0

Friends,

I would like to reformat a file ( fort.80) to fort.90! For that I used type constructs for reading the input ( fort.80) as well as writing it to output ( fort.90). I can successfully do copying all but one case (dihedral), where the output file looks blank ( please see the last column of fort.90). When I tried to write individually within the loop in which I copied the corresponding data (backbonedihedral) from fort.80, it works fine. But when I write the same data along with other variables (reorderedresiseqNumber,resiName, alphadistance, calphaangle), it (backbonedihedral ) gives me only blanks.( please see the wrapped code!)

Other details:

I use dynamic memory allocation for both type structures!

 module internal
! first module
      type internalcoordfile ! for reading the internal variables
!        sequence
       character (len=5) :: recordName
       integer :: resiseqNumber ! to check the different residues
        character (len=3) :: resiName
       real  :: angle
       real :: distance
      end type  internalcoordfile
!  second module      
      type configurationmatrix ! stores the configuration of a protein
!        sequence
       integer reorderedresiseqNumber
       character(len=3) ::  resiName
       real calphadistance ! d
       real calphaangle ! theta
       real:: backbonedihedral ! gamma
              end type  configurationmatrix
      end module internal ! total five variables
! module ends here!!
! These two TYPES will be read by the subroutine written at the end of
! the main program!
!*****************************************************************
      program internalcoordinatematrix
        use internal
       implicit none
       character(len=80), allocatable, dimension (:) :: line
       integer :: lineNumber, ierr, i
! NOTE: insert module "internal" before the final compilation of the
! software
       type (internalcoordfile), allocatable, target :: internalmatrix(:)
        open(unit=80, file='fort.80', status='old')
      counting_linenumber: do
                             read(80,fmt='(a80)',iostat=ierr,end=10)line
                             lineNumber=lineNumber + 1
                             if (ierr.ne.0)exit
                           enddo  counting_linenumber
10       close(80)
  write(*,*)"Number of lines in the internal coordinate file", lineNumber
!     allocating  number of files from fort.80 (internal coordinates)
      allocate(internalmatrix(lineNumber))
       test_allocation: if(allocated (internalmatrix)) then
          write(*,*) "Internal file allocation is successful"
                        endif test_allocation
        open(unit=80, file='fort.80', status='old')
          do i=1,lineNumber
            read(80,'(a,1x,i4,1x,a,1x,2f12.6)')internalmatrix(i)%recordName, &
       & internalmatrix(i)%resiseqNumber,internalmatrix(i)%resiName,&
       & internalmatrix(i)%angle, internalmatrix(i)%distance !
          enddo
       close(80)
! Loop for counting line number  ends here
        !  subroutine writes out internal coordinates
      call internalout
      call readinternal(lineNumber,internalmatrix(1)%resiseqNumber)
! The following loop will count the number of residues in the file
! loop ended
      end
!******************************************************************      
      subroutine readinternal(internalfilelineNumber,matrixdimension)
      use internal
      implicit none
      integer i,j,k! loop counter
      integer, intent(in) :: internalfilelineNumber,matrixdimension
      type (internalcoordfile), allocatable, target :: internalfile(:)
! internalcoordfile is fort.80
      type(configurationmatrix), allocatable, target :: confmatrix(:)
! configuration matrix is confmatrix
      write(*,*)'number of residues',matrixdimension,'number of lines in &
     & internal files', internalfilelineNumber
!      allocate this type : internalfile
         allocate(internalfile(internalfilelineNumber))
