JED_Testing.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# <u>JED Testing\n",
    "# This notebook contains tests for the JED Software</u>\n",
    "#### Last Revision: May, 2018\n",
    "#### Author: Charles David"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Define Project:\n",
    "* Define Variables and Bash Functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "USER=\"cflcyd\"\n",
    "NAME=\"JED\"\n",
    "PROJECT=\"/workspace/${USER}/git/${NAME}\"\n",
    "NOTES=\"${PROJECT}/NOTES\"\n",
    "TEMP=\"/workspace/${USER}/tmp\"\n",
    "\n",
    "TMPFS=\"/dev/shm/${USER}/${NAME}\"\n",
    "JTMP=\"/dev/shm/${USER}/JAVATMP\"\n",
    "\n",
    "JED=\"/workspace/cflcyd/git/JED/jars/version1.1/JED_Driver.jar\"\n",
    "FES=\"/workspace/cflcyd/git/JED/jars/version1.1/FES_Driver.jar\"\n",
    "FSSA=\"/workspace/cflcyd/git/JED/jars/version1.1/FSSA_Driver.jar\"\n",
    "FSSA_Iterated=\"/workspace/cflcyd/git/version1.1/JED/jars/FSSA_Iterated_Driver.jar\"\n",
    "POOL=\"/workspace/cflcyd/git/JED/jars/version1.1/POOL_Driver.jar\"\n",
    "SSA=\"/workspace/cflcyd/git/JED/jars/version1.1/SSA_Driver.jar\"\n",
    "VIZ=\"/workspace/cflcyd/git/JED/jars/version1.1/VIZ_Driver.jar\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### setJava () is used to define the java command that sets up the java VM:\n",
    "* The function has Two required args and One optional arg:\n",
    "    * ` Xms   Xmx   [-jar] `\n",
    "    * Create enough heap space\n",
    "    * Idealy, set `Xms=Xmx`\n",
    "    * Specify `-jar` if running a jar file\n",
    "        * Example usage: `setJava 16G 16G -jar`\n",
    "        * NOTE: Currently, the JVM cannot access shared memory and large pages\n",
    "        * Currently using Java version 1.8"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "setJava () {\n",
    "JAVA=\"java \\\n",
    "      -d64 \\\n",
    "      -server \\\n",
    "      -Xms${1} \\\n",
    "      -Xmx${2} \\\n",
    "      -Xconcurrentio \\\n",
    "      -XX:+AggressiveOpts \\\n",
    "      -XX:+AlwaysPreTouch \\\n",
    "      -XX:+UseG1GC \\\n",
    "      -XX:MaxGCPauseMillis=500 \\\n",
    "      -XX:ParallelGCThreads=8 \\\n",
    "      -XX:ConcGCThreads=2 \\\n",
    "      -XX:+UseStringDeduplication \\\n",
    "      -XX:-UseGCOverheadLimit \\\n",
    "      -XX:InitiatingHeapOccupancyPercent=75 \\\n",
    "      -Djava.io.tmpdir=${TEMP} ${3}\"\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### SINGLE CHAIN PDBs PRE-PROCESSING JOB\n",
    "* JED Driver Input File:"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "1      0\n",
    "/workspace/cflcyd/git/JED/test/Single/PDBs/\n",
    "TEST_PRE-PROCESSING_SINGLE \t\t\t1A6N.pdb\t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running JED Driver: \n",
      "Getting the input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
      "Reading Input File... \n",
      "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
      "Below are the parameters to be processed:\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "1      0\t//SINGLE CHAIN PDBs PRE-PROCESSING JOB\n",
      "/workspace/cflcyd/git/JED/test/Single/PDBs/\n",
      "TEST_PRE-PROCESSING_SINGLE \t\t\t1A6N.pdb\t\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 3\n",
      "\n",
      "Processing line: 1\n",
      "\tREAD PDBs = true\n",
      "\tMULTI CHAIN PDBs = false\n",
      "Processing line: 2\n",
      "\tWorking Directory = /workspace/cflcyd/git/JED/test/Single/PDBs/\n",
      "Processing line: 3\n",
      "\tDescription = TEST_PRE-PROCESSING_SINGLE\n",
      "\tPDB Reference File = 1A6N.pdb\n",
      "Done.\n",
      "Reading PDB Reference File... \n",
      "Done.\n",
      "Reading PDB files... Done. (126.909 seconds)\n",
      "Performing Pre-Processing of PDB files for JED Analysis... Done. (13.853 seconds)\n",
      "JED successfully completed: 2018-05-18 02:41:09\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test/Single/PDBs\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${JED} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running JED Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
    "Reading Input File... \n",
    "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Single_PP.txt\n",
    "Below are the parameters to be processed:\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "1      0\t//SINGLE CHAIN PDBs PRE-PROCESSING JOB\n",
    "/workspace/cflcyd/git/JED/test/Single/PDBs/\n",
    "TEST_PRE-PROCESSING_SINGLE \t\t\t1A6N.pdb\t\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 3\n",
    "\n",
    "Processing line: 1\n",
    "\tREAD PDBs = true\n",
