From 1ec72a67f0ed434fb7a764a91e0098ba328fd825 Mon Sep 17 00:00:00 2001 From: t-kimber Date: Tue, 7 Dec 2021 10:17:10 +0100 Subject: [PATCH 1/6] Update README.md --- README.md | 62 +++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 42 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 72167c3..eb201d5 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,13 @@ Maxsmi: data augmentation for molecular property prediction using deep learning [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) [![Documentation Status](https://readthedocs.org/projects/maxsmi/badge/?version=latest)](https://maxsmi.readthedocs.io/en/latest/?badge=latest) +[![Anaconda-Server Badge](https://anaconda.org/conda-forge/maxsmi/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge) ![GitHub closed pr](https://img.shields.io/github/issues-pr-closed-raw/volkamerlab/maxsmi) ![GitHub open pr](https://img.shields.io/github/issues-pr-raw/volkamerlab/maxsmi) ![GitHub closed issues](https://img.shields.io/github/issues-closed-raw/volkamerlab/maxsmi) ![GitHub open issues](https://img.shields.io/github/issues/volkamerlab/maxsmi) # Table of contents - Project description +- Citation - Installation using conda - Prerequisites - How to install @@ -20,6 +22,7 @@ Maxsmi: data augmentation for molecular property prediction using deep learning - How to make predictions - Documentation - Repository structure and important files +- Acknowledgments # Project description ## SMILES augmentation for deep learning based molecular property and activity prediction. @@ -49,41 +52,57 @@ This repository provides the code basis to exploit data augmentation using the f The results of our study show that data augmentation improves the accuracy independently of the deep learning model and the size of the data. The best strategy leads to the Maxsmi models, which are available here for predictions on novel compounds on the provided data sets. +# Citation +If you use `maxsmi`, don't forget to reference the work. The paper can be found at [this link](https://doi.org/10.1016/j.ailsci.2021.100014). + +``` +@article{kimber_2021_AILSCI, + title = {Maxsmi: Maximizing molecular property prediction performance with confidence estimation using SMILES augmentation and deep learning}, + author = {Talia B. Kimber and Maxime Gagnebin and Andrea Volkamer} + journal = {Artificial Intelligence in the Life Sciences}, + volume = {1}, + pages = {100014}, + year = {2021}, + issn = {2667-3185}, + doi = {https://doi.org/10.1016/j.ailsci.2021.100014}, + url = {https://www.sciencedirect.com/science/article/pii/S2667318521000143} +} +``` + # Installation using conda ## Prerequisites -Anaconda and Git should be installed. See [Anaconda's website](https://www.anaconda.com/products/individual) and [Git's website](https://git-scm.com/downloads) for download. +Anaconda should be installed. See [Anaconda's website](https://www.anaconda.com/products/individual) for download. ## How to install -1. Clone the github repository: +1. Create a `conda` environment, called e.g. `maxsmi`: ```console -git clone https://github.com/volkamerlab/maxsmi.git +conda env create -n maxsmi ``` +2. Activate the environment: -2. Change directory: ```console -cd maxsmi -``` -3. Create the conda environment: - -```console -conda env create -n maxsmi -f devtools/conda-envs/test_env.yaml +conda activate maxsmi ``` -4. Activate the environment: +3. Install the `maxsmi` package: +For Linux / MacOS: ```console -conda activate maxsmi +conda install -c conda-forge maxsmi ``` -5. Install the maxsmi package: -```console -pip install -e . +For Windows: +``` +conda install maxsmi -c conda-forge -c defaults ``` + # How to use maxsmi + ## Examples + ### How to train and evaluate a model using augmentation To get an overview of all available options: @@ -156,12 +175,15 @@ The `maxsmi` package documentation is available [here](https://maxsmi.readthedoc | |-- tests ``` -### Copyright - -Copyright (c) 2020, Talia B. Kimber at [VolkamerLab](https://volkamerlab.org/). - -#### Acknowledgements +### Acknowledgements Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.4. + +Documentation and packaging: +A special thank you to @dominiquesydow for sharing her valuable knowledge with infinite kindness. + +### Copyright + +Copyright (c) 2020, Talia B. Kimber at [VolkamerLab](https://volkamerlab.org/). \ No newline at end of file From 9343a5ede5f8b95ab4d086d99f60048871102254 Mon Sep 17 00:00:00 2001 From: t-kimber Date: Tue, 7 Dec 2021 11:08:14 +0100 Subject: [PATCH 2/6] Update links. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index eb201d5..d41af48 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ Maxsmi: data augmentation for molecular property prediction using deep learning [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) [![Documentation Status](https://readthedocs.org/projects/maxsmi/badge/?version=latest)](https://maxsmi.readthedocs.io/en/latest/?badge=latest) -[![Anaconda-Server Badge](https://anaconda.org/conda-forge/maxsmi/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge) +[![Anaconda-Server Badge](https://anaconda.org/conda-forge/maxsmi/badges/installer/conda.svg)](https://anaconda.org/conda-forge/maxsmi) ![GitHub closed pr](https://img.shields.io/github/issues-pr-closed-raw/volkamerlab/maxsmi) ![GitHub open pr](https://img.shields.io/github/issues-pr-raw/volkamerlab/maxsmi) ![GitHub closed issues](https://img.shields.io/github/issues-closed-raw/volkamerlab/maxsmi) ![GitHub open issues](https://img.shields.io/github/issues/volkamerlab/maxsmi) @@ -72,7 +72,7 @@ If you use `maxsmi`, don't forget to reference the work. The paper can be found # Installation using conda ## Prerequisites -Anaconda should be installed. See [Anaconda's website](https://www.anaconda.com/products/individual) for download. +Anaconda should be installed. See [Anaconda's website](https://www.anaconda.com) for download. ## How to install @@ -182,7 +182,7 @@ Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.4. Documentation and packaging: -A special thank you to @dominiquesydow for sharing her valuable knowledge with infinite kindness. +A special thank you to [dominiquesydow](https://github.com/dominiquesydow) for sharing her valuable knowledge with infinite kindness. ### Copyright From 40be726b64374bed2b84d5b4f7abe5f06908d4ad Mon Sep 17 00:00:00 2001 From: t-kimber Date: Tue, 7 Dec 2021 11:08:39 +0100 Subject: [PATCH 3/6] Add conda badge. --- docs/index.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/index.rst b/docs/index.rst index 806b8cb..b34a0ac 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -26,6 +26,10 @@ Welcome to maxsmi's documentation! .. image:: https://readthedocs.org/projects/maxsmi/badge/?version=latest :target: https://maxsmi.readthedocs.io/en/latest/?badge=latest + +.. image:: + https://anaconda.org/conda-forge/maxsmi/badges/installer/conda.svg + :target: https://anaconda.org/conda-forge/maxsmi .. raw:: html From 0f2da7ee4d843ad4f706a713d6df5c642391bd0d Mon Sep 17 00:00:00 2001 From: t-kimber Date: Tue, 7 Dec 2021 11:09:59 +0100 Subject: [PATCH 4/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d41af48..7368a38 100644 --- a/README.md +++ b/README.md @@ -182,7 +182,7 @@ Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.4. Documentation and packaging: -A special thank you to [dominiquesydow](https://github.com/dominiquesydow) for sharing her valuable knowledge with infinite kindness. +A special thank you to [dominiquesydow](https://github.com/dominiquesydow) for sharing her valuable knowledge with patience and kindness. ### Copyright From 1e56c329936f76f58adae3bfe2b7ff0c7c742d5c Mon Sep 17 00:00:00 2001 From: t-kimber Date: Tue, 7 Dec 2021 11:12:15 +0100 Subject: [PATCH 5/6] Update installation instructions. --- docs/getting_started.rst | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/docs/getting_started.rst b/docs/getting_started.rst index 260350e..a66552c 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -10,4 +10,28 @@ You've come to the right place! Installation ------------- -For installation, please refer to `the Github page `_. +Prerequisites +~~~~~~~~~~~~~ + +Anaconda should be installed. See `Anaconda's website `_ for download. + +How to install +~~~~~~~~~~~~~~ + +1. Create a :code:`conda` environment, called e.g. :code:`maxsmi` + +:code:`conda env create -n maxsmi` + +2. Activate the environment: + +:code:`conda activate maxsmi` + +3. Install the :code:`maxsmi` package: + +For Linux / MacOS: + +:code:`conda install -c conda-forge maxsmi` + +For Windows: + +:code:`conda install maxsmi -c conda-forge -c defaults` From 5ffd23a1bd9c378deac165064414cb53107ac743 Mon Sep 17 00:00:00 2001 From: t-kimber Date: Wed, 8 Dec 2021 11:26:39 +0100 Subject: [PATCH 6/6] Trigger action