diff --git a/README.rst b/README.rst index af1b9a4..13a0942 100644 --- a/README.rst +++ b/README.rst @@ -1,6 +1,8 @@ alchemtest: the simple alchemistry test set =========================================== +|doi| |docs| + **alchemtest** is a collection of test datasets for alchemical free energy calculations. The datasets come from a variety of software packages, primarily molecular dynamics engines, and are used as the test set for `alchemlyb`_. @@ -15,3 +17,15 @@ modification, separation, for any purpose and without a charge. .. _`open license`: http://opendefinition.org/licenses/#recommended-conformant-licenses .. _`Open Definition 2.1`: http://opendefinition.org/od/2.1/en/ + + +.. |docs| image:: https://readthedocs.org/projects/alchemtest/badge/?version=latest + :alt: Documentation + :scale: 100% + :target: https://alchemtest.readthedocs.io/en/latest/ + +.. |doi| image:: https://zenodo.org/badge/XXXXX.svg + :alt: Zenodo DOI + :scale: 100% + :target: https://zenodo.org/badge/latestdoi/XXXXX + diff --git a/docs/index.rst b/docs/index.rst index 64c7d0f..f5902ed 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,17 +13,29 @@ package is standalone, however, and can be used for any purpose. Datasets are released under an `open license`_ that conforms to the `Open Definition 2.1`_ that allows free use, re-use, redistribution, modification, -separation, for any purpose and without a charge. +separation, for any purpose and without a charge. All data and code +can be found in the public GitHub repository `alchemistry/alchemtest`_. + +This library is **under active development**. We use `semantic +versioning`_ to indicate clearly what kind of changes you may expect +between releases. Although it is heavily used for the alchemlyb_ test +suite it may contain bugs. Please raise any issues or questions in the +`Issue Tracker`_. `Contributions of data sets`_ and code in the form +of pull requests are very welcome. .. _`alchemlyb`: https://github.com/alchemistry/alchemlyb .. _`open license`: http://opendefinition.org/licenses/#recommended-conformant-licenses .. _`Open Definition 2.1`: http://opendefinition.org/od/2.1/en/ - -.. note:: This library is in an **alpha** state. The library and the - documentation is incomplete. Use in production at your own risk. - +.. _`alchemistry/alchemtest`: + https://github.com/alchemistry/alchemtest +.. _`semantic versioning`: https://semver.org +.. _`Issue Tracker`: + https://github.com/alchemistry/alchemtest/issues +.. _`Contributions of data sets`: + https://github.com/alchemistry/alchemtest/wiki/contributing + .. toctree:: :maxdepth: 1 diff --git a/src/alchemtest/namd/tyr2ala/descr.rst b/src/alchemtest/namd/tyr2ala/descr.rst index e96f6a0..0996e68 100644 --- a/src/alchemtest/namd/tyr2ala/descr.rst +++ b/src/alchemtest/namd/tyr2ala/descr.rst @@ -1,6 +1,5 @@ -======================================================================= - NAMD: free energy of tyrosine to alanine mutation in aqueous solution -======================================================================= +NAMD: free energy of tyrosine to alanine mutation in aqueous solution +===================================================================== Free energy change from mutating a tyrosine (Y) residue into alanine (A) in the Ala-Tyr-Ala tripeptide in aqueous environment.