Using Andrew LF's PDBParser.Py .ipynb

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   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "An Intro/ Documenting the elucidation of the PDB Parser Obj\n",
      "===========================================================\n",
      "\n",
      "Found in  Rosetta/tools/python_pdb_structure/ or something like that\n",
      "\n",
      "\n",
      "SJB"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from pdb_structure import *\n",
      "\n",
      "file = \"/Users/stevebertolani/2e2r.pdb\"\n",
      "pdb1 = pdbstructure_from_file( file )\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Access the Chains"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for chains in pdb1.chainmap:\n",
      "    print chains"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "A\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#print pdb1.pdb_lines()  #this dumps the entire pdb as a list (including HETATM) and \"\\n\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#for chain in pdb1.chains:\n",
      "#    print chain.residue?"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "  #  print chain.residue"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Access using chainmaps and residue maps"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for ch in pdb1.chainmap:\n",
      "    for res in pdb1.chainmap[ ch ].resmap:\n",
      "        print (pdb1.residue(ch,res).resname,ch)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('ASP', 'A')\n",
        "('LEU', 'A')\n",
        "('ASN', 'A')\n",
        "('ASN', 'A')\n",
        "('ALA', 'A')\n",
        "('GLY', 'A')\n",
        "('LEU', 'A')\n",
        "('LEU', 'A')\n",
        "('ALA', 'A')\n",
        "('ILE', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
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        "('MET', 'A')\n",
        "('SER', 'A')\n",
        "('ASP', 'A')\n",
        "('GLN', 'A')\n",
        "('LEU', 'A')\n",
        "('ALA', 'A')\n",
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        "('SER', 'A')\n",
        "('SER', 'A')\n",
        "('THR', 'A')\n",
        "('ASP', 'A')\n",
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        "('ASP', 'A')\n",
        "('ARG', 'A')\n",
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        "('GLU', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('ASP', 'A')\n",
        "('GLN', 'A')\n",
        "('HOH', 'A')\n",
        "('LYS', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('GLU', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HIS', 'A')\n",
        "('LEU', 'A')\n",
        "('VAL', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n",
        "('HOH', 'A')\n"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Access the atom level objects"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for chain in pdb1.chains:\n",
      "        for res in chain.residues:\n",
      "                for atom in res.atoms:\n",
      "                    print atom.xyz"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "(11.437, -29.418, -24.737)\n",
        "(10.618, -29.046, -25.925)\n",
        "(9.149, -29.532, -25.917)\n",
        "(8.512, -29.562, -26.972)\n",
        "(11.343, -29.46, -27.212)\n",
        "(12.508, -28.518, -27.575)\n",
        "(12.22, -27.669, -28.835)\n",
        "(12.583, -26.19, -28.651)\n",
        "(13.746, -25.756, -29.492)\n",
        "(8.609, -29.929, -24.757)\n",
        "(7.251, -29.495, -24.408)\n",
        "(7.38, -27.988, -24.207)\n",
        "(8.395, -27.542, -23.659)\n",
        "(6.963, -30.219, -23.089)\n",
        "(8.281, -30.562, -22.553)\n",
        "(9.158, -30.837, -23.738)\n",
        "(6.41, -27.206, -24.656)\n",
        "(6.717, -25.815, -24.948)\n",
        "(6.802, -24.913, -23.734)\n",
        "(6.469, -25.276, -22.594)\n",
        "(5.779, -25.221, -26.018)\n",
        "(4.305, -25.236, -25.702)\n",
        "(3.443, -26.071, -26.417)\n",
        "(3.76, -24.402, -24.733)\n",
        "(2.09, -26.09, -26.165)\n",
        "(2.399, -24.418, -24.464)\n",
        "(1.568, -25.266, -25.192)\n",
        "(0.215, -25.314, -24.964)\n",
