NGLView - Basics

nglview.ipynb

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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# NGLView basics"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Display a molecule from rdkit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
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      "text/plain": [
       "NGLWidget()"
      ]
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     "metadata": {},
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    }
   ],
   "source": [
    "import nglview as nv\n",
    "from rdkit import Chem \n",
    "from rdkit.Chem import AllChem\n",
    "\n",
    "m = Chem.AddHs(Chem.MolFromSmiles('COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))\n",
    "_ = AllChem.EmbedMultipleConfs(m, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)\n",
    "view = nv.show_rdkit(m)\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download and display a PDB from RCSB"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "5485e7932afb40c7a751fced611dbb16",
       "version_major": 2,
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      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nv.NGLWidget()\n",
    "c = view.add_pdbid('1tsu')\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Display a PDB from Biopython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
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     "text": [
      "/home/ravila/Software/miniconda/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:90: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 3284.\n",
      "  PDBConstructionWarning)\n",
      "/home/ravila/Software/miniconda/lib/python3.6/site-packages/Bio/PDB/StructureBuilder.py:90: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3480.\n",
      "  PDBConstructionWarning)\n"
     ]
    },
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      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from Bio.PDB import PDBParser\n",
    "\n",
    "parser = PDBParser()\n",
    "structure = parser.get_structure(\"protein\", \"3PQR.pdb\")\n",
    "w = nv.show_biopython(structure[0][\"A\"])\n",
    "w"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Customize the representation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "w.clear_representations()\n",
    "w.add_surface(opacity=0.3)\n",
    "w.add_ball_and_stick()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Play a trajectory from Simpletraj"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "fa340fb613664efcad38db9760f95b9d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget(count=51)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import nglview as nv\n",
    "t = nv.SimpletrajTrajectory(nv.datafiles.XTC, nv.datafiles.GRO)\n",
    "w = nv.NGLWidget(t)\n",
    "w"
   ]
  }
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