          internalfile_allocation: if(allocated (internalfile)) then
                write(*,*) " internal file allocation is successful"
                           endif internalfile_allocation
!     allocate the type : confmatrix
         allocate(confmatrix(matrixdimension))
                confmatrix_allocation: if(allocated(confmatrix))then
               write(*,*) "conformation matrix allocation is successful"
                                       endif confmatrix_allocation
!      loop for reading lines     
      open(unit=80,file='fort.80', status='old')
       do i=1, internalfilelineNumber
!          if(trim(internalfile(i)%recordName).eq.'DIHEL') then
!           read(80,'(a,1x,i4,1x,a,1x,1f12.6)')internalfile(i)%recordName,&
!       & internalfile(i)%resiseqNumber,internalfile(i)%resiName, &
!       & internalfile(i)%dihedral
!           else if(trim(internalfile(i)%recordName).ne.'DIHEL')then
         read(80,'(a,1x,i4,1x,a,1x,2f12.6)')internalfile(i)%recordName,&
        &internalfile(i)%resiseqNumber,internalfile(i)%resiName,&
        &internalfile(i)%angle, internalfile(i)%distance ! 
!        endif
       enddo
! testing to write
         do i=1, internalfilelineNumber
!          if(trim(internalfile(i)%recordName).eq.'DIHEL') then
!           write(*,'(a,1x,i4,1x,a,1x,1f12.6)')internalfile(i)%recordName,&
!       & internalfile(i)%resiseqNumber, internalfile(i)%resiName, internalfile(i)%dihedral
!           else
         write(*,'(a,1x,i4,1x,a,1x,2f12.6)')internalfile(i)%recordName,&
        &internalfile(i)%resiseqNumber,internalfile(i)%resiName,&
        &internalfile(i)%angle, internalfile(i)%distance ! 
!        endif
       enddo
!--------------------------------------------------------------------
! COPYING RESIDUE TO CONFIGURATION MATRIX
!-------------------------------------------------------------------
!     We avoid the residue at the tails, both beginning and ending
!     So,set up the internalfile(1)%resiName='BEG'
        confmatrix(1)%resiName='BEG'
      internalloop1: do i=1, internalfilelineNumber
         if(internalfile(i)%recordName.eq.'TOTAL') cycle
          if(internalfile(i)%recordName.eq.'DIHEL')cycle
           if(internalfile(i)%recordName.eq.'SCANG')cycle
            if(internalfile(i)%recordName.eq.'SOANG')cycle
!        cycling TOTAL
     residueinternal: if(internalfile(i)%recordName.eq.'ANGLE') then
                confmatrixloop1:  do j=2,matrixdimension-1 !loop for 
                 confmatrix(j)%resiName=internalfile(j)%resiName
!                read(80,'(a,6x,a)') confmatrix(j)%resiName
!                write(90,*)confmatrix(j)%resiName
!                                  exit ! exit for the termination of the j loop                
                                  enddo confmatrixloop1
                    endif residueinternal
! We do not explicitly mention the end residue; simply write 'END'
       enddo internalloop1
          confmatrix(matrixdimension)%resiName='END'
! done!!
!------------------------------------------------------------------
!  REARRANGING RESIDUE NUMBER AND COPY TO CONFIGURATION MATRIX
!-----------------------------------------------------------------
! In this part of the program, rearranging the residue number is done
! Until this point, the residueNumber is appeared as in the original PDB
! file !!!
!    Set first residue(BEG) number as 1
       confmatrix(1)%reorderedresiseqNumber=1
!    Set final residue(END) number as the matrixdimension, that is the
!    total number of residue in the structure
       confmatrix(matrixdimension)%reorderedresiseqNumber=matrixdimension
        internalloop2: do i=1, internalfilelineNumber
         if(internalfile(i)%recordName.eq.'TOTAL') cycle
!     cycling TOTAL
      resiseqNumberinternal: if(internalfile(i)%recordName.eq.'ANGLE') then
      confmatrixloop2:  do j=2,matrixdimension-1 !loop for 
             confmatrix(j)%reorderedresiseqNumber=j
!                        write(90,*) confmatrix(j)%reorderedresiseqNumber
