integer nres,nres0,nsup,nstart_sup,nend_sup,nstart_seq,
& nchain,chain_border,chain_length,ireschain,npermchain,
- & tabpermchain,ishift_pdb,iz_sc
+ & tabpermchain,ishift_pdb,iz_sc,nres_chomo
double precision c,cref,crefjlee,cref_pdb,dc,xloc,xrot,dc_norm,
& t,r,prod,rt,chomo
common /chain/ c(3,maxres2+2),dc(3,maxres2),xloc(3,maxres),
& buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad,
& buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
- common /chomo_models/ chomo(3,maxres2+2,max_template)
+ common /chomo_models/ chomo(3,maxres2+2,max_template),
+ & nres_chomo(max_template)
& min_odl=distancek(kk)
enddo
endif
+
c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
subroutine read_constr_homology
-
+ implicit none
include 'DIMENSIONS'
#ifdef MPI
include 'mpif.h'
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
+ integer ki,i,ii,ik,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,
+ & lim_theta,lim_xx,irec,iistart,iishift,i10,i01
+ double precision distal
integer idomain(max_template,maxres)
- logical lprn /.true./
+ logical lfirst
integer ilen
external ilen
logical liiflag
+ integer nres_temp
c
c FP - Nov. 2014 Temporary specifications for new vars
c
- double precision rescore_tmp,x12,y12,z12,rescore2_tmp
+ 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
tpl_k_rescore="template"//kic2//".sco"
unres_pdb=.false.
+ nres_temp=nres
if (read2sigma) then
call readpdb_template(k)
close(ipdbin)
call readpdb(out_template_coord)
close(ipdbin)
endif
+ nres_chomo(k)=nres
+ nres=nres_temp
-c 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
+ do i=1,nres_chomo(k)
write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
& (crefjlee(j,i+nres),j=1,3)
enddo
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
- do i=1,2*nres
+ 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
lim_odl=ii
endif
+c write (iout,*) "Distance restraints set"
+c call flush(iout)
c
c Theta, dihedral and SC retraints
c
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))
+ & 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 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 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)
-c sigma_d(k,i)=rescore(k,i) ! right expression ?
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))
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
- if (ii_in_use(ii).eq.0.and.liiflag) then
+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.
- iistart=ii
+ 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.or.
- & .not.liiflag.and.ii.eq.lim_odl) then
- if (ii.eq.lim_odl) then
- iishift=ii-iistart+1
- else
- iishift=ii-iistart
- endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag) then
+ i01=ii
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
+ lim_odl=iistart-1
endif
-
- endif ! .not. klapaucjusz
+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
-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 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.lprn) return
+ if (.not.out_template_restr) return
cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
write (iout,*) "Distance restraints from templates"
character*500 controlcard
integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
integer idomain(max_template,maxres)
+ integer nres_temp
logical lprn /.true./
+ logical lfirst
integer ilen
external ilen
logical liiflag
stop
34 continue
unres_pdb=.false.
+ nres_temp=nres
call readpdb_template(k)
+ nres_chomo(k)=nres
+ nres=nres_temp
c do i=1,2*nres
c do j=1,3
c chomo(j,i,k)=c(j,i)
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)
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
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
& ' Gamma'
endif
endif
- do i=1,nres-1
+ do i=2,nres
iti=itype(i)
- if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
+c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
+ if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
+ & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-ctest stop
+c stop
endif
- vbld(i+1)=dist(i,i+1)
- vbld_inv(i+1)=1.0d0/vbld(i+1)
- if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
+ vbld(i)=dist(i-1,i)
+ vbld_inv(i)=1.0d0/vbld(i)
+ theta(i+1)=alpha(i-1,i,i+1)
if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
enddo
+
c if (unres_pdb) then
c if (itype(1).eq.ntyp1) then
c theta(3)=90.0d0*deg2rad
endif
endif
C Calculate internal coordinates.
- if (lprn) then
+ if (out_template_coord) then
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
enddo
endif
C Calculate internal coordinates.
+#ifdef DEBUG
write (iout,'(a)')
& "Backbone and SC coordinates as read from the PDB"
do ires=1,nres
& ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
& (c(j,nres+ires),j=1,3)
enddo
- call int_from_cart(.true.,.false.)
