include 'COMMON.NAMES'
character*3 seq,atom,res
character*80 card
- double precision sccor(3,20)
+ double precision sccor(3,50)
integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
double precision dcj
integer rescode,kkk,lll,icha,cou,kupa,iprzes
goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
- itype(ires_old)=21
+c ires_old=ires+1
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ itype(ires_old)=ntyp1
ibeg=2
c write (iout,*) "Chain ended",ires,ishift,ires_old
call sccenter(ires,iii,sccor)
endif
C Start new residue.
c write (iout,'(a80)') card
- read (card(24:26),*) ires
+ read (card(23:26),*) ires
read (card(18:20),'(a3)') res
if (ibeg.eq.1) then
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
- itype(1)=21
+ itype(1)=ntyp1
endif
c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
ibeg=0
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
- else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ & atom(1:1).ne.'Q' .and. atom(1:2).ne.'1H' .and.
+ & atom(1:2).ne.'2H' .and. atom(1:2).ne.'3H' .and.
& atom.ne.'N ' .and. atom.ne.'C ') then
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) 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
+
+ if (itype(i).eq.ntyp1) then
+ if (itype(i+1).eq.ntyp1) 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
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the last dummy residue
+C call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif !fail
+C do j=1,3
+C c(j,i)=c(j,i-1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+C endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+C if (unres_pdb) then
+C 2/15/2013 by Adam: corrected insertion of the first dummy residue
+C call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+C if (fail) then
+C e2(1)=0.0d0
+C e2(2)=1.0d0
+C e2(3)=0.0d0
+C endif
+C do j=1,3
+C c(j,i)=c(j,i+1)-1.9d0*e2(j)
+C enddo
+C else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+C endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
enddo
C Calculate the CM of the last side chain.
call sccenter(ires,iii,sccor)
nstart_sup=1
if (itype(nres).ne.10) then
nres=nres+1
- itype(nres)=21
+ itype(nres)=ntyp1
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
c(j,nres+1)=c(j,1)
c(j,2*nres)=c(j,nres)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
nsup=nsup-1
nstart_sup=2
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.21) then
+ if ((itype(i-1).eq.ntyp1).and.(i.gt.2).and.(i.ne.nres)) then
chain_length=lll-1
kkk=kkk+1
c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
endif
enddo
enddo
+ if (chain_length.eq.0) chain_length=nres
+ write (iout,*) chain_length
do j=1,3
chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
chain_rep(j,chain_length+nres,symetr)
do i=2,nres
iti=itype(i)
write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
- if (itype(i-1).ne.21 .and. itype(i).ne.21 .and.
- & (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0)) then
+ if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and.
+ & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
stop
endif
theta(i+1)=alpha(i-1,i,i+1)
if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
enddo
- if (itype(1).eq.21) then
+ if (itype(1).eq.ntyp1) then
do j=1,3
c(j,1)=c(j,2)+(c(j,3)-c(j,4))
enddo
endif
- if (itype(nres).eq.21) then
+ if (itype(nres).eq.ntyp1) then
do j=1,3
c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
enddo
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