read-structure-step


Nameread-structure-step JSON
Version 2022.8.5 PyPI version JSON
download
home_pagehttps://github.com/molssi-seamm/read_structure_step
SummaryA SEAMM plug-in to read common formats in computational chemistry
upload_time2022-08-05 18:43:02
maintainer
docs_urlNone
authorEliseo Marin-R-Rimoldi
requires_python
licenseBSD-3-Clause
keywords seamm plug-in flowchart open babel molecules atomistic files
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage
            ============================
SEAMM Read Structure Plug-in
============================

.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/read_structure_step
   :target: https://github.com/molssi-seamm/read_structure_step/pulls
   :alt: GitHub pull requests

.. image:: https://github.com/molssi-seamm/read_structure_step/workflows/CI/badge.svg
   :target: https://github.com/molssi-seamm/read_structure_step/actions
   :alt: Build Status

.. image:: https://codecov.io/gh/molssi-seamm/read_structure_step/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/molssi-seamm/read_structure_step
   :alt: Code Coverage

.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/read_structure_step.svg?logo=lgtm&logoWidth=18
   :target: https://lgtm.com/projects/g/molssi-seamm/read_structure_step/context:python
   :alt: Code Quality

.. image:: https://github.com/molssi-seamm/read_structure_step/workflows/Documentation/badge.svg
   :target: https://molssi-seamm.github.io/read_structure_step/index.html
   :alt: Documentation Status

.. image:: https://pyup.io/repos/github/molssi-seamm/read_structure_step/shield.svg
   :target: https://pyup.io/repos/github/molssi-seamm/read_structure_step/
   :alt: Updates for Dependencies

.. image:: https://img.shields.io/pypi/v/read_structure_step.svg
   :target: https://pypi.python.org/pypi/read_structure_step
   :alt: PyPi VERSION

A SEAMM plug-in to read common formats in computational chemistry

The current version uses Open Babel as an engine to parse various
formats such as PDB, Mol2 or XYZ and transform them into the SEAMM
structure format for further use in SEAMM flowcharts.

* Free software: BSD license
* Documentation: https://molssi-seamm.github.io/read_structure_step/index.html
* Code: https://github.com/molssi-seamm/read_structure_step

Features
--------

- Emphasis in ease-of-use and simplicity. The public interface
  consists of a single function.
- Automatic file type recognition.
- OpenBabel as an engine to parse formats, but other engines can be
  easily implemented.
- Easily extensible to new formats.
- Current support for PDB, Mol2 and XYZ files.

Example
+++++++

.. code:: python

 import read_structure_step
 seamm_structure = read_structure_step.read("spc.xyz")

Acknowledgements
----------------

This package was created with Cookiecutter_ and the `molssi-seamm/cookiecutter-seamm-plugin`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award ACI-1547580

.. _MolSSI: https://www.molssi.org
.. _`National Science Foundation`: https://www.nsf.gov


=======
History
=======

2021.2.12 (12 February 2021)
----------------------------

* Updated the README file to give a better description.
* Updated the short description in setup.py to work with the new installer.
* Added keywords for better searchability.

2021.2.4 (4 February 2021)
--------------------------

* Updated for compatibility with the new system classes in MolSystem
  2021.2.2 release.

2020.12.5 (5 December 2020)
---------------------------

* Internal: switching CI from TravisCI to GitHub Actions, and in the
  process moving documentation from ReadTheDocs to GitHub Pages where
  it is consolidated with the main SEAMM documentation.

2020.8.1 (1 August 2020)
------------------------

* Removed leftover debug print statements.

0.9 (15 April 2020)
-------------------

* General bug fixing and code cleanup.
* Part of release of all modules.


0.7.1 (23 November 2019)
------------------------

* First release on PyPI.

            

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