag
2158 if (rmscutfrag(1,j,i).lt.rmsup_lim) &
2159 rmscutfrag(1,j,i)=rmsup_lim
2160 if (rmscutfrag(1,j,i).gt.rmsupup_lim) &
2161 rmscutfrag(1,j,i)=rmsupup_lim
2164 write (iout,*) "Level",1," number of fragments:",nfrag(1)
2166 write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),&
2167 k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),&
2168 rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),&
2169 ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),&
2170 nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
2173 write (iout,*) "Level",i," number of fragments:",nfrag(i)
2175 write (iout,*) npiece(j,i),(ipiece(k,j,i),&
2176 k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),&
2177 rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),&
2178 nc_fragm(j,i),nc_req_setf(j,i)
2182 end subroutine proc_cont
2183 !------------------------------------------------------------------------------
2185 !------------------------------------------------------------------------------
2186 subroutine define_pairs
2188 ! use energy_data, only:nsccont_frag_ref
2189 ! implicit real*8 (a-h,o-z)
2190 ! include 'DIMENSIONS'
2191 ! include 'DIMENSIONS.ZSCOPT'
2192 ! include 'DIMENSIONS.COMPAR'
2193 ! include 'COMMON.IOUNITS'
2194 ! include 'COMMON.TIME1'
2195 ! include 'COMMON.SBRIDGE'
2196 ! include 'COMMON.CONTROL'
2197 ! include 'COMMON.COMPAR'
2198 ! include 'COMMON.FRAG'
2199 ! include 'COMMON.CHAIN'
2200 ! include 'COMMON.HEADER'
2201 ! include 'COMMON.GEO'
2202 ! include 'COMMON.CONTACTS1'
2203 ! include 'COMMON.PEPTCONT'
2204 integer :: j,k,i,length_frag,ind,ll1,ll2,len_cut
2209 length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
2211 len_frag(j,1)=length_frag
2212 write (iout,*) "Fragment",j," length",len_frag(j,1)
2218 if (istruct(i).le.1 .or. istruct(j).le.1) then
2219 if (istruct(i).le.1) then
2224 if (istruct(j).le.1) then
2229 len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
2231 if (istruct(i).eq.2 .or. istruct(i).eq.4) then
2236 if (istruct(j).eq.2 .or. istruct(j).eq.4) then
2241 len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
2243 write (iout,*) "Fragments",i,j," structure",istruct(i),&
2244 istruct(j)," # contacts",&
2245 ncont_frag_ref(ind),nsccont_frag_ref(ind),&
2246 " lengths",len_frag(i,1),len_frag(j,1),&
2247 " ll1",ll1," ll2",ll2," len_cut",len_cut
2248 if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and. &
2249 nsccont_frag_ref(ind).ge.len_cut ) then
2250 if (istruct(i).eq.1 .and. istruct(j).eq.1) then
2251 write (iout,*) "Adding pair of helices",i,j,&
2252 " based on SC contacts"
2254 write (iout,*) "Adding helix+strand/sheet pair",i,j,&
2255 " based on SC contacts"
2258 if (icont_pair.gt.0) then
2259 write (iout,*) "# SC contacts will be used",&
2261 isccont(nfrag(2),2)=1
2263 if (irms_pair.gt.0) then
2264 write (iout,*) "Fragment RMSD will be used",&
2268 npiece(nfrag(2),2)=2
2269 ipiece(1,nfrag(2),2)=i
2270 ipiece(2,nfrag(2),2)=j
2271 ielecont(nfrag(2),2)=0
2272 n_shift(1,nfrag(2),2)=nshift_pair
2273 n_shift(2,nfrag(2),2)=nshift_pair
2274 nc_fragm(nfrag(2),2)=ncfrac_pair
2275 nc_req_setf(nfrag(2),2)=ncreq_pair
2276 else if ((istruct(i).ge.2 .and. istruct(i).le.4) &
2277 .and. (istruct(j).ge.2 .and. istruct(i).le.4) &
2278 .and. ncont_frag_ref(ind).ge.len_cut ) then
2280 write (iout,*) "Adding pair strands/sheets",i,j,&
2281 " based on pp contacts"
2282 if (icont_pair.gt.0) then
2283 write (iout,*) "# pp contacts will be used",&
2285 ielecont(nfrag(2),2)=1
2287 if (irms_pair.gt.0) then
2288 write (iout,*) "Fragment RMSD will be used",&
2292 npiece(nfrag(2),2)=2
2293 ipiece(1,nfrag(2),2)=i
2294 ipiece(2,nfrag(2),2)=j
2295 ielecont(nfrag(2),2)=1
2296 isccont(nfrag(2),2)=0
2297 n_shift(1,nfrag(2),2)=nshift_pair
2298 n_shift(2,nfrag(2),2)=nshift_pair
2299 nc_fragm(nfrag(2),2)=ncfrac_bet
2300 nc_req_setf(nfrag(2),2)=ncreq_bet
2304 write (iout,*) "Pairs found"
2306 write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
2309 end subroutine define_pairs
2310 !------------------------------------------------------------------------------
2312 !------------------------------------------------------------------------------
2313 INTEGER FUNCTION ICANT(I,J)
2322 !------------------------------------------------------------------------------
2324 !------------------------------------------------------------------------------
2325 subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
