subroutine readpdb
C Read the PDB file and convert the peptide geometry into virtual-chain
C geometry.
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.NAMES'
include 'COMMON.CONTROL'
- include 'COMMON.DISTFIT'
+ include 'COMMON.FRAG'
include 'COMMON.SETUP'
include 'COMMON.SBRIDGE'
character*3 seq,atom,res
character*80 card
- dimension sccor(3,50)
+ double precision sccor(3,50)
double precision e1(3),e2(3),e3(3)
integer rescode,iterter(maxres),cou
logical fail
+ integer i,j,iii,ires,ires_old,ishift,ibeg
+ double precision dcj
bfac=0.0d0
do i=1,maxres
iterter(i)=0
return
end
c---------------------------------------------------------------------------
- subroutine int_from_cart(lside,lprn)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
-#ifdef MPI
- include "mpif.h"
-#endif
- 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'
- character*3 seq,atom,res
- character*80 card
- dimension sccor(3,50)
- integer rescode
- logical lside,lprn
-#ifdef MPI
- if(me.eq.king.or..not.out1file)then
-#endif
- if (lprn) then
- write (iout,'(/a)')
- & 'Internal coordinates calculated from crystal structure.'
- if (lside) then
- write (iout,'(8a)') ' Res ',' dvb',' Theta',
- & ' Phi',' Dsc_id',' Dsc',' Alpha',
- & ' Omega'
- else
- write (iout,'(4a)') ' Res ',' dvb',' Theta',
- & ' Phi'
- endif
- endif
-#ifdef MPI
- endif
-#endif
- do i=1,nres-1
- iti=itype(i)
- if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
- & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
- write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-ctest stop
- endif
- vbld(i+1)=dist(i,i+1)
- vbld_inv(i+1)=1.0d0/vbld(i+1)
-c write (iout,*) "i",i+1," vbld",vbld(i+1)," vbld_inv",
-c & vbld_inv(i+1)
- if (i.gt.1) 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
-c if (unres_pdb) then
-c if (itype(1).eq.21) then
-c theta(3)=90.0d0*deg2rad
-c phi(4)=180.0d0*deg2rad
-c vbld(2)=3.8d0
-c vbld_inv(2)=1.0d0/vbld(2)
-c endif
-c if (itype(nres).eq.21) then
-c theta(nres)=90.0d0*deg2rad
-c phi(nres)=180.0d0*deg2rad
-c vbld(nres)=3.8d0
-c vbld_inv(nres)=1.0d0/vbld(2)
-c endif
-c endif
-c print *,"A TU2"
- if (lside) then
- do i=2,nres-1
- do j=1,3
- c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
- & +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
- enddo
- iti=itype(i)
- di=dist(i,nres+i)
- vbld(i+nres)=di
- if (itype(i).ne.10) then
- vbld_inv(i+nres)=1.0d0/di
- else
- vbld_inv(i+nres)=0.0d0
- endif
- if (iti.ne.10) then
- alph(i)=alpha(nres+i,i,maxres2)
- omeg(i)=beta(nres+i,i,maxres2,i+1)
- endif
- if(me.eq.king.or..not.out1file)then
- if (lprn)
- & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
- & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
- & rad2deg*alph(i),rad2deg*omeg(i)
- endif
- enddo
- if (lprn) then
- i=nres
- iti=itype(nres)
- write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
- & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
- & rad2deg*alph(i),rad2deg*omeg(i)
- endif
- else if (lprn) then
- do i=2,nres
- iti=itype(i)
- if(me.eq.king.or..not.out1file)
- & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
- & rad2deg*theta(i),rad2deg*phi(i)
- enddo
- endif
- return
- end
-c-------------------------------------------------------------------------------
- subroutine sc_loc_geom(lprn)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
-#ifdef MPI
- include "mpif.h"
-#endif
- 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
-c write (iout,*) "i",i," dc",(dc_norm(j,i),j=1,3),
-c & " vbld",vbld_inv(i+1)
- 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
-c write (iout,*) "i",i," dc",(dc_norm(j,i+nres),j=1,3),
-c & " vbld",vbld_inv(i+nres)
- 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)
-c write (iout,*) "i",i," costab",costtab(i+1),
-c & " sintab",sinttab(i+1)
-c write (iout,*) "dc_norm_b",(dc_norm(j,i-1),j=1,3)
-c write (iout,*) "dc_norm_s",(dc_norm(j,i+nres),j=1,3)
- 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
-c write (iout,*) "x_prime",(x_prime(j),j=1,3)
-c write (iout,*) "y_prime",(y_prime(j),j=1,3)
- call vecpr(x_prime,y_prime,z_prime)
-c write (iout,*) "z_prime",(z_prime(j),j=1,3)
-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
-#ifdef MPI
- if (me.eq.king.or..not.out1file) then
-#endif
- write (iout,*) "xxref,yyref,zzref"
- do i=2,nres
- write (iout,'(a3,i4,3f10.5)')
- & restyp(itype(i)),i,xxref(i),yyref(i),zzref(i)
- enddo
-#ifdef MPI
- endif
-#endif
- endif
- return
- end
-c---------------------------------------------------------------------------
- subroutine sccenter(ires,nscat,sccor)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CHAIN'
- dimension sccor(3,50)
- do j=1,3
- sccmj=0.0D0
- do i=1,nscat
- sccmj=sccmj+sccor(j,i)
- enddo
- dc(j,ires)=sccmj/nscat
- enddo
- return
- end
-c---------------------------------------------------------------------------
- subroutine bond_regular
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.VAR'
- include 'COMMON.LOCAL'
- include 'COMMON.CALC'
- include 'COMMON.INTERACT'
- include 'COMMON.CHAIN'
- do i=1,nres-1
- vbld(i+1)=vbl
- vbld_inv(i+1)=vblinv
- vbld(i+1+nres)=dsc(iabs(itype(i+1)))
- vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
-c print *,vbld(i+1),vbld(i+1+nres)
- enddo
-c Adam 2/26/20 Alter virtual bonds for non-blocking end groups of each chain
- do i=1,nchain
- i1=chain_border(1,i)
- i2=chain_border(2,i)
- if (i1.gt.1) then
- vbld(i1)=vbld(i1)/2
- vbld_inv(i1)=vbld_inv(i1)*2
- endif
- if (i2.lt.nres) then
- vbld(i2+1)=vbld(i2+1)/2
- vbld_inv(i2+1)=vbld_inv(i2+1)*2
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------------
subroutine readpdb_template(k)
C Read the PDB file for read_constr_homology with read2sigma
C and convert the peptide geometry into virtual-chain geometry.
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.NAMES'
include 'COMMON.CONTROL'
- include 'COMMON.DISTFIT'
+ include 'COMMON.FRAG'
include 'COMMON.SETUP'
- integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
- & ishift_pdb
+ integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
+ & ishift_pdb,ires_ca
logical lprn /.false./,fail
double precision e1(3),e2(3),e3(3)
double precision dcj,efree_temp
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
- & "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
+ & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
do ires=1,nres
- write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
+ write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
& restyp(itype(ires)),ires,(c(j,ires),j=1,3),
& (c(j,ires+nres),j=1,3)
enddo
projects / unres.git / blobdiff