                        enddo confmatrixloop2
                        exit
                     endif resiseqNumberinternal
       enddo internalloop2
! Done!
!---------------------------------------------------------------------
!    COPYING CALPHA DISTANCE TO CONFIGURATION MATRIX
!---------------------------------------------------------------------
!  This snippet deals with copying the Calphadistance in the internal
!  file into the configuration matrix
!  SET first residue, (beg) : second residue value=3.88888
      confmatrix(1)%calphadistance=3.80000
! SET last residue( END) - penultimate residue length, also equal to
! 3.8000
      confmatrix(matrixdimension)%calphadistance=3.80000
      internalloop3: do i=1, internalfilelineNumber
         if(internalfile(i)%recordName.eq.'TOTAL') cycle
!     cycling TOTAL
      distanceinternal: if(internalfile(i)%recordName.eq.'ANGLE')then
      confmatrixloop3:  do j=2,matrixdimension-1 !loop for 
             confmatrix(j)%calphadistance=internalfile(j)%distance
!                        write(90,*) confmatrix(j)%calphadistance
!                        exit
                        enddo confmatrixloop3
                        exit
                     endif distanceinternal
       enddo internalloop3
! Done !
!---------------------------------------------------
! COPYING THE ANGLE TO CONFIGURATION MATRIX
!--------------------------------------------------
! This snippet deals with copying the angle in the internalfile into
! the configuration matrix
! SET Calpha angle for the first (BEG)  equal to 0.00
       confmatrix(1)%calphaangle=0.00000
        internalloop4: do i=1, internalfilelineNumber
         if(internalfile(i)%recordName.eq.'TOTAL') cycle
!     cycling TOTAL
      angleinternal: if(internalfile(i)%recordName.eq.'ANGLE')then
      confmatrixloop4:  do j=2,matrixdimension-1 !loop for 
             confmatrix(j)%calphaangle=internalfile(j)%angle
!                        write(90,*) confmatrix(j)%calphaangle
                        enddo confmatrixloop4
!                       exit ! exiting to avoid multiple writing!!
                     endif angleinternal
                      enddo internalloop4
! SET Calpha angle for the last residue (END)  equal to 0.00
       confmatrix(matrixdimension)%calphaangle=0.00000
! Done !! 
!       write(*,*) matrixdimension
  COPYING THE DIHEDRAL ANGLE To CONFIGURATION MATRIX
!----------------------------------------------------
!   This snippet deals with copying the dihedral in the internalfile
!   into the configuration matrix
!   Setting confmatrix(1) equal to 0.0
       confmatrix(1)%backbonedihedral=0.00000
       confmatrix(matrixdimension-1)%backbonedihedral=0.00000
       confmatrix(matrixdimension)%backbonedihedral=0.00000
        internalloop5: do i=1, internalfilelineNumber
         if(internalfile(i)%recordName.eq.'TOTAL') cycle
          if(internalfile(i)%recordName.eq.'ANGLE') cycle
           if(internalfile(i)%recordName.eq.'SCANG')cycle
            if(internalfile(i)%recordName.eq.'SOANG')cycle
!     cycling TOTAL, ANGLE, SCANG & SOANG
      dihedralinternal: if(internalfile(i)%recordName.eq.'DIHEL')then
      confmatrixloop5:  do j=2,matrixdimension-2!loop for dihedral ! DON'T DELETE
             confmatrix(j)%backbonedihedral=internalfile(i)%angle ! the
! Value has not been stored, that is the problem !!
!            confmatrix(j)%backbonedihedral=temp
!                   internalfile(j)%angle=internalfile(i)%angle
!                  write(*,*)  internalfile(j)%angle
                 write(90,'(34x,f12.6)') confmatrix(j)%backbonedihedral
                    exit
                       enddo confmatrixloop5
                     endif dihedralinternal
       enddo internalloop5
      do j=1,matrixdimension
        write(90,'(i4,1x,a,1x,1f12.6,1x,2f12.6)') confmatrix(j)%reorderedresiseqNumber, &
       &  confmatrix(j)%resiName, confmatrix(j)%calphadistance,  confmatrix(j)%calphaangle, &
       &  confmatrix(j)%backbonedihedral