        "(7.294, -23.733, -24.038)\n",
        "(7.463, -22.631, -23.136)\n",
        "(6.507, -22.534, -21.94)\n",
        "(5.291, -22.605, -22.111)\n",
        "(7.326, -21.392, -23.989)\n",
        "(7.687, -20.198, -23.262)\n",
        "(6.844, -19.557, -22.665)\n",
        "(8.968, -19.88, -23.259)\n",
        "(7.063, -22.348, -20.743)\n",
        "(6.274, -22.336, -19.507)\n",
        "(6.263, -22.347, -19.517)\n",
        "(5.368, -21.117, -19.407)\n",
        "(4.232, -21.214, -18.951)\n",
        "(7.195, -22.413, -18.274)\n",
        "(7.166, -22.474, -18.279)\n",
        "(6.482, -22.341, -16.94)\n",
        "(6.432, -22.701, -16.978)\n",
        "(5.566, -23.525, -16.73)\n",
        "(5.636, -23.988, -16.968)\n",
        "(4.919, -23.511, -15.362)\n",
        "(5.217, -24.36, -15.55)\n",
        "(5.836, -23.984, -14.293)\n",
        "(4.004, -25.201, -15.523)\n",
        "(5.857, -19.948, -19.808)\n",
        "(5.036, -18.749, -19.753)\n",
        "(3.796, -18.953, -20.624)\n",
        "(2.695, -18.588, -20.204)\n",
        "(5.828, -17.482, -20.153)\n",
        "(6.854, -17.181, -19.056)\n",
        "(4.88, -16.307, -20.398)\n",
        "(7.713, -15.942, -19.318)\n",
        "(3.967, -19.546, -21.797)\n",
        "(2.818, -19.814, -22.675)\n",
        "(1.848, -20.766, -21.981)\n",
        "(0.639, -20.512, -21.943)\n",
        "(3.223, -20.364, -24.055)\n",
        "(1.997, -20.731, -24.864)\n",
        "(4.04, -19.347, -24.803)\n",
        "(2.361, -21.856, -21.425)\n",
        "(1.545, -22.826, -20.684)\n",
        "(1.472, -22.801, -20.758)\n",
        "(0.778, -22.153, -19.549)\n",
        "(-0.4, -22.444, -19.29)\n",
        "(2.431, -23.939, -20.095)\n",
        "(2.198, -24.098, -20.381)\n",
        "(2.941, -24.778, -21.108)\n",
        "(3.196, -23.856, -19.426)\n",
        "(1.461, -21.258, -18.84)\n",
        "(0.892, -20.544, -17.711)\n",
        "(-0.225, -19.611, -18.163)\n",
        "(-1.281, -19.555, -17.565)\n",
        "(2.001, -19.766, -17.003)\n",
        "(1.565, -19.094, -15.751)\n",
        "(1.231, -19.802, -14.611)\n",
        "(1.389, -17.792, -15.449)\n",
        "(0.895, -18.952, -13.664)\n",
        "(0.979, -17.727, -14.144)\n",
        "(-0.002, -18.877, -19.239)\n",
        "(-1.048, -17.994, -19.738)\n",
        "(-2.275, -18.792, -20.174)\n",
        "(-3.416, -18.339, -19.987)\n",
        "(-0.524, -17.147, -20.89)\n",
        "(0.573, -16.151, -20.529)\n",
        "(1.085, -15.473, -21.793)\n",
        "(0.123, -15.119, -19.506)\n",
        "(-2.058, -19.97, -20.739)\n",
        "(-3.189, -20.803, -21.148)\n",
        "(-4.056, -21.184, -19.955)\n",
        "(-5.282, -21.1, -20.035)\n",
        "(-2.719, -22.064, -21.83)\n",
        "(-2.249, -21.987, -23.258)\n",
        "(-1.737, -23.354, -23.67)\n",
        "(-3.385, -21.525, -24.196)\n",
        "(-3.455, -21.592, -18.832)\n",
        "(-4.286, -21.949, -17.656)\n",
        "(-4.858, -20.754, -16.906)\n",
        "(-5.831, -20.888, -16.145)\n",
        "(-3.578, -22.883, -16.624)\n",
        "(-3.295, -24.21, -17.256)\n",
        "(-2.346, -22.265, -16.033)\n",
        "(-4.289, -19.579, -17.118)\n",
        "(-4.804, -18.338, -16.555)\n",
        "(-5.965, -17.757, -17.386)\n",
        "(-6.549, -16.762, -16.989)\n",
        "(-3.71, -17.32, -16.454)\n",
        "(-6.264, -18.359, -18.533)\n",
        "(-7.272, -17.807, -19.45)\n",
        "(-8.625, -17.815, -18.752)\n",
        "(-9.032, -18.865, -18.26)\n",
        "(-7.343, -18.629, -20.723)\n",
        "(-8.355, -18.143, -21.759)\n",
        "(-8.014, -16.794, -22.376)\n",
        "(-6.935, -16.21, -22.102)\n",
        "(-8.888, -16.327, -23.128)\n",
        "(-9.302, -16.676, -18.685)\n",
        "(-10.656, -16.664, -18.132)\n",
        "(-11.665, -17.498, -18.9)\n",
        "(-11.531, -17.774, -20.082)\n",
        "(-11.042, -15.202, -18.209)\n",
        "(-9.723, -14.479, -18.195)\n",
        "(-8.867, -15.317, -19.056)\n",
        "(-12.69, -17.911, -18.163)\n",
        "(-13.821, -18.608, -18.733)\n",
        "(-14.65, -17.692, -19.627)\n",
        "(-14.615, -16.481, -19.472)\n",
        "(-14.726, -19.079, -17.608)\n",
        "(-14.107, -20.1, -16.665)\n",
