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.
- `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 version, the following commands have to be executed in
the terminal:
::
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.
Citation and mathematical background
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The theory behind chemcoord is described in `this paper <https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.27029>`__.
If this package is used in a project that leads to a scientific
publication, please acknowledge it by citing.
::
@article{https://doi.org/10.1002/jcc.27029,
author = {Weser, Oskar and Hein-Janke, Björn and Mata, Ricardo A.},
title = {Automated handling of complex chemical structures in Z-matrix coordinates—The chemcoord library},
journal = {Journal of Computational Chemistry},
volume = {44},
number = {5},
pages = {710-726},
keywords = {analytical gradients, geometry optimization, non-linear constraints, transition state search, Z-matrix},
doi = {10.1002/jcc.27029},
year = {2023}
}
My (Oskar Weser) master thesis including a more detailed 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>`__.
Acknowledgement
~~~~~~~~~~~~~~~
.. image:: https://github.com/zulip/zulip/blob/main/static/images/logo/zulip-icon-circle.svg
:width: 80
:align: left
:target: https://zulip.com/
Zulip is an open-source modern team chat app designed to keep both live and asynchronous conversations organized,
that supports the development of chemcoord with a free plan.
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"description": "chemcoord: A python module for coordinates of molecules\n=======================================================\n\n\n.. list-table::\n :widths: 25 25\n :header-rows: 0\n\n * - Latest Release\n - .. image:: https://img.shields.io/pypi/v/chemcoord.svg\n :target: https://pypi.python.org/pypi/chemcoord\n * - Package Status\n - .. image:: https://img.shields.io/pypi/status/chemcoord.svg\n :target: https://pypi.python.org/pypi/chemcoord\n * - Documentation\n - .. image:: https://readthedocs.org/projects/chemcoord/badge/?&style=plastic\n :target: https://chemcoord.readthedocs.io/\n :alt: Documentation Status\n * - License\n - .. image:: https://img.shields.io/pypi/l/chemcoord.svg\n :target: https://www.gnu.org/licenses/lgpl-3.0.en.html\n * - Build Status\n - .. image:: https://circleci.com/gh/mcocdawc/chemcoord/tree/master.svg?style=shield\n :target: https://app.circleci.com/pipelines/github/mcocdawc/chemcoord\n * - Coverage\n - .. image:: https://codecov.io/gh/mcocdawc/chemcoord/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/mcocdawc/chemcoord\n\n\nWebsite\n-------\n\nThe project's website with documentation is:\nhttp://chemcoord.readthedocs.org/\n\nFeatures\n--------\n\n- Molecules are reliably transformed between cartesian space and non\n redundant internal coordinates (Zmatrices). Dummy atoms are inserted\n and removed automatically on the fly if necessary.\n- The created Zmatrix is not only a structure expressed in internal\n coordinates, it is a \"chemical\" Zmatrix. \"Chemical\" Zmatrix means,\n that e.g. distances are along bonds or dihedrals are defined as they\n are drawn in chemical textbooks (Newman projections).\n- Analytical gradients for the transformations between the different\n coordinate systems are implemented.\n- Performance intensive functions/methods are implemented with\n Fortran/C like speed using `numba <http://numba.pydata.org/>`__.\n- Geometries may be defined with symbolic expressions using\n `sympy <http://www.sympy.org/en/index.html>`__.\n- Built on top of `pandas <http://pandas.pydata.org/>`__ with very\n similar syntax. This allows for example distinct label or row based\n indexing.\n- It derived from my own work and I heavily use it during the day. So\n all functions are tested and tailored around the work flow in\n theoretical chemistry.\n- `It as a python module ;) <https://xkcd.com/353/>`__\n\nInstallation guide\n------------------\n\nA working python 3 installation is required (>=3.7 are possible).\n\nIt is highly recommended to use this module in combination with\n`Ipython <http://ipython.org/>`__ and `jupyter <http://jupyter.org/>`__.\nThey come shipped by default with the `anaconda3\ninstaller <https://www.continuum.io/downloads/>`__\n\nUnix\n~~~~\n\nFor the packaged version, the following commands have to be executed in\nthe terminal:\n\n::\n\n pip install chemcoord\n\nFor the up to date development version (experimental):\n\n::\n\n git clone https://github.com/mcocdawc/chemcoord.git\n cd chemcoord\n pip install .\n\nWindows\n~~~~~~~\n\nNeither installation nor running the module are tested on windows. To\nthe best of my knowledge it should work there as well. Just use the same\nsteps as for UNIX.\n\n\nCitation and mathematical background\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe theory behind chemcoord is described in `this paper <https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.27029>`__.\nIf this package is used in a project that leads to a scientific\npublication, please acknowledge it by citing.\n\n::\n\n @article{https://doi.org/10.1002/jcc.27029,\n author = {Weser, Oskar and Hein-Janke, Bj\u00f6rn and Mata, Ricardo A.},\n title = {Automated handling of complex chemical structures in Z-matrix coordinates\u2014The chemcoord library},\n journal = {Journal of Computational Chemistry},\n volume = {44},\n number = {5},\n pages = {710-726},\n keywords = {analytical gradients, geometry optimization, non-linear constraints, transition state search, Z-matrix},\n doi = {10.1002/jcc.27029},\n year = {2023}\n }\n\n\nMy (Oskar Weser) master thesis including a more detailed derivation of implemented equations and\nthe mathematical background can be found\n`here <https://github.com/mcocdawc/chemcoord/blob/master/docs/source/files/master_thesis_oskar_weser_chemcoord.pdf>`__.\n\n\n\nAcknowledgement\n~~~~~~~~~~~~~~~\n\n\n.. image:: https://github.com/zulip/zulip/blob/main/static/images/logo/zulip-icon-circle.svg\n :width: 80\n :align: left\n :target: https://zulip.com/\n\nZulip is an open-source modern team chat app designed to keep both live and asynchronous conversations organized,\nthat supports the development of chemcoord with a free plan.\n\n\n",
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