X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc%2Freadrtns.F;h=d862542cf5e08cf71d94cb4ddfd467b2fc82a7b5;hb=357148eb01c1ea7e5cfd362d34f1e1ab61c8f2a8;hp=1d2fd437ad3a1d55ab7726f08af890aa31b919e2;hpb=478a9d9a1c99eb3f4bc4ca676ff3162bdd01d633;p=unres.git diff --git a/source/cluster/wham/src/readrtns.F b/source/cluster/wham/src/readrtns.F index 1d2fd43..d862542 100644 --- a/source/cluster/wham/src/readrtns.F +++ b/source/cluster/wham/src/readrtns.F @@ -24,12 +24,14 @@ C call card_concat(controlcard) call readi(controlcard,'NRES',nres,0) + write (iout,*) "NRES",NRES call readi(controlcard,'RESCALE',rescale_mode,2) call readi(controlcard,'PDBOUT',outpdb,0) call readi(controlcard,'MOL2OUT',outmol2,0) refstr=(index(controlcard,'REFSTR').gt.0) write (iout,*) "REFSTR",refstr pdbref=(index(controlcard,'PDBREF').gt.0) + dyn_ss=(index(controlcard,'DYN_SS').gt.0) iscode=index(controlcard,'ONE_LETTER') tree=(index(controlcard,'MAKE_TREE').gt.0) min_var=(index(controlcard,'MINVAR').gt.0) @@ -59,6 +61,16 @@ C write (iout,*) 'beta_h',(beta_h(i),i=1,nT) lprint_cart=index(controlcard,"PRINT_CART") .gt.0 lprint_int=index(controlcard,"PRINT_INT") .gt.0 + with_dihed_constr = index(controlcard,"WITH_DIHED_CONSTR").gt.0 + call readi(controlcard,'CONSTR_DIST',constr_dist,0) + write (iout,*) "with_dihed_constr ",with_dihed_constr, + & " CONSTR_DIST",constr_dist + + call readi(controlcard,'CONSTR_HOMOL',constr_homology,0) + write (iout,*) "with_homology_constr ",with_dihed_constr, + & " CONSTR_HOMOLOGY",constr_homology + + call flush(iout) if (min_var) iopt=1 return end @@ -82,6 +94,7 @@ C include 'COMMON.CONTROL' include 'COMMON.CONTACTS' include 'COMMON.TIME1' + include 'COMMON.TORCNSTR' #ifdef MPL include 'COMMON.INFO' #endif @@ -92,6 +105,7 @@ C integer itype_pdb(maxres) logical seq_comp integer i,j + write (iout,*) " MOLREAD: NRES",NRES C C Body C @@ -119,9 +133,49 @@ C Read weights of the subsequent energy terms. call reada(weightcard,'SCALSCP',scalscp,1.0d0) call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0) call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) + call reada(weightcard,'WSCCOR',wsccor,1.0D0) + call reada(weightcard,"D0CM",d0cm,3.78d0) + call reada(weightcard,"AKCM",akcm,15.1d0) + call reada(weightcard,"AKTH",akth,11.0d0) + call reada(weightcard,"AKCT",akct,12.0d0) + call reada(weightcard,"V1SS",v1ss,-1.08d0) + call reada(weightcard,"V2SS",v2ss,7.61d0) + call reada(weightcard,"V3SS",v3ss,13.7d0) + call reada(weightcard,"EBR",ebr,-5.50D0) +C Bartek + call reada(weightcard,'WDFAD',wdfa_dist,0.0d0) + call reada(weightcard,'WDFAT',wdfa_tor,0.0d0) + call reada(weightcard,'WDFAN',wdfa_nei,0.0d0) + call reada(weightcard,'WDFAB',wdfa_beta,0.0d0) if (index(weightcard,'SOFT').gt.0) ipot=6 C 12/1/95 Added weight for the multi-body term WCORR call reada(weightcard,'WCORRH',wcorr,1.0D0) + do i=1,maxres-1 + do j=i+1,maxres + dyn_ssbond_ij(i,j)=1.0d300 + enddo + enddo + call reada(weightcard,"HT",Ht,0.0D0) + if (dyn_ss) then + ss_depth=ebr/wsc-0.25*eps(1,1) + Ht=Ht/wsc-0.25*eps(1,1) + akcm=akcm*wstrain/wsc + akth=akth*wstrain/wsc + akct=akct*wstrain/wsc + v1ss=v1ss*wstrain/wsc + v2ss=v2ss*wstrain/wsc + v3ss=v3ss*wstrain/wsc + else + ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain + endif + write (iout,'(/a)') "Disulfide bridge parameters:" + write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr + write (iout,'(a,f10.2)') 'S-S depth: ',ss_depth + write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm + write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct + write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss, + & ' v3ss:',v3ss + write (iout,'(2(a,f10.2))') 'ht:',ht,' eps:', eps(1,1) if (wcorr4.gt.0.0d0) wcorr=wcorr4 weights(1)=wsc weights(2)=wscp @@ -141,9 +195,13 @@ C 12/1/95 Added weight for the multi-body term WCORR weights(16)=wvdwpp weights(17)=wbond weights(18)=scal14 + weights(22)=wdfa_dist + weights(23)=wdfa_tor + weights(24)=wdfa_nei + weights(25)=wdfa_beta write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor, & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wturn3, - & wturn4,wturn6 + & wturn4,wturn6,wsccor,wdfa_dist,wdfa_tor,wdfa_nei,wdfa_beta 10 format (/'Energy-term weights (unscaled):'// & 'WSCC= ',f10.6,' (SC-SC)'/ & 'WSCP= ',f10.6,' (SC-p)'/ @@ -161,7 +219,12 @@ C 12/1/95 Added weight for the multi-body term WCORR & 'WCORR6= ',f10.6,' (multi-body 6th order)'/ & 'WTURN3= ',f10.6,' (turns, 3rd order)'/ & 'WTURN4= ',f10.6,' (turns, 4th order)'/ - & 'WTURN6= ',f10.6,' (turns, 6th order)') + & 'WTURN6= ',f10.6,' (turns, 6th order)'/ + & 'WSCCOR= ',f10.6,' (SC-backbone torsional correalations)'/ + & 'WDFAD= ',f10.6,' (DFA distance)'/ + & 'WDFAT= ',f10.6,' (DFA torsional)'/ + & 'WDFAN= ',f10.6,' (DFA neighbors)'/ + & 'WDFAB= ',f10.6,' (DFA beta)'/) if (wcorr4.gt.0.0d0) then write (iout,'(/2a/)') 'Local-electrostatic type correlation ', & 'between contact pairs of peptide groups' @@ -224,6 +287,26 @@ C Convert sequence to numeric code print *,'Call Read_Bridge.' call read_bridge + if (with_dihed_constr) then + + read (inp,*) ndih_constr + if (ndih_constr.gt.0) then + read (inp,*) ftors + write (iout,*) 'FTORS',ftors + read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr) + write (iout,*) + & 'There are',ndih_constr,' constraints on phi angles.' + do i=1,ndih_constr + write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i) + enddo + do i=1,ndih_constr + phi0(i)=deg2rad*phi0(i) + drange(i)=deg2rad*drange(i) + enddo + endif + + endif + nnt=1 nct=nres print *,'NNT=',NNT,' NCT=',NCT @@ -233,6 +316,29 @@ C Convert sequence to numeric code if (nend.gt.nct .or. nend.eq.0) nend=nct write (iout,*) "nstart",nstart," nend",nend nres0=nres + +C Juyong:READ init_vars +C Initialize variables! +C Juyong:READ read_info +C READ fragment information!! +C both routines should be in dfa.F file!! + + if (.not. (wdfa_dist.eq.0.0 .and. wdfa_tor.eq.0.0 .and. + & wdfa_nei.eq.0.0 .and. wdfa_beta.eq.0.0)) then + write (iout,*) "Calling init_dfa_vars" + call flush(iout) + call init_dfa_vars + write (iout,*) 'init_dfa_vars finished!' + call flush(iout) + call read_dfa_info + write (iout,*) 'read_dfa_info finished!' + call flush(iout) + endif + + if (constr_homology.gt.0) then + call read_constr_homology + endif + c if (pdbref) then c read(inp,'(a)') pdbfile c write (iout,'(2a)') 'PDB data will be read from file ',pdbfile @@ -302,6 +408,11 @@ c endif endif call contact(.true.,ncont_ref,icont_ref) endif +c Read distance restraints + if (constr_dist.gt.0) then + call read_dist_constr + call hpb_partition + endif return end c----------------------------------------------------------------------------- @@ -341,7 +452,7 @@ C Read information about disulfide bridges. integer i,j C Read bridging residues. read (inp,*) ns,(iss(i),i=1,ns) - print *,'ns=',ns + write(iout,*)'ns=',ns C Check whether the specified bridging residues are cystines. do i=1,ns if (itype(iss(i)).ne.1) then @@ -390,8 +501,8 @@ C bridging residues. enddo write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.' 