        "(-13.773, -21.398, -17.357)\n",
        "(-14.645, -21.964, -18.061)\n",
        "(-12.618, -21.844, -17.222)\n",
        "(-15.403, -18.311, -20.53)\n",
        "(-16.332, -17.591, -21.413)\n",
        "(-17.357, -16.812, -20.595)\n",
        "(-17.745, -17.231, -19.501)\n",
        "(-17.064, -18.582, -22.338)\n",
        "(-16.189, -19.229, -23.412)\n",
        "(-16.932, -19.507, -24.734)\n",
        "(-17.584, -20.892, -24.806)\n",
        "(-17.838, -21.319, -26.237)\n",
        "(-17.783, -15.657, -21.12)\n",
        "(-18.783, -14.773, -20.499)\n",
        "(-18.848, -14.915, -20.477)\n",
        "(-19.933, -14.601, -21.509)\n",
        "(-19.68, -14.448, -22.698)\n",
        "(-18.14, -13.396, -20.142)\n",
        "(-18.3, -13.698, -19.662)\n",
        "(-17.165, -13.538, -18.963)\n",
        "(-18.655, -12.34, -20.255)\n",
        "(-19.199, -12.352, -19.761)\n",
        "(-16.767, -13.795, -19.453)\n",
        "(-16.2, -12.38, -18.814)\n",
        "(-18.595, -11.228, -19.247)\n",
        "(-21.172, -14.604, -21.033)\n",
        "(-22.325, -14.431, -21.915)\n",
        "(-22.355, -14.398, -21.855)\n",
        "(-22.721, -12.942, -21.893)\n",
        "(-22.559, -12.239, -20.907)\n",
        "(-23.512, -15.34, -21.492)\n",
        "(-23.513, -15.163, -21.225)\n",
        "(-23.503, -16.793, -22.011)\n",
        "(-23.242, -16.628, -21.21)\n",
        "(-23.934, -17.123, -23.294)\n",
        "(-23.607, -17.422, -22.282)\n",
        "(-23.107, -17.842, -21.184)\n",
        "(-22.565, -17.218, -20.142)\n",
        "(-23.939, -18.458, -23.748)\n",
        "(-23.341, -18.77, -22.287)\n",
        "(-23.107, -19.168, -21.626)\n",
        "(-22.293, -18.574, -20.138)\n",
        "(-23.524, -19.473, -22.904)\n",
        "(-22.68, -19.341, -21.218)\n",
        "(-23.522, -20.793, -23.317)\n",
        "(-22.422, -20.68, -21.234)\n",
        "(-23.219, -12.449, -23.032)\n",
        "(-23.658, -11.051, -23.128)\n",
        "(-24.997, -10.774, -22.461)\n",
        "(-25.185, -9.724, -21.879)\n",
        "(-23.746, -10.637, -24.601)\n",
        "(-25.907, -11.729, -22.606)\n",
        "(-27.258, -11.647, -22.011)\n",
        "(-27.98, -10.354, -22.409)\n",
        "(-28.359, -9.542, -21.553)\n",
        "(-27.194, -11.764, -20.478)\n",
        "(-26.99, -13.183, -20.056)\n",
        "(-26.6, -13.413, -18.31)\n",
        "(-24.833, -12.935, -18.194)\n",
        "(-28.18, -10.162, -23.716)\n",
        "(-28.984, -9.023, -24.151)\n",
        "(-30.376, -9.214, -23.529)\n",
        "(-30.837, -10.362, -23.424)\n",
        "(-29.023, -9.183, -25.67)\n",
        "(-28.776, -10.597, -25.952)\n",
        "(-27.802, -11.011, -24.85)\n",
        "(-30.993, -8.123, -23.128)\n",
        "(-32.286, -8.151, -22.42)\n",
        "(-33.395, -8.528, -23.41)\n",
        "(-33.679, -7.752, -24.341)\n",
        "(-32.518, -6.793, -21.785)\n",
        "(-33.737, -6.736, -20.903)\n",
        "(-34.69, -7.483, -21.162)\n",
        "(-33.809, -5.916, -19.98)\n",
        "(-34.017, -9.698, -23.251)\n",
        "(-34.967, -10.184, -24.25)\n",
        "(-36.286, -9.411, -24.215)\n",
        "(-37.09, -9.6, -25.141)\n",
        "(-35.215, -11.641, -23.819)\n",
        "(-35.019, -11.625, -22.371)\n",
        "(-33.883, -10.653, -22.127)\n",
        "(-36.488, -8.554, -23.225)\n",
        "(-37.699, -7.736, -23.156)\n",
        "(-37.553, -6.4, -23.867)\n",
        "(-38.548, -5.709, -24.072)\n",
        "(-38.153, -7.473, -21.694)\n",
        "(-37.264, -6.572, -21.014)\n",
        "(-38.14, -8.75, -20.843)\n",
        "(-36.329, -6.032, -24.248)\n",
        "(-36.067, -4.71, -24.828)\n",
        "(-36.103, -4.819, -26.341)\n",
        "(-35.532, -5.738, -26.934)\n",
        "(-34.679, -4.184, -24.36)\n",
        "(-34.287, -2.913, -25.11)\n",
        "(-34.669, -3.932, -22.847)\n",
        "(-36.798, -3.896, -27.016)\n",
        "(-36.791, -3.902, -28.476)\n",
        "(-35.385, -3.711, -29.045)\n",
        "(-34.608, -2.946, -28.476)\n",
        "(-37.682, -2.708, -28.839)\n",
        "(-38.468, -2.42, -27.627)\n",
        "(-37.611, -2.81, -26.455)\n",
        "(-35.086, -4.411, -30.123)\n",
        "(-33.807, -4.223, -30.818)\n",
