06_AdvancedTutorials/Visualisation_with_NGLView.ipynb

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    "## NGLview and MDAnalysis\n",
    "\n",
    "NGLview is a Python package for visualising your simulation data from within a notebook!\n",
    "\n",
    "NGLview is developed by Alexander Rose, for more details, you can check out the publication:\n",
    "\n",
    "https://academic.oup.com/bioinformatics/article-abstract/34/7/1241/4721781\n",
    "\n",
    "or their website:\n",
    "\n",
    "http://nglviewer.org/#page-top"
   ]
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   "source": [
    "import MDAnalysis as mda\n",
    "import MDAnalysisData as data\n",
    "\n",
    "import nglview"
   ]
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   "source": [
    "adk_eq = data.datasets.fetch_adk_equilibrium()\n",
    "\n",
    "u = mda.Universe(adk_eq['topology'], adk_eq['trajectory'])"
   ]
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   "source": [
    "nglview is able to display, within a notebook, objects from `MDAnalysis` using the `nglview.show_mdanalysis()` function.\n",
    "\n",
    "This should display a image of the system, which you can drag, rotate and zoom, and play the trajectory too."
   ]
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      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'icodes' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'\n",
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   "source": [
    "view = nglview.show_mdanalysis(u)\n",
    "\n",
    "view"
   ]
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   "source": [
    "Alternative representations can also be displayed, for example"
   ]
  },
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      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'icodes' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'\n",
      "  \"\".format(attrname, default))\n"
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   "source": [
    "view = nglview.show_mdanalysis(u)\n",
    "view.clear_representations()\n",
    "view.add_representation('ball+stick')\n",
    "view"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "### Displaying selections\n",
    "\n",
    "Selections from the overall Universe can be displayed by passing an AtomGroup to the `show_mdanalysis` function:"
   ]
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      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'icodes' Using default value of ' '\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'\n",
      "  \"\".format(attrname, default))\n",
      "/Users/richardgowers/miniconda3/envs/mda/lib/python3.6/site-packages/MDAnalysis/coordinates/PDB.py:902: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'\n",
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   "source": [
    "ag = u.select_atoms('not type H*')\n",
    "\n",
    "view = nglview.show_mdanalysis(ag)\n",
    "view.add_spacefill()\n",
    "\n",
    "view"
   ]
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