! include 'COMMON.NAMES'
real(kind=8) :: facont=1.569D0 ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
integer :: ncont
- integer,dimension(2,12*nres) :: icont!(2,12*nres) !(2,maxcont) (maxcont=12*maxres)
+ integer,dimension(2,100*nres) :: icont!(2,100*nres) !(2,maxcont) (maxcont=12*maxres)
logical :: lprint
!el local variables
real(kind=8) :: co,rcomp
- integer :: kkk,i,j,i1,i2,it1,it2,iti,itj
+ integer :: kkk,i,j,i1,i2,it1,it2,iti,itj,inum,jnum
ncont=0
kkk=3
- do i=nnt+kkk,nct
- iti=iabs(itype(i))
+ do i=nnt_molec(1)+kkk,nct_molec(1)
+ iti=iabs(itype(i,molnum(i)))
+ if (molnum(i).lt.3) then
+ inum=i+nres
+ else
+ inum=i
+ endif
+
do j=nnt,i-kkk
- itj=iabs(itype(j))
+ itj=iabs(itype(j,molnum(i)))
+ if (molnum(j).lt.3) then
+ jnum=j+nres
+ else
+ jnum=j
+ endif
if (ipot.ne.4) then
! rcomp=sigmaii(iti,itj)+1.0D0
rcomp=facont*sigmaii(iti,itj)
endif
! rcomp=6.5D0
! print *,'rcomp=',rcomp,' dist=',dist(nres+i,nres+j)
- if (dist(nres+i,nres+j).lt.rcomp) then
+ if (dist(inum,jnum).lt.rcomp) then
ncont=ncont+1
+ if (ncont.gt.nres*100) ncont=nres*100
icont(1,ncont)=i
icont(2,ncont)=j
endif
do i=1,ncont
i1=icont(1,i)
i2=icont(2,i)
- it1=itype(i1)
- it2=itype(i2)
+ it1=itype(i1,1)
+ it2=itype(i2,1)
write (iout,'(i3,2x,a,i4,2x,a,i4)') &
- i,restyp(it1),i1,restyp(it2),i2
+ i,restyp(it1,1),i1,restyp(it2,1),i2
enddo
endif
co = 0.0d0
! include 'DIMENSIONS'
! include 'COMMON.IOUNITS'
integer :: ncont,ncont_ref
- integer,dimension(2,12*nres) :: icont,icont_ref !(2,12*nres) (2,maxcont) (maxcont=12*maxres)
+ integer,dimension(2,100*nres) :: icont,icont_ref !(2,100*nres) (2,maxcont) (maxcont=12*maxres)
!el local variables
integer :: i,j,nmatch
nmatch=0
! include 'DIMENSIONS'
! include 'COMMON.IOUNITS'
integer :: ncont,ncont_ref
- integer,dimension(2,12*nres) :: icont,icont_ref !(2,12*nres) (2,maxcont) (maxcont=12*maxres)
+ integer,dimension(2,100*nres) :: icont,icont_ref !(2,100*nres) (2,maxcont) (maxcont=12*maxres)
!el local variables
integer :: i,j,nmatch
nmatch=0
! include 'COMMON.FFIELD'
! include 'COMMON.NAMES'
integer :: ncont
- integer,dimension(2,12*nres) :: icont !(2,maxcont) (maxcont=12*maxres)
+ integer,dimension(:,:),allocatable :: icont !(2,maxcont) (maxcont=12*maxres)
integer :: nharp
- integer,dimension(4,nres/3) :: iharp !(4,nres/3)(4,maxres/3)
+ integer,dimension(4,nres) :: iharp !(4,nres/3)(4,maxres/3)
logical :: lprint,not_done
real(kind=8) :: rcomp=6.0d0
!el local variables
integer :: i,j,kkk,k,i1,i2,it1,it2,j1,ii1,jj1
-! allocate(icont(2,12*nres))
-
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
ncont=0
kkk=0
! print *,'nnt=',nnt,' nct=',nct
