Metadata-Version: 2.1
Name: chemcoord
Version: 2.0.5
Summary: Python module for dealing with chemical coordinates.
Home-page: https://github.com/mcocdawc/chemcoord
Author: Oskar Weser
Author-email: oskar.weser@gmail.com
License: LGPLv3
Keywords: chemcoord,transformation,cartesian,internal,chemistry,zmatrix,xyz,zmat,coordinates,coordinate system
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Natural Language :: English
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
License-File: LICENSE.md
Requires-Dist: numpy (>=1.21)
Requires-Dist: scipy
Requires-Dist: pandas (>=1.0)
Requires-Dist: numba (>=0.35)
Requires-Dist: sortedcontainers
Requires-Dist: sympy
Requires-Dist: six
Requires-Dist: pymatgen

chemcoord: A python module for coordinates of molecules
=======================================================


.. list-table::
   :widths: 25 25
   :header-rows: 0

   * - Latest Release
     - .. image:: https://img.shields.io/pypi/v/chemcoord.svg
            :target: https://pypi.python.org/pypi/chemcoord
   * - Package Status
     - .. image:: https://img.shields.io/pypi/status/chemcoord.svg
            :target: https://pypi.python.org/pypi/chemcoord
   * - Documentation
     - .. image:: https://readthedocs.org/projects/chemcoord/badge/?&style=plastic
            :target: https://chemcoord.readthedocs.io/
            :alt: Documentation Status
   * - License
     - .. image:: https://img.shields.io/pypi/l/chemcoord.svg
            :target: https://www.gnu.org/licenses/lgpl-3.0.en.html
   * - Build Status
     - .. image:: https://circleci.com/gh/mcocdawc/chemcoord/tree/master.svg?style=shield
            :target: https://app.circleci.com/pipelines/github/mcocdawc/chemcoord
   * - Coverage
     - .. image:: https://codecov.io/gh/mcocdawc/chemcoord/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/mcocdawc/chemcoord


Website
-------

The project’s website with documentation is:
http://chemcoord.readthedocs.org/

Features
--------

-  Molecules are reliably transformed between cartesian space and non
   redundant internal coordinates (Zmatrices). Dummy atoms are inserted
   and removed automatically on the fly if necessary.
-  The created Zmatrix is not only a structure expressed in internal
   coordinates, it is a “chemical” Zmatrix. “Chemical” Zmatrix means,
   that e.g. distances are along bonds or dihedrals are defined as they
   are drawn in chemical textbooks (Newman projections).
-  Analytical gradients for the transformations between the different
   coordinate systems are implemented.
-  Performance intensive functions/methods are implemented with
   Fortran/C like speed using `numba <http://numba.pydata.org/>`__.
-  Geometries may be defined with symbolic expressions using
   `sympy <http://www.sympy.org/en/index.html>`__.
-  Built on top of `pandas <http://pandas.pydata.org/>`__ with very
   similar syntax. This allows for example distinct label or row based
   indexing.
-  It derived from my own work and I heavily use it during the day. So
   all functions are tested and tailored around the work flow in
   theoretical chemistry.
-  The classes are safe to inherit from and can easily be customized.
-  `It as a python module ;) <https://xkcd.com/353/>`__

Installation guide
------------------

A working python 3 installation is required (>=3.7 are possible).

It is highly recommended to use this module in combination with
`Ipython <http://ipython.org/>`__ and `jupyter <http://jupyter.org/>`__.
They come shipped by default with the `anaconda3
installer <https://www.continuum.io/downloads/>`__

Unix
~~~~

For the packaged versions, the following commands have to be executed in
the terminal:

::

   conda install -c mcocdawc chemcoord

or

::

   pip install chemcoord

For the up to date development version (experimental):

::

   git clone https://github.com/mcocdawc/chemcoord.git
   cd chemcoord
   pip install .

Windows
~~~~~~~

Neither installation nor running the module are tested on windows. To
the best of my knowledge it should work there as well. Just use the same
steps as for UNIX.

Changelog
~~~~~~~~~

The changelog can be found
`here <https://github.com/mcocdawc/chemcoord/blob/master/CHANGELOG.md>`__.

Citation and mathematical background
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If chemcoord is used in a project that leads to a scientific
publication, please acknowledge this fact by citing `this preprint <https://chemrxiv.org/engage/chemrxiv/article-details/615c0ae97d3da5630aed6dc0>`__.

My (Oskar Weser) master thesis including the derivation of implemented equations and
the mathematical background can be found
`here <https://github.com/mcocdawc/chemcoord/blob/master/docs/source/files/master_thesis_oskar_weser_chemcoord.pdf>`__.