20 continue - dhpb(i)=dbr - forcon(i)=fbr +c dhpb(i)=dbr +c forcon(i)=fbr enddo do i=1,nss ihpb(i)=ihpb(i)+nres @@ -399,6 +510,22 @@ C bridging residues. enddo endif endif + if (ns.gt.0.and.dyn_ss) then + do i=nss+1,nhpb + ihpb(i-nss)=ihpb(i) + jhpb(i-nss)=jhpb(i) + forcon(i-nss)=forcon(i) + dhpb(i-nss)=dhpb(i) + enddo + nhpb=nhpb-nss + nss=0 + call hpb_partition + do i=1,ns + dyn_ss_mask(iss(i))=.true. +c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU" + enddo + endif + print *, "Leaving brigde read" return end c---------------------------------------------------------------------------- @@ -473,6 +600,24 @@ c---------------------------------------------------------------------------- return end c---------------------------------------------------------------------------- + subroutine multreadi(rekord,lancuch,tablica,dim,default) + implicit none + integer dim,i + integer tablica(dim),default + character*(*) rekord,lancuch + character*80 aux + integer ilen,iread + external ilen + do i=1,dim + tablica(i)=default + enddo + iread=index(rekord,lancuch(:ilen(lancuch))//"=") + if (iread.eq.0) return + iread=iread+ilen(lancuch)+1 + read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim) + 10 return + end +c---------------------------------------------------------------------------- subroutine card_concat(card) include 'DIMENSIONS' include 'COMMON.IOUNITS' @@ -573,3 +718,523 @@ C #endif return end +c------------------------------------------------------------------------------- + subroutine read_dist_constr + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CONTROL' + include 'COMMON.CHAIN' + include 'COMMON.IOUNITS' + include 'COMMON.SBRIDGE' + integer ifrag_(2,100),ipair_(2,100) + double precision wfrag_(100),wpair_(100) + character*500 controlcard +c write (iout,*) "Calling read_dist_constr" +c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup + call card_concat(controlcard) +c call flush(iout) +c write (iout,'(a)') controlcard + call readi(controlcard,"NFRAG",nfrag_,0) + call readi(controlcard,"NPAIR",npair_,0) + call readi(controlcard,"NDIST",ndist_,0) + call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) + call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0) + call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0) + call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0) + call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0) + write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_ + write (iout,*) "IFRAG" + do i=1,nfrag_ + write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) + enddo + write (iout,*) "IPAIR" + do i=1,npair_ + write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i) + enddo + call flush(iout) + if (.not.refstr .and. nfrag_.gt.0) then + write (iout,*) + & "ERROR: no reference structure to compute distance restraints" + write (iout,*) + & "Restraints must be specified explicitly (NDIST=number)" + stop + endif + if (nfrag_.lt.2 .and. npair_.gt.0) then + write (iout,*) "ERROR: Less than 2 fragments specified", + & " but distance restraints between pairs requested" + stop + endif + call flush(iout) + do i=1,nfrag_ + if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup + if (ifrag_(2,i).gt.nstart_sup+nsup-1) + & ifrag_(2,i)=nstart_sup+nsup-1 +c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) + call flush(iout) + if (wfrag_(i).gt.0.0d0) then + do j=ifrag_(1,i),ifrag_(2,i)-1 + do k=j+1,ifrag_(2,i) + write (iout,*) "j",j," k",k + ddjk=dist(j,k) + if (constr_dist.eq.1) then + nhpb=nhpb+1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i) + else if (constr_dist.eq.2) then + if (ddjk.le.dist_cut) then + nhpb=nhpb+1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i) + endif + else + nhpb=nhpb+1 + ihpb(nhpb)=j + jhpb(nhpb)=k + dhpb(nhpb)=ddjk + forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2) + endif + write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) + enddo + enddo + endif + enddo + do i=1,npair_ + if (wpair_(i).gt.0.0d0) then + ii = ipair_(1,i) + jj = ipair_(2,i) + if (ii.gt.jj) then + itemp=ii + ii=jj + jj=itemp + endif + do j=ifrag_(1,ii),ifrag_(2,ii) + do k=ifrag_(1,jj),ifrag_(2,jj) + nhpb=nhpb+1 + ihpb(nhpb)=j + jhpb(nhpb)=k + forcon(nhpb)=wpair_(i) + dhpb(nhpb)=dist(j,k) + write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) + enddo + enddo + endif + enddo + do i=1,ndist_ + read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i), + & ibecarb(i),forcon(nhpb+1) + if (forcon(nhpb+1).gt.0.0d0) then + nhpb=nhpb+1 + if (ibecarb(i).gt.0) then + ihpb(i)=ihpb(i)+nres + jhpb(i)=jhpb(i)+nres + endif + if (dhpb(nhpb).eq.0.0d0) + & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) + endif + enddo + do i=1,nhpb + write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ", + & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i) + enddo + call flush(iout) + return + end + +c====------------------------------------------------------------------- + subroutine read_constr_homology + + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' +#endif + include 'COMMON.SETUP' + include 'COMMON.CONTROL' + include 'COMMON.CHAIN' + include 'COMMON.IOUNITS' + include 'COMMON.GEO' + include 'COMMON.INTERACT' + include 'COMMON.HOMRESTR' +c +c For new homol impl +c + include 'COMMON.VAR' +c include 'include_unres/COMMON.VAR' +c + +c double precision odl_temp,sigma_odl_temp,waga_theta,waga_d, +c & dist_cut +c common /przechowalnia/ odl_temp(maxres,maxres,max_template), +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, j, k, l + logical lprn /.true./ +c +c FP - Nov. 2014 Temporary specifications for new vars +c + double precision rescore_tmp,x12,y12,z12 + double precision, dimension (max_template,maxres) :: rescore + character*24 tpl_k_rescore +c ----------------------------------------------------------------- +c Reading multiple PDB ref structures and calculation of retraints +c not using pre-computed ones stored in files model_ki_{dist,angle} +c FP (Nov., 2014) +c ----------------------------------------------------------------- +c +c +c Alternative: reading from input + write (iout,*) "BEGIN READ HOMOLOGY INFO" + call flush(iout) + call card_concat(controlcard) + call reada(controlcard,"HOMOL_DIST",waga_dist,1.0d0) + call reada(controlcard,"HOMOL_ANGLE",waga_angle,1.0d0) + call reada(controlcard,"HOMOL_THETA",waga_theta,1.0d0) ! new + call reada(controlcard,"HOMOL_SCD",waga_d,1.0d0) ! new + call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma + + call readi(controlcard,"HOMOL_NSET",homol_nset,1) + if (homol_nset.gt.1)then + 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 " +#ifdef DEBUG + homol_nset=1 + call reada(controlcard,"WAGA_HOMOLOGY",waga_homology(1),1.0d0) +#endif + endif + iset=mod(kolor,homol_nset)+1 + else + iset=1 + waga_homology(1)=1.0 + endif +c + write(iout,*) "read_constr_homology" + write(iout,*) "waga_homology(",iset,")",waga_homology(iset) + call flush(iout) + + +cd write (iout,*) "nnt",nnt," nct",nct +cd call flush(iout) + + + lim_odl=0 + lim_dih=0 +c +c New +c + lim_theta=0 + lim_xx=0 +c +c Reading HM global scores (prob not required) +c +c open (4,file="HMscore") +c do k=1,constr_homology +c read (4,*,end=521) hmscore_tmp +c hmscore(k)=hmscore_tmp ! Another transformation can be used +c write(*,*) "Model", k, ":", hmscore(k) +c enddo +c521 continue + +c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d + + write (iout,*) "CONSTR_HOMOLOGY",constr_homology + do k=1,constr_homology + + read(inp,'(a)') pdbfile + write (iout,*) "k ",k," pdbfile ",pdbfile +c Next stament causes error upon compilation (?) +c if(me.eq.king.or. .not. out1file) +c write (iout,'(2a)') 'PDB data will be read from file ', +c & pdbfile(:ilen(pdbfile)) + open(ipdbin,file=pdbfile,status='old',err=33) + goto 34 + 33 write (iout,'(a)') 'Error opening PDB file.' + stop + 34 continue +c print *,'Begin reading pdb data' +c +c Files containing res sim or local scores (former containing sigmas) +c + + write(kic2,'(bz,i2.2)') k + + tpl_k_rescore="template"//kic2//".sco" +c tpl_k_sigma_odl="template"//kic2//".sigma_odl" +c tpl_k_sigma_dih="template"//kic2//".sigma_dih" +c tpl_k_sigma_theta="template"//kic2//".sigma_theta" +c tpl_k_sigma_d="template"//kic2//".sigma_d" + + unres_pdb=.false. + call readpdb + do i=1,2*nres + do j=1,3 + crefjlee(j,i)=c(j,i) + enddo + enddo +#ifdef DEBUG + do i=1,nres + write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3), + & (crefjlee(j,i+nres),j=1,3) + enddo +#endif + write (iout,*) "READ HOMOLOGY INFO" + write (iout,*) "read_constr_homology x: after reading pdb file" + write (iout,*) "waga_homology(",iset,")",waga_homology(iset) + write (iout,*) "waga_dist",waga_dist + write (iout,*) "waga_angle",waga_angle + write (iout,*) "waga_theta",waga_theta + write (iout,*) "waga_d",waga_d + write (iout,*) "dist_cut",dist_cut + call flush(iout) + +c +c Distance restraints +c +c ... --> odl(k,ii) +C Copy the coordinates from reference coordinates (?) + do i=1,2*nres + do j=1,3 + c(j,i)=cref(j,i) +c write (iout,*) "c(",j,i,") =",c(j,i) + enddo + enddo +c +c From read_dist_constr (commented out 25/11/2014 <-> res sim) +c +c write(iout,*) "tpl_k_rescore - ",tpl_k_rescore + open (ientin,file=tpl_k_rescore,status='old') + do irec=1,maxdim ! loop for reading res sim + if (irec.eq.1) then + rescore(k,irec)=0.0d0 + goto 1301 + endif + read (ientin,*,end=1401) rescore_tmp +c rescore(k,irec)=rescore_tmp+1.0d0 ! to avoid 0 values + rescore(k,irec)=0.5d0*(rescore_tmp+0.5d0) ! alt transf to reduce scores +c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec) + 1301 continue + enddo + 1401 continue + close (ientin) +c open (ientin,file=tpl_k_sigma_odl,status='old') +c do irec=1,maxdim ! loop for reading sigma_odl +c read (ientin,*,end=1401) i, j, +c & sigma_odl_temp(i+nnt-1,j+nnt-1,k) ! new variable (?) +c sigma_odl_temp(j+nnt-1,i+nnt-1,k)= ! which purpose? +c & sigma_odl_temp(i+nnt-1,j+nnt-1,k) +c enddo +c 1401 continue +c close (ientin) + if (waga_dist.ne.0.0d0) then + ii=0 + do i = nnt,nct-2 ! right? without parallel. + do j=i+2,nct ! right? +c do i = 1,nres ! alternative for bounds as used to set initial values in orig. read_constr_homology +c do j=i+2,nres ! ibid +c