visualization.ipynb

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   "source": [
    "import py3Dmol\n",
    "from rdkit import Chem\n",
    "from copy import deepcopy\n",
    "import pickle\n",
    "\n",
    "\n",
    "def visualize_mol(mol, size=(300, 300), surface=False, opacity=0.5):\n",
    "    \"\"\"Draw molecule in 3D\n",
    "    \n",
    "    Args:\n",
    "    ----\n",
    "        mol: rdMol, molecule to show\n",
    "        size: tuple(int, int), canvas size\n",
    "        style: str, type of drawing molecule\n",
    "               style can be 'line', 'stick', 'sphere', 'carton'\n",
    "        surface, bool, display SAS\n",
    "        opacity, float, opacity of surface, range 0.0-1.0\n",
    "    Return:\n",
    "    ----\n",
    "        viewer: py3Dmol.view, a class for constructing embedded 3Dmol.js views in ipython notebooks.\n",
    "    \"\"\"\n",
    "    # assert style in ('line', 'stick', 'sphere', 'carton')\n",
    "    mblock = Chem.MolToMolBlock(mol)\n",
    "    viewer = py3Dmol.view(width=size[0], height=size[1])\n",
    "    viewer.addModel(mblock, 'mol')\n",
    "    viewer.setStyle({'stick':{}, 'sphere':{'radius':0.35}})\n",
    "    if surface:\n",
    "        viewer.addSurface(py3Dmol.SAS, {'opacity': opacity})\n",
    "    viewer.zoomTo()\n",
    "    return viewer\n",
    "\n",
    "def set_rdmol_positions(rdkit_mol, pos):\n",
    "    \"\"\"\n",
    "    Args:\n",
    "        rdkit_mol:  An `rdkit.Chem.rdchem.Mol` object.\n",
    "        pos: (N_atoms, 3)\n",
    "    \"\"\"\n",
    "    mol = deepcopy(rdkit_mol)\n",
    "    set_rdmol_positions_(mol, pos)\n",
    "    return mol\n",
    "\n",
    "\n",
    "def set_rdmol_positions_(mol, pos):\n",
    "    \"\"\"\n",
    "    Args:\n",
    "        rdkit_mol:  An `rdkit.Chem.rdchem.Mol` object.\n",
    "        pos: (N_atoms, 3)\n",
    "    \"\"\"\n",
    "    for i in range(pos.shape[0]):\n",
    "        mol.GetConformer(0).SetAtomPosition(i, pos[i].tolist())\n",
    "    return mol"
   ]
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      "checkpoints/qm9_500steps/samples/samples_all.pkl\n",
      "Ground true 0: \n"
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       "\tviewer_1707104251442736.setStyle({\"stick\": {}, \"sphere\": {\"radius\": 0.35}});\n",
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       "viewer_1707104251442736.render();\n",
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      ]
     },
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    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Ground true 1: \n"
     ]
    },
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
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       "viewer_170710425144347 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_170710425144347\"),{backgroundColor:\"white\"});\n",
       "viewer_170710425144347.zoomTo();\n",
       "\tviewer_170710425144347.addModel(\"\\n     RDKit          3D\\n\\n 19 18  0  0  0  0  0  0  0  0999 V2000\\n   -0.7494   -1.6076    0.8369 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2901   -1.4622   -0.4855 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9278   -2.0319   -1.1769 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2348    0.0017   -0.9583 C   0  0  1  0  0  0  0  0  0  0  0  0\\n   -1.6396    0.6291   -0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2711    0.6258    0.2793 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.6727    1.0769    0.9000 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5700    1.6553   -1.3688 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.2905    0.0547   -1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.1577    0.0108   -1.9797 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7209    0.8404   -0.0730 C   0  0  2  0  0  0  0  0  0  0  0  0\\n    2.0786    0.3138   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.1837   -0.1453   -0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    4.1590   -0.5304   -0.2190 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2856    0.9093    1.2708 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2336   -0.0044    1.6003 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7255    1.8799   -0.4313 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.7148   -1.8939   -0.5068 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.6213   -1.1791    0.8844 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  1 19  1  0\\n  2  3  1  0\\n  2  4  1  0\\n  2 18  1  0\\n  4  5  1  0\\n  4 10  1  6\\n  4 11  1  0\\n  5  6  1  0\\n  5  8  1  0\\n  5  9  1  0\\n  6  7  1  0\\n 11 12  1  0\\n 11 15  1  0\\n 11 17  1  6\\n 12 13  3  0\\n 13 14  1  0\\n 15 16  1  0\\nM  END\\n\",\"mol\");\n",
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     },
     "metadata": {},
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    },
    {
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     "output_type": "stream",
     "text": [
      "generated 1:\n"
     ]
    },
    {
     "data": {
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      "text/html": [
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       "        <p id=\"3dmolwarning_17071042514441347\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
       "  return new Promise((resolve, reject) => {\n",
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       "  $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.3/3Dmol-min.js');\n",
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       "\n",