+#endif
+ call int_from_cart(.true.,out_template_coord)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
integer nres,nres0,nsup,nstart_sup,nend_sup,nstart_seq,
& ishift_pdb,chain_length,chain_border,chain_border1,ichanres,
- & tabpermchain,nchain ,npermchain,ireschain,iz_sc
+ & tabpermchain,nchain ,npermchain,ireschain,iz_sc,nres_chomo
double precision c,cref,crefjlee,dc,xloc,xrot,dc_norm,t,r,prod,rt,
& rmssing,anatemp,chomo
common /chain/ c(3,maxres2+2),dc(3,maxres2),xloc(3,maxres),
& buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad,
& buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
- common /chomo_models/ chomo(3,maxres2+2,max_template)
+ common /chomo_models/ chomo(3,maxres2+2,max_template),
+ & nres_chomo(max_template)
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
endif
#endif
-c write (iout,*) "nsaxs",nsaxs
c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr
if (nsaxs.gt.0 .and. saxs_mode.eq.0) then
call e_saxs(Esaxs_constr)
subroutine read_constr_homology
+ implicit none
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
include 'DIMENSIONS.FREE'
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
+ integer ki,i,ii,ik,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,
+ & lim_theta,lim_xx,irec,iistart,iishift,i10,i01
+ double precision distal
integer idomain(max_template,maxres)
- logical lprn /.true./
+ logical lfirst
integer ilen
external ilen
logical liiflag
+ integer nres_temp
c
c FP - Nov. 2014 Temporary specifications for new vars
c
tpl_k_rescore="template"//kic2//".sco"
unres_pdb=.false.
+ nres_temp=nres
if (read2sigma) then
call readpdb_template(k)
close(ipdbin)
call readpdb
close(ipdbin)
endif
+ nres_chomo(k)=nres
+ nres=nres_temp
-c call readpdb
- do i=1,2*nres
+ do i=1,2*nres_chomo(k)
do j=1,3
crefjlee(j,i)=c(j,i)
enddo
enddo
#ifdef DEBUG
- do i=1,nres
+ do i=1,nres_chmo(k)
write (iout,'(i5,3f8.3,5x,3f8.3)') i,(crefjlee(j,i),j=1,3),
& (crefjlee(j,i+nres),j=1,3)
enddo
c
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
- do i=1,2*nres
+ 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
lim_odl=ii
endif
+c write (iout,*) "Distance restraints set"
+c call flush(iout)
c
c Theta, dihedral and SC retraints
c
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))
+ & 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 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 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)
-c sigma_d(k,i)=rescore(k,i) ! right expression ?
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))
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
- if (ii_in_use(ii).eq.0.and.liiflag) then
+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.
- iistart=ii
+ 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.or.
- & .not.liiflag.and.ii.eq.lim_odl) then
- if (ii.eq.lim_odl) then
- iishift=ii-iistart+1
- else
- iishift=ii-iistart
- endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag) then
+ i01=ii
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
+ lim_odl=iistart-1
endif
-
- endif ! .not. klapaucjusz
+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
-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 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.lprn) return
+ if (.not.out_template_restr) return
cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
c if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
write (iout,*) "Distance restraints from templates"
end
c----------------------------------------------------------------------
subroutine read_klapaucjusz
-
+ implicit none
include 'DIMENSIONS'
include 'DIMENSIONS.ZSCOPT'
include 'DIMENSIONS.FREE'
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
+ integer i,ii,ik,ki,j,k,l,ll,ii_in_use(maxdim),i_tmp,idomain_tmp,
+ & nclust,iistart,iishift,lim_xx
+ integer nres_temp
integer idomain(max_template,maxres)
+ double precision distal
logical lprn /.true./
integer ilen
external ilen
call getenv("FRAGFILE",fragfile)
open(ientin,file=fragfile,status="old",err=10)
read(ientin,*) constr_homology,nclust
+ lim_xx=0
l_homo = .false.
sigma_theta=0.0
sigma_d=0.0
stop
34 continue
unres_pdb=.false.
+ nres_temp=nres
call readpdb_template(k)
+ nres_chomo(k)=nres
+ nres=nres_temp
c do i=1,2*nres
c do j=1,3
c chomo(j,i,k)=c(j,i)
c Loop over clusters
c
do l=1,nclust
+c write (iout,*) "CLUSTER",l," members:",ninclust(l)
do ll = 1,ninclust(l)
k = inclust(ll,l)
c ... --> odl(k,ii)
C Copy the coordinates from reference coordinates (?)
c write (iout,*) "k",k
+ 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
-c call cartprint
c write (iout,*) "read_klapaucjusz: calling int_from_cart"
+c call cartprint
+c write (iout,*) "idomain"
+c write (iout,'(2i5)') (i,idomain(k,i),i=1,nres)
call int_from_cart(.true.,.false.)
call sc_loc_geom(.false.)
c write (iout,*) "en"
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
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires_old)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
endif
C Calculate internal coordinates.
c call int_from_cart1(.false.)
- call int_from_cart(.true.,.true.)
- call sc_loc_geom(.true.)
+ call int_from_cart(.true.,out_template_coord)
+ call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
projects / unres.git / commitdiff