+ subroutine read_constr_homology
+ use control, only:init_int_table,homology_partition
+ use MD_data, only:iset
+! 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'
+! include 'COMMON.VAR'
+!
+
+! double precision odl_temp,sigma_odl_temp,waga_theta,waga_d,
+! & dist_cut
+! common /przechowalnia/ odl_temp(maxres,maxres,max_template),
+! & 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
+ integer, dimension (:), allocatable :: ii_in_use
+ integer :: i_tmp,idomain_tmp,&
+ irec,ik,iistart,nres_temp
+! integer :: iset
+! external :: ilen
+ logical :: liiflag,lfirst
+ integer :: i01,i10
+!
+! FP - Nov. 2014 Temporary specifications for new vars
+!
+ real(kind=8) :: rescore_tmp,x12,y12,z12,rescore2_tmp,&
+ rescore3_tmp, dist_cut
+ real(kind=8), dimension (:,:),allocatable :: rescore
+ real(kind=8), dimension (:,:),allocatable :: rescore2
+ real(kind=8), dimension (:,:),allocatable :: rescore3
+ real(kind=8) :: distal
+ character*24 tpl_k_rescore
+ character*256 pdbfile
+
+! -----------------------------------------------------------------
+! Reading multiple PDB ref structures and calculation of retraints
+! not using pre-computed ones stored in files model_ki_{dist,angle}
+! FP (Nov., 2014)
+! -----------------------------------------------------------------
+!
+!
+! 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 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.
+ iranconf=(indpdb.le.0)
+ 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 (start_from_model) nmodel_start=constr_homology
+ if(.not.allocated(waga_homology)) allocate (waga_homology(homol_nset))
+ 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 "
+ 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
+
+!d write (iout,*) "nnt",nnt," nct",nct
+!d call flush(iout)
+
+ if (read_homol_frag) then
+ call read_klapaucjusz
+ else
+
+ lim_odl=0
+ lim_dih=0
+!
+! write(iout,*) 'nnt=',nnt,'nct=',nct
+!
+! do i = nnt,nct
+! do k=1,constr_homology
+! idomain(k,i)=0
+! enddo
+! enddo
+ idomain=0
+
+! ii=0
+! do i = nnt,nct-2
+! do j=i+2,nct
+! ii=ii+1
+! ii_in_use(ii)=0
+! enddo
+! enddo
+ ii_in_use=0
+ if(.not.allocated(pdbfiles_chomo)) allocate(pdbfiles_chomo(constr_homology))
+ if(.not.allocated(chomo)) allocate(chomo(3,nres,constr_homology))
+
+ do k=1,constr_homology
+
+ read(inp,'(a)') pdbfile
+ pdbfiles_chomo(k)=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
+! print *,'Begin reading pdb data'
+!
+! Files containing res sim or local scores (former containing sigmas)
+!
+
+ write(kic2,'(bz,i2.2)') k
+
+ tpl_k_rescore="template"//kic2//".sco"
+ write(iout,*) "tpl_k_rescore=",tpl_k_rescore
+ unres_pdb=.false.
