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jupyter-marvinjs

MarvinJS and Chython integration

Usage

In jupyter notebook:

from jupyter_marvinjs import MarvinJS
mjs = MarvinJS()
mjs  # this render MJS

Draw structure in MJS and press Upload button on top panel for transferring to python side.

For accessing structure use mjs.structure property:

mol = mjs.structure

For loading structure to editor:

mol = chython.smiles('CCO')
mol.clean2d()
mjs.structure = mol

Installation

First of all download MarvinJS distributive from chemaxon website. Unpack it to project with name mjs. Make sure mjs directory contains editor.html and located at same level as setup.py.

To install use pip:

$ python setup.py bdist_wheel
$ pip install jupyter_marvinjs-<version>.whl

If not working:

$ jupyter nbextension install --py --sys-prefix jupyter_marvinjs
$ jupyter nbextension enable --py --sys-prefix jupyter_marvinjs

For a development installation (requires Node.js and Yarn version 1),

$ git clone https://github.com/stsouko/marvin_jupyter.git
$ cd marvin_jupyter
$ pip install -e .
$ jupyter nbextension install --py --symlink --overwrite --sys-prefix jupyter_marvinjs
$ jupyter nbextension enable --py --sys-prefix jupyter_marvinjs
$ jupyter labextension develop --overwrite jupyter_marvinjs

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