X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadrtns.F;h=93ed3a46f28a372862f86cdbfb41d572ac4c1767;hb=3e42b5f53e0ec03cd03009f3b857931ce7ee25c2;hp=056bfd43c91cba638c14e21ae33bc7310187ed72;hpb=c3d632cf84fd647434c093cb3fd69ea605293f75;p=unres.git diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F index 056bfd4..93ed3a4 100644 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@ -8,6 +8,7 @@ include 'COMMON.CONTROL' include 'COMMON.SBRIDGE' include 'COMMON.IOUNITS' + include 'COMMON.CHAIN' logical file_exist C Read force-field parameters except weights call parmread @@ -130,6 +131,7 @@ C Set up the time limit (caution! The time must be input in minutes!) sideadd=(index(controlcard,'SIDEADD').gt.0) energy_dec=(index(controlcard,'ENERGY_DEC').gt.0) outpdb=(index(controlcard,'PDBOUT').gt.0) + outx=(index(controlcard,'XOUT').gt.0) outmol2=(index(controlcard,'MOL2OUT').gt.0) pdbref=(index(controlcard,'PDBREF').gt.0) refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0) @@ -148,6 +150,7 @@ C Set up the time limit (caution! The time must be input in minutes!) modecalc=1 refstr=.true. endif + call reada(controlcard,"CHECKGRAD_INC",checkgrad_inc,1.0d-4) if (index(controlcard,'CHECKGRAD').gt.0) then modecalc=5 if (index(controlcard,'CART').gt.0) then @@ -386,6 +389,11 @@ C large = index(controlcard,"LARGE").gt.0 print_compon = index(controlcard,"PRINT_COMPON").gt.0 rattle = index(controlcard,"RATTLE").gt.0 + preminim = index(controlcard,"PREMINIM").gt.0 + if (preminim) then + dccart=(index(controlcard,'CART').gt.0) + call read_minim + endif c if performing umbrella sampling, fragments constrained are read from the fragment file nset=0 if(usampl) then @@ -426,6 +434,10 @@ c if performing umbrella sampling, fragments constrained are read from the frag write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx if (rattle) write (iout,'(a60)') & "Rattle algorithm used to constrain the virtual bonds" + if (preminim .or. iranconf.gt.0) then + write (iout,'(a60)') + & "Initial structure will be energy-minimized" + endif endif reset_fricmat=1000 if (lang.gt.0) then @@ -627,6 +639,7 @@ C common /pizda/ itype_pdb logical seq_comp,fail double precision energia(0:n_ene) + integer ilen external ilen C @@ -922,6 +935,17 @@ C 12/1/95 Added weight for the multi-body term WCORR 34 continue c print *,'Begin reading pdb data' 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 c print *,'Finished reading pdb data' if(me.eq.king.or..not.out1file) & write (iout,'(a,i3,a,i3)')'nsup=',nsup, @@ -974,6 +998,20 @@ C Convert sequence to numeric code do i=1,nres itype(i)=rescode(i,sequence(i),iscode) enddo + if (itype(2).eq.10.and.itype(1).eq.ntyp1) then + write (iout,*) + & "Glycine is the first full residue, initial dummy deleted" + do i=1,nres + itype(i)=itype(i+1) + enddo + nres=nres-1 + endif + if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then + write (iout,*) + & "Glycine is the last full residue, terminal dummy deleted" + nres=nres-1 + endif + C Assign initial virtual bond lengths do i=2,nres vbld(i)=vbl @@ -1064,6 +1102,7 @@ C Juyong:READ read_info C READ fragment information!! C both routines should be in dfa.F file!! +#ifdef DFA 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 call init_dfa_vars @@ -1071,6 +1110,7 @@ C both routines should be in dfa.F file!! call read_dfa_info print*, 'read_dfa_info finished!' endif +#endif C if (pdbref) then if(me.eq.king.or..not.out1file) @@ -1165,6 +1205,44 @@ c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup if (constr_homology.gt.0) then call read_constr_homology + if (indpdb.gt.0 .or. pdbref) then + do i=1,2*nres + do j=1,3 + c(j,i)=crefjlee(j,i) + cref(j,i)=crefjlee(j,i) + enddo + enddo + endif +#ifdef DEBUG + write (iout,*) "Array C" + do i=1,nres + write (iout,'(i5,3f8.3,5x,3f8.3)') i,(c(j,i),j=1,3), + & (c(j,i+nres),j=1,3) + enddo + write (iout,*) "Array Cref" + do i=1,nres + write (iout,'(i5,3f8.3,5x,3f8.3)') i,(cref(j,i),j=1,3), + & (cref(j,i+nres),j=1,3) + enddo +#endif + call int_from_cart1(.false.) + call sc_loc_geom(.false.) + do i=1,nres + thetaref(i)=theta(i) + phiref(i)=phi(i) + enddo + do i=1,nres-1 + do j=1,3 + dc(j,i)=c(j,i+1)-c(j,i) + dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) + enddo + enddo + do i=2,nres-1 + do j=1,3 + dc(j,i+nres)=c(j,i+nres)-c(j,i) + dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) + enddo + enddo else homol_nset=0 endif @@ -1182,6 +1260,8 @@ C initial geometry. if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) & write (iout,'(a)') 'Initial geometry will be read in.' if (read_cart) then + read (inp,*) time,potE,uconst,t_bath, + & nss,(ihpb(j),jhpb(j),j=1,nss), nn, (qfrag(i),i=1,nn) read(inp,'(8f10.5)',end=36,err=36) & ((c(l,k),l=1,3),k=1,nres), & ((c(l,k+nres),l=1,3),k=nnt,nct) @@ -1200,7 +1280,7 @@ C initial geometry. enddo endif enddo - return +c return else call read_angles(inp,*36) endif @@ -1284,6 +1364,8 @@ C Generate distance constraints, if the PDB structure is to be regularized. if (nthread.gt.0) then call read_threadbase endif + write (iout,*) "READRTNS: Calling setup_var" + call flush(iout) call setup_var if (me.eq.king .or. .not. out1file) & call intout @@ -2262,6 +2344,8 @@ c print *,"Processor",myrank," fg_rank",fg_rank & //'.pdb' mol2name=prefix(:lenpre)//'_'//pot(:lenpot)// & liczba(:ilen(liczba))//'.mol2' + cartname=prefix(:lenpre)//'_'//pot(:lenpot)// + & liczba(:ilen(liczba))//'.x' statname=prefix(:lenpre)//'_'//pot(:lenpot)// & liczba(:ilen(liczba))//'.stat' if (lentmp.gt.0) @@ -2280,6 +2364,7 @@ c print *,"Processor",myrank," fg_rank",fg_rank intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int' pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb' mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2' + cartname=prefix(:lenpre)//'_'//pot(:lenpot)//'.x' statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat' if (lentmp.gt.0) & call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) @@ -2440,33 +2525,36 @@ c------------------------------------------------------------------------------- include 'COMMON.IOUNITS' include 'COMMON.MD' include 'COMMON.CONTROL' + integer iset1 read(inp,*) nset,nfrag,npair,nfrag_back if(me.eq.king.or..not.out1file) & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair, & " nfrag_back",nfrag_back - do iset=1,nset - read(inp,*) mset(iset) + do iset1=1,nset + read(inp,*) mset(iset1) do i=1,nfrag - read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset), - & qinfrag(i,iset) + read(inp,*) wfrag(i,iset1),ifrag(1,i,iset1),ifrag(2,i,iset1), + & qinfrag(i,iset1) if(me.eq.king.or..not.out1file) - & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset), - & ifrag(2,i,iset), qinfrag(i,iset) + & write(iout,*) "R ",i,wfrag(i,iset1),ifrag(1,i,iset1), + & ifrag(2,i,iset1), qinfrag(i,iset1) enddo do i=1,npair - read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset), - & qinpair(i,iset) + read(inp,*) wpair(i,iset1),ipair(1,i,iset1),ipair(2,i,iset1), + & qinpair(i,iset1) if(me.eq.king.or..not.out1file) - & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset), - & ipair(2,i,iset), qinpair(i,iset) + & write(iout,*) "R ",i,wpair(i,iset1),ipair(1,i,iset1), + & ipair(2,i,iset1), qinpair(i,iset1) enddo do i=1,nfrag_back - read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset), - & wfrag_back(3,i,iset), - & ifrag_back(1,i,iset),ifrag_back(2,i,iset) + read(inp,*) wfrag_back(1,i,iset1),wfrag_back(2,i,iset1), + & wfrag_back(3,i,iset1), + & ifrag_back(1,i,iset1),ifrag_back(2,i,iset1) if(me.eq.king.or..not.out1file) - & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset), - & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset) + & write(iout,*) "A",i,wfrag_back(1,i,iset1), + & wfrag_back(2,i,iset1), + & wfrag_back(3,i,iset1),ifrag_back(1,i,iset1), + & ifrag_back(2,i,iset1) enddo enddo return @@ -2494,6 +2582,7 @@ c call flush(iout) 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) @@ -2593,8 +2682,14 @@ c write (iout,*) "j",j," k",k endif enddo do i=1,ndist_ + if (constr_dist.eq.11) then + read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i), + & ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1) + fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1) + else read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i), & ibecarb(i),forcon(nhpb+1) + endif if (forcon(nhpb+1).gt.0.0d0) then nhpb=nhpb+1 if (ibecarb(i).gt.0) then @@ -2609,8 +2704,14 @@ c write (iout,*) "j",j," k",k if (.not.out1file .or. me.eq.king) then #endif do i=1,nhpb + if (constr_dist.eq.11) then + write (iout,'(a,3i5,2f8.2,i2,2f10.1)') "+dist.constr11 ", + & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i), + & fordepth(i) + else write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ", & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i) + endif enddo call flush(iout) #ifdef MPI @@ -2633,6 +2734,7 @@ c------------------------------------------------------------------------------- include 'COMMON.MD' include 'COMMON.GEO' include 'COMMON.INTERACT' + include 'COMMON.NAMES' c c For new homol impl c @@ -2646,13 +2748,17 @@ 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 + integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp logical lprn /.true./ + integer ilen + external ilen + logical liiflag c c FP - Nov. 2014 Temporary specifications for new vars c - double precision rescore_tmp,x12,y12,z12 + double precision rescore_tmp,x12,y12,z12,rescore2_tmp double precision, dimension (max_template,maxres) :: rescore + double precision, dimension (max_template,maxres) :: rescore2 character*24 pdbfile,tpl_k_rescore c ----------------------------------------------------------------- c Reading multiple PDB ref structures and calculation of retraints @@ -2668,47 +2774,57 @@ c Alternative: reading from input 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 reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0) call readi(controlcard,"HOMOL_NSET",homol_nset,1) + read2sigma=(index(controlcard,'READ2SIGMA').gt.0) + start_from_model=(index(controlcard,'START_FROM_MODELS').gt.0) + if(.not.read2sigma.and.start_from_model) then + write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA' + start_from_model=.false. + endif + if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON' + if(start_from_model .and. rest) then + write(iout,*) 'START_FROM_MODELS is OFF' + write(iout,*) 'remove restart keyword from input' + endif if (homol_nset.gt.1)then call card_concat(controlcard) - read(controlcard,*) (waga_dist1(i),i=1,homol_nset) - call card_concat(controlcard) - read(controlcard,*) (waga_angle1(i),i=1,homol_nset) - write(iout,*) "iset distance_weight angle_weight" - do i=1,homol_nset - write(iout,*) i,waga_dist1(i),waga_angle1(i) - enddo + 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 " + do i=1,homol_nset + write(iout,*) i,waga_homology(i) + enddo + endif iset=mod(kolor,homol_nset)+1 else iset=1 -c call reada(controlcard,"HOMOL_DIST",waga_dist(1),1.0d0) -c call reada(controlcard,"HOMOL_ANGLE",waga_angle(1),1.0d0) + waga_homology(1)=1.0 endif - write (iout,*) "nnt",nnt," nct",nct - 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 + write(iout,*) 'nnt=',nnt,'nct=',nct 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 + 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 + do k=1,constr_homology read(inp,'(a)') pdbfile @@ -2716,9 +2832,12 @@ 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)) + write (iout,'(a,5x,a)') 'HOMOL: Opening PDB file', + & pdbfile(:ilen(pdbfile)) open(ipdbin,file=pdbfile,status='old',err=33) goto 34 - 33 write (iout,'(a)') 'Error opening PDB file.' + 33 write (iout,'(a,5x,a)') 'Error opening PDB file', + & pdbfile(:ilen(pdbfile)) stop 34 continue c print *,'Begin reading pdb data' @@ -2729,12 +2848,13 @@ 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" - call readpdb + unres_pdb=.false. + if (read2sigma) then + call readpdb_template(k) + else + call readpdb + endif c c Distance restraints c @@ -2751,89 +2871,82 @@ 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 + if (nnt.gt.1) rescore(k,1)=0.0d0 + do irec=nnt,nct ! loop for reading res sim + if (read2sigma) then + read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp, + & idomain_tmp + i_tmp=i_tmp+nnt-1 + idomain(k,i_tmp)=idomain_tmp + rescore(k,i_tmp)=rescore_tmp + rescore2(k,i_tmp)=rescore2_tmp + write(iout,'(a7,i5,2f10.5,i5)') "rescore", + & i_tmp,rescore2_tmp,rescore_tmp, + & idomain_tmp + else + idomain(k,irec)=1 + 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 + 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 + endif 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.gt.0.0d0) then + 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 + do i = nnt,nct-2 + do j=i+2,nct + + 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) +c write (iout,*) k,i,j,distal,dist2_cut + + if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 + & .and. distal.le.dist2_cut ) then + ii=ii+1 + ii_in_use(ii)=1 + l_homo(k,ii)=.true. + 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 + if (read2sigma) then + sigma_odl(k,ii)=0 + do ik=i,j + sigma_odl(k,ii)=sigma_odl(k,ii)+rescore2(k,ik) + enddo + sigma_odl(k,ii)=sigma_odl(k,ii)/(j-i+1) + if (odl(k,ii).gt.dist_cut) sigma_odl(k,ii) = + & sigma_odl(k,ii)*dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0) + else + if (odl(k,ii).le.dist_cut) then + sigma_odl(k,ii)=rescore(k,i)+rescore(k,j) + else +#ifdef OLDSIGMA + sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* & 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) +#else + sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* + & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0) +#endif + endif + endif + sigma_odl(k,ii)=1.0d0/(sigma_odl(k,ii)*sigma_odl(k,ii)) + else + ii=ii+1 + l_homo(k,ii)=.false. 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 + lim_odl=ii endif c c Theta, dihedral and SC retraints @@ -2848,10 +2961,11 @@ 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. + do i = nnt+3,nct + if (idomain(k,i).eq.0) then + sigma_dih(k,i)=0.0 + cycle + endif dih(k,i)=phiref(i) ! right? c read (ientin,*) sigma_dih(k,i) ! original variant c write (iout,*) "dih(",k,i,") =",dih(k,i) @@ -2860,19 +2974,19 @@ 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 + sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+ + & rescore(k,i-2)+rescore(k,i-3))/4.0 +c if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0 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)) + if (sigma_dih(k,i).ne.0) + & 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 + lim_dih=nct-nnt-2 endif if (waga_theta.gt.0.0d0) then @@ -2888,20 +3002,25 @@ 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. + if (idomain(k,i).eq.0) then + sigma_theta(k,i)=0.0 + cycle + endif 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)) + sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+ + & rescore(k,i-2))/3.0 +c if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0 + if (sigma_theta(k,i).ne.0) + & 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 @@ -2913,12 +3032,15 @@ c sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use 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? + if (itype(i).eq.10) cycle + if (idomain(k,i).eq.0 ) then + sigma_d(k,i)=0.0 + cycle + endif xxtpl(k,i)=xxref(i) yytpl(k,i)=yyref(i) zztpl(k,i)=zzref(i) @@ -2927,51 +3049,92 @@ 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)) + if (sigma_d(k,i).ne.0) + & 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.gt.0.0d0) lim_odl=ii +c +c remove distance restraints not used in any model from the list +c shift data in all arrays +c + if (waga_dist.ne.0.0d0) then + ii=0 + liiflag=.true. + do i=nnt,nct-2 + do j=i+2,nct + ii=ii+1 + if (ii_in_use(ii).eq.0.and.liiflag) then + liiflag=.false. + iistart=ii + 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 + 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 + endif if (constr_homology.gt.0) call homology_partition if (constr_homology.gt.0) call init_int_table - write (iout,*) "homology_partition: lim_theta= ",lim_theta, - & "lim_xx=",lim_xx +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 - write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d - 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), +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,'(3i5,100(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)), + & (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), + 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)), + & (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, + enddo + write (iout,*) "SC restraints from templates" + do i=nnt,nct + write(iout,'(i5,100(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 - + enddo + endif c ----------------------------------------------------------------- return end