01-PyRosseta-test.ipynb

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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import os\n",
      "import numpy as np\n",
      "import rosetta as r\n",
      "import random\n",
      "r.init()\n",
      "os.getcwd()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 25,
       "text": [
        "'/home/ajasja/notebooks'"
       ]
      }
     ],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "pose = r.pose_from_sequence('A'*10) \n",
      "scorefxn = r.get_fa_scorefxn() "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 18
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#pmm = r.PyMOLMover(target_host=\"XXXXX\")\n",
      "pmm = r.PyMOLMover(target_host=\"localhost\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "pose.set_psi(random.randint(1,10),(random.random()-0.5)*180)\n",
      "pose.set_phi(random.randint(1,10),(random.random()-0.5)*180)\n",
      "print scorefxn(pose)\n",
      "pmm.apply(pose)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "27.0474905598\n"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "pose.set_psi(5,-50)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 21
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print scorefxn(pose)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "27.8830412834\n"
       ]
      }
     ],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#test the scoring\n",
      "import time\n",
      "import random\n",
      "\n",
      "start = time.time()\n",
      "minscore = +100000000 \n",
      "numrun=10000;\n",
      "for i in xrange(numrun):\n",
      "    pose.set_psi(random.randint(1,10),(random.random()-0.5)*180)\n",
      "    pose.set_phi(random.randint(1,10),(random.random()-0.5)*180)\n",
      "    score = scorefxn(pose)\n",
      "    if score<minscore:\n",
      "        minscore=score\n",
      "\n",
      "end = time.time()\n",
      "elapsed = end - start\n",
      "print \"Time taken: \", elapsed, \"seconds.\"\n",
      "print \"Min Score is: \", minscore\n",
      "print \"Time per run: \", elapsed*1000.0/numrun, \"msec\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Time taken:  2.63420510292 seconds.\n",
        "Min Score is:  16.4718879927\n",
        "Time per run:  0.263420510292 msec\n"
       ]
      }
     ],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#test only the loops\n",
      "import time\n",
      "import random\n",
      "\n",
      "start = time.time()\n",
      "minscore = +100000000 \n",
      "numrun=10000;\n",
      "for i in xrange(numrun):\n",
      "    pass\n",
      "    random.randint(1,10); (random.random()-0.5)*180;\n",
      "    random.randint(1,10);score=(random.random()-0.5)*180;\n",
      "    #score = scorefxn(pose)\n",
      "    if score<minscore:\n",
      "        minscore=score\n",
      "\n",
      "end = time.time()\n",
      "elapsed = end - start\n",
      "print \"Time taken: \", elapsed, \"seconds.\"\n",
      "print \"Min Score is: \", minscore\n",
      "print \"Time per run: \", elapsed*1000.0/numrun, \"msec\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Time taken:  0.0392308235168 seconds.\n",
        "Min Score is:  -89.9782554597\n",
        "Time per run:  0.00392308235168 msec\n"
       ]
      }
     ],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      " r.mm_twist?"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 26
    }
   ],
   "metadata": {}
  }
 ]
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