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https://github.com/tridentbio/trident-chemwidgets

Jupyter Widgets to interact with molecular datasets.
https://github.com/tridentbio/trident-chemwidgets

chemistry jupyter jupyter-notebook molecule notebook visualization

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Jupyter Widgets to interact with molecular datasets.

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README 

        







    





   



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## Summary



- [About](#About)

- [Installation](#Installation)

- [Documentation](#Documentation)

- [Usage](#Usage)



## About



The Trident Chemwidgets (TCW) package provides a set of Jupyter widgets to improve data visibility in cheminformatics and molecular machine learning. 



Trident Chemwidgets is a product of Trident Bioscience. Trident Bioscience builds machine learning applications for the biotech and pharmaceutical industries. If you're interested in learning more, you can visit us at [trident.bio](https://www.trident.bio) or email us at [[email protected]](mailto:[email protected]).



## Installation



Trident Chemwidgets is available from pip and conda:



pip:

```bash

pip install trident-chemwidgets

```



conda:

```

conda install -c conda-forge trident-chemwidgets

```



Then, for Jupyter Lab, run:



```

jupyter labextension install trident-chemwidgets

```



[Full instructions here.](https://www.trident.bio/trident-chemwidgets/html/installing.html)



## [Documentation](https://www.trident.bio/trident-chemwidgets)



Click the link above to access the [documentation](https://www.trident.bio/trident-chemwidgets). If you're looking for example notebooks, check out the links below (clone this repository to use them directly).



- [JSME widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/JSME_widget.ipynb)

- [Histogram widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Histogram_widget.ipynb)

- [Scatter widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Scatter_widget.ipynb)

- [InteractiveMolecule widget](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/InteractiveMolecule_widget.ipynb)



## Usage



We suggest importing Trident Chemwidgets using the convention `tcw`, as shown below. 



```python

import trident_chemwidgets as tcw

```



---



### Input functions



#### JSME



To facilitate molecular input, TCW provides an interface to the [JSME Molecule Editor](https://jsme-editor.github.io/) with added functionality.



```python

editor = tcw.JSME()

editor

```





    




You can play with JSME widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/JSME_widget.ipynb).



---



### Plotting functions



Understanding the distribution of your data is critical to many cheminformatic tasks. To this end, we supply a number of interactive plotting functions that allow you to display both the data and underlying molecular structures. You can even subset and save the data based on the property values for use in downstream analysis.



#### Histogram



For 1-dimensional datasets, TCW provides a histogram plot function:



```python

histogram = tcw.Histogram(data=data, smiles='smiles', x='tpsa', x_label='TPSA')

histogram

```





    




You can play with Histogram widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Histogram_widget.ipynb).



#### Scatter plot



For 2-dimensional datasets, TCW provides a scatter plot function:



```python

scatter = tcw.Scatter(data=data, smiles='smiles', x='mwt', y='logp',

                      x_label='Molecular Weight', y_label='logP')

```





    




You can play with Scatter widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/Scatter_widget.ipynb).



---



### Output functions



#### Interactive molecule



To examine features at the atom level, TCW provides a function to plot a molecule and allow users to explore the atom-specific features:



```python

mol = tcw.InteractiveMolecule('CC(C)CC1=CC=C(C=C1)C(C)C(=O)O', data=atom_data)

mol

```





    




You can play with InteractiveMolecule widget in this [notebook](https://github.com/tridentbio/trident-chemwidgets/raw/master/examples/InteractiveMolecule_widget.ipynb).