semvec/pypi-packages huggingface dataset:
scipion-chem-toxCSM 0.1
Scipion framework plugin for the use of toxCSM software tool
Keywords: scipion toxCSM scipion-3.0 cheminformatics

.. |organization| replace:: scipion-chem
.. |repository| replace:: scipion-chem-toxCSM

====================================================
Toxicity prediction of small ligands scipion plugin
====================================================
**Documentation under development, sorry for the inconvenience**
Scipion framework plugin for the use of toxCSM software tool.
  
========================================
Install this plugin
========================================
You will need to use `Scipion3 <https://scipion-em.github.io/docs/docs/scipion
-modes/how-to-install.html>`_ to run these protocols.


- **Install the stable version**

    Through the plugin manager GUI by launching Scipion and following **Others** >> **Plugin Manager**

    or

.. parsed-literal::

    scipion3 installp -p \ |repository|\ 


- **Developer's version**

    1. Download repository:

    .. parsed-literal::

        git clone \https://github.com/\ |organization|\ /\ |repository|\ .git

    2. Install:

    .. parsed-literal::

        scipion3 installp -p /path/to/\ |repository|\  --devel
  
========================================
Protocols
========================================
This plugin contains the following protocols:

**None for now**

========================================
Packages & enviroments
========================================
Packages installed by this plugin can be located in ``/path/to/scipion/software/em/``.


As of today, Scipion does not automatically uninstall the conda enviroments created in the installation process when uninstalling a plugin, so keep this list in mind if you want to clean up some disk space if you need to uninstall this one.


========================================
Changelog
========================================
All the recent version changes can be found `here <https://github.com/scipion-chem/scipion-chem-toxCSM/blob/devel/CHANGES.rst>`_.
rhodent 1.1
Analyzing hot-carrier distributions from TD-DFT simulations
Requires Python: >=3.9
Keywords: chemistry, physics, scientific

rhodent
=======

**rhodent** is a tool for analyzing hot-carrier distributions based on input from real-time time-dependent density functional theory simulations.
A detailed description of the functionality provided as well as tutorials can be found in the `user guide <https://rhodent.materialsmodeling.org/>`_.

**rhodent** can be installed via `pip`::

    pip3 install rhodent

**rhodent** has been developed at the `Department of Physics <https://www.chalmers.se/en/departments/physics/>`_ at `Chalmers University of Technology <https://www.chalmers.se/>`_ (Gothenburg, Sweden) in the `Condensed Matter and Materials Theory division <http://www.materialsmodeling.org>`_.


Development
-----------

The test suite is run using `pytest`::

  pytest tests/

The tests should also pass in parallel MPI execution, on any number of ranks::

  mpirun -np 2 pytest -x tests/
  mpirun -np 3 pytest -x tests/
  mpirun -np 4 pytest -x tests/
  mpirun -np 5 pytest -x tests/
  mpirun -np 6 pytest -x tests/

Tests are configured such that they are skipped if the number of ranks is incompatible with the particular test.

Only a subset of data required for testing is included in the repository.
Large data files are included in a `zenodo record <https://doi.org/10.5281/zenodo.14832606>`_ that needs to be extracted into the `tests/data` directory.

The subset of tests that does not require the large data files (mostly unit-tests) can be run via::

  pytest -m 'not bigdata' tests/
smpl 1.5.6
SiMPLe plotting and fitting
Requires Python: >=3.9

# smpl
Simplified plotting and fitting in python.

[![PyPI version][pypi image]][pypi link]
[![PyPI version][pypi versions]][pypi link]
![downloads](https://img.shields.io/pypi/dm/smpl.svg)
[![test][a t image]][a t link]
[![Coverage Status][c t i]][c t l]
[![Codacy Badge][cc c i]][cc c l]
[![Codacy Badge][cc q i]][cc q l]
[![Documentation][rtd t i]][rtd t l]

## Documentation

-   <https://smpl.readthedocs.io/en/latest/>

## Versions

### Stable

```sh
pip install smpl
```

Optional: --user or --upgrade

[doc stable]: https://apn-pucky.github.io/smpl/index.html
[doc test]: https://apn-pucky.github.io/smpl/test/index.html

[pypi image]: https://badge.fury.io/py/smpl.svg
[pypi link]: https://pypi.org/project/smpl/
[pypi versions]: https://img.shields.io/pypi/pyversions/smpl.svg

[a s image]: https://github.com/APN-Pucky/smpl/actions/workflows/stable.yml/badge.svg
[a s link]: https://github.com/APN-Pucky/smpl/actions/workflows/stable.yml
[a t link]: https://github.com/APN-Pucky/smpl/actions/workflows/ci.yml
[a t image]: https://github.com/APN-Pucky/smpl/actions/workflows/ci.yml/badge.svg

[cc s q i]: https://app.codacy.com/project/badge/Grade/38630d0063814027bd4d0ffaa73790a2?branch=stable
[cc s q l]: https://www.codacy.com/gh/APN-Pucky/smpl/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=APN-Pucky/smpl&amp;utm_campaign=Badge_Grade?branch=stable
[cc s c i]: https://app.codacy.com/project/badge/Coverage/38630d0063814027bd4d0ffaa73790a2?branch=stable
[cc s c l]: https://www.codacy.com/gh/APN-Pucky/smpl/dashboard?utm_source=github.com&utm_medium=referral&utm_content=APN-Pucky/smpl&utm_campaign=Badge_Coverage?branch=stable

[cc q i]: https://app.codacy.com/project/badge/Grade/38630d0063814027bd4d0ffaa73790a2
[cc q l]: https://www.codacy.com/gh/APN-Pucky/smpl/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=APN-Pucky/smpl&amp;utm_campaign=Badge_Grade
[cc c i]: https://app.codacy.com/project/badge/Coverage/38630d0063814027bd4d0ffaa73790a2
[cc c l]: https://www.codacy.com/gh/APN-Pucky/smpl/dashboard?utm_source=github.com&utm_medium=referral&utm_content=APN-Pucky/smpl&utm_campaign=Badge_Coverage

[c s i]: https://coveralls.io/repos/github/APN-Pucky/smpl/badge.svg?branch=stable
[c s l]: https://coveralls.io/github/APN-Pucky/smpl?branch=stable
[c t l]: https://coveralls.io/github/APN-Pucky/smpl?branch=master
[c t i]: https://coveralls.io/repos/github/APN-Pucky/smpl/badge.svg?branch=master

[rtd s i]: https://readthedocs.org/projects/smpl/badge/?version=stable
[rtd s l]: https://smpl.readthedocs.io/en/stable/?badge=stable
[rtd t i]: https://readthedocs.org/projects/smpl/badge/?version=latest
[rtd t l]: https://smpl.readthedocs.io/en/latest/?badge=latest