do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
#else
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
include 'COMMON.HOMRESTR'
c
c For new homol impl
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
+ double precision, dimension (max_template,maxres) :: rescore3
character*24 tpl_k_rescore
c -----------------------------------------------------------------
c Reading multiple PDB ref structures and calculation of retraints
c
c New
c
- lim_theta=0
- lim_xx=0
c
c Reading HM global scores (prob not required)
c
c 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,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
- & idomain_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
+ 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
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
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
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & 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
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& 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))
+ if (sigma_theta(k,i).ne.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 rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
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)
- sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(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))
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
enddo
c
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
-c write (iout,*) "dih_diff(",k,") =",dih_diff(k)
+cd write (iout,'(a8,2i4,2f15.8)') "dih_diff",i,k,dih_diff(k)
+cd & ,sigma_dih(k,i)
c if (dih_diff(i,k).gt.3.14159) dih_diff(i,k)=
c & -(6.28318-dih_diff(i,k))
c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
c dtheta_i=theta(j)-thetaref(j,iref)
c dtheta_i=thetaref(k,i)-theta(i) ! original form without indexing
theta_diff(k)=thetatpl(k,i)-theta(i)
+cd write (iout,'(a8,2i4,2f15.8)') "theta_diff",i,k,theta_diff(k)
+cd & ,sigma_theta(k,i)
+
c
utheta_i=-0.5d0*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta rmvd from Gaussian argument
c utheta_i=-0.5d0*waga_theta*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta?
dyy=-yytpl(k,i)+yytab(i) ! ibid y
dzz=-zztpl(k,i)+zztab(i) ! ibid z
c write(iout,*) "dxx, dyy, dzz"
-c write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
+cd write(iout,'(2i5,4f8.2)') k,i,dxx,dyy,dzz,sigma_d(k,i)
c
usc_diff_i=-0.5d0*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d rmvd from Gaussian argument
c usc_diff(i)=-0.5d0*waga_d*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d?
#ifdef MPI
if (me.eq.king .or. .not. out1file) write (iout,*) "MPI"
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
write (iout,*) "Not MPI"
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
include 'COMMON.MD'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
c
c For new homol impl
c
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
+ double precision, dimension (max_template,maxres) :: rescore3
character*24 pdbfile,tpl_k_rescore
c -----------------------------------------------------------------
c Reading multiple PDB ref structures and calculation of retraints
lim_odl=0
lim_dih=0
c
-c New
-c
- lim_theta=0
- lim_xx=0
-c
write(iout,*) 'nnt=',nnt,'nct=',nct
c
do i = nnt,nct
c 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,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
- & idomain_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
+ 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
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
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
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & 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
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& 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))
+ if (sigma_theta(k,i).ne.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 rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
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)
- sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(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))
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
enddo
c
endif
if (constr_homology.gt.0) call homology_partition
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
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
- betai = phi(i+3)
+ betai = phi(i)
c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
& " lim_dih",lim_dih
#ifdef MPL
call int_bounds(lim_odl,link_start_homo,link_end_homo)
- call int_bounds(lim_dih-nnt+1,idihconstr_start_homo,
+ call int_bounds(lim_dih,idihconstr_start_homo,
& idihconstr_end_homo)
- idihconstr_start_homo=idihconstr_start_homo+nnt-1
- idihconstr_end_homo=idihconstr_end_homo+nnt-1
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
if (me.eq.king .or. .not. out1file)
& write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
#else
link_start_homo=1
link_end_homo=lim_odl
- idihconstr_start_homo=nnt
- idihconstr_end_homo=lim_dih
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+3
write (iout,*)
& ' lim_odl',lim_odl,' link_start=',link_start_homo,
& ' link_end',link_end_homo,' lim_dih',lim_dih,
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
+ include 'include_unres/COMMON.NAMES'
include 'COMMON.HOMRESTR'
c
c For new homol impl
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
+ double precision, dimension (max_template,maxres) :: rescore3
character*24 tpl_k_rescore
c -----------------------------------------------------------------
c Reading multiple PDB ref structures and calculation of retraints
c
c New
c
- lim_theta=0
- lim_xx=0
c
c Reading HM global scores (prob not required)
c
c 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,maxdim ! loop for reading res sim
+ do irec=nnt,nct ! loop for reading res sim
if (read2sigma) then
read (ientin,*,end=1401) i_tmp,rescore2_tmp,rescore_tmp,
- & idomain_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
+ 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
c sigma_dih(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)*
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
- sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i))
+ if (sigma_dih(k,i).ne.0)
+ & 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
sigma_theta(k,i)=(rescore(k,i)+rescore(k,i-1)+
& 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))
+ if (sigma_theta(k,i).ne.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 rescore(k,i-2) ! right expression ?
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
- lim_theta=nct-nnt-1
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)
- sigma_d(k,i)=rescore(k,i) ! right expression ?
- sigma_d(k,i)=1.0d0/(sigma_d(k,i)*sigma_d(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))
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
enddo
c
& ki=1,constr_homology)
enddo
write (iout,*) "Dihedral angle restraints from templates"
- do i=nnt+3,lim_dih
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*dih(ki,i),
+ do i=nnt+3,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
- write (iout,'(i5,100(2f8.2,4x))') i,(rad2deg*thetatpl(ki,i),
+ do i=nnt+2,nct
+ write (iout,'(i5,a4,100(2f8.2,4x))') i,restyp(itype(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
+ do i=nnt,nct
write(iout,'(i5,100(4f8.2,4x))') i,
& (xxtpl(ki,i),yytpl(ki,i),zztpl(ki,i),
& 1.0d0/dsqrt(sigma_d(ki,i)),ki=1,constr_homology)