X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc%2Fmolread_zs.F;h=b12fcfd079b9a4a48b764142cd01ac77b1470257;hb=f38a5bce43e7aa0071f0a3862eff6e9866ff03a1;hp=87a34953ecd4fd1559fb7dffbfe4e260c4f08629;hpb=24bbf0f3f06452c69bf4b69b4a9ba620e0260d7b;p=unres.git diff --git a/source/wham/src/molread_zs.F b/source/wham/src/molread_zs.F index 87a3495..b12fcfd 100644 --- a/source/wham/src/molread_zs.F +++ b/source/wham/src/molread_zs.F @@ -8,6 +8,7 @@ C include 'COMMON.IOUNITS' include 'COMMON.GEO' include 'COMMON.VAR' +c include 'include_unres/COMMON.VAR' include 'COMMON.INTERACT' include 'COMMON.LOCAL' include 'COMMON.NAMES' @@ -27,6 +28,13 @@ C call reada(controlcard,'SCALSCP',scalscp,1.0d0) call reada(controlcard,'CUTOFF',cutoff_corr,7.0d0) call reada(controlcard,'DELT_CORR',delt_corr,0.5d0) +C Bartek + call reada(controlcard,'WDFAD',wdfa_dist,0.0d0) + call reada(controlcard,'WDFAT',wdfa_tor,0.0d0) + call reada(controlcard,'WDFAN',wdfa_nei,0.0d0) + call reada(controlcard,'WDFAB',wdfa_beta,0.0d0) + write (iout,*) "wdfa_dist",wdfa_dist," wdfa_tor",wdfa_tor, + & " wdfa_nei",wdfa_nei," wdfa_beta",wdfa_beta r0_corr=cutoff_corr-delt_corr call readi(controlcard,"NRES",nres,0) iscode=index(controlcard,"ONE_LETTER") @@ -94,12 +102,84 @@ C Convert sequence to numeric code if (itype(1).eq.21) nnt=2 if (itype(nres).eq.21) nct=nct-1 write(iout,*) 'NNT=',NNT,' NCT=',NCT + +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 + c Read distance restraints if (constr_dist.gt.0) then + if (refstr) call read_ref_structure(*11) call read_dist_constr call hpb_partition endif + if (constr_homology.gt.0) then +c write (iout,*) "About to call read_constr_homology" +c call flush(iout) + call read_constr_homology +c write (iout,*) "Exit read_constr_homology" +c call flush(iout) + 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 +#ifdef DEBUG + call int_from_cart1(.false.) + call sc_loc_geom(.false.) + do i=1,nres + thetaref(i)=theta(i) + phiref(i)=phi(i) + write (iout,*) i," phiref",phiref(i)," thetaref",thetaref(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 +#endif + else + homol_nset=0 + endif + + call setup_var call init_int_table if (ns.gt.0) then @@ -119,6 +199,7 @@ c Read distance restraints endif write (iout,'(a)') return + 11 stop "Error reading reference structure" end c----------------------------------------------------------------------------- logical function seq_comp(itypea,itypeb,length) @@ -202,6 +283,25 @@ C bridging residues. enddo endif endif + if (ns.gt.0.and.dyn_ss) then +C /06/28/2013 Adasko:ns is number of Cysteins bonded also called half of +C the bond + do i=nss+1,nhpb +C /06/28/2013 Adasko: nss number of full SS bonds + 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 /06/28/2013 Adasko: dyn_ss_mask which Cysteins can form disulfidebond +c write(iout,*) i,iss(i),dyn_ss_mask(iss(i)),"ATU" + enddo + endif return end c------------------------------------------------------------------------------ @@ -252,6 +352,7 @@ c------------------------------------------------------------------------------- subroutine read_dist_constr implicit real*8 (a-h,o-z) include 'DIMENSIONS' + include 'DIMENSIONS.ZSCOPT' include 'COMMON.CONTROL' include 'COMMON.CHAIN' include 'COMMON.IOUNITS' @@ -374,3 +475,382 @@ c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) call flush(iout) return end + + + +c====------------------------------------------------------------------- + subroutine read_constr_homology + + include 'DIMENSIONS' + include 'DIMENSIONS.ZSCOPT' +#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 + call card_concat(controlcard,.true.) + 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,.true.) + 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 do i=1,homol_nset +c write(iout,*) i,waga_homology(i) +c enddo + endif + iset=mod(kolor,homol_nset)+1 + else + iset=1 + waga_homology(1)=1.0 + endif +c write(iout,*) "waga_homology(",iset,")",waga_homology(iset) + +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 + + do k=1,constr_homology + + read(inp,'(a)') 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_constr_homology: after reading pdb file" + 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 +c----------------------------------------------------------------------