X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fio_config.F90;fp=source%2Funres%2Fio_config.F90;h=3dc6fa1fb4a2b3fbc17f17c97b8405907dfcec0c;hb=3d3780d89d2885ee8700324ef832ef07ee35c45b;hp=61cb7b474b80e9ffbc68a6808efb912211efd6dc;hpb=54770cd3e877e04f7b6b5a1addce86b9cb2f3fad;p=unres4.git

diff --git a/source/unres/io_config.F90 b/source/unres/io_config.F90
index 61cb7b4..3dc6fa1 100644
--- a/source/unres/io_config.F90
+++ b/source/unres/io_config.F90
@@ -4141,7 +4141,7 @@
       enddo
       endif
 
-!       print *,seqalingbegin,nres
+       print *,seqalingbegin,nres
       if(.not.allocated(vbld)) then
        allocate(vbld(2*nres))
        do i=1,2*nres
@@ -4177,13 +4177,17 @@
         allocate(dc_norm(3,0:2*nres+2))
         dc_norm(:,:)=0.d0
       endif
- 
+      write(iout,*) "before int_from_cart"
       call int_from_cart(.true.,.false.)
       call sc_loc_geom(.false.)
+      write(iout,*) "after int_from_cart"
+
+      
       do i=1,nres
         thetaref(i)=theta(i)
         phiref(i)=phi(i)
       enddo
+      write(iout,*) "after thetaref"
 !      do i=1,2*nres
 !        vbld_inv(i)=0.d0
 !        vbld(i)=0.d0
@@ -4213,6 +4217,13 @@
 !        enddo
 !      enddo
 !
+!      do i=1,2*nres
+!        do j=1,3
+!          chomo(j,i,k)=c(j,i)
+!        enddo
+!      enddo
+!      write(iout,*) "after chomo"
+
       if(.not.allocated(cref)) allocate(cref(3,2*nres+2,maxperm)) !(3,maxres2+2,maxperm)
       if(.not.allocated(chain_rep)) allocate(chain_rep(3,2*nres+2,maxsym)) !(3,maxres2+2,maxsym)
       if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
@@ -4376,7 +4387,8 @@
 
