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    "<!--NOTEBOOK_HEADER-->\n",
    "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n",
    "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*"
   ]
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   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.02-Analyzing-energy-between-residues.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
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   "source": [
    "# Practice: Analyzing energy between residues\n",
    "Keywords: pose_from_rcsb(), pdb2pose(), EMapVector()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install pyrosettacolabsetup\n",
    "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n",
    "import pyrosetta; pyrosetta.init()\n",
    "from pyrosetta import *\n",
    "from pyrosetta.teaching import *\n",
    "init()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# From previous section:\n",
    "sfxn = get_score_function(True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Analyze the energy between residues Y102 and Q408 in cetuximab (PDB code 1YY9, use the `pyrosetta.toolbox.pose_from_rcsb` function to download it and load it into a new `Pose` object) by following the steps below. \n",
    "\n",
    "A. Internally, a Pose object has a list of residues, numbered starting from 1. To find the residue numbers of Y102 of chain D and Q408 of chain A, use the residue chain identifier and the PDB residue number to convert to the pose numbering using the `pose2pdb()` method:\n",
    "\n",
    "```\n",
    "pose = pyrosetta.toolbox.pose_from_rcsb(\"1YY9\")\n",
    "res102 = pose.pdb_info().pdb2pose(\"D\", 102)\n",
    "res408 = pose.pdb_info().pdb2pose(\"A\", 408)\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# get the pose numbers for Y102 (chain D) and Q408 (chain A)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "nbgrader": {
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   "source": [
    "### BEGIN SOLUTION\n",
    "pose = pyrosetta.toolbox.pose_from_rcsb(\"1YY9\")\n",
    "res102 = pose.pdb_info().pdb2pose(\"D\", 102)\n",
    "res408 = pose.pdb_info().pdb2pose(\"A\", 408)\n",
    "### END SOLUTION"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "B. Score the pose and determine the van der Waals energies and solvation energy between these two residues. Use the following commands to isolate contributions from particular pairs of residues, where `rsd102` and `rsd408` are the two residue objects of interest from above (not the residue number -- use `pose.residue(res_num)` to access the objects): \n",
    "\n",
    "```\n",
    "emap = EMapVector()\n",
    "sfxn.eval_ci_2b(pose.residue(res102), pose.residue(res408), pose, emap)\n",
    "print(emap[fa_atr])\n",
    "print(emap[fa_rep])\n",
    "print(emap[fa_sol])\n",
    "```"
   ]
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  {
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   "source": [
    "### BEGIN SOLUTION\n",
    "emap = EMapVector()\n",
    "sfxn.eval_ci_2b(pose.residue(res102), pose.residue(res408), pose, emap)\n",
    "print(emap[fa_atr])\n",
    "print(emap[fa_rep])\n",
    "print(emap[fa_sol])\n",
    "### END SOLUTION"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
   "source": []
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   "cell_type": "markdown",
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   "source": [
    "<!--NAVIGATION-->\n",
    "< [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.02-Analyzing-energy-between-residues.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
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