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       "$3Dmolpromise.then(function() {\n",
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       "viewer_17071042514441347.zoomTo();\n",
       "\tviewer_17071042514441347.addModel(\"\\n     RDKit          3D\\n\\n 19 18  0  0  0  0  0  0  0  0999 V2000\\n    2.2780    0.5014   -1.3848 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.4354    0.6564   -0.2553 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.9794    0.2994    0.5751 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.1634   -0.1090   -0.3703 C   0  0  2  0  0  0  0  0  0  0  0  0\\n   -0.7229    0.4182   -1.5897 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.8097   -0.3427   -1.8682 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -2.3365   -0.4498   -1.0508 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9956    1.4666   -1.3480 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.0766    0.4317   -2.4813 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.3383   -1.1390   -0.5713 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.6859   -0.0218    0.9284 C   0  0  2  0  0  0  0  0  0  0  0  0\\n    0.1113   -0.4543    2.0219 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.6987   -0.9777    3.0021 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.0118   -1.5621    3.8104 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.8948   -0.7295    0.8637 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.6711   -1.6980    0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9531    1.0248    1.0937 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2053    1.7110   -0.1065 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.9246    0.9745   -2.1397 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  1 19  1  0\\n  2  3  1  0\\n  2  4  1  0\\n  2 18  1  0\\n  4  5  1  0\\n  4 10  1  1\\n  4 11  1  0\\n  5  6  1  0\\n  5  8  1  0\\n  5  9  1  0\\n  6  7  1  0\\n 11 12  1  0\\n 11 15  1  0\\n 11 17  1  1\\n 12 13  3  0\\n 13 14  1  0\\n 15 16  1  0\\nM  END\\n\",\"mol\");\n",
       "\tviewer_17071042514441347.setStyle({\"stick\": {}, \"sphere\": {\"radius\": 0.35}});\n",
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       "viewer_17071042514441347.render();\n",
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      ]
     },
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    },
    {
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     "output_type": "stream",
     "text": [
      "Ground true 2: \n"
     ]
    },
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
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       "$3Dmolpromise.then(function() {\n",
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       "viewer_1707104251444827.zoomTo();\n",
       "\tviewer_1707104251444827.addModel(\"\\n     RDKit          3D\\n\\n 19 19  0  0  0  0  0  0  0  0999 V2000\\n   -1.3912   -1.5020    0.7245 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.7037   -1.2722    1.3604 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.7693   -1.7955   -0.5121 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.3245   -0.5287   -1.2569 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.5042    0.3763   -0.3602 C   0  0  2  0  0  0  0  0  0  0  0  0\\n    1.6948   -0.2184    0.1650 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.6655   -0.7444    0.6316 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    3.5322   -1.1888    1.0205 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2509    1.3433    0.5398 C   0  0  1  0  0  0  0  0  0  0  0  0\\n    0.5097    1.8619   -0.6422 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.4191    2.4144   -0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.0659    2.2011   -1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.6342    1.3711    0.5147 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.9705    0.4694    0.6545 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.1768    1.5270    1.5261 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2523   -0.8196   -2.1370 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2061    0.0249   -1.5852 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.0907   -2.4574   -0.3546 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.5172   -2.3289   -1.1033 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  1  3  1  0\\n  3  4  1  0\\n  3 18  1  0\\n  3 19  1  0\\n  4  5  1  0\\n  4 16  1  0\\n  4 17  1  0\\n  5  6  1  1\\n  5  9  1  0\\n  5 10  1  0\\n  6  7  3  0\\n  7  8  1  0\\n  9 10  1  0\\n  9 13  1  0\\n  9 15  1  1\\n 10 11  1  0\\n 10 12  1  0\\n 13 14  1  0\\nM  END\\n\",\"mol\");\n",
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     "output_type": "stream",
     "text": [
      "generated 2:\n"
     ]
    },
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
       "var loadScriptAsync = function(uri){\n",
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     "text": [
      "Ground true 3: \n"
     ]
    },
    {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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     "text": [
      "generated 3:\n"
     ]
    },
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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     "text": [
      "Ground true 4: \n"
     ]
    },
    {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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     "text": [
      "generated 4:\n"
     ]
    },
    {
     "data": {
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       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
