Tools for Simulating Chemical Evoltion
Project description
Copyright (c) 2017 ELIFE
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Description: ======================================
ChemEvolve
======================================
ChemEvolve is a Python package which provides a suite of chemical evolution tools. ChemEvolve is designed to allow for the rapid development and exploration of a chemical reaction systems with standardized input and outputs. CoreEvolve (currently) utilizes the `Simplified Stochastic or Gillispie Algorithm <https://en.wikipedia.org/wiki/Gillespie_algorithm>`_ to exactly simulate chemical systems.
ChemEvolve provides a standard format to specify chemical reaction systems (including the rate constants, catalytic effects, and a choice of propensity functions). It also allows users to simulate these reaction systems in spatially explicit models (e.g. solve Reaction-Diffusion Equations). All ouptut files are saved in `Tidy Data <http://vita.had.co.nz/papers/tidy-data.pdf>`_ format, to allow for easy plotting using standard data visualization tools ( e.g. `Seaborn <http://seaborn.pydata.org/>`_ , or `R <https://www.r-project.org/>`_ )
Requirements
------------
ChemEvolve requires Python 2.7.x, with `NumPy <http://www.numpy.org/>`_, `pandas <http://pandas.pydata.org/>`_, and both `matplotlib <https://matplotlib.org/>`_ and `Seaborn <http://seaborn.pydata.org/>`_ for plotting and visualization.
Installation
--------------
To install, first download and install the package using pip,
.. code-block:: bash
$ pip install chemevolve
Then just throw this import line into the top of your python script:
.. code-block:: python
import chemevolve as ce
That's it! You should be good to go!
Platform: UNKNOWN
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Description: ======================================
ChemEvolve
======================================
ChemEvolve is a Python package which provides a suite of chemical evolution tools. ChemEvolve is designed to allow for the rapid development and exploration of a chemical reaction systems with standardized input and outputs. CoreEvolve (currently) utilizes the `Simplified Stochastic or Gillispie Algorithm <https://en.wikipedia.org/wiki/Gillespie_algorithm>`_ to exactly simulate chemical systems.
ChemEvolve provides a standard format to specify chemical reaction systems (including the rate constants, catalytic effects, and a choice of propensity functions). It also allows users to simulate these reaction systems in spatially explicit models (e.g. solve Reaction-Diffusion Equations). All ouptut files are saved in `Tidy Data <http://vita.had.co.nz/papers/tidy-data.pdf>`_ format, to allow for easy plotting using standard data visualization tools ( e.g. `Seaborn <http://seaborn.pydata.org/>`_ , or `R <https://www.r-project.org/>`_ )
Requirements
------------
ChemEvolve requires Python 2.7.x, with `NumPy <http://www.numpy.org/>`_, `pandas <http://pandas.pydata.org/>`_, and both `matplotlib <https://matplotlib.org/>`_ and `Seaborn <http://seaborn.pydata.org/>`_ for plotting and visualization.
Installation
--------------
To install, first download and install the package using pip,
.. code-block:: bash
$ pip install chemevolve
Then just throw this import line into the top of your python script:
.. code-block:: python
import chemevolve as ce
That's it! You should be good to go!
Platform: UNKNOWN
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