| Name | alchemlyb JSON |
| Version |
2.2.0
JSON |
| download |
| home_page | None |
| Summary | the simple alchemistry library |
| upload_time | 2024-04-06 19:25:32 |
| maintainer | Oliver Beckstein |
| docs_url | None |
| author | David Dotson |
| requires_python | >=3.9 |
| license | BSD |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
alchemlyb: the simple alchemistry library
=========================================
|doi| |docs| |build| |cov| |anaconda|
**alchemlyb** makes alchemical free energy calculations easier to do
by leveraging the full power and flexibility of the PyData stack. It
includes:
1. Parsers for extracting raw data from output files of common
molecular dynamics engines such as `GROMACS`_, `AMBER`_, `NAMD`_
and `other simulation codes`_.
2. Subsamplers for obtaining uncorrelated samples from timeseries data
(including extracting independent, equilibrated samples
[Chodera2016]_ as implemented in the pymbar_ package).
3. Estimators for obtaining free energies directly from this data, using
best-practices approaches for multistate Bennett acceptance ratio (MBAR)
[Shirts2008]_ and BAR (from pymbar_) and thermodynamic integration (TI).
.. _GROMACS: http://www.gromacs.org/
.. _AMBER: http://ambermd.org/
.. _NAMD: http://www.ks.uiuc.edu/Research/namd/
.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html
.. _`pymbar`: http://pymbar.readthedocs.io/
Installation
------------
**Install** via ``pip`` from `PyPi (alchemlyb)`_ ::
pip install alchemlyb
or as a `conda`_ package from the `conda-forge (alchemlyb)`_ channel
::
conda install -c conda-forge alchemlyb
**Update** with ``pip`` ::
pip install --update alchemlyb
or with ``conda`` run ::
conda update -c conda-forge alchemlyb
to get the latest released version.
.. _`PyPi (alchemlyb)`: https://pypi.org/project/alchemlyb/
.. _`conda`: https://conda.io/
.. _`conda-forge (alchemlyb)`: https://anaconda.org/conda-forge/alchemlyb
Getting involved
----------------
Contributions of all kinds are very welcome.
If you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_.
If you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_.
We also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.
.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions
.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide
.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues
.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb
References
----------
.. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal
analysis of samples from multiple equilibrium states. The Journal of Chemical
Physics 129, 124105.
.. [Chodera2016] Chodera, J.D. (2016). A Simple Method for Automated
Equilibration Detection in Molecular Simulations. Journal of Chemical Theory
and Computation 12, 1799–1805.
.. |doi| image:: https://zenodo.org/badge/68669096.svg
:alt: Zenodo DOI
:scale: 100%
:target: https://zenodo.org/badge/latestdoi/68669096
.. |docs| image:: https://readthedocs.org/projects/alchemlyb/badge/?version=latest
:alt: Documentation
:scale: 100%
:target: http://alchemlyb.readthedocs.io/en/latest/
.. |build| image:: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml/badge.svg?branch=master
:alt: Build Status
:scale: 100%
:target: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml
.. |cov| image:: https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg
:alt: Code coverage
:scale: 100%
:target: https://codecov.io/gh/alchemistry/alchemlyb
.. |anaconda| image:: https://anaconda.org/conda-forge/alchemlyb/badges/version.svg
:alt: anaconda package
:scale: 100%
:target: https://anaconda.org/conda-forge/alchemlyb
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"description": "alchemlyb: the simple alchemistry library\n=========================================\n\n|doi| |docs| |build| |cov| |anaconda|\n\n**alchemlyb** makes alchemical free energy calculations easier to do\nby leveraging the full power and flexibility of the PyData stack. It\nincludes:\n\n1. Parsers for extracting raw data from output files of common\n molecular dynamics engines such as `GROMACS`_, `AMBER`_, `NAMD`_\n and `other simulation codes`_.\n\n2. Subsamplers for obtaining uncorrelated samples from timeseries data\n (including extracting independent, equilibrated samples\n [Chodera2016]_ as implemented in the pymbar_ package).\n\n3. Estimators for obtaining free energies directly from this data, using\n best-practices approaches for multistate Bennett acceptance ratio (MBAR)\n [Shirts2008]_ and BAR (from pymbar_) and thermodynamic integration (TI).\n\n.. _GROMACS: http://www.gromacs.org/\n.. _AMBER: http://ambermd.org/\n.. _NAMD: http://www.ks.uiuc.edu/Research/namd/\n.. _`other simulation codes`: https://alchemlyb.readthedocs.io/en/latest/parsing.html\n.. _`pymbar`: http://pymbar.readthedocs.io/\n\n\nInstallation\n------------\n\n**Install** via ``pip`` from `PyPi (alchemlyb)`_ ::\n\n pip install alchemlyb\n\nor as a `conda`_ package from the `conda-forge (alchemlyb)`_ channel\n::\n\n conda install -c conda-forge alchemlyb \n\n\n**Update** with ``pip`` ::\n\n pip install --update alchemlyb\n\nor with ``conda`` run ::\n\n conda update -c conda-forge alchemlyb\n\nto get the latest released version.\n\n.. _`PyPi (alchemlyb)`: https://pypi.org/project/alchemlyb/\n.. _`conda`: https://conda.io/\n.. _`conda-forge (alchemlyb)`: https://anaconda.org/conda-forge/alchemlyb\n\nGetting involved\n----------------\n\nContributions of all kinds are very welcome.\n\nIf you have questions or want to discuss alchemlyb please post in the `alchemlyb Discussions`_.\n\nIf you have bug reports or feature requests then please get in touch with us through the `Issue Tracker`_.\n\nWe also welcome code contributions: have a look at our `Developer Guide`_. Open an issue with the proposed fix or change in the `Issue Tracker`_ and submit a pull request against the `alchemistry/alchemlyb`_ GitHub repository.\n\n.. _`alchemlyb Discussions`: https://github.com/alchemistry/alchemlyb/discussions\n.. _`Developer Guide`: https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide\n.. _`Issue Tracker`: https://github.com/alchemistry/alchemlyb/issues\n.. _`alchemistry/alchemlyb`: https://github.com/alchemistry/alchemlyb\n\n \n\nReferences\n----------\n\n.. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal\n analysis of samples from multiple equilibrium states. The Journal of Chemical\n Physics 129, 124105.\n\n.. [Chodera2016] Chodera, J.D. (2016). A Simple Method for Automated\n Equilibration Detection in Molecular Simulations. Journal of Chemical Theory\n and Computation 12, 1799\u20131805.\n\n\n.. |doi| image:: https://zenodo.org/badge/68669096.svg\n :alt: Zenodo DOI\n :scale: 100%\n :target: https://zenodo.org/badge/latestdoi/68669096\n\n.. |docs| image:: https://readthedocs.org/projects/alchemlyb/badge/?version=latest\n :alt: Documentation\n :scale: 100%\n :target: http://alchemlyb.readthedocs.io/en/latest/\n\n.. |build| image:: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml/badge.svg?branch=master\n :alt: Build Status\n :scale: 100%\n :target: https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml\n\n.. |cov| image:: https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg\n :alt: Code coverage\n :scale: 100%\n :target: https://codecov.io/gh/alchemistry/alchemlyb\n\n\n.. |anaconda| image:: https://anaconda.org/conda-forge/alchemlyb/badges/version.svg\n :alt: anaconda package\n :scale: 100%\t \n :target: https://anaconda.org/conda-forge/alchemlyb\n",
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