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
call read_dfa_info
print*, 'read_dfa_info finished!'
endif
+#endif
C
if (pdbref) then
if(me.eq.king.or..not.out1file)
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
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)
logical lprn /.true./
+ integer ilen
+ external ilen
c
c FP - Nov. 2014 Temporary specifications for new vars
c
call readi(controlcard,"HOMOL_NSET",homol_nset,1)
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
c521 continue
c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+ 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
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'
c enddo
c 1401 continue
c close (ientin)
- if (waga_dist.gt.0.0d0) then
+ 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 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
+
+ if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0) 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
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
+#ifdef OLDSIGMA
sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
& dexp(0.5d0*(odl(k,ii)/dist_cut)**2)
+#else
+ sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))* ! sigma ~ rescore ~ error
+ & dexp(0.5d0*(odl(k,ii)/dist_cut)**2-0.5d0)
+#endif
c Following expr replaced by a positive exp argument
c sigma_odl(k,ii)=(rescore(k,i)+rescore(k,j))*
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
+ else
+ ii=ii+1
+ l_homo(k,ii)=.false.
+ endif
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
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
+ lim_dih=nct-nnt-2
endif
if (waga_theta.gt.0.0d0) then
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
+ lim_theta=nct-nnt-1
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right?
1 continue
enddo
+ lim_xx=nct-nnt+1
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
+ do i=nnt,nct-2
+ do j=i+2,nct
+ ii=ii+1
+ if (ii_in_use(ii).eq.0) then
+ do ki=ii,lim_odl-1
+ ires_homo(ki)=ires_homo(ki+1)
+ jres_homo(ki)=jres_homo(ki+1)
+ ii_in_use(ki)=ii_in_use(ki+1)
+ do k=1,constr_homology
+ odl(k,ki)=odl(k,ki+1)
+ sigma_odl(k,ki)=sigma_odl(k,ki+1)
+ l_homo(k,ki)=l_homo(k,ki+1)
+ enddo
+ enddo
+ ii=ii-1
+ lim_odl=lim_odl-1
+ 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
+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(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,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
+ 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
+ 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
-
+ enddo
+ endif
c -----------------------------------------------------------------
return
end
projects / unres.git / blobdiff