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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, Indigo and PIKAChU.

https://github.com/obrink/randepict

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

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, Indigo and PIKAChU.

Basic Info
  • Host: GitHub
  • Owner: OBrink
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 135 MB
Statistics
  • Stars: 27
  • Watchers: 4
  • Forks: 10
  • Open Issues: 4
  • Releases: 19
Created over 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Citation

README.md

License Maintenance Workflow GitHub issues GitHub contributors GitHub release PyPI version fury.io versions DOI Documentation Status

GitHub Logo

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, Indigo and PIKAChU.

Usage

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

Installation

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

Alternative

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

Install from PyPI

shell $ pip install RanDepict

Development

Note We recommend using 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 3.8). We recommend miniconda3. On Linux you can get it with:

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

```shell $ echo -e "channels:\n - conda-forge\n - nodefaults" > ~/.condarc $ conda update conda $ conda install conda-libmamba-solver $ conda config --set experimental_solver libmamba $ conda create --name RanDepict python=3.8 $ conda activate RanDepict

pypi has rdkit so not necessary to install it using conda

$ conda install -c rdkit rdkit

$ pip install -e ".[dev]" # will install pytest and tox

To run tests for python 3.8

$ tox -e py38 ```

Basic usage:

```python from RanDepict import RandomDepictor

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

with RandomDepictor() as depictor: image = depictor(smiles) ```

Have a look at the examples in our demo notebook. A more detailed documentation is provided here.

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

Cite Us

  • Brinkhaus, H.O., Rajan, K., Zielesny, A. et al. RanDepict: Random chemical structure depiction generator. J Cheminform 14, 31 (2022). https://doi.org/10.1186/s13321-022-00609-4

Acknowledgements

More information about our research group

GitHub Logo

Alt

Owner

  • Name: Otto Brinkhaus
  • Login: OBrink
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Brinkhaus"
  given-names: "Henning Otto"
  orcid: "https://orcid.org/0000-0002-6664-2183"
- family-names: "Rajan"
  given-names: "Kohulan"
  orcid: "https://orcid.org/0000-0003-1066-7792"
title: "RanDepict"
version: 1.3.0
doi: 10.5281/zenodo.5205528
date-released: 2021-08-17
url: "https://github.com/OBrink/RanDepict"
license: MIT

GitHub Events

Total
  • Issues event: 1
  • Watch event: 4
  • Issue comment event: 3
  • Pull request event: 1
  • Pull request review event: 1
Last Year
  • Issues event: 1
  • Watch event: 4
  • Issue comment event: 3
  • Pull request event: 1
  • Pull request review event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 325
  • Total Committers: 6
  • Avg Commits per committer: 54.167
  • Development Distribution Score (DDS): 0.431
Top Committers
Name Email Commits
OBrink b****s@g****m 185
Kohulan Rajan k****n@u****e 93
Otto Brinkhaus 5****k@u****m 23
Iagea i****3@g****m 12
Tulay Muezzinoglu t****u@s****m 11
Egon Willighagen e****n@g****m 1
Committer Domains (Top 20 + Academic)
sri.com: 1 uni-jena.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 19
  • Total pull requests: 37
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 4
  • Total pull request authors: 7
  • Average comments per issue: 1.53
  • Average comments per pull request: 0.46
  • Merged pull requests: 32
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 1
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • OBrink (13)
  • Kohulan (2)
  • tulay (2)
  • sralvins (1)
Pull Request Authors
  • OBrink (19)
  • Kohulan (9)
  • Iagea (3)
  • github-actions[bot] (2)
  • RvdPloeg (2)
  • egonw (1)
  • tulay (1)
Top Labels
Issue Labels
enhancement (9) bug (3) wontfix (2) To Do (1)
Pull Request Labels
enhancement (7) autorelease: tagged (3) autorelease: pending (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 56 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 15
  • Total maintainers: 2
pypi.org: randepict

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

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 56 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 12.5%
Stargazers count: 14.2%
Average: 19.1%
Dependent repos count: 21.7%
Downloads: 36.9%
Maintainers (2)
Kohulan OBrink
Last synced: 6 months ago

Dependencies

.github/workflows/ci_pypi_release.yml actions
  • actions/checkout master composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/ci_pytest_and_release.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • google-github-actions/release-please-action v3 composite
Python_requirements.txt pypi
  • epam.indigo *
  • ipyplot *
  • jpype1 *
  • numpy *
  • pikachu-chem >=1.0.7
  • rdkit *
  • scikit-image *
docs/requirements.txt pypi
  • epam.indigo *
  • furo *
  • imagecorruptions *
  • imgaug *
  • ipyplot *
  • jpype1 *
  • nbsphinx *
  • numpy >=1.19
  • omegaconf ==2.2.3
  • pikachu-chem >=1.0.7
  • pillow >=8
  • rdkit-pypi *
  • scikit-image *
  • sphinx-autodoc-typehints *
setup.py pypi
  • epam.indigo *
  • imagecorruptions *
  • imgaug *
  • ipyplot *
  • jpype1 *
  • numpy >=1.19
  • omegaconf *
  • pikachu-chem >=1.0.7
  • pillow >=8.2.0
  • rdkit *
  • scikit-image *
  • typing-extensions *