+ nres_temp=nres
+ write(iout,*) "read2sigma",read2sigma
+
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
+ write(iout,*) "after readpdb"
+ if(.not.allocated(nres_chomo)) allocate(nres_chomo(constr_homology))
+ nres_chomo(k)=nres
+ nres=nres_temp
+ if(.not.allocated(rescore)) allocate(rescore(constr_homology,nres))
+ if(.not.allocated(rescore2)) allocate(rescore2(constr_homology,nres))
+ if(.not.allocated(rescore3)) allocate(rescore3(constr_homology,nres))
+ if(.not.allocated(ii_in_use)) allocate(ii_in_use(nres*(nres-1)))
+ if(.not.allocated(idomain)) allocate(idomain(constr_homology,nres))
+ if(.not.allocated(l_homo)) allocate(l_homo(constr_homology,1000*nres))
+ if(.not.allocated(ires_homo)) allocate(ires_homo(nres*200))
+ if(.not.allocated(jres_homo)) allocate(jres_homo(nres*200))
+ if(.not.allocated(odl)) allocate(odl(constr_homology,nres*200))
+ if(.not.allocated(sigma_odl)) allocate(sigma_odl(constr_homology,nres*200))
+ if(.not.allocated(dih)) allocate(dih(constr_homology,nres))
+ if(.not.allocated(sigma_dih)) allocate(sigma_dih(constr_homology,nres))
+ if(.not.allocated(thetatpl)) allocate(thetatpl(constr_homology,nres))
+ if(.not.allocated(sigma_theta)) allocate(sigma_theta(constr_homology,nres))
+! if(.not.allocated(thetatpl)) allocate(thetatpl(constr_homology,nres))
+ if(.not.allocated(sigma_d)) allocate(sigma_d(constr_homology,nres))
+ if(.not.allocated(xxtpl)) allocate(xxtpl(constr_homology,nres))
+ if(.not.allocated(yytpl)) allocate(yytpl(constr_homology,nres))
+ if(.not.allocated(zztpl)) allocate(zztpl(constr_homology,nres))
+! if(.not.allocated(distance)) allocate(distance(constr_homology))
+! if(.not.allocated(distancek)) allocate(distancek(constr_homology))
+
+
+!
+! Distance restraints
+!
+! ... --> odl(k,ii)
+! Copy the coordinates from reference coordinates (?)
+ do i=1,2*nres_chomo(k)
+ do j=1,3
+ c(j,i)=cref(j,i,1)
+! write (iout,*) "c(",j,i,") =",c(j,i)
+ enddo
+ enddo
+!
+! From read_dist_constr (commented out 25/11/2014 <-> res sim)
+!
+! 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
+
+! 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
+! 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)
+! 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.
+
+! write (iout,*) "k",k
+! write (iout,*) "i",i," j",j," constr_homology",
+! & 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
+! write (iout,*) "Distance restraints set"
+! call flush(iout)
+!
+! Theta, dihedral and SC retraints
+!
+ if (waga_angle.gt.0.0d0) then
+! open (ientin,file=tpl_k_sigma_dih,status='old')
+! do irec=1,maxres-3 ! loop for reading sigma_dih
+! read (ientin,*,end=1402) i,j,ki,l,sigma_dih(k,i+nnt-1) ! j,ki,l what for?
+! if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! right?
+! sigma_dih(k,i+nnt-1)=sigma_dih(k,i+nnt-1)* ! not inverse because of use of res. similarity
+! & sigma_dih(k,i+nnt-1)
+! enddo
+!1402 continue
+! 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?
+! read (ientin,*) sigma_dih(k,i) ! original variant
+! write (iout,*) "dih(",k,i,") =",dih(k,i)
+! write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+! & "rescore(",k,i-1,") =",rescore(k,i-1),
+! & "rescore(",k,i-2,") =",rescore(k,i-2),
+! & "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
+! if (read2sigma) sigma_dih(k,i)=sigma_dih(k,i)/4.0
+! write (iout,*) "Raw sigmas for dihedral angle restraints"
+! write (iout,'(i5,10(2f8.2,4x))') i,sigma_dih(k,i)
+! sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+! rescore(k,i-2)*rescore(k,i-3) ! right expression ?
+! 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))
+! sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i)
+ enddo
+ lim_dih=nct-nnt-2
+ endif
+! write (iout,*) "Dihedral angle restraints set"
+! call flush(iout)
+
+ if (waga_theta.gt.0.0d0) then
+! open (ientin,file=tpl_k_sigma_theta,status='old')
+! do irec=1,maxres-2 ! loop for reading sigma_theta, right bounds?
+! read (ientin,*,end=1403) i,j,ki,sigma_theta(k,i+nnt-1) ! j,ki what for?
+! sigma_theta(k,i+nnt-1)=sigma_theta(k,i+nnt-1)* ! not inverse because of use of res. similarity
+! & sigma_theta(k,i+nnt-1)
+! enddo
+!1403 continue
+! close (ientin)
+
+ do i = nnt+2,nct ! right? without parallel.
+! do i = i=1,nres ! alternative for bounds acc to readpdb?