2328 integer :: x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
2329 real(kind=8) :: z2(n),z3(n),z4(n),z5(n)
2330 real(kind=8) :: xxtemp
2331 integer :: i,j,k,imax
2336 if (x(1,1,j).lt.xmin) then
2370 x(j,k,imax)=x(j,k,i)
2376 end subroutine imysort
2377 !------------------------------------------------------------------------------
2379 !-------------------------------------------------------------------------------
2380 real(kind=8) function qwolynes(ilevel,jfrag)
2382 use geometry_data, only:cref,nperm
2383 use control_data, only:symetr
2384 use energy_data, only:nnt,nct,itype,molnum
2386 ! include 'DIMENSIONS'
2387 ! include 'DIMENSIONS.ZSCOPT'
2388 ! include 'DIMENSIONS.COMPAR'
2389 ! include 'COMMON.IOUNITS'
2390 ! include 'COMMON.COMPAR'
2391 ! include 'COMMON.CHAIN'
2392 ! include 'COMMON.INTERACT'
2393 ! include 'COMMON.CONTROL'
2394 integer :: ilevel,jfrag,kkk
2395 integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp
2397 real(kind=8),dimension(:),allocatable :: tempus !(maxperm)
2398 real(kind=8) :: maxiQ !dist,
2399 real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
2400 logical :: lprn=.false.
2401 real(kind=8) :: x !el sigm
2402 !el sigm(x)=0.25d0*x
2408 ! write (iout,*) "QWolyes: " jfrag",jfrag,
2409 ! & " ilevel",ilevel
2410 allocate(tempus(nperm))
2413 if (ilevel.eq.0) then
2414 if (lprn) write (iout,*) "Q computed for whole molecule"
2425 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2426 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2427 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2429 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2430 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2433 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2434 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2435 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2436 dijCM=dist(il+nres,jl+nres)
2437 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2441 write (iout,*) "il",il," jl",jl,&
2442 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2443 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2444 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2449 if (lprn) write (iout,*) "nl",nl," qq",qq
2450 else if (ilevel.eq.1) then
2451 if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
2453 ! write (iout,*) "nlist_frag",nlist_frag(jfrag)
2454 do i=2,nlist_frag(jfrag)
2456 il=list_frag(i,jfrag)
2457 jl=list_frag(j,jfrag)
2458 if (iabs(il-jl).gt.nsep) then
2466 d0ij=dsqrt((cref(1,jl,kkk)-cref(1,il,kkk))**2+ &
2467 (cref(2,jl,kkk)-cref(2,il,kkk))**2+ &
2468 (cref(3,jl,kkk)-cref(3,il,kkk))**2)
2470 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2471 if (itype(il,molnum(il)).ne.10 .or. itype(jl,molnum(jl)).ne.10) then
2474 (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2475 (cref(2,jl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2476 (cref(3,jl+nres,kkk)-cref(3,il+nres,kkk))**2)
2477 dijCM=dist(il+nres,jl+nres)
2478 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
2482 write (iout,*) "i",i," j",j," il",il," jl",jl,&
2483 " itype",itype(il,molnum(il)),itype(jl,molnum(jl))
2484 write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,&
2485 " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2491 if (lprn) write (iout,*) "nl",nl," qq",qq
2492 else if (ilevel.eq.2) then
2493 np=npiece(jfrag,ilevel)
2496 ip=ipiece(i,jfrag,ilevel)
2497 do j=1,nlist_frag(ip)
2500 kp=ipiece(k,jfrag,ilevel)
2501 do l=1,nlist_frag(kp)
2503 if (iabs(kl-il).gt.nsep) then
2511 d0ij=dsqrt((cref(1,kl,kkk)-cref(1,il,kkk))**2+ &
2512 (cref(2,kl,kkk)-cref(2,il,kkk))**2+ &
2513 (cref(3,kl,kkk)-cref(3,il,kkk))**2)
2515 qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
2516 if (itype(il,molnum(il)).ne.10 .or. itype(kl,molnum(kl)).ne.10) then
2519 (cref(1,kl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
2520 (cref(2,kl+nres,kkk)-cref(2,il+nres,kkk))**2+ &
2521 (cref(3,kl+nres,kkk)-cref(3,il+nres,kkk))**2)
2522 dijCM=dist(il+nres,kl+nres)
2523 qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/ &
2528 write (iout,*) "i",i," j",j," k",k," l",l," il",il,&
2529 " kl",kl," itype",itype(il,molnum(il)), &
2530 itype(kl,molnum(kl))
2531 write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",&
2532 d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
2540 if (lprn) write (iout,*) "nl",nl," qq",qq
2542 write (iout,*)"Error: Q can be computed only for level 1 and 2."
