REM Dos Batch Script to run the TOXD MR Test
REM KJS : I couldn't for the life of me work out how to fix
REM the variables to work properly inside the text files.
REM There should be no issue except ccp4tmp has to be set to default.
echo off

echo. >NUL 2>TmpRVXDHW1.dat
echo. >NUL 2>TmpRVXDHW2.dat
echo. >NUL 2>TmpRVXDHW3.dat

call:EofCat ToxDRARun TmpRVXDHW1.dat
call:EofCat ToxDRBRun TmpRVXDHW2.dat
call:EofCat ToxDRCRun TmpRVXDHW3.dat

phaser < TmpRVXDHW1.dat
phaser < TmpRVXDHW2.dat
phaser < TmpRVXDHW2.dat

del TmpRVXDHW*.dat

exit /b

REM Rotation Search
goto:ToxDRARun
   MODE MR_FRF
   HKLIN ..\toxd\toxd.mtz
   LABIN F = FTOXD3 SIGF = SIGFTOXD3
   ENSEMBLE toxd PDBFILE ..\data\1D0D_B.pdb IDENTITY 0.364
   COMPOSITION PROTEIN MW 7139 NUM 1
   SEARCH ENSEMBLE toxd
   ROOT C:\ccp4tmp\ROT_toxd
:ToxDRARun

REM Rotation Ensemble Search
goto:ToxDRBRun
   MODE MR_FRF
   HKLIN ..\toxd\toxd.mtz
   LABIN F = FTOXD3 SIGF = SIGFTOXD3
   ENSEMBLE toxd PDBFILE ..\data\1D0D_B.pdb IDENTITY 0.364 &
                 PDBFILE ..\data\1BIK_2_1D0D_B.pdb IDENTITY 0.377
   COMPOSITION PROTEIN MW 7139 NUM 1
   SEARCH ENSEMBLE toxd
   ROOT C:\ccp4tmp\ROT_toxd
:ToxDRBRun

REM Translation Ensemble Search
goto:ToxDRCRun
   MODE MR_FTF
   HKLIN ..\toxd\toxd.mtz
   LABIN F = FTOXD3SIGF = SIGFTOXD3
   ENSEMBLE toxd PDBFILE ..\data\1D0D_B.pdb IDENTITY 0.364 &
                 PDBFILE ..\data\1BIK_2_1D0D_B.pdb IDENTITY 0.377
   COMPOSITION PROTEIN MW 7139 NUM 1
   SOLUTION TRIAL ENSEMBLE toxd EULER 138.405   18.970  207.570 RFZ 5.70
   ROOT C:\ccp4tmp\TRA_toxd
:ToxDRCRun

:EofCat
    ::Should call this function with 2 args, MYDELIM and outFile.txt
    ::where is to be catted to outFile.txt
    ::and text starts with <beginning of line>goto:MYDELIM
    ::and ends with <beginning of line>:MYDELIM
    set searchStart=goto:%~1
    set searchStop=:%~1
    set outFile=%~2
    set startLine=0
    set endLine=0
    for /f "delims=:" %%a in ('findstr -b -n %searchStart% %~dpnx0') do set "startLine=%%a"
    for /f "delims=:" %%a in ('findstr -b -n %searchStop%  %~dpnx0') do set "endLine=%%a"

    set /a linesLeftToRead=%endLine% - %startLine%
    del %outFile%
    if "%linesLeftToRead%" LEQ "0" (
        echo Error finding start and end delmieters for %searchStop% in catMyChunk routine
        exit /B 1
    )
    setlocal DisableDelayedExpansion
    for /f "usebackq skip=%startLine% delims=" %%a in (`"findstr /n ^^ %~dpnx0"`) do (
        set "oneLine=%%a"
        set /a linesLeftToRead-=1
        setlocal EnableDelayedExpansion
        set "oneLine=!oneLine:*:=!"
        if !linesLeftToRead! LEQ 0 exit /B
        echo(!oneLine!>>%outFile%
        endlocal
    )
    endlocal

goto: EOF