+! 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)
+! write (iout,*) "thetatpl(",k,i,") =",thetatpl(k,i)
+! write(iout,*) "rescore(",k,i,") =",rescore(k,i),
+! & "rescore(",k,i-1,") =",rescore(k,i-1),
+! & "rescore(",k,i-2,") =",rescore(k,i-2)
+! 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
+! 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))
+
+! sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
+! rescore(k,i-2) ! right expression ?
+! sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
+ enddo
+ endif
+! write (iout,*) "Angle restraints set"
+! call flush(iout)
+
+ if (waga_d.gt.0.0d0) then
+! open (ientin,file=tpl_k_sigma_d,status='old')
+! do irec=1,maxres-1 ! loop for reading sigma_theta, right bounds?
+! read (ientin,*,end=1404) i,j,sigma_d(k,i+nnt-1) ! j,ki what for?
+! sigma_d(k,i+nnt-1)=sigma_d(k,i+nnt-1)* ! not inverse because of use of res. similarity
+! & sigma_d(k,i+nnt-1)
+! enddo
+!1404 continue
+
+ do i = nnt,nct ! right? without parallel.
+! do i=2,nres-1 ! alternative for bounds acc to readpdb?
+! do i=loc_start,loc_end ! with FG parallel.
+ if (itype(i,1).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)
+! write (iout,*) "xxtpl(",k,i,") =",xxtpl(k,i)
+! write (iout,*) "yytpl(",k,i,") =",yytpl(k,i)
+! write (iout,*) "zztpl(",k,i,") =",zztpl(k,i)
+! 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))
+
+! sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ?
+! sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i)
+! read (ientin,*) sigma_d(k,i) ! 1st variant
+ enddo
+ endif
+ enddo
+! write (iout,*) "SC restraints set"
+! call flush(iout)
+!
+! remove distance restraints not used in any model from the list
+! shift data in all arrays
+!
+! 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
+! if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+! & .and. distal.le.dist2_cut ) then
+! write (iout,*) "i",i," j",j," ii",ii
+! 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
+! write (iout,*) "Removing distances completed"
+! call flush(iout)
+ endif ! .not. klapaucjusz
+
+ if (constr_homology.gt.0) call homology_partition
+ write (iout,*) "After homology_partition"
+ call flush(iout)
+ if (constr_homology.gt.0) call init_int_table
+ write (iout,*) "After init_int_table"
+ call flush(iout)
+! endif ! .not. klapaucjusz
+! endif
+! if (constr_homology.gt.0) call homology_partition
+! write (iout,*) "After homology_partition"
+! call flush(iout)
+! if (constr_homology.gt.0) call init_int_table
+! write (iout,*) "After init_int_table"
+! call flush(iout)
+! write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+! write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+!
+! Print restraints
+!
+ if (.not.out_template_restr) return
+!d 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,'(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,'(i7,a4,100(2f8.2,4x))') i,restyp(itype(i,1),1),&
+ (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,'(i7,a4,100(2f8.2,4x))') i,restyp(itype(i,1),1),&
+ (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,'(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
+ endif
+ return
+ end subroutine read_constr_homology
+!-----------------------------------------------------------------------------
+ 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(len=256) fragfile
+ integer, dimension(:), allocatable :: ninclust,nresclust,itype_temp,&
+ ii_in_use
+ integer, dimension(:,:), allocatable :: iresclust,inclust
+ integer :: nclust
+
+ character(len=2) :: kic2
+ character(len=24) :: model_ki_dist, model_ki_angle
+ character(len=500) :: controlcard
+ integer :: ki, i, j, jj,k, l, i_tmp,&
+ idomain_tmp,&
+ ik,ll,lll,ii_old,ii,iii,ichain,kk,iistart,iishift,lim_xx,igr,&
+ i01,i10,nnt_chain,nct_chain
+ real(kind=8) :: distal
+ logical :: lprn = .true.
+ integer :: nres_temp
+! integer :: ilen
+! external :: ilen
+ logical :: liiflag,lfirst
+
+ real(kind=8) rescore_tmp,x12,y12,z12,rescore2_tmp,dist_cut
+ real(kind=8), dimension (:,:), allocatable :: rescore
+ real(kind=8), dimension (:,:), allocatable :: rescore2
+ character(len=24) :: tpl_k_rescore
+ character(len=256) :: pdbfile
+
+!
