character*500 controlcard
integer ki, i, j, k, l, ii_in_use(maxdim),i_tmp,idomain_tmp
logical lprn /.true./
+ integer ilen
+ external ilen
c
c FP - Nov. 2014 Temporary specifications for new vars
c
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))
+ 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
tpl_k_rescore="template"//kic2//".sco"
+ unres_pdb=.false.
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
+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
endif
enddo
1401 continue
- close (ientin)
-
- 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'
-
- unres_pdb=.false.
- if (read2sigma) then
- call readpdb_template(k)
- else
- call readpdb
- endif
-c
-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
-
-
-
+ 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
+ do i = nnt,nct-2
+ do j=i+2,nct
if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0) then
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 (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) ! other exprs possible
-c sigma_odl(k,ii)=hmscore(k)*rescore(k,i)*rescore(k,j)
- else
+ 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) ! 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
+ 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
+ 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
- endif
- endif
+ endif
+ endif
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)
-
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 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.
+ do i = nnt+3,nct
if (idomain(k,i).eq.0) then
sigma_dih(k,i)=0.0
cycle
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
+ sigma_dih(k,i)=rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)+rescore(k,i-3)
+ 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-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
+ sigma_theta(k,i)=rescore(k,i)+rescore(k,i-1)+
+ & rescore(k,i-2)
+ if (read2sigma) sigma_theta(k,i)=sigma_theta(k,i)/3.0
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 & 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 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?
enddo
lim_xx=nct-nnt+1
endif
projects / unres.git / blobdiff