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chemcoord-2.0.5
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مشاهده بیشتر
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مشاهده بیشترتوضیحات
Python module for dealing with chemical coordinates.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | chemcoord-2.0.5 |
| نام | chemcoord |
| نسخه کتابخانه | 2.0.5 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Oskar Weser |
| ایمیل نویسنده | oskar.weser@gmail.com |
| آدرس صفحه اصلی | https://github.com/mcocdawc/chemcoord |
| آدرس اینترنتی | https://pypi.org/project/chemcoord/ |
| مجوز | LGPLv3 |
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>`__.
نیازمندی
| مقدار | نام |
|---|---|
| >=1.21 | numpy |
| - | scipy |
| >=1.0 | pandas |
| >=0.35 | numba |
| - | sortedcontainers |
| - | sympy |
| - | six |
| - | pymatgen |
نحوه نصب
نصب پکیج whl chemcoord-2.0.5:
pip install chemcoord-2.0.5.whl
نصب پکیج tar.gz chemcoord-2.0.5:
pip install chemcoord-2.0.5.tar.gz