rishiramraj / seepymol

See ipython render molecules.

seepymol

See IPython render molecules. Note that this code is very experimental.

Dependencies

In order to have IPython recognise and execute your plugin, you will need to use the jsonhandlers branch of IPython created by Brian E. Granger. You can find it here: https://github.com/ellisonbg/ipython/tree/jsonhandlers.

As per the setup.py file you will need the MMTK. You may have trouble fetching this package from pypi. You can find the package here: http://dirac.cnrs-orleans.fr/MMTK/. The MMTK depends on the ScientificPython package, which you can find here: http://dirac.cnrs-orleans.fr/plone/software/scientificpython/.

Installation

1. Install seepymol.
2. Under your static folder, create a folder called jsplugins.
   • Depending on your platform, this folder is in ~/.ipython/profile_default/static or ~/.config/ipython/profile_default/static.
3. Symlink the contents of the js folder into your jsplugins folder.
4. Activate WebGL in your browser.
5. Load the test notebook and run the example.

seepymol's Issues

JSON data is not Git-friendly

It turns out iPython notebooks DO store the json string in the notebook source. Here's an example from the test notebook source where we pass a water molecule PDB as a string. That's the non-git friendly string that Greg Wilson was talking about at the sprint.

    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from MMTK import Molecule\n",
      "h2o = Molecule('water')\n",
      "display(h2o)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "json": {
        "handler": "ChemicalObject",
        "pdb": "HETATM    1  H1  HOH     1      -0.757   0.000  -0.520  0.00  0.00           H\nHETATM    2  H2  HOH     1       0.757   0.000  -0.520  0.00  0.00           H\nHETATM    3  O   HOH     1       0.000   0.000   0.066  0.00  0.00           O\n"
       },
       "output_type": "display_data",
       "text": [
        "Molecule water"
       ]
      }
     ],
     "prompt_number": 5
    },

I'm not sure the solution to this, given the limitations of jsMol data inputs.

Support for ChemDoodle Visualization

jsMol may not be the best javascript molecule renderer given it's alpha-like quality. ChemDoodle has a lot of docs and may be a superior alternative once I take a closer look if it meets our requirements.

Here's a demo of a protein:
http://web.chemdoodle.com/demos/pdb-ribbons

Here's some documentation:
http://web.chemdoodle.com/docs/api
http://web.chemdoodle.com/docs/chemdoodle-json-format
http://web.chemdoodle.com/tutorial/advanced/working-with-pdb-files