    "\tMULTI CHAIN PDBs = false\n",
    "Processing line: 2\n",
    "\tWorking Directory = /workspace/cflcyd/git/JED/test/Single/PDBs/\n",
    "Processing line: 3\n",
    "\tDescription = TEST_PRE-PROCESSING_SINGLE\n",
    "\tPDB Reference File = 1A6N.pdb\n",
    "Done.\n",
    "Reading PDB Reference File... \n",
    "Done.\n",
    "Reading PDB files... Done. (131.689 seconds)\n",
    "Performing Pre-Processing of PDB files for JED Analysis... Done. (14.318 seconds)\n",
    "JED successfully completed: 2018-05-16 16:38:44"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### MULTI CHAIN PDBs PRE-PROCESSING JOB\n",
    "* JED Driver Input File:"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "1      1\n",
    "/workspace/cflcyd/git/JED/test/Multi/PDBs/\n",
    "TEST_PRE-PROCESSING_MULTI \t\t\tMVb_A_B_ATP.pdb\t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running JED Driver: \n",
      "Getting the input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
      "Reading Input File... \n",
      "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
      "Below are the parameters to be processed:\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "1    1 \n",
      "/workspace/cflcyd/git/JED/test/Multi/PDBs/\n",
      "TEST_PRE-PROCESSING_MULTI\t\tMVb_A_B_ATP.pdb\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 3\n",
      "\n",
      "Processing line: 1\n",
      "\tREAD PDBs = true\n",
      "\tMULTI CHAIN PDBs = true\n",
      "Processing line: 2\n",
      "\tWorking Directory = /workspace/cflcyd/git/JED/test/Multi/PDBs/\n",
      "Processing line: 3\n",
      "\tDescription = TEST_PRE-PROCESSING_MULTI\n",
      "\tPDB Reference File = MVb_A_B_ATP.pdb\n",
      "Done.\n",
      "Reading PDB Reference File... \n",
      "Done.\n",
      "Reading PDB files... Done. (25.659 seconds)\n",
      "Performing Pre-Processing of PDB files for JED Analysis... Done. (5.336 seconds)\n",
      "JED successfully completed: 2018-05-18 02:41:47\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test/Multi/PDBs\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${JED} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running JED Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
    "Reading Input File... \n",
    "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi_PP.txt\n",
    "Below are the parameters to be processed:\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "1    1 \n",
    "/workspace/cflcyd/git/JED/test/Multi/PDBs/\n",
    "TEST_PRE-PROCESSING_MULTI\t\tMVb_A_B_ATP.pdb\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 3\n",
    "\n",
    "Processing line: 1\n",
    "\tREAD PDBs = true\n",
    "\tMULTI CHAIN PDBs = true\n",
    "Processing line: 2\n",
    "\tWorking Directory = /workspace/cflcyd/git/JED/test/Multi/PDBs/\n",
    "Processing line: 3\n",
    "\tDescription = TEST_PRE-PROCESSING_MULTI\n",
    "\tPDB Reference File = MVb_A_B_ATP.pdb\n",
    "Done.\n",
    "Reading PDB Reference File... \n",
    "Done.\n",
    "Reading PDB files... Done. (26.995 seconds)\n",
    "Performing Pre-Processing of PDB files for JED Analysis... Done. (5.372 seconds)\n",
    "JED successfully completed: 2018-05-16 16:44:57"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### SINGLE CHAIN JOB\n",
    "* JED Driver Input File:\n",
    "    * cPCA\n",
    "    * dpPCA\n",
    "    * VIZ\n",
    "    * z-cutoff set to 3.0"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "0      0  \n",
    "/workspace/cflcyd/git/JED/test/Single/\n",
    "TEST_SINGLE\t\t\t1A6N.pdb\n",
    "0.00    3.00\n",
    "20     10     5     3.0\n",
    "residues.txt\n",
    "residue_pairs.txt\n",
    "original_PDB_Coordinates.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running JED Driver: \n",
      "Getting the input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
      "Reading Input File... \n",
      "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
      "Below are the parameters to be processed:\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "0      0 \n",
      "/workspace/cflcyd/git/JED/test/Single/\n",
      "TEST_SINGLE\t\t\t1A6N.pdb\n",
      "0.00    3.00\n",
      "20     10     5     3.0\n",
      "residues.txt\n",
      "residue_pairs.txt\n",
      "original_PDB_Coordinates.txt\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 8\n",
      "\n",
      "Processing line: 1\n",
      "\tREAD PDBs = false\n",
      "\tMULTI CHAIN PDBs = false\n",
      "Processing line: 2\n",
      "\tWorking Directory = /workspace/cflcyd/git/JED/test/Single/\n",
      "Processing line: 3\n",
      "\tDescription = TEST_SINGLE\n",