      enddo
deallocate(confmatrix)
!      deallocating internalfile
       deallocate(internalfile)
       close(80)
       end
       !  subroutine writes out internal coordinates
      subroutine internalout
      implicit none
      write(90,'(a)') '-----------------------------'
      write(90,'(a)') 'Conformation matrix of Protein backbone'
      write(90,'(a)')'-----------------------------------'
!      write(*,'(1x,a,2x,a,1x,a,1x,a,1x,a,1x,a,1x,a,1x,1a)')'Num','Res',' d',' Theta', &
!      & ' Phi', ' Dsc',' Alpha',' Omega'
      write(90,'(1x,a,1x,a,8x,a,8x,a,10x,a)')'Num','Res',' d','Theta','Phi'
       return
       end

Input fort.80

TOTAL   70
ANGLE    4 LYS    1.983920    3.822784
ANGLE    5 GLN    2.506508    3.822551
ANGLE    6 GLY    1.495086    3.821371
ANGLE    7 ARG    2.096276    3.820670
ANGLE    8 THR    2.364110    3.822508
ANGLE    9 ASP    2.094052    3.821672
ANGLE   10 CYS    1.963850    3.822539
ANGLE   11 PRO    1.677076    3.834944
ANGLE   12 ALA    1.799173    3.823198
ANGLE   13 LEU    2.063516    3.822105
ANGLE   14 PRO    1.965101    3.836382
ANGLE   15 PRO    1.949416    3.837436
ANGLE   16 GLY    1.705281    3.824572
ANGLE   17 TRP    1.892656    3.820108
ANGLE   18 LYS    2.242406    3.821930
ANGLE   19 LYS    2.308866    3.821398
ANGLE   20 GLU    2.313049    3.821454
ANGLE   21 GLU    2.083784    3.822719
ANGLE   22 VAL    2.100003    3.821506
ANGLE   23 ILE    2.052736    3.822493
ANGLE   24 ARG    1.751812    3.821769
ANGLE   25 LYS    1.626016    3.821603
ANGLE   26 SER    2.062574    3.821834
ANGLE   27 GLY    2.287319    3.824040
ANGLE   28 LEU    1.565828    3.821841
ANGLE   29 SER    1.451304    3.821571
ANGLE   30 ALA    1.934769    3.821035
ANGLE   31 GLY    1.747195    3.823237
ANGLE   32 LYS    1.926940    3.820865
ANGLE   33 SER    2.345152    3.821374
ANGLE   34 ASP    2.271087    3.821962
ANGLE   35 VAL    2.119246    3.821771
ANGLE   36 TYR    2.218048    3.821591
ANGLE   37 TYR    2.227151    3.822969
ANGLE   38 PHE    2.150835    3.821053
ANGLE   39 SER    2.169791    3.821796
ANGLE   40 PRO    1.548220    3.835462
ANGLE   41 SER    1.568206    3.823429
ANGLE   42 GLY    1.710068    3.822036
ANGLE   43 LYS    1.982734    3.822136
ANGLE   44 LYS    2.101412    3.821878
ANGLE   45 PHE    2.348185    3.821960
ANGLE   46 ARG    2.223365    3.821394
ANGLE   47 SER    2.249793    3.821801
ANGLE   48 LYS    1.592114    3.821490
ANGLE   49 PRO    1.549069    3.836537
ANGLE   50 GLN    1.674697    3.823194
ANGLE   51 LEU    1.598475    3.822194
ANGLE   52 ALA    1.579722    3.822999