2547 if (maxiQ.le.tempus(kkk)) maxiQ=tempus(kkk)
2549 qwolynes=1.0d0-maxiQ
2552 end function qwolynes
2553 !-------------------------------------------------------------------------------
2554 real(kind=8) function sigm(x)
2559 !-------------------------------------------------------------------------------
2560 subroutine fragment_list
2562 ! include 'DIMENSIONS'
2563 ! include 'DIMENSIONS.ZSCOPT'
2564 ! include 'DIMENSIONS.COMPAR'
2565 ! include 'COMMON.IOUNITS'
2566 ! include 'COMMON.COMPAR'
2567 logical :: lprn=.true.
2568 integer :: i,ilevel,j,k,jfrag
2571 do i=1,npiece(jfrag,1)
2572 if (lprn) write (iout,*) "jfrag=",jfrag,&
2573 "i=",i," fragment",ifrag(1,i,jfrag),&
2575 do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
2576 do k=1,nlist_frag(jfrag)
2577 if (list_frag(k,jfrag).eq.j) goto 10
2579 nlist_frag(jfrag)=nlist_frag(jfrag)+1
2580 list_frag(nlist_frag(jfrag),jfrag)=j
2585 write (iout,*) "Fragment list"
2587 write (iout,*)"Fragment",j," list",(list_frag(k,j),&
2591 end subroutine fragment_list
2592 !-------------------------------------------------------------------------------
2593 real(kind=8) function rmscalc(ishif,i,j,jcon,lprn)
2596 use control_data, only:symetr
2597 use geometry_data, only:nperm
2598 ! implicit real*8 (a-h,o-z)
2599 ! include 'DIMENSIONS'
2600 ! include 'DIMENSIONS.ZSCOPT'
2601 ! include 'DIMENSIONS.COMPAR'
2602 ! include 'COMMON.IOUNITS'
2603 ! include 'COMMON.COMPAR'
2604 ! include 'COMMON.CHAIN'
2605 ! include 'COMMON.INTERACT'
2606 ! include 'COMMON.VAR'
2607 ! include 'COMMON.CONTROL'
2608 real(kind=8) :: przes(3),obrot(3,3)
2609 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2610 !el logical :: iadded(nres)
2611 !el integer :: inumber(2,nres)
2612 !el common /ccc/ creff,cc,iadded,inumber
2615 integer :: ishif,i,j,jcon,idup,kkk,l,k,kk
2616 real(kind=8) :: rminrms,rms
2618 write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
2619 write (iout,*) "npiece",npiece(j,i)
2622 ! write (iout,*) "symetr",symetr
2628 ! write (iout,*) "nperm",nperm
2635 ! write (iout,*) "kkk",kkk
2640 write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",&
2641 ifrag(1,k,j),ifrag(2,k,j)
2644 call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,idup,kkk)
2645 ! write (iout,*) "Exit cprep"
2647 ! write (iout,*) "ii=",ii
2650 ! write (iout,*) "kk",kk," npiece",npiece(kk,1)
2653 write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,&
2654 " l=",l," adding fragment",&
2655 ifrag(1,l,kk),ifrag(2,l,kk)
2658 call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,idup,kkk)
2659 ! write (iout,*) "After cprep"
2666 write (iout,*) "tuszukaj"
2669 write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),&
2670 inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
2677 call fitsq(rms,cc(1,1),creff(1,1),idup,przes,obrot,non_conv)
2679 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2681 else if (rms.lt.-1.0d-6) then
2682 print *,'Error: rms^2 = ',rms,jcon,i
2684 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2687 ! write (iout,*) "rmsmin", rminrms, "rms", rms
2688 if (rms.le.rminrms) rminrms=rms
2690 rmscalc = dsqrt(rminrms)
2691 ! write (iout, *) "analysys", rmscalc,anatemp
2693 end function rmscalc
2694 !-------------------------------------------------------------------------
2695 subroutine cprep(if1,if2,ishif,idup,kwa)
2698 use control_data, only:symetr
2699 use geometry_data, only:nperm,cref,c
2700 ! implicit real*8 (a-h,o-z)
2701 ! include 'DIMENSIONS'
2702 ! include 'DIMENSIONS.ZSCOPT'
2703 ! include 'DIMENSIONS.COMPAR'
2704 ! include 'COMMON.CONTROL'
2705 ! include 'COMMON.IOUNITS'
2706 ! include 'COMMON.COMPAR'
2707 ! include 'COMMON.CHAIN'
2708 ! include 'COMMON.INTERACT'
2709 ! include 'COMMON.VAR'
2710 real(kind=8) :: przes(3),obrot(3,3)
2711 !el real(kind=8) :: creff(3,nres*2),cc(3,nres*2)
2712 !el logical :: iadded(nres)
2713 !el integer :: inumber(2,nres)
2714 integer :: iistrart,kwa,blar
2715 !el common /ccc/ creff,cc,iadded,inumber
2716 integer :: if1,if2,ishif,idup,kkk,l,m
2717 ! write (iout,*) "Calling cprep symetr",symetr," kwa",kwa
2722 ! write (iout,*) "nperm",nperm
2726 ! write (iout,*) "l",l," iadded",iadded(l)
2728 if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l)) &
