diff --git a/CHANGELOG.txt b/CHANGELOG.txt index c517b5637ff1e422282281668c60f7c07944bb3b..fd3d775e7d4322e6df69b7858fb9aa8af98da7e5 100644 --- a/CHANGELOG.txt +++ b/CHANGELOG.txt @@ -1,18 +1,21 @@ Changes in Release <RELEASE NUMBER> -------------------------------------------------------------------------------- - * nonstandard C++ module was moved from ost.conop to ost.mol.alg. This implies - change in the API. Mapping functions CopyResidue, CopyConserved and - CopyNonConserved that were previousely imported from ost.conop are now - to be imported from ost.mol.alg. + * Introduced recipes to generate Docker and Singularity containers. + * Moved "nonstandard" functions from ost.conop to ost.mol.alg. Mapping + functions CopyResidue, CopyConserved and CopyNonConserved that were + previousely imported from ost.conop are now to be imported from ost.mol.alg. * Removed habit of changing secondary structure of entities when loading from mmCIF PDB files. Before, OST would turn secondary structure 'EEH' into 'ECH' to make it look nicer in DNG. Now, 'EEH' stays 'EEH'. * Added Molck API to the ost.mol.alg module. * Extended lDDT API in ost.mol.alg module to reproduce functionality of lddt - binary. + binary and fixed issues in stereo chemistry checks there. * Added `actions` interface including one action to compare structures. * Updated HHblits binding (minor changes for optional arguments). + * Added functionality to find optimal membrane position of protein. + * Support for recent compilers which use C++-11 by default. + * Several minor bug fixes, improvements, and speed-ups. Changes in Release 1.7.1 -------------------------------------------------------------------------------- diff --git a/modules/doc/contributing.rst b/modules/doc/contributing.rst index c171b7c0ddf1304876a2a78e60d063ff6fc63cb2..21f56abca9215334d2379e0811954735a3803b17 100644 --- a/modules/doc/contributing.rst +++ b/modules/doc/contributing.rst @@ -143,7 +143,7 @@ To get the new action recognised by ``make`` to be placed in :file:`stage/libexec/openstructure`, it has to be registered with ``cmake`` in :file:`actions/CMakeLists.txt`: -.. code-block:: console +.. code-block:: cmake :linenos: add_custom_target(actions ALL) @@ -165,10 +165,10 @@ directory. There are only two really important points: environment your action is running in. Actions are called by :file:`ost`, that's enough to get everything just right. -* The action of your action happens in the ost branch of the script. +* The code of your action belongs in the :attr:`__main__` branch of the script. Your action will have own function definitions, variables and all the bells - and whistles. Hiding behind ost keeps everything separated and makes - things easier when it gets to debugging. So just after + and whistles. Hiding behind :attr:`__main__` keeps everything separated and + makes things easier when it gets to debugging. So just after .. code-block:: python