Added putting secondary-structure information to the pdbfiles generated by xdrf2pdb...

diff --git a/bin/xdrfpdb/xdrf2pdb b/bin/xdrfpdb/xdrf2pdb
index 2d2cb08..bf524ed 100755 (executable)
Binary files a/bin/xdrfpdb/xdrf2pdb and b/bin/xdrfpdb/xdrf2pdb differ

diff --git a/source/xdrfpdb/src/COMMON.DISTFIT b/source/xdrfpdb/src/COMMON.DISTFIT
index bbc98ad..683228a 100644 (file)
--- a/source/xdrfpdb/src/COMMON.DISTFIT
+++ b/source/xdrfpdb/src/COMMON.DISTFIT
@@ -1,6 +1,14 @@
+c      parameter (maxres22=maxres*(maxres+1)/2)
+      parameter (maxres22=1)
+      double precision w,d0,DRDG,DD,H,XX
       integer nbfrag,bfrag,nhfrag,hfrag,bvar_frag,hvar_frag,nhpb0,
      1        lvar_frag,svar_frag,avar_frag
       COMMON /c_frag/ nbfrag,bfrag(4,maxres/3),nhfrag,hfrag(2,maxres/3)
-      COMMON /frag/ bvar_frag(mxio,6),hvar_frag(mxio,3),
-     1              lvar_frag(mxio,3),svar_frag(mxio,3),
-     2              avar_frag(mxio,5)
+csa      COMMON /frag/ bvar_frag(mxio,6),hvar_frag(mxio,3),
+csa     1              lvar_frag(mxio,3),svar_frag(mxio,3),
+csa     2              avar_frag(mxio,5)
+      COMMON /WAGI/ w(MAXRES22),d0(MAXRES22)
+      COMMON /POCHODNE/ NX,NY,DRDG(MAXRES22,MAXRES),DD(MAXRES22),                 
+     1 H(MAXRES,MAXRES),XX(MAXRES)         
+      COMMON /frozen/ mask(maxres)
+      COMMON /store0/ nhpb0

diff --git a/source/xdrfpdb/src/Makefile_ifort b/source/xdrfpdb/src/Makefile_ifort
index a828e35..ed3051e 100644 (file)
--- a/source/xdrfpdb/src/Makefile_ifort
+++ b/source/xdrfpdb/src/Makefile_ifort
@@ -25,7 +25,7 @@ OPT =
 
 FFLAGS = -c ${OPT} 
 
-CPPFLAGS = -DNEWUNRES
+CPPFLAGS = -DNEWUNRES -DSECONDARY
 
 M4     = m4
 M4FILE = underscore.m4
@@ -38,8 +38,8 @@ M4FILE        = underscore.m4
 
 all:xdrf2pdb xdrf2pdb-m
 
-xdrf2pdb: xdrf2pdb.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
-       ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb xdrf2pdb.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
+xdrf2pdb: xdrf2pdb.o elecont.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
+       ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb xdrf2pdb.o elecont.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a
 
 xdrf2pdb-m: xdrf2pdb-m.o geomout.o misc.o rescode.o nazwy.o xdrf/libxdrf.a
        ${FC} -Bstatic -o ${BINDIR}/xdrf2pdb-m xdrf2pdb-m.o geomout.o rescode.o misc.o nazwy.o xdrf/libxdrf.a

