From 54c61f17cd8467a7dfcaabb8975e08487eb4a489 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 31 Oct 2017 13:04:16 -0700 Subject: [PATCH 1/2] state that data sets come under an Open license --- README.rst | 12 ++++++++---- docs/index.rst | 13 +++++++++---- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/README.rst b/README.rst index f5058f6..6f8a8b4 100644 --- a/README.rst +++ b/README.rst @@ -1,13 +1,17 @@ alchemtest: the simple alchemistry test set =========================================== -**Warning**: This library is young. It is **not** API stable. It is a -nucleation point. By all means use and help improve it, but note that it will -change with time. - **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`_. The 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. + + .. _`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/ diff --git a/docs/index.rst b/docs/index.rst index 61ad6cf..828c628 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -6,13 +6,18 @@ alchemtest: the simple alchemistry test set =========================================== -.. warning:: This library is in an **alpha** state. The library and the documentation is incomplete. Use in production at your own risk. +**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`_. The 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. -**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`_. -The package is standalone, however, and can be used for any purpose. .. _`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. + .. toctree:: :maxdepth: 1 From 7099ac56d6b90c8bbc6f77f0e536462539889615 Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Tue, 31 Oct 2017 13:04:58 -0700 Subject: [PATCH 2/2] explicitly put GMX data set under CC0 --- src/alchemtest/gmx/benzene/descr.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/alchemtest/gmx/benzene/descr.rst b/src/alchemtest/gmx/benzene/descr.rst index cded468..a9892e6 100644 --- a/src/alchemtest/gmx/benzene/descr.rst +++ b/src/alchemtest/gmx/benzene/descr.rst @@ -12,18 +12,18 @@ Data Set Characteristics: :Pressure: 1 bar :Alchemical Pathway: vdw + coul --> vdw --> vacuum :Experimental Hydration Free Energy: -0.90 +- 0.2 kcal/mol - :Missing Values: None :Creator: \I. Kenney :Donor: Ian Kenney (ian.kenney@asu.edu) :Date: March 2017 - + :License: `CC0 `_ Public Domain Dedication + Benzene in water, alchemically turned into benzene in vacuum separated from water This dataset was generated using `MDPOW `_, with the `Gromacs `_ molecular dynamics engine. -Experimental value sourced from [Mobley2013]. +Experimental value sourced from [Mobley2013]_. .. [Mobley2013] Mobley, David L. (2013). Experimental and Calculated Small Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical