{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "py3Dmol\n",
    "=======\n",
    "\n",
    "A simple [IPython/Jupyter](http://jupyter.org/) widget to\n",
    "embed an interactive [3Dmol.js](http://3dmol.csb.pitt.edu) viewer in a notebook.\n",
    "\n",
    "The widget is completely static, which means the viewer doesn't need a running\n",
    "IPython kernel to be useful and web pages and presentations generated from\n",
    "the notebook will work as expected.  However, this also means there is only\n",
    "one-way communication between the notebook and the viewer.\n",
    "\n",
    "Installation\n",
    "------------\n",
    "\n",
    "From PyPI:\n",
    "\n",
    "    pip install py3Dmol\n",
    "    \n",
    "API\n",
    "---\n",
    "\n",
    "The returned view object has the exact same API as [3Dmol.GLViewer](http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html)\n",
    "with the exception that functions return None.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import py3Dmol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false,
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496787217\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496787217 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496787217 = $3Dmol.createViewer($(\"#3dmolviewer_149496787217\"),{backgroundColor:\"white\"});\n",
       "$3Dmol.download(\"pdb:1ycr\", viewer_149496787217, {}, function() {\n",
       "\tviewer_149496787217.setStyle({\"cartoon\": {\"color\": \"spectrum\"}});\n",
       "viewer_149496787217.render();\n",
       "})\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = py3Dmol.view(query='pdb:1ycr')\n",
    "p.setStyle({'cartoon': {'color':'spectrum'}})\n",
    "p.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "xyz = '''4\n",
    "* (null), Energy   -1000.0000000\n",
    "N     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746\n",
    "H     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108\n",
    "H    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024\n",
    "H    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260\n",
    "'''"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_14949678722\"  style=\"position: relative; width: 400px; height: 400px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_14949678722 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_14949678722 = $3Dmol.createViewer($(\"#3dmolviewer_14949678722\"),{backgroundColor:\"white\"});\n",
       "\tviewer_14949678722.addModel(\"4\\n* (null), Energy   -1000.0000000\\nN     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746\\nH     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108\\nH    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024\\nH    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260\\n\",\"xyz\",{\"vibrate\": {\"frames\": 10, \"amplitude\": 1}});\n",
       "\tviewer_14949678722.setStyle({\"stick\": {}});\n",
       "\tviewer_14949678722.setBackgroundColor(\"0xeeeeee\");\n",
       "\tviewer_14949678722.animate({\"loop\": \"backAndForth\"});\n",
       "\tviewer_14949678722.zoomTo();\n",
       "viewer_14949678722.render();\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "xyzview = py3Dmol.view(width=400,height=400)\n",
    "xyzview.addModel(xyz,'xyz',{'vibrate': {'frames':10,'amplitude':1}})\n",
    "xyzview.setStyle({'stick':{}})\n",
    "xyzview.setBackgroundColor('0xeeeeee')\n",
    "xyzview.animate({'loop': 'backAndForth'})\n",
    "xyzview.zoomTo()\n",
    "xyzview.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496787222\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496787222 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496787222 = $3Dmol.createViewer($(\"#3dmolviewer_149496787222\"),{backgroundColor:\"white\"});\n",
       "$3Dmol.download(\"pdb:1dc9\", viewer_149496787222, {}, function() {\n",
       "\tviewer_149496787222.setViewStyle({\"color\": \"black\", \"width\": 0.1, \"style\": \"outline\"});\n",
       "\tviewer_149496787222.setStyle({\"cartoon\": {\"color\": \"white\", \"tubes\": true, \"style\": \"oval\", \"arrows\": true}});\n",
       "viewer_149496787222.render();\n",
       "})\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<py3Dmol.view at 0x10c328c10>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "view = py3Dmol.view(query='pdb:1dc9')\n",
    "view.setViewStyle({'style':'outline','color':'black','width':0.1})\n",
    "view.setStyle({'cartoon':{'arrows':True, 'tubes':True, 'style':'oval', 'color':'white'}})\n",
    "view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496787226\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496787226 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496787226 = $3Dmol.createViewer($(\"#3dmolviewer_149496787226\"),{backgroundColor:\"white\"});\n",
       "$3Dmol.download(\"pdb:1ycr\", viewer_149496787226, {}, function() {\n",
       "\tviewer_149496787226.setStyle({\"chain\": \"A\"},{\"cartoon\": {\"color\": \"spectrum\"}});\n",
       "\tviewer_149496787226.addSurface(1,{\"opacity\": 0.7, \"color\": \"white\"},{\"chain\": \"A\"});\n",
       "\tviewer_149496787226.setStyle({\"chain\": \"B\"},{\"stick\": {}});\n",
       "viewer_149496787226.render();\n",
       "})\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "view = py3Dmol.view(query='pdb:1ycr')\n",
