source/unres/src-HCD-5D/readpdb_template.F

   1       subroutine readpdb_template(k)
   2 C Read the PDB file for read_constr_homology with read2sigma
   3 C and convert the peptide geometry into virtual-chain geometry.
   4       implicit none
   5       include 'DIMENSIONS'
   6       include 'COMMON.LOCAL'
   7       include 'COMMON.VAR'
   8       include 'COMMON.CHAIN'
   9       include 'COMMON.INTERACT'
  10       include 'COMMON.IOUNITS'
  11       include 'COMMON.GEO'
  12       include 'COMMON.NAMES'
  13       include 'COMMON.CONTROL'
  14       include 'COMMON.FRAG'
  15       include 'COMMON.SETUP'
  16       integer i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
  17      &  ishift_pdb,ires_ca
  18       logical lprn /.false./,fail
  19       double precision e1(3),e2(3),e3(3)
  20       double precision dcj,efree_temp
  21       character*3 seq,res
  22       character*5 atom
  23       character*80 card
  24       double precision sccor(3,20)
  25       integer rescode,iterter(maxres)
  26       do i=1,maxres
  27          iterter(i)=0
  28       enddo
  29       ibeg=1
  30       ishift1=0
  31       ishift=0
  32 c      write (2,*) "UNRES_PDB",unres_pdb
  33       ires=0
  34       ires_old=0
  35       iii=0
  36       lsecondary=.false.
  37       nhfrag=0
  38       nbfrag=0
  39       do
  40         read (ipdbin,'(a80)',end=10) card
  41         if (card(:3).eq.'END') then
  42           goto 10
  43         else if (card(:3).eq.'TER') then
  44 C End current chain
  45           ires_old=ires+2
  46           itype(ires_old-1)=ntyp1
  47           iterter(ires_old-1)=1
  48           itype(ires_old)=ntyp1
  49           iterter(ires_old)=1
  50           ibeg=2
  51 c          write (iout,*) "Chain ended",ires,ishift,ires_old
  52           if (unres_pdb) then
  53             do j=1,3
  54               dc(j,ires)=sccor(j,iii)
  55             enddo
  56           else
  57             call sccenter(ires,iii,sccor)
  58           endif
  59         endif
  60 C Fish out the ATOM cards.
  61         if (index(card(1:4),'ATOM').gt.0) then
  62           read (card(12:16),*) atom
  63 c          write (iout,*) "! ",atom," !",ires
  64 c          if (atom.eq.'CA' .or. atom.eq.'CH3') then
  65           read (card(23:26),*) ires
  66           read (card(18:20),'(a3)') res
  67 c          write (iout,*) "ires",ires,ires-ishift+ishift1,
  68 c     &      " ires_old",ires_old
  69 c          write (iout,*) "ishift",ishift," ishift1",ishift1
  70 c          write (iout,*) "IRES",ires-ishift+ishift1,ires_old
  71           if (ires-ishift+ishift1.ne.ires_old) then
  72 C Calculate the CM of the preceding residue.
  73             if (ibeg.eq.0) then
  74               if (unres_pdb) then
  75                 do j=1,3
  76                   dc(j,ires_old)=sccor(j,iii)
  77                 enddo
  78               else
  79                 call sccenter(ires_old,iii,sccor)