+! For new homol impl
+!
+! include 'COMMON.VAR'
+!
+! write (iout,*) "READ_KLAPAUCJUSZ"
+! print *,"READ_KLAPAUCJUSZ"
+! call flush(iout)
+ call getenv("FRAGFILE",fragfile)
+ write (iout,*) "Opening", fragfile
+ call flush(iout)
+ open(ientin,file=fragfile,status="old",err=10)
+! write (iout,*) " opened"
+! call flush(iout)
+
+ sigma_theta=0.0
+ sigma_d=0.0
+ sigma_dih=0.0
+ l_homo = .false.
+
+ nres_temp=nres
+ itype_temp(:)=itype(:,1)
+ ii=0
+ lim_odl=0
+
+! write (iout,*) "Entering loop"
+! call flush(iout)
+
+ DO IGR = 1,NCHAIN_GROUP
+
+! 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
+! write (iout,*) "nnt_chain",nnt_chain," nct_chain",nct_chain
+
+! Read pdb files
+ if(.not.allocated(pdbfiles_chomo)) allocate(pdbfiles_chomo(constr_homology))
+ if(.not.allocated(nres_chomo)) allocate(nres_chomo(constr_homology))
+ do k=1,constr_homology
+ read(ientin,'(a)') pdbfile
+ write (iout,'(a,5x,a)') 'KLAPAUCJUSZ: Opening PDB file', &
+ pdbfile(:ilen(pdbfile))
+ pdbfiles_chomo(k)=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
+! 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
+!
+! Loop over clusters
+!
+ do l=1,nclust
+ do ll = 1,ninclust(l)
+
+ k = inclust(ll,l)
+! write (iout,*) "l",l," ll",ll," k",k
+ 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
+!
+! Distance restraints
+!
+! ... --> odl(k,ii)
+! 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)
+! 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=ii_old
+! do i = nnt,nct-2
+ do i = nnt_chain,nct_chain-2
+! 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)
+ z12=c(3,i)-c(3,j)
+ distal=dsqrt(x12*x12+y12*y12+z12*z12)
+! 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.
+
+! write (iout,*) "k",k
+! write (iout,*) "i",i," j",j," constr_homology",
+! & 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
+ 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
+!
+! Theta, dihedral and SC retraints
+!
+ if (waga_angle.gt.0.0d0) then
+ do i = nnt_chain+3,nct_chain
+ iii=i+chain_border1(1,igr)-1
+ if (idomain(k,i).eq.0) then
+! sigma_dih(k,i)=0.0
+ cycle
+ endif
+ 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
+! write (iout,*) "k",k," l",l," i",i," rescore",rescore(k,i),
+! & " sigma_dihed",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
+ endif
+
+ if (waga_theta.gt.0.0d0) then
+ do i = nnt_chain+2,nct_chain
+ iii=i+chain_border1(1,igr)-1
+ if (idomain(k,i).eq.0) then
+! sigma_theta(k,i)=0.0
+ cycle
+ endif
+ 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,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_chain,nct_chain
+ iii=i+chain_border1(1,igr)-1
+ if (itype(i,1).eq.10) cycle
+ if (idomain(k,i).eq.0 ) then
+! sigma_d(k,i)=0.0
+ cycle
+ endif
+ 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))
+! if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1
+ enddo
+ endif
+ enddo ! l
+ enddo ! ll
+!
+! remove distance restraints not used in any model from the list
+! shift data in all arrays
+!
+! write (iout,*) "ii_old",ii_old
+ if (waga_dist.ne.0.0d0) then
+#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.
+ lfirst=.true.
+ do i=nnt_chain,nct_chain-2
+ do j=i+2,nct_chain
+ ii=ii+1
+! if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+! & .and. distal.le.dist2_cut ) then
+! write (iout,*) "i",i," j",j," ii",ii," i_in_use",ii_in_use(ii)
+! 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
+
+ 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))
+! 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(:,1)=itype_temp(:)
+
+ return
+ 10 stop "Error in fragment file"
+ end subroutine read_klapaucjusz
projects / unres4.git / blobdiff