2733 inumber(2,idup)=l+ishif
2735 creff(m,idup)=cref(m,l,kkk)
2736 cc(m,idup)=c(m,l+ishif)
2741 end subroutine cprep
2742 !-------------------------------------------------------------------------
2743 real(kind=8) function rmsnat(jcon)
2745 use control_data, only:symetr
2746 use geometry_data, only:nperm,cref,c
2747 use energy_data, only:itype,molnum
2748 ! implicit real*8 (a-h,o-z)
2749 ! include 'DIMENSIONS'
2750 ! include 'DIMENSIONS.ZSCOPT'
2751 ! include 'DIMENSIONS.COMPAR'
2752 ! include 'COMMON.IOUNITS'
2753 ! include 'COMMON.COMPAR'
2754 ! include 'COMMON.CHAIN'
2755 ! include 'COMMON.INTERACT'
2756 ! include 'COMMON.VAR'
2757 ! include 'COMMON.CONTROL'
2758 real(kind=8) :: przes(3),obrot(3,3),cc(3,2*nres),ccref(3,2*nres)
2760 integer :: ishif,i,j,resprzesun,jcon,kkk,nnsup
2761 real(kind=8) :: rminrms,rmsminsing,rms
2771 if (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
2775 ccref(j,nnsup)=cref(j,i,kkk)
2779 call fitsq(rms,cc(1,1),ccref(1,1),nnsup,przes,obrot,non_conv)
2781 print *,'Error: FITSQ non-convergent, jcon',jcon,i
2783 else if (rms.lt.-1.0d-6) then
2784 print *,'Error: rms^2 = ',rms,jcon,i
2786 else if (rms.ge.1.0d-6 .and. rms.lt.0) then
2789 if (rms.le.rminrms) rminrms=rms
2790 ! write (iout,*) "kkk",kkk," rmsnat",rms , rminrms
2792 rmsnat = dsqrt(rminrms)
2793 ! write (iout,*) "analysys",rmsnat, anatemp
2794 ! liczenie rmsdla pojedynczego lancucha
2797 !-------------------------------------------------------------------------------
2798 subroutine define_fragments
2800 use geometry_data, only:rad2deg
2801 use energy_data, only:itype,molnum
2802 use compare_data, only:nhfrag,nbfrag,bfrag,hfrag
2803 ! implicit real*8 (a-h,o-z)
2804 ! include 'DIMENSIONS'
2805 ! include 'DIMENSIONS.ZSCOPT'
2806 ! include 'DIMENSIONS.COMPAR'
2807 ! include 'COMMON.IOUNITS'
2808 ! include 'COMMON.TIME1'
2809 ! include 'COMMON.FRAG'
2810 ! include 'COMMON.SBRIDGE'
2811 ! include 'COMMON.CONTROL'
2812 ! include 'COMMON.COMPAR'
2813 ! include 'COMMON.CHAIN'
2814 ! include 'COMMON.HEADER'
2815 ! include 'COMMON.GEO'
2816 ! include 'COMMON.CONTACTS'
2817 ! include 'COMMON.PEPTCONT'
2818 ! include 'COMMON.INTERACT'
2819 ! include 'COMMON.NAMES'
2820 integer :: nstrand,istrand(2,nres/2)
2821 integer :: nhairp,ihairp(2,nres/5),mnum
2822 character(len=16) :: strstr(4)=reshape((/'helix','hairpin',&
2823 'strand','strand pair'/),shape(strstr))
2824 integer :: j,i,ii,i1,i2,i3,i4,it1,it2,it3,it4
2826 write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,&
2827 'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,&
2828 'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,&
2829 ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
2830 write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,&
2831 ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
2832 write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,&
2833 ' MAXANG_HEL',angcut1_hel*rad2deg
2834 write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,&
2835 ' MAXANG_BET',angcut1_bet*rad2deg
2836 write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,&
2837 ' MAXANG_STRAND',angcut1_strand*rad2deg
2838 write (iout,*) 'FRAC_MIN',frac_min_set
2839 ! Find secondary structure elements (helices and beta-sheets)
2840 call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,&
2842 ! Define primary fragments. First include the helices.
2846 ! AL 12/23/03 - to avoid splitting helices into very small fragments
2847 if (merge_helices) then
2848 write (iout,*) "Before merging helices: nhfrag",nhfrag
2850 write (2,*) hfrag(1,i),hfrag(2,i)
2853 do while (i.lt.nhfrag)
2854 if (hfrag(1,i+1)-hfrag(2,i).le.1) then
2856 hfrag(2,i)=hfrag(2,i+1)
2858 hfrag(1,j)=hfrag(1,j+1)
2859 hfrag(2,j)=hfrag(2,j+1)
2864 write (iout,*) "After merging helices: nhfrag",nhfrag
2866 write (2,*) hfrag(1,i),hfrag(2,i)
2872 ifrag(1,1,i)=hfrag(1,i)
2873 ifrag(2,1,i)=hfrag(2,i)
2875 n_shift(2,i,1)=nshift_hel
2876 ang_cut(i)=angcut_hel
2877 ang_cut1(i)=angcut1_hel
2878 frac_min(i)=frac_min_set
2879 nc_fragm(i,1)=ncfrac_hel
2880 nc_req_setf(i,1)=ncreq_hel
2883 write (iout,*) "isplit_bet",isplit_bet
2884 if (isplit_bet.gt.1) then
2885 ! Split beta-sheets into strands and store strands as primary fragments.