      "\tPDB Reference File = 1A6N.pdb\n",
      "Processing line: 4\n",
      "\tPercent = 0.0\n",
      "\tZ-Cutoff = 3.0\n",
      "Processing line: 5\n",
      "\t#Cartesian Modes = 20\n",
      "\t#Distance-Pair-Modes = 10\n",
      "\t#Modes-Viz = 5\n",
      "\tMode Amplitude = 3.0\n",
      "Processing line: 6\n",
      "\tCartesian Residue List = residues.txt\n",
      "Processing line: 7\n",
      "\tResidue Pairs List = residue_pairs.txt\n",
      "Processing line: 8\n",
      "\tMatrix of Coordinates = original_PDB_Coordinates.txt\n",
      "Done.\n",
      "Reading PDB Reference File... \n",
      "Done.\n",
      "Reading Coordinate File... Done. (0.718 seconds)\n",
      "Performing cPCA analysis... Done. (66.318 seconds)\n",
      "Performing dpPCA analysis... Done. (3.870 seconds)\n",
      "Performing mode visualization... Done. (62.320 seconds)\n",
      "Performing Free Energy Calculations... Done. (50.167 seconds)\n",
      "JED successfully completed: 2018-05-18 02:44:58\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test/Single\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${JED} ${INPUT}\"\n",
    "\n",
    "${COMMAND}\n"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running JED Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
    "Reading Input File... \n",
    "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Single.txt\n",
    "Below are the parameters to be processed:\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "0      0 \n",
    "/workspace/cflcyd/git/JED/test/Single/\n",
    "TEST_SINGLE\t\t\t1A6N.pdb\n",
    "0.00    3.00\n",
    "20     10     5     3.0\n",
    "residues.txt\n",
    "residue_pairs.txt\n",
    "original_PDB_Coordinates.txt\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 8\n",
    "\n",
    "Processing line: 1\n",
    "\tREAD PDBs = false\n",
    "\tMULTI CHAIN PDBs = false\n",
    "Processing line: 2\n",
    "\tWorking Directory = /workspace/cflcyd/git/JED/test/Single/\n",
    "Processing line: 3\n",
    "\tDescription = TEST_SINGLE\n",
    "\tPDB Reference File = 1A6N.pdb\n",
    "Processing line: 4\n",
    "\tPercent = 0.0\n",
    "\tZ-Cutoff = 3.0\n",
    "Processing line: 5\n",
    "\t#Cartesian Modes = 20\n",
    "\t#Distance Pair Modes = 10\n",
    "\t#Modes Viz = 5\n",
    "\tMode Amplitude = 3.0\n",
    "Processing line: 6\n",
    "\tCartesian Residue List = residues.txt\n",
    "Processing line: 7\n",
    "\tResidue Pairs List = residue_pairs.txt\n",
    "Processing line: 8\n",
    "\tMatrix of Coordinates = original_PDB_Coordinates.txt\n",
    "Done.\n",
    "Reading PDB Reference File... \n",
    "Done.\n",
    "Reading Coordinate File... Done. (0.751 seconds)\n",
    "Performing cPCA analysis... Done. (64.946 seconds)\n",
    "Performing dpPCA analysis... Done. (2.681 seconds)\n",
    "Performing mode visualization... Done. (54.568 seconds)\n",
    "JED successfully completed: 2018-05-16 17:10:50"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### MULTI CHAIN JOB\n",
    "* JED Driver Input File:\n",
    "    * cPCA\n",
    "    * dpPCA\n",
    "    * VIZ\n",
    "    * z-cutoff set to 3.0"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "0      1  \n",
    "/workspace/cflcyd/git/JED/test/Multi/\n",
    "TEST_MULTI\t\t\tMVb_A_B_ATP.pdb\n",
    "0.00     3.00\n",
    "20     5     5     3.0\n",
    "residues.txt\n",
    "residue_pairs.txt\n",
    "original_PDB_Coordinates.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running JED Driver: \n",
      "Getting the input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
      "Reading Input File... \n",
      "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
      "Below are the parameters to be processed:\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "0      1 \n",
      "/workspace/cflcyd/git/JED/test/Multi/\n",
      "TEST_MULTI\t\t\tMVb_A_B_ATP.pdb\n",
      "0.00     0.00\n",
      "20     5     5     3.0\n",
      "residues.txt\n",
      "residue_pairs.txt\n",
      "original_PDB_Coordinates.txt\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 8\n",
      "\n",
      "Processing line: 1\n",
      "\tREAD PDBs = false\n",
      "\tMULTI CHAIN PDBs = true\n",
      "Processing line: 2\n",
      "\tWorking Directory = /workspace/cflcyd/git/JED/test/Multi/\n",
      "Processing line: 3\n",
      "\tDescription = TEST_MULTI\n",
      "\tPDB Reference File = MVb_A_B_ATP.pdb\n",
      "Processing line: 4\n",
      "\tPercent = 0.0\n",
      "\tZ-Cutoff = 0.0\n",
      "Processing line: 5\n",
      "\t#Cartesian Modes = 20\n",
      "\t#Distance-Pair-Modes = 5\n",
      "\t#Modes-Viz = 5\n",
