chemical-dataset-comparator

ChemIcal DatasEt comparatoR (CIDER) is a Python package and ready-to-use Jupyter Notebook workflow which primarily utilizes RDKit to compare two or more chemical structure datasets (SD files) in different aspects, e.g. size, overlap, molecular descriptor distributions, chemical space clustering, etc., most of which can be visually inspected.

https://github.com/steinbeck-lab/chemical-dataset-comparator

Science Score: 75.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Institutional organization owner
Organization steinbeck-lab has institutional domain (cheminf.uni-jena.de)
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: Steinbeck-Lab
License: other
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 19.2 MB

Statistics

Stars: 9
Watchers: 4
Forks: 4
Open Issues: 3
Releases: 1

Created about 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

README.md

Overview of ChemIcal DatasEt comparatoR (CIDER) :globewithmeridians:

ChemIcal DatasEt comparatoR (CIDER) is a Python package and ready-to-use Jupyter Notebook workflow which primarily utilizes RDKit to compare two or more chemical structure datasets (SD files) in different aspects, e.g. size, overlap, molecular descriptor distributions, chemical space clustering, etc., most of which can be visually inspected in the notebook.

Usage

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

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

Conda can be downloaded as part of the Anaconda or the Miniconda platforms (Python 3.10). We recommend to install miniconda3. Using 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

Installation

shell $ git clone https://github.com/Steinbeck-Lab/ChemIcal_DatasEt_compaRator.git $ cd ChemIcal_DatasEt_compaRator $ conda create --name cider_chem python=3.10 $ conda activate cider_chem $ conda install pip $ python -m pip install -U pip #Upgrade pip $ pip install . - Note: Make sure all installations are working correctly by running the tests. You can do this by running the pytest command in the repository root folder.

Alternative

shell $ python -m pip install -U pip #Upgrade pip $ pip install git+https://github.com/Steinbeck-Lab/ChemIcal_DatasEt_compaRator.git

Install from PyPI

shell $ pip install cider-chem

Basic usage:

```python from CIDER import ChemicalDatasetComparator cider = ChemicalDatasetComparator()

datadir = './data/' # dir with sd files containing molecules testdict = cider.importasdatadict(datadir) cider.getnumberofmolecules(testdict)

```

Documentation

The documentation for the CIDER package can be found here.

Cite us

Busch, H., Schaub, J., Brinkhaus, H. O., Rajan, K., & Steinbeck, C. (2022). ChemIcal DatasEt comparatoR CIDER (Version 0.0.1-dev) [Computer software]. https://doi.org/10.5281/zenodo.6630494

Maintained by :wrench:

ChemIcal DatasEt comparatoR is developed and maintained by the Steinbeck group at the Friedrich Schiller University Jena, Germany. The code for this web application is released under the MIT license. Copyright © CC-BY-SA 2024

Owner

Name: Steinbeck-Lab
Login: Steinbeck-Lab
Kind: organization

Website: https://cheminf.uni-jena.de
Repositories: 28
Profile: https://github.com/Steinbeck-Lab

Official GitHub organization for the Steinbeck group Jena, Germany

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Busch"
    given-names: "Hannah"
    orcid: "https://orcid.org/0000-0002-9674-6450"
  - family-names: "Schaub"
    given-names: "Jonas"
    orcid: "https://orcid.org/0000-0003-1554-6666"
  - 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"
  - family-names: "Steinbeck"
    given-names: "Christoph"
    orcid: "https://orcid.org/0000-0001-6966-0814"
title: "ChemIcal DatasEt comparatoR CIDER"
version: 1.0.0
doi: 10.5281/??
date-released: 2022.06.09
url: "https://github.com/hannbus/ChemIcal_DatasEt_compaRator"
license: MIT

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Dependencies

setup.py pypi

FPDF ==1.7.2
chemplot ==1.2.0
matplotlib ==3.5.1
matplotlib_venn ==0.11.6
notebook *
rdkit-pypi *
seaborn ==0.11.2

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/setup-python v1 composite

docs/requirements.txt pypi

FPDF ==1.7.2
IPython *
bokeh ==2.4.3
chemplot ==1.2.0
matplotlib ==3.5.1
matplotlib_venn ==0.11.6
nbsphinx *
rdkit-pypi *
seaborn ==0.11.2
sphinx-autodoc-typehints *
sphinx_rtd_theme *

ecosyste.ms

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