X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M-newcorr%2Freadpdb.F;fp=source%2Funres%2Fsrc_MD-M-newcorr%2Freadpdb.F;h=f2daaddb90a8887c232c7997d2ef3877cd4f5f5d;hb=7308760ff07636ef6b1ee28d8c3a67a23c14b34b;hp=0000000000000000000000000000000000000000;hpb=9a54ab407f6d0d9d564d52763b3e2136450b9ffc;p=unres.git

diff --git a/source/unres/src_MD-M-newcorr/readpdb.F b/source/unres/src_MD-M-newcorr/readpdb.F
new file mode 100644
index 0000000..f2daadd
--- /dev/null
+++ b/source/unres/src_MD-M-newcorr/readpdb.F
@@ -0,0 +1,557 @@
+      subroutine readpdb
+C Read the PDB file and convert the peptide geometry into virtual-chain 
+C 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'
+      character*3 seq,atom,res
+      character*80 card
+      dimension sccor(3,20)
+      double precision e1(3),e2(3),e3(3)
+      integer rescode
+      logical fail
+      ibeg=1
+      lsecondary=.false.
+      nhfrag=0
+      nbfrag=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+1 
+          itype(ires_old)=ntyp1
+          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(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(24:26),*) 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)
+            if(me.eq.king.or..not.out1file)
+     &       write (iout,'(2i3,2x,a,3f8.3)') 
+     &       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)
+        if (itype(i).eq.ntyp1) then
+c          write (iout,*) "dummy",i,itype(i)
+          do j=1,3
+            c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
+c            c(j,i)=(c(j,i-1)+c(j,i+1))/2
+            dc(j,i)=c(j,i)
+          enddo
+        endif
+      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)-3.8d0*e2(j)
+          enddo
+        else
+        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
+      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)-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(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 int_from_cart(.true.,.false.)
+      call sc_loc_geom(.true.)
+      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
+C Splits to single chain if occurs
+      kkk=1
+      lll=0
+      cou=1
+      do i=1,nres
+      lll=lll+1
+cc      write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+      if (i.gt.1) then
+      if ((itype(i-1).eq.ntyp1).and.(i.gt.2)) then
+      chain_length=lll-1
+      kkk=kkk+1
+c       write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+      lll=1
+      endif
+      endif
+        do j=1,3
+          cref(j,i,cou)=c(j,i)
+          cref(j,i+nres,cou)=c(j,i+nres)
+          if (i.le.nres) then
+          chain_rep(j,lll,kkk)=c(j,i)
+          chain_rep(j,lll+nres,kkk)=c(j,i+nres)
+          endif
+         enddo
+      enddo
+      write (iout,*) chain_length
+      if (chain_length.eq.0) chain_length=nres
+      do j=1,3
+      chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
+      chain_rep(j,chain_length+nres,symetr)
+     &=chain_rep(j,chain_length+nres,1)
+      enddo
+c diagnostic
+c       write (iout,*) "spraw lancuchy",chain_length,symetr
+c       do i=1,4
+c         do kkk=1,chain_length
+c           write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
+c         enddo
+c        enddo
+c enddiagnostic       
+C makes copy of chains
+        write (iout,*) "symetr", symetr
+       
+      if (symetr.gt.1) then
+       call permut(symetr)
+       nperm=1
+       do i=1,symetr
+       nperm=nperm*i
+       enddo
+       do i=1,nperm
+       write(iout,*) (tabperm(i,kkk),kkk=1,4)
+       enddo
+       do i=1,nperm
+        cou=0
+        do kkk=1,symetr
+         icha=tabperm(i,kkk)
+c         write (iout,*) i,icha
+         do lll=1,chain_length
+          cou=cou+1
+           if (cou.le.nres) then
+           do j=1,3
+            kupa=mod(lll,chain_length)
+            iprzes=(kkk-1)*chain_length+lll
+            if (kupa.eq.0) kupa=chain_length
+c            write (iout,*) "kupa", kupa
+            cref(j,iprzes,i)=chain_rep(j,kupa,icha)
+            cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
+          enddo
+          endif
+         enddo
+        enddo
+       enddo
+       endif
+C-koniec robienia kopii
+c diag
+      do kkk=1,nperm
+      write (iout,*) "nowa struktura", nperm
+      do i=1,nres
+        write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
+     &cref(2,i,kkk),
+     &cref(3,i,kkk),cref(1,nres+i,kkk),
+     &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
+      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)
+      
+      enddo
+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 int_from_cart(lside,lprn)
+      implicit real*8 (a-h,o-z)
+      include 'DIMENSIONS'
+#ifdef MPI
+      include "mpif.h"
+#endif 
+      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.SETUP'
+      character*3 seq,atom,res
+      character*80 card
+      dimension sccor(3,20)
+      integer rescode
+      logical lside,lprn
+#ifdef MPI
+      if(me.eq.king.or..not.out1file)then
+#endif
+       if (lprn) then 
+        write (iout,'(/a)') 
+     &  'Internal coordinates calculated from crystal structure.'
+        if (lside) then 
+          write (iout,'(8a)') '  Res  ','       dvb','     Theta',
+     & '       Phi','    Dsc_id','       Dsc','     Alpha',
+     & '     Omega'
+        else 
+          write (iout,'(4a)') '  Res  ','       dvb','     Theta',
+     & '       Phi'
+        endif
+       endif
+#ifdef MPI
+      endif
+#endif
+      do i=1,nres-1
+        iti=itype(i)
+        if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and. 