do i = nnt,nct-2 ! alternative for bounds as used to assign dist restraints in orig. read_constr_homology (s. above) +c do j=i+2,nct ! ibid + ii=ii+1 +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 +c Attempt to replace dist(i,j) by its definition in ... +c + x12=c(1,i)-c(1,j) + y12=c(2,i)-c(2,j) + z12=c(3,i)-c(3,j) + distal=dsqrt(x12*x12+y12*y12+z12*z12) + odl(k,ii)=distal +c +c odl(k,ii)=dist(i,j) +c write (iout,*) "dist(",i,j,") =",dist(i,j) +c write (iout,*) "distal = ",distal +c write (iout,*) "odl(",k,ii,") =",odl(k,ii) +c write(iout,*) "rescore(",k,i,") =",rescore(k,i), +c & "rescore(",k,j,") =",rescore(k,j) +c +c Calculation of sigma from res sim +c +c if (odl(k,ii).le.6.0d0) then +c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j) +c Other functional forms possible depending on odl(k,ii), eg. +c + if (odl(k,ii).le.dist_cut) then + sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) ! other exprs possible +c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j) + else + sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error + & dexp(0.5d0*(odl(k,ii)/dist_cut)**2) + +c Following expr replaced by a positive exp argument +c sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* +c & dexp(-0.5d0*(odl(k,ii)/dist_cut)**2) + +c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)* +c & dexp(-0.5d0*(odl(k,ii)/dist_cut)**2) + endif +c + sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) ! rescore ~ error +c sigma_odl(k,ii)=sigma_odl(k,ii)*sigma_odl(k,ii) +c +c sigma_odl(k,ii)=sigma_odl_temp(i,j,k)* ! new var read from file (?) +c & sigma_odl_temp(i,j,k) ! not inverse because of use of res. similarity + enddo +c read (ientin,*) sigma_odl(k,ii) ! 1st variant + enddo +c lim_odl=ii +c if (constr_homology.gt.0) call homology_partition + endif +c +c Theta, dihedral and SC retraints +c + if (waga_angle.gt.0.0d0) then +c open (ientin,file=tpl_k_sigma_dih,status='old') +c do irec=1,maxres-3 ! loop for reading sigma_dih +c read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for? +c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right? +c sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity +c & sigma_dih(k,i+nnt-1) +c enddo +c1402 continue +c close (ientin) + do i = nnt+3,nct ! right? without parallel. +c do i=1,nres ! alternative for bounds acc to readpdb? +c do i=1,nres-3 ! alternative for bounds as used to set initial values in orig. read_constr_homology +c do i=idihconstr_start_homo,idihconstr_end_homo ! with FG parallel. + dih(k,i)=phiref(i) ! right? +c read (ientin,*) sigma_dih(k,i) ! original variant +c write (iout,*) "dih(",k,i,") =",dih(k,i) +c write(iout,*) "rescore(",k,i,") =",rescore(k,i), +c & "rescore(",k,i-1,") =",rescore(k,i-1), +c & "rescore(",k,i-2,") =",rescore(k,i-2), +c & "rescore(",k,i-3,") =",rescore(k,i-3) + + sigma_dih(k,i)=rescore(k,i)+rescore(k,i-1)+ + & rescore(k,i-2)+rescore(k,i-3) ! right expression ? +c +c write (iout,*) "Raw sigmas for dihedral angle restraints" +c write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i) +c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)* +c rescore(k,i-2)*rescore(k,i-3) ! right expression ? +c Instead of res sim other local measure of b/b str reliability possible + sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i)) +c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i) + if (i-nnt-2.gt.lim_dih) lim_dih=i-nnt-2 ! right? +c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! original