ANGLE   53 ARG    1.552630    3.822948
ANGLE   54 TYR    1.618652    3.820822
ANGLE   55 LEU    1.551953    3.821788
ANGLE   56 GLY    1.941157    3.823335
ANGLE   57 ASN    1.670169    3.821963
ANGLE   58 ALA    1.670174    3.822638
ANGLE   59 VAL    2.385202    3.822763
ANGLE   60 ASP    2.025180    3.822024
ANGLE   61 LEU    1.613844    3.822328
ANGLE   62 SER    1.572482    3.821428
ANGLE   63 CYS    1.563730    3.822332
ANGLE   64 PHE    1.985124    3.822651
ANGLE   65 ASP    1.873640    3.821861
ANGLE   66 PHE    1.604218    3.822503
ANGLE   67 ARG    1.503885    3.822784
ANGLE   68 THR    1.725750    3.822031
ANGLE   69 GLY    1.684116    3.822909
ANGLE   70 LYS    2.322768    3.821630
ANGLE   71 MET    2.160215    3.821827
DIHEL    4 LYS    1.496096
DIHEL    5 GLN    1.333776
DIHEL    6 GLY    1.618819
DIHEL    7 ARG    3.022177
DIHEL    8 THR    1.924051
DIHEL    9 ASP    1.888155
DIHEL   10 CYS    2.865580
DIHEL   11 PRO    0.401756
DIHEL   12 ALA    1.320498
DIHEL   13 LEU    1.123235
DIHEL   14 PRO    1.543718
DIHEL   15 PRO    0.679356
DIHEL   16 GLY    2.250174
DIHEL   17 TRP    2.817974
DIHEL   18 LYS    3.010844
DIHEL   19 LYS    2.874462
DIHEL   20 GLU    2.587237
DIHEL   21 GLU    3.022746
DIHEL   22 VAL    2.629759
DIHEL   23 ILE    1.910234
DIHEL   24 ARG    3.043501
DIHEL   25 LYS    1.402398
DIHEL   26 SER    0.567028
DIHEL   27 GLY    1.768409
DIHEL   28 LEU    1.379249
DIHEL   29 SER    2.861548
DIHEL   30 ALA    1.259526
DIHEL   31 GLY    2.028536
DIHEL   32 LYS    3.091765
DIHEL   33 SER    2.684078
DIHEL   34 ASP    2.468847
DIHEL   35 VAL    2.898226
DIHEL   36 TYR    2.754847
DIHEL   37 TYR    2.714195
DIHEL   38 PHE    2.481630
DIHEL   39 SER    1.858816
DIHEL   40 PRO    1.072759
DIHEL   41 SER    1.911607
DIHEL   42 GLY    2.517043
DIHEL   43 LYS    2.322621
DIHEL   44 LYS    3.080138
DIHEL   45 PHE    2.650866
DIHEL   46 ARG    0.100788
DIHEL   47 SER    1.493801
DIHEL   48 LYS    1.103461
DIHEL   49 PRO    0.833585
DIHEL   50 GLN    0.718795
DIHEL   51 LEU    0.960888
DIHEL   52 ALA    0.881929
DIHEL   53 ARG    0.938154
DIHEL   54 TYR    0.788985
DIHEL   55 LEU    3.072032
DIHEL   56 GLY    0.478359
DIHEL   57 ASN    1.665880
DIHEL   58 ALA    0.289608
DIHEL   59 VAL    2.222054
DIHEL   60 ASP    3.100946
DIHEL   61 LEU    1.918940
DIHEL   62 SER    0.638466
DIHEL   63 CYS    1.665067
DIHEL   64 PHE    2.750731
DIHEL   65 ASP    3.065837
DIHEL   66 PHE    1.269825
DIHEL   67 ARG    0.177735
DIHEL   68 THR    2.174371
DIHEL   69 GLY    2.276402
DIHEL   70 LYS    2.202347