- do i=nnt,nct-3
+ do i=nnt_molec(1),nct_molec(1)-3
do k=1,3
c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
enddo
do i=1,ncont
i1=icont(1,i)
i2=icont(2,i)
- it1=itype(i1)
- it2=itype(i2)
+ it1=itype(i1,1)
+ it2=itype(i2,1)
write (iout,'(i3,2x,a,i4,2x,a,i4)') &
- i,restyp(it1),i1,restyp(it2),i2
+ i,restyp(it1,1),i1,restyp(it2,1),i2
enddo
endif
! finding hairpins
ii1=iharp(3,i)
jj1=iharp(4,i)
write (iout,*)
- write (iout,'(20(a,i3,1x))') (restyp(itype(k)),k,k=i1,ii1)
- write (iout,'(20(a,i3,1x))') (restyp(itype(k)),k,k=j1,jj1,-1)
+ write (iout,'(20(a,i3,1x))') (restyp(itype(k,1),1),k,k=i1,ii1)
+ write (iout,'(20(a,i3,1x))') (restyp(itype(k,1),1),k,k=j1,jj1,-1)
! do k=jj1,j1,-1
-! write (iout,'(a,i3,$)') restyp(itype(k)),k
+! write (iout,'(a,i3,$)') restyp(itype(k,1)),k
! enddo
enddo
endif
real(kind=8) :: ael6_i,ael3_i
real(kind=8),dimension(2,2) :: app_,bpp_,rpp_
integer :: ncont
- integer,dimension(2,12*nres) :: icont !(2,12*nres)(2,maxcont) (maxcont=12*maxres)
- real(kind=8),dimension(12*nres) :: econt !(maxcont)
+ integer,dimension(:,:),allocatable :: icont !(2,100*nres)(2,maxcont) (maxcont=12*maxres)
+ real(kind=8),dimension(:),allocatable :: econt !(maxcont)
!el local variables
integer :: i,j,k,iteli,itelj,i1,i2,it1,it2,ic1,ic2
real(kind=8) :: elcutoff,elecutoff_14,rri,ees,evdw
data elpp_6 /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
data elpp_3 / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
-!el allocate(econt(12*nres)) !(maxcont)
-
+!el allocate(econt(100*nres)) !(maxcont)
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
+ if (.not.allocated(econt)) then
+ allocate(econt(100*nres_molec(1)+1))
+ endif
elcutoff = -0.3d0
elecutoff_14 = -0.5d0
if (lprint) write (iout,'(a)') &
ncont=0
ees=0.0
evdw=0.0
- do 1 i=nnt,nct-2
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) goto 1
+! print *, "nntt,nct",nnt,nct-2
+ do 1 i=nnt_molec(1),nct_molec(1)-2
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) goto 1
xi=c(1,i)
yi=c(2,i)
zi=c(3,i)
ymedi=yi+0.5*dyi
zmedi=zi+0.5*dzi
do 4 j=i+2,nct-1
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) goto 4
+ if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) goto 4
iteli=itel(i)
itelj=itel(j)
if (j.eq.i+2 .and. itelj.eq.2) iteli=2
do i=1,ncont
i1=icont(1,i)
i2=icont(2,i)
- it1=itype(i1)
- it2=itype(i2)
+ it1=itype(i1,1)
+ it2=itype(i2,1)
write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
- i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ i,restyp(it1,1),i1,restyp(it2,1),i2,econt(i)
enddo
endif
! For given residues keep only the contacts with the greatest energy.