when readin i from file + enddo + endif + + if (waga_theta.gt.0.0d0) then +c open (ientin,file=tpl_k_sigma_theta,status='old') +c do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds? +c read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for? +c sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity +c & sigma_theta(k,i+nnt-1) +c enddo +c1403 continue +c close (ientin) + + do i = nnt+2,nct ! right? without parallel. +c do i = i=1,nres ! alternative for bounds acc to readpdb? +c do i=ithet_start,ithet_end ! with FG parallel. + thetatpl(k,i)=thetaref(i) +c write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i) +c write(iout,*) "rescore(",k,i,") =",rescore(k,i), +c & "rescore(",k,i-1,") =",rescore(k,i-1), +c & "rescore(",k,i-2,") =",rescore(k,i-2) +c read (ientin,*) sigma_theta(k,i) ! 1st variant + sigma_theta(k,i)=rescore(k,i)+rescore(k,i-1)+ + & rescore(k,i-2) ! right expression ? + sigma_theta(k,i)=1.0d0/(sigma_theta(k,i)*sigma_theta(k,i)) + +c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)* +c rescore(k,i-2) ! right expression ? +c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) + if (i-nnt-1.gt.lim_theta) lim_theta=i-nnt-1 ! right? + enddo + endif + + if (waga_d.gt.0.0d0) then +c open (ientin,file=tpl_k_sigma_d,status='old') +c do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds? +c read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for? +c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity +c & sigma_d(k,i+nnt-1) +c enddo +c1404 continue + close (ientin) + + do i = nnt,nct ! right? without parallel. +c do i=2,nres-1 ! alternative for bounds acc to readpdb? +c do i=loc_start,loc_end ! with FG parallel. + if (itype(i).eq.10) goto 1 ! right? + xxtpl(k,i)=xxref(i) + yytpl(k,i)=yyref(i) + zztpl(k,i)=zzref(i) +c write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i) +c write (iout,*) "yytpl(",k,i,") =",yytpl(k,i) +c write (iout,*) "zztpl(",k,i,") =",zztpl(k,i) +c write(iout,*) "rescore(",k,i,") =",rescore(k,i) + sigma_d(k,i)=rescore(k,i) ! right expression ? + sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(k,i)) + +c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ? +c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i) +c read (ientin,*) sigma_d(k,i) ! 1st variant + if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right? + 1 continue + enddo + endif + close(ientin) + enddo + if (waga_dist.ne.0.0d0) lim_odl=ii + if (constr_homology.gt.0) call homology_partition + if (constr_homology.gt.0) call init_int_table +cd write (iout,*) "homology_partition: lim_theta= ",lim_theta, +cd & "lim_xx=",lim_xx +c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end +c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end +c +c Print restraints +c + if (.not.lprn) return +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,'(3i5,10(2f16.2,4x))') ii,ires_homo(ii),jres_homo(ii), + & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),ki=1,constr_homology) + enddo + write (iout,*) "Dihedral angle restraints from templates" + do i=nnt+3,lim_dih + write (iout,'(i5,10(2f8.2,4x))') 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,lim_theta + write (iout,'(i5,10(2f8.2,4x))') 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,lim_xx + write(iout,'(i5,10(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 + endif +c ----------------------------------------------------------------- + return + end + +