py3Dmol/updating.ipynb

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    "py3Dmol - in place updates\n",
    "=======\n",
    "\n",
    "Per @dr_greg_landrum's request, support updating an already existing viewer in-place.\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_156233516553\"  style=\"position: relative; width: 640px; height: 480px\">\n        <p id=\"3dmolwarning_156233516553\" 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\nvar loadScriptAsync = function(uri){\n  return new Promise((resolve, reject) => {\n    var tag = document.createElement('script');\n    tag.src = uri;\n    tag.async = true;\n    tag.onload = () => {\n      resolve();\n    };\n  var firstScriptTag = document.getElementsByTagName('script')[0];\n  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_156233516553 = null;\nvar warn = document.getElementById(\"3dmolwarning_156233516553\");\nif(warn) {\n    warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_156233516553 = $3Dmol.createViewer($(\"#3dmolviewer_156233516553\"),{backgroundColor:\"white\"});\n\tviewer_156233516553.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_156233516553.setStyle({\"stick\": {}});\n\tviewer_156233516553.zoomTo();\nviewer_156233516553.render();\n});\n</script>",
      "text/html": [
       "<div id=\"3dmolviewer_156233516553\"  style=\"position: relative; width: 640px; height: 480px\">\n",
       "        <p id=\"3dmolwarning_156233516553\" 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",
       "    var tag = document.createElement('script');\n",
       "    tag.src = uri;\n",
       "    tag.async = true;\n",
       "    tag.onload = () => {\n",
       "      resolve();\n",
       "    };\n",
       "  var firstScriptTag = document.getElementsByTagName('script')[0];\n",
       "  firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
       "});\n",
       "};\n",
       "\n",
       "if(typeof $3Dmolpromise === 'undefined') {\n",
       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_156233516553 = null;\n",
       "var warn = document.getElementById(\"3dmolwarning_156233516553\");\n",
       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
       "viewer_156233516553 = $3Dmol.createViewer($(\"#3dmolviewer_156233516553\"),{backgroundColor:\"white\"});\n",
       "\tviewer_156233516553.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$$$$\",\"sdf\");\n",
       "\tviewer_156233516553.setStyle({\"stick\": {}});\n",
       "\tviewer_156233516553.zoomTo();\n",
       "viewer_156233516553.render();\n",
       "});\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import py3Dmol\n",
    "\n",
    "benz='''\n",
    "     RDKit          3D\n",
    "\n",
    "  6  6  0  0  0  0  0  0  0  0999 V2000\n",
    "   -0.9517    0.7811   -0.6622 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.2847    1.3329   -0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    1.2365    0.5518    0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "    0.9517   -0.7811    0.6644 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -0.2847   -1.3329    0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "   -1.2365   -0.5518   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
    "  1  2  2  0\n",
    "  2  3  1  0\n",
    "  3  4  2  0\n",
    "  4  5  1  0\n",
    "  5  6  2  0\n",
    "  6  1  1  0\n",
    "M  END\n",
    "$$$$'''\n",
    "view = py3Dmol.view()\n",
    "view.addModel(benz,'sdf')\n",
    "view.setStyle({'stick':{}})\n",
    "view.zoomTo()\n",
    "view.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<script>\n            $3Dmolpromise.then(function() { //wrap in promise for non-interactive functionality\n                \tviewer_156233516553.setStyle({\"stick\": {\"color\": \"blue\"}});\n\n                viewer_156233516553.render();\n            });\n            </script>",
      "text/html": [
       "<script>\n",
       "            $3Dmolpromise.then(function() { //wrap in promise for non-interactive functionality\n",
       "                \tviewer_156233516553.setStyle({\"stick\": {\"color\": \"blue\"}});\n",
       "\n",
       "                viewer_156233516553.render();\n",
       "            });\n",
       "            </script>"
      ]
     },
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    }
   ],
   "source": [
    "view.setStyle({'stick':{'color':'blue'}})\n",
    "view.update()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/3dmoljs_load.v0": "<script>\n            $3Dmolpromise.then(function() { //wrap in promise for non-interactive functionality\n                \tviewer_156233516553.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_156233516553.setStyle({\"model\": 1},{\"stick\": {}});\n\tviewer_156233516553.setBackgroundColor(\"0xeeeeee\");\n\tviewer_156233516553.animate({\"loop\": \"backAndForth\"});\n\tviewer_156233516553.zoomTo();\n\n                viewer_156233516553.render();\n            });\n            </script>",
      "text/html": [
       "<script>\n",
       "            $3Dmolpromise.then(function() { //wrap in promise for non-interactive functionality\n",
       "                \tviewer_156233516553.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_156233516553.setStyle({\"model\": 1},{\"stick\": {}});\n",
       "\tviewer_156233516553.setBackgroundColor(\"0xeeeeee\");\n",
       "\tviewer_156233516553.animate({\"loop\": \"backAndForth\"});\n",
       "\tviewer_156233516553.zoomTo();\n",
       "\n",
       "                viewer_156233516553.render();\n",
       "            });\n",
       "            </script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "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",
    "'''\n",
    "view.addModel(xyz,'xyz',{'vibrate': {'frames':10,'amplitude':1}})\n",
    "view.setStyle({'model':1},{'stick':{}})\n",
    "view.setBackgroundColor('0xeeeeee')\n",
    "view.animate({'loop': 'backAndForth'})\n",
    "view.zoomTo()\n",
    "view.update()"
   ]
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