Merge branch 'master' into develop

CHANGELOG.txt

-Changes in Release 1.X.0
+Changes in Release 1.9.0
 --------------------------------------------------------------------------------
 
  * Improved compare-structures action (chain mapping handling and documentation).

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
 project(OpenStructure CXX C)
 set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
 set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 8)
+set (OST_VERSION_MINOR 9)
 set (OST_VERSION_PATCH 0)
 set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)

modules/doc/actions.rst

@@ -38,6 +38,12 @@ In summary it performs the following steps:
   :class:`single chain lDDT scores <ost.mol.alg.lDDTScorer>`,
   :attr:`weighted average of single chain lDDT scores <ost.mol.alg.qsscoring.OligoLDDTScorer.weighted_lddt>`,
   :attr:`lDDT score of oligomer <ost.mol.alg.qsscoring.OligoLDDTScorer.oligo_lddt>`).
+  Note that while the QS score is symmetric (same result when swapping reference
+  and model), the lDDT scores are not. Extra atoms in the model for mapped
+  chains have no effect on the score, while extra atoms in the reference reduce
+  the score. For the oligomeric variants (weighted-lDDT & oligo-lDDT), we do
+  :attr:`penalize for extra chains <ost.mol.alg.qsscoring.OligoLDDTScorer.penalize_extra_chains>`
+  in both reference and model.
 
 .. note ::
 

singularity/README.rst

@@ -9,7 +9,7 @@ In order to build OST Singularity image:
 .. code-block:: bash
 
   cd <OST ROOT>/singularity
-  sudo singularity build ost.img Singularity.1.8.0
+  sudo singularity build ost.img Singularity.1.9.0
 
 .. note::
 

singularity/Singularity.1.8.0 → singularity/Singularity.1.9.0

@@ -17,7 +17,7 @@ export CPUS_FOR_MAKE=8
 export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
 # When changing OPENSTRUCTURE_VERSION make sure to change it also in the
 # environment section of singularity recipe (this file).
-export OPENSTRUCTURE_VERSION="1.8.0"
+export OPENSTRUCTURE_VERSION="1.9.0"
 export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
 export MSMS_VERSION="2.6.1"
 export OPENMM_VERSION="7.1.1"
@@ -223,7 +223,7 @@ cd /home
 # ENVIRONMENT
 ##############################################################################
 export OST_ROOT="/usr/local"
-export OPENSTRUCTURE_VERSION="1.8.0"
+export OPENSTRUCTURE_VERSION="1.9.0"
 export OPENMM_LIB_PATH=/usr/local/openmm/lib/
 export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"