--- /dev/null
+ subroutine read_constr_homology
+ implicit none
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.HOMOLOGY'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.QRESTR'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+c
+c For new homol impl
+c
+ include '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,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec,
+ & ik,iistart,nres_temp
+ integer ilen
+ external ilen
+ logical liiflag,lfirst
+ integer i01,i10
+c
+c FP - Nov. 2014 Temporary specifications for new vars
+c
+ double precision rescore_tmp,x12,y12,z12,rescore2_tmp,
+ & rescore3_tmp
+ double precision, dimension (max_template,maxres) :: rescore
+ double precision, dimension (max_template,maxres) :: rescore2
+ double precision, dimension (max_template,maxres) :: rescore3
+ double precision distal
+ character*24 pdbfile,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)
+ 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 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
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
+ & write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+ start_from_model=.false.
+ endif
+ if(start_from_model .and. (me.eq.king .or. .not. out1file))
+ & write(iout,*) 'START_FROM_MODELS is ON'
+ if(start_from_model .and. rest) then
+ if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) 'START_FROM_MODELS is OFF'
+ write(iout,*) 'remove restart keyword from input'
+ endif
+ endif
+ 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 "
+ do i=1,homol_nset
+ write(iout,*) i,waga_homology(i)
+ enddo
+ endif
+ iset=mod(kolor,homol_nset)+1
+ else
+ iset=1
+ waga_homology(1)=1.0
+ endif
+
+cd write (iout,*) "nnt",nnt," nct",nct
+cd call flush(iout)
+
+
+ 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
+
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+ if(me.eq.king .or. .not. out1file)
+ & 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,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ 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"
+
+ unres_pdb=.false.
+ nres_temp=nres
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
+ nres_chomo(k)=nres
+ nres=nres_temp
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres_chomo(k)
+ 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')
+ 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,
+ & rescore3_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
+ rescore3(k,i_tmp)=rescore3_tmp
+ if (.not. out1file .or. me.eq.king)
+ & write(iout,'(a7,i5,3f10.5,i5)') "rescore",
+ & i_tmp,rescore2_tmp,rescore_tmp,
+ & rescore3_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
+c write(iout,*) "rescore(",k,irec,") =",rescore(k,irec)
+ endif
+ enddo
+ 1401 continue
+ close (ientin)
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ 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
+ odl(k,ii)=distal
+ 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)
+#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
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c write (iout,*) "Distance restraints set"
+c call flush(iout)
+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
+ 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)
+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))/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
+ 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)
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+c write (iout,*) "Dihedral angle restraints set"
+c call flush(iout)
+
+ 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.
+ 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))/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)
+ enddo
+ endif
+c write (iout,*) "Angle restraints set"
+c call flush(iout)
+
+ 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
+
+ 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) 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)
+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)=rescore3(k,i) ! right expression ?
+ 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
+ enddo
+ endif
+ enddo
+c write (iout,*) "SC restraints set"
+c call flush(iout)
+c
+c remove distance restraints not used in any model from the list
+c shift data in all arrays
+c
+c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ liiflag=.true.
+ lfirst=.true.
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+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
+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.
+ 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) then
+ i01=ii
+ liiflag=.true.
+ endif
+ enddo
+ enddo
+ lim_odl=iistart-1
+ endif
+c write (iout,*) "Removing distances completed"
+c call flush(iout)
+ endif ! .not. klapaucjusz
+
+ if (constr_homology.gt.0) call homology_partition
+c write (iout,*) "After homology_partition"
+c call flush(iout)
+ if (constr_homology.gt.0) call init_int_table
+c write (iout,*) "After init_int_table"
+c call flush(iout)
+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.out_template_restr) 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,'(3i5,100(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,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,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
+ endif
+c -----------------------------------------------------------------
+ return
+ end
+c----------------------------------------------------------------------
+ subroutine read_klapaucjusz
+ implicit none
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.HOMOLOGY'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.MD'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ character*256 fragfile
+ integer ninclust(maxclust),inclust(max_template,maxclust),
+ & nresclust(maxclust),iresclust(maxres,maxclust),nclust
+
+ 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
+ double precision distal
+ logical lprn /.true./
+ integer nres_temp
+ integer ilen
+ external ilen
+ logical liiflag
+c
+c
+ 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 For new homol impl
+c
+ include 'COMMON.VAR'
+c
+ call getenv("FRAGFILE",fragfile)
+ open(ientin,file=fragfile,status="old",err=10)
+ read(ientin,*) constr_homology,nclust
+ l_homo = .false.
+ sigma_theta=0.0
+ sigma_d=0.0
+ sigma_dih=0.0
+c Read pdb files
+ do k=1,constr_homology
+ read(ientin,'(a)') pdbfile
+ write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a,5x,a)') 'Error opening PDB file',
+ & pdbfile(:ilen(pdbfile))
+ stop
+ 34 continue
+ unres_pdb=.false.
+ nres_temp=nres
+ call readpdb_template(k)
+ nres_chomo(k)=nres
+ nres=nres_temp
+ do i=1,nres
+ rescore(k,i)=0.2d0
+ rescore2(k,i)=1.0d0
+ enddo
+ enddo
+c Read clusters
+ do i=1,nclust
+ read(ientin,*) ninclust(i),nresclust(i)
+ read(ientin,*) (inclust(k,i),k=1,ninclust(i))
+ read(ientin,*) (iresclust(k,i),k=1,nresclust(i))
+ enddo
+c
+c Loop over clusters
+c
+ do l=1,nclust
+ do ll = 1,ninclust(l)
+
+ k = inclust(ll,l)
+ do i=1,nres
+ idomain(k,i)=0
+ enddo
+ do i=1,nresclust(l)
+ if (nnt.gt.1) then
+ idomain(k,iresclust(i,l)+1) = 1
+ else
+ idomain(k,iresclust(i,l)) = 1
+ endif
+ enddo
+c
+c Distance restraints
+c
+c ... --> odl(k,ii)
+C Copy the coordinates from reference coordinates (?)
+ nres_temp=nres
+ nres=nres_chomo(k)
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=chomo(j,i,k)
+c write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+ call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ nres=nres_temp
+ if (waga_dist.ne.0.0d0) then
+ ii=0
+ 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
+ odl(k,ii)=distal
+ 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)
+#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
+c l_homo(k,ii)=.false.
+ endif
+ enddo
+ enddo
+ lim_odl=ii
+ endif
+c
+c Theta, dihedral and SC retraints
+c
+ if (waga_angle.gt.0.0d0) then
+ do i = nnt+3,nct
+ 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)+
+ & 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))
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+ do i = nnt+2,nct
+ 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)+
+ & 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))
+ enddo
+ endif
+
+ if (waga_d.gt.0.0d0) then
+ do i = nnt,nct
+ 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
+ enddo
+ endif
+ enddo ! l
+ enddo ! ll
+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
+
+ return
+ 10 stop "Error in fragment file"
+ end
+
projects / unres.git / blobdiff