- subroutine gen_rand_conf(nstart,*)
+ subroutine gen_rand_conf(nstart,nend,*)
C Generate random conformation or chain cut and regrowth.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
include 'COMMON.MCM'
include 'COMMON.GEO'
include 'COMMON.CONTROL'
- logical overlap,back,fail
-cd print *,' CG Processor',me,' maxgen=',maxgen
+ logical overlap,back,fail,ldir
+ maxgen=10000
+ write (iout,*) ' CG Processor',me,' maxgen=',maxgen
maxsi=100
-cd write (iout,*) 'Gen_Rand_conf: nstart=',nstart
+ ldir = nstart.le.nend
+ write (iout,*) 'Gen_Rand_conf: nstart=',nstart,' nend',nend,
+ & ' ldir',ldir
+
+ if (ldir) then
+
if (nstart.lt.5) then
- it1=itype(2)
- phi(4)=gen_phi(4,itype(2),itype(3))
+ it1=iabs(itype(2))
+ phi(4)=gen_phi(4,iabs(itype(2)),iabs(itype(3)))
c write(iout,*)'phi(4)=',rad2deg*phi(4)
- if (nstart.lt.3) theta(3)=gen_theta(itype(2),pi,phi(4))
+ if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2)),pi,phi(4))
c write(iout,*)'theta(3)=',rad2deg*theta(3)
if (it1.ne.10) then
nsi=0
nit=0
niter=0
back=.false.
- do while (i.le.nres .and. niter.lt.maxgen)
+ do while (i.le.nend .and. niter.lt.maxgen)
if (i.lt.nstart) then
if(iprint.gt.1) then
write (iout,'(/80(1h*)/2a/80(1h*))')
endif
return1
endif
- it1=itype(i-1)
- it2=itype(i-2)
- it=itype(i)
+ it1=iabs(itype(i-1))
+ it2=iabs(itype(i-2))
+ it=iabs(itype(i))
c print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,
c & ' nit=',nit,' niter=',niter,' maxgen=',maxgen
phi(i+1)=gen_phi(i+1,it1,it)
phi(i)=gen_phi(i+1,it2,it1)
c print *,'phi(',i,')=',phi(i)
theta(i-1)=gen_theta(it2,phi(i-1),phi(i))
- if (it2.ne.10) then
+ if (it2.ne.10 .and. it2.ne.ntyp1) then
nsi=0
fail=.true.
do while (fail.and.nsi.le.maxsi)
call locate_next_res(i-1)
endif
theta(i)=gen_theta(it1,phi(i),phi(i+1))
- if (it1.ne.10) then
+ if (it1.ne.10 .and. it1.ne.ntyp1) then
nsi=0
fail=.true.
do while (fail.and.nsi.le.maxsi)
if (nsi.gt.maxsi) return1
endif
call locate_next_res(i)
- if (overlap(i-1)) then
+ if (overlap(i-1,ldir)) then
if (nit.lt.maxnit) then
back=.true.
nit=nit+1
c(j,nres+1)=c(j,1)
c(j,nres+nres)=c(j,nres)
enddo
+
+ else
+
+ maxnit=100
+
+ i=nstart
+ nit=0
+ niter=0
+ back=.false.
+ do while (i.ge.nend .and. niter.lt.maxgen)
+ if (i.gt.nstart) then
+ if(iprint.gt.1) then
+ write (iout,'(/80(1h*)/2a/80(1h*))')
+ & 'Generation procedure went down to ',
+ & 'chain beginning. Cannot continue...'
+ write (*,'(/80(1h*)/2a/80(1h*))')
+ & 'Generation procedure went down to ',
+ & 'chain beginning. Cannot continue...'
+ endif
+ return1
+ endif
+ it1=iabs(itype(i+1))
+ it2=iabs(itype(i+2))
+ it3=iabs(itype(i+3))
+c print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,
+c & ' nit=',nit,' niter=',niter,' maxgen=',maxgen
+ phi(i+2)=gen_phi(i+2,it1,it2)
+ if (back) then
+ phi(i+3)=gen_phi(i+3,it2,it3)
+ phi(i+4)=gen_phi(i+3,it2,it3)
+c print *,'phi(',i+3,')=',phi(i+3)
+ theta(i+3)=gen_theta(it2,phi(i+3),phi(i+4))
+ if (it2.ne.10 .and. it2.ne.ntyp1) then
+ nsi=0
+ fail=.true.
+ do while (fail.and.nsi.le.maxsi)
+ call gen_side(it2,theta(i+3),alph(i+2),omeg(i+2),fail)
+ nsi=nsi+1
+ enddo
+ if (nsi.gt.maxsi) return1
+ endif
+ call locate_prev_res(i+1)
+ endif
+ theta(i+2)=gen_theta(it1,phi(i+2),phi(i+3))
+ write (iout,*) "i"," theta",theta(i+2)," phi",phi(i+2),phi(i+3)
+ if (it1.ne.10 .and. it1.ne.ntyp1) then
+ nsi=0
+ fail=.true.