output: fort.90

----------------------

1 BEG     3.800000     0.000000    0.000000
   2 LYS     3.822784     1.983920    2.202347
   3 GLN     3.822551     2.506508    0.000000
   4 GLY     3.821371     1.495086    0.000000
   5 ARG     3.820670     2.096276    0.000000
   6 THR     3.822508     2.364110    0.000000
   7 ASP     3.821672     2.094052    0.000000
   8 CYS     3.822539     1.963850    0.000000
   9 PRO     3.834944     1.677076    0.000000
  10 ALA     3.823198     1.799173    0.000000
  11 LEU     3.822105     2.063516    0.000000
  12 PRO     3.836382     1.965101    0.000000
  13 PRO     3.837436     1.949416    0.000000
  14 GLY     3.824572     1.705281    0.000000
  15 TRP     3.820108     1.892656    0.000000
  16 LYS     3.821930     2.242406    0.000000
  17 LYS     3.821398     2.308866    0.000000
  18 GLU     3.821454     2.313049    0.000000
  19 GLU     3.822719     2.083784    0.000000
  20 VAL     3.821506     2.100003    0.000000
  21 ILE     3.822493     2.052736    0.000000
  22 ARG     3.821769     1.751812    0.000000
  23 LYS     3.821603     1.626016    0.000000
  24 SER     3.821834     2.062574    0.000000
  25 GLY     3.824040     2.287319    0.000000
  26 LEU     3.821841     1.565828    0.000000
  27 SER     3.821571     1.451304    0.000000
  28 ALA     3.821035     1.934769    0.000000
  29 GLY     3.823237     1.747195    0.000000
  30 LYS     3.820865     1.926940    0.000000
  31 SER     3.821374     2.345152    0.000000
  32 ASP     3.821962     2.271087    0.000000
  33 VAL     3.821771     2.119246    0.000000
  34 TYR     3.821591     2.218048    0.000000
  35 TYR     3.822969     2.227151    0.000000
  36 PHE     3.821053     2.150835    0.000000
  37 SER     3.821796     2.169791    0.000000
  38 PRO     3.835462     1.548220    0.000000
  39 SER     3.823429     1.568206    0.000000
  40 GLY     3.822036     1.710068    0.000000
  41 LYS     3.822136     1.982734    0.000000
  42 LYS     3.821878     2.101412    0.000000
  43 PHE     3.821960     2.348185    0.000000
  44 ARG     3.821394     2.223365    0.000000
  45 SER     3.821801     2.249793    0.000000
  46 LYS     3.821490     1.592114    0.000000
  47 PRO     3.836537     1.549069    0.000000
  48 GLN     3.823194     1.674697    0.000000
  49 LEU     3.822194     1.598475    0.000000
  50 ALA     3.822999     1.579722    0.000000
  51 ARG     3.822948     1.552630    0.000000
  52 TYR     3.820822     1.618652    0.000000
  53 LEU     3.821788     1.551953    0.000000
  54 GLY     3.823335     1.941157    0.000000
  55 ASN     3.821963     1.670169    0.000000
  56 ALA     3.822638     1.670174    0.000000
  57 VAL     3.822763     2.385202    0.000000
  58 ASP     3.822024     2.025180    0.000000
  59 LEU     3.822328     1.613844    0.000000
  60 SER     3.821428     1.572482    0.000000
  61 CYS     3.822332     1.563730    0.000000
  62 PHE     3.822651     1.985124    0.000000
  63 ASP     3.821861     1.873640    0.000000
  64 PHE     3.822503     1.604218    0.000000
  65 ARG     3.822784     1.503885    0.000000
  66 THR     3.822031     1.725750    0.000000
  67 GLY     3.822909     1.684116    0.000000
  68 LYS     3.821630     2.322768    0.000000
  69 MET     3.821827     2.160215    0.000000
  70 END     3.800000     0.000000    0.000000

Edited by mike_2000_17: Fixed formatting

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6 Years
Discussion Span
Last Post by jmandumpal
1

I got the program correct:

What I did is that remove the innerloop5 and insert a variable and incremented with every iteration of internalloop5

internalloop5: do i=1, internalfilelineNumber
....................
dihedralinternal: if(internalfile(i)%recordName.eq.'DIHEL')then
.....................................
confmatrix(j)%backbonedihedral=internalfile(i)%angle ! the
! Value has not been stored, that is the problem !!
! confmatrix(j)%backbonedihedral=temp
! internalfile(j)%angle=internalfile(i)%angle
! write(*,*) internalfile(j)%angle
write(90,'(34x,f12.6)') confmatrix(j)%backbonedihedral
exit
enddo confmatrixloop5
endif dihedralinternal
enddo internalloop5

replaced by
confmatrix(1)%backbonedihedral=0.0000 !
confmatrix(matrixdimension-1)%backbonedihedral=0.0000 !
confmatrix(matrixdimension)%backbonedihedral=0.0000 !
j=2
internalloop5: do i=1, internalfilelineNumber
dihedralinternal: if(internalfile(i)%recordName.eq.'DIHEL')then
confmatrix(j)%backbonedihedral=internalfile(i)%angle !
j=j+1
endif dihedralinternal
enddo internalloop5
do j=1,matrixdimension
write(90,'(i4,1x,a,1x,1f12.6,1x,2f12.6)') confmatrix(j)%reorderedresiseqNumber, &
& confmatrix(j)%resiName, confmatrix(j)%calphadistance, confmatrix(j)%calphaangle, &
& confmatrix(j)%backbonedihedral
enddo

Votes + Comments
Wow. Fortran
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