2886 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2890 ifrag(1,1,ii)=istrand(1,i)
2891 ifrag(2,1,ii)=istrand(2,i)
2892 n_shift(1,ii,1)=nshift_strand
2893 n_shift(2,ii,1)=nshift_strand
2894 ang_cut(ii)=angcut_strand
2895 ang_cut1(ii)=angcut1_strand
2896 frac_min(ii)=frac_min_set
2901 nfrag(1)=nfrag(1)+nstrand
2902 else if (isplit_bet.eq.1) then
2903 ! Split only far beta-sheets; does not split hairpins.
2904 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2905 call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
2909 ifrag(1,1,ii)=ihairp(1,i)
2910 ifrag(2,1,ii)=ihairp(2,i)
2911 n_shift(1,ii,1)=nshift_bet
2912 n_shift(2,ii,1)=nshift_bet
2913 ang_cut(ii)=angcut_bet
2914 ang_cut1(ii)=angcut1_bet
2915 frac_min(ii)=frac_min_set
2916 nc_fragm(ii,1)=ncfrac_bet
2917 nc_req_setf(ii,1)=ncreq_bet
2920 nfrag(1)=nfrag(1)+nhairp
2924 ifrag(1,1,ii)=istrand(1,i)
2925 ifrag(2,1,ii)=istrand(2,i)
2926 n_shift(1,ii,1)=nshift_strand
2927 n_shift(2,ii,1)=nshift_strand
2928 ang_cut(ii)=angcut_strand
2929 ang_cut1(ii)=angcut1_strand
2930 frac_min(ii)=frac_min_set
2935 nfrag(1)=nfrag(1)+nstrand
2937 ! Do not split beta-sheets; each pair of strands is a primary element.
2938 call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
2942 ifrag(1,1,ii)=ihairp(1,i)
2943 ifrag(2,1,ii)=ihairp(2,i)
2944 n_shift(1,ii,1)=nshift_bet
2945 n_shift(2,ii,1)=nshift_bet
2946 ang_cut(ii)=angcut_bet
2947 ang_cut1(ii)=angcut1_bet
2948 frac_min(ii)=frac_min_set
2949 nc_fragm(ii,1)=ncfrac_bet
2950 nc_req_setf(ii,1)=ncreq_bet
2953 nfrag(1)=nfrag(1)+nhairp
2957 ifrag(1,1,ii)=bfrag(1,i)
2958 ifrag(2,1,ii)=bfrag(2,i)
2959 if (bfrag(3,i).lt.bfrag(4,i)) then
2960 ifrag(1,2,ii)=bfrag(3,i)
2961 ifrag(2,2,ii)=bfrag(4,i)
2963 ifrag(1,2,ii)=bfrag(4,i)
2964 ifrag(2,2,ii)=bfrag(3,i)
2966 n_shift(1,ii,1)=nshift_bet
2967 n_shift(2,ii,1)=nshift_bet
2968 ang_cut(ii)=angcut_bet
2969 ang_cut1(ii)=angcut1_bet
2970 frac_min(ii)=frac_min_set
2971 nc_fragm(ii,1)=ncfrac_bet
2972 nc_req_setf(ii,1)=ncreq_bet
2975 nfrag(1)=nfrag(1)+nbfrag
2977 write (iout,*) "The following primary fragments were found:"
2978 write (iout,*) "Helices:",nhfrag
2985 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
2986 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
2988 write (iout,*) "Hairpins:",nhairp
2989 do i=nhfrag+1,nhfrag+nhairp
2992 it1=itype(i1,molnum(i1))
2993 it2=itype(i2,molnum(i2))
2994 write (iout,'(i3,2x,a,i4,2x,a,i4,2x)') &
2995 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2
2997 write (iout,*) "Far strand pairs:",nbfrag
2998 do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
3001 it1=itype(i1,molnum(i1))
3002 it2=itype(i2,molnum(i1))
3005 it3=itype(i3,molnum(i3))
3006 it4=itype(i4,molnum(i4))
3007 write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)') &
3008 i,restyp(it1,molnum(i1)),i1,restyp(it2,molnum(i2)),i2,&
3009 restyp(it3,molnum(i3)),i3,restyp(it4,molnum(i4)),i4
3011 write (iout,*) "Strands:",nstrand
3012 do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
3018 write (iout,'(i3,2x,a,i4,2x,a,i4)') &
3019 i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
3021 call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),&
3022 istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),&
3023 nc_fragm(1,1),nc_req_setf(1,1))
3024 write (iout,*) "Fragments after sorting:"
3031 write (iout,'(i3,2x,a,i4,2x,a,i4,$)') &
3032 i,restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2
3033 if (npiece(i,1).eq.1) then
3034 write (iout,'(2x,a)') strstr(istruct(i))