        "(-33.684, -2.786, -31.309)\n",
        "(-34.632, -2.202, -31.867)\n",
        "(-33.644, -5.214, -31.967)\n",
        "(-33.27, -6.616, -31.491)\n",
        "(-32.838, -6.824, -30.317)\n",
        "(-33.352, -7.591, -32.253)\n",
        "(-32.507, -2.211, -31.075)\n",
        "(-32.166, -0.859, -31.487)\n",
        "(-30.663, -0.687, -31.409)\n",
        "(-29.958, -1.53, -30.854)\n",
        "(-32.832, 0.191, -30.596)\n",
        "(-32.301, 0.234, -29.284)\n",
        "(-30.169, 0.416, -31.95)\n",
        "(-28.777, 0.752, -31.761)\n",
        "(-28.44, 0.929, -30.284)\n",
        "(-27.391, 0.454, -29.823)\n",
        "(-28.364, 1.975, -32.604)\n",
        "(-29.141, 3.251, -32.283)\n",
        "(-30.169, 3.247, -31.577)\n",
        "(-28.759, 4.359, -32.739)\n",
        "(-29.333, 1.553, -29.521)\n",
        "(-29.091, 1.756, -28.096)\n",
        "(-28.983, 0.4, -27.382)\n",
        "(-28.104, 0.214, -26.545)\n",
        "(-30.196, 2.639, -27.453)\n",
        "(-30.247, 4.025, -28.111)\n",
        "(-29.989, 2.775, -25.958)\n",
        "(-28.964, 4.794, -28.013)\n",
        "(-29.862, -0.547, -27.711)\n",
        "(-29.812, -1.864, -27.073)\n",
        "(-28.474, -2.551, -27.367)\n",
        "(-27.829, -3.098, -26.458)\n",
        "(-30.956, -2.771, -27.534)\n",
        "(-30.969, -4.128, -26.811)\n",
        "(-32.022, -5.049, -27.376)\n",
        "(-32.0, -6.407, -26.713)\n",
        "(-33.098, -7.272, -27.254)\n",
        "(-28.073, -2.531, -28.63)\n",
        "(-26.841, -3.201, -29.04)\n",
        "(-25.633, -2.61, -28.317)\n",
        "(-24.804, -3.343, -27.777)\n",
        "(-26.66, -3.141, -30.565)\n",
        "(-25.546, -1.29, -28.289)\n",
        "(-24.393, -0.616, -27.697)\n",
        "(-24.407, -0.79, -26.184)\n",
        "(-23.374, -0.969, -25.556)\n",
        "(-24.371, 0.869, -28.086)\n",
        "(-24.144, 1.104, -29.58)\n",
        "(-24.453, 2.541, -29.952)\n",
        "(-22.718, 0.774, -29.994)\n",
        "(-25.592, -0.772, -25.587)\n",
        "(-25.721, -1.013, -24.159)\n",
        "(-25.225, -2.419, -23.807)\n",
        "(-24.461, -2.607, -22.851)\n",
        "(-27.201, -0.856, -23.716)\n",
        "(-27.607, 0.508, -23.868)\n",
        "(-27.341, -1.124, -22.209)\n",
        "(-25.667, -3.389, -24.582)\n",
        "(-25.309, -4.781, -24.376)\n",
        "(-23.798, -4.943, -24.485)\n",
        "(-23.182, -5.586, -23.652)\n",
        "(-25.97, -5.67, -25.427)\n",
        "(-27.414, -5.541, -25.322)\n",
        "(-25.674, -7.14, -25.178)\n",
        "(-23.231, -4.369, -25.533)\n",
        "(-21.79, -4.491, -25.763)\n",
        "(-20.968, -3.838, -24.663)\n",
        "(-19.969, -4.41, -24.229)\n",
        "(-21.415, -3.906, -27.128)\n",
        "(-21.87, -4.754, -28.305)\n",
        "(-21.711, -3.885, -29.547)\n",
        "(-21.088, -6.045, -28.43)\n",
        "(-21.362, -2.652, -24.212)\n",
        "(-20.607, -1.961, -23.16)\n",
        "(-20.756, -2.64, -21.819)\n",
        "(-19.844, -2.612, -21.004)\n",
        "(-20.994, -0.496, -23.071)\n",
        "(-20.514, 0.438, -24.548)\n",
        "(-21.909, -3.271, -21.595)\n",
        "(-22.134, -4.022, -20.376)\n",
        "(-21.23, -5.252, -20.353)\n",
        "(-20.591, -5.548, -19.344)\n",
        "(-23.617, -4.42, -20.317)\n",
        "(-23.985, -5.133, -19.041)\n",
        "(-23.798, -6.345, -18.946)\n",
        "(-24.468, -4.538, -18.072)\n",
        "(-21.147, -5.942, -21.475)\n",
        "(-20.29, -7.1, -21.626)\n",
        "(-18.838, -6.681, -21.396)\n",
        "(-18.125, -7.349, -20.667)\n",
        "(-20.478, -7.697, -23.021)\n",
        "(-19.512, -8.788, -23.471)\n",
        "(-19.616, -10.027, -22.627)\n",
        "(-19.736, -9.139, -24.917)\n",
        "(-18.418, -5.58, -22.004)\n",
        "(-17.037, -5.084, -21.838)\n",
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        "(-15.648, -5.148, -19.884)\n",
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       "output_type": "stream",
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       "text": [
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        "(-13.808, 0.079, -7.5)\n",
        "(-10.804, 11.525, -25.432)\n",
        "(-15.603, -24.904, -18.624)\n",