      "\tMode Amplitude = 3.0\n",
      "Processing line: 6\n",
      "\tCartesian Residue List = residues.txt\n",
      "Processing line: 7\n",
      "\tResidue Pairs List = residue_pairs.txt\n",
      "Processing line: 8\n",
      "\tMatrix of Coordinates = original_PDB_Coordinates.txt\n",
      "Done.\n",
      "Reading PDB Reference File... \n",
      "Done.\n",
      "Reading Coordinate File... Done. (0.314 seconds)\n",
      "Performing cPCA analysis... Done. (12.424 seconds)\n",
      "Performing dpPCA analysis... Done. (2.080 seconds)\n",
      "Performing mode visualization... Done. (43.818 seconds)\n",
      "Performing Free Energy Calculations... Done. (3.169 seconds)\n",
      "JED successfully completed: 2018-05-18 02:46:07\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test/Multi\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${JED} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running JED Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
    "Reading Input File... \n",
    "Reading the input file: /workspace/cflcyd/git/JED/input_files/JED_Driver_Multi.txt\n",
    "Below are the parameters to be processed:\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "0      1 \n",
    "/workspace/cflcyd/git/JED/test/Multi/\n",
    "TEST_MULTI\t\t\tMVb_A_B_ATP.pdb\n",
    "0.00     0.00\n",
    "20     5     5     3.0\n",
    "residues.txt\n",
    "residue_pairs.txt\n",
    "original_PDB_Coordinates.txt\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 8\n",
    "\n",
    "Processing line: 1\n",
    "\tREAD PDBs = false\n",
    "\tMULTI CHAIN PDBs = true\n",
    "Processing line: 2\n",
    "\tWorking Directory = /workspace/cflcyd/git/JED/test/Multi/\n",
    "Processing line: 3\n",
    "\tDescription = TEST_MULTI\n",
    "\tPDB Reference File = MVb_A_B_ATP.pdb\n",
    "Processing line: 4\n",
    "\tPercent = 0.0\n",
    "\tZ-Cutoff = 0.0\n",
    "Processing line: 5\n",
    "\t#Cartesian Modes = 20\n",
    "\t#Distance Pair Modes = 5\n",
    "\t#Modes Viz = 5\n",
    "\tMode Amplitude = 3.0\n",
    "Processing line: 6\n",
    "\tCartesian Residue List = residues.txt\n",
    "Processing line: 7\n",
    "\tResidue Pairs List = residue_pairs.txt\n",
    "Processing line: 8\n",
    "\tMatrix of Coordinates = original_PDB_Coordinates.txt\n",
    "Done.\n",
    "Reading PDB Reference File... \n",
    "Done.\n",
    "Reading Coordinate File... Done. (0.314 seconds)\n",
    "Performing cPCA analysis... Done. (12.194 seconds)\n",
    "Performing dpPCA analysis... Done. (1.530 seconds)\n",
    "Performing mode visualization... Done. (43.063 seconds)\n",
    "JED successfully completed: 2018-05-16 17:13:42"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### FES\n",
    "* FES Driver Input File:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "3\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/FES/\n",
    "Test_FES\n",
    "******************************************************************************************************\n",
    "Test_1\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "1     2     2000     0     0\n",
    "******************************************************************************************************\n",
    "Test_2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "1     3     2000     0     0\n",
    "******************************************************************************************************\n",
    "Test_3\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "2     3     2000     0     0\n",
    "******************************************************************************************************\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running FES Driver: \n",
      "Getting the input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/FES.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/FES.txt\n",
      "Reading Input File... \n",
      "Below is the input file that was read: /workspace/cflcyd/git/JED/input_files/FES.txt\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "3\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/FES/\n",
      "Test_FES\n",
      "******************************************************************************************************\n",
      "Test_1\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "1     2     2000     0     0\n",
      "******************************************************************************************************\n",
      "Test_2\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "1     3     2000     0     0\n",
      "******************************************************************************************************\n",
