X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fcluster%2Fwham%2Fsrc-M%2Freadpdb.f;h=5913aa670b4fc4523587491607c11917b2170035;hb=ecdaefb55cd2370287e648c14fb657d5c7ad5145;hp=993b5c69f895dd87080a73285b64aff29944c319;hpb=7006db11d703450fb82ce20cfc53f74614334362;p=unres.git

diff --git a/source/cluster/wham/src-M/readpdb.f b/source/cluster/wham/src-M/readpdb.f
index 993b5c6..5913aa6 100644
--- a/source/cluster/wham/src-M/readpdb.f
+++ b/source/cluster/wham/src-M/readpdb.f
@@ -298,7 +298,7 @@ c        write (iout,*) i,dist(i,i-1)
         if ((dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0)
      &.and.(iti.ne.ntyp1).and.(itype(i-1).ne.ntyp1)) then
           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
-          stop
+c          stop
         endif
         theta(i+1)=alpha(i-1,i,i+1)
         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
@@ -432,3 +432,372 @@ c---------------------------------------------------------------------------
       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 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.SETUP'
+      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity
+      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)
+      logical unres_pdb
+      unres_pdb=.false.
+      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
+          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
+              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)
+c#ifdef DEBUG
+c            write (iout,'(2i3,2x,a,3f8.3)') 
+c     &      ires,itype(ires),res,(c(j,ires),j=1,3)
+c#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 (lprn) 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,i3,3f8.3,5x,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.
+      if(me.eq.king.or..not.out1file)then
+       write (iout,'(a)') 
+     &   "Backbone and SC coordinates as read from the PDB"
+       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_cart1(.false.)
+      call int_from_cart(.true.,.false.)
+      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
+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
+c      do i=1,2*nres
+c        do j=1,3
+c          chomo(j,i,k)=c(j,i)
+c        enddo
+c      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       
+
+      return
+      end