RanDepict 1.0.1

RanDepict is an easy-to-use utility to generate a big variety of chemical structure depictions (random depiction styles and image augmentations).

RanDepict

This repository contains RanDepict, an easy-to-use utility to generate a big variety of chemical structure depictions (random depiction styles and image augmentations) based on RDKit, CDK and Indigo.

Usage

• To use RanDepict, clone the repository to your local disk and make sure you install all the necessary requirements.

We recommend to use RanDepict inside a Conda environment to facilitate the installation of the dependencies.

• Conda can be downloaded as part of the Anaconda or the Miniconda plattforms (Python 3.7). We recommend to install miniconda3. Using Linux you can get it with:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Installation

$ git clone https://github.com/OBrink/RanDepict.git
$ cd RanDepict
$ conda create --name RanDepict python=3.7
$ conda activate RanDepict
$ conda install -c rdkit rdkit
$ conda install pip
$ python -m pip install -U pip #Upgrade pip
$ pip install numpy scikit-image epam.indigo jpype1 ipyplot imagecorruptions imgaug

Alternative

$ python -m pip install -U pip #Upgrade pip
$ pip install git+https://github.com/OBrink/RanDepict.git

Install from PyPI

$ pip install RanDepict

Basic usage:

from RanDepict import random_depictor

smiles = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"

with random_depictor() as depictor:
    image = depictor(smiles)

Have a look in the RanDepictNotebook.ipynb for more examples and a more detailed documentation.

Here are some examples of depictions of caffeine without augmentations (left) and with augmentations (right) that were automatically created using RanDepict.

Cite Us

@misc{Brinkhaus2021,
  title={RanDepict},
  author={Brinkhaus, Henning Otto and Rajan, Kohulan},
  doi = {10.5281/zenodo.5205528},
  year={2021},
  publisher={Github},
  journal={GitHub repository},
  howpublished={\url{https://github.com/OBrink/RanDepict}},
  url={https://doi.org/10.5281/zenodo.5205528},
 }

More information about our research group