C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'DIMENSIONS.ZSCOPT'
include 'DIMENSIONS.FREE'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.IOUNITS'
dimension ggg(3)
ehpb=0.0D0
-cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
-cd print *,'link_start=',link_start,' link_end=',link_end
-C write(iout,*) link_end, "link_end"
+ do i=1,3
+ ggg(i)=0.0d0
+ enddo
+C write (iout,*) ,"link_end",link_end,constr_dist
+cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
+c write(iout,*)'link_start=',link_start,' link_end=',link_end,
+c & " constr_dist",constr_dist
if (link_end.eq.0) return
do i=link_start,link_end
C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
iii=ii
jjj=jj
endif
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
C 24/11/03 AL: SS bridges handled separately because of introducing a specific
C distance and angle dependent SS bond potential.
-C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
C & iabs(itype(jjj)).eq.1) then
-C write(iout,*) constr_dist,"const"
- if (.not.dyn_ss .and. i.le.nss) then
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
- & iabs(itype(jjj)).eq.1) then
- call ssbond_ene(iii,jjj,eij)
- ehpb=ehpb+2*eij
- endif !ii.gt.neres
- else if (ii.gt.nres .and. jj.gt.nres) then
-c Restraints from contact prediction
+cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
+ if (.not.dyn_ss .and. i.le.nss) then
+C 15/02/13 CC dynamic SSbond - additional check
+ if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+ & iabs(itype(jjj)).eq.1) then
+ call ssbond_ene(iii,jjj,eij)
+ ehpb=ehpb+2*eij
+ endif
+cd write (iout,*) "eij",eij
+cd & ' waga=',waga,' fac=',fac
+! else if (ii.gt.nres .and. jj.gt.nres) then
+ else
+C Calculate the distance between the two points and its difference from the
+C target distance.
dd=dist(ii,jj)
- if (constr_dist.eq.11) then
-C ehpb=ehpb+fordepth(i)**4.0d0
-C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
- ehpb=ehpb+fordepth(i)**4.0d0
- & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
- fac=fordepth(i)**4.0d0
- & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
-C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
-C & ehpb,fordepth(i),dd
-C write(iout,*) ehpb,"atu?"
-C ehpb,"tu?"
-C fac=fordepth(i)**4.0d0
-C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
- else
- if (dhpb1(i).gt.0.0d0) then
- ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ if (irestr_type(i).eq.11) then
+ ehpb=ehpb+fordepth(i)!**4.0d0
+ & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ fac=fordepth(i)!**4.0d0
+ & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+c if (energy_dec) write (iout,'(a6,2i5,6f10.3,i5)')
+c & "edisL",ii,jj,dd,dhpb(i),dhpb1(i),forcon(i),fordepth(i),
+c & ehpb,irestr_type(i)
+ else if (irestr_type(i).eq.10) then
+c AL 6//19/2018 cross-link restraints
+ xdis = 0.5d0*(dd/forcon(i))**2
+ expdis = dexp(-xdis)
+c aux=(dhpb(i)+dhpb1(i)*xdis)*expdis+fordepth(i)
+ aux=(dhpb(i)+dhpb1(i)*xdis*xdis)*expdis+fordepth(i)
+c write (iout,*)"HERE: xdis",xdis," expdis",expdis," aux",aux,
+c & " wboltzd",wboltzd
+ ehpb=ehpb-wboltzd*xlscore(i)*dlog(aux)
+c fac=-wboltzd*(dhpb1(i)*(1.0d0-xdis)-dhpb(i))
+ fac=-wboltzd*xlscore(i)*(dhpb1(i)*(2.0d0-xdis)*xdis-dhpb(i))
+ & *expdis/(aux*forcon(i)**2)
+c if (energy_dec) write(iout,'(a6,2i5,6f10.3,i5)')
+c & "edisX",ii,jj,dd,dhpb(i),dhpb1(i),forcon(i),fordepth(i),
+c & -wboltzd*xlscore(i)*dlog(aux),irestr_type(i)
+ else if (irestr_type(i).eq.2) then
+c Quartic restraints
+ ehpb=ehpb+forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+c if (energy_dec) write(iout,'(a6,2i5,5f10.3,i5)')
+c & "edisQ",ii,jj,dd,dhpb(i),dhpb1(i),forcon(i),
+c & forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)),irestr_type(i)
fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
-c write (iout,*) "beta nmr",
-c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
else
- dd=dist(ii,jj)
+c Quadratic restraints
rdis=dd-dhpb(i)
C Get the force constant corresponding to this distance.
waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
-c write (iout,*) "beta reg",dd,waga*rdis*rdis
+ ehpb=ehpb+0.5d0*waga*rdis*rdis
+c if (energy_dec) write(iout,'(a6,2i5,5f10.3,i5)')
+c & "edisS",ii,jj,dd,dhpb(i),dhpb1(i),forcon(i),
+c & 0.5d0*waga*rdis*rdis,irestr_type(i)
C
C Evaluate gradient.