        "(-21.74, 7.007, -33.032)\n",
        "(11.589, -4.38, -11.256)\n",
        "(-25.871, -1.573, -18.84)\n",
        "(15.212, -16.047, -41.143)\n",
        "(10.67, -14.279, -35.997)\n",
        "(-14.013, -19.763, -42.098)\n",
        "(-36.366, -10.538, -27.616)\n",
        "(-18.642, -18.123, -17.115)\n",
        "(-8.561, 4.139, -40.239)\n",
        "(-16.251, 5.494, -13.501)\n",
        "(-25.047, 3.52, -16.042)\n",
        "(-10.295, 0.987, -41.208)\n",
        "(14.585, 4.589, -17.301)\n",
        "(-30.836, 0.242, -35.622)\n",
        "(0.175, -5.869, -6.98)\n",
        "(-6.765, 8.006, -15.543)\n",
        "(-10.351, 6.265, -40.385)\n",
        "(13.491, -11.985, -21.014)\n",
        "(12.387, -24.048, -25.664)\n",
        "(-19.8, -19.847, -42.654)\n",
        "(10.448, -23.696, -24.016)\n",
        "(-20.925, -13.766, -45.562)\n",
        "(-21.97, -10.061, -44.726)\n",
        "(-12.182, 9.626, -34.33)\n",
        "(15.755, -8.881, -20.158)\n",
        "(12.667, -1.85, -11.116)\n",
        "(-36.267, 0.087, -31.827)\n",
        "(-26.46, -4.703, -16.592)\n",
        "(-10.622, -21.916, -26.452)\n",
        "(-34.926, 2.813, -32.432)\n",
        "(-19.849, -8.56, -44.107)\n",
        "(-6.58, -2.435, -9.488)\n",
        "(-13.083, -21.262, -25.58)\n",
        "(-17.523, -12.925, -24.269)\n",
        "(-4.703, -9.977, -44.57)\n",
        "(-15.184, -12.722, -22.8)\n",
        "(8.506, 1.379, -20.783)\n",
        "(12.072, -18.622, -46.969)\n",
        "(-6.154, 5.319, -40.286)\n",
        "(-15.904, -18.615, -27.942)\n",
        "(-23.057, -8.171, -46.375)\n",
        "(-12.932, -18.227, -43.928)\n",
        "(6.365, 1.459, -22.321)\n",
        "(17.308, -13.899, -20.393)\n",
        "(15.249, -17.5, -18.553)\n",
        "(11.469, -17.319, -32.857)\n",
        "(-31.597, -2.152, -34.495)\n",
        "(-29.922, -3.964, -33.453)\n",
        "(-37.095, -0.885, -23.36)\n",
        "(-42.591, -4.271, -24.825)\n",
        "(-3.534, -24.391, -36.272)\n",
        "(-5.792, -23.291, -36.737)\n",
        "(-12.237, -20.648, -29.935)\n",
        "(-17.64, -17.038, -26.763)\n",
        "(-16.635, -15.587, -24.055)\n",
        "(-11.337, -8.216, -44.047)\n",
        "(-16.565, -4.756, -46.479)\n",
        "(-8.56, 2.569, -14.244)\n",
        "(-9.503, -23.602, -14.756)\n",
        "(10.16, -22.378, -20.847)\n",
        "(9.289, -19.848, -19.927)\n"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for res in pdb1.chainmap[ 'A' ].resmap :\n",
      "        print pdb1.residue('A',res).resname"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "HOH\n",
        "HOH\n",
        "ASP\n",
        "LEU\n",
        "ASN\n",
        "ASN\n",
        "ALA\n",
        "GLY\n",
        "LEU\n",
        "LEU\n",
        "ALA\n",
        "ILE\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "MET\n",
        "SER\n",
        "ASP\n",
        "GLN\n",
        "LEU\n",
        "ALA\n",
        "LEU\n",
        "SER\n",
        "SER\n",
        "THR\n",
        "ASP\n",
        "LEU\n",
        "ALA\n",
        "ASP\n",
        "ARG\n",
        "GLU\n",
        "LEU\n",
        "VAL\n",
        "VAL\n",
        "ILE\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "2OH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "LEU\n",
        "LYS\n",
        "LYS\n",
        "GLY\n",
        "GLU\n",
        "LEU\n",
        "HIS\n",
        "MET\n",
        "PRO\n",
        "VAL\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "ILE\n",
        "LYS\n",
        "TYR\n",
        "ASN\n",
        "HIS\n",
        "PHE\n",
        "VAL\n",
        "GLN\n",
        "LYS\n",
        "ALA\n",
        "LEU\n",
        "LYS\n",
        "ASP\n",
        "GLU\n",
        "SER\n",
        "GLN\n",
        "ILE\n",
        "TYR\n",
        "ASP\n",
        "MET\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "VAL\n",
        "SER\n",
        "TYR\n",
        "ASN\n",
        "LYS\n",
        "ILE\n",
        "LYS\n",
        "PRO\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HIS\n",
        "GLN\n",
        "GLY\n",
        "ALA\n",
        "GLU\n",
        "TYR\n",
        "ASP\n",
        "GLN\n",
