X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc-HCD-5D%2Freadrtns_CSA.F;fp=source%2Funres%2Fsrc-HCD-5D%2Freadrtns_CSA.F;h=58b86cc200e81964edeae8b447addcd2401c7cbd;hb=58980cd5a21077fd523753ffccc036765ef70d82;hp=b24a58257ab087b5605e8669cd6dcd450b68ee97;hpb=d02292725c202ff9c2749beac934bf1630f9017e;p=unres.git diff --git a/source/unres/src-HCD-5D/readrtns_CSA.F b/source/unres/src-HCD-5D/readrtns_CSA.F index b24a582..58b86cc 100644 --- a/source/unres/src-HCD-5D/readrtns_CSA.F +++ b/source/unres/src-HCD-5D/readrtns_CSA.F @@ -149,6 +149,7 @@ C constrains on theta angles WITH_THETA_CONSTR is the keyword out_template_coord = index(controlcard,"OUT_TEMPLATE_COORD").gt.0 out_template_restr = index(controlcard,"OUT_TEMPLATE_RESTR").gt.0 call readi(controlcard,'SYM',symetr,1) + call readi(controlcard,'PERMUT',npermut,1) call reada(controlcard,'TIMLIM',timlim,2800.0D0) ! default 16 hours unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0 call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes @@ -167,6 +168,8 @@ c write (iout,'(a,f10.1)') 'Time limit (min):',timlim c endif call readi(controlcard,'NZ_START',nz_start,0) call readi(controlcard,'NZ_END',nz_end,0) + call readi(controlcard,'NRAN_START',nran_start,0) + write (iout,*) "nran_start",nran_start c call readi(controlcard,'IZ_SC',iz_sc,0) timlim=60.0D0*timlim safety = 60.0d0*safety @@ -481,6 +484,7 @@ C call readi(controlcard,"NSTEP",n_timestep,1000000) call readi(controlcard,"NTWE",ntwe,100) call readi(controlcard,"NTWX",ntwx,1000) + call readi(controlcard,"REST_FREQ",irest_freq,1000) call reada(controlcard,"DT",d_time,1.0d-1) call reada(controlcard,"DVMAX",dvmax,2.0d1) call reada(controlcard,"DAMAX",damax,1.0d1) @@ -556,6 +560,7 @@ c if performing umbrella sampling, fragments constrained are read from the frag & " A" write(iout,'(a60,i5)')"Frequency of updating interaction list", & imatupdate + write(iout,'(a60,i5)')"Restart writing frequency",irest_freq if (RESPA) then write (iout,'(2a,i4,a)') & "A-MTS algorithm used; initial time step for fast-varying", @@ -741,7 +746,7 @@ C integer ilen external ilen integer iperm,tperm - integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2,nres_temp,itemp + integer i,j,ii,k,l,itrial,itmp,i1,i2,it1,it2,nres_temp double precision sumv C C Read PDB structure if applicable @@ -857,16 +862,19 @@ cd print *,'NNT=',NNT,' NCT=',NCT & chain_border(2,i),chain_border1(1,i),chain_border1(2,i) enddo call chain_symmetry(nchain,nres,itype,chain_border, - & chain_length,npermchain,tabpermchain) + & chain_length,npermchain,tabpermchain,nchain_group,nequiv, + & iequiv,mapchain) c do i=1,nres c write(iout,*) i,(tperm(ireschain(i),ii,tabpermchain), c & ii=1,npermchain) c enddo +#ifdef DEBUG write(iout,*) "residue permutations" do i=1,nres write(iout,*) i,(iperm(i,ii),ii=1,npermchain) enddo call flush(iout) +#endif if (itype(1).eq.ntyp1) nnt=2 if (itype(nres).eq.ntyp1) nct=nct-1 write (iout,*) "nnt",nnt," nct",nct @@ -971,25 +979,34 @@ C & write (iout,*) 'FTORS',ftors call reada(weightcard,"WDIHC",wdihc,0.591D0) write (iout,*) "Weight of dihedral angle restraints",wdihc read(inp,'(9x,3f7.3)') +c & (secprob(1,i),secprob(2,i),secprob(3,i),i=nnt,nct) & (secprob(1,i),secprob(2,i),secprob(3,i),i=nnt,nct) write (iout,*) "The secprob array" do i=nnt,nct write (iout,'(i5,3f8.3)') i,(secprob(j,i),j=1,3) enddo