C
fac=waga*rdis/dd
- endif !end dhpb1(i).gt.0
- endif !end const_dist=11
+ endif
+c Calculate Cartesian gradient
do j=1,3
ggg(j)=fac*(c(j,jj)-c(j,ii))
enddo
- do j=1,3
- ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
- ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
- enddo
- do k=1,3
- ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
- ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
- enddo
- else !ii.gt.nres
-C write(iout,*) "before"
- dd=dist(ii,jj)
-C write(iout,*) "after",dd
- if (constr_dist.eq.11) then
- ehpb=ehpb+fordepth(i)**4.0d0
- & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
- fac=fordepth(i)**4.0d0
- & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
-C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
-C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
-C print *,ehpb,"tu?"
-C write(iout,*) ehpb,"btu?",
-C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i)
-C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
-C & ehpb,fordepth(i),dd
- else
- if (dhpb1(i).gt.0.0d0) then
- ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
- fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
-c write (iout,*) "alph nmr",
-c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
- else
- rdis=dd-dhpb(i)
-C Get the force constant corresponding to this distance.
- waga=forcon(i)
-C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
-c write (iout,*) "alpha reg",dd,waga*rdis*rdis
-C
-C Evaluate gradient.
-C
- fac=waga*rdis/dd
- endif
- endif
-
- do j=1,3
- ggg(j)=fac*(c(j,jj)-c(j,ii))
- enddo
cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
C If this is a SC-SC distance, we need to calculate the contributions to the
C Cartesian gradient in the SC vectors (ghpbx).
- if (iii.lt.ii) then
- do j=1,3
- ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
- ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
- enddo
- endif
- do j=iii,jjj-1
+ if (iii.lt.ii) then
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ endif
do k=1,3
- ghpbc(k,j)=ghpbc(k,j)+ggg(k)
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
enddo
- enddo
endif
enddo
- if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
j = jres_homo(ii)
dij=dist(i,j)
c write (iout,*) "dij(",i,j,") =",dij
+ nexl=0
do k=1,constr_homology
- if(.not.l_homo(k,ii)) cycle
+ if(.not.l_homo(k,ii)) then
+ nexl=nexl+1
+ cycle
+ endif
distance(k)=odl(k,ii)-dij
c write (iout,*) "distance(",k,") =",distance(k)
c
write (iout,*) "distancek",(distancek(k),k=1,constr_homology)
write (iout,* )"min_odl",min_odl
#endif
+#ifdef OLDRESTR
odleg2=0.0d0
+#else
+ if (waga_dist.ge.0.0d0) then
+ odleg2=nexl
+ else
+ odleg2=0.0d0
+ endif
+#endif
do k=1,constr_homology
c Nie wiem po co to liczycie jeszcze raz!
c odleg3=-waga_dist(iset)*((distance(i,j,k)**2)/
c & -(6.28318-dih_diff(i,k))
c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
c & 6.28318+dih_diff(i,k)
-
+#ifdef OLD_DIHED
kat3=-0.5d0*dih_diff(k)**2*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
+#else
+ kat3=(dcos(dih_diff(k))-1)*sigma_dih(k,i)
+#endif
c kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
gdih(k)=dexp(kat3)
kat2=kat2+gdih(k)
sum_gdih=kat2
sum_sgdih=0.0d0
do k=1,constr_homology
+#ifdef OLD_DIHED
sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i) ! waga_angle rmvd
+#else
+ sgdih=-gdih(k)*dsin(dih_diff(k))*sigma_dih(k,i)
+#endif
c sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
sum_sgdih=sum_sgdih+sgdih
enddo
return
end
