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README.md

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![Beautiful :)](https://raw.githubusercontent.com/wjm41/molplotly/main/images/pca.gif)
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![Beautiful :)](https://raw.githubusercontent.com/wjm41/molplotly/main/images/multiple_smiles.gif)
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➡️  A readable walkthrough of how to use the package together with some useful examples can be found in [this blog post](https://www.wmccorkindale.com/post/introducing-molplotly) while a runnable notebook can be found in `examples/example.ipynb` :)
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A readable walkthrough of how to use the package together with some useful examples can be found in [this blog post](https://www.wmccorkindale.com/post/introducing-molplotly) while a runnable notebook can be found in `examples/simple_usage_and_formatting.ipynb` :)
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## ⬇️ Installation
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## Installation
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```sh
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pip install molplotly
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conda install rdkit
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```
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## 📜  Usage
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## Usage
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```python
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import pandas as pd
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- The recommended `height` of the app is `50+(height of the plotly figure)`.
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- For the `port` of the app, make sure you don't pick the same `port` as another `molplotly` plot otherwise the tooltips will clash with each other. Also, apparently on windows port numbers below `8700` are used by other processes so for safety processes keep to numbers above that.
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## 💻   Can I run this in colab?
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## Can I run this in colab?
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JupyterDash is supposed to have support for Google Colab but at some point that seems to have broken.. Keep an eye on the raised issue [here](https://github.com/plotly/jupyter-dash/issues/10)!
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Update (1st March 2022): The plots seem to be running again but the hoverboxes are not showing so I don't think it has been fully fixed - I will keep an eye on it in the meantime.
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## 💾   Can I save these plots?
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## Can I save these plots?
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An issue/feature request for this has already been raised [here](https://github.com/wjm41/molplotly/issues/4).
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`moltplotly` works using a Dash app which is non-trivial to export because server side javascript is needed in addition to HTML/CSS styling ([as detailed here](https://stackoverflow.com/questions/60097577/how-to-export-a-plotly-dashboard-app-into-a-html-standalone-file-to-share-with-t))
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Until I find a way to get around that, the best alternative is to either host the plot on an app/server, exporting the plotly figure without molecules showing :( as detailed in this [page](https://plotly.com/python/interactive-html-export/). If you want to use it in a presentation I'd suggest keeping the figure open in a browser and changing windows to it during your talk!
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## 🛑  Warning about memory size
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## Warning about memory size
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Just adding a warning here that memory usage in a notebook can increase significanly when using plotly (not `molplotly`'s fault!). If you notice your jupyter notebook slowing down, plotly itself is a likely culprit... In that case I'd consider either using plotly with [static image rendering](https://plotly.com/python/renderers/#static-image-renderers), or ... use [seaborn](https://seaborn.pydata.org/index.html) :P
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