X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc-HCD-5D%2Freadpdb.F;fp=source%2Funres%2Fsrc-HCD-5D%2Freadpdb.F;h=94fe78fbf22a54220397b3735c5f8001eb496512;hb=ba90a41f4674924a0bdc00452b59506a2acfa54a;hp=0000000000000000000000000000000000000000;hpb=ab695e2bb5e28825f160d84875b68d48c5c0f493;p=unres.git

diff --git a/source/unres/src-HCD-5D/readpdb.F b/source/unres/src-HCD-5D/readpdb.F
new file mode 100644
index 0000000..94fe78f
--- /dev/null
+++ b/source/unres/src-HCD-5D/readpdb.F
@@ -0,0 +1,392 @@
+      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,sccalc
+      integer i,j,iii,ires,ires_old,ishift,ishift1,ibeg,ifree
+      double precision dcj!,efree_temp
+      logical zero
+      bfac=0.0d0
+      do i=1,maxres
+         iterter(i)=0
+      enddo
+      ibeg=1
+      ishift1=0
+      lsecondary=.false.
+      nhfrag=0
+      nbfrag=0
+      iii=0
+      sccalc=.false.
+      do
+        read (ipdbin,'(a80)',end=10) card
+c        write (iout,'(a)') card
+c        call flush(iout)
+        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)
+!rc----------------------------------------
+!rc  to be corrected !!!
+          bfrag(3,nbfrag)=bfrag(1,nbfrag)
+          bfrag(4,nbfrag)=bfrag(2,nbfrag)
+!rc----------------------------------------
+        endif
+        if (card(:3).eq.'END') then
+          goto 10
+        else if (card(:3).eq.'TER') then
+! 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
+          ishift1=ishift1+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
+          iii=0
+          sccalc=.true.
+        endif
+! Read free energy
+c        if (index(card,"FREE ENERGY").gt.0) then
+c          ifree=index(card,"FREE ENERGY")+12
+c          read(card(ifree:),*,err=1115,end=1115) efree_temp
+c 1115     continue
+c        endif
+! Fish out the ATOM cards.
+        if (index(card(1:4),'ATOM').gt.0) then  
+          sccalc=.false.
+          read (card(12:16),*) atom
+c          write (2,'(a)') card
+c          write (iout,*) "ibeg",ibeg
+c          write (iout,*) "! ",atom," !",ires
+!          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
+! Calculate the CM of the preceding residue.
+!            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+            if (ibeg.eq.0) then
+c              write (iout,*) "Calculating sidechain center iii",iii
+c              write (iout,*) "ires",ires
+              if (unres_pdb) then
+c                write (iout,'(i5,3f10.5)') ires,(sccor(j,iii),j=1,3)
+                do j=1,3
+                  dc(j,ires_old)=sccor(j,iii)
+                enddo
+              else
+                call sccenter(ires_old,iii,sccor)
+              endif
+              iii=0
+              sccalc=.true.
+            endif
+! 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
+!              write (iout,*) "ishift",ishift," ires",ires,&
+!               " ires_old",ires_old
+              ibeg=0 
+            else if (ibeg.eq.2) then
+! Start a new chain
+              ishift=-ires_old+ires-1 !!!!!
+              ishift1=ishift1-1    !!!!!
+c              write (iout,*) "New chain started",ires,ishift,ishift1,"!"
+              ires=ires-ishift+ishift1
+              ires_old=ires
+              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
+!            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)
+            write (iout,*) "backbone ",atom
+            write (iout,*) ires,res,(c(j,ires),j=1,3)
+#ifdef DEBUG
+            write (iout,'(i6,i3,2x,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
+c            write (2,*) card(23:27),ires,itype(ires),iii
+          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
+!            write (iout,*) "sidechain ",atom
+            iii=iii+1
+            read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+c            write (2,*) "iii",iii
+          endif
+        endif
+      enddo
+   10 if(me.eq.king.or..not.out1file) 
+     & write (iout,'(a,i5)') ' Nres: ',ires
+c      write (iout,*) "iii",iii
+C Calculate dummy residue coordinates inside the "chain" of a multichain
+C system
+      nres=ires
+c      write (iout,*) "dc"
+c      do i=1,nres
+c        write (iout,'(i5,3f10.5)') i,(dc(j,i),j=1,3)
+c      enddo
+      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
+c            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
+c            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)
+             dC(j,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)
+            dC(j,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 (.not. sccalc) then
+      if (unres_pdb) then
+        do j=1,3
+          dc(j,ires)=sccor(j,iii)
+        enddo
+      else 
+c        write (iout,*) "Calling sccenter iii",iii
+        call sccenter(ires,iii,sccor)
+      endif
+      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
+      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
+      call flush(iout)
+      endif
+      zero=.false.
+      do ires=1,nres
+        zero=zero.or.itype(ires).eq.0
+      enddo
+      if (zero) then
+        write (iout,'(2a)') "Gaps in PDB coordinates detected;",
+     &    " look for ZERO in the control output above."
+        write (iout,'(2a)') "Repair the PDB file using MODELLER",
+     &    " or other softwared and resubmit."
+        call flush(iout)
+        stop
+      endif
+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
+      dc(:,0)=c(:,1)
+      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          '       ', 7X,'X',11X,'Y',11X,'Z',
+     &                          10X,'X',11X,'Y',11X,'Z')
+  110 format (a,'(',i4,')',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
+