c----------------------------------------------------------------------------
+ double precision function sscale2(r,r_cut,r0,rlamb)
+ implicit none
+ double precision r,gamm,r_cut,r0,rlamb,rr
+ rr = dabs(r-r0)
+c write (2,*) "r",r," r_cut",r_cut," r0",r0," rlamb",rlamb
+c write (2,*) "rr",rr
+ if(rr.lt.r_cut-rlamb) then
+ sscale2=1.0d0
+ else if(rr.le.r_cut.and.rr.ge.r_cut-rlamb) then
+ gamm=(rr-(r_cut-rlamb))/rlamb
+ sscale2=1.0d0+gamm*gamm*(2*gamm-3.0d0)
+ else
+ sscale2=0d0
+ endif
+ return
+ end
+C-----------------------------------------------------------------------
+ double precision function sscalgrad2(r,r_cut,r0,rlamb)
+ implicit none
+ double precision r,gamm,r_cut,r0,rlamb,rr
+ rr = dabs(r-r0)
+ if(rr.lt.r_cut-rlamb) then
+ sscalgrad2=0.0d0
+ else if(rr.le.r_cut.and.rr.ge.r_cut-rlamb) then
+ gamm=(rr-(r_cut-rlamb))/rlamb
+ if (r.ge.r0) then
+ sscalgrad2=gamm*(6*gamm-6.0d0)/rlamb
+ else
+ sscalgrad2=-gamm*(6*gamm-6.0d0)/rlamb
+ endif
+ else
+ sscalgrad2=0.0d0
+ endif
+ return
+ end
+c----------------------------------------------------------------------------
subroutine e_saxs(Esaxs_constr)
implicit none
include 'DIMENSIONS'
& sigma2CACA,sigma2CASC,sigma2SCCA,sigma2SCSC,expCACA,expCASC,
& expSCCA,expSCSC,CASCgrad,SCCAgrad,SCSCgrad,aux,auxC,auxC1,
& auxX,auxX1,CACAgrad,Cnorm
+ double precision sss2,ssgrad2,rrr,sscalgrad2,sscale2
double precision dist
external dist
c SAXS restraint penalty function
enddo
enddo
do i=iatsc_s,iatsc_e
+ if (itype(i).eq.ntyp1) cycle
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
+ if (itype(j).eq.ntyp1) cycle
#ifdef ALLSAXS
dijCACA=dist(i,j)
dijCASC=dist(i,j+nres)
enddo ! k
#else
dijCACA=dist(i,j)
- sigma2CACA=0.25d0/(restok(itype(j))**2+restok(itype(i))**2)
+ sigma2CACA=scal_rad**2*0.25d0/
+ & (restok(itype(j))**2+restok(itype(i))**2)
+
+ IF (saxs_cutoff.eq.0) THEN
do k=1,nsaxs
dk = distsaxs(k)
expCACA = dexp(-0.5d0*sigma2CACA*(dijCACA-dk)**2)
Pcalc(k) = Pcalc(k)+expCACA
+ CACAgrad = sigma2CACA*(dijCACA-dk)*expCACA
+ do l=1,3
+ aux = CACAgrad*(C(l,j)-C(l,i))/dijCACA
+ PgradC(k,l,i) = PgradC(k,l,i)-aux
+ PgradC(k,l,j) = PgradC(k,l,j)+aux
+ enddo ! l
+ enddo ! k
+ ELSE
+ rrr = saxs_cutoff*2.0d0/dsqrt(sigma2CACA)
+ do k=1,nsaxs
+ dk = distsaxs(k)
+c write (2,*) "ijk",i,j,k
+ sss2 = sscale2(dijCACA,rrr,dk,0.3d0)
+ if (sss2.eq.0.0d0) cycle
+ ssgrad2 = sscalgrad2(dijCACA,rrr,dk,0.3d0)
+ expCACA = dexp(-0.5d0*sigma2CACA*(dijCACA-dk)**2)*sss2
+ Pcalc(k) = Pcalc(k)+expCACA
#ifdef DEBUG
write(iout,*) "i j k Pcalc",i,j,Pcalc(k)
#endif
- CACAgrad = sigma2CACA*(dijCACA-dk)*expCACA
+ CACAgrad = -sigma2CACA*(dijCACA-dk)*expCACA+
+ & ssgrad2*expCACA/sss2
do l=1,3
c CA CA
aux = CACAgrad*(C(l,j)-C(l,i))/dijCACA
- PgradC(k,l,i) = PgradC(k,l,i)-aux
- PgradC(k,l,j) = PgradC(k,l,j)+aux
+ PgradC(k,l,i) = PgradC(k,l,i)+aux
+ PgradC(k,l,j) = PgradC(k,l,j)-aux
enddo ! l
enddo ! k
+ ENDIF
#endif
enddo ! j
enddo ! iint
do k=1,nsaxs
Cnorm = Cnorm + Pcalc(k)
enddo
- Esaxs_constr = dlog(Cnorm)
+ Esaxs_constr = dlog(Cnorm)-wsaxs0
do k=1,nsaxs
- Esaxs_constr = Esaxs_constr - Psaxs(k)*dlog(Pcalc(k))
+ if (Pcalc(k).gt.0.0d0)
+ & Esaxs_constr = Esaxs_constr - Psaxs(k)*dlog(Pcalc(k))
#ifdef DEBUG
write (iout,*) "k",k," Esaxs_constr",Esaxs_constr
#endif
auxX=0.0d0
auxX1=0.d0
do k=1,nsaxs
- auxC = auxC +Psaxs(k)*PgradC(k,l,i)/Pcalc(k)
+ if (Pcalc(k).gt.0)
+ & auxC = auxC +Psaxs(k)*PgradC(k,l,i)/Pcalc(k)
auxC1 = auxC1+PgradC(k,l,i)
#ifdef ALLSAXS
auxX = auxX +Psaxs(k)*PgradX(k,l,i)/Pcalc(k)
projects / unres.git / blobdiff