do i=1,ncont
i1=icont(1,i)
i2=icont(2,i)
- it1=itype(i1)
- it2=itype(i2)
+ it1=itype(i1,1)
+ it2=itype(i2,1)
write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)') &
- i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ i,restyp(it1,1),i1,restyp(it2,1),i2,econt(i)
enddo
endif
return
! include 'COMMON.CONTROL'
integer :: ncont,i,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,nhelix,&
iii1,jjj1
- integer,dimension(2,12*nres) :: icont !(2,maxcont) (maxcont=12*maxres)
- integer,dimension(nres,4) :: isec !(maxres,4)
+ integer,dimension(:,:),allocatable :: icont !(2,maxcont) (maxcont=12*maxres)
+ integer,dimension(nres,0:4) :: isec !(maxres,4)
integer,dimension(nres) :: nsec !(maxres)
logical :: lprint,not_done !,freeres
real(kind=8) :: p1,p2
!el external freeres
-!el allocate(icont(2,12*nres),isec(nres,4),nsec(nres))
-
- if(.not.dccart) call chainbuild
+!el allocate(icont(2,100*nres),isec(nres,4),nsec(nres))
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres+1))
+ endif
+ if(.not.dccart) call chainbuild_cart
if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
!d call write_pdb(99,'sec structure',0d0)
ncont=0
enddo
call elecont(lprint,ncont,icont)
+! print *,"after elecont"
+ if (nres_molec(1).eq.0) return
! finding parallel beta
!d write (iout,*) '------- looking for parallel beta -----------'
write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
write(12,'(a20)') "XMacStand ribbon.mac"
-
+ if (nres_molec(1).eq.0) return
write(iout,*) 'UNRES seq:'
do j=1,nbfrag
write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
! & obr,non_conv)
! rms=dsqrt(rms)
call rmsd(rms)
+! print *,"before contact"
!elte(iout,*) "rms_nacc before contact"
call contact(.false.,ncont,icont,co)
frac=contact_fract(ncont,ncont_ref,icont,icont_ref)
!el local variables
real(kind=8) :: drms,rminroz,roznica
- integer :: i,j,iatom,kkk,iti,k
+ integer :: i,j,iatom,kkk,iti,k,mnum
!el allocate(ccopy(3,2*nres+2),crefcopy(3,2*nres+2)) !(3,maxres2+2) maxres2=2*maxres
do kkk=1,nperm
! do i=nz_start,nz_end
! iatom=iatom+1
-! iti=itype(i)
+! iti=itype(i,1)
! do k=1,3
! ccopy(k,iatom)=c(k,i+nstart_seq-nstart_sup)
! crefcopy(k,iatom,kkk)=cref(k,i,kkk)
! else
! do kkk=1,nperm
iatom=0
+! print *,nz_start,nz_end,nstart_seq-nstart_sup
do i=nz_start,nz_end
+! iatom=iatom+1
+ iti=itype(i+nstart_seq-nstart_sup,molnum(i))
+ if (iti.eq.ntyp1_molec(molnum(i))) cycle
iatom=iatom+1
- iti=itype(i)
+ mnum=molnum(i+nstart_seq-nstart_sup)
do k=1,3
ccopy(k,iatom)=c(k,i+nstart_seq-nstart_sup)
crefcopy(k,iatom)=cref(k,i,kkk)
enddo
- if (iz_sc.eq.1.and.iti.ne.10) then
+ if (iz_sc.eq.1.and.iti.ne.10.and.mnum.lt.4) then
iatom=iatom+1
do k=1,3
ccopy(k,iatom)=c(k,nres+i+nstart_seq-nstart_sup)
iatom=0
do i=nz_start,nz_end
iatom=iatom+1
- iti=itype(i)
+ iti=itype(i,1)
do k=1,3
ccopy(k,iatom)=c(k,i)
crefcopy(k,iatom)=crefjlee(k,i)
! include 'COMMON.IOUNITS'
! include 'COMMON.DISTFIT'
- integer :: ncont,icont(2,nres*nres/2),isec(nres,3)
+ integer :: ncont,isec(nres,3)
logical :: lprint,not_done
- real(kind=4) :: dcont(nres*nres/2),d
+ real(kind=4) :: d
real(kind=4) :: rcomp = 7.0
real(kind=4) :: rbeta = 5.2
real(kind=4) :: ralfa = 5.2
real(kind=8),dimension(3) :: xpi,xpj
integer :: i,k,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,iii1,jjj1,&
