Metadata-Version: 2.1
Name: molsystem
Version: 2023.3.30
Summary: molsystem
Home-page: https://github.com/molssi-seamm/molsystem
Author: Paul Saxe
Author-email: psaxe@molssi.org
License: GNU Lesser General Public License v3 or later (LGPLv3+)
Keywords: molsystem,SEAMM
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
License-File: LICENSE
License-File: AUTHORS.rst

=============
MolSystem
=============


.. image:: https://img.shields.io/travis/molssi-seamm/molsystem.svg
           :target: https://travis-ci.org/molssi-seamm/molsystem
	   :alt: Build Status

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	   :target: https://codecov.io/gh/molssi-seamm/molsystem
	   :alt: Code Coverage

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	   :target: https://lgtm.com/projects/g/molssi-seamm/molsystem/context:python
	   :alt: Code Quality

.. image:: https://readthedocs.org/projects/molsystem/badge/?version=latest
           :target: https://molsystem.readthedocs.io/en/latest/?badge=latest
	   :alt: Documentation Status

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	   :target: https://pyup.io/repos/github/molssi-seamm/molsystem/
	   :alt: Updates for Dependencies

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

Molsystem provides a general class for handling molecular and periodic systems


* Free software: GNU Lesser General Public License v3+
* Documentation: https://molsystem.readthedocs.io.


Features
--------

* Complete the initial version!

  * Remove the coordinates from the Atoms class and allow for multiple
    sets of coordinates -- conformers, trajectories, etc.
  * Provide a concept of the 'current' system

Credits
---------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award OAC-1547580 and CHE-2136142.

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


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

2023.3.30 -- Enhancements to QCSchema support
    * Improved naming of molecule in QCSchema
    * Added creation of configurations from QCSchema objects.

2023.2.13 -- Fixed issue with valence in RDkit for cations like NH4+

2022.11.20 -- Added a method to copy a configuration.
  Added a new method to the `system` class, `copy_configuration`, that creates a copy of
  the configuration using the same atomset and bonset, but new coordinates and cell so
  that any changes to coordinates and cell are not shared between the configurations. By
  default it copies the current configuration.

2022.11.18 -- Fixed bug with handling for Open Babel
  The total charge and multiplicity were not correctly set when creating an Open Babel
  molecule.

2022.11.3 -- Add handling of strain and improved handling of properties
  Added methods for straining the unit cell, and also straining a configuration,
  correctly handling the coordinates for an affine transformation. In the future will
  add e.g. affine transformation of the centers of molecules, which is useful for
  molecular fluids.

  Added the system for properties, in addition to the configuration. This allows system
  properties that are not associated with a particular configuration, which is often
  appropriate for experimental results. It also makes it much easier to search for
  systems where any configuration has a particular property.

2022.10.26 -- Improved database write performance.
  Switched to write-ahead mode and tweaked memory settings. This gives a large
  performance improvement (10x or more) for large database (~1 GB).