  80               endif
  81               iii=0
  82             endif
  83 C Start new residue.
  84             if (res.eq.'Cl-' .or. res.eq.'Na+') then
  85               ires=ires_old
  86               cycle
  87             else if (ibeg.eq.1) then
  88 c              write (iout,*) "BEG ires",ires
  89               ishift=ires-1
  90               if (res.ne.'GLY' .and. res.ne. 'ACE') then
  91                 ishift=ishift-1
  92                 itype(1)=ntyp1
  93               endif
  94               ires=ires-ishift+ishift1
  95               ires_old=ires
  96 c              write (iout,*) "ishift",ishift," ires",ires,
  97 c     &         " ires_old",ires_old
  98 c              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
  99               ibeg=0
 100             else if (ibeg.eq.2) then
 101 c Start a new chain
 102               ishift=-ires_old+ires-1
 103               ires=ires_old+1
 104 c              write (iout,*) "New chain started",ires,ishift
 105               ibeg=0
 106             else
 107               ishift=ishift-(ires-ishift+ishift1-ires_old-1)
 108               ires=ires-ishift+ishift1
 109               ires_old=ires
 110             endif
 111             if (res.eq.'ACE' .or. res.eq.'NHE') then
 112               itype(ires)=10
 113             else
 114               itype(ires)=rescode(ires,res,0)
 115             endif
 116           else
 117             ires=ires-ishift+ishift1
 118           endif
 119 c          write (iout,*) "ires_old",ires_old," ires",ires
 120 c          if (card(27:27).eq."A" .or. card(27:27).eq."B") then
 121 c            ishift1=ishift1+1
 122 c          endif
 123 c          write (2,*) "ires",ires," res ",res," ity",ity
 124           if (atom.eq.'CA' .or. atom.eq.'CH3' .or.
 125      &       res.eq.'NHE'.and.atom(:2).eq.'HN') then
 126             read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
 127 c            write (iout,*) "backbone ",atom ,ires,res, (c(j,ires),j=1,3)
 128 #ifdef DEBUG
 129             write (iout,'(2i3,2x,a,3f8.3)')
 130      &      ires,itype(ires),res,(c(j,ires),j=1,3)
 131 #endif
 132             iii=iii+1
 133             do j=1,3
 134               sccor(j,iii)=c(j,ires)
 135             enddo
 136             if (ishift.ne.0) then
 137               ires_ca=ires+ishift-ishift1
 138             else
 139               ires_ca=ires
 140             endif
 141 c            write (*,*) card(23:27),ires,itype(ires)
 142           else if (atom.ne.'O'.and.atom(1:1).ne.'H' .and.
 143      &             atom.ne.'N' .and. atom.ne.'C' .and.
 144      &             atom(:2).ne.'1H' .and. atom(:2).ne.'2H' .and.
 145      &             atom.ne.'OXT' .and. atom(:2).ne.'3H') then
 146 c            write (iout,*) "sidechain ",atom
 147             iii=iii+1
 148             read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
 149           endif
 150         endif
 151       enddo
 152    10 if(me.eq.king.or..not.out1file)
 153      & write (iout,'(a,i5)') ' Nres: ',ires
 154 C Calculate dummy residue coordinates inside the "chain" of a multichain
 155 C system
 156       nres=ires
 157       do i=2,nres-1
 158 c        write (iout,*) i,itype(i),itype(i+1)
 159         if (itype(i).eq.ntyp1.and.iterter(i).eq.1) then
 160          if (itype(i+1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
 161 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
 162 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
 163 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
 164            if (unres_pdb) then
 165 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 166             call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
 167             if (fail) then
 168               e2(1)=0.0d0
 169               e2(2)=1.0d0
 170               e2(3)=0.0d0
 171             endif !fail
 172             do j=1,3
 173              c(j,i)=c(j,i-1)-1.9d0*e2(j)
 174             enddo
 175            else   !unres_pdb
 176            do j=1,3
 177              dcj=(c(j,i-2)-c(j,i-3))/2.0
 178             if (dcj.eq.0) dcj=1.23591524223
 179              c(j,i)=c(j,i-1)+dcj
 180              c(j,nres+i)=c(j,i)
 181            enddo
 182           endif   !unres_pdb
 183          else     !itype(i+1).eq.ntyp1
 184           if (unres_pdb) then
 185 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 186             call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
 187             if (fail) then
 188               e2(1)=0.0d0
 189               e2(2)=1.0d0
 190               e2(3)=0.0d0
 191             endif
 192             do j=1,3
 193               c(j,i)=c(j,i+1)-1.9d0*e2(j)
 194             enddo
 195           else !unres_pdb
 196            do j=1,3
 197             dcj=(c(j,i+3)-c(j,i+2))/2.0
 198             if (dcj.eq.0) dcj=1.23591524223
 199             c(j,i)=c(j,i+1)-dcj
 200             c(j,nres+i)=c(j,i)
