Run.java.csh

This is the csh script that we run to generate our binding footprints.

  #! /bin/csh -fe
  cd /home1/balius/RCR/projects_BNL/EGFR/active_erlotinib/009_footprint
  set get_java = "/home1/balius/RCR/projects_BNL/noel_binding_footprint/trajanalyzer2_mod"
  set parm_name =  "active_erlotinib.com.gas.leap.parm"
  set traj_name =  "active_erlotinib.com.ptraj.stripfit.trj"
  set get_parm_file = "/home1/balius/RCR/projects_BNL/EGFR/active_erlotinib/002_gas.wat.e16.prep_ssbonds/${parm_name}"
  set get_trj_file = "/home1/balius/RCR/projects_BNL/EGFR/active_erlotinib/005_mdwat.com.pointprop/${traj_name}"
  cp ${get_java}/* .
  cp ${get_parm_file} .
  cp ${get_trj_file} .
  #####################################################################
  cat <<EOF2 >  mk_input_file.csh
  cd /home1/balius/RCR/projects_BNL/EGFR/active_erlotinib/009_footprint
  sed s/PARM_FILE/${parm_name}/g  input.txt > temp1.txt
  sed s/TRJ_FILE/${traj_name}/g   temp1.txt > temp2.txt
  sed s/NUMSS/"5000"/g            temp2.txt > temp1.txt
  sed s/START/"1"/g               temp1.txt > temp2.txt
  sed s/STOP/"5001"/g             temp2.txt > temp1.txt
  sed s/RESNUM/"275"/g            temp1.txt > temp2.txt
  sed s/RESNUM/"275"/g            temp2.txt > temp1.txt
  sed s/RESFIRST/"1"/g            temp1.txt > temp2.txt
  sed s/RESLAST/274/g             temp2.txt > temp1.txt
  EOF2
  #####################################################################
  csh mk_input_file.csh
  rm -f mk_input_file.csh
  cat temp1.txt > input.txt
  cp /home1/balius/RCR/projects_BNL/program_scrips_develop/get_values_from_parm.py .
  sed s/'PUT FILE NAME HERE'/'active_erlotinib.com.gas.leap.parm'/g get_values_from_parm.py > temp.py
  mv temp.py get_values_from_parm.py
  python get_values_from_parm.py > parm_val.txt
  set input = `cat parm_val.txt`
  set res_atom_num = $input[1]
  set lig_atom_num = $input[2]
  #####################################################################
  cat <<EOF3 >  mk_analysis2.csh
  cd /home1/balius/RCR/projects_BNL/EGFR/active_erlotinib/009_footprint
  sed s/NUMOFRESIDUES/274/g  analysis2.java > temp1.txt
  sed s/TOTALNUMOFSS/5000/g  temp1.txt      > temp2.txt
  sed s/NUMOFATOMSPRO/$res_atom_num/g temp2.txt      > temp1.txt
  sed s/NUMOFATOMSLIG/${lig_atom_num}/g   temp1.txt      > temp2.txt
  EOF3
  #####################################################################
  csh mk_analysis2.csh
  rm -f mk_input_file.csh
  cat temp2.txt > analysis2.java
  rm -f temp1.txt temp2.txt
  javac Main.java
  java Main