      "Test_3\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "2     3     2000     0     0\n",
      "******************************************************************************************************\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 19\n",
      "\n",
      "Reading line 1\n",
      "\tThe number of jobs =  3\n",
      "Reading line 2\n",
      "\tOutput Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/FES/\n",
      "Reading line 3\n",
      "\tBatch Description = Test_FES\n",
      "Reading line 4\n",
      "******************************************************************************************************\n",
      "\n",
      "Reading line 5,  LINE 1 of job: 1\n",
      "\tJob Description = Test_1\n",
      "Reading line 6,  LINE 2 of job: 1\n",
      "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "Reading line 7,  LINE 3 of job: 1\n",
      "\tThe principal components = ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "Reading line 8,  LINE 4 of job: 1\n",
      "\tOP1 = 0\n",
      "\tOP2 = 1\n",
      "\tNumber of points to use = 2000\n",
      "\tOffset = 0\n",
      "\tCellsize = 0.0\n",
      "Program will automatically calculate a cellsize.\n",
      "Reading line 9\n",
      "******************************************************************************************************\n",
      "\n",
      "The bounds for the KDE are: OP1(-2221.124,377.048); OP2(-185.114,699.442)\n",
      "The effective cellsize is: 10.149109374999998\n",
      "Kernel Bandwidths are: 7.823\t3.313\n",
      "Reading line 10,  LINE 1 of job: 2\n",
      "\tJob Description = Test_2\n",
      "Reading line 11,  LINE 2 of job: 2\n",
      "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "Reading line 12,  LINE 3 of job: 2\n",
      "\tThe principal components = ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "Reading line 13,  LINE 4 of job: 2\n",
      "\tOP1 = 0\n",
      "\tOP2 = 2\n",
      "\tNumber of points to use = 2000\n",
      "\tOffset = 0\n",
      "\tCellsize = 0.0\n",
      "Program will automatically calculate a cellsize.\n",
      "Reading line 14\n",
      "******************************************************************************************************\n",
      "\n",
      "The bounds for the KDE are: OP1(-2221.124,377.048); OP2(-541.931,331.489)\n",
      "The effective cellsize is: 10.149109374999998\n",
      "Kernel Bandwidths are: 6.584\t1.983\n",
      "Reading line 15,  LINE 1 of job: 3\n",
      "\tJob Description = Test_3\n",
      "Reading line 16,  LINE 2 of job: 3\n",
      "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
      "Reading line 17,  LINE 3 of job: 3\n",
      "\tThe principal components = ss_151_top_20_weighted_DVPs_CORR.txt\n",
      "Reading line 18,  LINE 4 of job: 3\n",
      "\tOP1 = 1\n",
      "\tOP2 = 2\n",
      "\tNumber of points to use = 2000\n",
      "\tOffset = 0\n",
      "\tCellsize = 0.0\n",
      "Program will automatically calculate a cellsize.\n",
      "Reading line 19\n",
      "******************************************************************************************************\n",
      "\n",
      "The bounds for the KDE are: OP1(-185.114,699.442); OP2(-541.931,331.489)\n",
      "The effective cellsize is: 3.455296875\n",
      "Kernel Bandwidths are: 2.957\t2.169\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/FES.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${FES} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running FES Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/FES.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/FES.txt\n",
    "Reading Input File... \n",
    "Below is the input file that was read: /workspace/cflcyd/git/JED/input_files/FES.txt\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "3\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/FES/\n",
    "Test_FES\n",
    "******************************************************************************************************\n",
    "Test_1\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "1     2     2000     0     0\n",
    "******************************************************************************************************\n",
    "Test_2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "1     3     2000     0     0\n",
    "******************************************************************************************************\n",
    "Test_3\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "2     3     2000     0     0\n",