+     &      (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
+          write (iout,'(a,i4)') 'Bad Cartesians for residue',i
+ctest          stop
+        endif
+        vbld(i+1)=dist(i,i+1)
+        vbld_inv(i+1)=1.0d0/vbld(i+1)
+        if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
+        if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+      enddo
+c      if (unres_pdb) then
+c        if (itype(1).eq.21) then
+c          theta(3)=90.0d0*deg2rad
+c          phi(4)=180.0d0*deg2rad
+c          vbld(2)=3.8d0
+c          vbld_inv(2)=1.0d0/vbld(2)
+c        endif
+c        if (itype(nres).eq.21) then
+c          theta(nres)=90.0d0*deg2rad
+c          phi(nres)=180.0d0*deg2rad
+c          vbld(nres)=3.8d0
+c          vbld_inv(nres)=1.0d0/vbld(2)
+c        endif
+c      endif
+      if (lside) then
+        do i=2,nres-1
+          do j=1,3
+            c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i)
+     &     +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
+          enddo
+          iti=itype(i)
+          di=dist(i,nres+i)
+          vbld(i+nres)=di
+          if (itype(i).ne.10) then
+            vbld_inv(i+nres)=1.0d0/di
+          else
+            vbld_inv(i+nres)=0.0d0
+          endif
+          if (iti.ne.10) then
+            alph(i)=alpha(nres+i,i,maxres2)
+            omeg(i)=beta(nres+i,i,maxres2,i+1)
+          endif
+          if(me.eq.king.or..not.out1file)then
+           if (lprn)
+     &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),
+     &     rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),
+     &     rad2deg*alph(i),rad2deg*omeg(i)
+          endif
+        enddo
+      else if (lprn) then
+        do i=2,nres
+          iti=itype(i)
+          if(me.eq.king.or..not.out1file)
+     &     write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
+     &     rad2deg*theta(i),rad2deg*phi(i)
+        enddo
+      endif
+      return
+      end
+c-------------------------------------------------------------------------------
+      subroutine sc_loc_geom(lprn)
+      implicit real*8 (a-h,o-z)
+      include 'DIMENSIONS'
+#ifdef MPI
+      include "mpif.h"
+#endif 
+      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.SETUP'
+      double precision x_prime(3),y_prime(3),z_prime(3)
+      logical lprn
+      do i=1,nres-1
+        do j=1,3
+          dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
+        enddo
+      enddo
+      do i=2,nres-1
+        if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+          do j=1,3
+            dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
+          enddo
+        else
+          do j=1,3
+            dc_norm(j,i+nres)=0.0d0
+          enddo
+        endif
+      enddo
+      do i=2,nres-1
+        costtab(i+1) =dcos(theta(i+1))
+        sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+        cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+        sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+        cosfac2=0.5d0/(1.0d0+costtab(i+1))
+        cosfac=dsqrt(cosfac2)
+        sinfac2=0.5d0/(1.0d0-costtab(i+1))
+        sinfac=dsqrt(sinfac2)
+        it=itype(i)
+        if (it.ne.10 .and. itype(i).ne.ntyp1) then
+c
+C  Compute the axes of tghe local cartesian coordinates system; store in
+c   x_prime, y_prime and z_prime 
+c
+        do j=1,3
+          x_prime(j) = 0.00
+          y_prime(j) = 0.00
+          z_prime(j) = 0.00
+        enddo
+        do j = 1,3
+          x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+          y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+        enddo
+        call vecpr(x_prime,y_prime,z_prime)
+c
+C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
+C to local coordinate system. Store in xx, yy, zz.
+c
+        xx=0.0d0
+        yy=0.0d0
+        zz=0.0d0
+        do j = 1,3
+          xx = xx + x_prime(j)*dc_norm(j,i+nres)
+          yy = yy + y_prime(j)*dc_norm(j,i+nres)
+          zz = zz + z_prime(j)*dc_norm(j,i+nres)
+        enddo
+
+        xxref(i)=xx
+        yyref(i)=yy
+        zzref(i)=zz
+        else
+        xxref(i)=0.0d0
+        yyref(i)=0.0d0
+        zzref(i)=0.0d0
+        endif
+      enddo
+      if (lprn) then
+        do i=2,nres
+          iti=itype(i)
+#ifdef MPI
+          if(me.eq.king.or..not.out1file)
+     &     write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
+     &      yyref(i),zzref(i)
+#else
+          write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),yyref(i),
+     &     zzref(i)
+#endif
+        enddo
+      endif
+      return
+      end
+c---------------------------------------------------------------------------
+      subroutine sccenter(ires,nscat,sccor)
+      implicit real*8 (a-h,o-z)
+      include 'DIMENSIONS'
+      include 'COMMON.CHAIN'
+      dimension sccor(3,20)
+      do j=1,3
+        sccmj=0.0D0
+        do i=1,nscat
+          sccmj=sccmj+sccor(j,i) 
+        enddo
+        dc(j,ires)=sccmj/nscat
+      enddo
+      return
+      end
+c---------------------------------------------------------------------------
+      subroutine bond_regular
+      implicit real*8 (a-h,o-z)
+      include 'DIMENSIONS'   
+      include 'COMMON.VAR'
+      include 'COMMON.LOCAL'      
+      include 'COMMON.CALC'
+      include 'COMMON.INTERACT'
+      include 'COMMON.CHAIN'
+      do i=1,nres-1
+       vbld(i+1)=vbl
+       vbld_inv(i+1)=1.0d0/vbld(i+1)
+       vbld(i+1+nres)=dsc(iabs(itype(i+1)))
+       vbld_inv(i+1+nres)=dsc_inv(iabs(itype(i+1)))
+c       print *,vbld(i+1),vbld(i+1+nres)
+      enddo
+      return
+      end
+