ndih_constr=0 + iconstr_dih=0 do i=nnt+3,nct if (itype(i-3).ne.ntyp1 .and. itype(i-2).ne.ntyp1 & .and. itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1) then ndih_constr=ndih_constr+1 idih_constr(ndih_constr)=i + iconstr_dih(i)=ndih_constr sumv=0.0d0 do j=1,3 vpsipred(j,ndih_constr)=secprob(j,i-1)*secprob(j,i-2) sumv=sumv+vpsipred(j,ndih_constr) enddo - do j=1,3 - vpsipred(j,ndih_constr)=vpsipred(j,ndih_constr)/sumv - enddo + if (sumv.gt.0.0d0) then + do j=1,3 + vpsipred(j,ndih_constr)=vpsipred(j,ndih_constr)/sumv + enddo + else + vpsipred(1,ndih_constr)=1.0d0 + vpsipred(2,ndih_constr)=0.0d0 + vpsipred(3,ndih_constr)=0.0d0 + endif phibound(1,ndih_constr)=phihel*deg2rad phibound(2,ndih_constr)=phibet*deg2rad sdihed(1,ndih_constr)=sigmahel*deg2rad @@ -1125,8 +1142,11 @@ c write (iout,*) "After read_dist_constr nhpb",nhpb endif write (iout,*) "calling read_saxs_consrtr",nsaxs if (nsaxs.gt.0) call read_saxs_constr - +c write (iout,*) "After read_saxs_constr" +c call flush(iout) if (constr_homology.gt.0) then +c write (iout,*) "Calling read_constr_homology" +c call flush(iout) call read_constr_homology if (indpdb.gt.0 .or. pdbref) then do i=1,2*nres @@ -1184,7 +1204,8 @@ c write (iout,*) "After read_dist_constr nhpb",nhpb 335 continue unres_pdb=.false. nres_temp=nres - call readpdb +c call readpdb + call readpdb_template(nmodel_start+1) close(ipdbin) if (nres.ge.nres_temp) then nmodel_start=nmodel_start+1 @@ -1195,22 +1216,11 @@ c write (iout,*) "After read_dist_constr nhpb",nhpb enddo enddo else -c itemp=nres -c nres=nres_temp -c call gen_rand_conf(itemp,*115) -c nmodel_start=nmodel_start+1 -c do i=1,2*nres -c do j=1,3 -c chomo(j,i,nmodel_start)=c(j,i) -c enddo -c enddo -c goto 116 - 115 if (me.eq.king .or. .not. out1file) - & write (iout,'(a,2i5,1x,a)') + if (me.eq.king .or. .not. out1file) + & write (iout,'(a,2i7,1x,a)') & "Different number of residues",nres_temp,nres, & " model skipped." endif - 116 continue nres=nres_temp enddo 332 continue @@ -2341,6 +2351,7 @@ c1out open(iout,file=outname,status='unknown') #else if (me.eq.king .or. .not.out1file) & open(iout,file=outname,status='unknown') +#define DEBUG #ifdef DEBUG if (fg_rank.gt.0) then write (liczba,'(i3.3)') myrank/nfgtasks @@ -2349,6 +2360,7 @@ c1out open(iout,file=outname,status='unknown') & status='unknown') endif #endif +#undef DEBUG if(me.eq.king) then open(igeom,file=intname,status='unknown',access='append') open(ipdb,file=pdbname,status='unknown') @@ -2734,10 +2746,10 @@ c write (iout,*) "j",j," k",k endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", + & write (iout,'(a,3i6,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #else - write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", + write (iout,'(a,3i6,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #endif enddo @@ -2781,10 +2793,10 @@ c write (iout,*) "j",j," k",k endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", + & write (iout,'(a,3i6,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #else - write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.restr ", + write (iout,'(a,3i6,f8.2,1pe12.2)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) #endif enddo @@ -2811,13 +2823,13 @@ c & fordepth_peak(nhpb_peak+1),npeak ipeak(2,npeak)=i #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,5i5,2f8.2,2f10.5,i5)') "+dist.restr ", + & write (iout,'(a,5i6,2f8.2,2f10.5,i5)') "+dist.restr ", & nhpb_peak,ihpb_peak(nhpb_peak),jhpb_peak(nhpb_peak), & ibecarb_peak(nhpb_peak),npeak,dhpb_peak(nhpb_peak), & dhpb1_peak(nhpb_peak),forcon_peak(nhpb_peak), & fordepth_peak(nhpb_peak),irestr_type_peak(nhpb_peak) #else - write (iout,'(a,5i5,2f8.2,2f10.5,i5)') "+dist.restr ", + write (iout,'(a,5i6,2f8.2,2f10.5,i5)') "+dist.restr ", & nhpb_peak,ihpb_peak(nhpb_peak),jhpb_peak(nhpb_peak), & ibecarb_peak(nhpb_peak),npeak,dhpb_peak(nhpb_peak), & dhpb1_peak(nhpb_peak),forcon_peak(nhpb_peak), @@ -2840,11 +2852,11 @@ c fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1) irestr_type(nhpb)=11 #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,4i5,2f8.2,2f10.5,i5)') "+dist.restr ", + & write (iout,'(a,4i6,2f8.2,2f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),irestr_type(nhpb) #else - write (iout,'(a,4i5,2f8.2,2f10.5,i5)') "+dist.restr ", + write (iout,'(a,4i6,2f8.2,2f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),irestr_type(nhpb) #endif @@ -2904,12 +2916,12 @@ c & dhpb(nhpb+1),dhpb1(nhpb+1),forcon(nhpb+1),fordepth(nhpb+1) endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + & write (iout,'(a,4i6,2f8.2,3f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), & irestr_type(nhpb) #else - write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + write (iout,'(a,4i6,2f8.2,3f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), & irestr_type(nhpb) @@ -2938,10 +2950,10 @@ C print *,"in else" endif #ifdef MPI if (.not.out1file .or. me.eq.king) - & write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ", + & write (iout,'(a,4i6,f8.2,f10.1)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb) #else - write (iout,'(a,4i5,f8.2,f10.1)') "+dist.restr ", + write (iout,'(a,4i6,f8.2,f10.1)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(i),dhpb(nhpb),forcon(nhpb) #endif endif @@ -2984,13 +2996,13 @@ C dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) dhpb(nhpb)=dist(i+nres*ii,j+nres*jj) #ifdef MPI if (.not.out1file .or. me.eq.king) then - write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + write (iout,'(a,4i6,2f8.2,3f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), & irestr_type(nhpb) endif #else - write (iout,'(a,4i5,2f8.2,3f10.5,i5)') "+dist.restr ", + write (iout,'(a,4i6,2f8.2,3f10.5,i5)') "+dist.restr ", & nhpb,ihpb(nhpb),jhpb(nhpb),ibecarb(nhpb),dhpb(nhpb), & dhpb1(nhpb),forcon(nhpb),fordepth(nhpb),xlscore(nhpb), & irestr_type(nhpb) @@ -3054,8 +3066,8 @@ c & sigma_odl_temp(maxres,maxres,max_template) character*2 kic2 character*24 model_ki_dist, model_ki_angle character*500 controlcard - integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec, - & ik,iistart,nres_temp + integer ki,i,ii,j,k,l,ii_in_use(maxdim_cont),i_tmp,idomain_tmp, + & irec,ik,iistart,nres_temp integer ilen external ilen logical liiflag,lfirst @@ -3108,7 +3120,7 @@ c endif call card_concat(controlcard) read(controlcard,*) (waga_homology(i),i=1,homol_nset) if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then - write(iout,*) "iset homology_weight " +c write(iout,*) "iset homology_weight " do i=1,homol_nset write(iout,*) i,waga_homology(i) enddo @@ -3122,30 +3134,30 @@ c endif cd write (iout,*) "nnt",nnt," nct",nct cd call flush(iout) + if (read_homol_frag) then + call read_klapaucjusz + else lim_odl=0 lim_dih=0 c c write(iout,*) 'nnt=',nnt,'nct=',nct c - do i = nnt,nct - do k=1,constr_homology - idomain(k,i)=0 - enddo - enddo - - ii=0 - do i = nnt,nct-2 - do j=i+2,nct - ii=ii+1 - ii_in_use(ii)=0 - enddo - enddo - - if (read_homol_frag) then - call read_klapaucjusz - else +c do i = nnt,nct +c do k=1,constr_homology +c idomain(k,i)=0 +c enddo +c enddo + idomain=0 +c ii=0 +c do i = nnt,nct-2 +c do j=i+2,nct +c ii=ii+1 +c ii_in_use(ii)=0 +c enddo +c enddo + ii_in_use=0 do k=1,constr_homology read(inp,'(a)') pdbfile @@ -3265,8 +3277,8 @@ c & constr_homology endif sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) else -ct ii=ii+1 -ct l_homo(k,ii)=.false. +c ii=ii+1 +c l_homo(k,ii)=.false. endif enddo enddo @@ -3456,26 +3468,26 @@ cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then write (iout,*) "Distance restraints from templates" do ii=1,lim_odl - write(iout,'(i8,2i5,100(f8.2,e12.4,1x,l1,4x))') + write(iout,'(3i7,100(2f8.2,1x,l1,4x))') & ii,ires_homo(ii),jres_homo(ii), & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii), & ki=1,constr_homology) enddo write (iout,*) "Dihedral angle restraints from templates" do i=nnt+3,nct - write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)), + write (iout,'(i7,a4,100(2f8.2,4x))') i,restyp(itype(i)), & (rad2deg*dih(ki,i), & rad2deg/dsqrt(sigma_dih(ki,i)),ki=1,constr_homology) enddo write (iout,*) "Virtual-bond angle restraints from templates" do i=nnt+2,nct - write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(i)), + write (iout,'(i7,a4,100(2f8.2,4x))') i,restyp(itype(i)), & (rad2deg*thetatpl(ki,i), & rad2deg/dsqrt(sigma_theta(ki,i)),ki=1,constr_homology) enddo write (iout,*) "SC restraints from templates" do i=nnt,nct - write(iout,'(i5,100(4f8.2,4x))') i, + write(iout,'(i7,100(4f8.2,4x))') i, & (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i), & 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology) enddo @@ -3641,14 +3653,17 @@ c---------------------------------------------------------------------- character*2 kic2 character*24 model_ki_dist, model_ki_angle character*500 controlcard - integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp, - & ik,ll,ii,kk,iistart,iishift,lim_xx + integer ki, i, j, jj,k, l, ii_in_use(maxdim_cont),i_tmp, + & idomain_tmp, + & ik,ll,lll,ii_old,ii,iii,ichain,kk,iistart,iishift,lim_xx,igr, + & i01,i10,nnt_chain,nct_chain + integer itype_temp(maxres) double precision distal logical lprn /.true./ integer nres_temp integer ilen external ilen - logical liiflag + logical liiflag,lfirst c c double precision rescore_tmp,x12,y12,z12,rescore2_tmp @@ -3662,14 +3677,48 @@ c For new homol impl c include 'COMMON.VAR' c +c write (iout,*) "READ_KLAPAUCJUSZ" +c print *,"READ_KLAPAUCJUSZ" +c call flush(iout) call getenv("FRAGFILE",fragfile) + write (iout,*) "Opening", fragfile + call flush(iout) open(ientin,file=fragfile,status="old",err=10) - read(ientin,*) constr_homology,nclust - nmodel_start=constr_homology - l_homo = .false. +c write (iout,*) " opened" +c call flush(iout) + sigma_theta=0.0 sigma_d=0.0 sigma_dih=0.0 + l_homo = .false. + + nres_temp=nres + itype_temp=itype + ii=0 + lim_odl=0 + +c write (iout,*) "Entering loop" +c call flush(iout) + + DO IGR = 1,NCHAIN_GROUP + +c write (iout,*) "igr",igr + call flush(iout) + read(ientin,*) constr_homology,nclust + + if (start_from_model) then + nmodel_start=constr_homology + else + nmodel_start=0 + endif + + ii_old=lim_odl + + ichain=iequiv(1,igr) + nnt_chain=chain_border(1,ichain)-chain_border1(1,ichain)+1 + nct_chain=chain_border(2,ichain)-chain_border1(1,ichain)+1 +c write (iout,*) "nnt_chain",nnt_chain," nct_chain",nct_chain + c Read pdb files do k=1,constr_homology read(ientin,'(a)') pdbfile @@ -3683,10 +3732,10 @@ c Read pdb files stop 34 continue unres_pdb=.false. - nres_temp=nres +c nres_temp=nres call readpdb_template(k) nres_chomo(k)=nres - nres=nres_temp +c nres=nres_temp do i=1,nres rescore(k,i)=0.2d0 rescore2(k,i)=1.0d0 @@ -3705,6 +3754,7 @@ c do ll = 1,ninclust(l) k = inclust(ll,l) +c write (iout,*) "l",l," ll",ll," k",k do i=1,nres idomain(k,i)=0 enddo @@ -3720,7 +3770,7 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) - nres_temp=nres +c nres_temp=nres nres=nres_chomo(k) do i=1,2*nres do j=1,3 @@ -3734,11 +3784,13 @@ c write (iout,*) "c(",j,i,") =",c(j,i) thetaref(i)=theta(i) phiref(i)=phi(i) enddo - nres=nres_temp +c nres=nres_temp if (waga_dist.ne.0.0d0) then - ii=0 - do i = nnt,nct-2 - do j=i+2,nct + ii=ii_old +c do i = nnt,nct-2 + do i = nnt_chain,nct_chain-2 +c do j=i+2,nct + do j=i+2,nct_chain x12=c(1,i)-c(1,j) y12=c(2,i)-c(2,j) @@ -3755,9 +3807,9 @@ c write (iout,*) k,i,j,distal,dist2_cut c write (iout,*) "k",k c write (iout,*) "i",i," j",j," constr_homology", -c & constr_homology - ires_homo(ii)=i - jres_homo(ii)=j +c & constr_homology + ires_homo(ii)=i+chain_border1(1,igr)-1 + jres_homo(ii)=j+chain_border1(1,igr)-1 odl(k,ii)=distal if (read2sigma) then sigma_odl(k,ii)=0 @@ -3793,50 +3845,55 @@ c c Theta, dihedral and SC retraints c if (waga_angle.gt.0.0d0) then - do i = nnt+3,nct + do i = nnt_chain+3,nct_chain + iii=i+chain_border1(1,igr)-1 if (idomain(k,i).eq.0) then c sigma_dih(k,i)=0.0 cycle endif - dih(k,i)=phiref(i) - sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+ + dih(k,iii)=phiref(i) + sigma_dih(k,iii)= + & (rescore(k,i)+rescore(k,i-1)+ & rescore(k,i-2)+rescore(k,i-3))/4.0 c write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i), c & " sigma_dihed",sigma_dih(k,i) - if (sigma_dih(k,i).ne.0) - & sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i)) + if (sigma_dih(k,iii).ne.0) + & sigma_dih(k,iii)=1.0d0/(sigma_dih(k,iii)*sigma_dih(k,iii)) enddo - lim_dih=nct-nnt-2 +c lim_dih=nct-nnt-2 endif if (waga_theta.gt.0.0d0) then - do i = nnt+2,nct + do i = nnt_chain+2,nct_chain + iii=i+chain_border1(1,igr)-1 if (idomain(k,i).eq.0) then c sigma_theta(k,i)=0.0 cycle endif - thetatpl(k,i)=thetaref(i) - sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+ + thetatpl(k,iii)=thetaref(i) + sigma_theta(k,iii)=(rescore(k,i)+rescore(k,i-1)+ & rescore(k,i-2))/3.0 - if (sigma_theta(k,i).ne.0) - & sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i)) + if (sigma_theta(k,iii).ne.0) + & sigma_theta(k,iii)=1.0d0/ + & (sigma_theta(k,iii)*sigma_theta(k,iii)) enddo endif if (waga_d.gt.0.0d0) then - do i = nnt,nct + do i = nnt_chain,nct_chain + iii=i+chain_border1(1,igr)-1 if (itype(i).eq.10) cycle if (idomain(k,i).eq.0 ) then c sigma_d(k,i)=0.0 cycle endif - xxtpl(k,i)=xxref(i) - yytpl(k,i)=yyref(i) - zztpl(k,i)=zzref(i) - sigma_d(k,i)=rescore(k,i) - if (sigma_d(k,i).ne.0) - & sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i)) - if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 + xxtpl(k,iii)=xxref(i) + yytpl(k,iii)=yyref(i) + zztpl(k,iii)=zzref(i) + sigma_d(k,iii)=rescore(k,i) + if (sigma_d(k,iii).ne.0) + & sigma_d(k,iii)=1.0d0/(sigma_d(k,iii)*sigma_d(k,iii)) +c if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 enddo endif enddo ! l @@ -3845,41 +3902,101 @@ c c remove distance restraints not used in any model from the list c shift data in all arrays c +c write (iout,*) "ii_old",ii_old if (waga_dist.ne.0.0d0) then - ii=0 +#ifdef DEBUG + write (iout,*) "Distance restraints from templates" + do iii=1,lim_odl + write(iout,'(4i5,100(2f8.2,1x,l1,4x))') + & iii,ii_in_use(iii),ires_homo(iii),jres_homo(iii), + & (odl(ki,iii),1.0d0/dsqrt(sigma_odl(ki,iii)),l_homo(ki,iii), + & ki=1,constr_homology) + enddo +#endif + ii=ii_old liiflag=.true. - do i=nnt,nct-2 - do j=i+2,nct + lfirst=.true. + do i=nnt_chain,nct_chain-2 + do j=i+2,nct_chain ii=ii+1 - if (ii_in_use(ii).eq.0.and.liiflag) then +c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 +c & .and. distal.le.dist2_cut ) then +c write (iout,*) "i",i," j",j," ii",ii," i_in_use",ii_in_use(ii) +c call flush(iout) + if (ii_in_use(ii).eq.0.and.liiflag.or. + & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then liiflag=.false. - iistart=ii + i10=ii + if (lfirst) then + lfirst=.false. + iistart=ii + else + if(i10.eq.lim_odl) i10=i10+1 + do ki=0,i10-i01-1 + ires_homo(iistart+ki)=ires_homo(ki+i01) + jres_homo(iistart+ki)=jres_homo(ki+i01) + ii_in_use(iistart+ki)=ii_in_use(ki+i01) + do k=1,constr_homology + odl(k,iistart+ki)=odl(k,ki+i01) + sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01) + l_homo(k,iistart+ki)=l_homo(k,ki+i01) + enddo + enddo + iistart=iistart+i10-i01 + endif endif - if (ii_in_use(ii).ne.0.and..not.liiflag.or. - & .not.liiflag.and.ii.eq.lim_odl) then - if (ii.eq.lim_odl) then - iishift=ii-iistart+1 - else - iishift=ii-iistart - endif + if (ii_in_use(ii).ne.0.and..not.liiflag) then + i01=ii liiflag=.true. - do ki=iistart,lim_odl-iishift - ires_homo(ki)=ires_homo(ki+iishift) - jres_homo(ki)=jres_homo(ki+iishift) - ii_in_use(ki)=ii_in_use(ki+iishift) - do k=1,constr_homology - odl(k,ki)=odl(k,ki+iishift) - sigma_odl(k,ki)=sigma_odl(k,ki+iishift) - l_homo(k,ki)=l_homo(k,ki+iishift) - enddo - enddo - ii=ii-iishift - lim_odl=lim_odl-iishift endif enddo enddo + lim_odl=iistart-1 endif + lll=lim_odl-ii_old + + do i=2,nequiv(igr) + + ichain=iequiv(i,igr) + + do j=nnt_chain,nct_chain + jj=j+chain_border1(1,ichain)-chain_border1(1,iequiv(1,igr)) + do k=1,constr_homology + dih(k,jj)=dih(k,j) + sigma_dih(k,jj)=sigma_dih(k,j) + thetatpl(k,jj)=thetatpl(k,j) + sigma_theta(k,jj)=sigma_theta(k,j) + xxtpl(k,jj)=xxtpl(k,j) + yytpl(k,jj)=yytpl(k,j) + zztpl(k,jj)=zztpl(k,j) + sigma_d(k,jj)=sigma_d(k,j) + enddo + enddo + + jj=chain_border1(1,ichain)-chain_border1(1,iequiv(i-1,igr)) +c write (iout,*) "igr",igr," i",i," ichain",ichain," jj",jj + do j=ii_old+1,lim_odl + ires_homo(j+lll)=ires_homo(j)+jj + jres_homo(j+lll)=jres_homo(j)+jj + do k=1,constr_homology + odl(k,j+lll)=odl(k,j) + sigma_odl(k,j+lll)=sigma_odl(k,j) + l_homo(k,j+lll)=l_homo(k,j) + enddo + enddo + + ii_old=ii_old+lll + lim_odl=lim_odl+lll + + enddo + + ENDDO ! IGR + + if (waga_angle.gt.0.0d0) lim_dih=nct-nnt-2 + nres=nres_temp + itype=itype_temp + return 10 stop "Error in fragment file" end