Metadata-Version: 2.1
Name: molsystem
Version: 2023.7.18.1
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
=============

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Description
-----------
Molsystem provides a general class for handling molecular and periodic systems. This is
the heart of SEAMM.

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


Features
--------

* Supports molecular and periodic (crystalline) systems.
* Support for pointgroup and spacegroup symmetry.
* Implemented as a SQL database, currently using SQLite, which provides permanence and a
  disk file.
* Handles multiple systems, and for each system any number of
  configurations. Configurations are different structures, generally having different
  coordinates. Examples are conformers or frames in an MD trajectory.
* Configurations can have differing bonds, supporting reactive forcefields such as
  ReaxFF.
* Configurations can also have differing numbers of atoms, supporting e.g. grand
  canonical Monte Carlo.
* Support for templates and subsets. Templates can be used for creating or finding
  structures in systems and subsets hold substes of atoms. An atom can be in multiple
  subsets. For proteins, subsets can be used for residues and chains; for polymers,
  monomers; and for fluids the subsets can track individual molecules.
* Subsets and templates handle the correspondance between atoms so if, for instance, the
  ordering of atoms in residues are different, that can be handled using the
  correspondances.
* Direct connection to and support of RDKit and OpenBabel molecules, allowing direct
  transfer back and forth between configurations and those libraries.
* Properties of systems and configurations are stored in fact tables of integers,
  floats, strings, and JSON, using a star schema. One of the dimensions is metadata
  describing the property. This data warehousing approach is almost identical to that
  used in CIF files, with the metadata being the CIF dictionaries.
* Good support of CIF files, with the ability to store data other than the actual atoms
  using the properties warehouse.
* Direct support for SMILES, SMARTS and substructure searching.
* Scales to millions of systems and configurations, and databases in excess of 100 GB.

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
=======

2023.7.18.1 -- Added support for creating structures from InChIKeys
    * Uses PubChem to translate the InChiKey to InChI.
      
2023.7.18 -- Added support for InChI and InChIKeys

2023.7.9 -- Added JSON properties
    * Added properties stored as JSON, which allows, vectors, tensors, etc.
      
2023.4.6 -- Enhancements for CIF files
    * Handle uncertainties in CIF files expressed as '(x)' at end of value.

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).