    "******************************************************************************************************\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 19\n",
    "\n",
    "Reading line 1\n",
    "\tThe number of jobs =  3\n",
    "Reading line 2\n",
    "\tOutput Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/FES/\n",
    "\tThe output directory does not exist.\n",
    "\tAttempting to create it:\n",
    "\t\tSuccess.\n",
    "Reading line 3\n",
    "\tBatch Description = Test_FES\n",
    "Reading line 4\n",
    "******************************************************************************************************\n",
    "\n",
    "Reading line 5,  LINE 1 of job: 1\n",
    "\tJob Description = Test_1\n",
    "Reading line 6,  LINE 2 of job: 1\n",
    "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "Reading line 7,  LINE 3 of job: 1\n",
    "\tThe Delta Vectors = ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "Reading line 8,  LINE 4 of job: 1\n",
    "\tOP1 = 0\n",
    "\tOP2 = 1\n",
    "\tNumber of points to use = 2000\n",
    "\tOffset = 0\n",
    "\tCellsize = 0.0\n",
    "Program will automatically calculate a cellsize.\n",
    "Reading line 9\n",
    "******************************************************************************************************\n",
    "\n",
    "The bounds for the KDE are: OP1(-2221.124,377.048); OP2(-185.114,699.442)\n",
    "The effective cellsize is: 10.149109374999998\n",
    "Kernel Bandwidths are: 7.823\t3.313\n",
    "Reading line 10,  LINE 1 of job: 2\n",
    "\tJob Description = Test_2\n",
    "Reading line 11,  LINE 2 of job: 2\n",
    "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "Reading line 12,  LINE 3 of job: 2\n",
    "\tThe Delta Vectors = ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "Reading line 13,  LINE 4 of job: 2\n",
    "\tOP1 = 0\n",
    "\tOP2 = 2\n",
    "\tNumber of points to use = 2000\n",
    "\tOffset = 0\n",
    "\tCellsize = 0.0\n",
    "Program will automatically calculate a cellsize.\n",
    "Reading line 14\n",
    "******************************************************************************************************\n",
    "\n",
    "The bounds for the KDE are: OP1(-2221.124,377.048); OP2(-541.931,331.489)\n",
    "The effective cellsize is: 10.149109374999998\n",
    "Kernel Bandwidths are: 6.584\t1.983\n",
    "Reading line 15,  LINE 1 of job: 3\n",
    "\tJob Description = Test_3\n",
    "Reading line 16,  LINE 2 of job: 3\n",
    "\tJob Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "Reading line 17,  LINE 3 of job: 3\n",
    "\tThe Delta Vectors = ss_151_top_20_weighted_DVPs_CORR.txt\n",
    "Reading line 18,  LINE 4 of job: 3\n",
    "\tOP1 = 1\n",
    "\tOP2 = 2\n",
    "\tNumber of points to use = 2000\n",
    "\tOffset = 0\n",
    "\tCellsize = 0.0\n",
    "Program will automatically calculate a cellsize.\n",
    "Reading line 19\n",
    "******************************************************************************************************\n",
    "\n",
    "The bounds for the KDE are: OP1(-185.114,699.442); OP2(-541.931,331.489)\n",
    "The effective cellsize is: 3.455296875\n",
    "Kernel Bandwidths are: 2.957\t2.169"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### SSA\n",
    "* SSA Driver Input File:"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/SSA/\n",
    "MG_PCA_Model_Test\n",
    "*******************************************************************************************************************\n",
    "MG1\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/COV/ss_151_top_20_eigenvectors_COV.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "*******************************************************************************************************************\n",
    "MG2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/COV/     ss_10_Residue_Pairs_top_10_eigenvectors_COV.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/CORR/     ss_10_Residue_Pairs_top_10_eigenvectors_CORR.txt\n",
    "*******************************************************************************************************************"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Running SSA Driver: \n",
      "Getting the SSA input file: \n",
      "User specified input file (must be the first program argument)\n",
      "These are the specified program args:\n",
      "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
      "Working Directory = /tmp/hsperfdata_cflcyd\n",
      "Input File Path = /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
      "Reading Input File... \n",
