issue-RepairGraph.ipynb

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   "outputs": [],
   "source": [
    "import networkx as nx\n",
    "import vermouth\n",
    "import vermouth.forcefield\n",
    "import collections"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
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     "end_time": "2018-04-11T19:30:47.224132Z",
     "start_time": "2018-04-11T19:30:46.956029Z"
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   "outputs": [],
   "source": [
    "molecule = vermouth.molecule.Molecule()\n",
    "molecule.add_nodes_from((\n",
    "    (0, {'resid': 1, 'resname': 'GLU', 'atomname': 'N', 'chain': 'A'}),\n",
    "    (1, {'resid': 1, 'resname': 'GLU', 'atomname': 'CA', 'chain': 'A'}),\n",
    "    (2, {'resid': 1, 'resname': 'GLU', 'atomname': 'C', 'chain': 'A'}),\n",
    "    (3, {'resid': 1, 'resname': 'GLU', 'atomname': 'O', 'chain': 'A'}),\n",
    "    (4, {'resid': 1, 'resname': 'GLU', 'atomname': 'CB', 'chain': 'A'}),\n",
    "    (5, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB1', 'chain': 'A'}),\n",
    "    (6, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB2', 'chain': 'A'}),\n",
    "    (7, {'resid': 1, 'resname': 'GLU', 'atomname': 'CG', 'chain': 'A'}),\n",
    "    (8, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG1', 'chain': 'A'}),\n",
    "    (9, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG2', 'chain': 'A'}),\n",
    "    (10, {'resid': 1, 'resname': 'GLU', 'atomname': 'CD', 'chain': 'A'}),\n",
    "    (11, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE2', 'chain': 'A'}),\n",
    "    (12, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE1', 'chain': 'A'}),\n",
    "    (13, {'resid': 1, 'resname': 'GLU', 'atomname': 'HE1', 'chain': 'A'}),\n",
    "    (14, {'resid': 1, 'resname': 'GLU', 'atomname': 'H', 'chain': 'A'}),\n",
    "    (15, {'resid': 1, 'resname': 'GLU', 'atomname': 'HA', 'chain': 'A'}),\n",
    "    (16, {'resid': 1, 'resname': 'GLU', 'atomname': 'HN', 'chain': 'A'}),\n",
    "))\n",
    "molecule.add_edges_from([\n",
    "    [0, 1], [1, 2], [2, 3], [1, 4], [4, 5], [4, 6], [4, 7], [7, 8],\n",
    "    [7, 9], [7, 10], [10, 11], [10, 12], [12, 13], [14, 0], [15, 1], [16, 0],\n",
    "])\n",
    "system = vermouth.System()\n",
    "system.molecules = [molecule]\n",
    "system.force_field = vermouth.forcefield.FORCE_FIELDS['universal']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
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     "end_time": "2018-04-11T19:30:50.818510Z",
     "start_time": "2018-04-11T19:30:50.801704Z"
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   },
   "outputs": [],
   "source": [
    "name_count_before = collections.Counter(\n",
    "    node['atomname']\n",
    "    for molecule in system.molecules\n",
    "    for node in molecule.nodes.values()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
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     "end_time": "2018-04-11T19:30:51.556554Z",
     "start_time": "2018-04-11T19:30:51.509980Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "Counter({'C': 1,\n",
       "         'CA': 1,\n",
       "         'CB': 1,\n",
       "         'CD': 1,\n",
       "         'CG': 1,\n",
       "         'H': 1,\n",
       "         'HA': 1,\n",
       "         'HB1': 1,\n",
       "         'HB2': 1,\n",
       "         'HE1': 1,\n",
       "         'HG1': 1,\n",
       "         'HG2': 1,\n",
       "         'HN': 1,\n",
       "         'N': 1,\n",
       "         'O': 1,\n",
       "         'OE1': 1,\n",
       "         'OE2': 1})"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "name_count_before"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
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     "end_time": "2018-04-11T19:30:53.509486Z",
     "start_time": "2018-04-11T19:30:53.490797Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "17"
      ]
     },
     "execution_count": 17,
     "metadata": {},
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   ],
   "source": [
    "sum(name_count_before.values())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:30:54.455205Z",
     "start_time": "2018-04-11T19:30:54.400514Z"
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   },
   "outputs": [],
   "source": [
    "vermouth.RepairGraph().run_system(system)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:30:55.633548Z",
     "start_time": "2018-04-11T19:30:55.621396Z"
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   },
   "outputs": [],
   "source": [
    "name_count_after = collections.Counter(\n",
    "    node['atomname']\n",
    "    for molecule in system.molecules\n",
    "    for node in molecule.nodes.values()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:30:56.525912Z",
     "start_time": "2018-04-11T19:30:56.519591Z"
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "Counter({'C': 1,\n",
       "         'CA': 1,\n",
       "         'CB': 1,\n",
       "         'CD': 1,\n",
       "         'CG': 1,\n",
       "         'HA': 1,\n",
       "         'HB1': 1,\n",
       "         'HB2': 1,\n",
       "         'HE1': 1,\n",
       "         'HG1': 1,\n",
       "         'HG2': 1,\n",
       "         'HN': 2,\n",
       "         'N': 1,\n",
       "         'O': 1,\n",
       "         'OE1': 1,\n",
       "         'OE2': 1})"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "name_count_after"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:31:00.075602Z",
     "start_time": "2018-04-11T19:31:00.065174Z"
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   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "17"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sum(name_count_after.values())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:31:00.730949Z",
     "start_time": "2018-04-11T19:31:00.719348Z"
    }
   },
   "outputs": [],
   "source": [
    "name_count_block = collections.Counter(\n",
    "    vermouth.forcefield.FORCE_FIELDS['universal'].blocks['GLU'].nodes.keys()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:31:01.303426Z",
     "start_time": "2018-04-11T19:31:01.293086Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Counter({'C': 1,\n",
       "         'CA': 1,\n",
       "         'CB': 1,\n",
       "         'CD': 1,\n",
       "         'CG': 1,\n",
       "         'HA': 1,\n",
       "         'HB1': 1,\n",
       "         'HB2': 1,\n",
       "         'HG1': 1,\n",
       "         'HG2': 1,\n",
       "         'HN': 1,\n",
       "         'N': 1,\n",
       "         'O': 1,\n",
       "         'OE1': 1,\n",
       "         'OE2': 1})"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "name_count_block"
   ]
  },
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   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:31:03.188035Z",
     "start_time": "2018-04-11T19:31:03.175735Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "15"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sum(name_count_block.values())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-11T19:31:05.371365Z",
     "start_time": "2018-04-11T19:31:05.352133Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<vermouth.molecule.Molecule at 0x7fb2ccf10940>]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "system.molecules"
   ]
  }
 ],
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