        "GLU\n",
        "MET\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "SER\n",
        "ASP\n",
        "HOH\n",
        "HOH\n",
        "ALA\n",
        "LYS\n",
        "ALA\n",
        "ILE\n",
        "ALA\n",
        "LEU\n",
        "SER\n",
        "ASN\n",
        "HOH\n",
        "HOH\n",
        "LEU\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "LEU\n",
        "ALA\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "GLU\n",
        "ALA\n",
        "GLU\n",
        "PRO\n",
        "LEU\n",
        "HIS\n",
        "VAL\n",
        "LEU\n",
        "HOH\n",
        "ILE\n",
        "LYS\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "VAL\n",
        "CYS\n",
        "PHE\n",
        "LEU\n",
        "GLU\n",
        "MET\n",
        "LEU\n",
        "GLU\n",
        "ALA\n",
        "LYS\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "ASP\n",
        "GLU\n",
        "PHE\n",
        "GLU\n",
        "TYR\n",
        "ALA\n",
        "LEU\n",
        "VAL\n",
        "ASP\n",
        "ASP\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "ALA\n",
        "GLY\n",
        "LYS\n",
        "MET\n",
        "ASP\n",
        "PRO\n",
        "ARG\n",
        "ARG\n",
        "LEU\n",
        "MET\n",
        "SER\n",
        "LEU\n",
        "VAL\n",
        "GLY\n",
        "LEU\n",
        "ILE\n",
        "SER\n",
        "ARG\n",
        "TYR\n",
        "VAL\n",
        "THR\n",
        "LEU\n",
        "PHE\n",
        "VAL\n",
        "GLU\n",
        "GLU\n",
        "GLU\n",
        "LYS\n",
        "LYS\n",
        "LEU\n",
        "HOH\n",
        "MET\n",
        "HIS\n",
        "ILE\n",
        "GLU\n",
        "ASP\n",
        "VAL\n",
        "GLU\n",
        "ALA\n",
        "VAL\n",
        "GLN\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "PRO\n",
        "ASP\n",
        "MET\n",
        "PRO\n",
        "TYR\n",
        "ALA\n",
        "THR\n",
        "VAL\n",
        "ASP\n",
        "PRO\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "GOL\n",
        "GOL\n",
        "GOL\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "LYS\n",
        "TYR\n",
        "LYS\n",
        "LYS\n",
        "VAL\n",
        "LEU\n",
        "GLN\n",
        "LEU\n",
        "HOH\n",
        "MET\n",
        "SER\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "PHE\n",
        "GLY\n",
        "HOH\n",
        "HOH\n",
        "GLY\n",
        "ILE\n",
        "ALA\n",
        "TRP\n",
        "HIS\n",
        "LYS\n",
        "PRO\n",
        "ILE\n",
        "LYS\n",
        "ILE\n",
        "ASP\n",
        "SER\n",
        "THR\n",
        "THR\n",
        "LEU\n",
        "ALA\n",
        "CYS\n",
        "LEU\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "THR\n",
        "SER\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "LEU\n",
        "THR\n",
        "LEU\n",
        "PRO\n",
        "ARG\n",
        "LEU\n",
        "THR\n",
        "GLN\n",
        "ILE\n",
        "LEU\n",
        "LEU\n",
        "LEU\n",
        "GLN\n",
        "SER\n",
        "ALA\n",
        "TRP\n",
        "MET\n",
        "GLU\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "ASP\n",
        "GLN\n",
        "HOH\n",
        "LYS\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "GLU\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HIS\n",
        "LEU\n",
        "VAL\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n",
        "HOH\n"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "pdbtuple = subset_from_pdb(pdb1)\n",
      "pdbtuple[0][1] #gives the starting residue number"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 9,
       "text": [
        "'232'"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "How to just cycle down the list of residues and access each value"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print \"Length before removing waters\"\n",
      "print len(pdb1.chainmap['A'].residues)\n",
      "\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Length before removing waters\n",
        "619\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Get rid of water and get subsets of hetatm and protein"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "nohohres=[]\n",