      "Below is the input file that was read: /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "2\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/SSA/\n",
      "MG_PCA_Model_Test\n",
      "**********************************************************************************************************************************\n",
      "MG1\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/COV/ss_151_top_20_eigenvectors_COV.txt\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
      "**********************************************************************************************************************************\n",
      "MG2\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/COV/ss_10_Residue_Pairs_top_10_eigenvectors_COV.txt\n",
      "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/CORR/ss_10_Residue_Pairs_top_10_eigenvectors_CORR.txt\n",
      "**********************************************************************************************************************************\n",
      "--------------------------------------------------------------------------------------------------------------------------------\n",
      "The number of lines of parameters in the input file is: 12\n",
      "\n",
      "Reading line 1\n",
      "\tThe number of jobs =  2\n",
      "Reading line 2\n",
      "\tOutput Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/SSA/\n",
      "Reading line 3\n",
      "\tBatch Description = MG_PCA_Model_Test\n",
      "Reading line 4\n",
      "**********************************************************************************************************************************\n",
      "\n",
      "Reading line 5, the FIRST LINE of job: 1\n",
      "\tJob Description = MG1\n",
      "Reading line 6, the SECOND LINE of job: 1\n",
      "\tEigenvector File 1 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/COV/ss_151_top_20_eigenvectors_COV.txt\n",
      "Reading line 7, the THIRD LINE of job: 1\n",
      "\tEigenvector File 2 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
      "Reading line 8\n",
      "**********************************************************************************************************************************\n",
      "\n",
      "Reading line 9, the FIRST LINE of job: 2\n",
      "\tJob Description = MG2\n",
      "Reading line 10, the SECOND LINE of job: 2\n",
      "\tEigenvector File 1 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/COV/ss_10_Residue_Pairs_top_10_eigenvectors_COV.txt\n",
      "Reading line 11, the THIRD LINE of job: 2\n",
      "\tEigenvector File 2 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/CORR/ss_10_Residue_Pairs_top_10_eigenvectors_CORR.txt\n",
      "Reading line 12\n",
      "**********************************************************************************************************************************\n",
      "\n"
     ]
    }
   ],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/SSA_Single.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${SSA} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "Running SSA Driver: \n",
    "Getting the input file: \n",
    "The path to the input file must be the first argument:\n",
    "These are the command args:\n",
    "Arg 1 Value = /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
    "Working Directory = /tmp/hsperfdata_cflcyd\n",
    "Input File Path = /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
    "Reading Input File... \n",
    "Below is the input file that was read: /workspace/cflcyd/git/JED/input_files/SSA_Single.txt\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/SSA/\n",
    "MG_PCA_Model_Test\n",
    "**********************************************************************************************************************\n",
    "MG1\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/COV/ss_151_top_20_eigenvectors_COV.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "**********************************************************************************************************************\n",
    "MG2\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/COV/ss_10_Residue_Pairs_top_10_eigenvectors_COV.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/CORR/ss_10_Residue_Pairs_top_10_eigenvectors_CORR.txt\n",
    "**********************************************************************************************************************\n",
    "----------------------------------------------------------------------------------------------------------------------\n",
    "The number of lines of parameters in the input file is: 12\n",
    "\n",
    "Reading line 1\n",
    "\tThe number of jobs =  2\n",
    "Reading line 2\n",