 201            enddo
 202           endif !unres_pdb
 203          endif !itype(i+1).eq.ntyp1
 204         endif  !itype.eq.ntyp1
 205       enddo
 206 C Calculate the CM of the last side chain.
 207       if (unres_pdb) then
 208         do j=1,3
 209           dc(j,ires)=sccor(j,iii)
 210         enddo
 211       else
 212         call sccenter(ires,iii,sccor)
 213       endif
 214       nsup=nres
 215       nstart_sup=1
 216       if (itype(nres).ne.10) then
 217         nres=nres+1
 218         itype(nres)=ntyp1
 219         if (unres_pdb) then
 220 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
 221           call refsys(nres-3,nres-2,nres-1,e1,e2,e3,fail)
 222           if (fail) then
 223             e2(1)=0.0d0
 224             e2(2)=1.0d0
 225             e2(3)=0.0d0
 226           endif
 227           do j=1,3
 228             c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
 229           enddo
 230         else
 231         do j=1,3
 232           dcj=(c(j,nres-2)-c(j,nres-3))/2.0
 233             if (dcj.eq.0) dcj=1.23591524223
 234           c(j,nres)=c(j,nres-1)+dcj
 235           c(j,2*nres)=c(j,nres)
 236         enddo
 237       endif
 238       endif
 239       do i=2,nres-1
 240         do j=1,3
 241           c(j,i+nres)=dc(j,i)
 242         enddo
 243       enddo
 244       do j=1,3
 245         c(j,nres+1)=c(j,1)
 246         c(j,2*nres)=c(j,nres)
 247       enddo
 248       if (itype(1).eq.ntyp1) then
 249         nsup=nsup-1
 250         nstart_sup=2
 251         if (unres_pdb) then
 252 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
 253           call refsys(2,3,4,e1,e2,e3,fail)
 254           if (fail) then
 255             e2(1)=0.0d0
 256             e2(2)=1.0d0
 257             e2(3)=0.0d0
 258           endif
 259           do j=1,3
 260             c(j,1)=c(j,2)-1.9d0*e2(j)
 261           enddo
 262         else
 263         do j=1,3
 264           dcj=(c(j,4)-c(j,3))/2.0
 265           c(j,1)=c(j,2)-dcj
 266           c(j,nres+1)=c(j,1)
 267         enddo
 268         endif
 269       endif
 270 C Copy the coordinates to reference coordinates
 271 c      do i=1,2*nres
 272 c        do j=1,3
 273 c          cref(j,i)=c(j,i)
 274 c        enddo
 275 c      enddo
 276 C Calculate internal coordinates.
 277       if (out_template_coord) then
 278       write (iout,'(/a)')
 279      &  "Cartesian coordinates of the reference structure"
 280       write (iout,'(a,3(3x,a5),5x,3(3x,a5))')
 281      & "Residue ","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
 282       do ires=1,nres
 283         write (iout,'(a3,1x,i4,3f8.3,5x,3f8.3)')
 284      &    restyp(itype(ires)),ires,(c(j,ires),j=1,3),
 285      &    (c(j,ires+nres),j=1,3)
 286       enddo
 287       endif
 288 C Calculate internal coordinates.
 289       call int_from_cart(.true.,out_template_coord)
 290       call sc_loc_geom(.false.)
 291       do i=1,nres
 292         thetaref(i)=theta(i)
 293         phiref(i)=phi(i)
 294       enddo
 295       do i=1,nres-1
 296         do j=1,3
 297           dc(j,i)=c(j,i+1)-c(j,i)
 298           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 299         enddo
 300       enddo
 301       do i=2,nres-1
 302         do j=1,3
 303           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 304           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 305         enddo
 306 c        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
 307 c     &   vbld_inv(i+nres)
 308       enddo
 309       do i=1,nres
 310         do j=1,3
 311           cref(j,i)=c(j,i)
 312           cref(j,i+nres)=c(j,i+nres)
 313         enddo
 314       enddo
 315       do i=1,2*nres
 316         do j=1,3
 317           chomo(j,i,k)=c(j,i)
 318         enddo
 319       enddo
 320
 321       return
 322       end
 323
 324