Demo rosetta scripts wrapper component.

rosetta_scripts_demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import logging\n",
    "reload(logging)\n",
    "logging.basicConfig(level=logging.INFO)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:rosetta:Found rosetta database at: /work/fordas/python_local/rosetta/database\n",
      "INFO:rosetta:Version: 1afb81950d464d6243055cb6a566fd124985cd5f\n",
      "INFO:rosetta:core.init: Rosetta version  from\n",
      "INFO:rosetta:core.init: command: pyrosetta -ex1 -ex2aro -database /work/fordas/python_local/rosetta/database\n",
      "INFO:rosetta:core.init: 'RNG device' seed mode, using '/dev/urandom', seed=151738479 seed_offset=0 real_seed=151738479\n",
      "INFO:rosetta:core.init.random: RandomGenerator:init: Normal mode, seed=151738479 RG_type=mt19937\n"
     ]
    }
   ],
   "source": [
    "import rosetta\n",
    "rosetta.init()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from rosetta.protocols.rosetta_scripts import RosettaScriptsParser\n",
    "from rosetta.utility.tag import Tag\n",
    "from rosetta.protocols.jd2 import JobDistributor, Job\n",
    "\n",
    "class RosettaScriptWrapper(object):\n",
    "    \"\"\"Wrapper object that handles parsing a string RosettaScripts protocol and applying the protocol to target poses.\"\"\"\n",
    "    \n",
    "    def __init__(self, protocol_xml, starting_pose = None):\n",
    "        \"\"\"Parse protocol xml, using optional starting_pose if needed by defined movers/filters.\"\"\"\n",
    "        tag = Tag.create(protocol_xml)\n",
    "\n",
    "        if starting_pose is None:\n",
    "            self.protocol = RosettaScriptsParser().parse_protocol_tag(tag)\n",
    "        else:\n",
    "            self.protocol = RosettaScriptsParser().parse_protocol_tag(starting_pose, tag)\n",
    "            \n",
    "        JobDistributor.get_instance().restart()\n",
    "        self.blank_job = JobDistributor.get_instance().current_job()\n",
    "    \n",
    "    def apply(self, target_pose):\n",
    "        \"\"\"Apply protocol to pose.\n",
    "        \n",
    "        Returns:\n",
    "            (result_pose, filter_score)\n",
    "        \"\"\"\n",
    "        \n",
    "        self.protocol.apply(target_pose)\n",
    "        record_job = Job(self.blank_job)\n",
    "        self.protocol.add_values_to_job( target_pose, record_job )\n",
    "        \n",
    "        results = {}\n",
    "        results.update( record_job.get_string_real_pairs() )\n",
    "        results.update( record_job.get_string_string_pairs() )\n",
    "        \n",
    "        return target_pose, results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:rosetta:core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013\n"
     ]
    }
   ],
   "source": [
    "test_sf = rosetta.core.scoring.getScoreFunction()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "test_script = \"\"\"\n",
    "<ROSETTASCRIPTS>\n",
    "        <SCOREFXNS>\n",
    "        </SCOREFXNS>\n",
    "        <TASKOPERATIONS>\n",
    "        </TASKOPERATIONS>\n",
    "        <FILTERS>\n",
    "        <ScoreType name=\"total_score\" score_type=\"total_score\" threshold=100/>\n",
    " \n",
    "        </FILTERS>\n",
    "        <MOVERS>\n",
    "        <FastRelax name=\"fastrelax\" repeats=1 />\n",
    "        </MOVERS>\n",
    "        <PROTOCOLS>\n",
    "        <Add mover=\"fastrelax\" filter=\"total_score\"/>\n",
    "        </PROTOCOLS>\n",
    "</ROSETTASCRIPTS>\n",
    "\"\"\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:rosetta:core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013\n",
      "INFO:rosetta:protocols.simple_filters.ScoreTypeFilter: ScoreType filter for score_type total_score with threshold 100\n",
      "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named \"total_score\" of type ScoreType\n",
      "INFO:rosetta:protocols.relax.FastRelax: ================== Using default script ==================\n",
      "INFO:rosetta:protocols.relax.FastRelax: ================== Using default script ==================\n",
      "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named \"fastrelax\" of type FastRelax\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters\n",
      "added mover \"fastrelax\" with filter \"total_score\"\n",
      "INFO:rosetta:protocols::checkpoint: Deleting checkpoints of FastRelax\n",
      "INFO:rosetta:protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...\n",
      "INFO:rosetta:protocols::checkpoint: Deleting checkpoints of FastRelax\n"
     ]
    }
   ],
   "source": [
    "wrapper = TestScriptWrapper( test_script )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "test_pose = rosetta.pose_from_sequence(\"TESTTESTTEST\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - fastrelax=======================\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: repeat  1981.38  0  0  0.44\n",
      "INFO:rosetta:core.pack.task: Packer task: initialize from command line()\n",
      "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n",
      "INFO:rosetta:core.pack.pack_rotamers: built 297 rotamers at 12 positions.\n",
      "INFO:rosetta:core.pack.pack_rotamers: IG: 58660 bytes\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: ramp_repack_min  7.06057  0.000112984  0.000112984  0.0088\n",
      "INFO:rosetta:core.pack.task: Packer task: initialize from command line()\n",
      "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n",
      "INFO:rosetta:core.pack.pack_rotamers: built 283 rotamers at 12 positions.\n",
      "INFO:rosetta:core.pack.pack_rotamers: IG: 53980 bytes\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: ramp_repack_min  8.24648  0.000228142  0.000228142  0.11\n",
      "INFO:rosetta:core.pack.task: Packer task: initialize from command line()\n",
      "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n",
      "INFO:rosetta:core.pack.pack_rotamers: built 270 rotamers at 12 positions.\n",
      "INFO:rosetta:core.pack.pack_rotamers: IG: 50152 bytes\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: ramp_repack_min  9.79296  0.000347425  0.000347425  0.242\n",
      "INFO:rosetta:core.pack.task: Packer task: initialize from command line()\n",
      "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\n",
      "INFO:rosetta:core.pack.pack_rotamers: built 253 rotamers at 12 positions.\n",
      "INFO:rosetta:core.pack.pack_rotamers: IG: 44316 bytes\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: ramp_repack_min  -1.90835  1.47654  1.47654  0.44\n",
      "INFO:rosetta:protocols.relax.FastRelax: MRP: 0  -1.90835  -1.90835  1.47654  1.47654\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: accept_to_best  -1.90835  1.47654  1.47654  0.44\n",
      "INFO:rosetta:protocols.relax.FastRelax: CMD: endrepeat  -1.90835  1.47654  1.47654  0.44\n",
      "INFO:rosetta:protocols::checkpoint: Deleting checkpoints of FastRelax\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER total_score=======================\n",
      "INFO:rosetta:protocols.simple_filters.ScoreTypeFilter: score total_score is -1.90835. passing.\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER total_score=======================\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: setting status to success\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for total_score==================\n",
      "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: Weighted score of total_score -1.90835\n",
      "============End report for total_score==================\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(<rosetta.core.pose.__pose_all_at_once_.Pose at 0xd990730>,\n",
       " {'total_score': -1.9083521765116358})"
      ]
     },
     "execution_count": 71,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "wrapper.apply(test_pose)"
   ]
  }
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