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       "viewer_1707104251448795 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1707104251448795\"),{backgroundColor:\"white\"});\n",
       "viewer_1707104251448795.zoomTo();\n",
       "\tviewer_1707104251448795.addModel(\"\\n     RDKit          3D\\n\\n 19 18  0  0  0  0  0  0  0  0999 V2000\\n   -0.5289   -0.8936   -2.1602 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.6903   -0.4257   -1.5171 N   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2064   -1.2042   -1.1614 H   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.5006    0.5719   -0.5173 C   0  0  2  0  0  0  0  0  0  0  0  0\\n    1.8293    1.1861   -0.1186 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.0096    2.3516    0.0614 O   0  0  0  0  0  0  0  0  0  0  0  0\\n    2.5861    0.4361    0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.0922    0.0818    0.7873 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2288   -1.0935    1.1563 N   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.8309   -1.7973    1.8329 O   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.3617   -2.1879    2.6201 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.9674    0.9977    1.5678 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.1981    0.5541    2.5153 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.9020    1.1346    1.0102 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.5149    1.9566    1.6742 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.1410    1.3728   -0.9288 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2432   -1.5768   -2.9655 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.0687   -0.0475   -2.5696 H   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2019   -1.4169   -1.4391 H   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  1  0\\n  1 17  1  0\\n  1 18  1  0\\n  1 19  1  0\\n  2  3  1  0\\n  2  4  1  0\\n  4  5  1  0\\n  4  8  1  0\\n  4 16  1  1\\n  5  6  2  0\\n  5  7  1  0\\n  8  9  2  0\\n  8 12  1  0\\n  9 10  1  0\\n 10 11  1  0\\n 12 13  1  0\\n 12 14  1  0\\n 12 15  1  0\\nM  END\\n\",\"mol\");\n",
       "\tviewer_1707104251448795.setStyle({\"stick\": {}, \"sphere\": {\"radius\": 0.35}});\n",
       "\tviewer_1707104251448795.zoomTo();\n",
       "viewer_1707104251448795.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "import pickle\n",
    "import numpy as np\n",
    "from tqdm.auto import tqdm\n",
    "from rdkit.Chem import AllChem\n",
    "import os\n",
    "\n",
    "\n",
    "\n",
    "generated=\"checkpoints/qm9_500steps/samples/samples_all.pkl\" # or traj saved by test.py --save_traj\n",
    "\n",
    "\n",
    "num_confs=1\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "def generate_conformer(rdmol, confs):    \n",
    "    conf_idx = np.arange(confs.shape[0])\n",
    "    # np.random.RandomState(2021).shuffle(conf_idx)\n",
    "    conf_idx = conf_idx[:num_confs]\n",
    "    for idx in conf_idx:\n",
    "        mol = set_rdmol_positions(rdmol, confs[idx])\n",
    "    return mol\n",
    "\n",
    "\n",
    "viewers=[]\n",
    "original_viewers=[]\n",
    "confs_all=[]\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "with open(generated, 'rb') as f:\n",
    "    gens = pickle.load(f)\n",
    "gens_prop = []\n",
    "for data in tqdm(gens):\n",
    "    # if not isinstance(data, Data):\n",
    "    #     data = EasyDict(data)\n",
    "    data.num_nodes = data.rdmol.GetNumAtoms()\n",
    "    \n",
    "    rdmol = data.rdmol\n",
    "    mol_orginal = set_rdmol_positions(rdmol,data.pos)\n",
    "\n",
    "    if len(data.pos_gen.shape)==3: #traj torch.Size([n_steps, n_atoms, 3])\n",
    "        data.pos_prop = data.pos_gen.reshape(data.pos_gen.shape[0], -1, data.num_nodes,3)\n",
    "        mol  = rdmol\n",
    "        num_conformers = data.pos_gen.shape[0]\n",
    "\n",
    "        AllChem.EmbedMultipleConfs(mol, numConfs=num_conformers)\n",
    "        for step,confs in enumerate(data.pos_prop):\n",
    "            # mol = generate_conformer(rdmol=rdmol, confs=confs)\n",
    "            pos = confs[0]\n",
    "            for i in range(pos.shape[0]):\n",
    "                # mol.GetConformer(step).GetPositions()\n",
    "                mol.GetConformer(step).SetAtomPosition(i, pos[i].tolist())\n",
    "                # mol.GetConformer(step).GetPositions()\n",
    "            confs_all.append(mol)\n",
    "        writer = Chem.PDBWriter(f'{os.path.dirname(generated)}/{data.smiles}_traj.pdb')\n",
    "        writer.write(mol)\n",
    "        writer.close()\n",
    "        # Chem.MolToPDBFile(mol, f'{os.path.dirname(generated)}/{data.smiles}_traj.pdb')\n",
    "        print(\"save to\",  f'{os.path.dirname(generated)}/{data.smiles}_traj.pdb')\n",
    "        # break\n",
    "    else:\n",
    "        data.pos_prop = data.pos_gen.reshape(-1, data.num_nodes, 3)\n",
    "        confs = data.pos_prop\n",
    "        mol = generate_conformer(rdmol, confs)\n",
    "        confs_all.append(mol)\n",
    "        viewers.append(visualize_mol(mol))\n",
    "        original_viewers.append(visualize_mol(mol_orginal))\n",
    "        # Chem.MolToPDBFile(mol, f'{os.path.dirname(generated)}/{data.smiles}_{idx}.pdb')\n",
    "    # break\n",
    "\n",
    "print(generated)\n",
    "for num, viewer in enumerate(viewers[0:5]):\n",
    "    print(f\"Ground true {num}: \")\n",
    "    original_viewers[num].show()\n",
    "    print(f\"generated {num}:\")\n",
    "    viewer.show()\n"
   ]
  }
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