nhelix
- call chainbuild
+ integer, dimension(:,:),allocatable :: icont
+ real(kind=4),dimension(:),allocatable :: dcont
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
+ if (.not.allocated(dcont)) then
+ allocate(dcont(100*nres_molec(1)+1))
+ endif
+ call chainbuild_cart
!d call write_pdb(99,'sec structure',0d0)
ncont=0
nbfrag=0
(xpi(2)-xpj(2))*(xpi(2)-xpj(2)) + &
(xpi(3)-xpj(3))*(xpi(3)-xpj(3))
if ( d.lt.rcomp*rcomp) then
+ if (ncont.gt.(100*nres_molec(1)+1)) ncont=100*nres_molec(1)+1
ncont=ncont+1
icont(1,ncont)=i
icont(2,ncont)=j
c(j,i)=cart_base(j,i+ist,ii)
! cref(j,i)=c(j,i)
enddo
-!d write (iout,'(a,i4,3f10.5)') restyp(itype(i)),i,(c(j,i),j=1,3)
+!d write (iout,'(a,i4,3f10.5)') restyp(itype(i,1)),i,(c(j,i),j=1,3)
enddo
!d call fitsq(rms,c(1,nnt),cref(1,nnt),nct-nnt+1,przes,obr,
!d non_conv)
!d write (iout,'(a,f10.5)')
!d & 'Initial RMS deviation from reference structure:',rms
- if (itype(nres).eq.ntyp1) then
+ if (itype(nres,1).eq.ntyp1) then
do j=1,3
dcj=c(j,nres-2)-c(j,nres-3)
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
endif
- if (itype(1).eq.ntyp1) then
+ if (itype(1,1).eq.ntyp1) then
do j=1,3
dcj=c(j,4)-c(j,3)
c(j,1)=c(j,2)-dcj
link_end0=link_end
link_end=min0(link_end,nss)
do i=nnt,nct
- if (itype(i).ne.10) then
-!d print *,'i=',i,' itype=',itype(i),' theta=',theta(i+1)
- call gen_side(itype(i),theta(i+1),alph(i),omeg(i),fail)
+ if (itype(i,1).ne.10) then
+!d print *,'i=',i,' itype=',itype(i,1),' theta=',theta(i+1)
+ call gen_side(itype(i,1),theta(i+1),alph(i),omeg(i),fail,1)
endif
enddo
call chainbuild
glycine=.true.
do while(glycine)
ind_sc=iran_num(nnt,nct)
- glycine=(itype(ind_sc).eq.10)
+ glycine=(itype(ind_sc,1).eq.10)
enddo
alph0=alph(ind_sc)
omeg0=omeg(ind_sc)
- call gen_side(itype(ind_sc),theta(ind_sc+1),alph(ind_sc),&
- omeg(ind_sc),fail)
+ call gen_side(itype(ind_sc,1),theta(ind_sc+1),alph(ind_sc),&
+ omeg(ind_sc),fail,1)
call chainbuild
call etotal(energia)
!d write (iout,'(a,i5,a,i4,2(a,f8.3),2(a,1pe14.5))')
if(.not.allocated(bfrag)) allocate(bfrag(4,nres/3)) !(4,maxres/3)
if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
! COMMON /WAGI/
- allocate(w(maxres22),d0(maxres22)) !(maxres22)
+#ifndef FIVEDIAG
+ if(.not.allocated(w)) allocate(w(maxres22),d0(maxres22)) !(maxres22)
! COMMON /POCHODNE/
!el allocate(DRDG(maxres22,maxres22)) !(MAXRES22,MAXRES)
- allocate(DDD(maxres22)) !(maxres22)
- allocate(H(nres,nres)) !(MAXRES,MAXRES)
- allocate(XX(nres)) !(MAXRES)
+ if (.not.allocated(DDD)) allocate(DDD(maxres22)) !(maxres22)
+ if (.not.allocated(H)) allocate(H(nres,nres)) !(MAXRES,MAXRES)
+#endif
+ if (.not.allocated(XX)) allocate(XX(nres)) !(MAXRES)
! COMMON /frozen/
- allocate(mask(nres)) !(maxres)
+ if (.not.allocated(mask)) allocate(mask(nres)) !(maxres)
! common.thread
! common /thread/
- allocate(iexam(2,maxthread),ipatt(2,maxthread)) !(2,maxthread)
+ if (.not.allocated(iexam))allocate(iexam(2,maxthread),ipatt(2,maxthread)) !(2,maxthread)
! common /thread1/
- allocate(ener0(n_ene+2,maxthread),ener(n_ene+2,maxthread)) !(n_ene+2,maxthread)
+ if (.not.allocated(ener0)) allocate(ener0(n_ene+2,maxthread),ener(n_ene+2,maxthread)) !(n_ene+2,maxthread)
return
end subroutine alloc_compare_arrays
projects / unres4.git / blobdiff