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   "source": [
    "# 08. Molecules CG Mapping \n",
    "\n",
    "In this tutorial, we show how to generate a CG mapping matrix for a molecule given a bead distribution."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "import hoomd, hoomd.htf as htf, hoomd.md\n",
    "import numpy as np\n",
    "import MDAnalysis as mda"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[0.8224383  0.05918723 0.05918723 0.05918723 0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.44409524 0.03726984\n",
      "  0.44409524 0.03726984 0.03726984 0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.15577257 0.15577257 0.01307291\n",
      "  0.15577257 0.01307291 0.15577257 0.01307291 0.15577257 0.01307291\n",
      "  0.15577257 0.01307291 0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
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      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.42880501 0.57119499 0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.93286579 0.06713421\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.44409524 0.03726984 0.44409524 0.03726984 0.03726984 0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.15577257\n",
      "  0.15577257 0.01307291 0.15577257 0.01307291 0.15577257 0.01307291\n",
      "  0.15577257 0.01307291 0.15577257 0.01307291 0.         0.\n",
      "  0.        ]\n",
      " [0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.         0.\n",
      "  0.         0.         0.         0.         0.27291648 0.36354176\n",
      "  0.36354176]]\n"
     ]
    }
   ],
   "source": [
    "# Loading inputs\n",
    "TPR = 'Molecules_CG_Mapping/nvt_prod.tpr'\n",
    "tpr = mda.Universe(TPR)\n",
    "TRAJECTORY = 'Molecules_CG_Mapping/traj.trr'\n",
    "u = mda.Universe(TPR, TRAJECTORY)\n",
    "\n",
    "# Generating Mapping Matrix for FF\n",
    "protein_FF = u.select_atoms(\"resname PHE and resid 0:1\")\n",
    "Beads_distribution = [['N','H1','H2','H3'],\n",
    "                     ['CA','HA','CB','HB1','HB2'],\n",
    "                     ['CG','CD1','HD1','CD2','HD2','CE1','HE1','CE2','HE2','CZ','HZ'],\n",
    "                     ['C','O'],\n",
    "                     ['N','H'],\n",
    "                     ['CA','HA','CB','HB1','HB2'],\n",
    "                     ['CG','CD1','HD1','CD2','HD2','CE1','HE1','CE2','HE2','CZ','HZ'],\n",
    "                     ['C','O1','O2']]\n",
    "mapping_FF = htf.matrix_mapping(protein_FF,Beads_distribution)\n",
    "print (mapping_FF)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[0.88809574 0.05595213 0.05595213]]\n"
     ]
    }
   ],
   "source": [
    "# Generating Mapping Matrix for Water\n",
    "water = u.select_atoms(\"resname SOL and resid 500\")\n",
    "Beads_distribution = [['OW','HW1','HW2']]\n",
    "mapping_water = htf.matrix_mapping(water,Beads_distribution)             \n",
    "print (mapping_water)"
   ]
  }
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