character*3 seq,atom,res
character*80 card
dimension sccor(3,20)
- integer rescode
+ double precision e1(3),e2(3),e3(3)
+ integer rescode,iterter(maxres)
+ logical fail
+ do i=1,maxres
+ iterter(i)=0
+ enddo
ibeg=1
lsecondary=.false.
nhfrag=0
goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
itype(ires_old)=ntyp1
+ iterter(ires_old)=1
ibeg=2
-c write (iout,*) "Chain ended",ires,ishift,ires_old
+ write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
ires=ires-ishift
c write (2,*) "ires",ires," ishift",ishift
if (res.eq.'ACE') then
- ity=10
+ itype(ires)=10
else
itype(ires)=rescode(ires,res,0)
endif
C system
nres=ires
do i=2,nres-1
-c write (iout,*) i,itype(i)
- if (itype(i).eq.ntyp1) then
-c write (iout,*) "dummy",i,itype(i)
- do j=1,3
- c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
-c c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+ write (iout,*) i,itype(i),itype(i+1)
+ if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
+ if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
+C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ print *,i,'tu dochodze'
+ call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif !fail
+ print *,i,'a tu?'
+ do j=1,3
+ c(j,i)=c(j,i-1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+ if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
enddo
C Calculate the CM of the last side chain.
if (unres_pdb) then
nres=nres+1
itype(nres)=ntyp1
if (unres_pdb) then
- c(1,nres)=c(1,nres-1)+3.8d0
- c(2,nres)=c(2,nres-1)
- c(3,nres)=c(3,nres-1)
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+ call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
+ enddo
else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
nsup=nsup-1
nstart_sup=2
if (unres_pdb) then
- c(1,1)=c(1,2)-3.8d0
- c(2,1)=c(2,2)
- c(3,1)=c(3,2)
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(2,3,4,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,1)=c(j,2)-1.9d0*e2(j)
+ enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
lll=lll+1
cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
if (i.gt.1) then
- if ((itype(i-1).eq.ntyp1)) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
+ write (iout,*) chain_length
+ if (chain_length.eq.0) chain_length=nres
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
-
return
end
c---------------------------------------------------------------------------
projects / unres.git / blobdiff