include 'COMMON.CONTROL'
include 'COMMON.DISTFIT'
include 'COMMON.SETUP'
- character*3 seq,atom,res
- character*80 card
- dimension sccor(3,20)
+ integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
+ & ishift_pdb
+ logical lprn /.false./,fail
double precision e1(3),e2(3),e3(3)
- logical fail
+ double precision dcj,efree_temp
+ character*3 seq,res
+ character*5 atom
+ character*80 card
+ double precision sccor(3,20)
integer rescode
+ efree_temp=0.0d0
ibeg=1
+ ishift1=0
+ ishift=0
+c write (2,*) "UNRES_PDB",unres_pdb
+ ires=0
+ ires_old=0
+ iii=0
lsecondary=.false.
nhfrag=0
nbfrag=0
do i=1,10000
read (ipdbin,'(a80)',end=10) card
+c write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
crc----------------------------------------
endif
if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+c Read free energy
+ if (index(card,"FREE ENERGY").gt.0) read(card(35:),*) efree_temp
C Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
- read (card(14:16),'(a3)') atom
- if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ read (card(12:16),*) atom
+c write (iout,*) "! ",atom," !",ires
+c if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ read (card(23:26),*) ires
+ read (card(18:20),'(a3)') res
+c write (iout,*) "ires",ires,ires-ishift+ishift1,
+c & " ires_old",ires_old
+c write (iout,*) "ishift",ishift," ishift1",ishift1
+c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+ if (ires-ishift+ishift1.ne.ires_old) then
C Calculate the CM of the preceding residue.
+c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
if (ibeg.eq.0) then
+c write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires)=sccor(j,iii)
enddo
else
- call sccenter(ires,iii,sccor)
+ call sccenter(ires_old,iii,sccor)
endif
+ iii=0
endif
C Start new residue.
- read (card(24:26),*) ires
- read (card(18:20),'(a3)') res
- if (ibeg.eq.1) then
+ if (res.eq.'Cl-' .or. res.eq.'Na+') then
+ ires=ires_old
+ cycle
+ else if (ibeg.eq.1) then
+c write (iout,*) "BEG ires",ires
ishift=ires-1
if (res.ne.'GLY' .and. res.ne. 'ACE') then
ishift=ishift-1
itype(1)=21
endif
+ ires=ires-ishift+ishift1
+ ires_old=ires
+c write (iout,*) "ishift",ishift," ires",ires,
+c & " ires_old",ires_old
ibeg=0
+ else
+ ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+ ires=ires-ishift+ishift1
+ ires_old=ires
endif
- ires=ires-ishift
- if (res.eq.'ACE') then
- ity=10
+ if (res.eq.'ACE' .or. res.eq.'NHE') then
+ itype(ires)=10
else
itype(ires)=rescode(ires,res,0)
endif
+ else
+ ires=ires-ishift+ishift1
+ endif
+c write (iout,*) "ires_old",ires_old," ires",ires
+ if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+c ishift1=ishift1+1
+ endif
+c write (2,*) "ires",ires," res ",res," ity",ity
+ if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
+ & res.eq.'NHE'.and.atom(:2).eq.'HN') then
read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
-c if(me.eq.king.or..not.out1file)
-c & write (iout,'(2i3,2x,a,3f8.3)')
-c & ires,itype(ires),res,(c(j,ires),j=1,3)
- iii=1
+c write (iout,*) "backbone ",atom
+#ifdef DEBUG
+ write (iout,'(2i3,2x,a,3f8.3)')
+ & ires,itype(ires),res,(c(j,ires),j=1,3)
+#endif
+ iii=iii+1
do j=1,3
sccor(j,iii)=c(j,ires)
enddo
- else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
- & atom.ne.'N ' .and. atom.ne.'C ') then
+ if (ishift.ne.0) then
+ ires_ca=ires+ishift-ishift1
+ else
+ ires_ca=ires
+ endif
+c write (*,*) card(23:27),ires,itype(ires)
+ else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N' .and. atom.ne.'C' .and.
+ & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+ & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+c write (iout,*) "sidechain ",atom
iii=iii+1
read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
endif
endif
enddo
- 10 if(me.eq.king.or..not.out1file)
- & write (iout,'(a,i5)') ' Nres: ',ires
+ 10 continue
+#ifdef DEBUG
+ write (iout,'(a,i5)') ' Number of residues found: ',ires
+#endif
+ if (ires.eq.0) return
C Calculate the CM of the last side chain.
+ if (iii.gt.0) then
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires)=sccor(j,iii)
enddo
- else
+ else
call sccenter(ires,iii,sccor)
endif
+ endif
nres=ires
nsup=nres
nstart_sup=1
enddo
endif
endif
+C Copy the coordinates to reference coordinates
+c do i=1,2*nres
+c do j=1,3
+c cref(j,i)=c(j,i)
+c enddo
+c enddo
+C Calculate internal coordinates.
+ if (lprn) then
+ 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)"
+ do ires=1,nres
+ write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
+ & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
+ & (c(j,ires+nres),j=1,3)
+ enddo
+ endif
C Calculate internal coordinates.
if(me.eq.king.or..not.out1file)then
write (iout,'(a)')
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
-
+ ishift_pdb=ishift
return
end
c---------------------------------------------------------------------------
include 'COMMON.NAMES'
include 'COMMON.CONTROL'
include 'COMMON.SETUP'
- character*3 seq,atom,res
+ character*3 seq,res
+c character*5 atom
character*80 card
dimension sccor(3,20)
integer rescode
enddo
return
end
+ subroutine readpdb_template(k)
+C Read the PDB file with gaps for read_constr_homology with read2sigma
+C and convert the peptide geometry into virtual-chain geometry.
+ 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.DISTFIT'
+ include 'COMMON.SETUP'
+ include 'COMMON.MD'
+ integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
+ & ishift_pdb
+ logical lprn /.false./,fail
+ double precision e1(3),e2(3),e3(3)
+ double precision dcj,efree_temp
+ character*3 seq,res
+ character*5 atom
+ character*80 card
+ double precision sccor(3,20)
+ integer rescode
+ efree_temp=0.0d0
+ ibeg=1
+ ishift1=0
+ ishift=0
+c write (2,*) "UNRES_PDB",unres_pdb
+ ires=0
+ ires_old=0
+ iii=0
+ lsecondary=.false.
+ nhfrag=0
+ nbfrag=0
+ do i=1,10000
+ read (ipdbin,'(a80)',end=10) card
+c write (iout,'(a)') card
+ if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+C Fish out the ATOM cards.
+ if (index(card(1:4),'ATOM').gt.0) then
+ read (card(12:16),*) atom
+c write (iout,*) "! ",atom," !",ires
+c if (atom.eq.'CA' .or. atom.eq.'CH3') then
+ read (card(23:26),*) ires
+ read (card(18:20),'(a3)') res
+c write (iout,*) "ires",ires,ires-ishift+ishift1,
+c & " ires_old",ires_old
+c write (iout,*) "ishift",ishift," ishift1",ishift1
+c write (iout,*) "IRES",ires-ishift+ishift1,ires_old
+ if (ires-ishift+ishift1.ne.ires_old) then
+C Calculate the CM of the preceding residue.
+c if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+ if (ibeg.eq.0) then
+c write (iout,*) "Calculating sidechain center iii",iii
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires_old,iii,sccor)
+ endif
+ iii=0
+ endif
+C Start new residue.
