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.SETUP'
include 'COMMON.FRAG'
- 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
+ include 'COMMON.SETUP'
+ include 'COMMON.SBRIDGE'
+ character*3 seq,atom,res
character*80 card
double precision sccor(3,50)
- integer rescode
- efree_temp=0.0d0
+ 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
+ enddo
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
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
if (card(:5).eq.'HELIX') then
nhfrag=nhfrag+1
lsecondary=.true.
bfrag(4,nbfrag)=bfrag(2,nbfrag)
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
+ if (card(:3).eq.'END') then
+ goto 10
+ else if (card(:3).eq.'TER') then
+C End current chain
+ ires_old=ires+2
+ itype(ires_old-1)=ntyp1
+ iterter(ires_old-1)=1
+ itype(ires_old)=ntyp1
+ iterter(ires_old)=1
+ ibeg=2
+ write (iout,*) "Chain ended",ires,ishift,ires_old
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
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
+ read (card(14:16),'(a3)') atom
+ if (atom.eq.'CA' .or. atom.eq.'CH3') 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)
+ dc(j,ires+nres)=sccor(j,iii)
enddo
else
- call sccenter(ires_old,iii,sccor)
+ call sccenter(ires,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
+c write (iout,'(a80)') card
+ 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)=ntyp1
endif
- ires=ires-ishift+ishift1
- ires_old=ires
-c write (iout,*) "ishift",ishift," ires",ires,
-c & " ires_old",ires_old
+c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
ibeg=0
- else
- ishift=ishift-(ires-ishift+ishift1-ires_old-1)
- ires=ires-ishift+ishift1
- ires_old=ires
+ else if (ibeg.eq.2) then
+c Start a new chain
+ ishift=-ires_old+ires-1
+c write (iout,*) "New chain started",ires,ishift
+ ibeg=0
endif
- if (res.eq.'ACE' .or. res.eq.'NHE') then
+ ires=ires-ishift
+c write (2,*) "ires",ires," ishift",ishift
+ if (res.eq.'ACE') 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
+ read(card(61:66),*) bfac(ires)
+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
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
+ else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N ' .and. atom.ne.'C ') then
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
+ 10 if(me.eq.king.or..not.out1file)
+ & write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
+ nres=ires
+ do i=2,nres-1
+c write (iout,*) i,itype(i),itype(i+1),ntyp1,iterter(i)
+ 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*(-e1(j)+e2(j))/sqrt(2.0d0)
+ 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
+ write (iout,*) "After loop in readpbd"
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
+ else
call sccenter(ires,iii,sccor)
endif
- endif
- nres=ires
nsup=nres
nstart_sup=1
if (itype(nres).ne.10) then
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ c(j,nres)=c(j,nres-1)+1.9d0*(-e1(j)+e2(j))/sqrt(2.0d0)
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
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
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
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)')
- & "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 flush(iout)
+c write(iout,*)"before int_from_cart nres",nres
call int_from_cart(.true.,.false.)
- call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
dc(j,i)=c(j,i+1)-c(j,i)
dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
enddo
+c write (iout,*) i,(dc(j,i),j=1,3),(dc_norm(j,i),j=1,3),
+c & vbld_inv(i+1)
enddo
do i=2,nres-1
do j=1,3
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
+ call sc_loc_geom(.false.)
+ call int_from_cart1(.false.)
c call chainbuild
C Copy the coordinates to reference coordinates
- do i=1,2*nres
+ do i=1,nres
do j=1,3
cref(j,i)=c(j,i)
+ cref(j,i+nres)=c(j,i+nres)
enddo
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)
+cc enddiag
do j=1,nbfrag
do i=1,4
bfrag(i,j)=bfrag(i,j)-ishift
hfrag(i,j)=hfrag(i,j)-ishift
enddo
enddo
- ishift_pdb=ishift
return
end
-c-----------------------------------------------------------------------
+c---------------------------------------------------------------------------
subroutine readpdb_template(k)
-C Read the PDB file with gaps for read_constr_homology with read2sigma
+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'
- include 'COMMON.MD'
- 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
character*3 seq,res
character*5 atom
character*80 card
- double precision sccor(3,50)
- integer rescode
- efree_temp=0.0d0
+ double precision sccor(3,20)
+ integer rescode,iterter(maxres)
+ do i=1,maxres
+ iterter(i)=0
+ enddo
ibeg=1
ishift1=0
ishift=0
lsecondary=.false.
nhfrag=0
nbfrag=0
- do
+ do
read (ipdbin,'(a80)',end=10) card
-c write (iout,'(a)') card
- if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+ if (card(:3).eq.'END') then
+ goto 10
+ else if (card(:3).eq.'TER') then
+C End current chain
+ 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
+ if (unres_pdb) then
+ do j=1,3
+ dc(j,ires)=sccor(j,iii)
+ enddo
+ else
+ call sccenter(ires,iii,sccor)
+ endif
+ endif
C Fish out the ATOM cards.
if (index(card(1:4),'ATOM').gt.0) then
read (card(12:16),*) atom
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)
ires_old=ires
c write (iout,*) "ishift",ishift," ires",ires,
c & " ires_old",ires_old
+c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+ ibeg=0
+ else if (ibeg.eq.2) then
+c Start a new chain
+ ishift=-ires_old+ires-1
+ ires=ires_old+1
+c write (iout,*) "New chain started",ires,ishift
ibeg=0
else
ishift=ishift-(ires-ishift+ishift1-ires_old-1)
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 if (card(27:27).eq."A" .or. card(27:27).eq."B") then
c ishift1=ishift1+1
- endif
+c 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
+c write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
#ifdef DEBUG
write (iout,'(2i3,2x,a,3f8.3)')
& ires,itype(ires),res,(c(j,ires),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
+ 10 if(me.eq.king.or..not.out1file)
+ & write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
+ nres=ires
+ do i=2,nres-1
+c 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
+ 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
+ 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 (iii.gt.0) then
if (unres_pdb) then
do j=1,3
dc(j,ires)=sccor(j,iii)
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)=ntyp1
+ if (unres_pdb) then
+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
endif
+ endif
do i=2,nres-1
do j=1,3
c(j,i+nres)=dc(j,i)
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ 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
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
+ if (out_template_coord) then
write (iout,'(/a)')
& "Cartesian coordinates of the reference structure"
write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
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 int_from_cart(.true.,.true.)
call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(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
-c call chainbuild
-C Copy the coordinates to reference coordinates
- do i=1,2*nres
+ do i=1,nres
do j=1,3
cref(j,i)=c(j,i)
+ cref(j,i+nres)=c(j,i+nres)
+ enddo
+ enddo
+ do i=1,2*nres
+ do j=1,3
chomo(j,i,k)=c(j,i)
enddo
enddo
-
- ishift_pdb=ishift
return
end
+
projects / unres.git / commitdiff