3040 write (iout,'(2x,a,i4,2x,a,i4,2x,a)') &
3041 restyp(it1,molnum(it1)),i1,restyp(it2,molnum(it2)),i2,strstr(istruct(i))
3045 end subroutine define_fragments
3046 !------------------------------------------------------------------------------
3047 subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
3048 ! implicit real*8 (a-h,o-z)
3049 ! include 'DIMENSIONS'
3050 ! include 'DIMENSIONS.ZSCOPT'
3051 ! include 'DIMENSIONS.COMPAR'
3052 ! include 'COMMON.IOUNITS'
3053 integer :: nbfrag,bfrag(4,nres/3)
3054 integer :: nhairp,ihairp(2,nres/5)
3056 write (iout,*) "Entered find_and_remove_hairpins"
3057 write (iout,*) "nbfrag",nbfrag
3059 write (iout,*) i,(bfrag(k,i),k=1,4)
3063 do while (i.le.nbfrag)
3064 write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
3065 if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5) &
3067 write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
3069 ihairp(1,nhairp)=bfrag(1,i)
3070 ihairp(2,nhairp)=bfrag(3,i)
3074 bfrag(k,j)=bfrag(k,j+1)
3081 write (iout,*) "After finding hairpins:"
3082 write (iout,*) "nhairp",nhairp
3084 write (iout,*) i,ihairp(1,i),ihairp(2,i)
3086 write (iout,*) "nbfrag",nbfrag
3088 write (iout,*) i,(bfrag(k,i),k=1,4)
3091 end subroutine find_and_remove_hairpins
3092 !------------------------------------------------------------------------------
3093 subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
3094 ! implicit real*8 (a-h,o-z)
3095 ! include 'DIMENSIONS'
3096 ! include 'DIMENSIONS.ZSCOPT'
3097 ! include 'DIMENSIONS.COMPAR'
3098 ! include 'COMMON.IOUNITS'
3099 integer :: nbfrag,bfrag(4,nres/3)
3100 integer :: nstrand,istrand(2,nres/2)
3101 integer :: nhairp,ihairp(2,nres/5)
3104 write (iout,*) "Entered split_beta"
3105 write (iout,*) "nbfrag",nbfrag
3107 write (iout,*) i,(bfrag(k,i),k=1,4)
3111 write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
3112 call add_strand(nstrand,istrand,nhairp,ihairp,&
3113 bfrag(1,i),bfrag(2,i),found)
3114 if (bfrag(3,i).lt.bfrag(4,i)) then
3115 write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
3116 call add_strand(nstrand,istrand,nhairp,ihairp,&
3117 bfrag(3,i),bfrag(4,i),found)
3119 write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
3120 call add_strand(nstrand,istrand,nhairp,ihairp,&
3121 bfrag(4,i),bfrag(3,i),found)
3125 write (iout,*) "Strands found:",nstrand
3127 write (iout,*) i,istrand(1,i),istrand(2,i)
3130 end subroutine split_beta
3131 !------------------------------------------------------------------------------
3132 subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
3133 ! implicit real*8 (a-h,o-z)
3134 ! include 'DIMENSIONS'
3135 ! include 'DIMENSIONS.ZSCOPT'
3136 ! include 'DIMENSIONS.COMPAR'
3137 ! include 'COMMON.IOUNITS'
3138 integer :: nstrand,istrand(2,nres/2)
3139 integer :: nhairp,ihairp(2,nres/5)
3141 integer :: is1,is2,j,idelt
3144 idelt=(ihairp(2,j)-ihairp(1,j))/6
3145 if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
3146 write (iout,*) "strand",is1,is2," is part of hairpin",&
3147 ihairp(1,j),ihairp(2,j)
3152 idelt=(istrand(2,j)-istrand(1,j))/3
3153 if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt) &
3155 ! The strand already exists in the array; update its ends if necessary.
3156 write (iout,*) "strand",is1,is2," found at position",j,&
3157 ":",istrand(1,j),istrand(2,j)
3158 istrand(1,j)=min0(istrand(1,j),is1)
3159 istrand(2,j)=max0(istrand(2,j),is2)
3163 ! The strand has not been found; add it to the array.
3164 write (iout,*) "strand",is1,is2," added to the array."