+ if (res.eq.'Cl-' .or. res.eq.'Na+') then
+ ires=ires_old
+ cycle
+ else if (ibeg.eq.1) then
+c write (iout,*) "BEG ires",ires
+ ishift=ires-1
+ if (res.ne.'GLY' .and. res.ne. 'ACE') then
+ ishift=ishift-1
+ itype(1)=21
+ endif
+ ires=ires-ishift+ishift1
+ ires_old=ires
+c write (iout,*) "ishift",ishift," ires",ires,
+c & " ires_old",ires_old
+ ibeg=0
+ else
+ ishift=ishift-(ires-ishift+ishift1-ires_old-1)
+ ires=ires-ishift+ishift1
+ ires_old=ires
+ endif
+ if (res.eq.'ACE' .or. res.eq.'NHE') then
+ itype(ires)=10
+ else
+ itype(ires)=rescode(ires,res,0)
+ endif
+ else
+ ires=ires-ishift+ishift1
+ endif
+c write (iout,*) "ires_old",ires_old," ires",ires
+ if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+c ishift1=ishift1+1
+ endif
+c write (2,*) "ires",ires," res ",res," ity",ity
+ if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
+ & res.eq.'NHE'.and.atom(:2).eq.'HN') then
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+c write (iout,*) "backbone ",atom
+#ifdef DEBUG
+ write (iout,'(2i3,2x,a,3f8.3)')
+ & ires,itype(ires),res,(c(j,ires),j=1,3)
+#endif
+ iii=iii+1
+ do j=1,3
+ sccor(j,iii)=c(j,ires)
+ enddo
+ if (ishift.ne.0) then
+ ires_ca=ires+ishift-ishift1
+ else
+ ires_ca=ires
+ endif
+c write (*,*) card(23:27),ires,itype(ires)
+ else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N' .and. atom.ne.'C' .and.
+ & atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
+ & atom.ne.'OXT' .and. atom(:2).ne.'3H') then
+c write (iout,*) "sidechain ",atom
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
+ endif
+ enddo
+ 10 continue
+#ifdef DEBUG
+ write (iout,'(a,i5)') ' Number of residues found: ',ires
+#endif
+ if (ires.eq.0) return
+C Calculate the CM of the last side chain.
+ if (iii.gt.0) then
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
+ nres=ires
+ nsup=nres
+ nstart_sup=1
+ if (itype(nres).ne.10) then
+ nres=nres+1
+ itype(nres)=21
+ 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
+ do i=2,nres-1
+ do j=1,3
+ c(j,i+nres)=dc(j,i)
+ enddo
+ enddo
+ do j=1,3
+ c(j,nres+1)=c(j,1)
+ c(j,2*nres)=c(j,nres)
+ enddo
+ if (itype(1).eq.21) then
+ nsup=nsup-1
+ nstart_sup=2
+ if (unres_pdb) then
+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)-3.8d0*e2(j)
+ enddo
+ else
+ do j=1,3
+ dcj=c(j,4)-c(j,3)
+ c(j,1)=c(j,2)-dcj
+ c(j,nres+1)=c(j,1)
+ enddo
+ endif
+ endif
+C Calculate internal coordinates.
+ if (lprn) then
+ 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)"
+ do ires=1,nres
+ write (iout,'(a3,1x,i3,3f8.3,5x,3f8.3)')
+ & restyp(itype(ires)),ires,(c(j,ires),j=1,3),
+ & (c(j,ires+nres),j=1,3)
+ enddo
+ endif
+C Calculate internal coordinates.
+ if(me.eq.king.or..not.out1file)then
+ write (iout,'(a)')
+ & "Backbone and SC coordinates as read from the PDB"
+ do ires=1,nres
+ write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
+ & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
+ & (c(j,nres+ires),j=1,3)
+ enddo
+ endif
+ call int_from_cart(.true.,.false.)
+ call sc_loc_geom(.false.)
+ do i=1,nres
+ thetaref(i)=theta(i)
+ phiref(i)=phi(i)
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=2,nres-1
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+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
+c call chainbuild
+C Copy the coordinates to reference coordinates
+ do i=1,2*nres
+ do j=1,3
+ cref(j,i)=c(j,i)
+ chomo(j,i,k)=c(j,i)
+ enddo
+ enddo
+
+
+ ishift_pdb=ishift
+ return
+ end
projects / unres.git / blobdiff