Shell_Sh_Code_Example

#   Shell  ，  Python     

#!/bin/sh
# Run scripts with Python (and modpy.sh if needed) if possible, rather
# than the modXXX script (which only works correctly if Python 2.3 is installed)
modpy="../../bin/modpy.sh"
# If modpy.sh doesn't exist, assume we have Python set up correctly already
# (e.g. Mac or RPM install, or PYTHONPATH and LD_LIBRARY_PATH set):
if test "${PYTHON}x" != "x"; then
  pyint="${PYTHON}"
else
  pyint="python"
fi
if test ! -f ${modpy}; then
  modpy="${pyint}"
else
  modpy="${modpy} ${pyint}"
fi
# Only use Modeller through Python if 1) an import succeeds, 2) the 'modeller'
# module imported is really Modeller (not a spurious modeller.py in the path
# somewhere) and 3) the version matches that these examples were built with
run_version=`${modpy} - 2>/dev/null <<END
import sys
from modeller import *
v = info.version_info
if isinstance(v, tuple):
    v = ".".join([str(i) for i in v])
sys.stdout.write(v + '
')
END
`
build_version="9.11"

#-- Rewrite By JunH
workPath="../ModellerWorkFolder/TvLDH"
PDBID="TvLDH"
PYFULLPATH="/home/protein/JunHWorkSpace/SimpleModeller"

if [ $# != 2 ]
then
  echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  echo "!!                         !!"
  echo "!!          ，           !!"
  echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
  exit 1
fi

workPath=$1
PDBID=$2

# run_script build_profile
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/build_profile.py $PYFULLPATH $workPath $PDBID.ali > $workPath/temp/build_profile.log"
else
  cmd="mod9.11 $PYFULLPATH/build_profile.py"
fi
echo "$cmd"
#   Cmd
eval "$cmd"

# translate workPath + '/temp/build_profile.prf' File
#     $workPath/temp/build_profile.prf  1-7     $workPath/temp/build_profile.prf.copy
sed '1,7d' $workPath/temp/build_profile.prf > $workPath/temp/build_profile.prf.copy

#     $workPath/temp/build_profile.prf.copy  12        
minilize=`awk 'BEGIN { a = 1 } { if ($12 < a) a = $12; } END { print a }' $workPath/temp/build_profile.prf.copy`
#     $workPath/temp/build_profile.prf.copy       
ProteinPDBIDList=`awk '{ if ($12 == '$minilize') print $2 }' $workPath/temp/build_profile.prf.copy`

# format ProteinPDBIDList
#  $ProteinPDBIDList    "  "  " "
pPDBIDList=`echo $ProteinPDBIDList | sed 's/ / /g'`

#run_script compare
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/compare.py $PYFULLPATH $workPath $pPDBIDList > $workPath/temp/compare.log"
else
  cmd="mod9.11 $PYFULLPATH/compare.py"
fi
echo "$cmd"
eval "$cmd"

# translate workPath + '/temp/family.mat' File
# remove the first count line
sed '1,1d' $workPath/temp/family.mat > $workPath/temp/family.mat.copy

# search minilize score
minScore=1000
# while    $workPath/temp/family.mat.copy   
while read line
do
  #  line " "      2   atScore
   atScore=`echo $line | cut -d" " -f2`
   #  atScore  2             score
   score=`echo $atScore | cut -c2-`
   #   score       minScore        socre  minScore
   if (echo ${score} ${minScore} | awk '!($1<$2){exit 1}') then
        tpdbID=`echo $line | cut -d" " -f1`
 minScore=$score
   fi
done < $workPath/temp/family.mat.copy

#  tpdbID  1   4        pdbCode
pdbCode=`echo $tpdbID | cut -c-4`
#  tpdbID  5             pdbChain
pdbChain=`echo $tpdbID | cut -c5-`

#run_script align2d
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/align2d.py $PYFULLPATH $workPath $PDBID $pdbCode $pdbChain > $workPath/temp/align2d.log"
else
  cmd="mod9.11 $PYFULLPATH/align2d.py"
fi
echo "$cmd"
eval "$cmd"

#run_script model-single
if test "${run_version}" = "${build_version}"; then
  cmd="${modpy} $PYFULLPATH/model-single.py $workPath $PDBID $tpdbID > $workPath/temp/model-single.log"
else
  cmd="mod9.11 $PYFULLPATH/model-single.py"
fi
echo "$cmd"
eval "$cmd"

mv "$PDBID.B99990001.pdb" "$workPath/$PDBID.pdb"
rm -f $PDBID*