+ do while (fail.and.nsi.le.maxsi)
+ call gen_side(it1,theta(i+2),alph(i+1),omeg(i+1),fail)
+ nsi=nsi+1
+ enddo
+ write (iout,*) "i",i," alpha",alph(i+1)," omeg",omeg(i+1),
+ & " fail",fail
+ if (nsi.gt.maxsi) return1
+ endif
+ call locate_prev_res(i)
+ write (iout,*) "After locate_prev_res i=",i
+ write (iout,'(3f10.5,5x,3f10.5)') (c(l,i),l=1,3),
+ & (c(l,i+nres),l=1,3)
+ write (iout,'(3f10.5,5x,3f10.5)') (c(l,i+1),l=1,3),
+ & (c(l,i+1+nres),l=1,3)
+ call flush(iout)
+ if (overlap(i+1,ldir)) then
+ write (iout,*) "OVERLAP",nit
+ call flush(iout)
+ if (nit.lt.maxnit) then
+ back=.true.
+ nit=nit+1
+ else
+ nit=0
+ if (i.gt.3) then
+ back=.true.
+ i=i+1
+ else
+ write (iout,'(a)')
+ & 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
+ write (*,'(a)')
+ & 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
+ return1
+ endif
+ endif
+ else
+ write (iout,*) "================>> NO OVERLAP",i
+ call flush(iout)
+ back=.false.
+ nit=0
+ i=i-1
+ endif
+ niter=niter+1
+ write (iout,*) "iter",niter
+ enddo
+ if (niter.ge.maxgen) then
+ write (iout,'(a,2i5)')
+ &'Too many trials in backward conformation generation',niter,maxgen
+ write (*,'(a,2i5)')
+ &'Too many trials in backward conformation generation',niter,maxgen
+ return1
+ endif
+
+ endif
+
+ write (iout,*) "HERE!!!!"
+
return
end
c-------------------------------------------------------------------------
- logical function overlap(i)
+ logical function overlap(i,ldir)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.INTERACT'
include 'COMMON.FFIELD'
data redfac /0.5D0/
+ logical ldir
+ logical lprn /.false./
overlap=.false.
- iti=itype(i)
+ iti=iabs(itype(i))
if (iti.gt.ntyp) return
C Check for SC-SC overlaps.
cd print *,'nnt=',nnt,' nct=',nct
+c write (iout,*) "overlap i",i," ldir",ldir
+
+ if (ldir) then
+
do j=nnt,i-1
- itj=itype(j)
+ itj=iabs(itype(j))
if (j.lt.i-1 .or. ipot.ne.4) then
rcomp=sigmaii(iti,itj)
else
cd print *,'j=',j
if (dist(nres+i,nres+j).lt.redfac*rcomp) then
overlap=.true.
-c print *,'overlap, SC-SC: i=',i,' j=',j,
-c & ' dist=',dist(nres+i,nres+j),' rcomp=',
-c & rcomp
+ if (lprn) write (iout,*) 'overlap, SC-SC: i=',i,' j=',j,
+ & ' dist=',dist(nres+i,nres+j),' rcomp=',
+ & rcomp
return
endif
enddo
c(j,maxres2+1)=0.5D0*(c(j,i)+c(j,i+1))
enddo
do j=nnt,i-2
- itj=itype(j)
-cd print *,'overlap, p-Sc: i=',i,' j=',j,
-cd & ' dist=',dist(nres+j,maxres2+1)
+ itj=iabs(itype(j))
if (dist(nres+j,maxres2+1).lt.4.0D0*redfac) then
+ if (lprn) write (iout,*) 'overlap, p-Sc: i=',i,' j=',j,
+ & ' dist=',dist(nres+j,maxres2+1)
overlap=.true.
return
endif
do k=1,3
c(k,maxres2+1)=0.5D0*(c(k,j)+c(k,j+1))
enddo
-cd print *,'overlap, SC-p: i=',i,' j=',j,
-cd & ' dist=',dist(nres+i,maxres2+1)
if (dist(nres+i,maxres2+1).lt.4.0D0*redfac) then
+ if (lprn) write (iout,*) 'overlap, SC-p: i=',i,' j=',j,
+ & ' dist=',dist(nres+i,maxres2+1)
overlap=.true.
return
endif
do k=1,3
c(k,maxres2+2)=0.5D0*(c(k,j)+c(k,j+1))
enddo
-cd print *,'overlap, p-p: i=',i,' j=',j,
-cd & ' dist=',dist(maxres2+1,maxres2+2)
if(iteli.ne.0.and.itelj.ne.0)then
if (dist(maxres2+1,maxres2+2).lt.rpp(iteli,itelj)*redfac) then
+ if (lprn) write (iout,*) 'overlap, p-p: i=',i,' j=',j,
+ & ' dist=',dist(maxres2+1,maxres2+2)
+ overlap=.true.
