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https://github.com/theochem/procrustes

Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other.
https://github.com/theochem/procrustes

chemical-structure-similarity generalized-procrustes-analysis generalized-procrustes-problem gpa matrix-transformations molecular-alignment optimization optimization-algorithms orthogonal-procrustes-problem permutation-procrustes-problem procrustes procrustes-analysis quadratic-assignment-problem rotational-procrustes-problem softassign-method symmetric-procrustes-problem

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Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other.

Host: GitHub
URL: https://github.com/theochem/procrustes
Owner: theochem
License: gpl-3.0
Created: 2020-02-17T22:11:29.000Z (almost 5 years ago)
Default Branch: main
Last Pushed: 2024-09-17T20:19:34.000Z (4 months ago)
Last Synced: 2024-09-18T15:40:48.211Z (4 months ago)
Topics: chemical-structure-similarity, generalized-procrustes-analysis, generalized-procrustes-problem, gpa, matrix-transformations, molecular-alignment, optimization, optimization-algorithms, orthogonal-procrustes-problem, permutation-procrustes-problem, procrustes, procrustes-analysis, quadratic-assignment-problem, rotational-procrustes-problem, softassign-method, symmetric-procrustes-problem
Language: Python
Homepage: https://procrustes.qcdevs.org/
Size: 19.5 MB
Stars: 109
Watchers: 12
Forks: 20
Open Issues: 18
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff

Awesome Lists containing this project

README

        # Procrustes Python Library

[![This project supports Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg)](https://python.org/downloads)

[![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://opensource.org/licenses/)

[![CI Tox](https://github.com/theochem/procrustes/actions/workflows/ci_tox.yml/badge.svg?branch=main)](https://github.com/theochem/procrustes/actions/workflows/ci_tox.yml)

[![docs](https://github.com/theochem/procrustes/actions/workflows/deploy_website.yaml/badge.svg?branch=main)](https://github.com/theochem/procrustes/actions/workflows/deploy_website.yaml)

[![codecov](https://codecov.io/gh/theochem/procrustes/graph/badge.svg?token=3L96J5QQOT)](https://codecov.io/gh/theochem/procrustes)

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/theochem/procrustes/main?filepath=doc%2Fnotebooks%2F)

The Procrustes library provides a set of functions for transforming a matrix to make it

as similar as possible to a target matrix. For more information, visit

[**Procrustes Documentation**](https://procrustes.qcdevs.org/).

## Citation

Please use [the following citation](https://doi.org/10.1016/j.cpc.2022.108334)

in any publication using Procrustes library:

```md

@article{Meng2022procrustes,

    title = {Procrustes: A python library to find transformations that maximize the similarity between matrices},

    author = {Fanwang Meng and Michael Richer and Alireza Tehrani and Jonathan La and Taewon David Kim and Paul W. Ayers and Farnaz Heidar-Zadeh},

    journal = {Computer Physics Communications},

    volume = {276},

    number = {108334},

    pages = {1--37},

    year = {2022},

    issn = {0010-4655},

    doi = {https://doi.org/10.1016/j.cpc.2022.108334},

    url = {https://www.sciencedirect.com/science/article/pii/S0010465522000522},

    keywords = {Procrustes analysis, Orthogonal, Symmetric, Rotational, Permutation, Softassign},

}

```

## Dependencies

The following dependencies are required to run Procrustes properly,

* Python >= 3.9: 

* NumPy >= 1.21.5: 

* SciPy >= 1.9.0: 

To test Procrustes, the following dependencies are required,

* PyTest >= 8.3.0: 

* PyTest-Cov >= 5.0.0: 

## Installation

It is recommended to install `qc-procrustes` within a virtual environment.To create a virtual

environment, we can use the `venv` module (Python 3.3+,

https://docs.python.org/3/tutorial/venv.html), `miniconda` (https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html), or

`pipenv` (https://pipenv.pypa.io/en/latest/).

### Installing from PyPI

To install `procrustes` with `pip`, we can install the latest stable release from the Python Package Index (PyPI) as follows:

```bash

    # install the stable release.

    pip install qc-procrustes

```

### Installing from The Prebuild Wheel Files

To download the prebuilt wheel files, visit the [PyPI page](https://pypi.org/project/qc-procrustes/)

and [GitHub releases](https://github.com/theochem/procrustes/tags).

```bash

    # download the wheel file first to your local machine

    # then install the wheel file

    pip install file_path/qc_procrustes-1.0.2a1-py3-none-any.whl

```

### Installing from the Source Code

In addition, we can install the latest development version from the GitHub repository as follows:

```bash

    # install the latest development version

    pip install git+https://github.com/theochem/procrustes.git

```

We can also clone the repository to access the latest development version, test it and install it as follows:

```bash

    # clone the repository

    git clone [email protected]:theochem/procrustes.git

    # change into the working directory

    cd procrustes

    # run the tests

    python -m pytest .

    # install the package

    pip install .

```

## More

See https://procrustes.qcdevs.org for full details.