06-Rotamers.ipynb

{
 "worksheets": [
  {
   "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
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pmm = r.PyMOLMover(target_host=\"127.0.0.1\")",
     "prompt_number": 2,
     "outputs": [],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "#Makin a mutation after the helix is created also works\n#Create sequence \nseq = 'R'*5 + 'R'+'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#Make mutation    \nmut = r.MutateResidue(6 , 'R1A')\nmut.apply(pose)    \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)\npmm.apply(pose)",
     "prompt_number": 3,
     "outputs": [
      {
       "output_type": "stream",
       "text": "RRRRRRRRRRR\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\tR1A\n7\tTRUE\tFALSE\tARG\n8\tTRUE\tFALSE\tARG\n9\tTRUE\tFALSE\tARG\n10\tTRUE\tFALSE\tARG\n11\tTRUE\tFALSE\tARG:CtermProteinFull\n",
       "stream": "stdout"
      },
      {
       "output_type": "stream",
       "text": "\n-1.05767090814",
       "stream": "stdout"
      },
      {
       "output_type": "stream",
       "text": "\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "pose.chi(5,6)",
     "prompt_number": 4,
     "outputs": [
      {
       "text": "-100.07056096817568",
       "output_type": "pyout",
       "metadata": {},
       "prompt_number": 4
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "[attr for attr in dir(pose.residue(6)) if \"ch\" in attr]",
     "prompt_number": 5,
     "outputs": [
      {
       "text": "['atomic_charge',\n 'attached_H_begin',\n 'attached_H_end',\n 'chain',\n 'chi',\n 'chi_atoms',\n 'chi_rotamers',\n 'connections_match',\n 'first_sidechain_atom',\n 'first_sidechain_hydrogen',\n 'is_branch_lower_terminus',\n 'is_charged',\n 'mainchain_atom',\n 'mainchain_atoms',\n 'mainchain_torsion',\n 'mainchain_torsions',\n 'n_mainchain_atoms',\n 'nchi',\n 'set_all_chi',\n 'set_chi',\n 'sidechainAtoms_begin']",
       "output_type": "pyout",
       "metadata": {},
       "prompt_number": 5
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "#First try the obvious chi_rotamers!\npose.residue(6).chi_rotamers(1)",
     "prompt_number": 6,
     "outputs": [
      {
       "output_type": "pyerr",
       "ename": "TypeError",
       "evalue": "No Python class registered for C++ class utility::vector1<std::pair<double, double>, std::allocator<std::pair<double, double> > >",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-6-8a0ba53d69e7>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[1;31m#First try the obvious chi_rotamers!\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0mpose\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mresidue\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m6\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mchi_rotamers\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;31mTypeError\u001b[0m: No Python class registered for C++ class utility::vector1<std::pair<double, double>, std::allocator<std::pair<double, double> > >"
       ]
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "# Try advice from https://www.rosettacommons.org/content/rotamer-libraries-pyrosetta\nimport rosetta.core.pack.dunbrack as dr",
     "prompt_number": 7,
     "outputs": [],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "dir(dr)\nrot = dr.SingleResidueDunbrackLibrary()\nprint rot",
     "prompt_number": 8,
     "outputs": [
      {
       "output_type": "pyerr",
       "ename": "RuntimeError",
       "evalue": "This class cannot be instantiated from Python",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-8-7f65fdefc8df>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[0mdir\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdr\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0mrot\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdr\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mSingleResidueDunbrackLibrary\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      3\u001b[0m \u001b[1;32mprint\u001b[0m \u001b[0mrot\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
        "\u001b[1;31mRuntimeError\u001b[0m: This class cannot be instantiated from Python"
       ]
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "#As per the FAQ this should work\n#http://www.pyrosetta.org/faq#TOC-5.-How-do-I-convert-AP-or-CAP-objects-to-regular-class-objects-\nrot = dr.SingleResidueDunbrackLibraryCAP().get()\nprint rot\n#But it just return None",
     "prompt_number": 9,
     "outputs": [
      {
       "output_type": "stream",
       "text": "None\n",
       "stream": "stdout"
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    },
    {
     "metadata": {},
     "cell_type": "code",
     "input": "#Maybe it's in the pack_mover\nb = r.utility.OStringStream()\npack_mover.show(b)\nprint b.str()\npack_mover.rotamer_sets()",
     "prompt_number": 10,
     "outputs": [
      {
       "output_type": "stream",
       "text": "Mover name: PackRotamersMover, Mover type: PackRotamersMover, Mover current tag:NoTag\nScore function: talaris2013\n\n",
       "stream": "stdout"
      },
      {
       "output_type": "pyerr",
       "ename": "TypeError",
       "evalue": "No to_python (by-value) converter found for C++ type: utility::pointer::owning_ptr<core::pack::rotamer_set::RotamerSets const>",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-10-07a6709b0baa>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[0mpack_mover\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshow\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mb\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[1;32mprint\u001b[0m \u001b[0mb\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mstr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0mpack_mover\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrotamer_sets\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;31mTypeError\u001b[0m: No to_python (by-value) converter found for C++ type: utility::pointer::owning_ptr<core::pack::rotamer_set::RotamerSets const>"
       ]
      }
     ],
     "language": "python",
     "trusted": true,
     "collapsed": false
    }
   ],
   "metadata": {}
  }
 ],
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