diff --git a/source/xdrfpdb/src/geomout.F b/source/xdrfpdb/src/geomout.F
index af7043b..07e344e 100644 (file)
--- a/source/xdrfpdb/src/geomout.F
+++ b/source/xdrfpdb/src/geomout.F
@@ -7,76 +7,77 @@
       include 'COMMON.IOUNITS'
       include 'COMMON.HEADER'
       include 'COMMON.SBRIDGE'
-c      include 'COMMON.DISTFIT'
+      include 'COMMON.DISTFIT'
 c      include 'COMMON.MD'
       character*50 tytul
       dimension ica(maxres)
       write (iunit,'(3a,1pe15.5)') 'REMARK ',tytul,' ENERGY ',etot
+#ifdef SECONDARY
 cmodel      write (iunit,'(a5,i6)') 'MODEL',1
-c      if (nhfrag.gt.0) then
-c       do j=1,nhfrag
-c        iti=itype(hfrag(1,j))
-c        itj=itype(hfrag(2,j))
-c        if (j.lt.10) then
-c           write (iunit,'(a5,i5,1x,a1,i1,2x,a3,i7,2x,a3,i7,i3,t76,i5)') 
-c     &           'HELIX',j,'H',j,
-c     &           restyp(iti),hfrag(1,j)-1,
-c     &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
-c        else
-c             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
-c     &           'HELIX',j,'H',j,
-c     &           restyp(iti),hfrag(1,j)-1,
-c     &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
-c        endif
-c       enddo
-c      endif
+      if (nhfrag.gt.0) then
+       do j=1,nhfrag
+        iti=itype(hfrag(1,j))
+        itj=itype(hfrag(2,j))
+        if (j.lt.10) then
+           write (iunit,'(a5,i5,1x,a1,i1,2x,a3,i7,2x,a3,i7,i3,t76,i5)') 
+     &           'HELIX',j,'H',j,
+     &           restyp(iti),hfrag(1,j)-1,
+     &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
+        else
+             write (iunit,'(a5,i5,1x,a1,i2,1x,a3,i7,2x,a3,i7,i3)') 
+     &           'HELIX',j,'H',j,
+     &           restyp(iti),hfrag(1,j)-1,
+     &           restyp(itj),hfrag(2,j)-1,1,hfrag(2,j)-hfrag(1,j)
+        endif
+       enddo
+      endif
+
+      if (nbfrag.gt.0) then
+
+       do j=1,nbfrag
+
+        iti=itype(bfrag(1,j))
+        itj=itype(bfrag(2,j)-1)
+
+        write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3)') 
+     &           'SHEET',1,'B',j,2,
+     &           restyp(iti),bfrag(1,j)-1,
+     &           restyp(itj),bfrag(2,j)-2,0
+
+        if (bfrag(3,j).gt.bfrag(4,j)) then
+
+         itk=itype(bfrag(3,j))
+         itl=itype(bfrag(4,j)+1)
 
-c      if (nbfrag.gt.0) then
-c
-c       do j=1,nbfrag
-c
-c        iti=itype(bfrag(1,j))
-c        itj=itype(bfrag(2,j)-1)
-c
-c        write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3)') 
-c     &           'SHEET',1,'B',j,2,
-c     &           restyp(iti),bfrag(1,j)-1,
-c     &           restyp(itj),bfrag(2,j)-2,0
-c
-c        if (bfrag(3,j).gt.bfrag(4,j)) then
-c
-c         itk=itype(bfrag(3,j))
-c         itl=itype(bfrag(4,j)+1)
-c
-c         write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3,
-c     &              2x,a1,2x,a3,i6,3x,a1,2x,a3,i6)') 
-c     &           'SHEET',2,'B',j,2,
-c     &           restyp(itl),bfrag(4,j),
-c     &           restyp(itk),bfrag(3,j)-1,-1,
-c     &           "N",restyp(itk),bfrag(3,j)-1,
-c     &           "O",restyp(iti),bfrag(1,j)-1
-c
-c        else
-c
-c         itk=itype(bfrag(3,j))
-c         itl=itype(bfrag(4,j)-1)
-c
-c
-c        write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3,
-c     &              2x,a1,2x,a3,i6,3x,a1,2x,a3,i6)') 
-c     &           'SHEET',2,'B',j,2,
-c     &           restyp(itk),bfrag(3,j)-1,
-c     &           restyp(itl),bfrag(4,j)-2,1,
-c     &           "N",restyp(itk),bfrag(3,j)-1,
-c     &           "O",restyp(iti),bfrag(1,j)-1
-c
-c
-c
-c        endif
-c         
-c       enddo
-c      endif 
+         write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3,
+     &              2x,a1,2x,a3,i6,3x,a1,2x,a3,i6)') 
+     &           'SHEET',2,'B',j,2,
+     &           restyp(itl),bfrag(4,j),
+     &           restyp(itk),bfrag(3,j)-1,-1,
+     &           "N",restyp(itk),bfrag(3,j)-1,
+     &           "O",restyp(iti),bfrag(1,j)-1
 
