+++ /dev/null
- subroutine readpdb
-C Read the PDB file and convert the peptide geometry into virtual-chain
-C geometry.
- implicit none
- 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.FRAG'
- include 'COMMON.SETUP'
- include 'COMMON.SBRIDGE'
- character*3 seq,atom,res
- character*80 card
- 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
- enddo
- ibeg=1
- lsecondary=.false.
- nhfrag=0
- nbfrag=0
- ires=0
- do
- read (ipdbin,'(a80)',end=10) card
- if (card(:5).eq.'HELIX') then
- nhfrag=nhfrag+1
- lsecondary=.true.
- read(card(22:25),*) hfrag(1,nhfrag)
- read(card(34:37),*) hfrag(2,nhfrag)
- endif
- if (card(:5).eq.'SHEET') then
- nbfrag=nbfrag+1
- lsecondary=.true.
- read(card(24:26),*) bfrag(1,nbfrag)
- read(card(35:37),*) bfrag(2,nbfrag)
-crc----------------------------------------
-crc to be corrected !!!
- bfrag(3,nbfrag)=bfrag(1,nbfrag)
- bfrag(4,nbfrag)=bfrag(2,nbfrag)
-crc----------------------------------------
- endif
- 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(14:16),'(a3)') atom
- if (atom.eq.'CA' .or. atom.eq.'CH3') then
-C Calculate the CM of the preceding residue.
- if (ibeg.eq.0) then
- if (unres_pdb) then
- do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- endif
-C Start new residue.
-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
-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
-c write (iout,*) "New chain started",ires,ishift
- ibeg=0
- endif
- 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
- read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
- 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
- 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 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 (unres_pdb) then
- do j=1,3
- dc(j,ires)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- 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*(-e1(j)+e2(j))/sqrt(2.0d0)
- enddo
- else
- do j=1,3
- 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)
- 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.ntyp1) 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)+1.9d0*(e1(j)-e2(j))/dsqrt(2.0d0)
- enddo
- else
- do j=1,3
- 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 Calculate internal coordinates.
- if(me.eq.king.or..not.out1file)then
- 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.)
- 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
-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
- 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
- call sc_loc_geom(.false.)
- call int_from_cart1(.false.)
-c call chainbuild
-C Copy the coordinates to reference coordinates
- 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
- enddo
- enddo
-
- do j=1,nhfrag
- do i=1,2
- hfrag(i,j)=hfrag(i,j)-ishift
- enddo
- 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 none
- 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.FRAG'
- include 'COMMON.SETUP'
- 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(3,20)
- integer rescode,iterter(maxres)
- 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
- 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,*) "! ",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.
- if (ibeg.eq.0) then
- 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)=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 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
- 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
-c if (card(27:27).eq."A" .or. card(27:27).eq."B") then
-c ishift1=ishift1+1
-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 ,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
- 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 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 (unres_pdb) then
- do j=1,3
- dc(j,ires)=sccor(j,iii)
- enddo
- else
- call sccenter(ires,iii,sccor)
- endif
- 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))/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)
- 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.ntyp1) 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)-1.9d0*e2(j)
- enddo
- else
- do j=1,3
- 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 (out_template_coord) 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,i4,3f8.3,5x,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.
- call int_from_cart(.true.,.true.)
- 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
- 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
-
- return
- end
-