    "chA = {'chain':'A'}\n",
    "chB = {'chain':'B'}\n",
    "view.setStyle(chA,{'cartoon': {'color':'spectrum'}})\n",
    "view.addSurface(py3Dmol.VDW,{'opacity':0.7,'color':'white'}, chA)\n",
    "view.setStyle(chB,{'stick':{}})\n",
    "view.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496787229\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496787229 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496787229 = $3Dmol.createViewer($(\"#3dmolviewer_149496787229\"),{backgroundColor:\"white\"});\n",
       "$3Dmol.download(\"pdb:5ire\", viewer_149496787229, {\"doAssembly\": true}, function() {\n",
       "\tviewer_149496787229.setStyle({\"cartoon\": {\"color\": \"spectrum\"}});\n",
       "viewer_149496787229.render();\n",
       "})\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "view = py3Dmol.view(query='pdb:5ire',options={'doAssembly':True})\n",
    "view.setStyle({'cartoon':{'color':'spectrum'}})\n",
    "view.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "Color by temperature factors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496789334\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496789334 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496789334 = $3Dmol.createViewer($(\"#3dmolviewer_149496789334\"),{backgroundColor:\"white\"});\n",
       "$3Dmol.download(\"pdb:1ycr\", viewer_149496789334, {}, function() {\n",
       "\tviewer_149496789334.setStyle({\"cartoon\": {\"color\": \"white\"}});\n",
       "\tviewer_149496789334.addSurface(1,{\"opacity\": 0.7, \"colorscheme\": {\"gradient\": \"sinebow\", \"max\": 70, \"min\": 0, \"prop\": \"b\"}});\n",
       "viewer_149496789334.render();\n",
       "})\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<py3Dmol.view at 0x10c2f5b90>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "view = py3Dmol.view(query='pdb:1ycr')\n",
    "view.setStyle({'cartoon': {'color':'white'}})\n",
    "view.addSurface(py3Dmol.VDW,{'opacity':0.7,'colorscheme':{'prop':'b','gradient':'sinebow','min':0,'max':70}})"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Generate an inline image of what is currently in the viewer (all white if the structure hasn't loaded yet)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<img id=\"img_149496789334\">\n",
       "            <script>\n",
       "            var png = $('canvas','#3dmolviewer_149496789334')[0].toDataURL();\n",
       "            $('#img_149496789334').attr('src', png)\n",
       "            </script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "png = view.png()\n",
    "png"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "Display local file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div id=\"3dmolviewer_149496788184\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "<script>\n",
       "if(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\n",
       "var viewer_149496788184 = null;\n",
       "$3Dmolpromise.done(function() {\n",
       "viewer_149496788184 = $3Dmol.createViewer($(\"#3dmolviewer_149496788184\"),{backgroundColor:\"white\"});\n",
       "\tviewer_149496788184.addModel(\"\\n     RDKit          3D\\n\\n  6  6  0  0  0  0  0  0  0  0999 V2000\\n   -0.9517    0.7811   -0.6622 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.2847    1.3329   -0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    1.2365    0.5518    0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0\\n    0.9517   -0.7811    0.6644 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -0.2847   -1.3329    0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0\\n   -1.2365   -0.5518   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0\\n  1  2  2  0\\n  2  3  1  0\\n  3  4  2  0\\n  4  5  1  0\\n  5  6  2  0\\n  6  1  1  0\\nM  END\\n$$$$\",\"sdf\");\n",
       "\tviewer_149496788184.setStyle({\"stick\": {}});\n",
       "\tviewer_149496788184.zoomTo();\n",
       "viewer_149496788184.render();\n",
       "});\n",
       "</script>"
      ],
      "text/plain": [
       "<py3Dmol.view at 0x10c328f90>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "benz='''\n",
    "     RDKit          3D\n",
    "\n",
    "  6  6  0  0  0  0  0  0  0  0999 V2000\n",
    "   -0.9517    0.7811   -0.6622 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.2847    1.3329   -0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    1.2365    0.5518    0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.9517   -0.7811    0.6644 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.2847   -1.3329    0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.2365   -0.5518   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "  1  2  2  0\n",
    "  2  3  1  0\n",
    "  3  4  2  0\n",
    "  4  5  1  0\n",
    "  5  6  2  0\n",
    "  6  1  1  0\n",
    "M  END\n",
    "$$$$'''\n",
    "view = py3Dmol.view()\n",
    "view.addModel(benz,'sdf')\n",
    "view.setStyle({'stick':{}})\n",
    "view.zoomTo()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
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   "outputs": [],
   "source": []
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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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