+ return
+ endif
+ endif
+ enddo
+
+ else
+
+ if (lprn) write (iout,*) "start",i+1," end",nres_start+nsup
+ do j=i+1,nres_start+nsup
+ itj=iabs(itype(j))
+ if (j.gt.i+1 .or. ipot.ne.4) then
+ rcomp=sigmaii(iti,itj)
+ else
+ rcomp=sigma(iti,itj)
+ endif
+cd print *,'j=',j
+c write (iout,*) "SCSC j",j," dist",dist(nres+i,nres+j),
+c & " radfac",redfac*rcomp
+ if (dist(nres+i,nres+j).lt.redfac*rcomp) then
+ overlap=.true.
+ if (lprn) write (iout,*) 'overlap, SC-SC: i=',i,' j=',j,
+ & ' dist=',dist(nres+i,nres+j),' rcomp=',
+ & rcomp
+ return
+ endif
+ enddo
+C Check for overlaps between the added peptide group and the succeeding
+C SCs.
+ iteli=itel(i)
+ do j=1,3
+ c(j,maxres2+1)=0.5D0*(c(j,i)+c(j,i+1))
+ enddo
+ do j=i+2,nstart_res+nsup
+ itj=iabs(itype(j))
+cd write (iout,*) "pSC j",j," dist",dist(nres+j,maxres2+1)
+ if (dist(nres+j,maxres2+1).lt.4.0D0*redfac) then
+ if (lprn) write (iout,*) 'overlap, p-Sc: i=',i,' j=',j,
+ & ' dist=',dist(nres+j,maxres2+1)
+ overlap=.true.
+ return
+ endif
+ enddo
+C Check for overlaps between the added side chain and the succeeding peptide
+C groups.
+ do j=i+2,nstart_seq+nsup
+ do k=1,3
+ c(k,maxres2+1)=0.5D0*(c(k,j)+c(k,j+1))
+ enddo
+cd write (iout,*) "SCp j",j," dist",dist(nres+i,maxres2+1)
+ if (dist(nres+i,maxres2+1).lt.4.0D0*redfac) then
+ if (lprn) write (iout,*) 'overlap, SC-p: i=',i,' j=',j,
+ & ' dist=',dist(nres+i,maxres2+1)
+ overlap=.true.
+ return
+ endif
+ enddo
+C Check for p-p overlaps
+ do j=1,3
+ c(j,maxres2+2)=0.5D0*(c(j,i)+c(j,i+1))
+ enddo
+ do j=i+2,nres_start+nsup
+ itelj=itel(j)
+ do k=1,3
+ c(k,maxres2+2)=0.5D0*(c(k,j)+c(k,j+1))
+ enddo
+ if(iteli.ne.0.and.itelj.ne.0)then
+cd write (iout,*) "pp j",j," dist",dist(maxres2+1,maxres2+2)
+ if (dist(maxres2+1,maxres2+2).lt.rpp(iteli,itelj)*redfac) then
+ if (lprn) write (iout,*) 'overlap, p-p: i=',i,' j=',j,
+ & ' dist=',dist(maxres2+1,maxres2+2)
overlap=.true.
return
endif
endif
enddo
+
+ endif
+
return
end
c--------------------------------------------------------------------------
double precision function gen_phi(i,it1,it2)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
+ include "COMMON.TORCNSTR"
include 'COMMON.GEO'
include 'COMMON.BOUNDS'
-c gen_phi=ran_number(-pi,pi)
+ if (raw_psipred .or. ndih_constr.eq.0) then
+ gen_phi=ran_number(-pi,pi)
+ else
C 8/13/98 Generate phi using pre-defined boundaries
- gen_phi=ran_number(phibound(1,i),phibound(2,i))
+ gen_phi=ran_number(phibound(1,i),phibound(2,i))
+ endif
return
end
c---------------------------------------------------------------------------
endif
thet_pred_mean=a0thet(it)
do k=1,2
- thet_pred_mean=thet_pred_mean+athet(k,it)*y(k)+bthet(k,it)*z(k)
+ thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k)
+ & +bthet(k,it,1,1)*z(k)
enddo
sig=polthet(3,it)
do j=2,0,-1
do ires=1,ioverlap_last
i=ioverlap(ires)
- iti=itype(i)
+ iti=iabs(itype(i))
if (iti.ne.10) then
nsi=0
fail=.true.
endif
enddo
- call chainbuild
+ call chainbuild_extconf
call overlap_sc_list(ioverlap,ioverlap_last)
c write (iout,*) 'Overlaping residues ',ioverlap_last,
c & (ioverlap(j),j=1,ioverlap_last)
c print *,'>>overlap_sc nnt=',nnt,' nct=',nct
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
projects / unres.git / blobdiff