character*80 card
dimension sccor(3,20)
integer rescode
- call permut(symetr)
+c call permut(symetr)
ibeg=1
+ write(iout,*) 'pdbread'
do
read (ipdbin,'(a80)',end=10) card
if (card(:3).eq.'END') then
goto 10
else if (card(:3).eq.'TER') then
C End current chain
- ires_old=ires+1
- itype(ires_old)=21
+ 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)
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
nres=ires
do i=2,nres-1
c write (iout,*) i,itype(i)
- if (itype(i).eq.21) then
+ if (itype(i).eq.ntyp1) then
+ if (itype(i+1).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 do j=1,3
+C 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
+C dc(j,i)=c(j,i)
+C enddo
+ 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
+ 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
& ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
& (c(j,nres+ires),j=1,3)
enddo
+ call int_from_cart1(.false.)
call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.true.)
+ write (iout,*) "After int_from_cart"
+ call flush(iout)
do i=1,nres-1
do j=1,3
dc(j,i)=c(j,i+1)-c(j,i)
c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
c & vbld_inv(i+nres)
enddo
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+c
+ phi_ref(i)=phi(i)
+ theta_ref(i)=theta(i)
+ alph_ref(i)=alph(i)
+ omeg_ref(i)=omeg(i)
+ enddo
+
c call chainbuild
C Copy the coordinates to reference coordinates
- do i=1,2*nres
+c do i=1,2*nres
+c do j=1,3
+c cref(j,i)=c(j,i)
+c enddo
+c enddo
+
+ kkk=1
+ lll=0
+ cou=1
+ do i=1,nres
+ 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).and.(i.gt.2)) then
+ chain_length=lll-1
+ kkk=kkk+1
+c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+ lll=1
+ endif
+ endif
do j=1,3
- cref(j,i)=c(j,i)
+ cref(j,i,cou)=c(j,i)
+ cref(j,i+nres,cou)=c(j,i+nres)
+ if (i.le.nres) then
+ chain_rep(j,lll,kkk)=c(j,i)
+ chain_rep(j,lll+nres,kkk)=c(j,i+nres)
+ endif
+ enddo
+ enddo
+ do j=1,3
+ chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
+ chain_rep(j,chain_length+nres,symetr)
+ &=chain_rep(j,chain_length+nres,1)
+ enddo
+
+ if (symetr.gt.1) then
+ call permut(symetr)
+ nperm=1
+ do i=1,symetr
+ nperm=nperm*i
+ enddo
+c do i=1,nperm
+c write(iout,*) "tabperm", (tabperm(i,kkk),kkk=1,4)
+c enddo
+ do i=1,nperm
+ cou=0
+ do kkk=1,symetr
+ icha=tabperm(i,kkk)
+c write (iout,*) i,icha
+ do lll=1,chain_length
+ cou=cou+1
+ if (cou.le.nres) then
+ do j=1,3
+ kupa=mod(lll,chain_length)
+ iprzes=(kkk-1)*chain_length+lll
+ if (kupa.eq.0) kupa=chain_length
+c write (iout,*) "kupa", kupa
+ cref(j,iprzes,i)=chain_rep(j,kupa,icha)
+ cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
+ enddo
+ endif
+ enddo
enddo
+ enddo
+ endif
+
+C-koniec robienia kopidm
+ nperm=0
+ do kkk=1,nperm
+ write (iout,*) "nowa struktura", nperm
+ do i=1,nres
+ write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
+ &cref(2,i,kkk),
+ &cref(3,i,kkk),cref(1,nres+i,kkk),
+ &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
enddo
+ 100 format (//' alpha-carbon coordinates ',
+ & ' centroid coordinates'/
+ 1 ' ', 6X,'X',11X,'Y',11X,'Z',
+ & 10X,'X',11X,'Y',11X,'Z')
+ 110 format (a,'(',i3,')',6f12.5)
+ enddo
+
ishift_pdb=ishift
return
do i=nnt+1,nct
iti=itype(i)
c write (iout,*) i,dist(i,i-1)
- if (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0) then
+ if ((dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0)
+ &.and.(iti.ne.ntyp1).and.(itype(i-1).ne.ntyp1)) then
write (iout,'(a,i4)') 'Bad Cartesians for residue',i
stop
endif
endif
return
end
+
+c-------------------------------------------------------------------------------
+ subroutine sc_loc_geom(lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SETUP'
+ double precision x_prime(3),y_prime(3),z_prime(3)
+ logical lprn
+ do i=1,nres-1
+ do j=1,3
+ dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
+ enddo
+ enddo
+ do i=2,nres-1
+ if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ do j=1,3
+ dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
+ enddo
+ else
+ do j=1,3
+ dc_norm(j,i+nres)=0.0d0
+ enddo
+ endif
+ enddo
+ do i=2,nres-1
+ costtab(i+1) =dcos(theta(i+1))
+ sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+ cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+ sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+ cosfac2=0.5d0/(1.0d0+costtab(i+1))
+ cosfac=dsqrt(cosfac2)
+ sinfac2=0.5d0/(1.0d0-costtab(i+1))
+ sinfac=dsqrt(sinfac2)
+ it=itype(i)
+ if (it.ne.10 .and. itype(i).ne.ntyp1) then
+c
+C Compute the axes of tghe local cartesian coordinates system; store in
+c x_prime, y_prime and z_prime
+c
+ do j=1,3
+ x_prime(j) = 0.00
+ y_prime(j) = 0.00
+ z_prime(j) = 0.00
+ enddo
+ do j = 1,3
+ x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+ y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+ enddo
+ call vecpr(x_prime,y_prime,z_prime)
+c
+C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
+C to local coordinate system. Store in xx, yy, zz.
+c
+ xx=0.0d0
+ yy=0.0d0
+ zz=0.0d0
+ do j = 1,3
+ xx = xx + x_prime(j)*dc_norm(j,i+nres)
+ yy = yy + y_prime(j)*dc_norm(j,i+nres)
+ zz = zz + z_prime(j)*dc_norm(j,i+nres)
+ enddo
+
+ xxref(i)=xx
+ yyref(i)=yy
+ zzref(i)=zz
+ else
+ xxref(i)=0.0d0
+ yyref(i)=0.0d0
+ zzref(i)=0.0d0
+ endif
+ enddo
+ if (lprn) then
+ do i=2,nres
+ iti=itype(i)
+ if(me.eq.king.or..not.out1file)
+ & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
+ & yyref(i),zzref(i)
+ enddo
+ endif
+ return
+ end
c---------------------------------------------------------------------------
subroutine sccenter(ires,nscat,sccor)
implicit real*8 (a-h,o-z)
projects / unres.git / blobdiff