    "\tOutput Directory = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/SSA/\n",
    "\tThe output directory does not exist.\n",
    "\tAttempting to create it:\n",
    "\t\tSuccess.\n",
    "Reading line 3\n",
    "\tBatch Description = MG_PCA_Model_Test\n",
    "Reading line 4\n",
    "**********************************************************************************************************************\n",
    "\n",
    "Reading line 5, the FIRST LINE of job: 1\n",
    "\tJob Description = MG1\n",
    "Reading line 6, the SECOND LINE of job: 1\n",
    "\tDirectory 1 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/COV/\n",
    "\tFirst Eigenvector File = ss_151_top_20_eigenvectors_COV.txt\n",
    "Reading line 7, the THIRD LINE of job: 1\n",
    "\tDirectory 2 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/\n",
    "\tFirst Eigenvector File = ss_151_top_20_eigenvectors_CORR.txt\n",
    "Reading line 8\n",
    "**********************************************************************************************************************\n",
    "\n",
    "Reading line 9, the FIRST LINE of job: 2\n",
    "\tJob Description = MG2\n",
    "Reading line 10, the SECOND LINE of job: 2\n",
    "\tDirectory 1 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/COV/\n",
    "\tFirst Eigenvector File = ss_10_Residue_Pairs_top_10_eigenvectors_COV.txt\n",
    "Reading line 11, the THIRD LINE of job: 2\n",
    "\tDirectory 2 = /workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/dpPCA/CORR/\n",
    "\tFirst Eigenvector File = ss_10_Residue_Pairs_top_10_eigenvectors_CORR.txt\n",
    "Reading line 12\n",
    "**********************************************************************************************************************\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### VIZ\n",
    "* VIZ Driver Input File:"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "7\n",
    "**********************************************************************************************************************\n",
    "1     1     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST1/\n",
    "**********************************************************************************************************************\n",
    "1     2     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST2/\n",
    "**********************************************************************************************************************\n",
    "1     3     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST3/\n",
    "**********************************************************************************************************************\n",
    "1     4     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST4/\n",
    "**********************************************************************************************************************\n",
    "1     5     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST5/\n",
    "**********************************************************************************************************************\n",
    "1     10     3.0     .05     .05     100     5     0     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST6/\n",
    "**********************************************************************************************************************\n",
    "1     20     3.0     .05     .05     100     5     1     CORR\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/ss_151_RMSF_edited.pdb\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_eigenvalues_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_eigenvectors_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_modes_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MAXES_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/cPCA/CORR/ss_151_top_20_square_pca_mode_MINS_CORR.txt\n",
    "/workspace/cflcyd/git/JED/test/Single/JED_RESULTS_TEST_SINGLE/VIZ_TEST7/\n",
    "**********************************************************************************************************************"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "module load java\n",
    "setJava 8G 8G -jar\n",
    "\n",
    "INPUT=\"/workspace/cflcyd/git/JED/input_files/VIZ.txt\"\n",
    "OUT=\"/workspace/cflcyd/git/JED/test\"\n",
    "\n",
    "COMMAND=\"${JAVA} ${VIZ} ${INPUT}\"\n",
    "\n",
    "${COMMAND}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Bash",
   "language": "bash",
   "name": "bash"
  },
  "language_info": {
   "codemirror_mode": "shell",
   "file_extension": ".sh",
   "mimetype": "text/x-sh",
   "name": "bash"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}