      "hetatm=[]\n",
      "protein=[]\n",
      "from amino_acids import *\n",
      "\n",
      "for res in pdb1.chainmap['A'].residues:\n",
      "    if (res.resname != \"HOH\"):\n",
      "        nohohres.append(res)\n",
      "\n",
      "for res in nohohres:\n",
      "    if (res.resname in longer_names):  #this assumes there arent' any noncanonicals\n",
      "        protein.append(res)\n",
      "    else:\n",
      "        hetatm.append(res)\n",
      "\n",
      "#    if (res.resname == \"ATOM\"):\n",
      "#        protein.append(res)\n",
      "\n",
      "count=0\n",
      "for res in hetatm:\n",
      "    for atom in res.atoms:\n",
      "        count += 1\n",
      "\n",
      "count_pro=0\n",
      "for res in protein:\n",
      "    count_pro +=1\n",
      "print \"number of residues (protein) is %s\" %count_pro\n",
      "\n",
      "print \"after removing waters\"\n",
      "print len(nohohres)\n",
      "#for res in nohohres:\n",
      "#    print res.resname\n",
      "\n",
      "print \"Number of hetatms is %s \" %count\n",
      "\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "number of residues (protein) is 228\n",
        "after removing waters\n",
        "232\n",
        "Number of hetatms is 35 \n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "How to remove alternative conformations (just remove off the array)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "\n",
      "#should add this upstream so that it accounts for ligands as well!\n",
      "for res in protein:\n",
      "    for atom in res.atoms:\n",
      "        if (atom.conformer != \" \"):\n",
      "            if (atom.conformer != \"A\" ):\n",
      "#                print \"removing alternate conformations for res %s\" %res.resname\n",
      "#                print atom.name\n",
      "                res.atoms.remove(atom)\n",
      "#for res in protein:\n",
      "#    for atom in res.atoms:\n",
      "#        print atom.name"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " ND2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " SG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " NE \n",
        " CZ \n",
        " NH1\n",
        " NH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " NE1\n",
        " CE2\n",
        " CE3\n",
        " CZ2\n",
        " CZ3\n",
        " CH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " NE1\n",
        " CE2\n",
        " CE3\n",
        " CZ2\n",
        " CZ3\n",
        " CH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " NE \n",
        " CZ \n",
        " NH1\n",
        " NH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " ND2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " ND2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " ND2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " OD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " NE \n",
        " CZ \n",
        " NH1\n",
        " NH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " NE \n",
        " CZ \n",
        " NH1\n",
        " NH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " NE \n",
        " CZ \n",
        " NH1\n",
        " NH2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " OG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " OH \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " OD1\n",
        " ND2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " CD1\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " ND1\n",
        " CD2\n",
        " CE1\n",
        " NE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " CE1\n",
        " CE2\n",
        " CZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " SD \n",
        " CE \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD1\n",
        " CD2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " OE1\n",
        " OE2\n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG \n",
        " CD \n",
        " CE \n",
        " NZ \n",
        " N  \n",
        " CA \n",
        " C  \n",
        " O  \n",
        " CB \n",
        " CG1\n",
        " CG2\n",