+        else
+
+         itk=itype(bfrag(3,j))
+         itl=itype(bfrag(4,j)-1)
+
+
+        write (iunit,'(a5,i5,1x,a1,i1,i3,1x,a3,i6,2x,a3,i6,i3,
+     &              2x,a1,2x,a3,i6,3x,a1,2x,a3,i6)') 
+     &           'SHEET',2,'B',j,2,
+     &           restyp(itk),bfrag(3,j)-1,
+     &           restyp(itl),bfrag(4,j)-2,1,
+     &           "N",restyp(itk),bfrag(3,j)-1,
+     &           "O",restyp(iti),bfrag(1,j)-1
+
+
+
+        endif
+         
+       enddo
+      endif 
+#endif
       if (nss.gt.0) then
         do i=1,nss
           write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') 

diff --git a/source/xdrfpdb/src/xdrf2pdb.F b/source/xdrfpdb/src/xdrf2pdb.F
index 592d552..1f7ce8e 100644 (file)
--- a/source/xdrfpdb/src/xdrf2pdb.F
+++ b/source/xdrfpdb/src/xdrf2pdb.F
@@ -3,6 +3,7 @@
       include 'COMMON.CHAIN'
       include 'COMMON.INTERACT'
       include 'COMMON.SBRIDGE'
+      include 'COMMON.DISTFIT'
       real*4 coord(3,2*maxres)
       real*4 prec,time,potE,uconst,t_bath,qfrag(100)
       real*8 etot
@@ -94,37 +95,44 @@
       if (itype(nres).eq.21) nct = nres-1
       print *,"nnt",nnt," nct",nct
       print *,"file",arg
+      do i=nnt,nct
+        if (itype(i).ne.20) then
+          itel(i)=1
+        else
+          itel(i)=2
+        endif 
+      enddo
       call xdrfopen(ixdrf,arg, "r", iret)
       if (iret.eq.0) stop
-      print *,"iret",iret
-      print *,"is",is," ie",ie
+c      print *,"iret",iret
+c      print *,"is",is," ie",ie
       kk = 0
       do while(is.eq.0 .or. kk.lt.ie) 
        call xdrffloat(ixdrf, time, iret)
-       print *,"time",time," iret",iret
+c       print *,"time",time," iret",iret
        if(iret.eq.0) exit
        kk = kk + 1
        call xdrffloat(ixdrf, potE, iret)
        call xdrffloat(ixdrf, uconst, iret)
-       print *,"potE",potE," uconst",uconst
+c       print *,"potE",potE," uconst",uconst
 #ifdef NEWUNRES
        call xdrffloat(ixdrf, uconst_back, iret)
-       print *,"uconst_back",uconst_back
+c       print *,"uconst_back",uconst_back
 #endif
        call xdrffloat(ixdrf, t_bath, iret)
-       print *,"t_bath",t_bath
+c       print *,"t_bath",t_bath
        call xdrfint(ixdrf, nss, iret) 
        do j=1,nss
         call xdrfint(ixdrf, ihpb(j), iret)
         call xdrfint(ixdrf, jhpb(j), iret)
        enddo
-       print *,"nss",nss
-       print *,"   ",(ihpb(j),"-",jhpb(j),j=1,nss)
+c       print *,"nss",nss
+c       print *,"   ",(ihpb(j),"-",jhpb(j),j=1,nss)
        call xdrfint(ixdrf, nfrag, iret)
        do i=1,nfrag
         call xdrffloat(ixdrf, qfrag(i), iret)
        enddo
-       print *,"nfrag",nfrag
+c       print *,"nfrag",nfrag
        prec=10000.0
 
        isize=0
@@ -167,6 +175,9 @@ c Calculate the CM
          enddo
          etot=potE
          write (tytul,'(a,i6)') "Structure",kk
+#ifdef SECONDARY
+         call secondary2(.false.)
+#endif
          call pdbout(etot,tytul,9)
        endif
       enddo