       real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
       integer i                 
-
+      usampl=.false. ! the default value of usample should be 0
+!      write(iout,*) "KURWA2",usampl
       nglob_csa=0
       eglob_csa=1d99
       nmin_csa=0
@@ -4398,6 +4410,10 @@
       call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
       call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
       call reada(controlcard,'DRMS',drms,0.1D0)
+      call readi(controlcard,'CONSTR_HOMOL',constr_homology,0)
+      read_homol_frag = index(controlcard,"READ_HOMOL_FRAG").gt.0
+      out_template_coord = index(controlcard,"OUT_TEMPLATE_COORD").gt.0
+      out_template_restr = index(controlcard,"OUT_TEMPLATE_RESTR").gt.0
       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
        write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc 
        write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1 
@@ -4750,6 +4766,7 @@
       rest = index(controlcard,"REST").gt.0
       tbf = index(controlcard,"TBF").gt.0
       usampl = index(controlcard,"USAMPL").gt.0
+!      write(iout,*) "KURWA",usampl
       mdpdb = index(controlcard,"MDPDB").gt.0
       call reada(controlcard,"T_BATH",t_bath,300.0d0)
       call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1) 
@@ -6021,6 +6038,332 @@
       return
       end subroutine write_stat_thread
 !-----------------------------------------------------------------------------
+      subroutine readpdb_template(k)
+! Read the PDB file for read_constr_homology with read2sigma
+! 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'
+      use compare_data, only:nhfrag,nbfrag
+      integer :: i,j,k,ibeg,ishift1,ires,iii,ires_old,ishift,ity, &
+       ishift_pdb,ires_ca
+      logical lprn /.false./,fail
+      real(kind=8), dimension (3):: e1,e2,e3
+      real(kind=8) :: dcj,efree_temp
+      character*3 seq,res
+      character*5 atom
+      character*80 card
+      real(kind=8), dimension (3,20) :: sccor
+!      integer rescode
+      integer, dimension (:), allocatable :: iterter
+      if(.not.allocated(iterter))allocate(iterter(nres))
+      do i=1,nres
+         iterter(i)=0
+      enddo
+      ibeg=1
+      ishift1=0
+      ishift=0
+      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
+! End current chain
+          ires_old=ires+2
+          itype(ires_old-1,1)=ntyp1 
+          iterter(ires_old-1)=1
+          itype(ires_old,1)=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
+! Fish out the ATOM cards.
+        if (index(card(1:4),'ATOM').gt.0) then  
+          read (card(12:16),*) atom
+!          write (iout,*) "! ",atom," !",ires
+!          if (atom.eq.'CA' .or. atom.eq.'CH3') then
+          read (card(23:26),*) ires
+          read (card(18:20),'(a3)') res
+!          write (iout,*) "ires",ires,ires-ishift+ishift1,
+!     &      " ires_old",ires_old
+!          write (iout,*) "ishift",ishift," ishift1",ishift1
+!          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) then
+              if (unres_pdb) then
+                do j=1,3
+                  dc(j,ires_old)=sccor(j,iii)
+                enddo
+              else
+                call sccenter(ires_old,iii,sccor)
+              endif
+              iii=0
+            endif
+! Start new residue.
+            if (res.eq.'Cl-' .or. res.eq.'Na+') then
+              ires=ires_old
+              cycle
+            else if (ibeg.eq.1) then
+!              write (iout,*) "BEG ires",ires
+              ishift=ires-1
+              if (res.ne.'GLY' .and. res.ne. 'ACE') then
+                ishift=ishift-1
+                itype(1,1)=ntyp1
+              endif
+              ires=ires-ishift+ishift1
+              ires_old=ires
+!              write (iout,*) "ishift",ishift," ires",ires,
+!     &         " ires_old",ires_old
+!              write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
+              ibeg=0          
+            else if (ibeg.eq.2) then
+! Start a new chain
+              ishift=-ires_old+ires-1
+              ires=ires_old+1
+!              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,1)=10
+            else
+              itype(ires,1)=rescode(ires,res,0,1)
+            endif
+          else
+            ires=ires-ishift+ishift1
+          endif
+!          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
+!          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 ,ires,res, (c(j,ires),j=1,3)
+#ifdef DEBUG
+            write (iout,'(2i3,2x,a,3f8.3)') &
+           ires,itype(ires,1),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
+!            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
+!            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
+! Calculate dummy residue coordinates inside the "chain" of a multichain
+! system
+      nres=ires
+      do i=2,nres-1
+!        write (iout,*) i,itype(i),itype(i+1)
+        if (itype(i,1).eq.ntyp1.and.iterter(i).eq.1) then
+         if (itype(i+1,1).eq.ntyp1.and.iterter(i+1).eq.1 ) then
+! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+! first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+           if (unres_pdb) then
+! 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
+! 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
+! 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,1).ne.10) then
+        nres=nres+1
+        itype(nres,1)=ntyp1
+        if (unres_pdb) then
+! 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(1,1).eq.ntyp1) then
+        nsup=nsup-1
+        nstart_sup=2
+        if (unres_pdb) then
+! 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
+! Copy the coordinates to reference coordinates
+!      do i=1,2*nres
+!        do j=1,3
+!          cref(j,i)=c(j,i)
+!        enddo
+!      enddo
+! 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,1),1),ires,(c(j,ires),j=1,3),&
+         (c(j,ires+nres),j=1,3)
+      enddo
+      endif
+! Calculate internal coordinates.
+      call int_from_cart(.true.,out_template_coord)
+      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
+!        write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
+!     &   vbld_inv(i+nres)
+      enddo
+      do i=1,nres
+        do j=1,3
+          cref(j,i,1)=c(j,i)
+          cref(j,i+nres,1)=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 subroutine readpdb_template
+!-----------------------------------------------------------------------------
 #endif
 !-----------------------------------------------------------------------------
       end module io_config