        " N  \n"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from find_neighbors import *\n",
      "interf_active = []\n",
      "\n",
      "int = count_nneighbs_wi_cbeta_cutoff(pdb1,5)\n",
      "## this gives the number of residues in contact with each residue as a dictionary\n",
      "# create a similar version of this that does the same for each atom in the hetatms to the other atoms\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "List of types for atoms and polar/apolar"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "bb_atoms=['N','CA','C','O']\n",
      "bb_polar=['N','O']\n",
      "bb_apolar=['CA','C']\n",
      "\n",
      "sc_atoms=[\n",
      "'CB',\n",
      "'CD',\n",
      "'CD1',\n",
      "'CD2',\n",
      "'CE',\n",
      "'CE1',\n",
      "'CE2',\n",
      "'CE3',\n",
      "'CG',\n",
      "'CG1',\n",
      "'CG2',\n",
      "'CH2',\n",
      "'CZ',\n",
      "'CZ2',\n",
      "'CZ3',\n",
      "'ND1',\n",
      "'ND2',\n",
      "'NE',\n",
      "'NE1',\n",
      "'NE2',\n",
      "'NH1',\n",
      "'NH2',\n",
      "'NV',\n",
      "'NZ',\n",
      "'OD1',\n",
      "'OD2',\n",
      "'OE1',\n",
      "'OE2',\n",
      "'OG',\n",
      "'OG1',\n",
      "'OH',\n",
      "'SD',\n",
      "'SG']\n",
      "\n",
      "sc_polar=[\n",
      "'ND1',\n",
      "'ND2',\n",
      "'NE',\n",
      "'NE1',\n",
      "'NE2',\n",
      "'NH1',\n",
      "'NH2',\n",
      "'NV',\n",
      "'NZ',\n",
      "'OD1',\n",
      "'OD2',\n",
      "'OE1',\n",
      "'OE2',\n",
      "'OG',\n",
      "'OG1',\n",
      "'OH',\n",
      "'SD',\n",
      "'SG']\n",
      "\n",
      "sc_apolar=[\n",
      "'CB',\n",
      "'CD',\n",
      "'CD1',\n",
      "'CD2',\n",
      "'CE',\n",
      "'CE1',\n",
      "'CE2',\n",
      "'CE3',\n",
      "'CG',\n",
      "'CG1',\n",
      "'CG2',\n",
      "'CH2',\n",
      "'CZ',\n",
      "'CZ2',\n",
      "'CZ3']\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 21
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "How to get the polar atoms in the ligand typed as polar"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import re\n",
      "\n",
      "class Contacts(object):\n",
      "    def __init__(self):\n",
      "        ''' Container Class for keeping all of the contact counts'''\n",
      "        self.pp_sc=0\n",
      "        self.pn_sc=0\n",
      "        self.np_sc=0\n",
      "        self.nn_sc=0\n",
      "        self.pp_bb=0\n",
      "        self.pn_bb=0\n",
      "        self.np_bb=0\n",
      "        self.nn_bb=0\n",
      "    \n",
      "    def open(self, filename , results )\n",
      "        try:\n",
      "            fh=open(\"%s.contact_results\" %filename,'w')\n",
      "            fh.write(\"pp_sc  pn_sc  np_sc  nn_sc  pp_bb  pn_bb  np_bb  nn_bb  num_lig  Extrastuff...\")\n",
      "            for line in results:\n",
      "                fh.write(results)\n",
      "            fh.close()\n",
      "        except:\n",
      "            print \"Error while trying to write the contact results\"\n",
      "        \n",
      "ctct = Contacts()\n",
      "\n",
      "for res in hetatm:\n",
      "    for atom in res.atoms:\n",
      "        atom_type = re.search(r'([a-zA-Z])\\d+',atom.name,).group(1)\n",
      "        \n",
      "        if atom_type in bb_polar:\n",
      "            # check against protein\n",
      "            # \n",
      "        if atom_type in bb_apolar:\n",
      "            pass\n",
      "            #check against protein\n",
      "\n",
      "def get_contacts_for_hetatm_line_over_protein(single_het_atom,all_protein_res):\n",
      "    ''' takes one line of a hetatm and loops over the entire protein, while counting the various contact properties'''\n",
      "    het_xyz = single_het_atom.atom.xyz\n",
      "    het_type = \n",
      "    \n",
      "    ###Better idea, also add the attributes of atom.polaritytype! then just loop over the different sets, using the dict/list I made above\n",
      "    "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n",
        "O\n"
       ]
      }
     ],
     "prompt_number": 36
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}