Set-chi.ipynb

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   "cells": [
    {
     "metadata": {},
     "cell_type": "code",
     "input": "import os\nimport numpy as np\nimport rosetta as r\nimport random\nr.init()\nr.__version__",
     "prompt_number": 1,
     "outputs": [
      {
       "text": "'56891:56891:6efc58f8abb54611ace5a6cdd7e69e6c970a01ef'",
       "output_type": "pyout",
       "metadata": {},
       "prompt_number": 1
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     ],
     "language": "python",
     "trusted": true,
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    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "#Makin a mutation after the helix is created also works\n#Create sequence \nseq = 'R'*5 + 'K'+'R'*5; print seq\npose = r.pose_from_sequence(seq, res_type=\"fa_standard\") \nscorefxn = r.get_fa_scorefxn()\n\n#Create perfect alpha helix\n#phi = -57.8, Psi -47.0\nfor i in range(1, pose.total_residue()+1):\n    pose.set_phi(i, -57.9)\n    pose.set_psi(i, -47.9)\n\n\n    #pack side chains\npacker_task = r.standard_packer_task(pose)\npacker_task.restrict_to_repacking() \nprint packer_task\npack_mover = r.PackRotamersMover(scorefxn, packer_task) \npack_mover.apply(pose) \n\n#show the resuls\nprint scorefxn(pose)\n",
     "prompt_number": 14,
     "outputs": [
      {
       "output_type": "stream",
       "text": "RRRRRKRRRRR\n#Packer_Task\n\nresid\tpack?\tdesign?\tallowed_aas\n1\tTRUE\tFALSE\tARG:NtermProteinFull\n2\tTRUE\tFALSE\tARG\n3\tTRUE\tFALSE\tARG\n4\tTRUE\tFALSE\tARG\n5\tTRUE\tFALSE\tARG\n6\tTRUE\tFALSE\tLYS\n7\tTRUE\tFALSE\tARG\n8\tTRUE\tFALSE\tARG\n9\tTRUE\tFALSE\tARG\n10\tTRUE\tFALSE\tARG\n11\tTRUE\tFALSE\tARG:CtermProteinFull\n\n-0.165960801682",
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       "text": "\n",
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      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pose.residue(6).chi(r.Vector1([1.,2.,3.,4.]))\nprint scorefxn(pose)\n#As expected energy not updated",
     "prompt_number": 15,
     "outputs": [
      {
       "output_type": "stream",
       "text": "-0.165960801682\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
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    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pack_mover.apply(pose) \nprint scorefxn(pose)\npose.residue(6).set_chi(1, 90.)\nprint scorefxn(pose)\n#Energy still not updated??",
     "prompt_number": 11,
     "outputs": [
      {
       "output_type": "stream",
       "text": "0.121413424414\n0.121413424414\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pack_mover.apply(pose) \nprint scorefxn(pose)\npose.residue(6).set_all_chi(r.Vector1([1.,2.,3.,4.]))\nprint scorefxn(pose)\n#Energy still not updated??",
     "prompt_number": 12,
     "outputs": [
      {
       "output_type": "stream",
       "text": "0.112666631125\n0.112666631125\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pack_mover.apply(pose) \nprint scorefxn(pose)\npose.set_chi(1,6,90.)\nprint scorefxn(pose)\n#Ahh, energy finally updated",
     "prompt_number": 13,
     "outputs": [
      {
       "output_type": "stream",
       "text": "-0.165960801682\n11.3687762064\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
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     "cell_type": "code",
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