3167 istrand(1,nstrand)=is1
3168 istrand(2,nstrand)=is2
3170 end subroutine add_strand
3171 !------------------------------------------------------------------------------
3172 subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
3174 use geometry_data, only:anatemp,rad2deg,phi,nstart_sup,nend_sup
3175 use energy_data, only:itype,maxcont,molnum
3176 use compare_data, only:bfrag,hfrag,nbfrag,nhfrag
3177 use compare, only:freeres
3178 ! implicit real*8 (a-h,o-z)
3179 ! include 'DIMENSIONS'
3180 ! include 'DIMENSIONS.ZSCOPT'
3181 ! include 'COMMON.IOUNITS'
3182 ! include 'COMMON.FRAG'
3183 ! include 'COMMON.VAR'
3184 ! include 'COMMON.GEO'
3185 ! include 'COMMON.CHAIN'
3186 ! include 'COMMON.NAMES'
3187 ! include 'COMMON.INTERACT'
3188 integer :: ncont,icont(2,maxcont),isec(nres,4),nsec(nres+1),&
3190 logical :: lprint,lprint_sec,not_done !el,freeres
3191 integer :: i,j,ii1,jj1,i1,j1,ij,k,ien,ist
3192 integer :: nstrand,nbeta,nhelix,iii1,jjj1,mnum
3193 real(kind=8) :: p1,p2
3194 !rel external freeres
3195 character(len=1) :: csec(0:2)=reshape((/'-','E','H'/),shape(csec))
3197 write (iout,*) "entered secondary2",ncont
3198 write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
3200 write (iout,*) icont(1,i),icont(2,i)
3214 ! finding parallel beta
3215 !d write (iout,*) '------- looking for parallel beta -----------'
3221 if (i1.ge.nstart_sup .and. i1.le.nend_sup &
3222 .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
3223 !d write (iout,*) "parallel",i1,j1
3224 if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
3227 !d write (iout,*) i1,j1
3233 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and. &
3234 freeres(i1,j1,nsec,isec)) goto 5
3238 !d write (iout,*) i1,j1,not_done
3242 if (i1-ii1.gt.1) then
3246 if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',&
3250 bfrag(1,nbfrag)=ii1+1
3251 bfrag(2,nbfrag)=i1+1
3252 bfrag(3,nbfrag)=jj1+1
3253 bfrag(4,nbfrag)=min0(j1+1,nres)
3257 isec(ij,nsec(ij))=nbeta
3261 isec(ij,nsec(ij))=nbeta
3266 if (nbeta.le.9) then
3267 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3268 "DefPropRes 'strand",nstrand,&
3269 "' 'num = ",ii1-1,"..",i1-1,"'"
3271 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3272 "DefPropRes 'strand",nstrand,&
3273 "' 'num = ",ii1-1,"..",i1-1,"'"
3276 if (nbeta.le.9) then
3277 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3278 "DefPropRes 'strand",nstrand,&
3279 "' 'num = ",jj1-1,"..",j1-1,"'"
3281 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3282 "DefPropRes 'strand",nstrand,&
3283 "' 'num = ",jj1-1,"..",j1-1,"'"
3285 write(12,'(a8,4i4)') &
3286 "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
3290 endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
3293 ! finding antiparallel beta
3294 !d write (iout,*) '--------- looking for antiparallel beta ---------'
3299 if (freeres(i1,j1,nsec,isec)) then
3302 !d write (iout,*) i1,j1
3309 if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and. &
3310 freeres(i1,j1,nsec,isec)) goto 6
3314 !d write (iout,*) i1,j1,not_done
3318 if (i1-ii1.gt.1) then
3322 bfrag(2,nbfrag)=min0(i1+1,nres)
3323 bfrag(3,nbfrag)=min0(jj1+1,nres)
3330 if (nsec(ij).le.2) then
3331 isec(ij,nsec(ij))=nbeta
3337 if (nsec(ij).le.2) then
3338 isec(ij,nsec(ij))=nbeta
3343 if (lprint_sec) then
3344 write (iout,'(a,i3,4i4)')'antiparallel beta',&
3345 nbeta,ii1-1,i1,jj1,j1-1
3347 if (nstrand.le.9) then
3348 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3349 "DefPropRes 'strand",nstrand,&
3350 "' 'num = ",ii1-2,"..",i1-1,"'"
3352 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3353 "DefPropRes 'strand",nstrand,&
3354 "' 'num = ",ii1-2,"..",i1-1,"'"
3357 if (nstrand.le.9) then
3358 write(12,'(a18,i1,a9,i3,a2,i3,a1)') &
3359 "DefPropRes 'strand",nstrand,&
3360 "' 'num = ",j1-2,"..",jj1-1,"'"
3362 write(12,'(a18,i2,a9,i3,a2,i3,a1)') &
3363 "DefPropRes 'strand",nstrand,&
3364 "' 'num = ",j1-2,"..",jj1-1,"'"
3366 write(12,'(a8,4i4)') &
3367 "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
3373 !d write (iout,*) "After beta:",nbfrag
3375 !d write (iout,*) (bfrag(j,i),j=1,4)
3378 if (nstrand.gt.0.and.lprint_sec) then
3379 write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
3382 write(12,'(a9,i1,$)') " | strand",i
3384 write(12,'(a9,i2,$)') " | strand",i
3387 write(12,'(a1)') "'"
3391 ! finding alpha or 310 helix
3397 p1=phi(i1+2)*rad2deg
