X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Freadpdb.F;h=eed985e003b6a5f01fe4f5a560eee891a95d246e;hb=3e42b5f53e0ec03cd03009f3b857931ce7ee25c2;hp=3ce8334606e37962aaaf15bb1ab712acfeadec49;hpb=b847bacd7f528a68d640b3d58d4f5b9ce3c6ede2;p=unres.git

diff --git a/source/unres/src_MD/readpdb.F b/source/unres/src_MD/readpdb.F
index 3ce8334..eed985e 100644
--- a/source/unres/src_MD/readpdb.F
+++ b/source/unres/src_MD/readpdb.F
@@ -15,7 +15,7 @@ C geometry.
       include 'COMMON.SETUP'
       integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
      &  ishift_pdb
-      logical lprn /.true./,fail
+      logical lprn /.false./,fail
       double precision e1(3),e2(3),e3(3)
       double precision dcj,efree_temp
       character*3 seq,res
@@ -144,7 +144,10 @@ c            write (iout,*) "sidechain ",atom
           endif
         endif
       enddo
-   10 write (iout,'(a,i5)') ' Number of residues found: ',ires
+   10 continue
+#ifdef DEBUG
+      write (iout,'(a,i5)') ' Number of residues found: ',ires
+#endif
       if (ires.eq.0) return
 C Calculate the CM of the last side chain.
       if (iii.gt.0)  then
@@ -162,11 +165,24 @@ C Calculate the CM of the last side chain.
       if (itype(nres).ne.10) then
         nres=nres+1
         itype(nres)=21
+        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
@@ -493,3 +509,244 @@ c       print *,vbld(i+1),vbld(i+1+nres)
       enddo
       return
       end
+      subroutine readpdb_template(k)
+C Read the PDB file with gaps 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.DISTFIT'
+      include 'COMMON.SETUP'
+      include 'COMMON.MD'
+      integer i,j,ibeg,ishift1,ires,iii,ires_old,ishift,ity,
+     &  ishift_pdb
+      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
+      efree_temp=0.0d0
+      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 i=1,10000
+        read (ipdbin,'(a80)',end=10) card
+c        write (iout,'(a)') card
+        if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+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.
+c            if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+            if (ibeg.eq.0) then
+c              write (iout,*) "Calculating sidechain center iii",iii
+              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)=21
+              endif
+              ires=ires-ishift+ishift1
+              ires_old=ires
+c              write (iout,*) "ishift",ishift," ires",ires,
+c     &         " ires_old",ires_old
+              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
+c            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)
+c            write (iout,*) "backbone ",atom 
+#ifdef DEBUG
+            write (iout,'(2i3,2x,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
+            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 continue
+#ifdef DEBUG
+      write (iout,'(a,i5)') ' Number of residues found: ',ires
+#endif
+      if (ires.eq.0) return
+C Calculate the CM of the last side chain.
+      if (iii.gt.0)  then
+      if (unres_pdb) then
+        do j=1,3
+          dc(j,ires)=sccor(j,iii)
+        enddo
+      else
+        call sccenter(ires,iii,sccor)
+      endif
+      endif
+      nres=ires
+      nsup=nres
+      nstart_sup=1
+      if (itype(nres).ne.10) then
+        nres=nres+1
+        itype(nres)=21
+        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
+      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.21) 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 (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_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
+      do i=1,2*nres
+        do j=1,3
+          cref(j,i)=c(j,i)
+          chomo(j,i,k)=c(j,i)
+        enddo
+      enddo
+
+
+      ishift_pdb=ishift
+      return
+      end