do i=1,nres
itype(i)=rescode(i,sequence(i),iscode)
enddo
+ if (itype(2).eq.10.and.itype(1).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the first full residue, initial dummy deleted"
+ do i=1,nres
+ itype(i)=itype(i+1)
+ enddo
+ nres=nres-1
+ endif
+ if (itype(nres-1).eq.10.and.itype(nres).eq.ntyp1) then
+ write (iout,*)
+ & "Glycine is the last full residue, terminal dummy deleted"
+ nres=nres-1
+ endif
+
C Assign initial virtual bond lengths
do i=2,nres
vbld(i)=vbl
call readi(controlcard,"NPAIR",npair_,0)
call readi(controlcard,"NDIST",ndist_,0)
call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
+ call reada(controlcard,'DIST2_CUT',dist2_cut,9999.0d0)
call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
c
c FP - Nov. 2014 Temporary specifications for new vars
c
- double precision rescore_tmp,x12,y12,z12
+ 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 Reading multiple PDB ref structures and calculation of retraints
call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) ! for diff ways of calc sigma
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
+ write(iout,*) 'START_FROM_MODELS works only with READ2SIGMA'
+ start_from_model=.false.
+ endif
+ if(start_from_model) write(iout,*) 'START_FROM_MODELS is ON'
+ if(start_from_model .and. rest) then
+ write(iout,*) 'START_FROM_MODELS is OFF'
+ write(iout,*) 'remove restart keyword from input'
+ endif
if (homol_nset.gt.1)then
call card_concat(controlcard)
read(controlcard,*) (waga_homology(i),i=1,homol_nset)
write(kic2,'(bz,i2.2)') k
tpl_k_rescore="template"//kic2//".sco"
-c tpl_k_sigma_odl="template"//kic2//".sigma_odl"
-c tpl_k_sigma_dih="template"//kic2//".sigma_dih"
-c tpl_k_sigma_theta="template"//kic2//".sigma_theta"
-c tpl_k_sigma_d="template"//kic2//".sigma_d"
unres_pdb=.false.
- call readpdb
+ if (read2sigma) then
+ call readpdb_template(k)
+ else
+ call readpdb
+ endif
c
c Distance restraints
c
& idomain_tmp
i_tmp=i_tmp+nnt-1
idomain(k,i_tmp)=idomain_tmp
- rescore(k,i_tmp)=0.5d0*(rescore_tmp+0.5d0)
- rescore2(k,i_tmp)=0.5d0*(rescore2_tmp+0.5d0)
+ rescore(k,i_tmp)=rescore_tmp
+ rescore2(k,i_tmp)=rescore2_tmp
else
idomain(k,irec)=1
read (ientin,*,end=1401) rescore_tmp
endif
enddo
1401 continue
- close (ientin)
-c open (ientin,file=tpl_k_sigma_odl,status='old')
-c do irec=1,maxdim ! loop for reading sigma_odl
-c read (ientin,*,end=1401) i, j,
-c & sigma_odl_temp(i+nnt-1,j+nnt-1,k) ! new variable (?)
-c sigma_odl_temp(j+nnt-1,i+nnt-1,k)= ! which purpose?
-c & sigma_odl_temp(i+nnt-1,j+nnt-1,k)
-c enddo
-c 1401 continue
-c close (ientin)
+ 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
-
- if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0) then
-
+ 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)
+
+
+ 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 & constr_homology
ires_homo(ii)=i
jres_homo(ii)=j
-c
-c Attempt to replace dist(i,j) by its definition in ...
-c
- 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)
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 (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)
+ 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))*
& 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))*
& 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 & 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)
- endif
-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
-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
+ 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
-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 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
+ 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)
sigma_dih(k,i)=(rescore(k,i)+rescore(k,i-1)+
& rescore(k,i-2)+rescore(k,i-3))/4.0
-c
+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)*
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-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
+ & rescore(k,i-2))/3.0
+c 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
- close (ientin)
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) goto 1 ! right?
+ 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 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?
- 1 continue
enddo
lim_xx=nct-nnt+1
endif
- close(ientin)
enddo
c
c remove distance restraints not used in any model from the list