Skip to content
New issue

Have a question about this project? # for a free GitHub account to open an issue and contact its maintainers and the community.

#

By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? # to your account

explicit dataset licenses #7

Merged
merged 2 commits into from
Oct 31, 2017
Merged

explicit dataset licenses #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
54c61f1
state that data sets come under an Open license
orbeckst Oct 31, 2017
7099ac5
explicitly put GMX data set under CC0
ianmkenney Oct 31, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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/
13 changes: 9 additions & 4 deletions docs/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
6 changes: 3 additions & 3 deletions src/alchemtest/gmx/benzene/descr.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 <https://creativecommons.org/publicdomain/zero/1.0/>`_ Public Domain Dedication

Benzene in water, alchemically turned into benzene in vacuum separated from water

This dataset was generated using `MDPOW <https://github.com/Becksteinlab/MDPOW>`_, with
the `Gromacs <http://www.gromacs.org/>`_ 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
Expand Down