3399 if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
3402 if (j1.eq.i1+3 .and. &
3403 ((p1.ge.10.and.p1.le.80).or.i1.le.2).and. &
3404 ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
3405 !d if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
3406 !o if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
3409 if (nsec(ii1).eq.0) then
3418 if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
3422 p1=phi(i1+2)*rad2deg
3423 p2=phi(j1+2)*rad2deg
3424 if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80) &
3427 !d write (iout,*) i1,j1,not_done,p1,p2
3430 if (j1-ii1.gt.4) then
3432 !d write (iout,*)'helix',nhelix,ii1,j1
3441 if (lprint_sec) then
3442 write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
3443 if (nhelix.le.9) then
3444 write(12,'(a17,i1,a9,i3,a2,i3,a1)') &
3445 "DefPropRes 'helix",nhelix,&
3446 "' 'num = ",ii1-1,"..",j1-2,"'"
3448 write(12,'(a17,i2,a9,i3,a2,i3,a1)') &
3449 "DefPropRes 'helix",nhelix,&
3450 "' 'num = ",ii1-1,"..",j1-2,"'"
3457 if (nhelix.gt.0.and.lprint_sec) then
3458 write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
3460 if (nhelix.le.9) then
3461 write(12,'(a8,i1,$)') " | helix",i
3463 write(12,'(a8,i2,$)') " | helix",i
3466 write(12,'(a1)') "'"
3469 if (lprint_sec) then
3470 write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
3471 write(12,'(a20)') "XMacStand ribbon.mac"
3476 write(iout,*) 'UNRES seq:',anatemp
3478 write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
3482 write(iout,*) 'helix ',(hfrag(i,j),i=1,2),anatemp
3488 do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
3491 do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
3496 do k=hfrag(1,j),hfrag(2,j)
3502 write (iout,*) "Secondary structure"
3508 write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
3509 write (iout,'(80a1)') (onelet(itype(k,mnum)),k=ist,ien)
3510 write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
3515 end subroutine secondary2
3516 !-------------------------------------------------
3517 ! logical function freeres(i,j,nsec,isec)
3518 ! include 'DIMENSIONS'
3519 ! integer :: isec(nres,4),nsec(nres)
3520 ! integer :: i,j,k,l
3523 ! if (nsec(i).gt.1.or.nsec(j).gt.1) return
3526 ! if (isec(i,k).eq.isec(j,l)) return
3531 ! end function freeres
3532 !-------------------------------------------------
3533 subroutine alloc_compar_arrays(nfrg,nlev)
3535 use energy_data, only:maxcont
3537 integer :: nfrg,nlev
3539 !write(iout,*) "in alloc conpar arrays: nlevel=", nlevel," nfrag(1)=",nfrag(1)
3540 !------------------------
3543 allocate(nsccont_frag_ref(mmaxfrag)) !(mmaxfrag) !wham
3544 allocate(isccont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag) !wham
3545 !------------------------
3548 allocate(rmsfrag(nfrg,nlev+1),nc_fragm(nfrg,nlev+1)) !(maxfrag,maxlevel)
3549 allocate(qfrag(nfrg,2)) !(maxfrag,2)
3550 allocate(rmscutfrag(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3551 allocate(ang_cut(nfrg),ang_cut1(nfrg),frac_min(nfrg)) !(maxfrag)
3552 allocate(nc_req_setf(nfrg,nlev+1),npiece(nfrg,nlev+1),&
3553 ielecont(nfrg,nlev+1),isccont(nfrg,nlev+1),irms(nfrg,nlev+1),&
3554 ishifft(nfrg,nlev+1),len_frag(nfrg,nlev+1)) !(maxfrag,maxlevel)
3555 allocate(ncont_nat(2,nfrg,nlev+1))
3556 allocate(n_shift(2,nfrg,nlev+1)) !(2,maxfrag,maxlevel)
3557 ! allocate(nfrag(nlev)) !(maxlevel)
3558 allocate(isnfrag(nlev+2)) !(maxlevel+1)
3559 allocate(ifrag(2,maxpiece,nfrg)) !(2,maxpiece,maxfrag)
3560 allocate(ipiece(maxpiece,nfrg,2:nlev+1)) !(maxpiece,maxfrag,2:maxlevel)
3561 allocate(istruct(nfrg),iloc(nfrg),nlist_frag(nfrg)) !(maxfrag)
3562 allocate(iclass(nlev*nfrg,nlev+1)) !(maxlevel*maxfrag,maxlevel)
3563 allocate(list_frag(nres,nfrg)) !(maxres,maxfrag)
3564 !------------------------
3567 ! integer,dimension(:,:),allocatable :: icont_pept_ref !(2,maxcont)
3568 allocate(ncont_frag_ref(mmaxfrag)) !(mmaxfrag)
3569 allocate(icont_frag_ref(2,maxcont,mmaxfrag)) !(2,maxcont,mmaxfrag)
3570 ! integer,dimension(:),allocatable :: isec_ref !(maxres)
3571 !------------------------
3572 ! module w_comm_local
3574 allocate(creff(3,2*nres),cc(3,2*nres)) !(3,nres*2)
3575 allocate(iadded(nres)) !(nres)
3576 allocate(inumber(2,nres)) !(2,nres)
3579 !-------------------------------------------------------------------------------
3580 end subroutine alloc_compar_arrays
3582 !-------------------------------------------------------------------------------
3583 end module conform_compar